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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "3f88f70c-970a-43d2-b03c-1b0676ad22bc",
+   "metadata": {},
+   "source": [
+    "<h1>Convert LIRICAL's 384 Phenopackets to GA4GH Version 2 Format</h1>\n",
+    "<p><a href=\"https://pubmed.ncbi.nlm.nih.gov/32755546/\" target=\"__blank\">Robinson PN, et al. (2020) Interpretable Clinical Genomics with a Likelihood Ratio Paradigm. Am J Hum Genet. 2020 Sep 3;107(3):403-417</a> presented 384 phenopackets formated according to the GA4GH Phenopacket Schema version 1. This notebook converts those phenopackets to version 2 of the Phenopacket Schema.</p>\n",
+    "<p>We use the Python json package to input the V1 phenopackets and apply a series of corrections to ensure the V2 phenopackets are correctly formated.</p>"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "33a1010e-60e4-4a96-b153-7a8cc9d9a5ff",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import phenopackets as PPKt\n",
+    "import json\n",
+    "import os\n",
+    "import re\n",
+    "from google import protobuf\n",
+    "from google.protobuf.json_format import MessageToJson\n",
+    "import time\n",
+    "import hpotk"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "ff3ce5a5-0677-4c32-82cd-9df4b5312987",
+   "metadata": {},
+   "source": [
+    "<h2>Import HPO object</h2>"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "a154a8eb-6f41-44d6-9e37-060dfa464169",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "hpo = hpotk.load_ontology('http://purl.obolibrary.org/obo/hp.json')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "32ff6443-3ae0-4603-9f62-7f8c956a92b5",
+   "metadata": {},
+   "source": [
+    "### Get all 384 json files"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "fa8afc86-540a-4a59-8328-6bcb4746336b",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Extracted total of 384 V1 Phenopacket V1 files\n"
+     ]
+    }
+   ],
+   "source": [
+    "from os import listdir\n",
+    "from os.path import isfile, join\n",
+    "v1dir = \"v1phenopackets\"\n",
+    "jsonfiles = [f for f in listdir(v1dir) if isfile(join(v1dir, f)) and f.endswith(\"json\")]\n",
+    "print(f\"Extracted total of {len(jsonfiles)} V1 Phenopacket V1 files\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "19f2659b-9ac5-4e5e-a683-3194bc56a82a",
+   "metadata": {},
+   "source": [
+    "### Create JSON objects from JSON files"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "8d42f9eb-f80e-4c51-b6dc-dc22d07ad8b8",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_json_object(fname, dirname):\n",
+    "    fpath = join(dirname, fname)\n",
+    "    if not isfile(fpath):\n",
+    "        raise FileNotFoundError(f\"Could not find {fpath}\")\n",
+    "    with open(fpath, \"r\") as f:\n",
+    "        json_string = f.read()\n",
+    "        json_dict = json.loads(json_string)\n",
+    "        return json_dict"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "b2d1c6d3-cdf1-469a-a4d0-c5bf416b95f0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_id(json_dict):\n",
+    "    if 'id' not in json_dict:\n",
+    "        raise ValueError(\"Could not extract id field\")\n",
+    "    else:\n",
+    "        return json_dict.get('id')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "3417ffd0-1859-4a35-bd2f-99d2a6d24517",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def validate_age(ageString):\n",
+    "    \"\"\"\n",
+    "    return true if we can parse age as an ISO 8601 Period\n",
+    "    \"\"\"\n",
+    "    if ageString == \"N/A\":\n",
+    "        return False\n",
+    "    # first check if the string contains digits\n",
+    "    _digits = re.compile('\\d')\n",
+    "    if not bool(_digits.search(ageString)):\n",
+    "        print(f\"invalid ageString {ageString}\")\n",
+    "        return False\n",
+    "    # now check that the string conforms to ISO 8601, e.g. P34Y2M\n",
+    "    match = re.match(\n",
+    "        r'P((?P<years>\\d+)Y)?((?P<months>\\d+)M)?((?P<weeks>\\d+)W)?((?P<days>\\d+)D)?(T((?P<hours>\\d+)H)?((?P<minutes>\\d+)M)?((?P<seconds>\\d+)S)?)?',\n",
+    "        ageString\n",
+    "    )\n",
+    "    return match"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "id": "a2a68ac7-335d-4154-a16e-5c5376e3f3a7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_subject(json_dict):\n",
+    "    if 'subject' not in json_dict:\n",
+    "        raise ValueError(\"Could not extract id field\")\n",
+    "    subject = json_dict.get('subject')\n",
+    "    proband_id = subject.get('id', None)\n",
+    "    ageAtCollection = subject.get('ageAtCollection', None)\n",
+    "    invalid_age_strings = { \"N/A\", \"ADULT\", \"FETUS\" }\n",
+    "    if ageAtCollection is not None:\n",
+    "        iso_age = ageAtCollection.get('age', None)\n",
+    "        iso_age = iso_age.upper()\n",
+    "        if not iso_age in invalid_age_strings:\n",
+    "            if not iso_age.startswith(\"P\"): \n",
+    "                iso_age = \"P\" + iso_age\n",
+    "            if not validate_age(iso_age):\n",
+    "                print(f\"Could not validate age for {proband_id}: \\\"{iso_age}\\\", will omit\")\n",
+    "                iso_age = None\n",
+    "    else:\n",
+    "        iso_age = None\n",
+    "        \n",
+    "    sex = subject.get('sex', 'UNKNOWN_SEX')\n",
+    "    return proband_id, iso_age, sex\n",
+    "    "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "id": "c83698bb-a15f-4a6c-81eb-cf10c93bde09",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_phenotypic_features_list(json_dict):\n",
+    "    if 'phenotypicFeatures' not in json_dict:\n",
+    "        raise ValueError(\"Could not extract phenotypicFeatures field\")\n",
+    "    pfeature_list = []\n",
+    "    for pfeat in json_dict.get('phenotypicFeatures'):\n",
+    "        pfeature = PPKt.PhenotypicFeature()\n",
+    "        ontology_term = pfeat.get('type')\n",
+    "        ontology_id = ontology_term.get('id')\n",
+    "        ontology_label = ontology_term.get('label')\n",
+    "        # The following code uses the HPO to update outdated term IDs and labels\n",
+    "        if ontology_id in hpo:\n",
+    "            hpo_term = hpo.get_term(ontology_id)\n",
+    "            ontology_id = hpo_term.identifier\n",
+    "            ontology_label = hpo_term.name\n",
+    "        hpo_term = PPKt.OntologyClass()\n",
+    "        hpo_term.id = ontology_id.value\n",
+    "        hpo_term.label = ontology_label\n",
+    "        pfeature.type.CopyFrom(hpo_term)\n",
+    "        if 'excluded' in pfeat:\n",
+    "            pfeature.excluded = pfeat.excluded\n",
+    "        evidence_list = pfeat.get('evidence')\n",
+    "        # The 384 v1 phenopackets always have exactly one evidence element\n",
+    "        # do not check here, things will crash if we were wrong\n",
+    "        evidence = evidence_list[0]\n",
+    "        evidence_code = evidence.get('evidenceCode')\n",
+    "        evidence_term = PPKt.OntologyClass()\n",
+    "        evidence_term.id = evidence_code.get('id')\n",
+    "        evidence_term.label = evidence_code.get('label')\n",
+    "        evi = PPKt.Evidence()\n",
+    "        evi.evidence_code.CopyFrom(evidence_term)\n",
+    "        reference_json = evidence.get('reference')\n",
+    "        if reference_json is not None:\n",
+    "            ref = PPKt.ExternalReference()\n",
+    "            ref.id = reference_json.get('id')\n",
+    "            ref.description = reference_json.get('description')\n",
+    "            evi.reference.CopyFrom(ref)\n",
+    "        pfeature.evidence.append(evi)\n",
+    "        pfeature_list.append(pfeature)\n",
+    "    return pfeature_list"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "9f2ecee5-e97a-4e6a-ae0e-7a360b6b36ae",
+   "metadata": {},
+   "source": [
+    "<h2>Disease</h2>\n",
+    "<p>This is the format of the disease entries in the V1 schema.</p>\n",
+    "<pre>'diseases': [{'term': {'id': 'OMIM:191900', 'label': 'MUCKLE-WELLS SYNDROME; MWS'}}]</pre>"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "id": "717b8899-3fa3-4712-b8ae-cbedbc6f183e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_disease(json_dict):\n",
+    "    if not 'diseases' in json_dict:\n",
+    "        raise ValueError(\"Could not extract disease field\")\n",
+    "    disease_list = json_dict.get('diseases')\n",
+    "    if len(disease_list) != 1:\n",
+    "        raise ValueError(f\"Got bad number of diseases, {len(disease_list)}\")\n",
+    "    disease_object = disease_list[0]\n",
+    "    return disease_object.get('term')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "id": "06ab9fdb-2ee1-4d68-87e8-d78a09295f3b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_gene(json_dict):\n",
+    "    \"\"\"\n",
+    "    We expect one and only one gene here\n",
+    "    \"\"\"\n",
+    "    if not 'genes' in json_dict:\n",
+    "        raise ValueError(\"Could not extract genes field\")\n",
+    "    gene_list = json_dict.get('genes')\n",
+    "    if len(gene_list) != 1:\n",
+    "        raise ValueError(f\"Got bad number of genes, {len(gene_list)}\")\n",
+    "    return gene_list[0]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "64f2a698-1931-414d-abcd-c0d5ec64b2a8",
+   "metadata": {},
+   "source": [
+    "<h2>Variants in v1 phenopacket</h2>\n",
+    "<p>This is the format of the variants entries in the V1 schema.</p>\n",
+    "\n",
+    "<pre>\n",
+    " 'variants': [{'vcfAllele': {'genomeAssembly': 'GRCh37', 'chr': '1', 'pos': 247587794, 'ref': 'C', 'alt': 'T'}, \n",
+    "    'zygosity': {'id': 'GENO:0000135', 'label': 'heterozygous'}}]\n",
+    " </pre>"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "id": "c488dc42-0868-49e0-8f4d-286c1c8dead3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_one_ga4gh_interpretation(vcf_allele, zygosity, gene, disease, var_id):\n",
+    "    vdescriptor = PPKt.VariationDescriptor()\n",
+    "    vdescriptor.id = var_id\n",
+    "    vdescriptor.gene_context.value_id = gene.get('id')\n",
+    "    vdescriptor.gene_context.symbol = gene.get('symbol')\n",
+    "    vdescriptor.molecule_context =  PPKt.MoleculeContext.genomic\n",
+    "    vdescriptor.allelic_state.id = zygosity.get('id')\n",
+    "    vdescriptor.allelic_state.label = zygosity.get('label')\n",
+    "    vinterpretation = PPKt.VariantInterpretation() \n",
+    "    vcf_record = PPKt.VcfRecord()\n",
+    "    vcf_record.genome_assembly =  vcf_allele.get('genomeAssembly')\n",
+    "    vcf_record.chrom = vcf_allele.get('chr')\n",
+    "    vcf_record.pos = vcf_allele.get('pos')\n",
+    "    vcf_record.ref = vcf_allele.get('ref')\n",
+    "    vcf_record.alt = vcf_allele.get('alt')\n",
+    "    vdescriptor.vcf_record.CopyFrom(vcf_record)\n",
+    "    vinterpretation.variation_descriptor.CopyFrom(vdescriptor)\n",
+    "    return vinterpretation"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "id": "f89c45dc-5e3d-421e-9633-3963754b21df",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_interpretation(json_dict, gene, disease, individual_id):\n",
+    "    if not 'variants' in json_dict:\n",
+    "        raise ValueError(\"Could not find variants\")\n",
+    "    ga4gh_var_list = []\n",
+    "    i = 0\n",
+    "    for v in json_dict.get('variants'):\n",
+    "        if 'vcfAllele' not in v:\n",
+    "            raise ValueError(\"Malformed variant\")\n",
+    "        if 'zygosity' not in v:\n",
+    "            raise ValueError(\"Malformed variant - no zygosity\")\n",
+    "        vcf_allele = v.get('vcfAllele')\n",
+    "        zygosity = v.get('zygosity')\n",
+    "        i += 1\n",
+    "        var_id = f\"variant-{i}\"\n",
+    "        ga4gh_int = get_one_ga4gh_interpretation(vcf_allele, zygosity, gene, disease, var_id)\n",
+    "        ga4gh_var_list.append(ga4gh_int)\n",
+    "    interpretation = PPKt.Interpretation()\n",
+    "    interpretation.id = \"interpretation-id\"\n",
+    "    interpretation.progress_status = PPKt.Interpretation.ProgressStatus.SOLVED\n",
+    "    interpretation.diagnosis.disease.id = disease.get('id')\n",
+    "    interpretation.diagnosis.disease.label = disease.get('label')\n",
+    "    for var in ga4gh_var_list:\n",
+    "        genomic_interpretation = PPKt.GenomicInterpretation()\n",
+    "        genomic_interpretation.subject_or_biosample_id = individual_id\n",
+    "        # by assumption, variants passed to this package are all causative\n",
+    "        genomic_interpretation.interpretation_status = PPKt.GenomicInterpretation.InterpretationStatus.CAUSATIVE\n",
+    "        genomic_interpretation.variant_interpretation.CopyFrom(var)\n",
+    "        interpretation.diagnosis.genomic_interpretations.append(genomic_interpretation)\n",
+    "    return interpretation  "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "b3146193-6f7a-490a-896d-be6ac5a37aaa",
+   "metadata": {},
+   "source": [
+    "<h2>Metadata (V1)</h2>"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "id": "abd90fb5-ca2e-439c-a338-a4bb25b1dcdc",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_metadata(json_dict):\n",
+    "    if not 'metaData' in json_dict:\n",
+    "        raise ValueError(\"Could not find metaData\")\n",
+    "    metadata = json_dict.get('metaData')\n",
+    "    createdBy = metadata.get('createdBy', 'n/a')\n",
+    "    submittedBy = metadata.get('submittedBy')\n",
+    "    ga4gh_metadata = PPKt.MetaData()\n",
+    "    resources = []\n",
+    "    for res in metadata.get('resources'):\n",
+    "        if res.get('id') == 'ncbitaxon':\n",
+    "            continue # superfluous to add taxon H. sapiens in thius context and we do not have iriPREFIX for this resource\n",
+    "        ga4gh_resource = PPKt.Resource()\n",
+    "        ga4gh_resource.id = res.get('id')\n",
+    "        ga4gh_resource.name = res.get('name')\n",
+    "        ga4gh_resource.url = res.get('url')\n",
+    "        ga4gh_resource.version = res.get('version', 'n/a')\n",
+    "        ga4gh_resource.namespace_prefix = res.get('namespacePrefix')\n",
+    "        ga4gh_resource.iri_prefix = res.get('iriPrefix', 'n/a')\n",
+    "        ga4gh_metadata.resources.append(ga4gh_resource)\n",
+    "    ga4gh_metadata.created_by = createdBy\n",
+    "    if submittedBy is not None:\n",
+    "        ga4gh_metadata.submitted_by = submittedBy\n",
+    "    now = time.time()\n",
+    "    seconds = int(now)\n",
+    "    nanos = int((now - seconds) * 10 ** 9)\n",
+    "    timestamp = protobuf.timestamp_pb2.Timestamp(seconds=seconds, nanos=nanos)\n",
+    "    ga4gh_metadata.created.CopyFrom(timestamp)\n",
+    "    ga4gh_metadata.phenopacket_schema_version = \"2.0\"\n",
+    "    for res in resources:\n",
+    "        metadata.resources.append(res)\n",
+    "    return ga4gh_metadata"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 16,
+   "id": "62022748-1fc4-47b2-b298-9d4443943510",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def construct_v2_phenopacket(json_dict):\n",
+    "    id = get_id(json_dict)\n",
+    "    proband_id, iso_age, sex= get_subject(json_dict)\n",
+    "    pfeatures_list = get_phenotypic_features_list(json_dict)\n",
+    "    gene = get_gene(json_dict)\n",
+    "    disease = get_disease(json_dict)\n",
+    "    interpretation = get_interpretation(json_dict, gene, disease, proband_id)\n",
+    "    # Create phenopacket\n",
+    "    phenopacket = PPKt.Phenopacket()\n",
+    "    phenopacket.id = id\n",
+    "    proband = PPKt.Individual()\n",
+    "    proband.id = proband_id\n",
+    "    if sex == \"MALE\":\n",
+    "        proband.sex  = PPKt.Sex.MALE\n",
+    "    elif sex == \"FEMALE\":\n",
+    "        proband.sex = PPKt.Sex.FEMALE\n",
+    "    else:\n",
+    "        proband.sex  = PPKt.Sex.UNKNOWN_SEX\n",
+    "    if iso_age is not None:\n",
+    "        proband.time_at_last_encounter.age.iso8601duration = iso_age\n",
+    "    phenopacket.subject.CopyFrom(proband)\n",
+    "    for pf in pfeatures_list:\n",
+    "        phenopacket.phenotypic_features.append(pf)\n",
+    "    phenopacket.interpretations.append(interpretation)\n",
+    "    metadata = get_metadata(json_dict)\n",
+    "    phenopacket.meta_data.CopyFrom(metadata)\n",
+    "    return phenopacket\n",
+    "    "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 17,
+   "id": "be420e84-8e20-4ebf-b703-ab4b257e6cc5",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def output_phenopacket(json_dict, output_dir):\n",
+    "    ppack = construct_v2_phenopacket(json_dict)\n",
+    "    json_string = MessageToJson(ppack)\n",
+    "    pp_id = ppack.id\n",
+    "    fname = pp_id.replace(\" \", \"\").replace(\":\", \"_\")\n",
+    "    fname = re.sub('[^A-Za-z0-9_-]', '', fname)  # remove any illegal characters from filename\n",
+    "    fname = fname.replace(\" \", \"_\") + \".json\"\n",
+    "    outpth = os.path.join(output_dir, fname)\n",
+    "    with open(outpth, \"wt\") as fh:\n",
+    "        fh.write(json_string)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "a1124962-d861-43be-be8a-8521fa2b3868",
+   "metadata": {},
+   "source": [
+    "<h2>Output</h2>\n",
+    "<p>Here we output the 384 phenopackets in version 2 format. Some of the original files do not have a valid age string, and so they produce a warning during the output. This can be ignored, the corresponding cases our output without an age (which is not required)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 18,
+   "id": "cdf192e7-66fe-4f70-bfdd-82688994bd7b",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "................................................................................................................................................................................................................................................................................................................................................................................................\n",
+      "Output 384 phenopackets\n"
+     ]
+    }
+   ],
+   "source": [
+    "out_dir = \"v2phenopackets\"\n",
+    "v1dir = \"v1phenopackets\"\n",
+    "os.makedirs(out_dir, exist_ok=True)\n",
+    "n = 0\n",
+    "for json_file in jsonfiles:\n",
+    "    json_dict = get_json_object(json_file, v1dir)\n",
+    "    output_phenopacket(json_dict, out_dir)\n",
+    "    print(\".\", end=\"\")\n",
+    "    n += 1\n",
+    "print(f\"\\nOutput {n} phenopackets\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6c535af8-e15e-4f84-890f-79df3df0cead",
+   "metadata": {},
+   "source": [
+    "<h2>Where to go from here</h2>\n",
+    "<p>Use <a href=\"http://phenopackets.org/phenopacket-tools/stable/cli.html\">phenopacket tools</a> to check the output V2 phenopackets.</p>\n",
+    "<p>I checked the phenopackets with <tt>pxf validate *.json</tt> and everything was OK (no errors reported).</p>"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "a5ce98dd-d164-4b21-9b09-fbfa0f061ea7",
+   "metadata": {},
+   "source": [
+    "<pre>\n",
+    "pxf validate --hpo /Users/robinp/data/hpo/hp.json *.json | cut -f3 -d,  errors.csv | sort | uniq\n",
+    "HpoAncestryValidator\n",
+    "HpoUniqueValidator\n",
+    "more than once but the feature was present 2 times\"\n",
+    "</pre>\n",
+    "<p>This means that the phenopackets may have redundant entries,but the term ids are up to date.</p>"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3af17457-c57e-4af2-a819-3a9b06043a06",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/notebooks/LIRICAL/v1phenopackets/Abdul_Wahab-2016-GCDH-Patient_5.json b/notebooks/LIRICAL/v1phenopackets/Abdul_Wahab-2016-GCDH-Patient_5.json
new file mode 100644
index 000000000..1d386fcf1
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Abdul_Wahab-2016-GCDH-Patient_5.json
@@ -0,0 +1,162 @@
+{
+  "id": "PMID:27672653-Abdul_Wahab-2016-GCDH-Patient_5",
+  "subject": {
+    "id": "Patient 5",
+    "ageAtCollection": {
+      "age": "P14Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000256",
+      "label": "Macrocephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27672653",
+        "description": "Clinical and Mutational Analysis of the GCDH Gene in Malaysian Patients with Glutaric Aciduria Type 1"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002059",
+      "label": "Cerebral atrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27672653",
+        "description": "Clinical and Mutational Analysis of the GCDH Gene in Malaysian Patients with Glutaric Aciduria Type 1"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100309",
+      "label": "Subdural hemorrhage"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27672653",
+        "description": "Clinical and Mutational Analysis of the GCDH Gene in Malaysian Patients with Glutaric Aciduria Type 1"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003150",
+      "label": "Glutaric aciduria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27672653",
+        "description": "Clinical and Mutational Analysis of the GCDH Gene in Malaysian Patients with Glutaric Aciduria Type 1"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001332",
+      "label": "Dystonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27672653",
+        "description": "Clinical and Mutational Analysis of the GCDH Gene in Malaysian Patients with Glutaric Aciduria Type 1"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2639",
+    "symbol": "GCDH"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "19",
+      "pos": 13007113,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:231670",
+      "label": "GLUTARIC ACIDEMIA I"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27672653",
+      "description": "Clinical and Mutational Analysis of the GCDH Gene in Malaysian Patients with Glutaric Aciduria Type 1"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Ajmal-2013-BBS1-IV-5_family_A.json b/notebooks/LIRICAL/v1phenopackets/Ajmal-2013-BBS1-IV-5_family_A.json
new file mode 100644
index 000000000..8418da628
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Ajmal-2013-BBS1-IV-5_family_A.json
@@ -0,0 +1,191 @@
+{
+  "id": "PMID:23559858-Ajmal-2013-BBS1-IV-5/family_A",
+  "subject": {
+    "id": "IV-5/family A",
+    "ageAtCollection": {
+      "age": "26Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0007843",
+      "label": "Attenuation of retinal blood vessels"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23559858",
+        "description": "Exome sequencing identifies a novel and a recurrent BBS1 mutation in Pakistani families with Bardet-Biedl syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001513",
+      "label": "Obesity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23559858",
+        "description": "Exome sequencing identifies a novel and a recurrent BBS1 mutation in Pakistani families with Bardet-Biedl syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000608",
+      "label": "Macular degeneration"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23559858",
+        "description": "Exome sequencing identifies a novel and a recurrent BBS1 mutation in Pakistani families with Bardet-Biedl syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000486",
+      "label": "Strabismus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23559858",
+        "description": "Exome sequencing identifies a novel and a recurrent BBS1 mutation in Pakistani families with Bardet-Biedl syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001328",
+      "label": "Specific learning disability"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23559858",
+        "description": "Exome sequencing identifies a novel and a recurrent BBS1 mutation in Pakistani families with Bardet-Biedl syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000510",
+      "label": "Rod-cone dystrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23559858",
+        "description": "Exome sequencing identifies a novel and a recurrent BBS1 mutation in Pakistani families with Bardet-Biedl syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23559858",
+        "description": "Exome sequencing identifies a novel and a recurrent BBS1 mutation in Pakistani families with Bardet-Biedl syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:582",
+    "symbol": "BBS1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "11",
+      "pos": 66278178,
+      "ref": "G",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:209900",
+      "label": "BARDET-BIEDL SYNDROME 1; BBS1"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:23559858",
+      "description": "Exome sequencing identifies a novel and a recurrent BBS1 mutation in Pakistani families with Bardet-Biedl syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Al-Dosari-2010-TFAP2A-10-year-old_girl.json b/notebooks/LIRICAL/v1phenopackets/Al-Dosari-2010-TFAP2A-10-year-old_girl.json
new file mode 100644
index 000000000..cf4a04f61
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Al-Dosari-2010-TFAP2A-10-year-old_girl.json
@@ -0,0 +1,284 @@
+{
+  "id": "PMID:20461149-Al-Dosari-2010-TFAP2A-10-year-old_girl",
+  "subject": {
+    "id": "10-year-old girl",
+    "ageAtCollection": {
+      "age": "P10Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20461149",
+        "description": "Ocular manifestations of branchio-oculo-facial syndrome: report of a novel mutation and review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008494",
+      "label": "Inferior lens subluxation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20461149",
+        "description": "Ocular manifestations of branchio-oculo-facial syndrome: report of a novel mutation and review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001597",
+      "label": "Abnormality of the nail"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20461149",
+        "description": "Ocular manifestations of branchio-oculo-facial syndrome: report of a novel mutation and review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000482",
+      "label": "Microcornea"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20461149",
+        "description": "Ocular manifestations of branchio-oculo-facial syndrome: report of a novel mutation and review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000568",
+      "label": "Microphthalmia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20461149",
+        "description": "Ocular manifestations of branchio-oculo-facial syndrome: report of a novel mutation and review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000612",
+      "label": "Iris coloboma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20461149",
+        "description": "Ocular manifestations of branchio-oculo-facial syndrome: report of a novel mutation and review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000567",
+      "label": "Chorioretinal coloboma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20461149",
+        "description": "Ocular manifestations of branchio-oculo-facial syndrome: report of a novel mutation and review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007678",
+      "label": "Lacrimal duct stenosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20461149",
+        "description": "Ocular manifestations of branchio-oculo-facial syndrome: report of a novel mutation and review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012210",
+      "label": "Abnormal renal morphology"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20461149",
+        "description": "Ocular manifestations of branchio-oculo-facial syndrome: report of a novel mutation and review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000677",
+      "label": "Oligodontia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20461149",
+        "description": "Ocular manifestations of branchio-oculo-facial syndrome: report of a novel mutation and review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000218",
+      "label": "High palate"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20461149",
+        "description": "Ocular manifestations of branchio-oculo-facial syndrome: report of a novel mutation and review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000410",
+      "label": "Mixed hearing impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20461149",
+        "description": "Ocular manifestations of branchio-oculo-facial syndrome: report of a novel mutation and review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004476",
+      "label": "Aplasia cutis congenita over parietal area"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20461149",
+        "description": "Ocular manifestations of branchio-oculo-facial syndrome: report of a novel mutation and review of the literature"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:7020",
+    "symbol": "TFAP2A"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "6",
+      "pos": 10404742,
+      "ref": "T",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:113620",
+      "label": "BRANCHIOOCULOFACIAL SYNDROME; BOFS"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.12-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:20461149",
+      "description": "Ocular manifestations of branchio-oculo-facial syndrome: report of a novel mutation and review of the literature"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Al-Hashmi-2018-SNX14-IV-1.json b/notebooks/LIRICAL/v1phenopackets/Al-Hashmi-2018-SNX14-IV-1.json
new file mode 100644
index 000000000..12ebaa30f
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Al-Hashmi-2018-SNX14-IV-1.json
@@ -0,0 +1,362 @@
+{
+  "id": "PMID:30473892-Al-Hashmi-2018-SNX14-IV-1",
+  "subject": {
+    "id": "IV-1",
+    "ageAtCollection": {
+      "age": "P6Y9M"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000280",
+      "label": "Coarse facial features"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:30473892",
+        "description": "Exome Sequencing Identifies a Novel Sorting Nexin 14 Gene Mutation Causing Cerebellar Atrophy and Intellectual Disability"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002783",
+      "label": "Recurrent lower respiratory tract infections"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Exome Sequencing Identifies a Novel Sorting Nexin 14 Gene Mutation Causing Cerebellar Atrophy and Intellectual Disability"
+      }
+    }]
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+      "label": "homozygous"
+    }
+  }],
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+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
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+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
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+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
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+      "namespacePrefix": "NCBITaxon"
+    }, {
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+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
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+      "namespacePrefix": "OMIM"
+    }],
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+    "externalReferences": [{
+      "id": "PMID:30473892",
+      "description": "Exome Sequencing Identifies a Novel Sorting Nexin 14 Gene Mutation Causing Cerebellar Atrophy and Intellectual Disability"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Al-Qattan-2018-SCARF2-proband.json b/notebooks/LIRICAL/v1phenopackets/Al-Qattan-2018-SCARF2-proband.json
new file mode 100644
index 000000000..f4fcc0372
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Al-Qattan-2018-SCARF2-proband.json
@@ -0,0 +1,343 @@
+{
+  "id": "PMID:29378527-Al-Qattan-2018-SCARF2-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P15Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002987",
+      "label": "Elbow flexion contracture"
+    },
+    "evidence": [{
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+        "description": "Inclusion of joint laxity, recurrent patellar dislocation, and short distal ulnae as a feature of Van Den Ende-Gupta syndrome: a case report"
+      }
+    }]
+  }, {
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+      "id": "HP:0012385",
+      "label": "Camptodactyly"
+    },
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+      "label": "Blepharophimosis"
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+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "22",
+      "pos": 20785386,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:600920",
+      "label": "VAN DEN ENDE-GUPTA SYNDROME; VDEGS"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
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+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29378527",
+      "description": "Inclusion of joint laxity, recurrent patellar dislocation, and short distal ulnae as a feature of Van Den Ende-Gupta syndrome: a case report"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Al-Semari-2013-FGD1-II-1.json b/notebooks/LIRICAL/v1phenopackets/Al-Semari-2013-FGD1-II-1.json
new file mode 100644
index 000000000..c21becc9e
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Al-Semari-2013-FGD1-II-1.json
@@ -0,0 +1,238 @@
+{
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+      "label": "Homo sapiens"
+    }
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+      "label": "Short stature"
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+    },
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+      "label": "Ptosis"
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+    },
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+        "description": "Novel FGD1 mutation underlying Aarskog-Scott syndrome with myopathy and distal arthropathy"
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+    }]
+  }],
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+    "symbol": "FGD1"
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+      "id": "GENO:0000134",
+      "label": "hemizygous"
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+  }],
+  "diseases": [{
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+      "id": "OMIM:305400",
+      "label": "AARSKOG-SCOTT SYNDROME; AAS"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
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+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:23211637",
+      "description": "Novel FGD1 mutation underlying Aarskog-Scott syndrome with myopathy and distal arthropathy"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/AlSubhi-2016-ALG9-IV_5.json b/notebooks/LIRICAL/v1phenopackets/AlSubhi-2016-ALG9-IV_5.json
new file mode 100644
index 000000000..24847b845
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/AlSubhi-2016-ALG9-IV_5.json
@@ -0,0 +1,327 @@
+{
+  "id": "PMID:26453364-AlSubhi-2016-ALG9-IV:5",
+  "subject": {
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+    "ageAtCollection": {
+      "age": "6Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001057",
+      "label": "Aplasia cutis congenita"
+    },
+    "evidence": [{
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+      },
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+        "id": "PMID:26453364",
+        "description": "Further Delineation of the ALG9-CDG Phenotype"
+      }
+    }]
+  }, {
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+      "id": "HP:0002827",
+      "label": "Hip dislocation"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:26453364",
+        "description": "Further Delineation of the ALG9-CDG Phenotype"
+      }
+    }]
+  }, {
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+      "id": "HP:0000965",
+      "label": "Cutis marmorata"
+    },
+    "evidence": [{
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+        "description": "Further Delineation of the ALG9-CDG Phenotype"
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+  }, {
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+        "description": "Further Delineation of the ALG9-CDG Phenotype"
+      }
+    }]
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+      "label": "Depressed nasal bridge"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:26453364",
+        "description": "Further Delineation of the ALG9-CDG Phenotype"
+      }
+    }]
+  }, {
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+      "id": "HP:0000154",
+      "label": "Wide mouth"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+        "description": "Further Delineation of the ALG9-CDG Phenotype"
+      }
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+  }, {
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+    }]
+  }, {
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+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
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+        "description": "Further Delineation of the ALG9-CDG Phenotype"
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+        "description": "Further Delineation of the ALG9-CDG Phenotype"
+      }
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+  }],
+  "genes": [{
+    "id": "NCBIGene:79796",
+    "symbol": "ALG9"
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+    },
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+      "label": "homozygous"
+    }
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+      "id": "OMIM:608776",
+      "label": "CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Il; CDG1L"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
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+      "id": "hp",
+      "name": "human phenotype ontology",
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+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:26453364",
+      "description": "Further Delineation of the ALG9-CDG Phenotype"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Alazami-2016-ATP6V1E1-Family_5_-_IV_2.json b/notebooks/LIRICAL/v1phenopackets/Alazami-2016-ATP6V1E1-Family_5_-_IV_2.json
new file mode 100644
index 000000000..ed652b4b9
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Alazami-2016-ATP6V1E1-Family_5_-_IV_2.json
@@ -0,0 +1,147 @@
+{
+  "id": "PMID:27023906-Alazami-2016-ATP6V1E1-Family_5_-_IV:2",
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+    "ageAtCollection": {
+      "age": "n/a"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000973",
+      "label": "Cutis laxa"
+    },
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27023906",
+        "description": "Expanding the clinical and genetic heterogeneity of hereditary disorders of connective tissue"
+      }
+    }]
+  }, {
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+      "id": "HP:0001627",
+      "label": "Abnormal heart morphology"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27023906",
+        "description": "Expanding the clinical and genetic heterogeneity of hereditary disorders of connective tissue"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000121",
+      "label": "Nephrocalcinosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27023906",
+        "description": "Expanding the clinical and genetic heterogeneity of hereditary disorders of connective tissue"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001999",
+      "label": "Abnormal facial shape"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27023906",
+        "description": "Expanding the clinical and genetic heterogeneity of hereditary disorders of connective tissue"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:529",
+    "symbol": "ATP6V1E1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "22",
+      "pos": 18075487,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617402",
+      "label": "Cutis laxa, autosomal recessive, type IIC"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27023906",
+      "description": "Expanding the clinical and genetic heterogeneity of hereditary disorders of connective tissue"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Ali-2017-MYH3-proband.json b/notebooks/LIRICAL/v1phenopackets/Ali-2017-MYH3-proband.json
new file mode 100644
index 000000000..1aed0a24b
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Ali-2017-MYH3-proband.json
@@ -0,0 +1,281 @@
+{
+  "id": "PMID:28584669-Ali-2017-MYH3-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P10D"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0005280",
+      "label": "Depressed nasal bridge"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28584669",
+        "description": "Freeman-Sheldon Syndrome: First Molecularly Confirmed Case from Sub-Saharan Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000346",
+      "label": "Whistling appearance"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28584669",
+        "description": "Freeman-Sheldon Syndrome: First Molecularly Confirmed Case from Sub-Saharan Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000047",
+      "label": "Hypospadias"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28584669",
+        "description": "Freeman-Sheldon Syndrome: First Molecularly Confirmed Case from Sub-Saharan Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000347",
+      "label": "Micrognathia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28584669",
+        "description": "Freeman-Sheldon Syndrome: First Molecularly Confirmed Case from Sub-Saharan Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000316",
+      "label": "Hypertelorism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28584669",
+        "description": "Freeman-Sheldon Syndrome: First Molecularly Confirmed Case from Sub-Saharan Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000369",
+      "label": "Low-set ears"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28584669",
+        "description": "Freeman-Sheldon Syndrome: First Molecularly Confirmed Case from Sub-Saharan Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008872",
+      "label": "Feeding difficulties in infancy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28584669",
+        "description": "Freeman-Sheldon Syndrome: First Molecularly Confirmed Case from Sub-Saharan Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001371",
+      "label": "Flexion contracture"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28584669",
+        "description": "Freeman-Sheldon Syndrome: First Molecularly Confirmed Case from Sub-Saharan Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001762",
+      "label": "Talipes equinovarus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28584669",
+        "description": "Freeman-Sheldon Syndrome: First Molecularly Confirmed Case from Sub-Saharan Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000041",
+      "label": "Chordee"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28584669",
+        "description": "Freeman-Sheldon Syndrome: First Molecularly Confirmed Case from Sub-Saharan Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000431",
+      "label": "Wide nasal bridge"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28584669",
+        "description": "Freeman-Sheldon Syndrome: First Molecularly Confirmed Case from Sub-Saharan Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000160",
+      "label": "Narrow mouth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28584669",
+        "description": "Freeman-Sheldon Syndrome: First Molecularly Confirmed Case from Sub-Saharan Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100490",
+      "label": "Camptodactyly of finger"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28584669",
+        "description": "Freeman-Sheldon Syndrome: First Molecularly Confirmed Case from Sub-Saharan Africa"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:4621",
+    "symbol": "MYH3"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "17",
+      "pos": 10544634,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:193700",
+      "label": "ARTHROGRYPOSIS, DISTAL, TYPE 2A; DA2A"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28584669",
+      "description": "Freeman-Sheldon Syndrome: First Molecularly Confirmed Case from Sub-Saharan Africa"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Alzahrani-2018-EPG5-18-month_son.json b/notebooks/LIRICAL/v1phenopackets/Alzahrani-2018-EPG5-18-month_son.json
new file mode 100644
index 000000000..7161a3ed8
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Alzahrani-2018-EPG5-18-month_son.json
@@ -0,0 +1,311 @@
+{
+  "id": "PMID:29983806-Alzahrani-2018-EPG5-18-month_son",
+  "subject": {
+    "id": "18-month son",
+    "ageAtCollection": {
+      "age": "P1Y6M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001270",
+      "label": "Motor delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29983806",
+        "description": "A Saudi Infant with Vici Syndrome: Case Report and Literature Review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000518",
+      "label": "Cataract"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29983806",
+        "description": "A Saudi Infant with Vici Syndrome: Case Report and Literature Review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012646",
+      "label": "Retractile testis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29983806",
+        "description": "A Saudi Infant with Vici Syndrome: Case Report and Literature Review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008897",
+      "label": "Postnatal growth retardation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29983806",
+        "description": "A Saudi Infant with Vici Syndrome: Case Report and Literature Review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001488",
+      "label": "Bilateral ptosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29983806",
+        "description": "A Saudi Infant with Vici Syndrome: Case Report and Literature Review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002007",
+      "label": "Frontal bossing"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29983806",
+        "description": "A Saudi Infant with Vici Syndrome: Case Report and Literature Review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000527",
+      "label": "Long eyelashes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29983806",
+        "description": "A Saudi Infant with Vici Syndrome: Case Report and Literature Review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000670",
+      "label": "Carious teeth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29983806",
+        "description": "A Saudi Infant with Vici Syndrome: Case Report and Literature Review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000347",
+      "label": "Micrognathia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29983806",
+        "description": "A Saudi Infant with Vici Syndrome: Case Report and Literature Review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002205",
+      "label": "Recurrent respiratory infections"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29983806",
+        "description": "A Saudi Infant with Vici Syndrome: Case Report and Literature Review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000365",
+      "label": "Hearing impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29983806",
+        "description": "A Saudi Infant with Vici Syndrome: Case Report and Literature Review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000343",
+      "label": "Long philtrum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29983806",
+        "description": "A Saudi Infant with Vici Syndrome: Case Report and Literature Review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29983806",
+        "description": "A Saudi Infant with Vici Syndrome: Case Report and Literature Review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008872",
+      "label": "Feeding difficulties in infancy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29983806",
+        "description": "A Saudi Infant with Vici Syndrome: Case Report and Literature Review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000319",
+      "label": "Smooth philtrum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29983806",
+        "description": "A Saudi Infant with Vici Syndrome: Case Report and Literature Review"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:57724",
+    "symbol": "EPG5"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "18",
+      "pos": 43435648,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:242840",
+      "label": "VICI SYNDROME; VICIS"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29983806",
+      "description": "A Saudi Infant with Vici Syndrome: Case Report and Literature Review"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Anazi-2017-NKX6-2-Patient_36-16DG1123.json b/notebooks/LIRICAL/v1phenopackets/Anazi-2017-NKX6-2-Patient_36-16DG1123.json
new file mode 100644
index 000000000..1e9c4cfbf
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Anazi-2017-NKX6-2-Patient_36-16DG1123.json
@@ -0,0 +1,162 @@
+{
+  "id": "PMID:28940097-Anazi-2017-NKX6-2-Patient_36-16DG1123",
+  "subject": {
+    "id": "Patient 36-16DG1123",
+    "ageAtCollection": {
+      "age": "P10Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0003429",
+      "label": "CNS hypomyelination"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28940097",
+        "description": "Expanding the genetic heterogeneity of intellectual disability"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28940097",
+        "description": "Expanding the genetic heterogeneity of intellectual disability"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001298",
+      "label": "Encephalopathy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28940097",
+        "description": "Expanding the genetic heterogeneity of intellectual disability"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000486",
+      "label": "Strabismus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28940097",
+        "description": "Expanding the genetic heterogeneity of intellectual disability"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002650",
+      "label": "Scoliosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28940097",
+        "description": "Expanding the genetic heterogeneity of intellectual disability"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:84504",
+    "symbol": "NKX6-2"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "10",
+      "pos": 134599256,
+      "ref": "CG",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617560",
+      "label": "Spastic ataxia 8, autosomal recessive, with hypomyelinating leukodystrophy"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
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+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28940097",
+      "description": "Expanding the genetic heterogeneity of intellectual disability"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Arno-2017-ARHGEF18-Individual_1.json b/notebooks/LIRICAL/v1phenopackets/Arno-2017-ARHGEF18-Individual_1.json
new file mode 100644
index 000000000..d645e54bc
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Arno-2017-ARHGEF18-Individual_1.json
@@ -0,0 +1,219 @@
+{
+  "id": "PMID:28132693-Arno-2017-ARHGEF18-Individual_1",
+  "subject": {
+    "id": "Individual 1",
+    "ageAtCollection": {
+      "age": "P37Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0007843",
+      "label": "Attenuation of retinal blood vessels"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132693",
+        "description": "Biallelic Mutation of ARHGEF18, Involved in the Determination of Epithelial Apicobasal Polarity, Causes Adult-Onset Retinal Degeneration"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000510",
+      "label": "Rod-cone dystrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132693",
+        "description": "Biallelic Mutation of ARHGEF18, Involved in the Determination of Epithelial Apicobasal Polarity, Causes Adult-Onset Retinal Degeneration"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000662",
+      "label": "Nyctalopia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132693",
+        "description": "Biallelic Mutation of ARHGEF18, Involved in the Determination of Epithelial Apicobasal Polarity, Causes Adult-Onset Retinal Degeneration"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0025159",
+      "label": "Hypoautofluorescent retinal lesion"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132693",
+        "description": "Biallelic Mutation of ARHGEF18, Involved in the Determination of Epithelial Apicobasal Polarity, Causes Adult-Onset Retinal Degeneration"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012512",
+      "label": "Diffuse optic disc pallor"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132693",
+        "description": "Biallelic Mutation of ARHGEF18, Involved in the Determination of Epithelial Apicobasal Polarity, Causes Adult-Onset Retinal Degeneration"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001123",
+      "label": "Visual field defect"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132693",
+        "description": "Biallelic Mutation of ARHGEF18, Involved in the Determination of Epithelial Apicobasal Polarity, Causes Adult-Onset Retinal Degeneration"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007663",
+      "label": "Reduced visual acuity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132693",
+        "description": "Biallelic Mutation of ARHGEF18, Involved in the Determination of Epithelial Apicobasal Polarity, Causes Adult-Onset Retinal Degeneration"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000580",
+      "label": "Pigmentary retinopathy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132693",
+        "description": "Biallelic Mutation of ARHGEF18, Involved in the Determination of Epithelial Apicobasal Polarity, Causes Adult-Onset Retinal Degeneration"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:23370",
+    "symbol": "ARHGEF18"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "19",
+      "pos": 7509101,
+      "ref": "A",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "19",
+      "pos": 7527145,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617433",
+      "label": "Retinitis pigmentosa 78"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28132693",
+      "description": "Biallelic Mutation of ARHGEF18, Involved in the Determination of Epithelial Apicobasal Polarity, Causes Adult-Onset Retinal Degeneration"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Arno-2017-ARHGEF18-Individual_2.json b/notebooks/LIRICAL/v1phenopackets/Arno-2017-ARHGEF18-Individual_2.json
new file mode 100644
index 000000000..0cce7aef3
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Arno-2017-ARHGEF18-Individual_2.json
@@ -0,0 +1,219 @@
+{
+  "id": "PMID:28132693-Arno-2017-ARHGEF18-Individual_2",
+  "subject": {
+    "id": "Individual 2",
+    "ageAtCollection": {
+      "age": "P51Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0007843",
+      "label": "Attenuation of retinal blood vessels"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132693",
+        "description": "Biallelic Mutation of ARHGEF18, Involved in the Determination of Epithelial Apicobasal Polarity, Causes Adult-Onset Retinal Degeneration"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000510",
+      "label": "Rod-cone dystrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132693",
+        "description": "Biallelic Mutation of ARHGEF18, Involved in the Determination of Epithelial Apicobasal Polarity, Causes Adult-Onset Retinal Degeneration"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000662",
+      "label": "Nyctalopia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132693",
+        "description": "Biallelic Mutation of ARHGEF18, Involved in the Determination of Epithelial Apicobasal Polarity, Causes Adult-Onset Retinal Degeneration"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0025159",
+      "label": "Hypoautofluorescent retinal lesion"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132693",
+        "description": "Biallelic Mutation of ARHGEF18, Involved in the Determination of Epithelial Apicobasal Polarity, Causes Adult-Onset Retinal Degeneration"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012512",
+      "label": "Diffuse optic disc pallor"
+    },
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+        "id": "ECO:0000033",
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+        "id": "PMID:28132693",
+        "description": "Biallelic Mutation of ARHGEF18, Involved in the Determination of Epithelial Apicobasal Polarity, Causes Adult-Onset Retinal Degeneration"
+      }
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+  }, {
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+      "label": "Visual field defect"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132693",
+        "description": "Biallelic Mutation of ARHGEF18, Involved in the Determination of Epithelial Apicobasal Polarity, Causes Adult-Onset Retinal Degeneration"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007663",
+      "label": "Reduced visual acuity"
+    },
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+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132693",
+        "description": "Biallelic Mutation of ARHGEF18, Involved in the Determination of Epithelial Apicobasal Polarity, Causes Adult-Onset Retinal Degeneration"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000580",
+      "label": "Pigmentary retinopathy"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132693",
+        "description": "Biallelic Mutation of ARHGEF18, Involved in the Determination of Epithelial Apicobasal Polarity, Causes Adult-Onset Retinal Degeneration"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:23370",
+    "symbol": "ARHGEF18"
+  }],
+  "variants": [{
+    "vcfAllele": {
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+      "chr": "19",
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+      "ref": "GCGAGCGGCTGGAGCAGGAGCGGGC",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "19",
+      "pos": 7532286,
+      "ref": "G",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617433",
+      "label": "Retinitis pigmentosa 78"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
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+    "externalReferences": [{
+      "id": "PMID:28132693",
+      "description": "Biallelic Mutation of ARHGEF18, Involved in the Determination of Epithelial Apicobasal Polarity, Causes Adult-Onset Retinal Degeneration"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Arora-2019-COG8-proband.json b/notebooks/LIRICAL/v1phenopackets/Arora-2019-COG8-proband.json
new file mode 100644
index 000000000..a2b95aeb5
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Arora-2019-COG8-proband.json
@@ -0,0 +1,496 @@
+{
+  "id": "PMID:30690882-Arora-2019-COG8-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P1D"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001942",
+      "label": "Metabolic acidosis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30690882",
+        "description": "The first case of antenatal presentation in COG8-congenital disorder of glycosylation with a novel splice site mutation and an extended phenotype"
+      }
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+        "description": "The first case of antenatal presentation in COG8-congenital disorder of glycosylation with a novel splice site mutation and an extended phenotype"
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+        "description": "The first case of antenatal presentation in COG8-congenital disorder of glycosylation with a novel splice site mutation and an extended phenotype"
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+      "label": "Hypertelorism"
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+        "description": "The first case of antenatal presentation in COG8-congenital disorder of glycosylation with a novel splice site mutation and an extended phenotype"
+      }
+    }]
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+      "label": "Short neck"
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+        "description": "The first case of antenatal presentation in COG8-congenital disorder of glycosylation with a novel splice site mutation and an extended phenotype"
+      }
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+      "label": "Deep philtrum"
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+        "description": "The first case of antenatal presentation in COG8-congenital disorder of glycosylation with a novel splice site mutation and an extended phenotype"
+      }
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+      "label": "Dandy-Walker malformation"
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+      }
+    }]
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+      "label": "Depressed nasal bridge"
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+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Asgharzade-2018-GIPC3-Ahv-14_23.json b/notebooks/LIRICAL/v1phenopackets/Asgharzade-2018-GIPC3-Ahv-14_23.json
new file mode 100644
index 000000000..2d7c7a5e7
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Asgharzade-2018-GIPC3-Ahv-14_23.json
@@ -0,0 +1,101 @@
+{
+  "id": "PMID:29605370-Asgharzade-2018-GIPC3-Ahv-14:23",
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+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000399",
+      "label": "Prelingual sensorineural hearing impairment"
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+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:29605370",
+        "description": "A novel missense mutation in GIPC3 causes sensorineural hearing loss in an Iranian family revealed by targeted next-generation sequencing"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:126326",
+    "symbol": "GIPC3"
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+    }
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+      "id": "OMIM:601869",
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+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
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+      "url": "http://purl.obolibrary.org/obo/pato.owl",
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+      "version": "19-03-2018",
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+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Avgeris-2017-TSC1-patient_6.json b/notebooks/LIRICAL/v1phenopackets/Avgeris-2017-TSC1-patient_6.json
new file mode 100644
index 000000000..9860f9806
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Avgeris-2017-TSC1-patient_6.json
@@ -0,0 +1,193 @@
+{
+  "id": "PMID:29196670-Avgeris-2017-TSC1-patient_6",
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+      "age": "n/a"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
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+  "phenotypicFeatures": [{
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+      "label": "Autistic behavior"
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:29196670",
+        "description": "Mutational analysis of TSC1 and TSC2 genes in Tuberous Sclerosis Complex patients from Greece"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010615",
+      "label": "Angiofibromas"
+    },
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Mutational analysis of TSC1 and TSC2 genes in Tuberous Sclerosis Complex patients from Greece"
+      }
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+      "id": "HP:0009717",
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+        "description": "Mutational analysis of TSC1 and TSC2 genes in Tuberous Sclerosis Complex patients from Greece"
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+        "description": "Mutational analysis of TSC1 and TSC2 genes in Tuberous Sclerosis Complex patients from Greece"
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+    }]
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+      "reference": {
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+        "description": "Mutational analysis of TSC1 and TSC2 genes in Tuberous Sclerosis Complex patients from Greece"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009719",
+      "label": "Hypomelanotic macule"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29196670",
+        "description": "Mutational analysis of TSC1 and TSC2 genes in Tuberous Sclerosis Complex patients from Greece"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:7248",
+    "symbol": "TSC1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "9",
+      "pos": 135787681,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:191100",
+      "label": "TUBEROUS SCLEROSIS 1; TSC1"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29196670",
+      "description": "Mutational analysis of TSC1 and TSC2 genes in Tuberous Sclerosis Complex patients from Greece"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Avrahami-2008-ST14-patient.json b/notebooks/LIRICAL/v1phenopackets/Avrahami-2008-ST14-patient.json
new file mode 100644
index 000000000..1ab107895
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Avrahami-2008-ST14-patient.json
@@ -0,0 +1,193 @@
+{
+  "id": "PMID:18445049-Avrahami-2008-ST14-patient",
+  "subject": {
+    "id": "patient",
+    "ageAtCollection": {
+      "age": "P2Y6M"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0007431",
+      "label": "Congenital ichthyosiform erythroderma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18445049",
+        "description": "Autosomal recessive ichthyosis with hypotrichosis syndrome: further delineation of the phenotype"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008070",
+      "label": "Sparse hair"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18445049",
+        "description": "Autosomal recessive ichthyosis with hypotrichosis syndrome: further delineation of the phenotype"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002231",
+      "label": "Sparse body hair"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Autosomal recessive ichthyosis with hypotrichosis syndrome: further delineation of the phenotype"
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+    }]
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+      "label": "Sparse eyebrow"
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+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:18445049",
+        "description": "Autosomal recessive ichthyosis with hypotrichosis syndrome: further delineation of the phenotype"
+      }
+    }]
+  }, {
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+      "id": "HP:0000498",
+      "label": "Blepharitis"
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+        "id": "PMID:18445049",
+        "description": "Autosomal recessive ichthyosis with hypotrichosis syndrome: further delineation of the phenotype"
+      }
+    }]
+  }, {
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+      "id": "HP:0000653",
+      "label": "Sparse eyelashes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:18445049",
+        "description": "Autosomal recessive ichthyosis with hypotrichosis syndrome: further delineation of the phenotype"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:6768",
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+  }],
+  "variants": [{
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+      "pos": 130029877,
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+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:602400",
+      "label": "ICHTHYOSIS, CONGENITAL, AUTOSOMAL RECESSIVE 11; ARCI11"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
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+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:18445049",
+      "description": "Autosomal recessive ichthyosis with hypotrichosis syndrome: further delineation of the phenotype"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Badin-2017-RUNX1-Pedigree_I,_V_2.json b/notebooks/LIRICAL/v1phenopackets/Badin-2017-RUNX1-Pedigree_I,_V_2.json
new file mode 100644
index 000000000..aa8a87d50
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Badin-2017-RUNX1-Pedigree_I,_V_2.json
@@ -0,0 +1,131 @@
+{
+  "id": "PMID:28181366-Badin-2017-RUNX1-Pedigree_I,_V:2",
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+    "id": "Pedigree I, V:2",
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+      "age": "n/a"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0012484",
+      "label": "Abnormal dense granules"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28181366",
+        "description": "Molecular phenotype and bleeding risks of an inherited platelet disorder in a family with a RUNX1 frameshift mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030402",
+      "label": "Abnormal platelet aggregation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28181366",
+        "description": "Molecular phenotype and bleeding risks of an inherited platelet disorder in a family with a RUNX1 frameshift mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004808",
+      "label": "Acute myeloid leukemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28181366",
+        "description": "Molecular phenotype and bleeding risks of an inherited platelet disorder in a family with a RUNX1 frameshift mutation"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:861",
+    "symbol": "RUNX1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "21",
+      "pos": 36259163,
+      "ref": "T",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:601399",
+      "label": "PLATELET DISORDER, FAMILIAL, WITH ASSOCIATED MYELOID MALIGNANCY; FPDMM"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
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+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
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+    "externalReferences": [{
+      "id": "PMID:28181366",
+      "description": "Molecular phenotype and bleeding risks of an inherited platelet disorder in a family with a RUNX1 frameshift mutation"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Baldi-2018-NKX6-2-F6,II-2.json b/notebooks/LIRICAL/v1phenopackets/Baldi-2018-NKX6-2-F6,II-2.json
new file mode 100644
index 000000000..36942091f
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Baldi-2018-NKX6-2-F6,II-2.json
@@ -0,0 +1,448 @@
+{
+  "id": "PMID:29388673-Baldi-2018-NKX6-2-F6,II-2",
+  "subject": {
+    "id": "F6,II-2",
+    "ageAtCollection": {
+      "age": "P12Y6M"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002415",
+      "label": "Leukodystrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29388673",
+        "description": "Expanding the clinical and genetic spectra of NKX6-2-related disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001238",
+      "label": "Slender finger"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29388673",
+        "description": "Expanding the clinical and genetic spectra of NKX6-2-related disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001285",
+      "label": "Spastic tetraparesis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Expanding the clinical and genetic spectra of NKX6-2-related disorder"
+      }
+    }]
+  }, {
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+      "id": "HP:0000486",
+      "label": "Strabismus"
+    },
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29388673",
+        "description": "Expanding the clinical and genetic spectra of NKX6-2-related disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+        "description": "Expanding the clinical and genetic spectra of NKX6-2-related disorder"
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+        "description": "Expanding the clinical and genetic spectra of NKX6-2-related disorder"
+      }
+    }]
+  }, {
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+      "label": "Hyperreflexia"
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+    "evidence": [{
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+        "description": "Expanding the clinical and genetic spectra of NKX6-2-related disorder"
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+    "evidence": [{
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+  }, {
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+      "label": "Long face"
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+        "description": "Expanding the clinical and genetic spectra of NKX6-2-related disorder"
+      }
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+  }, {
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+      "label": "Hearing impairment"
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+    "evidence": [{
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+      "label": "High palate"
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+    "evidence": [{
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+  }, {
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+      "label": "Overgrowth"
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+      "reference": {
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+        "description": "Expanding the clinical and genetic spectra of NKX6-2-related disorder"
+      }
+    }]
+  }, {
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+      "label": "Horizontal nystagmus"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:29388673",
+        "description": "Expanding the clinical and genetic spectra of NKX6-2-related disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001321",
+      "label": "Cerebellar hypoplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29388673",
+        "description": "Expanding the clinical and genetic spectra of NKX6-2-related disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000678",
+      "label": "Dental crowding"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29388673",
+        "description": "Expanding the clinical and genetic spectra of NKX6-2-related disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001332",
+      "label": "Dystonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29388673",
+        "description": "Expanding the clinical and genetic spectra of NKX6-2-related disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006808",
+      "label": "Cerebral hypomyelination"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:29388673",
+        "description": "Expanding the clinical and genetic spectra of NKX6-2-related disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007034",
+      "label": "Generalized hyperreflexia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "id": "PMID:29388673",
+        "description": "Expanding the clinical and genetic spectra of NKX6-2-related disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002079",
+      "label": "Hypoplasia of the corpus callosum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:29388673",
+        "description": "Expanding the clinical and genetic spectra of NKX6-2-related disorder"
+      }
+    }]
+  }, {
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+      "id": "HP:0002828",
+      "label": "Multiple joint contractures"
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+    "evidence": [{
+      "evidenceCode": {
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:29388673",
+        "description": "Expanding the clinical and genetic spectra of NKX6-2-related disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001290",
+      "label": "Generalized hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29388673",
+        "description": "Expanding the clinical and genetic spectra of NKX6-2-related disorder"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:84504",
+    "symbol": "NKX6-2"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "10",
+      "pos": 134598646,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617560",
+      "label": "Spastic ataxia 8, autosomal recessive, with hypomyelinating leukodystrophy"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29388673",
+      "description": "Expanding the clinical and genetic spectra of NKX6-2-related disorder"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Bao-2019-COL6A1-II.1.json b/notebooks/LIRICAL/v1phenopackets/Bao-2019-COL6A1-II.1.json
new file mode 100644
index 000000000..a83206a40
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Bao-2019-COL6A1-II.1.json
@@ -0,0 +1,409 @@
+{
+  "id": "PMID:30808312-Bao-2019-COL6A1-II.1",
+  "subject": {
+    "id": "II.1",
+    "ageAtCollection": {
+      "age": "14Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0008944",
+      "label": "Distal lower limb amyotrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30808312",
+        "description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001558",
+      "label": "Decreased fetal movement"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30808312",
+        "description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000988",
+      "label": "Skin rash"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30808312",
+        "description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001284",
+      "label": "Areflexia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30808312",
+        "description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0040083",
+      "label": "Toe walking"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:30808312",
+        "description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0040129",
+      "label": "Abnormal nerve conduction velocity"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30808312",
+        "description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report"
+      }
+    }]
+  }, {
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+      "id": "HP:0000969",
+      "label": "Edema"
+    },
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+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:30808312",
+        "description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report"
+      }
+    }]
+  }, {
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+      "id": "HP:0001324",
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+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:30808312",
+        "description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000010",
+      "label": "Recurrent urinary tract infections"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30808312",
+        "description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0040180",
+      "label": "Hyperkeratosis pilaris"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30808312",
+        "description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003724",
+      "label": "Shoulder girdle muscle atrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30808312",
+        "description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012587",
+      "label": "Macroscopic hematuria"
+    },
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+        "id": "ECO:0000033",
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+      "reference": {
+        "id": "PMID:30808312",
+        "description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report"
+      }
+    }]
+  }, {
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+      "id": "HP:0003458",
+      "label": "EMG: myopathic abnormalities"
+    },
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30808312",
+        "description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002829",
+      "label": "Arthralgia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+      },
+      "reference": {
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+        "description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report"
+      }
+    }]
+  }, {
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+      "id": "HP:0031910",
+      "label": "Abnormal cranial nerve physiology"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
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+        "description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003115",
+      "label": "Abnormal EKG"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
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+        "id": "PMID:30808312",
+        "description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report"
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+    }]
+  }, {
+    "type": {
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+      "label": "Global developmental delay"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
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+        "description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report"
+      }
+    }]
+  }, {
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+      "label": "Motor delay"
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+        "id": "PMID:30808312",
+        "description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003687",
+      "label": "Centrally nucleated skeletal muscle fibers"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:30808312",
+        "description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report"
+      }
+    }]
+  }, {
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+      "id": "HP:0002907",
+      "label": "Microscopic hematuria"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:30808312",
+        "description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000467",
+      "label": "Neck muscle weakness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30808312",
+        "description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:1291",
+    "symbol": "COL6A1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "21",
+      "pos": 47409540,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:158810",
+      "label": "BETHLEM MYOPATHY 1; BTHLM1"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30808312",
+      "description": "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria: a case report"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Bastaki-2017-CTCF-proband.json b/notebooks/LIRICAL/v1phenopackets/Bastaki-2017-CTCF-proband.json
new file mode 100644
index 000000000..92a7c6b3d
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Bastaki-2017-CTCF-proband.json
@@ -0,0 +1,507 @@
+{
+  "id": "PMID:28619046-Bastaki-2017-CTCF-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P2Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000527",
+      "label": "Long eyelashes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28619046",
+        "description": "Identification of a novel CTCF mutation responsible for syndromic intellectual disability - a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000463",
+      "label": "Anteverted nares"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28619046",
+        "description": "Identification of a novel CTCF mutation responsible for syndromic intellectual disability - a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002553",
+      "label": "Highly arched eyebrow"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28619046",
+        "description": "Identification of a novel CTCF mutation responsible for syndromic intellectual disability - a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000248",
+      "label": "Brachycephaly"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28619046",
+        "description": "Identification of a novel CTCF mutation responsible for syndromic intellectual disability - a case report"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Attached earlobe"
+    },
+    "evidence": [{
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+        "id": "PMID:28619046",
+        "description": "Identification of a novel CTCF mutation responsible for syndromic intellectual disability - a case report"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Short nose"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28619046",
+        "description": "Identification of a novel CTCF mutation responsible for syndromic intellectual disability - a case report"
+      }
+    }]
+  }, {
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+      "label": "Recurrent respiratory infections"
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+      "label": "Hypoplastic labia majora"
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+      "namespacePrefix": "OMIM"
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+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Bee-2015-BBS2-II_2.json b/notebooks/LIRICAL/v1phenopackets/Bee-2015-BBS2-II_2.json
new file mode 100644
index 000000000..e14d4b810
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Bee-2015-BBS2-II_2.json
@@ -0,0 +1,233 @@
+{
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+      "label": "Renal insufficiency"
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+    }
+  }],
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+    }, {
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+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
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+    "externalReferences": [{
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+      "description": "Whole Exome Sequencing Identifies a Novel and a Recurrent Mutation in BBS2 Gene in a Family with Bardet-Biedl Syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Ben_Ammar-2013-MUSK-patient.json b/notebooks/LIRICAL/v1phenopackets/Ben_Ammar-2013-MUSK-patient.json
new file mode 100644
index 000000000..8f0d79e5a
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Ben_Ammar-2013-MUSK-patient.json
@@ -0,0 +1,346 @@
+{
+  "id": "PMID:23326516-Ben_Ammar-2013-MUSK-patient",
+  "subject": {
+    "id": "patient",
+    "ageAtCollection": {
+      "age": "P12Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0010535",
+      "label": "Sleep apnea"
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+        "description": "A mutation causes MuSK reduced sensitivity to agrin and congenital myasthenia"
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+  }, {
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+      "id": "HP:0012473",
+      "label": "Tongue atrophy"
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+      "reference": {
+        "id": "PMID:23326516",
+        "description": "A mutation causes MuSK reduced sensitivity to agrin and congenital myasthenia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003323",
+      "label": "Progressive muscle weakness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23326516",
+        "description": "A mutation causes MuSK reduced sensitivity to agrin and congenital myasthenia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008944",
+      "label": "Distal lower limb amyotrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23326516",
+        "description": "A mutation causes MuSK reduced sensitivity to agrin and congenital myasthenia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007911",
+      "label": "Congenital bilateral ptosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23326516",
+        "description": "A mutation causes MuSK reduced sensitivity to agrin and congenital myasthenia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003473",
+      "label": "Fatigable weakness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23326516",
+        "description": "A mutation causes MuSK reduced sensitivity to agrin and congenital myasthenia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030208",
+      "label": "Acetylcholine receptor antibody positivity"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23326516",
+        "description": "A mutation causes MuSK reduced sensitivity to agrin and congenital myasthenia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002380",
+      "label": "Fasciculations"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23326516",
+        "description": "A mutation causes MuSK reduced sensitivity to agrin and congenital myasthenia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002515",
+      "label": "Waddling gait"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23326516",
+        "description": "A mutation causes MuSK reduced sensitivity to agrin and congenital myasthenia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002650",
+      "label": "Scoliosis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23326516",
+        "description": "A mutation causes MuSK reduced sensitivity to agrin and congenital myasthenia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0025331",
+      "label": "Upgaze palsy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "description": "A mutation causes MuSK reduced sensitivity to agrin and congenital myasthenia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003202",
+      "label": "Skeletal muscle atrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23326516",
+        "description": "A mutation causes MuSK reduced sensitivity to agrin and congenital myasthenia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003327",
+      "label": "Axial muscle weakness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23326516",
+        "description": "A mutation causes MuSK reduced sensitivity to agrin and congenital myasthenia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002875",
+      "label": "Exertional dyspnea"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23326516",
+        "description": "A mutation causes MuSK reduced sensitivity to agrin and congenital myasthenia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003391",
+      "label": "Gowers sign"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23326516",
+        "description": "A mutation causes MuSK reduced sensitivity to agrin and congenital myasthenia"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:4593",
+    "symbol": "MUSK"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "9",
+      "pos": 113563161,
+      "ref": "A",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616325",
+      "label": "MYASTHENIC SYNDROME, CONGENITAL, 9, ASSOCIATED WITH ACETYLCHOLINERECEPTOR DEFICIENCY; CMS9"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:23326516",
+      "description": "A mutation causes MuSK reduced sensitivity to agrin and congenital myasthenia"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Bhatia-2018-PRPF31-IV_3.json b/notebooks/LIRICAL/v1phenopackets/Bhatia-2018-PRPF31-IV_3.json
new file mode 100644
index 000000000..99928d504
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Bhatia-2018-PRPF31-IV_3.json
@@ -0,0 +1,161 @@
+{
+  "id": "PMID:30099644-Bhatia-2018-PRPF31-IV:3",
+  "subject": {
+    "id": "IV:3",
+    "ageAtCollection": {
+      "age": "35Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0007663",
+      "label": "Reduced visual acuity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30099644",
+        "description": "A novel mutation in the PRPF31 in a North Indian adRP family with incomplete penetrance"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007843",
+      "label": "Attenuation of retinal blood vessels"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30099644",
+        "description": "A novel mutation in the PRPF31 in a North Indian adRP family with incomplete penetrance"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000543",
+      "label": "Optic disc pallor"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30099644",
+        "description": "A novel mutation in the PRPF31 in a North Indian adRP family with incomplete penetrance"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007737",
+      "label": "Bone spicule pigmentation of the retina"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30099644",
+        "description": "A novel mutation in the PRPF31 in a North Indian adRP family with incomplete penetrance"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000662",
+      "label": "Nyctalopia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30099644",
+        "description": "A novel mutation in the PRPF31 in a North Indian adRP family with incomplete penetrance"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:26121",
+    "symbol": "PRPF31"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "19",
+      "pos": 54629943,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:600138",
+      "label": "RETINITIS PIGMENTOSA 11; RP11"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30099644",
+      "description": "A novel mutation in the PRPF31 in a North Indian adRP family with incomplete penetrance"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-1-1.json b/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-1-1.json
new file mode 100644
index 000000000..7e98c9b6b
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-1-1.json
@@ -0,0 +1,389 @@
+{
+  "id": "PMID:27040691-Bhoj-2016-TBCK-1-1",
+  "subject": {
+    "id": "1-1",
+    "ageAtCollection": {
+      "age": "P5Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000414",
+      "label": "Bulbous nose"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012444",
+      "label": "Brain atrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001562",
+      "label": "Oligohydramnios"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000582",
+      "label": "Upslanted palpebral fissure"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001290",
+      "label": "Generalized hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002376",
+      "label": "Developmental regression"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002283",
+      "label": "Global brain atrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001344",
+      "label": "Absent speech"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000496",
+      "label": "Abnormality of eye movement"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002099",
+      "label": "Asthma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001558",
+      "label": "Decreased fetal movement"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005946",
+      "label": "Ventilator dependence with inability to wean"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000964",
+      "label": "Eczema"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006829",
+      "label": "Severe muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010804",
+      "label": "Tented upper lip vermilion"
+    },
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
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+  }, {
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+      "id": "HP:0000340",
+      "label": "Sloping forehead"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
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+  }, {
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+      "label": "Severe global developmental delay"
+    },
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+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Seizures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:93627",
+    "symbol": "TBCK"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "4",
+      "pos": 107115874,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616900",
+      "label": "Hypotonia, infantile, with psychomotor retardation and characteristic facies 3"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
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+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27040691",
+      "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-1-2.json b/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-1-2.json
new file mode 100644
index 000000000..82ca9a52d
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-1-2.json
@@ -0,0 +1,207 @@
+{
+  "id": "PMID:27040691-Bhoj-2016-TBCK-1-2",
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+      "age": "P11Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
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+  "phenotypicFeatures": [{
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+      "id": "HP:0002283",
+      "label": "Global brain atrophy"
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+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
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+      "label": "Bulbous nose"
+    },
+    "evidence": [{
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+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
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+      }
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+    "id": "NCBIGene:93627",
+    "symbol": "TBCK"
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+    "submittedBy": "UNC:biocuration",
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+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "name": "Phenotype And Trait Ontology",
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+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
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+      "name": "Genotype Ontology",
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+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
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+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27040691",
+      "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-2-1.json b/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-2-1.json
new file mode 100644
index 000000000..d4f0d8647
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-2-1.json
@@ -0,0 +1,280 @@
+{
+  "id": "PMID:27040691-Bhoj-2016-TBCK-2-1",
+  "subject": {
+    "id": "2-1",
+    "ageAtCollection": {
+      "age": "P5Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001344",
+      "label": "Absent speech"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006970",
+      "label": "Periventricular leukomalacia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006829",
+      "label": "Severe muscular hypotonia"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
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+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
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+      "label": "Hypoplasia of the corpus callosum"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
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+    },
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+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
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+        "id": "PMID:27040691",
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+      "label": "Nystagmus"
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+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
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+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
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+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
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+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
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+  "genes": [{
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+    "symbol": "TBCK"
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+      "alt": "A"
+    },
+    "zygosity": {
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+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
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+      "pos": 107168395,
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+    },
+    "zygosity": {
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+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616900",
+      "label": "Hypotonia, infantile, with psychomotor retardation and characteristic facies 3"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27040691",
+      "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-3-1.json b/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-3-1.json
new file mode 100644
index 000000000..3a61da364
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-3-1.json
@@ -0,0 +1,314 @@
+{
+  "id": "PMID:27040691-Bhoj-2016-TBCK-3-1",
+  "subject": {
+    "id": "3-1",
+    "ageAtCollection": {
+      "age": "P11Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000218",
+      "label": "High palate"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001837",
+      "label": "Broad toe"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001250",
+      "label": "Seizures"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000717",
+      "label": "Autism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002376",
+      "label": "Developmental regression"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000490",
+      "label": "Deeply set eye"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
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+      "id": "HP:0001500",
+      "label": "Broad finger"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011342",
+      "label": "Mild global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007302",
+      "label": "Bipolar affective disorder"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000431",
+      "label": "Wide nasal bridge"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000286",
+      "label": "Epicanthus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002650",
+      "label": "Scoliosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:93627",
+    "symbol": "TBCK"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "4",
+      "pos": 107152924,
+      "ref": "A",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616900",
+      "label": "Hypotonia, infantile, with psychomotor retardation and characteristic facies 3"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27040691",
+      "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-4-1.json b/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-4-1.json
new file mode 100644
index 000000000..890d7f3e8
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-4-1.json
@@ -0,0 +1,252 @@
+{
+  "id": "PMID:27040691-Bhoj-2016-TBCK-4-1",
+  "subject": {
+    "id": "4-1",
+    "ageAtCollection": {
+      "age": "P4Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001315",
+      "label": "Reduced tendon reflexes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002119",
+      "label": "Ventriculomegaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001250",
+      "label": "Seizures"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000256",
+      "label": "Macrocephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001999",
+      "label": "Abnormal facial shape"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
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+      "label": "Severe global developmental delay"
+    },
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
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+      "label": "Intellectual disability"
+    },
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002376",
+      "label": "Developmental regression"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:93627",
+    "symbol": "TBCK"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "4",
+      "pos": 107092429,
+      "ref": "T",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "4",
+      "pos": 107168420,
+      "ref": "CTTCA",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616900",
+      "label": "Hypotonia, infantile, with psychomotor retardation and characteristic facies 3"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27040691",
+      "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-4-2.json b/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-4-2.json
new file mode 100644
index 000000000..8356d2c4e
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-4-2.json
@@ -0,0 +1,159 @@
+{
+  "id": "PMID:27040691-Bhoj-2016-TBCK-4-2",
+  "subject": {
+    "id": "4-2",
+    "ageAtCollection": {
+      "age": "p2y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001315",
+      "label": "Reduced tendon reflexes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:93627",
+    "symbol": "TBCK"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "4",
+      "pos": 107092429,
+      "ref": "T",
+      "alt": "C"
+    },
+    "zygosity": {
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+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "4",
+      "pos": 107168420,
+      "ref": "CTTCA",
+      "alt": "c"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616900",
+      "label": "Hypotonia, infantile, with psychomotor retardation and characteristic facies 3"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27040691",
+      "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-5-1.json b/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-5-1.json
new file mode 100644
index 000000000..b3261bad9
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-5-1.json
@@ -0,0 +1,357 @@
+{
+  "id": "PMID:27040691-Bhoj-2016-TBCK-5-1",
+  "subject": {
+    "id": "5-1",
+    "ageAtCollection": {
+      "age": "P10Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001007",
+      "label": "Hirsutism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000280",
+      "label": "Coarse facial features"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
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+      "id": "HP:0001265",
+      "label": "Hyporeflexia"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
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+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
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+    }]
+  }, {
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+    },
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+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
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+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
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+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
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+    }]
+  }, {
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+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
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+    }]
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+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
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+      "label": "Corneal opacity"
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+      }
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+      "label": "Growth hormone deficiency"
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+    "evidence": [{
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+      }
+    }]
+  }],
+  "genes": [{
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+  }],
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+      "label": "homozygous"
+    }
+  }],
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+    }
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+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
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+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27040691",
+      "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-6-1.json b/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-6-1.json
new file mode 100644
index 000000000..584a0a7f4
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-6-1.json
@@ -0,0 +1,283 @@
+{
+  "id": "PMID:27040691-Bhoj-2016-TBCK-6-1",
+  "subject": {
+    "id": "6-1",
+    "ageAtCollection": {
+      "age": "P12Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002750",
+      "label": "Delayed skeletal maturation"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27040691",
+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000414",
+      "label": "Bulbous nose"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
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+        "description": "Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia"
+      }
+    }]
+  }, {
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+      "id": "HP:0000194",
+      "label": "Open mouth"
+    },
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+  "diseases": [{
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+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-6-2.json b/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-6-2.json
new file mode 100644
index 000000000..14d812ee2
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-6-2.json
@@ -0,0 +1,162 @@
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+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-8-1.json b/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-8-1.json
new file mode 100644
index 000000000..a128b6547
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Bhoj-2016-TBCK-8-1.json
@@ -0,0 +1,298 @@
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+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Bicknell-2007-FLNB-19.json b/notebooks/LIRICAL/v1phenopackets/Bicknell-2007-FLNB-19.json
new file mode 100644
index 000000000..d2034db4b
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Bicknell-2007-FLNB-19.json
@@ -0,0 +1,267 @@
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+        "description": "A molecular and clinical study of Larsen syndrome caused by mutations in FLNB"
+      }
+    }]
+  }, {
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+      "id": "HP:0005191",
+      "label": "Congenital knee dislocation"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+        "label": "author statement supported by traceable reference"
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+      }
+    }]
+  }, {
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+      "id": "HP:0008438",
+      "label": "Vertebral arch anomaly"
+    },
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+      },
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+        "description": "A molecular and clinical study of Larsen syndrome caused by mutations in FLNB"
+      }
+    }]
+  }, {
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+      "id": "HP:0000175",
+      "label": "Cleft palate"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:16801345",
+        "description": "A molecular and clinical study of Larsen syndrome caused by mutations in FLNB"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2317",
+    "symbol": "FLNB"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "3",
+      "pos": 58131722,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:150250",
+      "label": "LARSEN SYNDROME; LRS"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.12-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:16801345",
+      "description": "A molecular and clinical study of Larsen syndrome caused by mutations in FLNB"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Blanco-Kelly-2017-CDH3-Patient.json b/notebooks/LIRICAL/v1phenopackets/Blanco-Kelly-2017-CDH3-Patient.json
new file mode 100644
index 000000000..ecd0d6388
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Blanco-Kelly-2017-CDH3-Patient.json
@@ -0,0 +1,312 @@
+{
+  "id": "PMID:28061825-Blanco-Kelly-2017-CDH3-Patient",
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+    "ageAtCollection": {
+      "age": "P12Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002209",
+      "label": "Sparse scalp hair"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28061825",
+        "description": "New CDH3 mutation in the first Spanish case of hypotrichosis with juvenile macular dystrophy, a case report"
+      }
+    }]
+  }, {
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+      "id": "HP:0007502",
+      "label": "Follicular hyperkeratosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "description": "New CDH3 mutation in the first Spanish case of hypotrichosis with juvenile macular dystrophy, a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001760",
+      "label": "Abnormality of the foot"
+    },
+    "negated": true,
+    "evidence": [{
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+      "label": "Dry skin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28061825",
+        "description": "New CDH3 mutation in the first Spanish case of hypotrichosis with juvenile macular dystrophy, a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006482",
+      "label": "Abnormality of dental morphology"
+    },
+    "negated": true,
+    "evidence": [{
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+      "id": "HP:0410400",
+      "label": "Absent sebaceous glands"
+    },
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+        "id": "ECO:0000033",
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+        "description": "New CDH3 mutation in the first Spanish case of hypotrichosis with juvenile macular dystrophy, a case report"
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+    }]
+  }, {
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+      "label": "Macular hyperpigmentation"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+  }, {
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+        "description": "New CDH3 mutation in the first Spanish case of hypotrichosis with juvenile macular dystrophy, a case report"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:1001",
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+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "16",
+      "pos": 68713838,
+      "ref": "AG",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:601553",
+      "label": "HYPOTRICHOSIS, CONGENITAL, WITH JUVENILE MACULAR DYSTROPHY; HJMD"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28061825",
+      "description": "New CDH3 mutation in the first Spanish case of hypotrichosis with juvenile macular dystrophy, a case report"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Bluteau-2018-SAMD9L-UB049.json b/notebooks/LIRICAL/v1phenopackets/Bluteau-2018-SAMD9L-UB049.json
new file mode 100644
index 000000000..78025c817
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Bluteau-2018-SAMD9L-UB049.json
@@ -0,0 +1,197 @@
+{
+  "id": "PMID:29146883-Bluteau-2018-SAMD9L-UB049",
+  "subject": {
+    "id": "UB049",
+    "ageAtCollection": {
+      "age": "P10M"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0005528",
+      "label": "Bone marrow hypocellularity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29146883",
+        "description": "A landscape of germ line mutations in a cohort of inherited bone marrow failure patients"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001510",
+      "label": "Growth delay"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29146883",
+        "description": "A landscape of germ line mutations in a cohort of inherited bone marrow failure patients"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031413",
+      "label": "Short telomere length"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+      }
+    }]
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+        "id": "PMID:29146883",
+        "description": "A landscape of germ line mutations in a cohort of inherited bone marrow failure patients"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:219285",
+    "symbol": "SAMD9L"
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+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:159550",
+      "label": "Ataxia-pancytopenia syndrome"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29146883",
+      "description": "A landscape of germ line mutations in a cohort of inherited bone marrow failure patients"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Bluteau-2018-SAMD9L-UB081.json b/notebooks/LIRICAL/v1phenopackets/Bluteau-2018-SAMD9L-UB081.json
new file mode 100644
index 000000000..bfc0ecba4
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Bluteau-2018-SAMD9L-UB081.json
@@ -0,0 +1,195 @@
+{
+  "id": "PMID:29146883-Bluteau-2018-SAMD9L-UB081",
+  "subject": {
+    "id": "UB081",
+    "ageAtCollection": {
+      "age": "P1Y1M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0005528",
+      "label": "Bone marrow hypocellularity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29146883",
+        "description": "A landscape of germ line mutations in a cohort of inherited bone marrow failure patients"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001510",
+      "label": "Growth delay"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
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+      },
+      "reference": {
+        "id": "PMID:29146883",
+        "description": "A landscape of germ line mutations in a cohort of inherited bone marrow failure patients"
+      }
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+  }, {
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+      "id": "HP:0000238",
+      "label": "Hydrocephalus"
+    },
+    "evidence": [{
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+      }
+    }]
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+        "id": "PMID:29146883",
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+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002721",
+      "label": "Immunodeficiency"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29146883",
+        "description": "A landscape of germ line mutations in a cohort of inherited bone marrow failure patients"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:219285",
+    "symbol": "SAMD9L"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "7",
+      "pos": 92760637,
+      "ref": "A",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:159550",
+      "label": "Ataxia-pancytopenia syndrome"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29146883",
+      "description": "A landscape of germ line mutations in a cohort of inherited bone marrow failure patients"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Bluteau-2018-SAMD9L-UB085.json b/notebooks/LIRICAL/v1phenopackets/Bluteau-2018-SAMD9L-UB085.json
new file mode 100644
index 000000000..972f176f1
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Bluteau-2018-SAMD9L-UB085.json
@@ -0,0 +1,269 @@
+{
+  "id": "PMID:29146883-Bluteau-2018-SAMD9L-UB085",
+  "subject": {
+    "id": "UB085",
+    "ageAtCollection": {
+      "age": "P1Y8M"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002500",
+      "label": "Abnormality of the cerebral white matter"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29146883",
+        "description": "A landscape of germ line mutations in a cohort of inherited bone marrow failure patients"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002317",
+      "label": "Unsteady gait"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29146883",
+        "description": "A landscape of germ line mutations in a cohort of inherited bone marrow failure patients"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002673",
+      "label": "Coxa valga"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29146883",
+        "description": "A landscape of germ line mutations in a cohort of inherited bone marrow failure patients"
+      }
+    }]
+  }, {
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+      "id": "HP:0000238",
+      "label": "Hydrocephalus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29146883",
+        "description": "A landscape of germ line mutations in a cohort of inherited bone marrow failure patients"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001321",
+      "label": "Cerebellar hypoplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+      },
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+    "evidence": [{
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+        "id": "PMID:29146883",
+        "description": "A landscape of germ line mutations in a cohort of inherited bone marrow failure patients"
+      }
+    }]
+  }, {
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+      "label": "Intellectual disability, mild"
+    },
+    "evidence": [{
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+        "id": "PMID:29146883",
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+        "id": "PMID:29146883",
+        "description": "A landscape of germ line mutations in a cohort of inherited bone marrow failure patients"
+      }
+    }]
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+      "id": "HP:0100702",
+      "label": "Arachnoid cyst"
+    },
+    "evidence": [{
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+        "description": "A landscape of germ line mutations in a cohort of inherited bone marrow failure patients"
+      }
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+      "label": "Asthma"
+    },
+    "evidence": [{
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+      "reference": {
+        "id": "PMID:29146883",
+        "description": "A landscape of germ line mutations in a cohort of inherited bone marrow failure patients"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001876",
+      "label": "Pancytopenia"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:29146883",
+        "description": "A landscape of germ line mutations in a cohort of inherited bone marrow failure patients"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:219285",
+    "symbol": "SAMD9L"
+  }],
+  "variants": [{
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+      "genomeAssembly": "GRCh37",
+      "chr": "7",
+      "pos": 92762185,
+      "ref": "C",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:159550",
+      "label": "Ataxia-pancytopenia syndrome"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29146883",
+      "description": "A landscape of germ line mutations in a cohort of inherited bone marrow failure patients"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Bluteau-2018-SAMD9L-UB612.json b/notebooks/LIRICAL/v1phenopackets/Bluteau-2018-SAMD9L-UB612.json
new file mode 100644
index 000000000..ba6227109
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Bluteau-2018-SAMD9L-UB612.json
@@ -0,0 +1,132 @@
+{
+  "id": "PMID:29146883-Bluteau-2018-SAMD9L-UB612",
+  "subject": {
+    "id": "UB612",
+    "ageAtCollection": {
+      "age": "P5Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0005528",
+      "label": "Bone marrow hypocellularity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29146883",
+        "description": "A landscape of germ line mutations in a cohort of inherited bone marrow failure patients"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001876",
+      "label": "Pancytopenia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29146883",
+        "description": "A landscape of germ line mutations in a cohort of inherited bone marrow failure patients"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000639",
+      "label": "Nystagmus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29146883",
+        "description": "A landscape of germ line mutations in a cohort of inherited bone marrow failure patients"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:219285",
+    "symbol": "SAMD9L"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "7",
+      "pos": 92762329,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:159550",
+      "label": "Ataxia-pancytopenia syndrome"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29146883",
+      "description": "A landscape of germ line mutations in a cohort of inherited bone marrow failure patients"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Boddrich-1997-NF1-0548.json b/notebooks/LIRICAL/v1phenopackets/Boddrich-1997-NF1-0548.json
new file mode 100644
index 000000000..92bfabb6e
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Boddrich-1997-NF1-0548.json
@@ -0,0 +1,206 @@
+{
+  "id": "PMID:9101303-Böddrich-1997-NF1-0548",
+  "subject": {
+    "id": "0548",
+    "ageAtCollection": {
+      "age": "2y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0009732",
+      "label": "Plexiform neurofibroma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:9101303",
+        "description": "New evidence for a mutation hotspot in exon 37 of the NF1 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001480",
+      "label": "Freckling"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:9101303",
+        "description": "New evidence for a mutation hotspot in exon 37 of the NF1 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007565",
+      "label": "Multiple cafe-au-lait spots"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:9101303",
+        "description": "New evidence for a mutation hotspot in exon 37 of the NF1 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000767",
+      "label": "Pectus excavatum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:9101303",
+        "description": "New evidence for a mutation hotspot in exon 37 of the NF1 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002751",
+      "label": "Kyphoscoliosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:9101303",
+        "description": "New evidence for a mutation hotspot in exon 37 of the NF1 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001010",
+      "label": "Hypopigmentation of the skin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:9101303",
+        "description": "New evidence for a mutation hotspot in exon 37 of the NF1 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001067",
+      "label": "Neurofibromas"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:9101303",
+        "description": "New evidence for a mutation hotspot in exon 37 of the NF1 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000957",
+      "label": "Cafe-au-lait spot"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:9101303",
+        "description": "New evidence for a mutation hotspot in exon 37 of the NF1 gene"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:4763",
+    "symbol": "NF1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "17",
+      "pos": 29665753,
+      "ref": "C",
+      "alt": "CTT"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:162200",
+      "label": "NEUROFIBROMATOSIS, TYPE I; NF1"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:9101303",
+      "description": "New evidence for a mutation hotspot in exon 37 of the NF1 gene"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Bordbar-2017-PRF1-8-year-old_boy.json b/notebooks/LIRICAL/v1phenopackets/Bordbar-2017-PRF1-8-year-old_boy.json
new file mode 100644
index 000000000..c74bcc856
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Bordbar-2017-PRF1-8-year-old_boy.json
@@ -0,0 +1,178 @@
+{
+  "id": "PMID:28468610-Bordbar-2017-PRF1-8-year-old_boy",
+  "subject": {
+    "id": "8-year-old boy",
+    "ageAtCollection": {
+      "age": "P8Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
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+      "label": "Elevated serum alanine aminotransferase"
+    },
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+        "description": "A case report of novel mutation in PRF1 gene, which causes familial autosomal recessive hemophagocytic lymphohistiocytosis"
+      }
+    }]
+  }, {
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+      "id": "HP:0025435",
+      "label": "Increased lactate dehydrogenase activity"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
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+      }
+    }]
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+      "label": "Increased serum ferritin"
+    },
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+  }],
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+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
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+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
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+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
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+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
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+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
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+    "externalReferences": [{
+      "id": "PMID:28468610",
+      "description": "A case report of novel mutation in PRF1 gene, which causes familial autosomal recessive hemophagocytic lymphohistiocytosis"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Bulut-2017-SETBP1-proposita.json b/notebooks/LIRICAL/v1phenopackets/Bulut-2017-SETBP1-proposita.json
new file mode 100644
index 000000000..9a809e00e
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Bulut-2017-SETBP1-proposita.json
@@ -0,0 +1,478 @@
+{
+  "id": "PMID:29333303-Bulut-2017-SETBP1-proposita",
+  "subject": {
+    "id": "proposita",
+    "ageAtCollection": {
+      "age": "P11M"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
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+    "type": {
+      "id": "HP:0001141",
+      "label": "Severely reduced visual acuity"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29333303",
+        "description": "Schinzel-Giedion Syndrome with Congenital Megacalycosis in a Turkish Patient: Report of SETBP1 Mutation and Literature Review of the Clinical Features"
+      }
+    }]
+  }, {
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+      "label": "Narrow forehead"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:29333303",
+        "description": "Schinzel-Giedion Syndrome with Congenital Megacalycosis in a Turkish Patient: Report of SETBP1 Mutation and Literature Review of the Clinical Features"
+      }
+    }]
+  }, {
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+      "label": "Growth delay"
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+      }
+    }]
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+      "label": "Hydronephrosis"
+    },
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:29333303",
+        "description": "Schinzel-Giedion Syndrome with Congenital Megacalycosis in a Turkish Patient: Report of SETBP1 Mutation and Literature Review of the Clinical Features"
+      }
+    }]
+  }, {
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+      }
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+      "label": "Bilateral fetal pyelectasis"
+    },
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+        "label": "author statement supported by traceable reference"
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+        "description": "Schinzel-Giedion Syndrome with Congenital Megacalycosis in a Turkish Patient: Report of SETBP1 Mutation and Literature Review of the Clinical Features"
+      }
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+  }, {
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+      "label": "Talipes equinovarus"
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+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+      }
+    }]
+  }, {
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+      "label": "Frontal bossing"
+    },
+    "evidence": [{
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+      }
+    }]
+  }, {
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+      }
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+      "label": "Wide anterior fontanel"
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+      }
+    }]
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+      "label": "Low-set ears"
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+  }, {
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+      "label": "Abnormal fundus morphology"
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+    "negated": true,
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+      "label": "Seizures"
+    },
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+      }
+    }]
+  }, {
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+      "id": "HP:0001655",
+      "label": "Patent foramen ovale"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Schinzel-Giedion Syndrome with Congenital Megacalycosis in a Turkish Patient: Report of SETBP1 Mutation and Literature Review of the Clinical Features"
+      }
+    }]
+  }, {
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+      "id": "HP:0011800",
+      "label": "Midface retrusion"
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+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:29333303",
+        "description": "Schinzel-Giedion Syndrome with Congenital Megacalycosis in a Turkish Patient: Report of SETBP1 Mutation and Literature Review of the Clinical Features"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:26040",
+    "symbol": "SETBP1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "18",
+      "pos": 42531913,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:269150",
+      "label": "SCHINZEL-GIEDION MIDFACE RETRACTION SYNDROME"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29333303",
+      "description": "Schinzel-Giedion Syndrome with Congenital Megacalycosis in a Turkish Patient: Report of SETBP1 Mutation and Literature Review of the Clinical Features"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Calado-2005-UMOD-proband.json b/notebooks/LIRICAL/v1phenopackets/Calado-2005-UMOD-proband.json
new file mode 100644
index 000000000..d5c01f5cc
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Calado-2005-UMOD-proband.json
@@ -0,0 +1,177 @@
+{
+  "id": "PMID:15673476-Calado-2005-UMOD-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P49Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000083",
+      "label": "Renal insufficiency"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:15673476",
+        "description": "A novel heterozygous missense mutation in the UMOD gene responsible for Familial Juvenile Hyperuricemic Nephropathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003774",
+      "label": "Stage 5 chronic kidney disease"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:15673476",
+        "description": "A novel heterozygous missense mutation in the UMOD gene responsible for Familial Juvenile Hyperuricemic Nephropathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002149",
+      "label": "Hyperuricemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:15673476",
+        "description": "A novel heterozygous missense mutation in the UMOD gene responsible for Familial Juvenile Hyperuricemic Nephropathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003259",
+      "label": "Elevated serum creatinine"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:15673476",
+        "description": "A novel heterozygous missense mutation in the UMOD gene responsible for Familial Juvenile Hyperuricemic Nephropathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000107",
+      "label": "Renal cyst"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:15673476",
+        "description": "A novel heterozygous missense mutation in the UMOD gene responsible for Familial Juvenile Hyperuricemic Nephropathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001997",
+      "label": "Gout"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:15673476",
+        "description": "A novel heterozygous missense mutation in the UMOD gene responsible for Familial Juvenile Hyperuricemic Nephropathy"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:7369",
+    "symbol": "UMOD"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "16",
+      "pos": 20359598,
+      "ref": "T",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:162000",
+      "label": "HYPERURICEMIC NEPHROPATHY, FAMILIAL JUVENILE, 1; HNFJ1"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:15673476",
+      "description": "A novel heterozygous missense mutation in the UMOD gene responsible for Familial Juvenile Hyperuricemic Nephropathy"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Canosa-2018-SOD1-patient.json b/notebooks/LIRICAL/v1phenopackets/Canosa-2018-SOD1-patient.json
new file mode 100644
index 000000000..b89b13b03
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Canosa-2018-SOD1-patient.json
@@ -0,0 +1,192 @@
+{
+  "id": "PMID:30236613-Canosa-2018-SOD1-patient",
+  "subject": {
+    "id": "patient",
+    "ageAtCollection": {
+      "age": "64Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001283",
+      "label": "Bulbar palsy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30236613",
+        "description": "A novel p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003487",
+      "label": "Babinski sign"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30236613",
+        "description": "A novel p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002015",
+      "label": "Dysphagia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30236613",
+        "description": "A novel p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002273",
+      "label": "Tetraparesis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30236613",
+        "description": "A novel p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011448",
+      "label": "Ankle clonus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30236613",
+        "description": "A novel p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001260",
+      "label": "Dysarthria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30236613",
+        "description": "A novel p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012473",
+      "label": "Tongue atrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30236613",
+        "description": "A novel p"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:6647",
+    "symbol": "SOD1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "21",
+      "pos": 33039650,
+      "ref": "C",
+      "alt": "CT"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:105400",
+      "label": "AMYOTROPHIC LATERAL SCLEROSIS 1; ALS1"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30236613",
+      "description": "A novel p"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Cao-2018-FBN1-Patient_1.json b/notebooks/LIRICAL/v1phenopackets/Cao-2018-FBN1-Patient_1.json
new file mode 100644
index 000000000..e6e8fc374
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Cao-2018-FBN1-Patient_1.json
@@ -0,0 +1,147 @@
+{
+  "id": "PMID:30101859-Cao-2018-FBN1-Patient_1",
+  "subject": {
+    "id": "Patient 1",
+    "ageAtCollection": {
+      "age": "P24Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002650",
+      "label": "Scoliosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30101859",
+        "description": "Three Novel Mutations in FBN1 and TGFBR2 in Patients with the Syndromic Form of Thoracic Aortic Aneurysms and Dissections"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011003",
+      "label": "High myopia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30101859",
+        "description": "Three Novel Mutations in FBN1 and TGFBR2 in Patients with the Syndromic Form of Thoracic Aortic Aneurysms and Dissections"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001519",
+      "label": "Disproportionate tall stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30101859",
+        "description": "Three Novel Mutations in FBN1 and TGFBR2 in Patients with the Syndromic Form of Thoracic Aortic Aneurysms and Dissections"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004970",
+      "label": "Ascending tubular aorta aneurysm"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30101859",
+        "description": "Three Novel Mutations in FBN1 and TGFBR2 in Patients with the Syndromic Form of Thoracic Aortic Aneurysms and Dissections"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2200",
+    "symbol": "FBN1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "15",
+      "pos": 48808561,
+      "ref": "T",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:154700",
+      "label": "MARFAN SYNDROME; MFS"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30101859",
+      "description": "Three Novel Mutations in FBN1 and TGFBR2 in Patients with the Syndromic Form of Thoracic Aortic Aneurysms and Dissections"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Cao-2018-FBN1-Patient_2.json b/notebooks/LIRICAL/v1phenopackets/Cao-2018-FBN1-Patient_2.json
new file mode 100644
index 000000000..2e17bbef2
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Cao-2018-FBN1-Patient_2.json
@@ -0,0 +1,252 @@
+{
+  "id": "PMID:30101859-Cao-2018-FBN1-Patient_2",
+  "subject": {
+    "id": "Patient 2",
+    "ageAtCollection": {
+      "age": "P36Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000486",
+      "label": "Strabismus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30101859",
+        "description": "Three Novel Mutations in FBN1 and TGFBR2 in Patients with the Syndromic Form of Thoracic Aortic Aneurysms and Dissections"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000483",
+      "label": "Astigmatism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30101859",
+        "description": "Three Novel Mutations in FBN1 and TGFBR2 in Patients with the Syndromic Form of Thoracic Aortic Aneurysms and Dissections"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001519",
+      "label": "Disproportionate tall stature"
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+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Cao-2018-FBN1-Patient_3.json b/notebooks/LIRICAL/v1phenopackets/Cao-2018-FBN1-Patient_3.json
new file mode 100644
index 000000000..fbd6b0386
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Cao-2018-FBN1-Patient_3.json
@@ -0,0 +1,147 @@
+{
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+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Cao-2018-TGFBR2-Patient_4.json b/notebooks/LIRICAL/v1phenopackets/Cao-2018-TGFBR2-Patient_4.json
new file mode 100644
index 000000000..6ea16fc70
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Cao-2018-TGFBR2-Patient_4.json
@@ -0,0 +1,312 @@
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+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30101859",
+      "description": "Three Novel Mutations in FBN1 and TGFBR2 in Patients with the Syndromic Form of Thoracic Aortic Aneurysms and Dissections"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Caputo-2014-SMAD4-patient.json b/notebooks/LIRICAL/v1phenopackets/Caputo-2014-SMAD4-patient.json
new file mode 100644
index 000000000..a69544782
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Caputo-2014-SMAD4-patient.json
@@ -0,0 +1,359 @@
+{
+  "id": "PMID:24715504-Caputo-2014-SMAD4-patient",
+  "subject": {
+    "id": "patient",
+    "ageAtCollection": {
+      "age": "15Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001156",
+      "label": "Brachydactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24715504",
+        "description": "Novel SMAD4 mutation causing Myhre syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001387",
+      "label": "Joint stiffness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24715504",
+        "description": "Novel SMAD4 mutation causing Myhre syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000527",
+      "label": "Long eyelashes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24715504",
+        "description": "Novel SMAD4 mutation causing Myhre syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001627",
+      "label": "Abnormal heart morphology"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24715504",
+        "description": "Novel SMAD4 mutation causing Myhre syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012210",
+      "label": "Abnormal renal morphology"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24715504",
+        "description": "Novel SMAD4 mutation causing Myhre syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008513",
+      "label": "Bilateral conductive hearing impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24715504",
+        "description": "Novel SMAD4 mutation causing Myhre syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002553",
+      "label": "Highly arched eyebrow"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24715504",
+        "description": "Novel SMAD4 mutation causing Myhre syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002684",
+      "label": "Thickened calvaria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24715504",
+        "description": "Novel SMAD4 mutation causing Myhre syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0032152",
+      "label": "Keratosis pilaris"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24715504",
+        "description": "Novel SMAD4 mutation causing Myhre syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001276",
+      "label": "Hypertonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24715504",
+        "description": "Novel SMAD4 mutation causing Myhre syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002942",
+      "label": "Thoracic kyphosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24715504",
+        "description": "Novel SMAD4 mutation causing Myhre syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012443",
+      "label": "Abnormality of brain morphology"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24715504",
+        "description": "Novel SMAD4 mutation causing Myhre syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004621",
+      "label": "Enlarged vertebral pedicles"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24715504",
+        "description": "Novel SMAD4 mutation causing Myhre syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001284",
+      "label": "Areflexia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24715504",
+        "description": "Novel SMAD4 mutation causing Myhre syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002938",
+      "label": "Lumbar hyperlordosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24715504",
+        "description": "Novel SMAD4 mutation causing Myhre syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002312",
+      "label": "Clumsiness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24715504",
+        "description": "Novel SMAD4 mutation causing Myhre syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000405",
+      "label": "Conductive hearing impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24715504",
+        "description": "Novel SMAD4 mutation causing Myhre syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000303",
+      "label": "Mandibular prognathia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24715504",
+        "description": "Novel SMAD4 mutation causing Myhre syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:4089",
+    "symbol": "SMAD4"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "18",
+      "pos": 48604664,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:139210",
+      "label": "MYHRE SYNDROME; MYHRS"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:24715504",
+      "description": "Novel SMAD4 mutation causing Myhre syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Caro-Contreras-2019-ERF-proband.json b/notebooks/LIRICAL/v1phenopackets/Caro-Contreras-2019-ERF-proband.json
new file mode 100644
index 000000000..b4b50483b
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Caro-Contreras-2019-ERF-proband.json
@@ -0,0 +1,343 @@
+{
+  "id": "PMID:30569521-Caro-Contreras-2019-ERF-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P3Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0004209",
+      "label": "Clinodactyly of the 5th finger"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30569521",
+        "description": "Molecular analysis provides further evidence that Chitayat syndrome is caused by the recurrent p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012471",
+      "label": "Thick vermilion border"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30569521",
+        "description": "Molecular analysis provides further evidence that Chitayat syndrome is caused by the recurrent p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30569521",
+        "description": "Molecular analysis provides further evidence that Chitayat syndrome is caused by the recurrent p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001561",
+      "label": "Polyhydramnios"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30569521",
+        "description": "Molecular analysis provides further evidence that Chitayat syndrome is caused by the recurrent p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001822",
+      "label": "Hallux valgus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30569521",
+        "description": "Molecular analysis provides further evidence that Chitayat syndrome is caused by the recurrent p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000768",
+      "label": "Pectus carinatum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30569521",
+        "description": "Molecular analysis provides further evidence that Chitayat syndrome is caused by the recurrent p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000520",
+      "label": "Proptosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30569521",
+        "description": "Molecular analysis provides further evidence that Chitayat syndrome is caused by the recurrent p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002098",
+      "label": "Respiratory distress"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30569521",
+        "description": "Molecular analysis provides further evidence that Chitayat syndrome is caused by the recurrent p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005469",
+      "label": "Flat occiput"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30569521",
+        "description": "Molecular analysis provides further evidence that Chitayat syndrome is caused by the recurrent p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001156",
+      "label": "Brachydactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30569521",
+        "description": "Molecular analysis provides further evidence that Chitayat syndrome is caused by the recurrent p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000341",
+      "label": "Narrow forehead"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30569521",
+        "description": "Molecular analysis provides further evidence that Chitayat syndrome is caused by the recurrent p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002020",
+      "label": "Gastroesophageal reflux"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30569521",
+        "description": "Molecular analysis provides further evidence that Chitayat syndrome is caused by the recurrent p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011951",
+      "label": "Aspiration pneumonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30569521",
+        "description": "Molecular analysis provides further evidence that Chitayat syndrome is caused by the recurrent p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000248",
+      "label": "Brachycephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30569521",
+        "description": "Molecular analysis provides further evidence that Chitayat syndrome is caused by the recurrent p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001561",
+      "label": "Polyhydramnios"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30569521",
+        "description": "Molecular analysis provides further evidence that Chitayat syndrome is caused by the recurrent p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005280",
+      "label": "Depressed nasal bridge"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30569521",
+        "description": "Molecular analysis provides further evidence that Chitayat syndrome is caused by the recurrent p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000316",
+      "label": "Hypertelorism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30569521",
+        "description": "Molecular analysis provides further evidence that Chitayat syndrome is caused by the recurrent p"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2077",
+    "symbol": "ERF"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "19",
+      "pos": 42754086,
+      "ref": "T",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617180",
+      "label": "Chitayat syndrome"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30569521",
+      "description": "Molecular analysis provides further evidence that Chitayat syndrome is caused by the recurrent p"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Carre-2014-FOXE1-patient.json b/notebooks/LIRICAL/v1phenopackets/Carre-2014-FOXE1-patient.json
new file mode 100644
index 000000000..a7418d936
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Carre-2014-FOXE1-patient.json
@@ -0,0 +1,191 @@
+{
+  "id": "PMID:24219130-Carré-2014-FOXE1-patient",
+  "subject": {
+    "id": "patient",
+    "ageAtCollection": {
+      "age": "P1M"
+    },
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+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0100786",
+      "label": "Hypersomnia"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24219130",
+        "description": "A novel FOXE1 mutation (R73S) in Bamforth-Lazarus syndrome causing increased thyroidal gene expression"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008191",
+      "label": "Thyroid agenesis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24219130",
+        "description": "A novel FOXE1 mutation (R73S) in Bamforth-Lazarus syndrome causing increased thyroidal gene expression"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031507",
+      "label": "Decreased circulating thyroxine level"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24219130",
+        "description": "A novel FOXE1 mutation (R73S) in Bamforth-Lazarus syndrome causing increased thyroidal gene expression"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Feeding difficulties"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24219130",
+        "description": "A novel FOXE1 mutation (R73S) in Bamforth-Lazarus syndrome causing increased thyroidal gene expression"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Increased thyroid-stimulating hormone level"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:24219130",
+        "description": "A novel FOXE1 mutation (R73S) in Bamforth-Lazarus syndrome causing increased thyroidal gene expression"
+      }
+    }]
+  }, {
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+      "label": "Cleft palate"
+    },
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:24219130",
+        "description": "A novel FOXE1 mutation (R73S) in Bamforth-Lazarus syndrome causing increased thyroidal gene expression"
+      }
+    }]
+  }, {
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+      "id": "HP:0000453",
+      "label": "Choanal atresia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24219130",
+        "description": "A novel FOXE1 mutation (R73S) in Bamforth-Lazarus syndrome causing increased thyroidal gene expression"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2304",
+    "symbol": "FOXE1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "9",
+      "pos": 100616413,
+      "ref": "C",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:241850",
+      "label": "HYPOTHYROIDISM, THYROIDAL OR ATHYROIDAL, WITH SPIKY HAIR AND CLEFTPALATE"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
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+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:24219130",
+      "description": "A novel FOXE1 mutation (R73S) in Bamforth-Lazarus syndrome causing increased thyroidal gene expression"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Chabas-2005-GBA-_boy_weighing_1690_g.json b/notebooks/LIRICAL/v1phenopackets/Chabas-2005-GBA-_boy_weighing_1690_g.json
new file mode 100644
index 000000000..e6241b210
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Chabas-2005-GBA-_boy_weighing_1690_g.json
@@ -0,0 +1,191 @@
+{
+  "id": "PMID:15967693-Chabás-2005-GBA-_boy_weighing_1690_g",
+  "subject": {
+    "id": " boy weighing 1690 g",
+    "ageAtCollection": {
+      "age": "25D"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001873",
+      "label": "Thrombocytopenia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:15967693",
+        "description": "Perinatal lethal phenotype with generalized ichthyosis in a type 2 Gaucher disease patient with the [L444P;E326K]/P182L genotype: effect of the E326K change in neonatal and classic forms of the disease"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004325",
+      "label": "Decreased body weight"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:15967693",
+        "description": "Perinatal lethal phenotype with generalized ichthyosis in a type 2 Gaucher disease patient with the [L444P;E326K]/P182L genotype: effect of the E326K change in neonatal and classic forms of the disease"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001290",
+      "label": "Generalized hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:15967693",
+        "description": "Perinatal lethal phenotype with generalized ichthyosis in a type 2 Gaucher disease patient with the [L444P;E326K]/P182L genotype: effect of the E326K change in neonatal and classic forms of the disease"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003656",
+      "label": "Decreased beta-glucocerebrosidase protein and activity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:15967693",
+        "description": "Perinatal lethal phenotype with generalized ichthyosis in a type 2 Gaucher disease patient with the [L444P;E326K]/P182L genotype: effect of the E326K change in neonatal and classic forms of the disease"
+      }
+    }]
+  }, {
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+      "id": "HP:0001433",
+      "label": "Hepatosplenomegaly"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:15967693",
+        "description": "Perinatal lethal phenotype with generalized ichthyosis in a type 2 Gaucher disease patient with the [L444P;E326K]/P182L genotype: effect of the E326K change in neonatal and classic forms of the disease"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001522",
+      "label": "Death in infancy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:15967693",
+        "description": "Perinatal lethal phenotype with generalized ichthyosis in a type 2 Gaucher disease patient with the [L444P;E326K]/P182L genotype: effect of the E326K change in neonatal and classic forms of the disease"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007479",
+      "label": "Congenital nonbullous ichthyosiform erythroderma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:15967693",
+        "description": "Perinatal lethal phenotype with generalized ichthyosis in a type 2 Gaucher disease patient with the [L444P;E326K]/P182L genotype: effect of the E326K change in neonatal and classic forms of the disease"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2629",
+    "symbol": "GBA"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 155204848,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:608013",
+      "label": "GAUCHER DISEASE, PERINATAL LETHAL"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:15967693",
+      "description": "Perinatal lethal phenotype with generalized ichthyosis in a type 2 Gaucher disease patient with the [L444P;E326K]/P182L genotype: effect of the E326K change in neonatal and classic forms of the disease"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Chebly-2018-ERCC6-Patient_B.json b/notebooks/LIRICAL/v1phenopackets/Chebly-2018-ERCC6-Patient_B.json
new file mode 100644
index 000000000..2727ca72f
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Chebly-2018-ERCC6-Patient_B.json
@@ -0,0 +1,162 @@
+{
+  "id": "PMID:30200888-Chebly-2018-ERCC6-Patient_B",
+  "subject": {
+    "id": "Patient B",
+    "ageAtCollection": {
+      "age": "P1Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000958",
+      "label": "Dry skin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30200888",
+        "description": "First molecular study in Lebanese patients with Cockayne syndrome and report of a novel mutation in ERCC8 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000519",
+      "label": "Developmental cataract"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:30200888",
+        "description": "First molecular study in Lebanese patients with Cockayne syndrome and report of a novel mutation in ERCC8 gene"
+      }
+    }]
+  }, {
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+      "id": "HP:0000992",
+      "label": "Cutaneous photosensitivity"
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+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:30200888",
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+      }
+    }]
+  }, {
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+      "id": "HP:0000490",
+      "label": "Deeply set eye"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:30200888",
+        "description": "First molecular study in Lebanese patients with Cockayne syndrome and report of a novel mutation in ERCC8 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000252",
+      "label": "Microcephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:30200888",
+        "description": "First molecular study in Lebanese patients with Cockayne syndrome and report of a novel mutation in ERCC8 gene"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2074",
+    "symbol": "ERCC6"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "10",
+      "pos": 50690894,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:133540",
+      "label": "COCKAYNE SYNDROME B; CSB"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30200888",
+      "description": "First molecular study in Lebanese patients with Cockayne syndrome and report of a novel mutation in ERCC8 gene"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Chebly-2018-ERCC8-Patient_A.json b/notebooks/LIRICAL/v1phenopackets/Chebly-2018-ERCC8-Patient_A.json
new file mode 100644
index 000000000..e0986cc7d
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Chebly-2018-ERCC8-Patient_A.json
@@ -0,0 +1,192 @@
+{
+  "id": "PMID:30200888-Chebly-2018-ERCC8-Patient_A",
+  "subject": {
+    "id": "Patient A",
+    "ageAtCollection": {
+      "age": "P17Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000670",
+      "label": "Carious teeth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30200888",
+        "description": "First molecular study in Lebanese patients with Cockayne syndrome and report of a novel mutation in ERCC8 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:30200888",
+        "description": "First molecular study in Lebanese patients with Cockayne syndrome and report of a novel mutation in ERCC8 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000992",
+      "label": "Cutaneous photosensitivity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:30200888",
+        "description": "First molecular study in Lebanese patients with Cockayne syndrome and report of a novel mutation in ERCC8 gene"
+      }
+    }]
+  }, {
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+      "label": "Generalized hypotonia"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:30200888",
+        "description": "First molecular study in Lebanese patients with Cockayne syndrome and report of a novel mutation in ERCC8 gene"
+      }
+    }]
+  }, {
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+      "id": "HP:0000407",
+      "label": "Sensorineural hearing impairment"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "description": "First molecular study in Lebanese patients with Cockayne syndrome and report of a novel mutation in ERCC8 gene"
+      }
+    }]
+  }, {
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+      "id": "HP:0000252",
+      "label": "Microcephaly"
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+    "evidence": [{
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+        "id": "PMID:30200888",
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+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000490",
+      "label": "Deeply set eye"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:30200888",
+        "description": "First molecular study in Lebanese patients with Cockayne syndrome and report of a novel mutation in ERCC8 gene"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:1161",
+    "symbol": "ERCC8"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "5",
+      "pos": 60186791,
+      "ref": "G",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:216400",
+      "label": "COCKAYNE SYNDROME A; CSA"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30200888",
+      "description": "First molecular study in Lebanese patients with Cockayne syndrome and report of a novel mutation in ERCC8 gene"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Chebly-2018-ERCC8-Patient_C.json b/notebooks/LIRICAL/v1phenopackets/Chebly-2018-ERCC8-Patient_C.json
new file mode 100644
index 000000000..03103e991
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Chebly-2018-ERCC8-Patient_C.json
@@ -0,0 +1,162 @@
+{
+  "id": "PMID:30200888-Chebly-2018-ERCC8-Patient_C",
+  "subject": {
+    "id": "Patient C",
+    "ageAtCollection": {
+      "age": "P3Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001510",
+      "label": "Growth delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30200888",
+        "description": "First molecular study in Lebanese patients with Cockayne syndrome and report of a novel mutation in ERCC8 gene"
+      }
+    }]
+  }, {
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+      "id": "HP:0000518",
+      "label": "Cataract"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:30200888",
+        "description": "First molecular study in Lebanese patients with Cockayne syndrome and report of a novel mutation in ERCC8 gene"
+      }
+    }]
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+      "id": "HP:0000520",
+      "label": "Proptosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:30200888",
+        "description": "First molecular study in Lebanese patients with Cockayne syndrome and report of a novel mutation in ERCC8 gene"
+      }
+    }]
+  }, {
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+      "label": "Hearing impairment"
+    },
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+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:30200888",
+        "description": "First molecular study in Lebanese patients with Cockayne syndrome and report of a novel mutation in ERCC8 gene"
+      }
+    }]
+  }, {
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+      "id": "HP:0000252",
+      "label": "Microcephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:30200888",
+        "description": "First molecular study in Lebanese patients with Cockayne syndrome and report of a novel mutation in ERCC8 gene"
+      }
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+  }],
+  "genes": [{
+    "id": "NCBIGene:1161",
+    "symbol": "ERCC8"
+  }],
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+      "genomeAssembly": "GRCh37",
+      "chr": "5",
+      "pos": 60194102,
+      "ref": "C",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:216400",
+      "label": "COCKAYNE SYNDROME A; CSA"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30200888",
+      "description": "First molecular study in Lebanese patients with Cockayne syndrome and report of a novel mutation in ERCC8 gene"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Chelban-2017-NKX6-2-III-1.json b/notebooks/LIRICAL/v1phenopackets/Chelban-2017-NKX6-2-III-1.json
new file mode 100644
index 000000000..b8a9486a3
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Chelban-2017-NKX6-2-III-1.json
@@ -0,0 +1,374 @@
+{
+  "id": "PMID:28575651-Chelban-2017-NKX6-2-III-1",
+  "subject": {
+    "id": "III-1",
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+      "age": "P27Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0003429",
+      "label": "CNS hypomyelination"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28575651",
+        "description": "Mutations in NKX6-2 Cause Progressive Spastic Ataxia and Hypomyelination"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003474",
+      "label": "Sensory impairment"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28575651",
+        "description": "Mutations in NKX6-2 Cause Progressive Spastic Ataxia and Hypomyelination"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000639",
+      "label": "Nystagmus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28575651",
+        "description": "Mutations in NKX6-2 Cause Progressive Spastic Ataxia and Hypomyelination"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007108",
+      "label": "Demyelinating peripheral neuropathy"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28575651",
+        "description": "Mutations in NKX6-2 Cause Progressive Spastic Ataxia and Hypomyelination"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000605",
+      "label": "Supranuclear gaze palsy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28575651",
+        "description": "Mutations in NKX6-2 Cause Progressive Spastic Ataxia and Hypomyelination"
+      }
+    }]
+  }, {
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+      "id": "HP:0001332",
+      "label": "Dystonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28575651",
+        "description": "Mutations in NKX6-2 Cause Progressive Spastic Ataxia and Hypomyelination"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000473",
+      "label": "Torticollis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28575651",
+        "description": "Mutations in NKX6-2 Cause Progressive Spastic Ataxia and Hypomyelination"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002540",
+      "label": "Inability to walk"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28575651",
+        "description": "Mutations in NKX6-2 Cause Progressive Spastic Ataxia and Hypomyelination"
+      }
+    }]
+  }, {
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+      "id": "HP:0002497",
+      "label": "Spastic ataxia"
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+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28575651",
+        "description": "Mutations in NKX6-2 Cause Progressive Spastic Ataxia and Hypomyelination"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000571",
+      "label": "Hypometric saccades"
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+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28575651",
+        "description": "Mutations in NKX6-2 Cause Progressive Spastic Ataxia and Hypomyelination"
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+    }]
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+      "id": "HP:0001270",
+      "label": "Motor delay"
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+        "description": "Mutations in NKX6-2 Cause Progressive Spastic Ataxia and Hypomyelination"
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+    }]
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+    "type": {
+      "id": "HP:0000511",
+      "label": "Vertical supranuclear gaze palsy"
+    },
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+        "id": "PMID:28575651",
+        "description": "Mutations in NKX6-2 Cause Progressive Spastic Ataxia and Hypomyelination"
+      }
+    }]
+  }, {
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+      "id": "HP:0030187",
+      "label": "Titubation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "description": "Mutations in NKX6-2 Cause Progressive Spastic Ataxia and Hypomyelination"
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+    }]
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+      "id": "HP:0001260",
+      "label": "Dysarthria"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28575651",
+        "description": "Mutations in NKX6-2 Cause Progressive Spastic Ataxia and Hypomyelination"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002062",
+      "label": "Morphological abnormality of the pyramidal tract"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+    }]
+  }, {
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+      "label": "Ataxia"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28575651",
+        "description": "Mutations in NKX6-2 Cause Progressive Spastic Ataxia and Hypomyelination"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012547",
+      "label": "Abnormal involuntary eye movements"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28575651",
+        "description": "Mutations in NKX6-2 Cause Progressive Spastic Ataxia and Hypomyelination"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001272",
+      "label": "Cerebellar atrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28575651",
+        "description": "Mutations in NKX6-2 Cause Progressive Spastic Ataxia and Hypomyelination"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009830",
+      "label": "Peripheral neuropathy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28575651",
+        "description": "Mutations in NKX6-2 Cause Progressive Spastic Ataxia and Hypomyelination"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:84504",
+    "symbol": "NKX6-2"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "10",
+      "pos": 134599332,
+      "ref": "T",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617560",
+      "label": "Spastic ataxia 8, autosomal recessive, with hypomyelinating leukodystrophy"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
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+      "name": "human phenotype ontology",
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+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
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+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
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+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28575651",
+      "description": "Mutations in NKX6-2 Cause Progressive Spastic Ataxia and Hypomyelination"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Chelban-2017-NKX6-2-IV-6.json b/notebooks/LIRICAL/v1phenopackets/Chelban-2017-NKX6-2-IV-6.json
new file mode 100644
index 000000000..23329a140
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Chelban-2017-NKX6-2-IV-6.json
@@ -0,0 +1,147 @@
+{
+  "id": "PMID:28575651-Chelban-2017-NKX6-2-IV-6",
+  "subject": {
+    "id": "IV-6",
+    "ageAtCollection": {
+      "age": "P6Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001257",
+      "label": "Spasticity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28575651",
+        "description": "Mutations in NKX6-2 Cause Progressive Spastic Ataxia and Hypomyelination"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000639",
+      "label": "Nystagmus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
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+        "id": "ECO:0000033",
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+        "id": "PMID:28575651",
+        "description": "Mutations in NKX6-2 Cause Progressive Spastic Ataxia and Hypomyelination"
+      }
+    }]
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+    "id": "NCBIGene:84504",
+    "symbol": "NKX6-2"
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+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
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+    "term": {
+      "id": "OMIM:617560",
+      "label": "Spastic ataxia 8, autosomal recessive, with hypomyelinating leukodystrophy"
+    }
+  }],
+  "metaData": {
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+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28575651",
+      "description": "Mutations in NKX6-2 Cause Progressive Spastic Ataxia and Hypomyelination"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Chen-2014-RUNX2-III_3.json b/notebooks/LIRICAL/v1phenopackets/Chen-2014-RUNX2-III_3.json
new file mode 100644
index 000000000..e285a3737
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Chen-2014-RUNX2-III_3.json
@@ -0,0 +1,237 @@
+{
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+    },
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+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002645",
+      "label": "Wormian bones"
+    },
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+      }
+    }]
+  }, {
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+      "label": "Delayed cranial suture closure"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+        "label": "author statement supported by traceable reference"
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+      }
+    }]
+  }, {
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+      "id": "HP:0002866",
+      "label": "Hypoplastic iliac wing"
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+    "evidence": [{
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+    }]
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+    }]
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+      "label": "Dental malocclusion"
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+      }
+    }]
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+    }
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+    }
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+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
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+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
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+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
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+    "externalReferences": [{
+      "id": "PMID:24966961",
+      "description": "A novel small deletion mutation in RUNX2 gene in one Chinese family with cleidocranial dysplasia"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Chen-2016-SAMD9L-II-4.json b/notebooks/LIRICAL/v1phenopackets/Chen-2016-SAMD9L-II-4.json
new file mode 100644
index 000000000..22a6796ca
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Chen-2016-SAMD9L-II-4.json
@@ -0,0 +1,177 @@
+{
+  "id": "PMID:27259050-Chen-2016-SAMD9L-II-4",
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+      "label": "Homo sapiens"
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+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002066",
+      "label": "Gait ataxia"
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+        "description": "Ataxia-Pancytopenia Syndrome Is Caused by Missense Mutations in SAMD9L"
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+      "id": "HP:0005528",
+      "label": "Bone marrow hypocellularity"
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+        "description": "Ataxia-Pancytopenia Syndrome Is Caused by Missense Mutations in SAMD9L"
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+      "label": "heterozygous"
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+  }],
+  "diseases": [{
+    "term": {
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+      "label": "Ataxia-pancytopenia syndrome"
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+  }],
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+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
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+      "namespacePrefix": "NCBITaxon"
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+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
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+      "id": "PMID:27259050",
+      "description": "Ataxia-Pancytopenia Syndrome Is Caused by Missense Mutations in SAMD9L"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Chen-2016-SAMD9L-IV-1.json b/notebooks/LIRICAL/v1phenopackets/Chen-2016-SAMD9L-IV-1.json
new file mode 100644
index 000000000..8b88528c4
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Chen-2016-SAMD9L-IV-1.json
@@ -0,0 +1,162 @@
+{
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+      "label": "Dysarthria"
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+        "description": "Ataxia-Pancytopenia Syndrome Is Caused by Missense Mutations in SAMD9L"
+      }
+    }]
+  }, {
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+    }
+  }],
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+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27259050",
+      "description": "Ataxia-Pancytopenia Syndrome Is Caused by Missense Mutations in SAMD9L"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Cheng-2018-FBN1-Family_1,_Patient_1.json b/notebooks/LIRICAL/v1phenopackets/Cheng-2018-FBN1-Family_1,_Patient_1.json
new file mode 100644
index 000000000..72896f5fc
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Cheng-2018-FBN1-Family_1,_Patient_1.json
@@ -0,0 +1,299 @@
+{
+  "id": "PMID:29191498-Cheng-2018-FBN1-Family_1,_Patient_1",
+  "subject": {
+    "id": "Family 1, Patient 1",
+    "ageAtCollection": {
+      "age": "P9Y6M"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29191498",
+        "description": "A report of three families with FBN1-related acromelic dysplasias and review of literature for genotype-phenotype correlation in geleophysic dysplasia"
+      }
+    }]
+  }, {
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+      "id": "HP:0001642",
+      "label": "Pulmonic stenosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29191498",
+        "description": "A report of three families with FBN1-related acromelic dysplasias and review of literature for genotype-phenotype correlation in geleophysic dysplasia"
+      }
+    }]
+  }, {
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+      "label": "Dysplastic pulmonary valve"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
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+        "id": "PMID:29191498",
+        "description": "A report of three families with FBN1-related acromelic dysplasias and review of literature for genotype-phenotype correlation in geleophysic dysplasia"
+      }
+    }]
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+      "label": "Lumbar hyperlordosis"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29191498",
+        "description": "A report of three families with FBN1-related acromelic dysplasias and review of literature for genotype-phenotype correlation in geleophysic dysplasia"
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+      }
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+  }, {
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+      "label": "Global developmental delay"
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+      "label": "Short phalanx of finger"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
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+        "description": "A report of three families with FBN1-related acromelic dysplasias and review of literature for genotype-phenotype correlation in geleophysic dysplasia"
+      }
+    }]
+  }, {
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+      "label": "Cone-shaped epiphysis"
+    },
+    "negated": true,
+    "evidence": [{
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+      }
+    }]
+  }, {
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+      "label": "Upslanted palpebral fissure"
+    },
+    "evidence": [{
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+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Internal notch of the femoral head"
+    },
+    "evidence": [{
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+      "label": "Depressed nasal bridge"
+    },
+    "evidence": [{
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+        "description": "A report of three families with FBN1-related acromelic dysplasias and review of literature for genotype-phenotype correlation in geleophysic dysplasia"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2200",
+    "symbol": "FBN1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "15",
+      "pos": 48752455,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:614185",
+      "label": "GELEOPHYSIC DYSPLASIA 2; GPHYSD2"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
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+    "externalReferences": [{
+      "id": "PMID:29191498",
+      "description": "A report of three families with FBN1-related acromelic dysplasias and review of literature for genotype-phenotype correlation in geleophysic dysplasia"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Chong-2016-TBCK-A-II-1.json b/notebooks/LIRICAL/v1phenopackets/Chong-2016-TBCK-A-II-1.json
new file mode 100644
index 000000000..6283f959e
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Chong-2016-TBCK-A-II-1.json
@@ -0,0 +1,507 @@
+{
+  "id": "PMID:27040692-Chong-2016-TBCK-A-II-1",
+  "subject": {
+    "id": "A-II-1",
+    "ageAtCollection": {
+      "age": "P14Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0011968",
+      "label": "Feeding difficulties"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000341",
+      "label": "Narrow forehead"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012736",
+      "label": "Profound global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001284",
+      "label": "Areflexia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010841",
+      "label": "Multifocal epileptiform discharges"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
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+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
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+      "label": "Subdural hemorrhage"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001338",
+      "label": "Partial agenesis of the corpus callosum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
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+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Cerebellar vermis hypoplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
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+      "id": "HP:0007359",
+      "label": "Focal-onset seizure"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002093",
+      "label": "Respiratory insufficiency"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
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+      "id": "HP:0002553",
+      "label": "Highly arched eyebrow"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
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+      "id": "HP:0002376",
+      "label": "Developmental regression"
+    },
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+        "label": "author statement supported by traceable reference"
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+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000280",
+      "label": "Coarse facial features"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000158",
+      "label": "Macroglossia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000463",
+      "label": "Anteverted nares"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002263",
+      "label": "Exaggerated cupid\u0027s bow"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000508",
+      "label": "Ptosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002155",
+      "label": "Hypertriglyceridemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000939",
+      "label": "Osteoporosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001297",
+      "label": "Stroke"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012697",
+      "label": "Small basal ganglia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006829",
+      "label": "Severe muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "namespacePrefix": "NCBITaxon"
+    }, {
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+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
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+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
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+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Chong-2016-TBCK-B-IV-4.json b/notebooks/LIRICAL/v1phenopackets/Chong-2016-TBCK-B-IV-4.json
new file mode 100644
index 000000000..90f3e071e
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Chong-2016-TBCK-B-IV-4.json
@@ -0,0 +1,447 @@
+{
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+      "version": "2018-03-02",
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+      "url": "http://purl.obolibrary.org/obo/eco.owl",
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+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
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+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Chong-2016-TBCK-B-IV-6.json b/notebooks/LIRICAL/v1phenopackets/Chong-2016-TBCK-B-IV-6.json
new file mode 100644
index 000000000..1a018d702
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Chong-2016-TBCK-B-IV-6.json
@@ -0,0 +1,327 @@
+{
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+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
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+      "label": "Feeding difficulties"
+    },
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+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
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+      "label": "Anteverted nares"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000341",
+      "label": "Narrow forehead"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002263",
+      "label": "Exaggerated cupid\u0027s bow"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002353",
+      "label": "EEG abnormality"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000505",
+      "label": "Visual impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
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+      "label": "Hypoplasia of the corpus callosum"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
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+      "id": "HP:0012736",
+      "label": "Profound global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
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+      "id": "HP:0012697",
+      "label": "Small basal ganglia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
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+      "label": "Cerebellar vermis hypoplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
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+      "label": "Ventriculomegaly"
+    },
+    "evidence": [{
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+      }
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+      "label": "Prominent nasal bridge"
+    },
+    "evidence": [{
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+    }]
+  }, {
+    "type": {
+      "id": "HP:0002093",
+      "label": "Respiratory insufficiency"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
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+      }
+    }]
+  }, {
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+      "label": "Highly arched eyebrow"
+    },
+    "evidence": [{
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+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
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+      "label": "Peripheral axonal neuropathy"
+    },
+    "evidence": [{
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+      }
+    }]
+  }, {
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+      "label": "Seizures"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:93627",
+    "symbol": "TBCK"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "4",
+      "pos": 107156512,
+      "ref": "T",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616900",
+      "label": "Hypotonia, infantile, with psychomotor retardation and characteristic facies 3"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27040692",
+      "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Chong-2016-TBCK-C-II-1.json b/notebooks/LIRICAL/v1phenopackets/Chong-2016-TBCK-C-II-1.json
new file mode 100644
index 000000000..9139e7dd9
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Chong-2016-TBCK-C-II-1.json
@@ -0,0 +1,482 @@
+{
+  "id": "PMID:27040692-Chong-2016-TBCK-C-II-1",
+  "subject": {
+    "id": "C-II-1",
+    "ageAtCollection": {
+      "age": "P2Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0011968",
+      "label": "Feeding difficulties"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000341",
+      "label": "Narrow forehead"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001284",
+      "label": "Areflexia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
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+      "label": "Profound global developmental delay"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000262",
+      "label": "Turricephaly"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
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+      "label": "Highly arched eyebrow"
+    },
+    "negated": true,
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001338",
+      "label": "Partial agenesis of the corpus callosum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
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+      "label": "Cerebellar vermis hypoplasia"
+    },
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+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000280",
+      "label": "Coarse facial features"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012020",
+      "label": "Right aortic arch"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000463",
+      "label": "Anteverted nares"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002263",
+      "label": "Exaggerated cupid\u0027s bow"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002353",
+      "label": "EEG abnormality"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
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+      "id": "HP:0001250",
+      "label": "Seizures"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000998",
+      "label": "Hypertrichosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
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+      "id": "HP:0002079",
+      "label": "Hypoplasia of the corpus callosum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002376",
+      "label": "Developmental regression"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012697",
+      "label": "Small basal ganglia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000878",
+      "label": "11 pairs of ribs"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000648",
+      "label": "Optic atrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000158",
+      "label": "Macroglossia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000565",
+      "label": "Esotropia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006829",
+      "label": "Severe muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002119",
+      "label": "Ventriculomegaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27040692",
+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000426",
+      "label": "Prominent nasal bridge"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
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+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:93627",
+    "symbol": "TBCK"
+  }],
+  "variants": [{
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+      "genomeAssembly": "GRCh37",
+      "chr": "4",
+      "pos": 107154202,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616900",
+      "label": "Hypotonia, infantile, with psychomotor retardation and characteristic facies 3"
+    }
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+    "submittedBy": "UNC:biocuration",
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+      "id": "hp",
+      "name": "human phenotype ontology",
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+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "name": "Phenotype And Trait Ontology",
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+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
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+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
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+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
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+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
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+      "namespacePrefix": "OMIM"
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+    "externalReferences": [{
+      "id": "PMID:27040692",
+      "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Chong-2016-TBCK-D-II-1.json b/notebooks/LIRICAL/v1phenopackets/Chong-2016-TBCK-D-II-1.json
new file mode 100644
index 000000000..401aa7d74
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Chong-2016-TBCK-D-II-1.json
@@ -0,0 +1,494 @@
+{
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+      "label": "Homo sapiens"
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+      "label": "Feeding difficulties"
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+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
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+    }]
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+      }
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+      }
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+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }, {
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+      "id": "HP:0002553",
+      "label": "Highly arched eyebrow"
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+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
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+    }]
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+      }
+    }]
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+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
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+  }, {
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+    },
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+        "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:93627",
+    "symbol": "TBCK"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "4",
+      "pos": 107183260,
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+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616900",
+      "label": "Hypotonia, infantile, with psychomotor retardation and characteristic facies 3"
+    }
+  }],
+  "metaData": {
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+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "name": "Phenotype And Trait Ontology",
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+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
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+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
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+    "externalReferences": [{
+      "id": "PMID:27040692",
+      "description": "Recessive Inactivating Mutations in TBCK, Encoding a Rab GTPase-Activating Protein, Cause Severe Infantile Syndromic Encephalopathy"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Claverie-Martin-2019-LMX1B-index.json b/notebooks/LIRICAL/v1phenopackets/Claverie-Martin-2019-LMX1B-index.json
new file mode 100644
index 000000000..e99975dc5
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Claverie-Martin-2019-LMX1B-index.json
@@ -0,0 +1,177 @@
+{
+  "id": "PMID:30881852-Claverie-Martin-2019-LMX1B-index",
+  "subject": {
+    "id": "index",
+    "ageAtCollection": {
+      "age": "P7Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0009781",
+      "label": "Lester\u0027s sign"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30881852",
+        "description": "Novel missense mutation affecting the LIM-A domain of LMX1B in a family with Nail-Patella syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30881852",
+        "description": "Novel missense mutation affecting the LIM-A domain of LMX1B in a family with Nail-Patella syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008404",
+      "label": "Nail dystrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30881852",
+        "description": "Novel missense mutation affecting the LIM-A domain of LMX1B in a family with Nail-Patella syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006443",
+      "label": "Patellar aplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:30881852",
+        "description": "Novel missense mutation affecting the LIM-A domain of LMX1B in a family with Nail-Patella syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001382",
+      "label": "Joint hypermobility"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30881852",
+        "description": "Novel missense mutation affecting the LIM-A domain of LMX1B in a family with Nail-Patella syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001290",
+      "label": "Generalized hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30881852",
+        "description": "Novel missense mutation affecting the LIM-A domain of LMX1B in a family with Nail-Patella syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:4010",
+    "symbol": "LMX1B"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "9",
+      "pos": 129377827,
+      "ref": "A",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:161200",
+      "label": "NAIL-PATELLA SYNDROME; NPS"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30881852",
+      "description": "Novel missense mutation affecting the LIM-A domain of LMX1B in a family with Nail-Patella syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Cuchanski-2018-KIF5A-proband.json b/notebooks/LIRICAL/v1phenopackets/Cuchanski-2018-KIF5A-proband.json
new file mode 100644
index 000000000..10dd670b0
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Cuchanski-2018-KIF5A-proband.json
@@ -0,0 +1,270 @@
+{
+  "id": "PMID:30057544-Cuchanski-2018-KIF5A-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P31Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001257",
+      "label": "Spasticity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057544",
+        "description": "Mutation in KIF5A c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003487",
+      "label": "Babinski sign"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057544",
+        "description": "Mutation in KIF5A c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002169",
+      "label": "Clonus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057544",
+        "description": "Mutation in KIF5A c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009830",
+      "label": "Peripheral neuropathy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057544",
+        "description": "Mutation in KIF5A c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031910",
+      "label": "Abnormal cranial nerve physiology"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057544",
+        "description": "Mutation in KIF5A c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002312",
+      "label": "Clumsiness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057544",
+        "description": "Mutation in KIF5A c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001251",
+      "label": "Ataxia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057544",
+        "description": "Mutation in KIF5A c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006886",
+      "label": "Impaired distal vibration sensation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057544",
+        "description": "Mutation in KIF5A c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012534",
+      "label": "Dysesthesia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057544",
+        "description": "Mutation in KIF5A c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002064",
+      "label": "Spastic gait"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057544",
+        "description": "Mutation in KIF5A c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100543",
+      "label": "Cognitive impairment"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057544",
+        "description": "Mutation in KIF5A c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003401",
+      "label": "Paresthesia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057544",
+        "description": "Mutation in KIF5A c"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:3798",
+    "symbol": "KIF5A"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "12",
+      "pos": 57961297,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:604187",
+      "label": "SPASTIC PARAPLEGIA 10, AUTOSOMAL DOMINANT; SPG10"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30057544",
+      "description": "Mutation in KIF5A c"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Curtis-1978-FLCN-253.json b/notebooks/LIRICAL/v1phenopackets/Curtis-1978-FLCN-253.json
new file mode 100644
index 000000000..8bf540a3c
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Curtis-1978-FLCN-253.json
@@ -0,0 +1,115 @@
+{
+  "id": "PMID:96481-Curtis-1978-FLCN-253",
+  "subject": {
+    "id": "253",
+    "ageAtCollection": {
+      "age": "n/a"
+    },
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0030436",
+      "label": "Fibrofolliculoma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:96481",
+        "description": "Response of a rat rhabdomyosarcoma to neon- and helium-ion irradiation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002108",
+      "label": "Spontaneous pneumothorax"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:96481",
+        "description": "Response of a rat rhabdomyosarcoma to neon- and helium-ion irradiation"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:201163",
+    "symbol": "FLCN"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "17",
+      "pos": 17129638,
+      "ref": "T",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:135150",
+      "label": "BIRT-HOGG-DUBE SYNDROME; BHD"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:96481",
+      "description": "Response of a rat rhabdomyosarcoma to neon- and helium-ion irradiation"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Dastsooz-2017-PANK2-Family_I_patient_I.json b/notebooks/LIRICAL/v1phenopackets/Dastsooz-2017-PANK2-Family_I_patient_I.json
new file mode 100644
index 000000000..59a8f266c
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Dastsooz-2017-PANK2-Family_I_patient_I.json
@@ -0,0 +1,195 @@
+{
+  "id": "PMID:28821231-Dastsooz-2017-PANK2-Family_I_patient_I",
+  "subject": {
+    "id": "Family I patient I",
+    "ageAtCollection": {
+      "age": "P9Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002370",
+      "label": "Poor coordination"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28821231",
+        "description": "Novel mutations in PANK2 and PLA2G6 genes in patients with neurodegenerative disorders: two case reports"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000238",
+      "label": "Hydrocephalus"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28821231",
+        "description": "Novel mutations in PANK2 and PLA2G6 genes in patients with neurodegenerative disorders: two case reports"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003155",
+      "label": "Elevated alkaline phosphatase"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28821231",
+        "description": "Novel mutations in PANK2 and PLA2G6 genes in patients with neurodegenerative disorders: two case reports"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012503",
+      "label": "Abnormality of the pituitary gland"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28821231",
+        "description": "Novel mutations in PANK2 and PLA2G6 genes in patients with neurodegenerative disorders: two case reports"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002454",
+      "label": "Eye of the tiger anomaly of globus pallidus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28821231",
+        "description": "Novel mutations in PANK2 and PLA2G6 genes in patients with neurodegenerative disorders: two case reports"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003236",
+      "label": "Elevated serum creatine kinase"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28821231",
+        "description": "Novel mutations in PANK2 and PLA2G6 genes in patients with neurodegenerative disorders: two case reports"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28821231",
+        "description": "Novel mutations in PANK2 and PLA2G6 genes in patients with neurodegenerative disorders: two case reports"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:80025",
+    "symbol": "PANK2"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "20",
+      "pos": 3897586,
+      "ref": "GATGA",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:234200",
+      "label": "NEURODEGENERATION WITH BRAIN IRON ACCUMULATION 1; NBIA1"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28821231",
+      "description": "Novel mutations in PANK2 and PLA2G6 genes in patients with neurodegenerative disorders: two case reports"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Dastsooz-2017-PLA2G6-family_II_patient_II.json b/notebooks/LIRICAL/v1phenopackets/Dastsooz-2017-PLA2G6-family_II_patient_II.json
new file mode 100644
index 000000000..07a4bacf5
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Dastsooz-2017-PLA2G6-family_II_patient_II.json
@@ -0,0 +1,209 @@
+{
+  "id": "PMID:28821231-Dastsooz-2017-PLA2G6-family_II_patient_II",
+  "subject": {
+    "id": "family II patient II",
+    "ageAtCollection": {
+      "age": "P1Y6M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0025435",
+      "label": "Increased lactate dehydrogenase activity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28821231",
+        "description": "Novel mutations in PANK2 and PLA2G6 genes in patients with neurodegenerative disorders: two case reports"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031956",
+      "label": "Elevated serum aspartate aminotransferase"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28821231",
+        "description": "Novel mutations in PANK2 and PLA2G6 genes in patients with neurodegenerative disorders: two case reports"
+      }
+    }]
+  }, {
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+      "id": "HP:0002376",
+      "label": "Developmental regression"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28821231",
+        "description": "Novel mutations in PANK2 and PLA2G6 genes in patients with neurodegenerative disorders: two case reports"
+      }
+    }]
+  }, {
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+      "label": "Elevated serum creatine kinase"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28821231",
+        "description": "Novel mutations in PANK2 and PLA2G6 genes in patients with neurodegenerative disorders: two case reports"
+      }
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+  }, {
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+        "id": "PMID:28821231",
+        "description": "Novel mutations in PANK2 and PLA2G6 genes in patients with neurodegenerative disorders: two case reports"
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+        "description": "Novel mutations in PANK2 and PLA2G6 genes in patients with neurodegenerative disorders: two case reports"
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+    }]
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+      "label": "Seizures"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28821231",
+        "description": "Novel mutations in PANK2 and PLA2G6 genes in patients with neurodegenerative disorders: two case reports"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:8398",
+    "symbol": "PLA2G6"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "22",
+      "pos": 38565431,
+      "ref": "C",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:610217",
+      "label": "NEURODEGENERATION WITH BRAIN IRON ACCUMULATION 2B; NBIA2B"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
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+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28821231",
+      "description": "Novel mutations in PANK2 and PLA2G6 genes in patients with neurodegenerative disorders: two case reports"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Dauber-2014-SLC35C1-Proband_1.json b/notebooks/LIRICAL/v1phenopackets/Dauber-2014-SLC35C1-Proband_1.json
new file mode 100644
index 000000000..edeccc76b
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Dauber-2014-SLC35C1-Proband_1.json
@@ -0,0 +1,406 @@
+{
+  "id": "PMID:24403049-Dauber-2014-SLC35C1-Proband_1",
+  "subject": {
+    "id": "Proband 1",
+    "ageAtCollection": {
+      "age": "P21Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000729",
+      "label": "Autistic behavior"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24403049",
+        "description": "Congenital disorder of fucosylation type 2c (LADII) presenting with short stature and developmental delay with minimal adhesion defect"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000349",
+      "label": "Widow\u0027s peak"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24403049",
+        "description": "Congenital disorder of fucosylation type 2c (LADII) presenting with short stature and developmental delay with minimal adhesion defect"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011893",
+      "label": "Abnormal leukocyte count"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24403049",
+        "description": "Congenital disorder of fucosylation type 2c (LADII) presenting with short stature and developmental delay with minimal adhesion defect"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030352",
+      "label": "Abnormal serum insulin-like growth factor 1 level"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24403049",
+        "description": "Congenital disorder of fucosylation type 2c (LADII) presenting with short stature and developmental delay with minimal adhesion defect"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010529",
+      "label": "Echolalia"
+    },
+    "evidence": [{
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+        "id": "PMID:24403049",
+        "description": "Congenital disorder of fucosylation type 2c (LADII) presenting with short stature and developmental delay with minimal adhesion defect"
+      }
+    }]
+  }, {
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+      "label": "Small hand"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:24403049",
+        "description": "Congenital disorder of fucosylation type 2c (LADII) presenting with short stature and developmental delay with minimal adhesion defect"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000414",
+      "label": "Bulbous nose"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:24403049",
+        "description": "Congenital disorder of fucosylation type 2c (LADII) presenting with short stature and developmental delay with minimal adhesion defect"
+      }
+    }]
+  }, {
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+      "id": "HP:0003355",
+      "label": "Aminoaciduria"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:24403049",
+        "description": "Congenital disorder of fucosylation type 2c (LADII) presenting with short stature and developmental delay with minimal adhesion defect"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000739",
+      "label": "Anxiety"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Congenital disorder of fucosylation type 2c (LADII) presenting with short stature and developmental delay with minimal adhesion defect"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001212",
+      "label": "Prominent fingertip pads"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:24403049",
+        "description": "Congenital disorder of fucosylation type 2c (LADII) presenting with short stature and developmental delay with minimal adhesion defect"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
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+    }]
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+      "label": "Short stature"
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+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
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+        "description": "Congenital disorder of fucosylation type 2c (LADII) presenting with short stature and developmental delay with minimal adhesion defect"
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+    }]
+  }, {
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+      "id": "HP:0000403",
+      "label": "Recurrent otitis media"
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+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:24403049",
+        "description": "Congenital disorder of fucosylation type 2c (LADII) presenting with short stature and developmental delay with minimal adhesion defect"
+      }
+    }]
+  }, {
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+      "id": "HP:0000280",
+      "label": "Coarse facial features"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:24403049",
+        "description": "Congenital disorder of fucosylation type 2c (LADII) presenting with short stature and developmental delay with minimal adhesion defect"
+      }
+    }]
+  }, {
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+      "label": "Organic aciduria"
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+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Congenital disorder of fucosylation type 2c (LADII) presenting with short stature and developmental delay with minimal adhesion defect"
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+    }]
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+      "label": "Brachydactyly"
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+    "evidence": [{
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+        "description": "Congenital disorder of fucosylation type 2c (LADII) presenting with short stature and developmental delay with minimal adhesion defect"
+      }
+    }]
+  }, {
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+      "label": "Abnormality of serum amino acid level"
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+    "negated": true,
+    "evidence": [{
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+      }
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+  }, {
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+      "label": "Oligosacchariduria"
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+    "negated": true,
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+        "id": "ECO:0000033",
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+    }]
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+      "label": "Delayed speech and language development"
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+        "description": "Congenital disorder of fucosylation type 2c (LADII) presenting with short stature and developmental delay with minimal adhesion defect"
+      }
+    }]
+  }],
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+    "symbol": "SLC35C1"
+  }],
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+      "chr": "11",
+      "pos": 45827443,
+      "ref": "G",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "11",
+      "pos": 45827852,
+      "ref": "CCTT",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:266265",
+      "label": "CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIc; CDG2C"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:24403049",
+      "description": "Congenital disorder of fucosylation type 2c (LADII) presenting with short stature and developmental delay with minimal adhesion defect"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Delahaye-2007-CHD7-B_III-3.json b/notebooks/LIRICAL/v1phenopackets/Delahaye-2007-CHD7-B_III-3.json
new file mode 100644
index 000000000..9f68c3155
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Delahaye-2007-CHD7-B_III-3.json
@@ -0,0 +1,297 @@
+{
+  "id": "PMID:17661815-Delahaye-2007-CHD7-B_III-3",
+  "subject": {
+    "id": "B III-3",
+    "ageAtCollection": {
+      "age": "P2Y6M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001635",
+      "label": "Congestive heart failure"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+      "version": "19-03-2018",
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+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Delahaye-2007-CHD7-Patient_A_III-2.json b/notebooks/LIRICAL/v1phenopackets/Delahaye-2007-CHD7-Patient_A_III-2.json
new file mode 100644
index 000000000..0e76158fa
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Delahaye-2007-CHD7-Patient_A_III-2.json
@@ -0,0 +1,297 @@
+{
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+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Devalla-2016-TECRL-Patient_1.json b/notebooks/LIRICAL/v1phenopackets/Devalla-2016-TECRL-Patient_1.json
new file mode 100644
index 000000000..ec5f6de56
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Devalla-2016-TECRL-Patient_1.json
@@ -0,0 +1,207 @@
+{
+  "id": "PMID:27861123-Devalla-2016-TECRL-Patient_1",
+  "subject": {
+    "id": "Patient 1",
+    "ageAtCollection": {
+      "age": "22"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
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+      "label": "Homo sapiens"
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+      "id": "HP:0001692",
+      "label": "Atrial arrhythmia"
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+        "label": "author statement supported by traceable reference"
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+        "description": "TECRL, a new life-threatening inherited arrhythmia gene associated with overlapping clinical features of both LQTS and CPVT"
+      }
+    }]
+  }, {
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+      "id": "HP:0031547",
+      "label": "Abnormal QT interval"
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+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "description": "TECRL, a new life-threatening inherited arrhythmia gene associated with overlapping clinical features of both LQTS and CPVT"
+      }
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+      }
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+        "description": "TECRL, a new life-threatening inherited arrhythmia gene associated with overlapping clinical features of both LQTS and CPVT"
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+      "label": "Prolonged QT interval"
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+  }, {
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+      "id": "HP:0001663",
+      "label": "Ventricular fibrillation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27861123",
+        "description": "TECRL, a new life-threatening inherited arrhythmia gene associated with overlapping clinical features of both LQTS and CPVT"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:253017",
+    "symbol": "TECRL"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "4",
+      "pos": 65175614,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:614021",
+      "label": "VENTRICULAR TACHYCARDIA, CATECHOLAMINERGIC POLYMORPHIC, 3; CPVT3"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:lccarmody",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27861123",
+      "description": "TECRL, a new life-threatening inherited arrhythmia gene associated with overlapping clinical features of both LQTS and CPVT"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Di_Nottia-2017-PARK7-proband.json b/notebooks/LIRICAL/v1phenopackets/Di_Nottia-2017-PARK7-proband.json
new file mode 100644
index 000000000..728be2f00
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Di_Nottia-2017-PARK7-proband.json
@@ -0,0 +1,284 @@
+{
+  "id": "PMID:27460976-Di_Nottia-2017-PARK7-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P47Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002174",
+      "label": "Postural tremor"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27460976",
+        "description": "DJ-1 modulates mitochondrial response to oxidative stress: clues from a novel diagnosis of PARK7"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003688",
+      "label": "Cytochrome C oxidase-negative muscle fibers"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27460976",
+        "description": "DJ-1 modulates mitochondrial response to oxidative stress: clues from a novel diagnosis of PARK7"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008619",
+      "label": "Bilateral sensorineural hearing impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27460976",
+        "description": "DJ-1 modulates mitochondrial response to oxidative stress: clues from a novel diagnosis of PARK7"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002355",
+      "label": "Difficulty walking"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27460976",
+        "description": "DJ-1 modulates mitochondrial response to oxidative stress: clues from a novel diagnosis of PARK7"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003693",
+      "label": "Distal amyotrophy"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
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+        "id": "PMID:27460976",
+        "description": "DJ-1 modulates mitochondrial response to oxidative stress: clues from a novel diagnosis of PARK7"
+      }
+    }]
+  }, {
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+      "id": "HP:0001761",
+      "label": "Pes cavus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27460976",
+        "description": "DJ-1 modulates mitochondrial response to oxidative stress: clues from a novel diagnosis of PARK7"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003200",
+      "label": "Ragged-red muscle fibers"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27460976",
+        "description": "DJ-1 modulates mitochondrial response to oxidative stress: clues from a novel diagnosis of PARK7"
+      }
+    }]
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+      "id": "HP:0001300",
+      "label": "Parkinsonism"
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+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27460976",
+        "description": "DJ-1 modulates mitochondrial response to oxidative stress: clues from a novel diagnosis of PARK7"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012049",
+      "label": "Laryngeal dystonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27460976",
+        "description": "DJ-1 modulates mitochondrial response to oxidative stress: clues from a novel diagnosis of PARK7"
+      }
+    }]
+  }, {
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+      "id": "HP:0000518",
+      "label": "Cataract"
+    },
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+        "id": "PMID:27460976",
+        "description": "DJ-1 modulates mitochondrial response to oxidative stress: clues from a novel diagnosis of PARK7"
+      }
+    }]
+  }, {
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+      "id": "HP:0002460",
+      "label": "Distal muscle weakness"
+    },
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27460976",
+        "description": "DJ-1 modulates mitochondrial response to oxidative stress: clues from a novel diagnosis of PARK7"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100660",
+      "label": "Dyskinesia"
+    },
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+        "description": "DJ-1 modulates mitochondrial response to oxidative stress: clues from a novel diagnosis of PARK7"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001765",
+      "label": "Hammertoe"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27460976",
+        "description": "DJ-1 modulates mitochondrial response to oxidative stress: clues from a novel diagnosis of PARK7"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:11315",
+    "symbol": "PARK7"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 8045005,
+      "ref": "C",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:606324",
+      "label": "PARKINSON DISEASE 7, AUTOSOMAL RECESSIVE EARLY-ONSET; PARK7"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27460976",
+      "description": "DJ-1 modulates mitochondrial response to oxidative stress: clues from a novel diagnosis of PARK7"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Dias-2013-TRPS1-girl.json b/notebooks/LIRICAL/v1phenopackets/Dias-2013-TRPS1-girl.json
new file mode 100644
index 000000000..428b9b15a
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Dias-2013-TRPS1-girl.json
@@ -0,0 +1,160 @@
+{
+  "id": "PMID:23691375-Dias-2013-TRPS1-girl",
+  "subject": {
+    "id": "girl",
+    "ageAtCollection": {
+      "age": "4PY"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23691375",
+        "description": "Trichorhinophalangeal Syndrome Type I: A Patient with Two Novel and Different Mutations in the TRPS1 Gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000752",
+      "label": "Hyperactivity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23691375",
+        "description": "Trichorhinophalangeal Syndrome Type I: A Patient with Two Novel and Different Mutations in the TRPS1 Gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005338",
+      "label": "Sparse lateral eyebrow"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23691375",
+        "description": "Trichorhinophalangeal Syndrome Type I: A Patient with Two Novel and Different Mutations in the TRPS1 Gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002750",
+      "label": "Delayed skeletal maturation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23691375",
+        "description": "Trichorhinophalangeal Syndrome Type I: A Patient with Two Novel and Different Mutations in the TRPS1 Gene"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:7227",
+    "symbol": "TRPS1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "8",
+      "pos": 116616998,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "8",
+      "pos": 116616110,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:190350",
+      "label": "TRICHORHINOPHALANGEAL SYNDROME, TYPE I; TRPS1"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13",
+    "submittedBy": "HP:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:23691375",
+      "description": "Trichorhinophalangeal Syndrome Type I: A Patient with Two Novel and Different Mutations in the TRPS1 Gene"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Dikoglu-2015-LONP1-Patient_1.json b/notebooks/LIRICAL/v1phenopackets/Dikoglu-2015-LONP1-Patient_1.json
new file mode 100644
index 000000000..72cec04e3
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Dikoglu-2015-LONP1-Patient_1.json
@@ -0,0 +1,219 @@
+{
+  "id": "PMID:25808063-Dikoglu-2015-LONP1-Patient_1",
+  "subject": {
+    "id": "Patient 1",
+    "ageAtCollection": {
+      "age": "3Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25808063",
+        "description": "Mutations in LONP1, a mitochondrial matrix protease, cause CODAS syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001272",
+      "label": "Cerebellar atrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25808063",
+        "description": "Mutations in LONP1, a mitochondrial matrix protease, cause CODAS syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008820",
+      "label": "Absent ossification of capital femoral epiphysis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25808063",
+        "description": "Mutations in LONP1, a mitochondrial matrix protease, cause CODAS syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001251",
+      "label": "Ataxia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25808063",
+        "description": "Mutations in LONP1, a mitochondrial matrix protease, cause CODAS syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000518",
+      "label": "Cataract"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25808063",
+        "description": "Mutations in LONP1, a mitochondrial matrix protease, cause CODAS syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009901",
+      "label": "Crumpled ear"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25808063",
+        "description": "Mutations in LONP1, a mitochondrial matrix protease, cause CODAS syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003417",
+      "label": "Coronal cleft vertebrae"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25808063",
+        "description": "Mutations in LONP1, a mitochondrial matrix protease, cause CODAS syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012368",
+      "label": "Flat face"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25808063",
+        "description": "Mutations in LONP1, a mitochondrial matrix protease, cause CODAS syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:9361",
+    "symbol": "LONP1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "19",
+      "pos": 5694473,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "19",
+      "pos": 5694418,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:600373",
+      "label": "CODAS SYNDROME"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:25808063",
+      "description": "Mutations in LONP1, a mitochondrial matrix protease, cause CODAS syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Dinani-2017-AAGAB-family_1_proband.json b/notebooks/LIRICAL/v1phenopackets/Dinani-2017-AAGAB-family_1_proband.json
new file mode 100644
index 000000000..044b18fd7
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Dinani-2017-AAGAB-family_1_proband.json
@@ -0,0 +1,149 @@
+{
+  "id": "PMID:28239884-Dinani-2017-AAGAB-family_1:proband",
+  "subject": {
+    "id": "family 1:proband",
+    "ageAtCollection": {
+      "age": "P43Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001595",
+      "label": "Abnormality of the hair"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28239884",
+        "description": "Mutations in AAGAB underlie autosomal dominant punctate palmoplantar keratoderma"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007530",
+      "label": "Punctate palmoplantar hyperkeratosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28239884",
+        "description": "Mutations in AAGAB underlie autosomal dominant punctate palmoplantar keratoderma"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006482",
+      "label": "Abnormality of dental morphology"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28239884",
+        "description": "Mutations in AAGAB underlie autosomal dominant punctate palmoplantar keratoderma"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001597",
+      "label": "Abnormality of the nail"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28239884",
+        "description": "Mutations in AAGAB underlie autosomal dominant punctate palmoplantar keratoderma"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:79719",
+    "symbol": "AAGAB"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "15",
+      "pos": 67524181,
+      "ref": "T",
+      "alt": "TTT"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:148600",
+      "label": "PALMOPLANTAR KERATODERMA, PUNCTATE TYPE IA; PPKP1A"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28239884",
+      "description": "Mutations in AAGAB underlie autosomal dominant punctate palmoplantar keratoderma"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Djamshidian-2009-VCP-II-3.json b/notebooks/LIRICAL/v1phenopackets/Djamshidian-2009-VCP-II-3.json
new file mode 100644
index 000000000..4dbe4023f
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Djamshidian-2009-VCP-II-3.json
@@ -0,0 +1,254 @@
+{
+  "id": "PMID:19208399-Djamshidian-2009-VCP-II-3",
+  "subject": {
+    "id": "II-3",
+    "ageAtCollection": {
+      "age": "P41Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0007126",
+      "label": "Proximal amyotrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:19208399",
+        "description": "A novel mutation in the VCP gene (G157R) in a German family with inclusion-body myopathy with Paget disease of bone and frontotemporal dementia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000407",
+      "label": "Sensorineural hearing impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:19208399",
+        "description": "A novel mutation in the VCP gene (G157R) in a German family with inclusion-body myopathy with Paget disease of bone and frontotemporal dementia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003805",
+      "label": "Rimmed vacuoles"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:19208399",
+        "description": "A novel mutation in the VCP gene (G157R) in a German family with inclusion-body myopathy with Paget disease of bone and frontotemporal dementia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008180",
+      "label": "Mildly elevated creatine kinase"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:19208399",
+        "description": "A novel mutation in the VCP gene (G157R) in a German family with inclusion-body myopathy with Paget disease of bone and frontotemporal dementia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003701",
+      "label": "Proximal muscle weakness"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
+      },
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+        "description": "A novel mutation in the VCP gene (G157R) in a German family with inclusion-body myopathy with Paget disease of bone and frontotemporal dementia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100543",
+      "label": "Cognitive impairment"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:19208399",
+        "description": "A novel mutation in the VCP gene (G157R) in a German family with inclusion-body myopathy with Paget disease of bone and frontotemporal dementia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000741",
+      "label": "Apathy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "A novel mutation in the VCP gene (G157R) in a German family with inclusion-body myopathy with Paget disease of bone and frontotemporal dementia"
+      }
+    }]
+  }, {
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+      "label": "Elevated alkaline phosphatase of bone origin"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "description": "A novel mutation in the VCP gene (G157R) in a German family with inclusion-body myopathy with Paget disease of bone and frontotemporal dementia"
+      }
+    }]
+  }, {
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+      "id": "HP:0002653",
+      "label": "Bone pain"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:19208399",
+        "description": "A novel mutation in the VCP gene (G157R) in a German family with inclusion-body myopathy with Paget disease of bone and frontotemporal dementia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002515",
+      "label": "Waddling gait"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+      },
+      "reference": {
+        "id": "PMID:19208399",
+        "description": "A novel mutation in the VCP gene (G157R) in a German family with inclusion-body myopathy with Paget disease of bone and frontotemporal dementia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003691",
+      "label": "Scapular winging"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:19208399",
+        "description": "A novel mutation in the VCP gene (G157R) in a German family with inclusion-body myopathy with Paget disease of bone and frontotemporal dementia"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:7415",
+    "symbol": "VCP"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "9",
+      "pos": 35065355,
+      "ref": "C",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:167320",
+      "label": "INCLUSION BODY MYOPATHY WITH EARLY-ONSET PAGET DISEASE WITH OR WITHOUTFRONTOTEMPORAL DEMENTIA 1; IBMPFD1"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:19208399",
+      "description": "A novel mutation in the VCP gene (G157R) in a German family with inclusion-body myopathy with Paget disease of bone and frontotemporal dementia"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Dobbs-2008-FLNB-patient.json b/notebooks/LIRICAL/v1phenopackets/Dobbs-2008-FLNB-patient.json
new file mode 100644
index 000000000..9d1d05e9e
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Dobbs-2008-FLNB-patient.json
@@ -0,0 +1,269 @@
+{
+  "id": "PMID:18322662-Dobbs-2008-FLNB-patient",
+  "subject": {
+    "id": "patient",
+    "ageAtCollection": {
+      "age": "P1Y10M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002987",
+      "label": "Elbow flexion contracture"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18322662",
+        "description": "Case report: Congenital knee dislocation in a patient with larsen syndrome and a novel filamin B mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000175",
+      "label": "Cleft palate"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18322662",
+        "description": "Case report: Congenital knee dislocation in a patient with larsen syndrome and a novel filamin B mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002827",
+      "label": "Hip dislocation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18322662",
+        "description": "Case report: Congenital knee dislocation in a patient with larsen syndrome and a novel filamin B mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002650",
+      "label": "Scoliosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18322662",
+        "description": "Case report: Congenital knee dislocation in a patient with larsen syndrome and a novel filamin B mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010049",
+      "label": "Short metacarpal"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:18322662",
+        "description": "Case report: Congenital knee dislocation in a patient with larsen syndrome and a novel filamin B mutation"
+      }
+    }]
+  }, {
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+      "label": "Breech presentation"
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+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18322662",
+        "description": "Case report: Congenital knee dislocation in a patient with larsen syndrome and a novel filamin B mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004976",
+      "label": "Knee dislocation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18322662",
+        "description": "Case report: Congenital knee dislocation in a patient with larsen syndrome and a novel filamin B mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002947",
+      "label": "Cervical kyphosis"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:18322662",
+        "description": "Case report: Congenital knee dislocation in a patient with larsen syndrome and a novel filamin B mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000316",
+      "label": "Hypertelorism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:18322662",
+        "description": "Case report: Congenital knee dislocation in a patient with larsen syndrome and a novel filamin B mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011432",
+      "label": "High maternal serum alpha-fetoprotein"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:18322662",
+        "description": "Case report: Congenital knee dislocation in a patient with larsen syndrome and a novel filamin B mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010301",
+      "label": "Spinal dysraphism"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18322662",
+        "description": "Case report: Congenital knee dislocation in a patient with larsen syndrome and a novel filamin B mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005280",
+      "label": "Depressed nasal bridge"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18322662",
+        "description": "Case report: Congenital knee dislocation in a patient with larsen syndrome and a novel filamin B mutation"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2317",
+    "symbol": "FLNB"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "3",
+      "pos": 58062988,
+      "ref": "G",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:150250",
+      "label": "LARSEN SYNDROME; LRS"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:18322662",
+      "description": "Case report: Congenital knee dislocation in a patient with larsen syndrome and a novel filamin B mutation"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Dorboz-2017-NKX6-2-Patient_1_II-1.json b/notebooks/LIRICAL/v1phenopackets/Dorboz-2017-NKX6-2-Patient_1_II-1.json
new file mode 100644
index 000000000..026cdb9d8
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Dorboz-2017-NKX6-2-Patient_1_II-1.json
@@ -0,0 +1,282 @@
+{
+  "id": "PMID:28969374-Dorboz-2017-NKX6-2-Patient_1_II-1",
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+      "age": "P8Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
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+      "id": "HP:0001257",
+      "label": "Spasticity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28969374",
+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008947",
+      "label": "Infantile muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28969374",
+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001583",
+      "label": "Rotary nystagmus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28969374",
+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
+      }
+    }]
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+      "label": "Cognitive impairment"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:28969374",
+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
+      }
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+  }, {
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+    },
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+    },
+    "evidence": [{
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+        "id": "PMID:28969374",
+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
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+    }]
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+      "label": "Poor gross motor coordination"
+    },
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+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
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+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
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+    }]
+  }, {
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+      "id": "HP:0000666",
+      "label": "Horizontal nystagmus"
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+        "label": "author statement supported by traceable reference"
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+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
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+    }]
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+      "label": "Poor head control"
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+      "label": "Dystonia"
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+        "id": "PMID:28969374",
+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
+      }
+    }]
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+      "label": "Gastrostomy tube feeding in infancy"
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+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Abnormality of visual evoked potentials"
+    },
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28969374",
+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:84504",
+    "symbol": "NKX6-2"
+  }],
+  "variants": [{
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+      "ref": "C",
+      "alt": "TA"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617560",
+      "label": "Spastic ataxia 8, autosomal recessive, with hypomyelinating leukodystrophy"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28969374",
+      "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Dorboz-2017-NKX6-2-Patient_3_II-3.json b/notebooks/LIRICAL/v1phenopackets/Dorboz-2017-NKX6-2-Patient_3_II-3.json
new file mode 100644
index 000000000..96ba91d7f
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Dorboz-2017-NKX6-2-Patient_3_II-3.json
@@ -0,0 +1,222 @@
+{
+  "id": "PMID:28969374-Dorboz-2017-NKX6-2-Patient_3_II-3",
+  "subject": {
+    "id": "Patient 3 II-3",
+    "ageAtCollection": {
+      "age": "P9Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0007015",
+      "label": "Poor gross motor coordination"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28969374",
+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002878",
+      "label": "Respiratory failure"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28969374",
+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000639",
+      "label": "Nystagmus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28969374",
+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008947",
+      "label": "Infantile muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28969374",
+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006855",
+      "label": "Cerebellar vermis atrophy"
+    },
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+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
+      }
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+      "label": "Reduced visual acuity"
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+        "id": "PMID:28969374",
+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
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+    }]
+  }, {
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+      "id": "HP:0001332",
+      "label": "Dystonia"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28969374",
+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
+      }
+    }]
+  }, {
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+      "id": "HP:0100543",
+      "label": "Cognitive impairment"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28969374",
+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000212",
+      "label": "Gingival overgrowth"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28969374",
+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:84504",
+    "symbol": "NKX6-2"
+  }],
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+      "chr": "10",
+      "pos": 134598798,
+      "ref": "C",
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+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617560",
+      "label": "Spastic ataxia 8, autosomal recessive, with hypomyelinating leukodystrophy"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28969374",
+      "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Dorboz-2017-NKX6-2-Patient_4_II-1.json b/notebooks/LIRICAL/v1phenopackets/Dorboz-2017-NKX6-2-Patient_4_II-1.json
new file mode 100644
index 000000000..0e6232319
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Dorboz-2017-NKX6-2-Patient_4_II-1.json
@@ -0,0 +1,249 @@
+{
+  "id": "PMID:28969374-Dorboz-2017-NKX6-2-Patient_4_II-1",
+  "subject": {
+    "id": "Patient 4 II-1",
+    "ageAtCollection": {
+      "age": "P3Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002015",
+      "label": "Dysphagia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28969374",
+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001257",
+      "label": "Spasticity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28969374",
+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008947",
+      "label": "Infantile muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28969374",
+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002300",
+      "label": "Mutism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28969374",
+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002421",
+      "label": "Poor head control"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28969374",
+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007663",
+      "label": "Reduced visual acuity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28969374",
+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011471",
+      "label": "Gastrostomy tube feeding in infancy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28969374",
+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000543",
+      "label": "Optic disc pallor"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28969374",
+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002194",
+      "label": "Delayed gross motor development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28969374",
+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012043",
+      "label": "Pendular nystagmus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28969374",
+        "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:84504",
+    "symbol": "NKX6-2"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "10",
+      "pos": 134598665,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "10",
+      "pos": 134598655,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617560",
+      "label": "Spastic ataxia 8, autosomal recessive, with hypomyelinating leukodystrophy"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28969374",
+      "description": "Biallelic mutations in the homeodomain of NKX6-2 underlie a severe hypomyelinating leukodystrophy"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Dougherty-2016-NPC1-The_proband.json b/notebooks/LIRICAL/v1phenopackets/Dougherty-2016-NPC1-The_proband.json
new file mode 100644
index 000000000..6376676f0
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Dougherty-2016-NPC1-The_proband.json
@@ -0,0 +1,308 @@
+{
+  "id": "PMID:27900365-Dougherty-2016-NPC1-The_proband",
+  "subject": {
+    "id": "The proband",
+    "ageAtCollection": {
+      "age": "54Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0007017",
+      "label": "Progressive forgetfulness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27900365",
+        "description": "Genome sequencing in a case of Niemann-Pick type C"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002448",
+      "label": "Progressive encephalopathy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27900365",
+        "description": "Genome sequencing in a case of Niemann-Pick type C"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002529",
+      "label": "Neuronal loss in central nervous system"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27900365",
+        "description": "Genome sequencing in a case of Niemann-Pick type C"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007369",
+      "label": "Atrophy/Degeneration affecting the cerebrum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27900365",
+        "description": "Genome sequencing in a case of Niemann-Pick type C"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007064",
+      "label": "Progressive language deterioration"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27900365",
+        "description": "Genome sequencing in a case of Niemann-Pick type C"
+      }
+    }]
+  }, {
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+      "label": "Progressive psychomotor deterioration"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27900365",
+        "description": "Genome sequencing in a case of Niemann-Pick type C"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002527",
+      "label": "Falls"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27900365",
+        "description": "Genome sequencing in a case of Niemann-Pick type C"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002354",
+      "label": "Memory impairment"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "description": "Genome sequencing in a case of Niemann-Pick type C"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007086",
+      "label": "Social and occupational deterioration"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27900365",
+        "description": "Genome sequencing in a case of Niemann-Pick type C"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007009",
+      "label": "Central nervous system degeneration"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27900365",
+        "description": "Genome sequencing in a case of Niemann-Pick type C"
+      }
+    }]
+  }, {
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+      "id": "HP:0002180",
+      "label": "Neurodegeneration"
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27900365",
+        "description": "Genome sequencing in a case of Niemann-Pick type C"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007164",
+      "label": "Slowed slurred speech"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27900365",
+        "description": "Genome sequencing in a case of Niemann-Pick type C"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001433",
+      "label": "Hepatosplenomegaly"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27900365",
+        "description": "Genome sequencing in a case of Niemann-Pick type C"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002361",
+      "label": "Psychomotor deterioration"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27900365",
+        "description": "Genome sequencing in a case of Niemann-Pick type C"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:4864",
+    "symbol": "NPC1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "18",
+      "pos": 21115443,
+      "ref": "T",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "18",
+      "pos": 21119382,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:257220",
+      "label": "NIEMANN-PICK DISEASE, TYPE C1; NPC1"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27900365",
+      "description": "Genome sequencing in a case of Niemann-Pick type C"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Du-2018-TINF2-proband.json b/notebooks/LIRICAL/v1phenopackets/Du-2018-TINF2-proband.json
new file mode 100644
index 000000000..8514898b5
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Du-2018-TINF2-proband.json
@@ -0,0 +1,271 @@
+{
+  "id": "PMID:29742735-Du-2018-TINF2-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P32Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0007898",
+      "label": "Exudative retinopathy"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29742735",
+        "description": "A case report of heterozygous TINF2 gene mutation associated with pulmonary fibrosis in a patient with dyskeratosis congenita"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002110",
+      "label": "Bronchiectasis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29742735",
+        "description": "A case report of heterozygous TINF2 gene mutation associated with pulmonary fibrosis in a patient with dyskeratosis congenita"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001010",
+      "label": "Hypopigmentation of the skin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29742735",
+        "description": "A case report of heterozygous TINF2 gene mutation associated with pulmonary fibrosis in a patient with dyskeratosis congenita"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002091",
+      "label": "Restrictive ventilatory defect"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29742735",
+        "description": "A case report of heterozygous TINF2 gene mutation associated with pulmonary fibrosis in a patient with dyskeratosis congenita"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002721",
+      "label": "Immunodeficiency"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29742735",
+        "description": "A case report of heterozygous TINF2 gene mutation associated with pulmonary fibrosis in a patient with dyskeratosis congenita"
+      }
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+  }, {
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+      "label": "Subpleural honeycombing"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29742735",
+        "description": "A case report of heterozygous TINF2 gene mutation associated with pulmonary fibrosis in a patient with dyskeratosis congenita"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008404",
+      "label": "Nail dystrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29742735",
+        "description": "A case report of heterozygous TINF2 gene mutation associated with pulmonary fibrosis in a patient with dyskeratosis congenita"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002664",
+      "label": "Neoplasm"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29742735",
+        "description": "A case report of heterozygous TINF2 gene mutation associated with pulmonary fibrosis in a patient with dyskeratosis congenita"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002745",
+      "label": "Oral leukoplakia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29742735",
+        "description": "A case report of heterozygous TINF2 gene mutation associated with pulmonary fibrosis in a patient with dyskeratosis congenita"
+      }
+    }]
+  }, {
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+      "id": "HP:0100792",
+      "label": "Acantholysis"
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+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:29742735",
+        "description": "A case report of heterozygous TINF2 gene mutation associated with pulmonary fibrosis in a patient with dyskeratosis congenita"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000962",
+      "label": "Hyperkeratosis"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29742735",
+        "description": "A case report of heterozygous TINF2 gene mutation associated with pulmonary fibrosis in a patient with dyskeratosis congenita"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001510",
+      "label": "Growth delay"
+    },
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+    "evidence": [{
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+        "id": "PMID:29742735",
+        "description": "A case report of heterozygous TINF2 gene mutation associated with pulmonary fibrosis in a patient with dyskeratosis congenita"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:26277",
+    "symbol": "TINF2"
+  }],
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+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "14",
+      "pos": 24709842,
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+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:613990",
+      "label": "DYSKERATOSIS CONGENITA, AUTOSOMAL DOMINANT 3; DKCA3"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29742735",
+      "description": "A case report of heterozygous TINF2 gene mutation associated with pulmonary fibrosis in a patient with dyskeratosis congenita"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Ekvall-2015-NRAS-case_1.json b/notebooks/LIRICAL/v1phenopackets/Ekvall-2015-NRAS-case_1.json
new file mode 100644
index 000000000..27b57134b
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Ekvall-2015-NRAS-case_1.json
@@ -0,0 +1,312 @@
+{
+  "id": "PMID:26467218-Ekvall-2015-NRAS-case_1",
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+    },
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+      "label": "Homo sapiens"
+    }
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+    "type": {
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+      "label": "Freckling"
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+        "id": "PMID:26467218",
+        "description": "Mutation in NRAS in familial Noonan syndrome--case report and review of the literature"
+      }
+    }]
+  }, {
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+      "label": "Short neck"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26467218",
+        "description": "Mutation in NRAS in familial Noonan syndrome--case report and review of the literature"
+      }
+    }]
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+      "label": "Low posterior hairline"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Mutation in NRAS in familial Noonan syndrome--case report and review of the literature"
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+      }
+    }]
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+      "label": "Cardiomyopathy"
+    },
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+    "evidence": [{
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+    }]
+  }, {
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+      "id": "HP:0000369",
+      "label": "Low-set ears"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "description": "Mutation in NRAS in familial Noonan syndrome--case report and review of the literature"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Cafe-au-lait spot"
+    },
+    "evidence": [{
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+        "description": "Mutation in NRAS in familial Noonan syndrome--case report and review of the literature"
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+    },
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+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:613224",
+      "label": "NOONAN SYNDROME 6; NS6"
+    }
+  }],
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+    "externalReferences": [{
+      "id": "PMID:26467218",
+      "description": "Mutation in NRAS in familial Noonan syndrome--case report and review of the literature"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/El-Harith-2009-MPL-FT2_VI_3.json b/notebooks/LIRICAL/v1phenopackets/El-Harith-2009-MPL-FT2_VI_3.json
new file mode 100644
index 000000000..1f910e403
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/El-Harith-2009-MPL-FT2_VI_3.json
@@ -0,0 +1,102 @@
+{
+  "id": "PMID:19036112-El-Harith-2009-MPL-FT2:VI:3",
+  "subject": {
+    "id": "FT2:VI:3",
+    "ageAtCollection": {
+      "age": "P9Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001894",
+      "label": "Thrombocytosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:19036112",
+        "description": "Familial thrombocytosis caused by the novel germ-line mutation p"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:4352",
+    "symbol": "MPL"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 43804317,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:601977",
+      "label": "THROMBOCYTHEMIA 2; THCYT2"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:19036112",
+      "description": "Familial thrombocytosis caused by the novel germ-line mutation p"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/El-Jaick-2007-TGIF1-male_proband.json b/notebooks/LIRICAL/v1phenopackets/El-Jaick-2007-TGIF1-male_proband.json
new file mode 100644
index 000000000..739d3a11c
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/El-Jaick-2007-TGIF1-male_proband.json
@@ -0,0 +1,191 @@
+{
+  "id": "PMID:16962354-El-Jaick-2007-TGIF1-male_proband",
+  "subject": {
+    "id": "male proband",
+    "ageAtCollection": {
+      "age": "n/a"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000161",
+      "label": "Median cleft lip"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:16962354",
+        "description": "Functional analysis of mutations in TGIF associated with holoprosencephaly"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005273",
+      "label": "Absent nasal septal cartilage"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:16962354",
+        "description": "Functional analysis of mutations in TGIF associated with holoprosencephaly"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000252",
+      "label": "Microcephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:16962354",
+        "description": "Functional analysis of mutations in TGIF associated with holoprosencephaly"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006870",
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+    },
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:16962354",
+        "description": "Functional analysis of mutations in TGIF associated with holoprosencephaly"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009099",
+      "label": "Median cleft palate"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:16962354",
+        "description": "Functional analysis of mutations in TGIF associated with holoprosencephaly"
+      }
+    }]
+  }, {
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+      "label": "Diabetes insipidus"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+      "reference": {
+        "id": "PMID:16962354",
+        "description": "Functional analysis of mutations in TGIF associated with holoprosencephaly"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000437",
+      "label": "Depressed nasal tip"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:16962354",
+        "description": "Functional analysis of mutations in TGIF associated with holoprosencephaly"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:7050",
+    "symbol": "TGIF1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "18",
+      "pos": 3456468,
+      "ref": "G",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:142946",
+      "label": "HOLOPROSENCEPHALY 4; HPE4"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
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+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:16962354",
+      "description": "Functional analysis of mutations in TGIF associated with holoprosencephaly"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Elsaadany-2016-WWOX-Patient_1.json b/notebooks/LIRICAL/v1phenopackets/Elsaadany-2016-WWOX-Patient_1.json
new file mode 100644
index 000000000..ae743160b
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Elsaadany-2016-WWOX-Patient_1.json
@@ -0,0 +1,359 @@
+{
+  "id": "PMID:27495153-Elsaadany-2016-WWOX-Patient_1",
+  "subject": {
+    "id": "Patient 1",
+    "ageAtCollection": {
+      "age": "P7Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001250",
+      "label": "Seizures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27495153",
+        "description": "W44X mutation in the WWOX gene causes intractable seizures and developmental delay: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000543",
+      "label": "Optic disc pallor"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27495153",
+        "description": "W44X mutation in the WWOX gene causes intractable seizures and developmental delay: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001290",
+      "label": "Generalized hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27495153",
+        "description": "W44X mutation in the WWOX gene causes intractable seizures and developmental delay: a case report"
+      }
+    }]
+  }, {
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+      "label": "Organic aciduria"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27495153",
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+      }
+    }]
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+      "id": "HP:0011470",
+      "label": "Nasogastric tube feeding in infancy"
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+        "id": "PMID:27495153",
+        "description": "W44X mutation in the WWOX gene causes intractable seizures and developmental delay: a case report"
+      }
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+    }]
+  }, {
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+      "id": "HP:0007305",
+      "label": "CNS demyelination"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+      "reference": {
+        "id": "PMID:27495153",
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+    }]
+  }, {
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+    },
+    "evidence": [{
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+      "label": "Hypoplastic hippocampus"
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+    }]
+  }, {
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+    "evidence": [{
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+        "description": "W44X mutation in the WWOX gene causes intractable seizures and developmental delay: a case report"
+      }
+    }]
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+      "label": "Progressive muscle weakness"
+    },
+    "evidence": [{
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+        "description": "W44X mutation in the WWOX gene causes intractable seizures and developmental delay: a case report"
+      }
+    }]
+  }, {
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+      "id": "HP:0002093",
+      "label": "Respiratory insufficiency"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27495153",
+        "description": "W44X mutation in the WWOX gene causes intractable seizures and developmental delay: a case report"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:51741",
+    "symbol": "WWOX"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "16",
+      "pos": 78142343,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616211",
+      "label": "EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 28; EIEE28"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27495153",
+      "description": "W44X mutation in the WWOX gene causes intractable seizures and developmental delay: a case report"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Elsaid-2017-NT5C2-II.3.json b/notebooks/LIRICAL/v1phenopackets/Elsaid-2017-NT5C2-II.3.json
new file mode 100644
index 000000000..1d6195050
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Elsaid-2017-NT5C2-II.3.json
@@ -0,0 +1,283 @@
+{
+  "id": "PMID:28327087-Elsaid-2017-NT5C2-II.3",
+  "subject": {
+    "id": "II.3",
+    "ageAtCollection": {
+      "age": "P3Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001762",
+      "label": "Talipes equinovarus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28327087",
+        "description": "NT5C2 novel splicing variant expands the phenotypic spectrum of Spastic Paraplegia (SPG45): case report of a new member of thin corpus callosum SPG-Subgroup"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28327087",
+        "description": "NT5C2 novel splicing variant expands the phenotypic spectrum of Spastic Paraplegia (SPG45): case report of a new member of thin corpus callosum SPG-Subgroup"
+      }
+    }]
+  }, {
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+      "id": "HP:0001348",
+      "label": "Brisk reflexes"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+    "type": {
+      "id": "HP:0001256",
+      "label": "Intellectual disability, mild"
+    },
+    "evidence": [{
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+      "name": "human phenotype ontology",
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+      "version": "2018-03-08",
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+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
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+      "version": "2018-03-28",
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+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
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+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
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+      "name": "NCBI organismal classification",
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+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
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+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Falik_Zaccai-2014-INSR-ISR1.json b/notebooks/LIRICAL/v1phenopackets/Falik_Zaccai-2014-INSR-ISR1.json
new file mode 100644
index 000000000..5b16cabb5
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Falik_Zaccai-2014-INSR-ISR1.json
@@ -0,0 +1,296 @@
+{
+  "id": "PMID:24498630-Falik_Zaccai-2014-INSR-ISR1",
+  "subject": {
+    "id": "ISR1",
+    "ageAtCollection": {
+      "age": "18M"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002090",
+      "label": "Pneumonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24498630",
+        "description": "Two novel mutations identified in familial cases with Donohue syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002035",
+      "label": "Rectal prolapse"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24498630",
+        "description": "Two novel mutations identified in familial cases with Donohue syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002719",
+      "label": "Recurrent infections"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24498630",
+        "description": "Two novel mutations identified in familial cases with Donohue syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003270",
+      "label": "Abdominal distention"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24498630",
+        "description": "Two novel mutations identified in familial cases with Donohue syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030796",
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+    },
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+      "label": "Hyperinsulinemia"
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+        "id": "PMID:24498630",
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+      }
+    }]
+  }, {
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+      "label": "Ovarian cyst"
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+        "id": "ECO:0000033",
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+        "id": "PMID:24498630",
+        "description": "Two novel mutations identified in familial cases with Donohue syndrome"
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+    }]
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+      }
+    }]
+  }, {
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+      "id": "HP:0008665",
+      "label": "Clitoral hypertrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:24498630",
+        "description": "Two novel mutations identified in familial cases with Donohue syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000388",
+      "label": "Otitis media"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:24498630",
+        "description": "Two novel mutations identified in familial cases with Donohue syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000105",
+      "label": "Enlarged kidney"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24498630",
+        "description": "Two novel mutations identified in familial cases with Donohue syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001712",
+      "label": "Left ventricular hypertrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24498630",
+        "description": "Two novel mutations identified in familial cases with Donohue syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001943",
+      "label": "Hypoglycemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24498630",
+        "description": "Two novel mutations identified in familial cases with Donohue syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000065",
+      "label": "Labial hypertrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24498630",
+        "description": "Two novel mutations identified in familial cases with Donohue syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:3643",
+    "symbol": "INSR"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "19",
+      "pos": 7184444,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:246200",
+      "label": "DONOHUE SYNDROME"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:24498630",
+      "description": "Two novel mutations identified in familial cases with Donohue syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Falik_Zaccai-2017-PLAA-A-VI3.json b/notebooks/LIRICAL/v1phenopackets/Falik_Zaccai-2017-PLAA-A-VI3.json
new file mode 100644
index 000000000..d7a01a42d
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Falik_Zaccai-2017-PLAA-A-VI3.json
@@ -0,0 +1,344 @@
+{
+  "id": "PMID:28007986-Falik_Zaccai-2017-PLAA-A-VI3",
+  "subject": {
+    "id": "A-VI3",
+    "ageAtCollection": {
+      "age": "P4M"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000998",
+      "label": "Hypertrichosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28007986",
+        "description": "Phospholipase A2-activating protein is associated with a novel form of leukoencephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001250",
+      "label": "Seizures"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28007986",
+        "description": "Phospholipase A2-activating protein is associated with a novel form of leukoencephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012444",
+      "label": "Brain atrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28007986",
+        "description": "Phospholipase A2-activating protein is associated with a novel form of leukoencephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001838",
+      "label": "Rocker bottom foot"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28007986",
+        "description": "Phospholipase A2-activating protein is associated with a novel form of leukoencephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002808",
+      "label": "Kyphosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "id": "PMID:28007986",
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+    "type": {
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+      "label": "Abnormal activity of mitochondrial respiratory chain"
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+    "negated": true,
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28007986",
+        "description": "Phospholipase A2-activating protein is associated with a novel form of leukoencephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012448",
+      "label": "Delayed myelination"
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+    "evidence": [{
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+        "id": "PMID:28007986",
+        "description": "Phospholipase A2-activating protein is associated with a novel form of leukoencephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007377",
+      "label": "Abnormality of somatosensory evoked potentials"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28007986",
+        "description": "Phospholipase A2-activating protein is associated with a novel form of leukoencephalopathy"
+      }
+    }]
+  }, {
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+      "id": "HP:0001371",
+      "label": "Flexion contracture"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28007986",
+        "description": "Phospholipase A2-activating protein is associated with a novel form of leukoencephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003487",
+      "label": "Babinski sign"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28007986",
+        "description": "Phospholipase A2-activating protein is associated with a novel form of leukoencephalopathy"
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+    }]
+  }, {
+    "type": {
+      "id": "HP:0000768",
+      "label": "Pectus carinatum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28007986",
+        "description": "Phospholipase A2-activating protein is associated with a novel form of leukoencephalopathy"
+      }
+    }]
+  }, {
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+      "id": "HP:0007410",
+      "label": "Palmoplantar hyperhidrosis"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "description": "Phospholipase A2-activating protein is associated with a novel form of leukoencephalopathy"
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+    }]
+  }, {
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+      "label": "Increased muscle glycogen content"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "description": "Phospholipase A2-activating protein is associated with a novel form of leukoencephalopathy"
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+    }]
+  }, {
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+      "label": "Failure to thrive"
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28007986",
+        "description": "Phospholipase A2-activating protein is associated with a novel form of leukoencephalopathy"
+      }
+    }]
+  }, {
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+      "label": "Joint hyperflexibility"
+    },
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28007986",
+        "description": "Phospholipase A2-activating protein is associated with a novel form of leukoencephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000253",
+      "label": "Progressive microcephaly"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28007986",
+        "description": "Phospholipase A2-activating protein is associated with a novel form of leukoencephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012713",
+      "label": "Moderate hearing impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28007986",
+        "description": "Phospholipase A2-activating protein is associated with a novel form of leukoencephalopathy"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:9373",
+    "symbol": "PLAA"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "9",
+      "pos": 26905643,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617527",
+      "label": "Neurodevelopmental disorder with progressive microcephaly, spasticity, and brain anomalies"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28007986",
+      "description": "Phospholipase A2-activating protein is associated with a novel form of leukoencephalopathy"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Fiscaletti-2018-SP7-II_5.json b/notebooks/LIRICAL/v1phenopackets/Fiscaletti-2018-SP7-II_5.json
new file mode 100644
index 000000000..6d7263c40
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Fiscaletti-2018-SP7-II_5.json
@@ -0,0 +1,328 @@
+{
+  "id": "PMID:29382611-Fiscaletti-2018-SP7-II:5",
+  "subject": {
+    "id": "II:5",
+    "ageAtCollection": {
+      "age": "P14Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0045086",
+      "label": "Knee joint hypermobility"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29382611",
+        "description": "Novel variant in Sp7/Osx associated with recessive osteogenesis imperfecta with bone fragility and hearing impairment"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000407",
+      "label": "Sensorineural hearing impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29382611",
+        "description": "Novel variant in Sp7/Osx associated with recessive osteogenesis imperfecta with bone fragility and hearing impairment"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000411",
+      "label": "Protruding ear"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29382611",
+        "description": "Novel variant in Sp7/Osx associated with recessive osteogenesis imperfecta with bone fragility and hearing impairment"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000218",
+      "label": "High palate"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29382611",
+        "description": "Novel variant in Sp7/Osx associated with recessive osteogenesis imperfecta with bone fragility and hearing impairment"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000703",
+      "label": "Dentinogenesis imperfecta"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29382611",
+        "description": "Novel variant in Sp7/Osx associated with recessive osteogenesis imperfecta with bone fragility and hearing impairment"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002650",
+      "label": "Scoliosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29382611",
+        "description": "Novel variant in Sp7/Osx associated with recessive osteogenesis imperfecta with bone fragility and hearing impairment"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000684",
+      "label": "Delayed eruption of teeth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29382611",
+        "description": "Novel variant in Sp7/Osx associated with recessive osteogenesis imperfecta with bone fragility and hearing impairment"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002757",
+      "label": "Recurrent fractures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29382611",
+        "description": "Novel variant in Sp7/Osx associated with recessive osteogenesis imperfecta with bone fragility and hearing impairment"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004349",
+      "label": "Reduced bone mineral density"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29382611",
+        "description": "Novel variant in Sp7/Osx associated with recessive osteogenesis imperfecta with bone fragility and hearing impairment"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004592",
+      "label": "Thoracic platyspondyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29382611",
+        "description": "Novel variant in Sp7/Osx associated with recessive osteogenesis imperfecta with bone fragility and hearing impairment"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011800",
+      "label": "Midface retrusion"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29382611",
+        "description": "Novel variant in Sp7/Osx associated with recessive osteogenesis imperfecta with bone fragility and hearing impairment"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011220",
+      "label": "Prominent forehead"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29382611",
+        "description": "Novel variant in Sp7/Osx associated with recessive osteogenesis imperfecta with bone fragility and hearing impairment"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000336",
+      "label": "Prominent supraorbital ridges"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29382611",
+        "description": "Novel variant in Sp7/Osx associated with recessive osteogenesis imperfecta with bone fragility and hearing impairment"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000160",
+      "label": "Narrow mouth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29382611",
+        "description": "Novel variant in Sp7/Osx associated with recessive osteogenesis imperfecta with bone fragility and hearing impairment"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005280",
+      "label": "Depressed nasal bridge"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29382611",
+        "description": "Novel variant in Sp7/Osx associated with recessive osteogenesis imperfecta with bone fragility and hearing impairment"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29382611",
+        "description": "Novel variant in Sp7/Osx associated with recessive osteogenesis imperfecta with bone fragility and hearing impairment"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:121340",
+    "symbol": "SP7"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "12",
+      "pos": 53722280,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:613849",
+      "label": "OSTEOGENESIS IMPERFECTA, TYPE XII; OI12"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13",
+    "submittedBy": "HP:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29382611",
+      "description": "Novel variant in Sp7/Osx associated with recessive osteogenesis imperfecta with bone fragility and hearing impairment"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_1.json b/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_1.json
new file mode 100644
index 000000000..770742494
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_1.json
@@ -0,0 +1,1470 @@
+{
+  "id": "PMID:27087320-Fregeau-2016-RERE-Subject_1",
+  "subject": {
+    "id": "Subject 1",
+    "ageAtCollection": {
+      "age": "P3Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000414",
+      "label": "Bulbous nose"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000218",
+      "label": "High palate"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000582",
+      "label": "Upslanted palpebral fissure"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030301",
+      "label": "Abnormality of the anterior commissure"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000659",
+      "label": "Peters anomaly"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007018",
+      "label": "Attention deficit hyperactivity disorder"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000752",
+      "label": "Hyperactivity"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000349",
+      "label": "Widow\u0027s peak"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000525",
+      "label": "Abnormality iris morphology"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010772",
+      "label": "Anomalous pulmonary venous return"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003186",
+      "label": "Inverted nipples"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001290",
+      "label": "Generalized hypotonia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0200055",
+      "label": "Small hand"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000581",
+      "label": "Blepharophimosis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011328",
+      "label": "Abnormality of fontanelles"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000076",
+      "label": "Vesicoureteral reflux"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000286",
+      "label": "Epicanthus"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002079",
+      "label": "Hypoplasia of the corpus callosum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006808",
+      "label": "Cerebral hypomyelination"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000601",
+      "label": "Hypotelorism"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001260",
+      "label": "Dysarthria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002650",
+      "label": "Scoliosis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000957",
+      "label": "Cafe-au-lait spot"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002247",
+      "label": "Duodenal atresia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001159",
+      "label": "Syndactyly"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011480",
+      "label": "Unilateral microphthalmos"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002020",
+      "label": "Gastroesophageal reflux"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001629",
+      "label": "Ventricular septal defect"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010490",
+      "label": "Abnormality of the palmar creases"
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+    "evidence": [{
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+        "id": "ECO:0000033",
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000534",
+      "label": "Abnormal eyebrow morphology"
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+        "id": "ECO:0000033",
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+    "type": {
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+      "label": "Narrow mouth"
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+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Hypoplastic nipples"
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+      }
+    }]
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+      "label": "Cryptorchidism"
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+      }
+    }]
+  }, {
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+      "label": "Thick vermilion border"
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+      }
+    }]
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+      "label": "Furrowed tongue"
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+      }
+    }]
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+      "label": "Pyloric stenosis"
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+      }
+    }]
+  }, {
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+      "label": "Hip dysplasia"
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+    }]
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+      "label": "Clinodactyly"
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+      }
+    }]
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+      "label": "Muscular hypotonia"
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+      }
+    }]
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+      "label": "Global developmental delay"
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+      }
+    }]
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+      "label": "Preauricular pit"
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+      }
+    }]
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+      }
+    }]
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+      "label": "Seizures"
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+      }
+    }]
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+      }
+    }]
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+      }
+    }]
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+      }
+    }]
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+      }
+    }]
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+      "label": "Small nail"
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+      }
+    }]
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+    "type": {
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+      "label": "Sacral hypertrichosis"
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+      }
+    }]
+  }, {
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+      }
+    }]
+  }, {
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+      "label": "Narrow palpebral fissure"
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+      }
+    }]
+  }, {
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+      "label": "Spastic tetraparesis"
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+      }
+    }]
+  }, {
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+      "label": "Placental infarction"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
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+      "label": "Smooth philtrum"
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+      }
+    }]
+  }, {
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+      "label": "Macrocephaly"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002015",
+      "label": "Dysphagia"
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+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000252",
+      "label": "Microcephaly"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001511",
+      "label": "Intrauterine growth retardation"
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+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001518",
+      "label": "Small for gestational age"
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+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
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+      "id": "HP:0008587",
+      "label": "Mild neurosensory hearing impairment"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
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+      "id": "HP:0000041",
+      "label": "Chordee"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Premature birth"
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+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Hypoplasia of the pons"
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+    "evidence": [{
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+        "id": "ECO:0000033",
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000453",
+      "label": "Choanal atresia"
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+    "negated": true,
+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002938",
+      "label": "Lumbar hyperlordosis"
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+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002119",
+      "label": "Ventriculomegaly"
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+    "negated": true,
+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000164",
+      "label": "Abnormality of the dentition"
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+    "negated": true,
+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000589",
+      "label": "Coloboma"
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+    "evidence": [{
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+        "id": "ECO:0000033",
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+      "reference": {
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000494",
+      "label": "Downslanted palpebral fissures"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002007",
+      "label": "Frontal bossing"
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+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000187",
+      "label": "Broad alveolar ridges"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012448",
+      "label": "Delayed myelination"
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+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000107",
+      "label": "Renal cyst"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+    }, {
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+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
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+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_10.json b/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_10.json
new file mode 100644
index 000000000..22f73578c
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_10.json
@@ -0,0 +1,177 @@
+{
+  "id": "PMID:27087320-Fregeau-2016-RERE-Subject_10",
+  "subject": {
+    "id": "Subject 10",
+    "ageAtCollection": {
+      "age": "P14Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
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+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000729",
+      "label": "Autistic behavior"
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+    "evidence": [{
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+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+    }]
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+    "id": "NCBIGene:473",
+    "symbol": "RERE"
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+    },
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+      "label": "heterozygous"
+    }
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+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
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+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
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+    "externalReferences": [{
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+      "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_2.json b/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_2.json
new file mode 100644
index 000000000..8ea8c9741
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_2.json
@@ -0,0 +1,1413 @@
+{
+  "id": "PMID:27087320-Fregeau-2016-RERE-Subject_2",
+  "subject": {
+    "id": "Subject 2",
+    "ageAtCollection": {
+      "age": "P1Y3M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000414",
+      "label": "Bulbous nose"
+    },
+    "negated": true,
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000218",
+      "label": "High palate"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000453",
+      "label": "Choanal atresia"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
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+      "label": "Upslanted palpebral fissure"
+    },
+    "negated": true,
+    "evidence": [{
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+      "reference": {
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+      "label": "Multicystic kidney dysplasia"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+      "label": "Abnormality of the anterior commissure"
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+    "negated": true,
+    "evidence": [{
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+      "reference": {
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+    }]
+  }, {
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+      "label": "Ventriculomegaly"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
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+      "label": "Peters anomaly"
+    },
+    "negated": true,
+    "evidence": [{
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+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+    }]
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+      "label": "Vesicoureteral reflux"
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+    }]
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+      "label": "Microcephaly"
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+      }
+    }]
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+      "label": "Cerebral hypomyelination"
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+      }
+    }]
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+    }]
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+      }
+    }]
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+      }
+    }]
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+      "label": "Hypospadias"
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+    }]
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+      "label": "Scoliosis"
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+      }
+    }]
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+      "label": "Cafe-au-lait spot"
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+      }
+    }]
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+      "label": "Duodenal atresia"
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+    }]
+  }, {
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+      "label": "Syndactyly"
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+      }
+    }]
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+      "label": "Ventricular septal defect"
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+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010490",
+      "label": "Abnormality of the palmar creases"
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+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
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+      "label": "Abnormal eyebrow morphology"
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+    "negated": true,
+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+    }]
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+    "type": {
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+      "label": "Narrow mouth"
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+    "negated": true,
+    "evidence": [{
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+    }]
+  }, {
+    "type": {
+      "id": "HP:0000377",
+      "label": "Abnormality of the pinna"
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+    "evidence": [{
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+    }]
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+    "type": {
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+      "label": "Hypoplastic nipples"
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+    "evidence": [{
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+    }]
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+      "label": "Thick vermilion border"
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+    }]
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+    "type": {
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+      "label": "Furrowed tongue"
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+      "label": "Pyloric stenosis"
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+      "label": "Hip dysplasia"
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+    }]
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+      "label": "Patent ductus arteriosus"
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+      "label": "Preauricular pit"
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+      "label": "Patent foramen ovale"
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+      "label": "Seizures"
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+    "evidence": [{
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+      "label": "Triangular face"
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+      "label": "Sacral hypertrichosis"
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+      "id": "HP:0045025",
+      "label": "Narrow palpebral fissure"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000319",
+      "label": "Smooth philtrum"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000256",
+      "label": "Macrocephaly"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008897",
+      "label": "Postnatal growth retardation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0025100",
+      "label": "Abnormal morphology of the hippocampus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000648",
+      "label": "Optic atrophy"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001511",
+      "label": "Intrauterine growth retardation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001317",
+      "label": "Abnormal cerebellum morphology"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002938",
+      "label": "Lumbar hyperlordosis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002020",
+      "label": "Gastroesophageal reflux"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000164",
+      "label": "Abnormality of the dentition"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000347",
+      "label": "Micrognathia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000494",
+      "label": "Downslanted palpebral fissures"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002007",
+      "label": "Frontal bossing"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000187",
+      "label": "Broad alveolar ridges"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000028",
+      "label": "Cryptorchidism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010772",
+      "label": "Anomalous pulmonary venous return"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001734",
+      "label": "Annular pancreas"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000463",
+      "label": "Anteverted nares"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000490",
+      "label": "Deeply set eye"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000998",
+      "label": "Hypertrichosis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000316",
+      "label": "Hypertelorism"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+      "reference": {
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
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+      "label": "Hyperlordosis"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000568",
+      "label": "Microphthalmia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001285",
+      "label": "Spastic tetraparesis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000708",
+      "label": "Behavioral abnormality"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0410030",
+      "label": "Cleft lip"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:473",
+    "symbol": "RERE"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 8418276,
+      "ref": "T",
+      "alt": "TGGTGGA"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616975",
+      "label": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27087320",
+      "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_3.json b/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_3.json
new file mode 100644
index 000000000..b8c368210
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_3.json
@@ -0,0 +1,1582 @@
+{
+  "id": "PMID:27087320-Fregeau-2016-RERE-Subject_3",
+  "subject": {
+    "id": "Subject 3",
+    "ageAtCollection": {
+      "age": "P2Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000414",
+      "label": "Bulbous nose"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000218",
+      "label": "High palate"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000365",
+      "label": "Hearing impairment"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030301",
+      "label": "Abnormality of the anterior commissure"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002119",
+      "label": "Ventriculomegaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007018",
+      "label": "Attention deficit hyperactivity disorder"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000589",
+      "label": "Coloboma"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002273",
+      "label": "Tetraparesis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000752",
+      "label": "Hyperactivity"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000098",
+      "label": "Tall stature"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000407",
+      "label": "Sensorineural hearing impairment"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000349",
+      "label": "Widow\u0027s peak"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
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+    }]
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+      "label": "Short stature"
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+    }]
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+      "label": "Anomalous pulmonary venous return"
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+    }]
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+    }]
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+      "label": "Small hand"
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+    }]
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+      "label": "Hydronephrosis"
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+    }]
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+      "label": "Blepharophimosis"
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+      }
+    }]
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+    }]
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+      "label": "Anterior creases of earlobe"
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+      }
+    }]
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+    }]
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+      }
+    }]
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+      "label": "Feeding difficulties"
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+      }
+    }]
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+      }
+    }]
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+      "label": "Vesicoureteral reflux"
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+      }
+    }]
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+      "label": "Generalized hypotonia"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+      "label": "Hypospadias"
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+      }
+    }]
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+      "label": "Scoliosis"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+      "label": "Cafe-au-lait spot"
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+      }
+    }]
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+      }
+    }]
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+      "label": "Renal hypoplasia"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+      "label": "Neoplasm of the liver"
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+      }
+    }]
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
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+      "label": "Abnormal eyebrow morphology"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+      }
+    }]
+  }, {
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+      "label": "Abnormality of the pinna"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+      "id": "HP:0000028",
+      "label": "Cryptorchidism"
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+      }
+    }]
+  }, {
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+      "label": "Annular pancreas"
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+    "evidence": [{
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+      }
+    }]
+  }, {
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+      "label": "Thick vermilion border"
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+    "evidence": [{
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+      }
+    }]
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+      "label": "Furrowed tongue"
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+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+      "label": "Pyloric stenosis"
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+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+    }]
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+      "label": "Prominent antihelix"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+    }]
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+      "id": "HP:0001385",
+      "label": "Hip dysplasia"
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+    "evidence": [{
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+    }]
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+      "label": "Global developmental delay"
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+    }]
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+      "label": "Abnormal morphology of the hippocampus"
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+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+    "type": {
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+      "label": "Patent foramen ovale"
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+    "negated": true,
+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
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+      "id": "HP:0045025",
+      "label": "Narrow palpebral fissure"
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+    "evidence": [{
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+      "reference": {
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
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+      "label": "CNS hypomyelination"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+      "label": "Triangular face"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+    }]
+  }, {
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+      "label": "Polyhydramnios"
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+    "evidence": [{
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+      "reference": {
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001792",
+      "label": "Small nail"
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+    "negated": true,
+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Hypoplastic nipples"
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+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+    }]
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+    "type": {
+      "id": "HP:0000568",
+      "label": "Microphthalmia"
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+    "evidence": [{
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+      "reference": {
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000319",
+      "label": "Smooth philtrum"
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+    "negated": true,
+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000256",
+      "label": "Macrocephaly"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+      "reference": {
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008897",
+      "label": "Postnatal growth retardation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000252",
+      "label": "Microcephaly"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+      "id": "HP:0000648",
+      "label": "Optic atrophy"
+    },
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+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000453",
+      "label": "Choanal atresia"
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+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+    }]
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+      "label": "Gastroesophageal reflux"
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+      "label": "Cerebellar vermis hypoplasia"
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+        "label": "author statement supported by traceable reference"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
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+      "label": "Abnormality of the dentition"
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+    "evidence": [{
+      "evidenceCode": {
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+      "label": "Upslanted palpebral fissure"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+  }, {
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+      "label": "Downslanted palpebral fissures"
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+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+      "label": "Broad alveolar ridges"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002007",
+      "label": "Frontal bossing"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000525",
+      "label": "Abnormality iris morphology"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
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+      "id": "HP:0000107",
+      "label": "Renal cyst"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000490",
+      "label": "Deeply set eye"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "id": "PMID:27087320",
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+      "label": "Patent ductus arteriosus"
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000286",
+      "label": "Epicanthus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004467",
+      "label": "Preauricular pit"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+        "label": "author statement supported by traceable reference"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
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+      "label": "Micrognathia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000316",
+      "label": "Hypertelorism"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
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+      "label": "Abnormal thumb morphology"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+      "label": "Absence seizure"
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+        "id": "ECO:0000033",
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+    }]
+  }, {
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+      "label": "Hyperlordosis"
+    },
+    "negated": true,
+    "evidence": [{
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+      }
+    }]
+  }, {
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+      "label": "Abnormal facial shape"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+        "label": "author statement supported by traceable reference"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+    }]
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+      "label": "Spastic tetraparesis"
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+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+      "label": "Clinodactyly of the 5th finger"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+    }]
+  }, {
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+      "label": "Duodenal atresia"
+    },
+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+    }]
+  }, {
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+      "label": "1-2 finger syndactyly"
+    },
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+      }
+    }]
+  }, {
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+      "label": "Intrauterine growth retardation"
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+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
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+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
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+    }]
+  }, {
+    "type": {
+      "id": "HP:0000708",
+      "label": "Behavioral abnormality"
+    },
+    "negated": true,
+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
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+      "label": "Cleft lip"
+    },
+    "negated": true,
+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
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+      "label": "Growth delay"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
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+      "id": "HP:0000610",
+      "label": "Abnormal choroid morphology"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:473",
+    "symbol": "RERE"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 8418810,
+      "ref": "G",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616975",
+      "label": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
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+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27087320",
+      "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_4.json b/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_4.json
new file mode 100644
index 000000000..afd60b98d
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_4.json
@@ -0,0 +1,1456 @@
+{
+  "id": "PMID:27087320-Fregeau-2016-RERE-Subject_4",
+  "subject": {
+    "id": "Subject 4",
+    "ageAtCollection": {
+      "age": "P9Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000414",
+      "label": "Bulbous nose"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000218",
+      "label": "High palate"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+    }]
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+      "label": "Furrowed tongue"
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+    }]
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+    }]
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+    }]
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+    }]
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+    }]
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+    }]
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+      }
+    }]
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+      "label": "Coloboma"
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+      }
+    }]
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+    }]
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+    }]
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+    }]
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+    }]
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+    }]
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+    }]
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+    }]
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+    }]
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+    }]
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+    }]
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+    }]
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+    }]
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+      "label": "Preauricular pit"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+      "label": "Patent foramen ovale"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+      "id": "HP:0004532",
+      "label": "Sacral hypertrichosis"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001250",
+      "label": "Seizures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0045025",
+      "label": "Narrow palpebral fissure"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+      "label": "Smooth philtrum"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001385",
+      "label": "Hip dysplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+      "label": "Ventriculomegaly"
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+    "negated": true,
+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
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+      "label": "Cerebellar vermis hypoplasia"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000164",
+      "label": "Abnormality of the dentition"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+      "id": "HP:0000347",
+      "label": "Micrognathia"
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+    "negated": true,
+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000187",
+      "label": "Broad alveolar ridges"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
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+      "label": "Downslanted palpebral fissures"
+    },
+    "negated": true,
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+      "label": "Frontal bossing"
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+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+      "label": "Renal cyst"
+    },
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+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001734",
+      "label": "Annular pancreas"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Anteverted nares"
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+    "negated": true,
+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
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+      "label": "Hypertrichosis"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001643",
+      "label": "Patent ductus arteriosus"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+    "type": {
+      "id": "HP:0000286",
+      "label": "Epicanthus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000316",
+      "label": "Hypertelorism"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
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+      "label": "Hyperlordosis"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+      "label": "Microphthalmia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
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+    },
+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+    }]
+  }, {
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+      "label": "Brachydactyly"
+    },
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+  }, {
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+    "negated": true,
+    "evidence": [{
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+      "label": "Spastic tetraparesis"
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+    "negated": true,
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+      "label": "Temperature instability"
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+    "evidence": [{
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+    }]
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+      "label": "Cleft lip"
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+    "negated": true,
+    "evidence": [{
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+    }]
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+      "label": "Single transverse palmar crease"
+    },
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+      "label": "Ventricular septal defect"
+    },
+    "negated": true,
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010490",
+      "label": "Abnormality of the palmar creases"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:473",
+    "symbol": "RERE"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 8418302,
+      "ref": "G",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616975",
+      "label": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27087320",
+      "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_5.json b/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_5.json
new file mode 100644
index 000000000..264913017
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_5.json
@@ -0,0 +1,1530 @@
+{
+  "id": "PMID:27087320-Fregeau-2016-RERE-Subject_5",
+  "subject": {
+    "id": "Subject 5",
+    "ageAtCollection": {
+      "age": "P12Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000582",
+      "label": "Upslanted palpebral fissure"
+    },
+    "negated": true,
+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+    }]
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
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+      "label": "Visual impairment"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+    }]
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
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+    }]
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+    }]
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+    }]
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+    }]
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+    }]
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+    }]
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+    }]
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+    }]
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+      }
+    }]
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+      }
+    }]
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+    }]
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+      }
+    }]
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+      }
+    }]
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+    }]
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+      }
+    }]
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+      }
+    }]
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+      }
+    }]
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+    }]
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+    }]
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+    }]
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+      }
+    }]
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+    }]
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+      }
+    }]
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+    }]
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+      }
+    }]
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+    }]
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+      }
+    }]
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
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+    }]
+  }, {
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000648",
+      "label": "Optic atrophy"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
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+      "label": "Intrauterine growth retardation"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000708",
+      "label": "Behavioral abnormality"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0410030",
+      "label": "Cleft lip"
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+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001629",
+      "label": "Ventricular septal defect"
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+    "negated": true,
+    "evidence": [{
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:473",
+    "symbol": "RERE"
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+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 8418302,
+      "ref": "G",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616975",
+      "label": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27087320",
+      "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_6.json b/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_6.json
new file mode 100644
index 000000000..48e3f81f4
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_6.json
@@ -0,0 +1,1315 @@
+{
+  "id": "PMID:27087320-Fregeau-2016-RERE-Subject_6",
+  "subject": {
+    "id": "Subject 6",
+    "ageAtCollection": {
+      "age": "P6Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000414",
+      "label": "Bulbous nose"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000218",
+      "label": "High palate"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012168",
+      "label": "Head-banging"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000708",
+      "label": "Behavioral abnormality"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000365",
+      "label": "Hearing impairment"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000659",
+      "label": "Peters anomaly"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007018",
+      "label": "Attention deficit hyperactivity disorder"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000589",
+      "label": "Coloboma"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002273",
+      "label": "Tetraparesis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000752",
+      "label": "Hyperactivity"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000098",
+      "label": "Tall stature"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000349",
+      "label": "Widow\u0027s peak"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000407",
+      "label": "Sensorineural hearing impairment"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000525",
+      "label": "Abnormality iris morphology"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001510",
+      "label": "Growth delay"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003186",
+      "label": "Inverted nipples"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000319",
+      "label": "Smooth philtrum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0200055",
+      "label": "Small hand"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000581",
+      "label": "Blepharophimosis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011328",
+      "label": "Abnormality of fontanelles"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000076",
+      "label": "Vesicoureteral reflux"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000463",
+      "label": "Anteverted nares"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000286",
+      "label": "Epicanthus"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011968",
+      "label": "Feeding difficulties"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000601",
+      "label": "Hypotelorism"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001290",
+      "label": "Generalized hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002650",
+      "label": "Scoliosis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000957",
+      "label": "Cafe-au-lait spot"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012170",
+      "label": "Nail-biting"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003307",
+      "label": "Hyperlordosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002247",
+      "label": "Duodenal atresia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002938",
+      "label": "Lumbar hyperlordosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001159",
+      "label": "Syndactyly"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000160",
+      "label": "Narrow mouth"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002557",
+      "label": "Hypoplastic nipples"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000256",
+      "label": "Macrocephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012471",
+      "label": "Thick vermilion border"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000221",
+      "label": "Furrowed tongue"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002021",
+      "label": "Pyloric stenosis"
+    },
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+    "evidence": [{
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+    "symbol": "RERE"
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+      "alt": "A"
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+    }
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+      "label": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart"
+    }
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+  "metaData": {
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+      "version": "2018-03-08",
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+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27087320",
+      "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_7.json b/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_7.json
new file mode 100644
index 000000000..cdaffadbe
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_7.json
@@ -0,0 +1,1479 @@
+{
+  "id": "PMID:27087320-Fregeau-2016-RERE-Subject_7",
+  "subject": {
+    "id": "Subject 7",
+    "ageAtCollection": {
+      "age": "P11Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000414",
+      "label": "Bulbous nose"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000218",
+      "label": "High palate"
+    },
+    "negated": true,
+    "evidence": [{
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+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_8.json b/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_8.json
new file mode 100644
index 000000000..9480e878a
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_8.json
@@ -0,0 +1,1555 @@
+{
+  "id": "PMID:27087320-Fregeau-2016-RERE-Subject_8",
+  "subject": {
+    "id": "Subject 8",
+    "ageAtCollection": {
+      "age": "P10Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000414",
+      "label": "Bulbous nose"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003429",
+      "label": "CNS hypomyelination"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002033",
+      "label": "Poor suck"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000218",
+      "label": "High palate"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000582",
+      "label": "Upslanted palpebral fissure"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000365",
+      "label": "Hearing impairment"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030301",
+      "label": "Abnormality of the anterior commissure"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002273",
+      "label": "Tetraparesis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000659",
+      "label": "Peters anomaly"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000729",
+      "label": "Autistic behavior"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000589",
+      "label": "Coloboma"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000098",
+      "label": "Tall stature"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011848",
+      "label": "Abdominal colic"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000407",
+      "label": "Sensorineural hearing impairment"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001510",
+      "label": "Growth delay"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000525",
+      "label": "Abnormality iris morphology"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010772",
+      "label": "Anomalous pulmonary venous return"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000494",
+      "label": "Downslanted palpebral fissures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001290",
+      "label": "Generalized hypotonia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001273",
+      "label": "Abnormal corpus callosum morphology"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000483",
+      "label": "Astigmatism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000581",
+      "label": "Blepharophimosis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011328",
+      "label": "Abnormality of fontanelles"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012448",
+      "label": "Delayed myelination"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002334",
+      "label": "Abnormality of the cerebellar vermis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000076",
+      "label": "Vesicoureteral reflux"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000286",
+      "label": "Epicanthus"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007361",
+      "label": "Abnormality of the pons"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000601",
+      "label": "Hypotelorism"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004209",
+      "label": "Clinodactyly of the 5th finger"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000047",
+      "label": "Hypospadias"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002650",
+      "label": "Scoliosis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000957",
+      "label": "Cafe-au-lait spot"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002247",
+      "label": "Duodenal atresia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001159",
+      "label": "Syndactyly"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002020",
+      "label": "Gastroesophageal reflux"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011968",
+      "label": "Feeding difficulties"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010490",
+      "label": "Abnormality of the palmar creases"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006808",
+      "label": "Cerebral hypomyelination"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000160",
+      "label": "Narrow mouth"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002557",
+      "label": "Hypoplastic nipples"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000028",
+      "label": "Cryptorchidism"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012471",
+      "label": "Thick vermilion border"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007018",
+      "label": "Attention deficit hyperactivity disorder"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010862",
+      "label": "Delayed fine motor development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001629",
+      "label": "Ventricular septal defect"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:473",
+    "symbol": "RERE"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 8555122,
+      "ref": "CT",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616975",
+      "label": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27087320",
+      "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_9.json b/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_9.json
new file mode 100644
index 000000000..6e3c8f09c
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Fregeau-2016-RERE-Subject_9.json
@@ -0,0 +1,1415 @@
+{
+  "id": "PMID:27087320-Fregeau-2016-RERE-Subject_9",
+  "subject": {
+    "id": "Subject 9",
+    "ageAtCollection": {
+      "age": "P9Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000414",
+      "label": "Bulbous nose"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000160",
+      "label": "Narrow mouth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000218",
+      "label": "High palate"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000582",
+      "label": "Upslanted palpebral fissure"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000365",
+      "label": "Hearing impairment"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007018",
+      "label": "Attention deficit hyperactivity disorder"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000659",
+      "label": "Peters anomaly"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002273",
+      "label": "Tetraparesis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000589",
+      "label": "Coloboma"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000098",
+      "label": "Tall stature"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000752",
+      "label": "Hyperactivity"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000407",
+      "label": "Sensorineural hearing impairment"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000349",
+      "label": "Widow\u0027s peak"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001510",
+      "label": "Growth delay"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000525",
+      "label": "Abnormality iris morphology"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010772",
+      "label": "Anomalous pulmonary venous return"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003186",
+      "label": "Inverted nipples"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001290",
+      "label": "Generalized hypotonia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0200055",
+      "label": "Small hand"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000581",
+      "label": "Blepharophimosis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011328",
+      "label": "Abnormality of fontanelles"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000957",
+      "label": "Cafe-au-lait spot"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000076",
+      "label": "Vesicoureteral reflux"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000286",
+      "label": "Epicanthus"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006808",
+      "label": "Cerebral hypomyelination"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000601",
+      "label": "Hypotelorism"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001671",
+      "label": "Abnormal cardiac septum morphology"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000047",
+      "label": "Hypospadias"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002247",
+      "label": "Duodenal atresia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001159",
+      "label": "Syndactyly"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001629",
+      "label": "Ventricular septal defect"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010490",
+      "label": "Abnormality of the palmar creases"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000534",
+      "label": "Abnormal eyebrow morphology"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002557",
+      "label": "Hypoplastic nipples"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000028",
+      "label": "Cryptorchidism"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000256",
+      "label": "Macrocephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0410030",
+      "label": "Cleft lip"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27087320",
+        "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:473",
+    "symbol": "RERE"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 8421296,
+      "ref": "C",
+      "alt": "CCCTGGAGGAGCTGAGGAGGGAG"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616975",
+      "label": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27087320",
+      "description": "De Novo Mutations of RERE Cause a Genetic Syndrome with Features that Overlap Those Associated with Proximal 1p36 Deletions"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Fusco-2017-PMP22-Proband.json b/notebooks/LIRICAL/v1phenopackets/Fusco-2017-PMP22-Proband.json
new file mode 100644
index 000000000..86a61903d
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Fusco-2017-PMP22-Proband.json
@@ -0,0 +1,195 @@
+{
+  "id": "PMID:29078790-Fusco-2017-PMP22-Proband",
+  "subject": {
+    "id": "Proband",
+    "ageAtCollection": {
+      "age": "P4Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0003448",
+      "label": "Decreased sensory nerve conduction velocity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29078790",
+        "description": "Hereditary neuropathy with liability to pressure palsy (HNPP): report of a family with a new point mutation in PMP22 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001284",
+      "label": "Areflexia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29078790",
+        "description": "Hereditary neuropathy with liability to pressure palsy (HNPP): report of a family with a new point mutation in PMP22 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031810",
+      "label": "Anti-ganglioside antibody positivity"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29078790",
+        "description": "Hereditary neuropathy with liability to pressure palsy (HNPP): report of a family with a new point mutation in PMP22 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006937",
+      "label": "Impaired distal tactile sensation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29078790",
+        "description": "Hereditary neuropathy with liability to pressure palsy (HNPP): report of a family with a new point mutation in PMP22 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003431",
+      "label": "Decreased motor nerve conduction velocity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29078790",
+        "description": "Hereditary neuropathy with liability to pressure palsy (HNPP): report of a family with a new point mutation in PMP22 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008959",
+      "label": "Distal upper limb muscle weakness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29078790",
+        "description": "Hereditary neuropathy with liability to pressure palsy (HNPP): report of a family with a new point mutation in PMP22 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001761",
+      "label": "Pes cavus"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29078790",
+        "description": "Hereditary neuropathy with liability to pressure palsy (HNPP): report of a family with a new point mutation in PMP22 gene"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:5376",
+    "symbol": "PMP22"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "17",
+      "pos": 15162409,
+      "ref": "A",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:162500",
+      "label": "NEUROPATHY, HEREDITARY, WITH LIABILITY TO PRESSURE PALSIES; HNPP"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29078790",
+      "description": "Hereditary neuropathy with liability to pressure palsy (HNPP): report of a family with a new point mutation in PMP22 gene"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Gan-Or-2016-CAPN1-Family_A-V_2.json b/notebooks/LIRICAL/v1phenopackets/Gan-Or-2016-CAPN1-Family_A-V_2.json
new file mode 100644
index 000000000..eb7f20a27
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Gan-Or-2016-CAPN1-Family_A-V_2.json
@@ -0,0 +1,207 @@
+{
+  "id": "PMID:27153400-Gan-Or-2016-CAPN1-Family_A-V:2",
+  "subject": {
+    "id": "Family A-V:2",
+    "ageAtCollection": {
+      "age": "P20Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001348",
+      "label": "Brisk reflexes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27153400",
+        "description": "Mutations in CAPN1 Cause Autosomal-Recessive Hereditary Spastic Paraplegia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002064",
+      "label": "Spastic gait"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27153400",
+        "description": "Mutations in CAPN1 Cause Autosomal-Recessive Hereditary Spastic Paraplegia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002355",
+      "label": "Difficulty walking"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27153400",
+        "description": "Mutations in CAPN1 Cause Autosomal-Recessive Hereditary Spastic Paraplegia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008081",
+      "label": "Pes valgus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27153400",
+        "description": "Mutations in CAPN1 Cause Autosomal-Recessive Hereditary Spastic Paraplegia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003487",
+      "label": "Babinski sign"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27153400",
+        "description": "Mutations in CAPN1 Cause Autosomal-Recessive Hereditary Spastic Paraplegia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000020",
+      "label": "Urinary incontinence"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27153400",
+        "description": "Mutations in CAPN1 Cause Autosomal-Recessive Hereditary Spastic Paraplegia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001258",
+      "label": "Spastic paraplegia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27153400",
+        "description": "Mutations in CAPN1 Cause Autosomal-Recessive Hereditary Spastic Paraplegia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001260",
+      "label": "Dysarthria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27153400",
+        "description": "Mutations in CAPN1 Cause Autosomal-Recessive Hereditary Spastic Paraplegia"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:823",
+    "symbol": "CAPN1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "11",
+      "pos": 64955466,
+      "ref": "G",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616907",
+      "label": "Spastic paraplegia 76, autosomal recessive"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27153400",
+      "description": "Mutations in CAPN1 Cause Autosomal-Recessive Hereditary Spastic Paraplegia"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Gan-Or-2016-CAPN1-Family_B-IV_1.json b/notebooks/LIRICAL/v1phenopackets/Gan-Or-2016-CAPN1-Family_B-IV_1.json
new file mode 100644
index 000000000..27f493a36
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Gan-Or-2016-CAPN1-Family_B-IV_1.json
@@ -0,0 +1,192 @@
+{
+  "id": "PMID:27153400-Gan-Or-2016-CAPN1-Family_B-IV:1",
+  "subject": {
+    "id": "Family B-IV:1",
+    "ageAtCollection": {
+      "age": "P35Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002355",
+      "label": "Difficulty walking"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27153400",
+        "description": "Mutations in CAPN1 Cause Autosomal-Recessive Hereditary Spastic Paraplegia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002600",
+      "label": "Hyporeflexia of lower limbs"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27153400",
+        "description": "Mutations in CAPN1 Cause Autosomal-Recessive Hereditary Spastic Paraplegia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002064",
+      "label": "Spastic gait"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27153400",
+        "description": "Mutations in CAPN1 Cause Autosomal-Recessive Hereditary Spastic Paraplegia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007067",
+      "label": "Distal peripheral sensory neuropathy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27153400",
+        "description": "Mutations in CAPN1 Cause Autosomal-Recessive Hereditary Spastic Paraplegia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001258",
+      "label": "Spastic paraplegia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27153400",
+        "description": "Mutations in CAPN1 Cause Autosomal-Recessive Hereditary Spastic Paraplegia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002460",
+      "label": "Distal muscle weakness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27153400",
+        "description": "Mutations in CAPN1 Cause Autosomal-Recessive Hereditary Spastic Paraplegia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001260",
+      "label": "Dysarthria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27153400",
+        "description": "Mutations in CAPN1 Cause Autosomal-Recessive Hereditary Spastic Paraplegia"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:823",
+    "symbol": "CAPN1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "11",
+      "pos": 64974264,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616907",
+      "label": "Spastic paraplegia 76, autosomal recessive"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27153400",
+      "description": "Mutations in CAPN1 Cause Autosomal-Recessive Hereditary Spastic Paraplegia"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Gan-Or-2016-CAPN1-Family_C-IV_13.json b/notebooks/LIRICAL/v1phenopackets/Gan-Or-2016-CAPN1-Family_C-IV_13.json
new file mode 100644
index 000000000..22d04b576
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Gan-Or-2016-CAPN1-Family_C-IV_13.json
@@ -0,0 +1,144 @@
+{
+  "id": "PMID:27153400-Gan-Or-2016-CAPN1-Family_C-IV:13",
+  "subject": {
+    "id": "Family C-IV:13",
+    "ageAtCollection": {
+      "age": "P33Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002355",
+      "label": "Difficulty walking"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27153400",
+        "description": "Mutations in CAPN1 Cause Autosomal-Recessive Hereditary Spastic Paraplegia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002064",
+      "label": "Spastic gait"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27153400",
+        "description": "Mutations in CAPN1 Cause Autosomal-Recessive Hereditary Spastic Paraplegia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001258",
+      "label": "Spastic paraplegia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27153400",
+        "description": "Mutations in CAPN1 Cause Autosomal-Recessive Hereditary Spastic Paraplegia"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:823",
+    "symbol": "CAPN1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "11",
+      "pos": 64951012,
+      "ref": "TC",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "11",
+      "pos": 64974295,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616907",
+      "label": "Spastic paraplegia 76, autosomal recessive"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27153400",
+      "description": "Mutations in CAPN1 Cause Autosomal-Recessive Hereditary Spastic Paraplegia"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Gao-2019-RUNX2-Family_A_II1.json b/notebooks/LIRICAL/v1phenopackets/Gao-2019-RUNX2-Family_A_II1.json
new file mode 100644
index 000000000..96d26bb6a
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Gao-2019-RUNX2-Family_A_II1.json
@@ -0,0 +1,372 @@
+{
+  "id": "PMID:31548836-Gao-2019-RUNX2-Family_A_II1",
+  "subject": {
+    "id": "Family_A_II1",
+    "ageAtCollection": {
+      "age": "P3Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000894",
+      "label": "Short clavicles"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008788",
+      "label": "Delayed pubic bone ossification"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008804",
+      "label": "Broad femoral head"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006297",
+      "label": "Hypoplasia of dental enamel"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011800",
+      "label": "Midface retrusion"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000774",
+      "label": "Narrow chest"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011223",
+      "label": "Metopic depression"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000680",
+      "label": "Delayed eruption of primary teeth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002007",
+      "label": "Frontal bossing"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002645",
+      "label": "Wormian bones"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002650",
+      "label": "Scoliosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005280",
+      "label": "Depressed nasal bridge"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003396",
+      "label": "Syringomyelia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005259",
+      "label": "Abnormal facility in opposing the shoulders"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002866",
+      "label": "Hypoplastic iliac wing"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000242",
+      "label": "Parietal bossing"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100864",
+      "label": "Short femoral neck"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000239",
+      "label": "Large fontanelles"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:860",
+    "symbol": "RUNX2"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "6",
+      "pos": 45399753,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:119600",
+      "label": "CLEIDOCRANIAL DYSPLASIA; CCD"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:31548836",
+      "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Gao-2019-RUNX2-Family_B_II1.json b/notebooks/LIRICAL/v1phenopackets/Gao-2019-RUNX2-Family_B_II1.json
new file mode 100644
index 000000000..0a1f7214f
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Gao-2019-RUNX2-Family_B_II1.json
@@ -0,0 +1,372 @@
+{
+  "id": "PMID:31548836-Gao-2019-RUNX2-Family_B_II1",
+  "subject": {
+    "id": "Family_B_II1",
+    "ageAtCollection": {
+      "age": "P1Y9M"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000894",
+      "label": "Short clavicles"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008788",
+      "label": "Delayed pubic bone ossification"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008804",
+      "label": "Broad femoral head"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006297",
+      "label": "Hypoplasia of dental enamel"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000347",
+      "label": "Micrognathia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011800",
+      "label": "Midface retrusion"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011223",
+      "label": "Metopic depression"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000680",
+      "label": "Delayed eruption of primary teeth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000316",
+      "label": "Hypertelorism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002007",
+      "label": "Frontal bossing"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002645",
+      "label": "Wormian bones"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002650",
+      "label": "Scoliosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005280",
+      "label": "Depressed nasal bridge"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005259",
+      "label": "Abnormal facility in opposing the shoulders"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002866",
+      "label": "Hypoplastic iliac wing"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000242",
+      "label": "Parietal bossing"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100864",
+      "label": "Short femoral neck"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000239",
+      "label": "Large fontanelles"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:860",
+    "symbol": "RUNX2"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "6",
+      "pos": 45399750,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:119600",
+      "label": "CLEIDOCRANIAL DYSPLASIA; CCD"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:31548836",
+      "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Gao-2019-RUNX2-Family_D_II1.json b/notebooks/LIRICAL/v1phenopackets/Gao-2019-RUNX2-Family_D_II1.json
new file mode 100644
index 000000000..07514d546
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Gao-2019-RUNX2-Family_D_II1.json
@@ -0,0 +1,372 @@
+{
+  "id": "PMID:31548836-Gao-2019-RUNX2-Family_D_II1",
+  "subject": {
+    "id": "Family_D_II1",
+    "ageAtCollection": {
+      "age": "P12Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000894",
+      "label": "Short clavicles"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008788",
+      "label": "Delayed pubic bone ossification"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008804",
+      "label": "Broad femoral head"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006297",
+      "label": "Hypoplasia of dental enamel"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011800",
+      "label": "Midface retrusion"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000774",
+      "label": "Narrow chest"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011223",
+      "label": "Metopic depression"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000680",
+      "label": "Delayed eruption of primary teeth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000316",
+      "label": "Hypertelorism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002007",
+      "label": "Frontal bossing"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002645",
+      "label": "Wormian bones"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002650",
+      "label": "Scoliosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005280",
+      "label": "Depressed nasal bridge"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005259",
+      "label": "Abnormal facility in opposing the shoulders"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002866",
+      "label": "Hypoplastic iliac wing"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000242",
+      "label": "Parietal bossing"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100864",
+      "label": "Short femoral neck"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000239",
+      "label": "Large fontanelles"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31548836",
+        "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:860",
+    "symbol": "RUNX2"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "6",
+      "pos": 45459710,
+      "ref": "AGTTT",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:119600",
+      "label": "CLEIDOCRANIAL DYSPLASIA; CCD"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:31548836",
+      "description": "Identification of RUNX2 variants associated with cleidocranial dysplasia"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Ge-2019-TJP2-proband.json b/notebooks/LIRICAL/v1phenopackets/Ge-2019-TJP2-proband.json
new file mode 100644
index 000000000..d06ec9e1b
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Ge-2019-TJP2-proband.json
@@ -0,0 +1,359 @@
+{
+  "id": "PMID:30658709-Ge-2019-TJP2-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P1Y11M"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0031964",
+      "label": "Elevated serum alanine aminotransferase"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30658709",
+        "description": "Novel compound heterozygote mutations of TJP2 in a Chinese child with progressive cholestatic liver disease"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003112",
+      "label": "Abnormality of serum amino acid level"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30658709",
+        "description": "Novel compound heterozygote mutations of TJP2 in a Chinese child with progressive cholestatic liver disease"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000952",
+      "label": "Jaundice"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30658709",
+        "description": "Novel compound heterozygote mutations of TJP2 in a Chinese child with progressive cholestatic liver disease"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000989",
+      "label": "Pruritus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30658709",
+        "description": "Novel compound heterozygote mutations of TJP2 in a Chinese child with progressive cholestatic liver disease"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012202",
+      "label": "Increased serum bile acid concentration"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30658709",
+        "description": "Novel compound heterozygote mutations of TJP2 in a Chinese child with progressive cholestatic liver disease"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002240",
+      "label": "Hepatomegaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30658709",
+        "description": "Novel compound heterozygote mutations of TJP2 in a Chinese child with progressive cholestatic liver disease"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001433",
+      "label": "Hepatosplenomegaly"
+    },
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+        "label": "author statement supported by traceable reference"
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+      }
+    }]
+  }, {
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+      "id": "HP:0002650",
+      "label": "Scoliosis"
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+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30658709",
+        "description": "Novel compound heterozygote mutations of TJP2 in a Chinese child with progressive cholestatic liver disease"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100810",
+      "label": "Pointed helix"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30658709",
+        "description": "Novel compound heterozygote mutations of TJP2 in a Chinese child with progressive cholestatic liver disease"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010701",
+      "label": "Abnormal immunoglobulin level"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30658709",
+        "description": "Novel compound heterozygote mutations of TJP2 in a Chinese child with progressive cholestatic liver disease"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002908",
+      "label": "Conjugated hyperbilirubinemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30658709",
+        "description": "Novel compound heterozygote mutations of TJP2 in a Chinese child with progressive cholestatic liver disease"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003573",
+      "label": "Increased total bilirubin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Novel compound heterozygote mutations of TJP2 in a Chinese child with progressive cholestatic liver disease"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001510",
+      "label": "Growth delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Novel compound heterozygote mutations of TJP2 in a Chinese child with progressive cholestatic liver disease"
+      }
+    }]
+  }, {
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+      "label": "Abnormal heart morphology"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
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+      }
+    }]
+  }, {
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+    },
+    "evidence": [{
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+      }
+    }]
+  }, {
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+      "label": "Elevated serum aspartate aminotransferase"
+    },
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+      "evidenceCode": {
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+      }
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+  }, {
+    "type": {
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+      "label": "Abnormality of coagulation"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:30658709",
+        "description": "Novel compound heterozygote mutations of TJP2 in a Chinese child with progressive cholestatic liver disease"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:9414",
+    "symbol": "TJP2"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "9",
+      "pos": 71853706,
+      "ref": "G",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "9",
+      "pos": 71855042,
+      "ref": "AC",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:615878",
+      "label": "CHOLESTASIS, PROGRESSIVE FAMILIAL INTRAHEPATIC, 4; PFIC4"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30658709",
+      "description": "Novel compound heterozygote mutations of TJP2 in a Chinese child with progressive cholestatic liver disease"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Gebbia-1997-ZIC3-III-1.json b/notebooks/LIRICAL/v1phenopackets/Gebbia-1997-ZIC3-III-1.json
new file mode 100644
index 000000000..13715d230
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Gebbia-1997-ZIC3-III-1.json
@@ -0,0 +1,267 @@
+{
+  "id": "PMID:9354794-Gebbia-1997-ZIC3-III-1",
+  "subject": {
+    "id": "III-1",
+    "ageAtCollection": {
+      "age": "7W"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002139",
+      "label": "Arrhinencephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:9354794",
+        "description": "X-linked situs abnormalities result from mutations in ZIC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001750",
+      "label": "Single ventricle"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:9354794",
+        "description": "X-linked situs abnormalities result from mutations in ZIC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001643",
+      "label": "Patent ductus arteriosus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:9354794",
+        "description": "X-linked situs abnormalities result from mutations in ZIC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001746",
+      "label": "Asplenia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:9354794",
+        "description": "X-linked situs abnormalities result from mutations in ZIC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004971",
+      "label": "Pulmonary artery hypoplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:9354794",
+        "description": "X-linked situs abnormalities result from mutations in ZIC3"
+      }
+    }]
+  }, {
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+      "id": "HP:0001674",
+      "label": "Complete atrioventricular canal defect"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:9354794",
+        "description": "X-linked situs abnormalities result from mutations in ZIC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001669",
+      "label": "Transposition of the great arteries"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:9354794",
+        "description": "X-linked situs abnormalities result from mutations in ZIC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012890",
+      "label": "Posteriorly placed anus"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+    }]
+  }, {
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+      "label": "Ventricular septal defect"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:9354794",
+        "description": "X-linked situs abnormalities result from mutations in ZIC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012262",
+      "label": "Abnormal ciliary motility"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      }
+    }]
+  }, {
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+      "id": "HP:0004935",
+      "label": "Pulmonary artery atresia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:9354794",
+        "description": "X-linked situs abnormalities result from mutations in ZIC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003363",
+      "label": "Abdominal situs inversus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:9354794",
+        "description": "X-linked situs abnormalities result from mutations in ZIC3"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:7547",
+    "symbol": "ZIC3"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "X",
+      "pos": 136649818,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000134",
+      "label": "hemizygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:306955",
+      "label": "HETEROTAXY, VISCERAL, 1, X-LINKED; HTX1"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:9354794",
+      "description": "X-linked situs abnormalities result from mutations in ZIC3"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Geiger-2017-TUBB2B-proband.json b/notebooks/LIRICAL/v1phenopackets/Geiger-2017-TUBB2B-proband.json
new file mode 100644
index 000000000..a7de0fcca
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Geiger-2017-TUBB2B-proband.json
@@ -0,0 +1,360 @@
+{
+  "id": "PMID:28966590-Geiger-2017-TUBB2B-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P31Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0003487",
+      "label": "Babinski sign"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28966590",
+        "description": "TUBB2B Mutation in an Adult Patient with Myoclonus-Dystonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003808",
+      "label": "Abnormal muscle tone"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28966590",
+        "description": "TUBB2B Mutation in an Adult Patient with Myoclonus-Dystonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007033",
+      "label": "Cerebellar dysplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28966590",
+        "description": "TUBB2B Mutation in an Adult Patient with Myoclonus-Dystonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001347",
+      "label": "Hyperreflexia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28966590",
+        "description": "TUBB2B Mutation in an Adult Patient with Myoclonus-Dystonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001302",
+      "label": "Pachygyria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28966590",
+        "description": "TUBB2B Mutation in an Adult Patient with Myoclonus-Dystonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000473",
+      "label": "Torticollis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28966590",
+        "description": "TUBB2B Mutation in an Adult Patient with Myoclonus-Dystonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002174",
+      "label": "Postural tremor"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28966590",
+        "description": "TUBB2B Mutation in an Adult Patient with Myoclonus-Dystonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007018",
+      "label": "Attention deficit hyperactivity disorder"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28966590",
+        "description": "TUBB2B Mutation in an Adult Patient with Myoclonus-Dystonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100021",
+      "label": "Cerebral palsy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28966590",
+        "description": "TUBB2B Mutation in an Adult Patient with Myoclonus-Dystonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002857",
+      "label": "Genu valgum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28966590",
+        "description": "TUBB2B Mutation in an Adult Patient with Myoclonus-Dystonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001339",
+      "label": "Lissencephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28966590",
+        "description": "TUBB2B Mutation in an Adult Patient with Myoclonus-Dystonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100543",
+      "label": "Cognitive impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28966590",
+        "description": "TUBB2B Mutation in an Adult Patient with Myoclonus-Dystonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001385",
+      "label": "Hip dysplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28966590",
+        "description": "TUBB2B Mutation in an Adult Patient with Myoclonus-Dystonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003307",
+      "label": "Hyperlordosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28966590",
+        "description": "TUBB2B Mutation in an Adult Patient with Myoclonus-Dystonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006956",
+      "label": "Dilation of lateral ventricles"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28966590",
+        "description": "TUBB2B Mutation in an Adult Patient with Myoclonus-Dystonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001336",
+      "label": "Myoclonus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28966590",
+        "description": "TUBB2B Mutation in an Adult Patient with Myoclonus-Dystonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002069",
+      "label": "Generalized tonic-clonic seizures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28966590",
+        "description": "TUBB2B Mutation in an Adult Patient with Myoclonus-Dystonia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001270",
+      "label": "Motor delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28966590",
+        "description": "TUBB2B Mutation in an Adult Patient with Myoclonus-Dystonia"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:347733",
+    "symbol": "TUBB2B"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "6",
+      "pos": 3225601,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:610031",
+      "label": "POLYMICROGYRIA, SYMMETRIC OR ASYMMETRIC; PMGYSA"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28966590",
+      "description": "TUBB2B Mutation in an Adult Patient with Myoclonus-Dystonia"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Gerding-2009-LITAF-Proband.json b/notebooks/LIRICAL/v1phenopackets/Gerding-2009-LITAF-Proband.json
new file mode 100644
index 000000000..4ccf547c7
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Gerding-2009-LITAF-Proband.json
@@ -0,0 +1,301 @@
+{
+  "id": "PMID:19541485-Gerding-2009-LITAF-Proband",
+  "subject": {
+    "id": "Proband",
+    "ageAtCollection": {
+      "age": "P57Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0007078",
+      "label": "Decreased amplitude of sensory action potentials"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:19541485",
+        "description": "Hereditary motor and sensory neuropathy caused by a novel mutation in LITAF"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003474",
+      "label": "Sensory impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:19541485",
+        "description": "Hereditary motor and sensory neuropathy caused by a novel mutation in LITAF"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002403",
+      "label": "Positive Romberg sign"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:19541485",
+        "description": "Hereditary motor and sensory neuropathy caused by a novel mutation in LITAF"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031910",
+      "label": "Abnormal cranial nerve physiology"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:19541485",
+        "description": "Hereditary motor and sensory neuropathy caused by a novel mutation in LITAF"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100543",
+      "label": "Cognitive impairment"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:19541485",
+        "description": "Hereditary motor and sensory neuropathy caused by a novel mutation in LITAF"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002070",
+      "label": "Limb ataxia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:19541485",
+        "description": "Hereditary motor and sensory neuropathy caused by a novel mutation in LITAF"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007141",
+      "label": "Sensorimotor neuropathy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:19541485",
+        "description": "Hereditary motor and sensory neuropathy caused by a novel mutation in LITAF"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001761",
+      "label": "Pes cavus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:19541485",
+        "description": "Hereditary motor and sensory neuropathy caused by a novel mutation in LITAF"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003401",
+      "label": "Paresthesia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:19541485",
+        "description": "Hereditary motor and sensory neuropathy caused by a novel mutation in LITAF"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002073",
+      "label": "Progressive cerebellar ataxia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:19541485",
+        "description": "Hereditary motor and sensory neuropathy caused by a novel mutation in LITAF"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000762",
+      "label": "Decreased nerve conduction velocity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:19541485",
+        "description": "Hereditary motor and sensory neuropathy caused by a novel mutation in LITAF"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009053",
+      "label": "Distal lower limb muscle weakness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:19541485",
+        "description": "Hereditary motor and sensory neuropathy caused by a novel mutation in LITAF"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000649",
+      "label": "Abnormality of visual evoked potentials"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:19541485",
+        "description": "Hereditary motor and sensory neuropathy caused by a novel mutation in LITAF"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002066",
+      "label": "Gait ataxia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:19541485",
+        "description": "Hereditary motor and sensory neuropathy caused by a novel mutation in LITAF"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:9516",
+    "symbol": "LITAF"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "16",
+      "pos": 11643549,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:601098",
+      "label": "CHARCOT-MARIE-TOOTH DISEASE, DEMYELINATING, TYPE 1C; CMT1C"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:19541485",
+      "description": "Hereditary motor and sensory neuropathy caused by a novel mutation in LITAF"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Giau-2018-PSEN2-proband.json b/notebooks/LIRICAL/v1phenopackets/Giau-2018-PSEN2-proband.json
new file mode 100644
index 000000000..eb3ec9bdf
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Giau-2018-PSEN2-proband.json
@@ -0,0 +1,132 @@
+{
+  "id": "PMID:30104866-Giau-2018-PSEN2-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P58Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000718",
+      "label": "Aggressive behavior"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30104866",
+        "description": "A pathogenic PSEN2 p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002354",
+      "label": "Memory impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30104866",
+        "description": "A pathogenic PSEN2 p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000726",
+      "label": "Dementia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30104866",
+        "description": "A pathogenic PSEN2 p"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:5664",
+    "symbol": "PSEN2"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 227075798,
+      "ref": "C",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:606889",
+      "label": "ALZHEIMER DISEASE 4"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30104866",
+      "description": "A pathogenic PSEN2 p"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Gong-2015-CBS-III_3.json b/notebooks/LIRICAL/v1phenopackets/Gong-2015-CBS-III_3.json
new file mode 100644
index 000000000..7c904e8c8
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Gong-2015-CBS-III_3.json
@@ -0,0 +1,278 @@
+{
+  "id": "PMID:26667307-Gong-2015-CBS-III:3",
+  "subject": {
+    "id": "III:3",
+    "ageAtCollection": {
+      "age": "7Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000577",
+      "label": "Exotropia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26667307",
+        "description": "Novel Compound Heterozygous CBS Mutations Cause Homocystinuria in a Han Chinese Family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001288",
+      "label": "Gait disturbance"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26667307",
+        "description": "Novel Compound Heterozygous CBS Mutations Cause Homocystinuria in a Han Chinese Family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007256",
+      "label": "Abnormal pyramidal sign"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26667307",
+        "description": "Novel Compound Heterozygous CBS Mutations Cause Homocystinuria in a Han Chinese Family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012444",
+      "label": "Brain atrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26667307",
+        "description": "Novel Compound Heterozygous CBS Mutations Cause Homocystinuria in a Han Chinese Family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001251",
+      "label": "Ataxia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:26667307",
+        "description": "Novel Compound Heterozygous CBS Mutations Cause Homocystinuria in a Han Chinese Family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001260",
+      "label": "Dysarthria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26667307",
+        "description": "Novel Compound Heterozygous CBS Mutations Cause Homocystinuria in a Han Chinese Family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:26667307",
+        "description": "Novel Compound Heterozygous CBS Mutations Cause Homocystinuria in a Han Chinese Family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001166",
+      "label": "Arachnodactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:26667307",
+        "description": "Novel Compound Heterozygous CBS Mutations Cause Homocystinuria in a Han Chinese Family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000545",
+      "label": "Myopia"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Novel Compound Heterozygous CBS Mutations Cause Homocystinuria in a Han Chinese Family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030854",
+      "label": "Scleral staphyloma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:26667307",
+        "description": "Novel Compound Heterozygous CBS Mutations Cause Homocystinuria in a Han Chinese Family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001083",
+      "label": "Ectopia lentis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "description": "Novel Compound Heterozygous CBS Mutations Cause Homocystinuria in a Han Chinese Family"
+      }
+    }]
+  }, {
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+      "id": "HP:0031284",
+      "label": "Flushing"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:26667307",
+        "description": "Novel Compound Heterozygous CBS Mutations Cause Homocystinuria in a Han Chinese Family"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:875",
+    "symbol": "CBS"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "21",
+      "pos": 44486397,
+      "ref": "A",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "21",
+      "pos": 44485784,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:236200",
+      "label": "HOMOCYSTINURIA DUE TO CYSTATHIONINE BETA-SYNTHASE DEFICIENCY"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:26667307",
+      "description": "Novel Compound Heterozygous CBS Mutations Cause Homocystinuria in a Han Chinese Family"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Gonzalez-Perez-2009-CAV3-I1.json b/notebooks/LIRICAL/v1phenopackets/Gonzalez-Perez-2009-CAV3-I1.json
new file mode 100644
index 000000000..16ba0889f
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Gonzalez-Perez-2009-CAV3-I1.json
@@ -0,0 +1,333 @@
+{
+  "id": "PMID:18930476-González-Pérez-2009-CAV3-I1",
+  "subject": {
+    "id": "I1",
+    "ageAtCollection": {
+      "age": "77"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0008981",
+      "label": "Calf muscle hypertrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18930476",
+        "description": "Phenotypic variability in a Spanish family with a Caveolin-3 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003128",
+      "label": "Lactic acidosis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18930476",
+        "description": "Phenotypic variability in a Spanish family with a Caveolin-3 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003393",
+      "label": "Thenar muscle atrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18930476",
+        "description": "Phenotypic variability in a Spanish family with a Caveolin-3 mutation"
+      }
+    }]
+  }, {
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+      "id": "HP:0001268",
+      "label": "Mental deterioration"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18930476",
+        "description": "Phenotypic variability in a Spanish family with a Caveolin-3 mutation"
+      }
+    }]
+  }, {
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+      "id": "HP:0001761",
+      "label": "Pes cavus"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+    },
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+        "id": "PMID:18930476",
+        "description": "Phenotypic variability in a Spanish family with a Caveolin-3 mutation"
+      }
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+      "label": "Muscle spasm"
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+    "evidence": [{
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+        "id": "PMID:18930476",
+        "description": "Phenotypic variability in a Spanish family with a Caveolin-3 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008954",
+      "label": "Intrinsic hand muscle atrophy"
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+    }]
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+      "label": "Myalgia"
+    },
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+      }
+    }]
+  }, {
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+      "label": "Fatigue"
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+    }]
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+      "label": "Finger flexor weakness"
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+        "description": "Phenotypic variability in a Spanish family with a Caveolin-3 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003760",
+      "label": "Percussion-induced rapid rolling muscle contractions"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18930476",
+        "description": "Phenotypic variability in a Spanish family with a Caveolin-3 mutation"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Hand muscle atrophy"
+    },
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+        "label": "author statement supported by traceable reference"
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+        "description": "Phenotypic variability in a Spanish family with a Caveolin-3 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008959",
+      "label": "Distal upper limb muscle weakness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18930476",
+        "description": "Phenotypic variability in a Spanish family with a Caveolin-3 mutation"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:859",
+    "symbol": "CAV3"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "3",
+      "pos": 8775642,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:614321",
+      "label": "MYOPATHY, DISTAL, TATEYAMA TYPE; MPDT"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:lccarmody",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:18930476",
+      "description": "Phenotypic variability in a Spanish family with a Caveolin-3 mutation"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Gowda-2017-MCOLN1-6_year_old_boy.json b/notebooks/LIRICAL/v1phenopackets/Gowda-2017-MCOLN1-6_year_old_boy.json
new file mode 100644
index 000000000..cbf7aabb7
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Gowda-2017-MCOLN1-6_year_old_boy.json
@@ -0,0 +1,206 @@
+{
+  "id": "PMID:28620732-Gowda-2017-MCOLN1-6_year_old_boy",
+  "subject": {
+    "id": "6 year old boy",
+    "ageAtCollection": {
+      "age": "6Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28620732",
+        "description": "Mucolipidosis Type IV Due to Novel MCOLN1 Mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001272",
+      "label": "Cerebellar atrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28620732",
+        "description": "Mucolipidosis Type IV Due to Novel MCOLN1 Mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002079",
+      "label": "Hypoplasia of the corpus callosum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28620732",
+        "description": "Mucolipidosis Type IV Due to Novel MCOLN1 Mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000639",
+      "label": "Nystagmus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28620732",
+        "description": "Mucolipidosis Type IV Due to Novel MCOLN1 Mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000252",
+      "label": "Microcephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
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+      }
+    }]
+  }, {
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+      "id": "HP:0000543",
+      "label": "Optic disc pallor"
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+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "description": "Mucolipidosis Type IV Due to Novel MCOLN1 Mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030890",
+      "label": "Hyperintensity of cerebral white matter on MRI"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28620732",
+        "description": "Mucolipidosis Type IV Due to Novel MCOLN1 Mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000485",
+      "label": "Megalocornea"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28620732",
+        "description": "Mucolipidosis Type IV Due to Novel MCOLN1 Mutation"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:57192",
+    "symbol": "MCOLN1"
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+    "vcfAllele": {
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+      "chr": "19",
+      "pos": 7592840,
+      "ref": "C",
+      "alt": "CC"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:252650",
+      "label": "MUCOLIPIDOSIS IV; ML4"
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+  }],
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+      "url": "http://purl.obolibrary.org/obo/hp.owl",
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+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
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+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28620732",
+      "description": "Mucolipidosis Type IV Due to Novel MCOLN1 Mutation"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Gregor-2018-FBXO11-Individual_1.json b/notebooks/LIRICAL/v1phenopackets/Gregor-2018-FBXO11-Individual_1.json
new file mode 100644
index 000000000..9f831d2b3
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Gregor-2018-FBXO11-Individual_1.json
@@ -0,0 +1,480 @@
+{
+  "id": "PMID:30057029-Gregor-2018-FBXO11-Individual_1",
+  "subject": {
+    "id": "Individual 1",
+    "ageAtCollection": {
+      "age": "P9Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0004780",
+      "label": "Elbow hypertrichosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057029",
+        "description": "De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001250",
+      "label": "Seizures"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057029",
+        "description": "De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000998",
+      "label": "Hypertrichosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057029",
+        "description": "De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001290",
+      "label": "Generalized hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057029",
+        "description": "De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000527",
+      "label": "Long eyelashes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057029",
+        "description": "De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002360",
+      "label": "Sleep disturbance"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057029",
+        "description": "De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002719",
+      "label": "Recurrent infections"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057029",
+        "description": "De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000817",
+      "label": "Poor eye contact"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057029",
+        "description": "De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000316",
+      "label": "Hypertelorism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057029",
+        "description": "De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000486",
+      "label": "Strabismus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057029",
+        "description": "De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008763",
+      "label": "No social interaction"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057029",
+        "description": "De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001212",
+      "label": "Prominent fingertip pads"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057029",
+        "description": "De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001388",
+      "label": "Joint laxity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057029",
+        "description": "De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000175",
+      "label": "Cleft palate"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057029",
+        "description": "De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002019",
+      "label": "Constipation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057029",
+        "description": "De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001344",
+      "label": "Absent speech"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057029",
+        "description": "De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000729",
+      "label": "Autistic behavior"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057029",
+        "description": "De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000520",
+      "label": "Proptosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057029",
+        "description": "De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000735",
+      "label": "Impaired social interactions"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057029",
+        "description": "De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057029",
+        "description": "De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000325",
+      "label": "Triangular face"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057029",
+        "description": "De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000337",
+      "label": "Broad forehead"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057029",
+        "description": "De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100716",
+      "label": "Self-injurious behavior"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057029",
+        "description": "De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001572",
+      "label": "Macrodontia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057029",
+        "description": "De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011344",
+      "label": "Severe global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057029",
+        "description": "De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011081",
+      "label": "Incisor macrodontia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30057029",
+        "description": "De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:80204",
+    "symbol": "FBXO11"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "2",
+      "pos": 48050286,
+      "ref": "T",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:618089",
+      "label": "Intellectual developmental disorder with dysmorphic facies and behavioral abnormalities"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30057029",
+      "description": "De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Grumach-2015-CARD9-Patient.json b/notebooks/LIRICAL/v1phenopackets/Grumach-2015-CARD9-Patient.json
new file mode 100644
index 000000000..00e0bad71
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Grumach-2015-CARD9-Patient.json
@@ -0,0 +1,210 @@
+{
+  "id": "PMID:26044242-Grumach-2015-CARD9-Patient",
+  "subject": {
+    "id": "Patient",
+    "ageAtCollection": {
+      "age": "P24Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0003212",
+      "label": "Increased circulating total IgE level"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26044242",
+        "description": "A homozygous CARD9 mutation in a Brazilian patient with deep dermatophytosis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001880",
+      "label": "Eosinophilia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26044242",
+        "description": "A homozygous CARD9 mutation in a Brazilian patient with deep dermatophytosis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003237",
+      "label": "Increased circulating IgG level"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26044242",
+        "description": "A homozygous CARD9 mutation in a Brazilian patient with deep dermatophytosis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001888",
+      "label": "Lymphopenia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26044242",
+        "description": "A homozygous CARD9 mutation in a Brazilian patient with deep dermatophytosis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031393",
+      "label": "Abnormal proportion of CD8 T cells"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26044242",
+        "description": "A homozygous CARD9 mutation in a Brazilian patient with deep dermatophytosis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008404",
+      "label": "Nail dystrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26044242",
+        "description": "A homozygous CARD9 mutation in a Brazilian patient with deep dermatophytosis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009098",
+      "label": "Chronic oral candidiasis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26044242",
+        "description": "A homozygous CARD9 mutation in a Brazilian patient with deep dermatophytosis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031392",
+      "label": "Abnormal proportion of CD4 T cells"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26044242",
+        "description": "A homozygous CARD9 mutation in a Brazilian patient with deep dermatophytosis"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:64170",
+    "symbol": "CARD9"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "9",
+      "pos": 139265796,
+      "ref": "C",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:212050",
+      "label": "CANDIDIASIS, FAMILIAL, 2; CANDF2"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:26044242",
+      "description": "A homozygous CARD9 mutation in a Brazilian patient with deep dermatophytosis"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Gu-2013-NOTCH2-proband.json b/notebooks/LIRICAL/v1phenopackets/Gu-2013-NOTCH2-proband.json
new file mode 100644
index 000000000..b3db00889
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Gu-2013-NOTCH2-proband.json
@@ -0,0 +1,268 @@
+{
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+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P60Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
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+      "label": "Short stature"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "description": "A mutation in NOTCH2 gene in a Chinese patient with Hajdu-Cheney syndrome"
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+    }]
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+        "id": "PMID:23566664",
+        "description": "A mutation in NOTCH2 gene in a Chinese patient with Hajdu-Cheney syndrome"
+      }
+    }]
+  }, {
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+      "id": "HP:0002953",
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+    },
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+        "description": "A mutation in NOTCH2 gene in a Chinese patient with Hajdu-Cheney syndrome"
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+      "id": "HP:0000365",
+      "label": "Hearing impairment"
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+      "label": "Macrotia"
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+        "id": "PMID:23566664",
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+    }]
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+      "id": "HP:0011927",
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+        "id": "PMID:23566664",
+        "description": "A mutation in NOTCH2 gene in a Chinese patient with Hajdu-Cheney syndrome"
+      }
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+  "genes": [{
+    "id": "NCBIGene:4853",
+    "symbol": "NOTCH2"
+  }],
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+    },
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+      "id": "GENO:0000135",
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+  }],
+  "diseases": [{
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+      "id": "OMIM:102500",
+      "label": "HAJDU-CHENEY SYNDROME; HJCYS"
+    }
+  }],
+  "metaData": {
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+    "submittedBy": "HPO:probinson",
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+      "name": "human phenotype ontology",
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+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
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+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
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+    }, {
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+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
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+    "externalReferences": [{
+      "id": "PMID:23566664",
+      "description": "A mutation in NOTCH2 gene in a Chinese patient with Hajdu-Cheney syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Gueguen-2013-ACTN1-proband.json b/notebooks/LIRICAL/v1phenopackets/Gueguen-2013-ACTN1-proband.json
new file mode 100644
index 000000000..df21933e9
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Gueguen-2013-ACTN1-proband.json
@@ -0,0 +1,164 @@
+{
+  "id": "PMID:24069336-Guéguen-2013-ACTN1-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "adult"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001873",
+      "label": "Thrombocytopenia"
+    },
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+        "id": "PMID:24069336",
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+      }
+    }]
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+      "label": "Abnormal platelet aggregation"
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+      }
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+    }]
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+  "genes": [{
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+    "symbol": "ACTN1"
+  }],
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+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
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+      "id": "OMIM:615193",
+      "label": "BLEEDING DISORDER, PLATELET-TYPE, 15; BDPLT15"
+    }
+  }],
+  "metaData": {
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+    "submittedBy": "HPO:probinson",
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+      "url": "http://purl.obolibrary.org/obo/hp.owl",
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+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
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+    "externalReferences": [{
+      "id": "PMID:24069336",
+      "description": "A missense mutation in the alpha-actinin 1 gene (ACTN1) is the cause of autosomal dominant macrothrombocytopenia in a large French family"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Guerreiro-2016-TBCK-II-3.json b/notebooks/LIRICAL/v1phenopackets/Guerreiro-2016-TBCK-II-3.json
new file mode 100644
index 000000000..ce059f2a7
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Guerreiro-2016-TBCK-II-3.json
@@ -0,0 +1,402 @@
+{
+  "id": "PMID:27275012-Guerreiro-2016-TBCK-II-3",
+  "subject": {
+    "id": "II-3",
+    "ageAtCollection": {
+      "age": "P16Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0006191",
+      "label": "Deep palmar crease"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27275012",
+        "description": "Mutation of TBCK causes a rare recessive developmental disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003739",
+      "label": "Myoclonic spasms"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27275012",
+        "description": "Mutation of TBCK causes a rare recessive developmental disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27275012",
+        "description": "Mutation of TBCK causes a rare recessive developmental disorder"
+      }
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+      "label": "Generalized tonic-clonic seizures"
+    },
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+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27275012",
+        "description": "Mutation of TBCK causes a rare recessive developmental disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002353",
+      "label": "EEG abnormality"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27275012",
+        "description": "Mutation of TBCK causes a rare recessive developmental disorder"
+      }
+    }]
+  }, {
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+      "id": "HP:0006380",
+      "label": "Knee flexion contracture"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27275012",
+        "description": "Mutation of TBCK causes a rare recessive developmental disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002421",
+      "label": "Poor head control"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27275012",
+        "description": "Mutation of TBCK causes a rare recessive developmental disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000248",
+      "label": "Brachycephaly"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "description": "Mutation of TBCK causes a rare recessive developmental disorder"
+      }
+    }]
+  }, {
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+      "label": "Precocious puberty"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Mutation of TBCK causes a rare recessive developmental disorder"
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+    }]
+  }, {
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+      "id": "HP:0001290",
+      "label": "Generalized hypotonia"
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+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27275012",
+        "description": "Mutation of TBCK causes a rare recessive developmental disorder"
+      }
+    }]
+  }, {
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+      "id": "HP:0000954",
+      "label": "Single transverse palmar crease"
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+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27275012",
+        "description": "Mutation of TBCK causes a rare recessive developmental disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000384",
+      "label": "Preauricular skin tag"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27275012",
+        "description": "Mutation of TBCK causes a rare recessive developmental disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008947",
+      "label": "Infantile muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27275012",
+        "description": "Mutation of TBCK causes a rare recessive developmental disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001239",
+      "label": "Wrist flexion contracture"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27275012",
+        "description": "Mutation of TBCK causes a rare recessive developmental disorder"
+      }
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+  }, {
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+      "label": "Hypotonia, infantile, with psychomotor retardation and characteristic facies 3"
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+    "submittedBy": "UNC:biocuration",
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+    }, {
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+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
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+    }, {
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+    "externalReferences": [{
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+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Guerreiro-2016-TBCK-II-4.json b/notebooks/LIRICAL/v1phenopackets/Guerreiro-2016-TBCK-II-4.json
new file mode 100644
index 000000000..289c1a535
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Guerreiro-2016-TBCK-II-4.json
@@ -0,0 +1,327 @@
+{
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+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Gul-2006-CENPJ-IV-5.json b/notebooks/LIRICAL/v1phenopackets/Gul-2006-CENPJ-IV-5.json
new file mode 100644
index 000000000..152a42f78
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Gul-2006-CENPJ-IV-5.json
@@ -0,0 +1,195 @@
+{
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+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Guo-2017-EXTL3-Patient_1.json b/notebooks/LIRICAL/v1phenopackets/Guo-2017-EXTL3-Patient_1.json
new file mode 100644
index 000000000..03ed6005e
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Guo-2017-EXTL3-Patient_1.json
@@ -0,0 +1,837 @@
+{
+  "id": "PMID:28331220-Guo-2017-EXTL3-Patient_1",
+  "subject": {
+    "id": "Patient 1",
+    "ageAtCollection": {
+      "age": "P2Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0003196",
+      "label": "Short nose"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002176",
+      "label": "Spinal cord compression"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003265",
+      "label": "Neonatal hyperbilirubinemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005280",
+      "label": "Depressed nasal bridge"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002090",
+      "label": "Pneumonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003016",
+      "label": "Metaphyseal widening"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008936",
+      "label": "Muscular hypotonia of the trunk"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000463",
+      "label": "Anteverted nares"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000212",
+      "label": "Gingival overgrowth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005306",
+      "label": "Capillary hemangioma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001270",
+      "label": "Motor delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100625",
+      "label": "Enlarged thorax"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001028",
+      "label": "Hemangioma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003307",
+      "label": "Hyperlordosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000960",
+      "label": "Sacral dimple"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002063",
+      "label": "Rigidity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000252",
+      "label": "Microcephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100865",
+      "label": "Broad ischia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000347",
+      "label": "Micrognathia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003690",
+      "label": "Limb muscle weakness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001156",
+      "label": "Brachydactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002867",
+      "label": "Abnormality of the ilium"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001265",
+      "label": "Hyporeflexia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002240",
+      "label": "Hepatomegaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001324",
+      "label": "Muscle weakness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004565",
+      "label": "Severe platyspondyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002007",
+      "label": "Frontal bossing"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005193",
+      "label": "Restricted large joint movement"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002808",
+      "label": "Kyphosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002850",
+      "label": "Decreased circulating total IgM"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001508",
+      "label": "Failure to thrive"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000924",
+      "label": "Abnormality of the skeletal system"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004060",
+      "label": "Trident hand"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002904",
+      "label": "Hyperbilirubinemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007340",
+      "label": "Lower limb muscle weakness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001407",
+      "label": "Hepatic cysts"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000670",
+      "label": "Carious teeth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003416",
+      "label": "Spinal canal stenosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000253",
+      "label": "Progressive microcephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004315",
+      "label": "Decreased circulating IgG level"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100543",
+      "label": "Cognitive impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009826",
+      "label": "Limb undergrowth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000520",
+      "label": "Proptosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001561",
+      "label": "Polyhydramnios"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005619",
+      "label": "Thoracolumbar kyphosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006532",
+      "label": "Recurrent pneumonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001548",
+      "label": "Overgrowth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001290",
+      "label": "Generalized hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002938",
+      "label": "Lumbar hyperlordosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28331220",
+        "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2137",
+    "symbol": "EXTL3"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "8",
+      "pos": 28574529,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617425",
+      "label": "Immunoskeletal dysplasia with neurodevelopmental abnormalities"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28331220",
+      "description": "Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Guo-2018-KDM6A-3_month_old_boy.json b/notebooks/LIRICAL/v1phenopackets/Guo-2018-KDM6A-3_month_old_boy.json
new file mode 100644
index 000000000..9f76f9322
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Guo-2018-KDM6A-3_month_old_boy.json
@@ -0,0 +1,406 @@
+{
+  "id": "PMID:30509212-Guo-2018-KDM6A-3_month_old_boy",
+  "subject": {
+    "id": "3 month old boy",
+    "ageAtCollection": {
+      "age": "3 months"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000437",
+      "label": "Depressed nasal tip"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30509212",
+        "description": "Novel KDM6A splice-site mutation in kabuki syndrome with congenital hydrocephalus: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001510",
+      "label": "Growth delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30509212",
+        "description": "Novel KDM6A splice-site mutation in kabuki syndrome with congenital hydrocephalus: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000369",
+      "label": "Low-set ears"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30509212",
+        "description": "Novel KDM6A splice-site mutation in kabuki syndrome with congenital hydrocephalus: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001612",
+      "label": "Weak cry"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30509212",
+        "description": "Novel KDM6A splice-site mutation in kabuki syndrome with congenital hydrocephalus: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000175",
+      "label": "Cleft palate"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30509212",
+        "description": "Novel KDM6A splice-site mutation in kabuki syndrome with congenital hydrocephalus: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001623",
+      "label": "Breech presentation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30509212",
+        "description": "Novel KDM6A splice-site mutation in kabuki syndrome with congenital hydrocephalus: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007655",
+      "label": "Eversion of lateral third of lower eyelids"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30509212",
+        "description": "Novel KDM6A splice-site mutation in kabuki syndrome with congenital hydrocephalus: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031508",
+      "label": "Abnormal thyroid hormone level"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:30509212",
+        "description": "Novel KDM6A splice-site mutation in kabuki syndrome with congenital hydrocephalus: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000411",
+      "label": "Protruding ear"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30509212",
+        "description": "Novel KDM6A splice-site mutation in kabuki syndrome with congenital hydrocephalus: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008897",
+      "label": "Postnatal growth retardation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30509212",
+        "description": "Novel KDM6A splice-site mutation in kabuki syndrome with congenital hydrocephalus: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001626",
+      "label": "Abnormality of the cardiovascular system"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30509212",
+        "description": "Novel KDM6A splice-site mutation in kabuki syndrome with congenital hydrocephalus: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001385",
+      "label": "Hip dysplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30509212",
+        "description": "Novel KDM6A splice-site mutation in kabuki syndrome with congenital hydrocephalus: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006956",
+      "label": "Dilation of lateral ventricles"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30509212",
+        "description": "Novel KDM6A splice-site mutation in kabuki syndrome with congenital hydrocephalus: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001743",
+      "label": "Abnormality of the spleen"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:30509212",
+        "description": "Novel KDM6A splice-site mutation in kabuki syndrome with congenital hydrocephalus: a case report"
+      }
+    }]
+  }, {
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+      "id": "HP:0000347",
+      "label": "Micrognathia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30509212",
+        "description": "Novel KDM6A splice-site mutation in kabuki syndrome with congenital hydrocephalus: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001392",
+      "label": "Abnormality of the liver"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30509212",
+        "description": "Novel KDM6A splice-site mutation in kabuki syndrome with congenital hydrocephalus: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000238",
+      "label": "Hydrocephalus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30509212",
+        "description": "Novel KDM6A splice-site mutation in kabuki syndrome with congenital hydrocephalus: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0045075",
+      "label": "Sparse eyebrow"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30509212",
+        "description": "Novel KDM6A splice-site mutation in kabuki syndrome with congenital hydrocephalus: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000218",
+      "label": "High palate"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30509212",
+        "description": "Novel KDM6A splice-site mutation in kabuki syndrome with congenital hydrocephalus: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000637",
+      "label": "Long palpebral fissure"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30509212",
+        "description": "Novel KDM6A splice-site mutation in kabuki syndrome with congenital hydrocephalus: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001290",
+      "label": "Generalized hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30509212",
+        "description": "Novel KDM6A splice-site mutation in kabuki syndrome with congenital hydrocephalus: a case report"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:7403",
+    "symbol": "KDM6A"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "X",
+      "pos": 44833910,
+      "ref": "G",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000134",
+      "label": "hemizygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:300867",
+      "label": "KABUKI SYNDROME 2; KABUK2"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30509212",
+      "description": "Novel KDM6A splice-site mutation in kabuki syndrome with congenital hydrocephalus: a case report"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Habarou-2017-LIPT2-P1.json b/notebooks/LIRICAL/v1phenopackets/Habarou-2017-LIPT2-P1.json
new file mode 100644
index 000000000..4ab81bdc9
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Habarou-2017-LIPT2-P1.json
@@ -0,0 +1,339 @@
+{
+  "id": "PMID:28757203-Habarou-2017-LIPT2-P1",
+  "subject": {
+    "id": "P1",
+    "ageAtCollection": {
+      "age": "P7Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001344",
+      "label": "Absent speech"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28757203",
+        "description": "Biallelic Mutations in LIPT2 Cause a Mitochondrial Lipoylation Defect Associated with Severe Neonatal Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003348",
+      "label": "Hyperalaninemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28757203",
+        "description": "Biallelic Mutations in LIPT2 Cause a Mitochondrial Lipoylation Defect Associated with Severe Neonatal Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031518",
+      "label": "Absent posterior alpha rhythm"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28757203",
+        "description": "Biallelic Mutations in LIPT2 Cause a Mitochondrial Lipoylation Defect Associated with Severe Neonatal Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002119",
+      "label": "Ventriculomegaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28757203",
+        "description": "Biallelic Mutations in LIPT2 Cause a Mitochondrial Lipoylation Defect Associated with Severe Neonatal Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004325",
+      "label": "Decreased body weight"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28757203",
+        "description": "Biallelic Mutations in LIPT2 Cause a Mitochondrial Lipoylation Defect Associated with Severe Neonatal Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000252",
+      "label": "Microcephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28757203",
+        "description": "Biallelic Mutations in LIPT2 Cause a Mitochondrial Lipoylation Defect Associated with Severe Neonatal Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012448",
+      "label": "Delayed myelination"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28757203",
+        "description": "Biallelic Mutations in LIPT2 Cause a Mitochondrial Lipoylation Defect Associated with Severe Neonatal Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002194",
+      "label": "Delayed gross motor development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28757203",
+        "description": "Biallelic Mutations in LIPT2 Cause a Mitochondrial Lipoylation Defect Associated with Severe Neonatal Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001332",
+      "label": "Dystonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28757203",
+        "description": "Biallelic Mutations in LIPT2 Cause a Mitochondrial Lipoylation Defect Associated with Severe Neonatal Encephalopathy"
+      }
+    }]
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+      "label": "Abnormality of the cerebral white matter"
+    },
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+        "description": "Biallelic Mutations in LIPT2 Cause a Mitochondrial Lipoylation Defect Associated with Severe Neonatal Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001250",
+      "label": "Seizures"
+    },
+    "evidence": [{
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+        "description": "Biallelic Mutations in LIPT2 Cause a Mitochondrial Lipoylation Defect Associated with Severe Neonatal Encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001285",
+      "label": "Spastic tetraparesis"
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+    "evidence": [{
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+    }]
+  }, {
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+    "id": "NCBIGene:387787",
+    "symbol": "LIPT2"
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+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
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+      "chr": "11",
+      "pos": 74204372,
+      "ref": "A",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617668",
+      "label": "Encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28757203",
+      "description": "Biallelic Mutations in LIPT2 Cause a Mitochondrial Lipoylation Defect Associated with Severe Neonatal Encephalopathy"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Haliloglu-2017-PIEZO2-Patient.json b/notebooks/LIRICAL/v1phenopackets/Haliloglu-2017-PIEZO2-Patient.json
new file mode 100644
index 000000000..5d48ebb80
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Haliloglu-2017-PIEZO2-Patient.json
@@ -0,0 +1,266 @@
+{
+  "id": "PMID:27974811-Haliloglu-2017-PIEZO2-Patient",
+  "subject": {
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+    "ageAtCollection": {
+      "age": "18Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001371",
+      "label": "Flexion contracture"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27974811",
+        "description": "Recessive PIEZO2 stop mutation causes distal arthrogryposis with distal muscle weakness, scoliosis and proprioception defects"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003557",
+      "label": "Increased variability in muscle fiber diameter"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Recessive PIEZO2 stop mutation causes distal arthrogryposis with distal muscle weakness, scoliosis and proprioception defects"
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+      "label": "Muscle weakness"
+    },
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+      "label": "Broad-based gait"
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+      }
+    }]
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+        "description": "Recessive PIEZO2 stop mutation causes distal arthrogryposis with distal muscle weakness, scoliosis and proprioception defects"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:63895",
+    "symbol": "PIEZO2"
+  }],
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+      "genomeAssembly": "GRCh37",
+      "chr": "18",
+      "pos": 10797515,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617146",
+      "label": "Arthrogryposis, distal, with impaired proprioception and touch"
+    }
+  }],
+  "metaData": {
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+    }, {
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+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27974811",
+      "description": "Recessive PIEZO2 stop mutation causes distal arthrogryposis with distal muscle weakness, scoliosis and proprioception defects"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Hall-2017-PLAA-Family_A-IV_6.json b/notebooks/LIRICAL/v1phenopackets/Hall-2017-PLAA-Family_A-IV_6.json
new file mode 100644
index 000000000..3bafca24e
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Hall-2017-PLAA-Family_A-IV_6.json
@@ -0,0 +1,417 @@
+{
+  "id": "PMID:28413018-Hall-2017-PLAA-Family_A-IV:6",
+  "subject": {
+    "id": "Family A-IV:6",
+    "ageAtCollection": {
+      "age": "P12D"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0008872",
+      "label": "Feeding difficulties in infancy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28413018",
+        "description": "PLAA Mutations Cause a Lethal Infantile Epileptic Encephalopathy by Disrupting Ubiquitin-Mediated Endolysosomal Degradation of Synaptic Proteins"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001522",
+      "label": "Death in infancy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28413018",
+        "description": "PLAA Mutations Cause a Lethal Infantile Epileptic Encephalopathy by Disrupting Ubiquitin-Mediated Endolysosomal Degradation of Synaptic Proteins"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000369",
+      "label": "Low-set ears"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28413018",
+        "description": "PLAA Mutations Cause a Lethal Infantile Epileptic Encephalopathy by Disrupting Ubiquitin-Mediated Endolysosomal Degradation of Synaptic Proteins"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000343",
+      "label": "Long philtrum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28413018",
+        "description": "PLAA Mutations Cause a Lethal Infantile Epileptic Encephalopathy by Disrupting Ubiquitin-Mediated Endolysosomal Degradation of Synaptic Proteins"
+      }
+    }]
+  }, {
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+      "id": "HP:0000851",
+      "label": "Congenital hypothyroidism"
+    },
+    "evidence": [{
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+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002015",
+      "label": "Dysphagia"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28413018",
+        "description": "PLAA Mutations Cause a Lethal Infantile Epileptic Encephalopathy by Disrupting Ubiquitin-Mediated Endolysosomal Degradation of Synaptic Proteins"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001561",
+      "label": "Polyhydramnios"
+    },
+    "evidence": [{
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+        "description": "PLAA Mutations Cause a Lethal Infantile Epileptic Encephalopathy by Disrupting Ubiquitin-Mediated Endolysosomal Degradation of Synaptic Proteins"
+      }
+    }]
+  }, {
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+      "id": "HP:0002871",
+      "label": "Central apnea"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "PLAA Mutations Cause a Lethal Infantile Epileptic Encephalopathy by Disrupting Ubiquitin-Mediated Endolysosomal Degradation of Synaptic Proteins"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031605",
+      "label": "Abnormality of fundus pigmentation"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
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+        "description": "PLAA Mutations Cause a Lethal Infantile Epileptic Encephalopathy by Disrupting Ubiquitin-Mediated Endolysosomal Degradation of Synaptic Proteins"
+      }
+    }]
+  }, {
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+      "id": "HP:0010576",
+      "label": "Intracranial cystic lesion"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "description": "PLAA Mutations Cause a Lethal Infantile Epileptic Encephalopathy by Disrupting Ubiquitin-Mediated Endolysosomal Degradation of Synaptic Proteins"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001007",
+      "label": "Hirsutism"
+    },
+    "evidence": [{
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+    }]
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+    }]
+  }, {
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+      "label": "Postaxial polydactyly"
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+    "evidence": [{
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+      }
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+  }, {
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+      "label": "High palate"
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+        "description": "PLAA Mutations Cause a Lethal Infantile Epileptic Encephalopathy by Disrupting Ubiquitin-Mediated Endolysosomal Degradation of Synaptic Proteins"
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+    }]
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+      "id": "HP:0100022",
+      "label": "Abnormality of movement"
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+      "evidenceCode": {
+        "id": "ECO:0000033",
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+      }
+    }]
+  }, {
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+      "id": "HP:0003196",
+      "label": "Short nose"
+    },
+    "evidence": [{
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+        "description": "PLAA Mutations Cause a Lethal Infantile Epileptic Encephalopathy by Disrupting Ubiquitin-Mediated Endolysosomal Degradation of Synaptic Proteins"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002509",
+      "label": "Limb hypertonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28413018",
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+      }
+    }]
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+      "id": "HP:0002033",
+      "label": "Poor suck"
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+    "evidence": [{
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+        "id": "ECO:0000033",
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+      }
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+    "type": {
+      "id": "HP:0008936",
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+    }]
+  }, {
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+      "label": "Fetal distress"
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+        "id": "ECO:0000033",
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+      }
+    }]
+  }, {
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+      "id": "HP:0007633",
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+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007598",
+      "label": "Bilateral single transverse palmar creases"
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+    "evidence": [{
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+        "description": "PLAA Mutations Cause a Lethal Infantile Epileptic Encephalopathy by Disrupting Ubiquitin-Mediated Endolysosomal Degradation of Synaptic Proteins"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:9373",
+    "symbol": "PLAA"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "9",
+      "pos": 26946976,
+      "ref": "C",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617527",
+      "label": "Neurodevelopmental disorder with progressive microcephaly, spasticity, and brain anomalies"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28413018",
+      "description": "PLAA Mutations Cause a Lethal Infantile Epileptic Encephalopathy by Disrupting Ubiquitin-Mediated Endolysosomal Degradation of Synaptic Proteins"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Hall-2017-PLAA-Family_D-Case_VIII-1.json b/notebooks/LIRICAL/v1phenopackets/Hall-2017-PLAA-Family_D-Case_VIII-1.json
new file mode 100644
index 000000000..2a5239c15
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Hall-2017-PLAA-Family_D-Case_VIII-1.json
@@ -0,0 +1,297 @@
+{
+  "id": "PMID:28413018-Hall-2017-PLAA-Family_D-Case_VIII-1",
+  "subject": {
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+    "ageAtCollection": {
+      "age": "P10M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
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+    "type": {
+      "id": "HP:0002719",
+      "label": "Recurrent infections"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
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+        "description": "PLAA Mutations Cause a Lethal Infantile Epileptic Encephalopathy by Disrupting Ubiquitin-Mediated Endolysosomal Degradation of Synaptic Proteins"
+      }
+    }]
+  }, {
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+      "id": "HP:0000400",
+      "label": "Macrotia"
+    },
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "PLAA Mutations Cause a Lethal Infantile Epileptic Encephalopathy by Disrupting Ubiquitin-Mediated Endolysosomal Degradation of Synaptic Proteins"
+      }
+    }]
+  }, {
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+      }
+    }]
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+      "label": "Breathing dysregulation"
+    },
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+      "label": "Postaxial polydactyly"
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+    }, {
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+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
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+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
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+      "description": "PLAA Mutations Cause a Lethal Infantile Epileptic Encephalopathy by Disrupting Ubiquitin-Mediated Endolysosomal Degradation of Synaptic Proteins"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Hamamy-2014-FYB1-IV_5.json b/notebooks/LIRICAL/v1phenopackets/Hamamy-2014-FYB1-IV_5.json
new file mode 100644
index 000000000..9da189b49
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Hamamy-2014-FYB1-IV_5.json
@@ -0,0 +1,148 @@
+{
+  "id": "PMID:25516138-Hamamy-2014-FYB1-IV:5",
+  "subject": {
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+      "age": "P6Y"
+    },
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+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
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+      "label": "Decreased mean platelet volume"
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+        "label": "author statement supported by traceable reference"
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+      }
+    }]
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+    }]
+  }],
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+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:25516138",
+      "description": "Recessive thrombocytopenia likely due to a homozygous pathogenic variant in the FYB gene: case report"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Hamzeh-2016-GPSM2-case_1.json b/notebooks/LIRICAL/v1phenopackets/Hamzeh-2016-GPSM2-case_1.json
new file mode 100644
index 000000000..8d44d1f9a
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Hamzeh-2016-GPSM2-case_1.json
@@ -0,0 +1,282 @@
+{
+  "id": "PMID:27180139-Hamzeh-2016-GPSM2-case_1",
+  "subject": {
+    "id": "case 1",
+    "ageAtCollection": {
+      "age": "P12Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0045086",
+      "label": "Knee joint hypermobility"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27180139",
+        "description": "A novel nonsense GPSM2 mutation in a Yemeni family underlying Chudley-McCullough syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000358",
+      "label": "Posteriorly rotated ears"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27180139",
+        "description": "A novel nonsense GPSM2 mutation in a Yemeni family underlying Chudley-McCullough syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000407",
+      "label": "Sensorineural hearing impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27180139",
+        "description": "A novel nonsense GPSM2 mutation in a Yemeni family underlying Chudley-McCullough syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27180139",
+        "description": "A novel nonsense GPSM2 mutation in a Yemeni family underlying Chudley-McCullough syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002099",
+      "label": "Asthma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27180139",
+        "description": "A novel nonsense GPSM2 mutation in a Yemeni family underlying Chudley-McCullough syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004691",
+      "label": "2-3 toe syndactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27180139",
+        "description": "A novel nonsense GPSM2 mutation in a Yemeni family underlying Chudley-McCullough syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001533",
+      "label": "Slender build"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27180139",
+        "description": "A novel nonsense GPSM2 mutation in a Yemeni family underlying Chudley-McCullough syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001338",
+      "label": "Partial agenesis of the corpus callosum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27180139",
+        "description": "A novel nonsense GPSM2 mutation in a Yemeni family underlying Chudley-McCullough syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010485",
+      "label": "Hyperextensibility at elbow"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27180139",
+        "description": "A novel nonsense GPSM2 mutation in a Yemeni family underlying Chudley-McCullough syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27180139",
+        "description": "A novel nonsense GPSM2 mutation in a Yemeni family underlying Chudley-McCullough syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100702",
+      "label": "Arachnoid cyst"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27180139",
+        "description": "A novel nonsense GPSM2 mutation in a Yemeni family underlying Chudley-McCullough syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0045075",
+      "label": "Sparse eyebrow"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27180139",
+        "description": "A novel nonsense GPSM2 mutation in a Yemeni family underlying Chudley-McCullough syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000325",
+      "label": "Triangular face"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27180139",
+        "description": "A novel nonsense GPSM2 mutation in a Yemeni family underlying Chudley-McCullough syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:29899",
+    "symbol": "GPSM2"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 109445849,
+      "ref": "C",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:604213",
+      "label": "CHUDLEY-MCCULLOUGH SYNDROME; CMCS"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27180139",
+      "description": "A novel nonsense GPSM2 mutation in a Yemeni family underlying Chudley-McCullough syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Han-2015-CHRDL1-III-1.json b/notebooks/LIRICAL/v1phenopackets/Han-2015-CHRDL1-III-1.json
new file mode 100644
index 000000000..b1a02f37e
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Han-2015-CHRDL1-III-1.json
@@ -0,0 +1,148 @@
+{
+  "id": "PMID:24073597-Han-2015-CHRDL1-III-1",
+  "subject": {
+    "id": "III-1",
+    "ageAtCollection": {
+      "age": "P11Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000505",
+      "label": "Visual impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24073597",
+        "description": "X-linked Megalocornea Associated with the Novel CHRDL1 Gene Mutation p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012632",
+      "label": "Abnormal intraocular pressure"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24073597",
+        "description": "X-linked Megalocornea Associated with the Novel CHRDL1 Gene Mutation p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000485",
+      "label": "Megalocornea"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24073597",
+        "description": "X-linked Megalocornea Associated with the Novel CHRDL1 Gene Mutation p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007765",
+      "label": "Deep anterior chamber"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24073597",
+        "description": "X-linked Megalocornea Associated with the Novel CHRDL1 Gene Mutation p"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:91851",
+    "symbol": "CHRDL1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "X",
+      "pos": 110005962,
+      "ref": "AG",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000134",
+      "label": "hemizygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:309300",
+      "label": "MEGALOCORNEA; MGC1"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13",
+    "submittedBy": "HP:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:24073597",
+      "description": "X-linked Megalocornea Associated with the Novel CHRDL1 Gene Mutation p"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Hara-2019-TGFBR1-patient.json b/notebooks/LIRICAL/v1phenopackets/Hara-2019-TGFBR1-patient.json
new file mode 100644
index 000000000..59c927a10
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Hara-2019-TGFBR1-patient.json
@@ -0,0 +1,357 @@
+{
+  "id": "PMID:30701076-Hara-2019-TGFBR1-patient",
+  "subject": {
+    "id": "patient",
+    "ageAtCollection": {
+      "age": "P31Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0012180",
+      "label": "Cystic medial necrosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30701076",
+        "description": "Activation of TGF-β signaling in an aortic aneurysm in a patient with Loeys-Dietz syndrome caused by a novel loss-of-function variant of TGFBR1"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000272",
+      "label": "Malar flattening"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30701076",
+        "description": "Activation of TGF-β signaling in an aortic aneurysm in a patient with Loeys-Dietz syndrome caused by a novel loss-of-function variant of TGFBR1"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000268",
+      "label": "Dolichocephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30701076",
+        "description": "Activation of TGF-β signaling in an aortic aneurysm in a patient with Loeys-Dietz syndrome caused by a novel loss-of-function variant of TGFBR1"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000316",
+      "label": "Hypertelorism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30701076",
+        "description": "Activation of TGF-β signaling in an aortic aneurysm in a patient with Loeys-Dietz syndrome caused by a novel loss-of-function variant of TGFBR1"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001166",
+      "label": "Arachnodactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30701076",
+        "description": "Activation of TGF-β signaling in an aortic aneurysm in a patient with Loeys-Dietz syndrome caused by a novel loss-of-function variant of TGFBR1"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002650",
+      "label": "Scoliosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30701076",
+        "description": "Activation of TGF-β signaling in an aortic aneurysm in a patient with Loeys-Dietz syndrome caused by a novel loss-of-function variant of TGFBR1"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000494",
+      "label": "Downslanted palpebral fissures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30701076",
+        "description": "Activation of TGF-β signaling in an aortic aneurysm in a patient with Loeys-Dietz syndrome caused by a novel loss-of-function variant of TGFBR1"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001065",
+      "label": "Striae distensae"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30701076",
+        "description": "Activation of TGF-β signaling in an aortic aneurysm in a patient with Loeys-Dietz syndrome caused by a novel loss-of-function variant of TGFBR1"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001634",
+      "label": "Mitral valve prolapse"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30701076",
+        "description": "Activation of TGF-β signaling in an aortic aneurysm in a patient with Loeys-Dietz syndrome caused by a novel loss-of-function variant of TGFBR1"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000193",
+      "label": "Bifid uvula"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30701076",
+        "description": "Activation of TGF-β signaling in an aortic aneurysm in a patient with Loeys-Dietz syndrome caused by a novel loss-of-function variant of TGFBR1"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100775",
+      "label": "Dural ectasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30701076",
+        "description": "Activation of TGF-β signaling in an aortic aneurysm in a patient with Loeys-Dietz syndrome caused by a novel loss-of-function variant of TGFBR1"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002616",
+      "label": "Aortic root aneurysm"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30701076",
+        "description": "Activation of TGF-β signaling in an aortic aneurysm in a patient with Loeys-Dietz syndrome caused by a novel loss-of-function variant of TGFBR1"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000767",
+      "label": "Pectus excavatum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30701076",
+        "description": "Activation of TGF-β signaling in an aortic aneurysm in a patient with Loeys-Dietz syndrome caused by a novel loss-of-function variant of TGFBR1"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003179",
+      "label": "Protrusio acetabuli"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+    "id": "NCBIGene:7046",
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+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
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+      "label": "LOEYS-DIETZ SYNDROME 1; LDS1"
+    }
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+    }, {
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+      "version": "2018-03-28",
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+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30701076",
+      "description": "Activation of TGF-β signaling in an aortic aneurysm in a patient with Loeys-Dietz syndrome caused by a novel loss-of-function variant of TGFBR1"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Harlalka-2013-HERC2-Pedigree_1A,VIII_8.json b/notebooks/LIRICAL/v1phenopackets/Harlalka-2013-HERC2-Pedigree_1A,VIII_8.json
new file mode 100644
index 000000000..d6e55f4d0
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Harlalka-2013-HERC2-Pedigree_1A,VIII_8.json
@@ -0,0 +1,222 @@
+{
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+      }
+    }]
+  }, {
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+      "label": "Intellectual disability"
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+    "evidence": [{
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+      }
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+      "label": "Delayed speech and language development"
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+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
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+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
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+    "externalReferences": [{
+      "id": "PMID:23243086",
+      "description": "Mutation of HERC2 causes developmental delay with Angelman-like features"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Hashemi-Gorji-2019-MED23-IV.8.json b/notebooks/LIRICAL/v1phenopackets/Hashemi-Gorji-2019-MED23-IV.8.json
new file mode 100644
index 000000000..97f788622
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Hashemi-Gorji-2019-MED23-IV.8.json
@@ -0,0 +1,192 @@
+{
+  "id": "PMID:30847200-Hashemi-Gorji-2019-MED23-IV.8",
+  "subject": {
+    "id": "IV.8",
+    "ageAtCollection": {
+      "age": "P25Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:30847200",
+        "description": "Novel mutation in the MED23 gene for intellectual disability: A case report and literature review"
+      }
+    }]
+  }, {
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+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+      },
+      "reference": {
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+        "description": "Novel mutation in the MED23 gene for intellectual disability: A case report and literature review"
+      }
+    }]
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+      "label": "Delayed speech and language development"
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+        "description": "Novel mutation in the MED23 gene for intellectual disability: A case report and literature review"
+      }
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+      "label": "Microcephaly"
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+      "label": "homozygous"
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+    }
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+  "metaData": {
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+    "submittedBy": "HPO:probinson",
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+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
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+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
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+    }],
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+    "externalReferences": [{
+      "id": "PMID:30847200",
+      "description": "Novel mutation in the MED23 gene for intellectual disability: A case report and literature review"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Hayette-1995-EPB42-proposita.json b/notebooks/LIRICAL/v1phenopackets/Hayette-1995-EPB42-proposita.json
new file mode 100644
index 000000000..57bf5ad36
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Hayette-1995-EPB42-proposita.json
@@ -0,0 +1,162 @@
+{
+  "id": "PMID:7803799-Hayette-1995-EPB42-proposita",
+  "subject": {
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+      "label": "Homo sapiens"
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+      "label": "Jaundice"
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:7803799",
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+      "label": "Reticulocytosis"
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+        "label": "author statement supported by traceable reference"
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+        "label": "author statement supported by traceable reference"
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+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:7803799",
+      "description": "A deletional frameshift mutation in protein 4"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Helmi-2017-LYST-patient.json b/notebooks/LIRICAL/v1phenopackets/Helmi-2017-LYST-patient.json
new file mode 100644
index 000000000..f4a10d305
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Helmi-2017-LYST-patient.json
@@ -0,0 +1,304 @@
+{
+  "id": "PMID:28183707-Helmi-2017-LYST-patient",
+  "subject": {
+    "id": "patient",
+    "ageAtCollection": {
+      "age": "P2Y6M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002013",
+      "label": "Vomiting"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28183707",
+        "description": "Chédiak-Higashi syndrome with novel gene mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28183707",
+        "description": "Chédiak-Higashi syndrome with novel gene mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002090",
+      "label": "Pneumonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28183707",
+        "description": "Chédiak-Higashi syndrome with novel gene mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001010",
+      "label": "Hypopigmentation of the skin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28183707",
+        "description": "Chédiak-Higashi syndrome with novel gene mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008070",
+      "label": "Sparse hair"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28183707",
+        "description": "Chédiak-Higashi syndrome with novel gene mutation"
+      }
+    }]
+  }, {
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+      "id": "HP:0003212",
+      "label": "Increased circulating total IgE level"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:28183707",
+        "description": "Chédiak-Higashi syndrome with novel gene mutation"
+      }
+    }]
+  }, {
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+      "id": "HP:0001945",
+      "label": "Fever"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28183707",
+        "description": "Chédiak-Higashi syndrome with novel gene mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001386",
+      "label": "Joint swelling"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28183707",
+        "description": "Chédiak-Higashi syndrome with novel gene mutation"
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+    }]
+  }, {
+    "type": {
+      "id": "HP:0000964",
+      "label": "Eczema"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28183707",
+        "description": "Chédiak-Higashi syndrome with novel gene mutation"
+      }
+    }]
+  }, {
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+      "label": "Abnormal bleeding"
+    },
+    "negated": true,
+    "evidence": [{
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+      "label": "Diarrhea"
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+    "negated": true,
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+        "id": "PMID:28183707",
+        "description": "Chédiak-Higashi syndrome with novel gene mutation"
+      }
+    }]
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+      "id": "HP:0012735",
+      "label": "Cough"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001433",
+      "label": "Hepatosplenomegaly"
+    },
+    "negated": true,
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28183707",
+        "description": "Chédiak-Higashi syndrome with novel gene mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004396",
+      "label": "Poor appetite"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28183707",
+        "description": "Chédiak-Higashi syndrome with novel gene mutation"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:1130",
+    "symbol": "LYST"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 235926112,
+      "ref": "TAC",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:214500",
+      "label": "CHEDIAK-HIGASHI SYNDROME; CHS"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28183707",
+      "description": "Chédiak-Higashi syndrome with novel gene mutation"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Hernan-2004-STK11-20-year-old_woman_.json b/notebooks/LIRICAL/v1phenopackets/Hernan-2004-STK11-20-year-old_woman_.json
new file mode 100644
index 000000000..105c8365c
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Hernan-2004-STK11-20-year-old_woman_.json
@@ -0,0 +1,132 @@
+{
+  "id": "PMID:15200509-Hernan-2004-STK11-20-year-old_woman_",
+  "subject": {
+    "id": "20-year-old woman ",
+    "ageAtCollection": {
+      "age": "P20Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0032454",
+      "label": "Labial melanotic macule"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:15200509",
+        "description": "De novo germline mutation in the serine-threonine kinase STK11/LKB1 gene associated with Peutz-Jeghers syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0032451",
+      "label": "Oral melanotic macule"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:15200509",
+        "description": "De novo germline mutation in the serine-threonine kinase STK11/LKB1 gene associated with Peutz-Jeghers syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004390",
+      "label": "Hamartomatous polyposis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:15200509",
+        "description": "De novo germline mutation in the serine-threonine kinase STK11/LKB1 gene associated with Peutz-Jeghers syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:6794",
+    "symbol": "STK11"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "19",
+      "pos": 1221215,
+      "ref": "C",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:175200",
+      "label": "PEUTZ-JEGHERS SYNDROME; PJS"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:15200509",
+      "description": "De novo germline mutation in the serine-threonine kinase STK11/LKB1 gene associated with Peutz-Jeghers syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Higuchi-2017-COL2A1-proband.json b/notebooks/LIRICAL/v1phenopackets/Higuchi-2017-COL2A1-proband.json
new file mode 100644
index 000000000..aa4f7209b
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Higuchi-2017-COL2A1-proband.json
@@ -0,0 +1,375 @@
+{
+  "id": "PMID:28841907-Higuchi-2017-COL2A1-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P2Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0410031",
+      "label": "Submucous cleft of soft and hard palate"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28841907",
+        "description": "A novel mutation in the COL2A1 gene in a patient with Stickler syndrome type 1: a case report and review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002684",
+      "label": "Thickened calvaria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28841907",
+        "description": "A novel mutation in the COL2A1 gene in a patient with Stickler syndrome type 1: a case report and review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000586",
+      "label": "Shallow orbits"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28841907",
+        "description": "A novel mutation in the COL2A1 gene in a patient with Stickler syndrome type 1: a case report and review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000518",
+      "label": "Cataract"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28841907",
+        "description": "A novel mutation in the COL2A1 gene in a patient with Stickler syndrome type 1: a case report and review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001382",
+      "label": "Joint hypermobility"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28841907",
+        "description": "A novel mutation in the COL2A1 gene in a patient with Stickler syndrome type 1: a case report and review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000520",
+      "label": "Proptosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28841907",
+        "description": "A novel mutation in the COL2A1 gene in a patient with Stickler syndrome type 1: a case report and review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28841907",
+        "description": "A novel mutation in the COL2A1 gene in a patient with Stickler syndrome type 1: a case report and review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011800",
+      "label": "Midface retrusion"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28841907",
+        "description": "A novel mutation in the COL2A1 gene in a patient with Stickler syndrome type 1: a case report and review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000369",
+      "label": "Low-set ears"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28841907",
+        "description": "A novel mutation in the COL2A1 gene in a patient with Stickler syndrome type 1: a case report and review of the literature"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Micrognathia"
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+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28841907",
+        "description": "A novel mutation in the COL2A1 gene in a patient with Stickler syndrome type 1: a case report and review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003311",
+      "label": "Hypoplasia of the odontoid process"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28841907",
+        "description": "A novel mutation in the COL2A1 gene in a patient with Stickler syndrome type 1: a case report and review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
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+      "namespacePrefix": "PATO",
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+    }, {
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+      "version": "2018-11-10",
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+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
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+      "description": "A novel mutation in the COL2A1 gene in a patient with Stickler syndrome type 1: a case report and review of the literature"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Hilgert-2008-TMC1-935-IV_1.json b/notebooks/LIRICAL/v1phenopackets/Hilgert-2008-TMC1-935-IV_1.json
new file mode 100644
index 000000000..dc33f5962
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Hilgert-2008-TMC1-935-IV_1.json
@@ -0,0 +1,118 @@
+{
+  "id": "PMID:18616530-Hilgert-2008-TMC1-935-IV:1",
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+    "sex": "MALE",
+    "taxonomy": {
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+      "label": "Homo sapiens"
+    }
+  },
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+      "id": "HP:0001751",
+      "label": "Vestibular dysfunction"
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+    "negated": true,
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+      }
+    }]
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+      "label": "Sensorineural hearing impairment"
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+      }
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+  "genes": [{
+    "id": "NCBIGene:117531",
+    "symbol": "TMC1"
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+    }
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+    "submittedBy": "HPO:probinson",
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+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "name": "Phenotype And Trait Ontology",
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+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
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+      "namespacePrefix": "NCBITaxon"
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+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
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+      "namespacePrefix": "OMIM"
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+      "description": "Mutation analysis of TMC1 identifies four new mutations and suggests an additional deafness gene at loci DFNA36 and DFNB7/11"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Hirabayashi-2018-SPINT2-two-month-old_male.json b/notebooks/LIRICAL/v1phenopackets/Hirabayashi-2018-SPINT2-two-month-old_male.json
new file mode 100644
index 000000000..5fd9eef04
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Hirabayashi-2018-SPINT2-two-month-old_male.json
@@ -0,0 +1,294 @@
+{
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+      "label": "Homo sapiens"
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+        "label": "author statement supported by traceable reference"
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+        "description": "Congenital sodium diarrhea and chorioretinal coloboma with optic disc coloboma in a patient with biallelic SPINT2 mutations, including p"
+      }
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+      "label": "Dehydration"
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+        "description": "Congenital sodium diarrhea and chorioretinal coloboma with optic disc coloboma in a patient with biallelic SPINT2 mutations, including p"
+      }
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+      "label": "Failure to thrive in infancy"
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+      "label": "Cleft palate"
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+      "label": "Decreased body weight"
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+      "id": "GENO:0000135",
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+  }, {
+    "vcfAllele": {
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+      "alt": "GTA"
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+    "zygosity": {
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+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:270420",
+      "label": "DIARRHEA 3, SECRETORY SODIUM, CONGENITAL, WITH OR WITHOUT OTHER CONGENITALANOMALIES; DIAR3"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
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+      "id": "hp",
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+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
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+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
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+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
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+      "description": "Congenital sodium diarrhea and chorioretinal coloboma with optic disc coloboma in a patient with biallelic SPINT2 mutations, including p"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Hirschhorn-1991-ADA-Patient.json b/notebooks/LIRICAL/v1phenopackets/Hirschhorn-1991-ADA-Patient.json
new file mode 100644
index 000000000..1b4085866
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Hirschhorn-1991-ADA-Patient.json
@@ -0,0 +1,176 @@
+{
+  "id": "PMID:1680289-Hirschhorn-1991-ADA-Patient",
+  "subject": {
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+      "age": "P2Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
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+      "id": "HP:0030273",
+      "label": "Reduced red cell adenosine deaminase activity"
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:1680289",
+        "description": "Homozygosity for a newly identified missense mutation in a patient with very severe combined immunodeficiency due to adenosine deaminase deficiency (ADA-SCID)"
+      }
+    }]
+  }, {
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+      "id": "HP:0002090",
+      "label": "Pneumonia"
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+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:1680289",
+        "description": "Homozygosity for a newly identified missense mutation in a patient with very severe combined immunodeficiency due to adenosine deaminase deficiency (ADA-SCID)"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001888",
+      "label": "Lymphopenia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:1680289",
+        "description": "Homozygosity for a newly identified missense mutation in a patient with very severe combined immunodeficiency due to adenosine deaminase deficiency (ADA-SCID)"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002720",
+      "label": "Decreased circulating IgA level"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:1680289",
+        "description": "Homozygosity for a newly identified missense mutation in a patient with very severe combined immunodeficiency due to adenosine deaminase deficiency (ADA-SCID)"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0032218",
+      "label": "Reduced proportion of CD4 T cells"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:1680289",
+        "description": "Homozygosity for a newly identified missense mutation in a patient with very severe combined immunodeficiency due to adenosine deaminase deficiency (ADA-SCID)"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031381",
+      "label": "Decreased lymphocyte proliferation in response to mitogen"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:1680289",
+        "description": "Homozygosity for a newly identified missense mutation in a patient with very severe combined immunodeficiency due to adenosine deaminase deficiency (ADA-SCID)"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:100",
+    "symbol": "ADA"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "20",
+      "pos": 43251680,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:102700",
+      "label": "SEVERE COMBINED IMMUNODEFICIENCY, AUTOSOMAL RECESSIVE, T CELL-NEGATIVE,B CELL-NEGATIVE, NK CELL-NEGATIVE, DUE TO ADENOSINE DEAMINASE DEFICIENCY"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:1680289",
+      "description": "Homozygosity for a newly identified missense mutation in a patient with very severe combined immunodeficiency due to adenosine deaminase deficiency (ADA-SCID)"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Ho-2018-GNPTAB-proband.json b/notebooks/LIRICAL/v1phenopackets/Ho-2018-GNPTAB-proband.json
new file mode 100644
index 000000000..ce7d474dd
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Ho-2018-GNPTAB-proband.json
@@ -0,0 +1,309 @@
+{
+  "id": "PMID:30208878-Ho-2018-GNPTAB-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P7M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000280",
+      "label": "Coarse facial features"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30208878",
+        "description": "GNPTAB c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005280",
+      "label": "Depressed nasal bridge"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30208878",
+        "description": "GNPTAB c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001357",
+      "label": "Plagiocephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30208878",
+        "description": "GNPTAB c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000768",
+      "label": "Pectus carinatum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30208878",
+        "description": "GNPTAB c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000252",
+      "label": "Microcephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30208878",
+        "description": "GNPTAB c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000023",
+      "label": "Inguinal hernia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30208878",
+        "description": "GNPTAB c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001508",
+      "label": "Failure to thrive"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30208878",
+        "description": "GNPTAB c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003307",
+      "label": "Hyperlordosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30208878",
+        "description": "GNPTAB c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000243",
+      "label": "Trigonocephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30208878",
+        "description": "GNPTAB c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000520",
+      "label": "Proptosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30208878",
+        "description": "GNPTAB c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001518",
+      "label": "Small for gestational age"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30208878",
+        "description": "GNPTAB c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002194",
+      "label": "Delayed gross motor development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30208878",
+        "description": "GNPTAB c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006801",
+      "label": "Hyperactive deep tendon reflexes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30208878",
+        "description": "GNPTAB c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001371",
+      "label": "Flexion contracture"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30208878",
+        "description": "GNPTAB c"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:79158",
+    "symbol": "GNPTAB"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "12",
+      "pos": 102158291,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "12",
+      "pos": 102157979,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:252500",
+      "label": "MUCOLIPIDOSIS II ALPHA/BETA"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30208878",
+      "description": "GNPTAB c"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Holmberg-1997-GP1BA-73_year_old_male.json b/notebooks/LIRICAL/v1phenopackets/Holmberg-1997-GP1BA-73_year_old_male.json
new file mode 100644
index 000000000..57e100582
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Holmberg-1997-GP1BA-73_year_old_male.json
@@ -0,0 +1,161 @@
+{
+  "id": "PMID:9233564-Holmberg-1997-GP1BA-73_year_old_male",
+  "subject": {
+    "id": "73 year old male",
+    "ageAtCollection": {
+      "age": "73Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001873",
+      "label": "Thrombocytopenia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:9233564",
+        "description": "Bernard-Soulier syndrome Karlstad: Trp 498--\u0026gt;Stop mutation resulting in a truncated glycoprotein Ib alpha that contains part of the transmembranous domain"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001902",
+      "label": "Giant platelets"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:9233564",
+        "description": "Bernard-Soulier syndrome Karlstad: Trp 498--\u0026gt;Stop mutation resulting in a truncated glycoprotein Ib alpha that contains part of the transmembranous domain"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011871",
+      "label": "Impaired ristocetin-induced platelet aggregation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:9233564",
+        "description": "Bernard-Soulier syndrome Karlstad: Trp 498--\u0026gt;Stop mutation resulting in a truncated glycoprotein Ib alpha that contains part of the transmembranous domain"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001892",
+      "label": "Abnormal bleeding"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:9233564",
+        "description": "Bernard-Soulier syndrome Karlstad: Trp 498--\u0026gt;Stop mutation resulting in a truncated glycoprotein Ib alpha that contains part of the transmembranous domain"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100309",
+      "label": "Subdural hemorrhage"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:9233564",
+        "description": "Bernard-Soulier syndrome Karlstad: Trp 498--\u0026gt;Stop mutation resulting in a truncated glycoprotein Ib alpha that contains part of the transmembranous domain"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2811",
+    "symbol": "GP1BA"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "17",
+      "pos": 4837519,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:231200",
+      "label": "BERNARD-SOULIER SYNDROME; BSS"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:9233564",
+      "description": "Bernard-Soulier syndrome Karlstad: Trp 498--\u0026gt;Stop mutation resulting in a truncated glycoprotein Ib alpha that contains part of the transmembranous domain"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Horvath-2014-GLRA1-proband.json b/notebooks/LIRICAL/v1phenopackets/Horvath-2014-GLRA1-proband.json
new file mode 100644
index 000000000..5ad24b485
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Horvath-2014-GLRA1-proband.json
@@ -0,0 +1,163 @@
+{
+  "id": "PMID:24969041-Horváth-2014-GLRA1-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P11D"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0100660",
+      "label": "Dyskinesia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24969041",
+        "description": "Identification of a novel missense GLRA1 gene mutation in hyperekplexia: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010946",
+      "label": "Dilatation of the renal pelvis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24969041",
+        "description": "Identification of a novel missense GLRA1 gene mutation in hyperekplexia: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001276",
+      "label": "Hypertonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24969041",
+        "description": "Identification of a novel missense GLRA1 gene mutation in hyperekplexia: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002107",
+      "label": "Pneumothorax"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24969041",
+        "description": "Identification of a novel missense GLRA1 gene mutation in hyperekplexia: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002011",
+      "label": "Morphological abnormality of the central nervous system"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24969041",
+        "description": "Identification of a novel missense GLRA1 gene mutation in hyperekplexia: a case report"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2741",
+    "symbol": "GLRA1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "5",
+      "pos": 151266323,
+      "ref": "T",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:149400",
+      "label": "HYPEREKPLEXIA, HEREDITARY 1; HKPX1"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:24969041",
+      "description": "Identification of a novel missense GLRA1 gene mutation in hyperekplexia: a case report"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Hsu-2017-SNAP29-The_patient.json b/notebooks/LIRICAL/v1phenopackets/Hsu-2017-SNAP29-The_patient.json
new file mode 100644
index 000000000..351f55862
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Hsu-2017-SNAP29-The_patient.json
@@ -0,0 +1,371 @@
+{
+  "id": "PMID:29051910-Hsu-2017-SNAP29-The_patient",
+  "subject": {
+    "id": "The patient",
+    "ageAtCollection": {
+      "age": "10Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0006532",
+      "label": "Recurrent pneumonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29051910",
+        "description": "CEDNIK: Phenotypic and Molecular Characterization of an Additional Patient and Review of the Literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006989",
+      "label": "Dysplastic corpus callosum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29051910",
+        "description": "CEDNIK: Phenotypic and Molecular Characterization of an Additional Patient and Review of the Literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000958",
+      "label": "Dry skin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29051910",
+        "description": "CEDNIK: Phenotypic and Molecular Characterization of an Additional Patient and Review of the Literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000664",
+      "label": "Synophrys"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29051910",
+        "description": "CEDNIK: Phenotypic and Molecular Characterization of an Additional Patient and Review of the Literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000574",
+      "label": "Thick eyebrow"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29051910",
+        "description": "CEDNIK: Phenotypic and Molecular Characterization of an Additional Patient and Review of the Literature"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Deeply set eye"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29051910",
+        "description": "CEDNIK: Phenotypic and Molecular Characterization of an Additional Patient and Review of the Literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001344",
+      "label": "Absent speech"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29051910",
+        "description": "CEDNIK: Phenotypic and Molecular Characterization of an Additional Patient and Review of the Literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000421",
+      "label": "Epistaxis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29051910",
+        "description": "CEDNIK: Phenotypic and Molecular Characterization of an Additional Patient and Review of the Literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000294",
+      "label": "Low anterior hairline"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29051910",
+        "description": "CEDNIK: Phenotypic and Molecular Characterization of an Additional Patient and Review of the Literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000448",
+      "label": "Prominent nose"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:29051910",
+        "description": "CEDNIK: Phenotypic and Molecular Characterization of an Additional Patient and Review of the Literature"
+      }
+    }]
+  }, {
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+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29051910",
+        "description": "CEDNIK: Phenotypic and Molecular Characterization of an Additional Patient and Review of the Literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001257",
+      "label": "Spasticity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29051910",
+        "description": "CEDNIK: Phenotypic and Molecular Characterization of an Additional Patient and Review of the Literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000527",
+      "label": "Long eyelashes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29051910",
+        "description": "CEDNIK: Phenotypic and Molecular Characterization of an Additional Patient and Review of the Literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002015",
+      "label": "Dysphagia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29051910",
+        "description": "CEDNIK: Phenotypic and Molecular Characterization of an Additional Patient and Review of the Literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000193",
+      "label": "Bifid uvula"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29051910",
+        "description": "CEDNIK: Phenotypic and Molecular Characterization of an Additional Patient and Review of the Literature"
+      }
+    }]
+  }, {
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+      "id": "HP:0002751",
+      "label": "Kyphoscoliosis"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29051910",
+        "description": "CEDNIK: Phenotypic and Molecular Characterization of an Additional Patient and Review of the Literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000486",
+      "label": "Strabismus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29051910",
+        "description": "CEDNIK: Phenotypic and Molecular Characterization of an Additional Patient and Review of the Literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001007",
+      "label": "Hirsutism"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29051910",
+        "description": "CEDNIK: Phenotypic and Molecular Characterization of an Additional Patient and Review of the Literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000982",
+      "label": "Palmoplantar keratoderma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29051910",
+        "description": "CEDNIK: Phenotypic and Molecular Characterization of an Additional Patient and Review of the Literature"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:9342",
+    "symbol": "SNAP29"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "22",
+      "pos": 21213483,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:609528",
+      "label": "CEREBRAL DYSGENESIS, NEUROPATHY, ICHTHYOSIS, AND PALMOPLANTAR KERATODERMASYNDROME"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29051910",
+      "description": "CEDNIK: Phenotypic and Molecular Characterization of an Additional Patient and Review of the Literature"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Huang-2017-P3H1-proband.json b/notebooks/LIRICAL/v1phenopackets/Huang-2017-P3H1-proband.json
new file mode 100644
index 000000000..1f4c9d780
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Huang-2017-P3H1-proband.json
@@ -0,0 +1,158 @@
+{
+  "id": "PMID:27864101-Huang-2017-P3H1-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "fetus"
+    },
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0005792",
+      "label": "Short humerus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27864101",
+        "description": "Targeted exome sequencing identifies novel compound heterozygous mutations in P3H1 in a fetus with osteogenesis imperfecta type VIII"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005736",
+      "label": "Short tibia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27864101",
+        "description": "Targeted exome sequencing identifies novel compound heterozygous mutations in P3H1 in a fetus with osteogenesis imperfecta type VIII"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002980",
+      "label": "Femoral bowing"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27864101",
+        "description": "Targeted exome sequencing identifies novel compound heterozygous mutations in P3H1 in a fetus with osteogenesis imperfecta type VIII"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002984",
+      "label": "Hypoplasia of the radius"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27864101",
+        "description": "Targeted exome sequencing identifies novel compound heterozygous mutations in P3H1 in a fetus with osteogenesis imperfecta type VIII"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:64175",
+    "symbol": "P3H1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 43232522,
+      "ref": "CGGCGAAGAGCAGATCA",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 43212415,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:610915",
+      "label": "OSTEOGENESIS IMPERFECTA, TYPE VIII; OI8"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27864101",
+      "description": "Targeted exome sequencing identifies novel compound heterozygous mutations in P3H1 in a fetus with osteogenesis imperfecta type VIII"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Hyun-2018-TP53RK-II-1.json b/notebooks/LIRICAL/v1phenopackets/Hyun-2018-TP53RK-II-1.json
new file mode 100644
index 000000000..93ead045b
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Hyun-2018-TP53RK-II-1.json
@@ -0,0 +1,237 @@
+{
+  "id": "PMID:30053862-Hyun-2018-TP53RK-II-1",
+  "subject": {
+    "id": "II-1",
+    "ageAtCollection": {
+      "age": "P10M"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002059",
+      "label": "Cerebral atrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30053862",
+        "description": "A familial case of Galloway-Mowat syndrome due to a novel TP53RK mutation: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000252",
+      "label": "Microcephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30053862",
+        "description": "A familial case of Galloway-Mowat syndrome due to a novel TP53RK mutation: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000776",
+      "label": "Congenital diaphragmatic hernia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30053862",
+        "description": "A familial case of Galloway-Mowat syndrome due to a novel TP53RK mutation: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009879",
+      "label": "Simplified gyral pattern"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30053862",
+        "description": "A familial case of Galloway-Mowat syndrome due to a novel TP53RK mutation: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008677",
+      "label": "Congenital nephrotic syndrome"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30053862",
+        "description": "A familial case of Galloway-Mowat syndrome due to a novel TP53RK mutation: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002580",
+      "label": "Volvulus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30053862",
+        "description": "A familial case of Galloway-Mowat syndrome due to a novel TP53RK mutation: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000369",
+      "label": "Low-set ears"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "description": "A familial case of Galloway-Mowat syndrome due to a novel TP53RK mutation: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000316",
+      "label": "Hypertelorism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:30053862",
+        "description": "A familial case of Galloway-Mowat syndrome due to a novel TP53RK mutation: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002036",
+      "label": "Hiatus hernia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "id": "PMID:30053862",
+        "description": "A familial case of Galloway-Mowat syndrome due to a novel TP53RK mutation: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000097",
+      "label": "Focal segmental glomerulosclerosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30053862",
+        "description": "A familial case of Galloway-Mowat syndrome due to a novel TP53RK mutation: a case report"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:112858",
+    "symbol": "TP53RK"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "20",
+      "pos": 45317860,
+      "ref": "T",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617730",
+      "label": "Galloway-Mowat syndrome 4"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30053862",
+      "description": "A familial case of Galloway-Mowat syndrome due to a novel TP53RK mutation: a case report"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Imani-2019-BBS5-II_2.json b/notebooks/LIRICAL/v1phenopackets/Imani-2019-BBS5-II_2.json
new file mode 100644
index 000000000..bbc07b87b
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Imani-2019-BBS5-II_2.json
@@ -0,0 +1,178 @@
+{
+  "id": "PMID:30850397-Imani-2019-BBS5-II:2",
+  "subject": {
+    "id": "II:2",
+    "ageAtCollection": {
+      "age": "P12Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000135",
+      "label": "Hypogonadism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30850397",
+        "description": "Novel splicing variant c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000662",
+      "label": "Nyctalopia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30850397",
+        "description": "Novel splicing variant c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000543",
+      "label": "Optic disc pallor"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30850397",
+        "description": "Novel splicing variant c"
+      }
+    }]
+  }, {
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+      "id": "HP:0000486",
+      "label": "Strabismus"
+    },
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+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:30850397",
+        "description": "Novel splicing variant c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001513",
+      "label": "Obesity"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30850397",
+        "description": "Novel splicing variant c"
+      }
+    }]
+  }, {
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+      "id": "HP:0007663",
+      "label": "Reduced visual acuity"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:30850397",
+        "description": "Novel splicing variant c"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:129880",
+    "symbol": "BBS5"
+  }],
+  "variants": [{
+    "vcfAllele": {
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+      "chr": "2",
+      "pos": 170343646,
+      "ref": "T",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:615983",
+      "label": "BARDET-BIEDL SYNDROME 5; BBS5"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30850397",
+      "description": "Novel splicing variant c"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Infante-2017-SMC3-patient_1.json b/notebooks/LIRICAL/v1phenopackets/Infante-2017-SMC3-patient_1.json
new file mode 100644
index 000000000..5aafbbe15
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Infante-2017-SMC3-patient_1.json
@@ -0,0 +1,432 @@
+{
+  "id": "PMID:28781842-Infante-2017-SMC3-patient_1",
+  "subject": {
+    "id": "patient 1",
+    "ageAtCollection": {
+      "age": "7m"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0004209",
+      "label": "Clinodactyly of the 5th finger"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28781842",
+        "description": "Rare form of autosomal dominant familial Cornelia de Lange syndrome due to a novel duplication in SMC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010044",
+      "label": "Short 4th metacarpal"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28781842",
+        "description": "Rare form of autosomal dominant familial Cornelia de Lange syndrome due to a novel duplication in SMC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001508",
+      "label": "Failure to thrive"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28781842",
+        "description": "Rare form of autosomal dominant familial Cornelia de Lange syndrome due to a novel duplication in SMC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000286",
+      "label": "Epicanthus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28781842",
+        "description": "Rare form of autosomal dominant familial Cornelia de Lange syndrome due to a novel duplication in SMC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000331",
+      "label": "Short chin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28781842",
+        "description": "Rare form of autosomal dominant familial Cornelia de Lange syndrome due to a novel duplication in SMC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004691",
+      "label": "2-3 toe syndactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28781842",
+        "description": "Rare form of autosomal dominant familial Cornelia de Lange syndrome due to a novel duplication in SMC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000574",
+      "label": "Thick eyebrow"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28781842",
+        "description": "Rare form of autosomal dominant familial Cornelia de Lange syndrome due to a novel duplication in SMC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000463",
+      "label": "Anteverted nares"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28781842",
+        "description": "Rare form of autosomal dominant familial Cornelia de Lange syndrome due to a novel duplication in SMC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012210",
+      "label": "Abnormal renal morphology"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28781842",
+        "description": "Rare form of autosomal dominant familial Cornelia de Lange syndrome due to a novel duplication in SMC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000278",
+      "label": "Retrognathia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28781842",
+        "description": "Rare form of autosomal dominant familial Cornelia de Lange syndrome due to a novel duplication in SMC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000341",
+      "label": "Narrow forehead"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28781842",
+        "description": "Rare form of autosomal dominant familial Cornelia de Lange syndrome due to a novel duplication in SMC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002553",
+      "label": "Highly arched eyebrow"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28781842",
+        "description": "Rare form of autosomal dominant familial Cornelia de Lange syndrome due to a novel duplication in SMC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010047",
+      "label": "Short 5th metacarpal"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28781842",
+        "description": "Rare form of autosomal dominant familial Cornelia de Lange syndrome due to a novel duplication in SMC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000508",
+      "label": "Ptosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28781842",
+        "description": "Rare form of autosomal dominant familial Cornelia de Lange syndrome due to a novel duplication in SMC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009623",
+      "label": "Proximal placement of thumb"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28781842",
+        "description": "Rare form of autosomal dominant familial Cornelia de Lange syndrome due to a novel duplication in SMC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001007",
+      "label": "Hirsutism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28781842",
+        "description": "Rare form of autosomal dominant familial Cornelia de Lange syndrome due to a novel duplication in SMC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005280",
+      "label": "Depressed nasal bridge"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28781842",
+        "description": "Rare form of autosomal dominant familial Cornelia de Lange syndrome due to a novel duplication in SMC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000252",
+      "label": "Microcephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28781842",
+        "description": "Rare form of autosomal dominant familial Cornelia de Lange syndrome due to a novel duplication in SMC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000664",
+      "label": "Synophrys"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28781842",
+        "description": "Rare form of autosomal dominant familial Cornelia de Lange syndrome due to a novel duplication in SMC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007665",
+      "label": "Curly eyelashes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
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+        "description": "Rare form of autosomal dominant familial Cornelia de Lange syndrome due to a novel duplication in SMC3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008872",
+      "label": "Feeding difficulties in infancy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Rare form of autosomal dominant familial Cornelia de Lange syndrome due to a novel duplication in SMC3"
+      }
+    }]
+  }, {
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+      "label": "High palate"
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28781842",
+        "description": "Rare form of autosomal dominant familial Cornelia de Lange syndrome due to a novel duplication in SMC3"
+      }
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+    "id": "NCBIGene:9126",
+    "symbol": "SMC3"
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+    "vcfAllele": {
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+      "alt": "TGCA"
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+      "id": "GENO:0000135",
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+    }
+  }],
+  "diseases": [{
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+      "id": "OMIM:610759",
+      "label": "CORNELIA DE LANGE SYNDROME 3; CDLS3"
+    }
+  }],
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+      "name": "human phenotype ontology",
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+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
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+      "namespacePrefix": "NCBITaxon"
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+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
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+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28781842",
+      "description": "Rare form of autosomal dominant familial Cornelia de Lange syndrome due to a novel duplication in SMC3"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Inlora-2017-APTX-V-3.json b/notebooks/LIRICAL/v1phenopackets/Inlora-2017-APTX-V-3.json
new file mode 100644
index 000000000..3879ba96a
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Inlora-2017-APTX-V-3.json
@@ -0,0 +1,147 @@
+{
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+      }
+    }]
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+  }],
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+  }],
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+      "label": "ATAXIA, EARLY-ONSET, WITH OCULOMOTOR APRAXIA AND HYPOALBUMINEMIA;EAOH"
+    }
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+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
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+      "url": "http://purl.obolibrary.org/obo/eco.owl",
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+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Inui-2017-LONP1-Proband.json b/notebooks/LIRICAL/v1phenopackets/Inui-2017-LONP1-Proband.json
new file mode 100644
index 000000000..685f576e6
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Inui-2017-LONP1-Proband.json
@@ -0,0 +1,297 @@
+{
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+    },
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+      "label": "Homo sapiens"
+    }
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+      "label": "Short stature"
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+    },
+    "zygosity": {
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+    },
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+  "diseases": [{
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+      "label": "CODAS SYNDROME"
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+  "metaData": {
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+    "submittedBy": "HPO:probinson",
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+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
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+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
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+      "url": "http://purl.obolibrary.org/obo/geno.owl",
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+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
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+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
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+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
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+      "namespacePrefix": "ECO",
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+    "externalReferences": [{
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+      "description": "A novel mutation in the proteolytic domain of LONP1 causes atypical CODAS syndrome"
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+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Irfanullah-2015-NPR2-IV-2_family-A.json b/notebooks/LIRICAL/v1phenopackets/Irfanullah-2015-NPR2-IV-2_family-A.json
new file mode 100644
index 000000000..a18a27a6b
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Irfanullah-2015-NPR2-IV-2_family-A.json
@@ -0,0 +1,238 @@
+{
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+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
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+        "label": "author statement supported by traceable reference"
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+        "description": "Homozygous sequence variants in the NPR2 gene underlying Acromesomelic dysplasia Maroteaux type (AMDM) in consanguineous families"
+      }
+    }]
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+      "label": "Broad hallux"
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+      }
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+      }
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+      "label": "Short stature"
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+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Ishii-2013-KCNT1-Patient-1.json b/notebooks/LIRICAL/v1phenopackets/Ishii-2013-KCNT1-Patient-1.json
new file mode 100644
index 000000000..88407a60e
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Ishii-2013-KCNT1-Patient-1.json
@@ -0,0 +1,162 @@
+{
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+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Itoh-Satoh-2002-TTN-JK109.json b/notebooks/LIRICAL/v1phenopackets/Itoh-Satoh-2002-TTN-JK109.json
new file mode 100644
index 000000000..a17d0d5b1
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Itoh-Satoh-2002-TTN-JK109.json
@@ -0,0 +1,147 @@
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+    }, {
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+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Jagadisan-2017-PYGL-2-year_5-month_old_child.json b/notebooks/LIRICAL/v1phenopackets/Jagadisan-2017-PYGL-2-year_5-month_old_child.json
new file mode 100644
index 000000000..d81dda541
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Jagadisan-2017-PYGL-2-year_5-month_old_child.json
@@ -0,0 +1,302 @@
+{
+  "id": "PMID:28984260-Jagadisan-2017-PYGL-2-year_5-month_old_child",
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+      "label": "Homo sapiens"
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+        "description": "Glycogen Storage Disease Type VI With a Novel Mutation in PYGL Gene"
+      }
+    }]
+  }, {
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+      "id": "HP:0003270",
+      "label": "Abdominal distention"
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+      "label": "GLYCOGEN STORAGE DISEASE VI; GSD6"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28984260",
+      "description": "Glycogen Storage Disease Type VI With a Novel Mutation in PYGL Gene"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Janecke-2015-SLC9A3-Patient_9.json b/notebooks/LIRICAL/v1phenopackets/Janecke-2015-SLC9A3-Patient_9.json
new file mode 100644
index 000000000..f76aec96b
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Janecke-2015-SLC9A3-Patient_9.json
@@ -0,0 +1,235 @@
+{
+  "id": "PMID:26358773-Janecke-2015-SLC9A3-Patient_9",
+  "subject": {
+    "id": "Patient 9",
+    "ageAtCollection": {
+      "age": "1.5"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0032368",
+      "label": "Acidemia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26358773",
+        "description": "Reduced sodium/proton exchanger NHE3 activity causes congenital sodium diarrhea"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001518",
+      "label": "Small for gestational age"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26358773",
+        "description": "Reduced sodium/proton exchanger NHE3 activity causes congenital sodium diarrhea"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0032484",
+      "label": "Elevated fecal sodium"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26358773",
+        "description": "Reduced sodium/proton exchanger NHE3 activity causes congenital sodium diarrhea"
+      }
+    }]
+  }, {
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+      "label": "Polyhydramnios"
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:26358773",
+        "description": "Reduced sodium/proton exchanger NHE3 activity causes congenital sodium diarrhea"
+      }
+    }]
+  }, {
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+      "id": "HP:0001510",
+      "label": "Growth delay"
+    },
+    "evidence": [{
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+        "description": "Reduced sodium/proton exchanger NHE3 activity causes congenital sodium diarrhea"
+      }
+    }]
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+      "id": "HP:0003270",
+      "label": "Abdominal distention"
+    },
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+        "id": "PMID:26358773",
+        "description": "Reduced sodium/proton exchanger NHE3 activity causes congenital sodium diarrhea"
+      }
+    }]
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+      "label": "Hyponatriuria"
+    },
+    "evidence": [{
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+        "id": "PMID:26358773",
+        "description": "Reduced sodium/proton exchanger NHE3 activity causes congenital sodium diarrhea"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0032487",
+      "label": "Reduced fecal osmolality"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26358773",
+        "description": "Reduced sodium/proton exchanger NHE3 activity causes congenital sodium diarrhea"
+      }
+    }]
+  }],
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+    "id": "NCBIGene:6550",
+    "symbol": "SLC9A3"
+  }],
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+      "genomeAssembly": "GRCh37",
+      "chr": "5",
+      "pos": 483385,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "5",
+      "pos": 477461,
+      "ref": "AG",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616868",
+      "label": "Diarrhea 8, secretory sodium, congenital"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "name": "Phenotype And Trait Ontology",
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+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:26358773",
+      "description": "Reduced sodium/proton exchanger NHE3 activity causes congenital sodium diarrhea"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Jansen-2016-TMEM199-F1-II2.json b/notebooks/LIRICAL/v1phenopackets/Jansen-2016-TMEM199-F1-II2.json
new file mode 100644
index 000000000..e14c868c3
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Jansen-2016-TMEM199-F1-II2.json
@@ -0,0 +1,252 @@
+{
+  "id": "PMID:26833330-Jansen-2016-TMEM199-F1-II2",
+  "subject": {
+    "id": "F1-II2",
+    "ageAtCollection": {
+      "age": "P6Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001397",
+      "label": "Hepatic steatosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26833330",
+        "description": "TMEM199 Deficiency Is a Disorder of Golgi Homeostasis Characterized by Elevated Aminotransferases, Alkaline Phosphatase, and Cholesterol and Abnormal Glycosylation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003124",
+      "label": "Hypercholesterolemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26833330",
+        "description": "TMEM199 Deficiency Is a Disorder of Golgi Homeostasis Characterized by Elevated Aminotransferases, Alkaline Phosphatase, and Cholesterol and Abnormal Glycosylation"
+      }
+    }]
+  }, {
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+      "id": "HP:0031964",
+      "label": "Elevated serum alanine aminotransferase"
+    },
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+        "description": "TMEM199 Deficiency Is a Disorder of Golgi Homeostasis Characterized by Elevated Aminotransferases, Alkaline Phosphatase, and Cholesterol and Abnormal Glycosylation"
+      }
+    }]
+  }, {
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+      "id": "HP:0003155",
+      "label": "Elevated alkaline phosphatase"
+    },
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+        "description": "TMEM199 Deficiency Is a Disorder of Golgi Homeostasis Characterized by Elevated Aminotransferases, Alkaline Phosphatase, and Cholesterol and Abnormal Glycosylation"
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+      }
+    }]
+  }, {
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+      "id": "HP:0010837",
+      "label": "Decreased serum ceruloplasmin"
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+        "label": "author statement supported by traceable reference"
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+      }
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+  }, {
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+      "label": "Reduced antithrombin III activity"
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+      }
+    }]
+  }, {
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+      "label": "Abnormal protein N-linked glycosylation"
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+      }
+    }]
+  }, {
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+      "id": "HP:0003141",
+      "label": "Increased LDL cholesterol concentration"
+    },
+    "evidence": [{
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+        "description": "TMEM199 Deficiency Is a Disorder of Golgi Homeostasis Characterized by Elevated Aminotransferases, Alkaline Phosphatase, and Cholesterol and Abnormal Glycosylation"
+      }
+    }]
+  }, {
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+      "label": "Abnormal circulating copper concentration"
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+      }
+    }]
+  }, {
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+      "label": "Abnormal protein O-linked glycosylation"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
+      },
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+        "description": "TMEM199 Deficiency Is a Disorder of Golgi Homeostasis Characterized by Elevated Aminotransferases, Alkaline Phosphatase, and Cholesterol and Abnormal Glycosylation"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:147007",
+    "symbol": "TMEM199"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "17",
+      "pos": 26684713,
+      "ref": "C",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616829",
+      "label": "Congenital disorder of glycosylation, type IIp"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13",
+    "submittedBy": "HP:probinson",
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+      "id": "hp",
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+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
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+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:26833330",
+      "description": "TMEM199 Deficiency Is a Disorder of Golgi Homeostasis Characterized by Elevated Aminotransferases, Alkaline Phosphatase, and Cholesterol and Abnormal Glycosylation"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Jansen-2016-TMEM199-F2-II2.json b/notebooks/LIRICAL/v1phenopackets/Jansen-2016-TMEM199-F2-II2.json
new file mode 100644
index 000000000..a824ed0c8
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Jansen-2016-TMEM199-F2-II2.json
@@ -0,0 +1,357 @@
+{
+  "id": "PMID:26833330-Jansen-2016-TMEM199-F2-II2",
+  "subject": {
+    "id": "F2-II2",
+    "ageAtCollection": {
+      "age": "P41Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000023",
+      "label": "Inguinal hernia"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:26833330",
+        "description": "TMEM199 Deficiency Is a Disorder of Golgi Homeostasis Characterized by Elevated Aminotransferases, Alkaline Phosphatase, and Cholesterol and Abnormal Glycosylation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000952",
+      "label": "Jaundice"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:26833330",
+        "description": "TMEM199 Deficiency Is a Disorder of Golgi Homeostasis Characterized by Elevated Aminotransferases, Alkaline Phosphatase, and Cholesterol and Abnormal Glycosylation"
+      }
+    }]
+  }, {
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+      "id": "HP:0031964",
+      "label": "Elevated serum alanine aminotransferase"
+    },
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+        "description": "TMEM199 Deficiency Is a Disorder of Golgi Homeostasis Characterized by Elevated Aminotransferases, Alkaline Phosphatase, and Cholesterol and Abnormal Glycosylation"
+      }
+    }]
+  }, {
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:26833330",
+        "description": "TMEM199 Deficiency Is a Disorder of Golgi Homeostasis Characterized by Elevated Aminotransferases, Alkaline Phosphatase, and Cholesterol and Abnormal Glycosylation"
+      }
+    }]
+  }, {
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+        "description": "TMEM199 Deficiency Is a Disorder of Golgi Homeostasis Characterized by Elevated Aminotransferases, Alkaline Phosphatase, and Cholesterol and Abnormal Glycosylation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0025321",
+      "label": "Copper accumulation in liver"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26833330",
+        "description": "TMEM199 Deficiency Is a Disorder of Golgi Homeostasis Characterized by Elevated Aminotransferases, Alkaline Phosphatase, and Cholesterol and Abnormal Glycosylation"
+      }
+    }]
+  }, {
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+      "id": "HP:0010837",
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+      "id": "GENO:0000135",
+      "label": "heterozygous"
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+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616829",
+      "label": "Congenital disorder of glycosylation, type IIp"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13",
+    "submittedBy": "HP:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
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+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
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+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
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+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
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+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
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+    "externalReferences": [{
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+      "description": "TMEM199 Deficiency Is a Disorder of Golgi Homeostasis Characterized by Elevated Aminotransferases, Alkaline Phosphatase, and Cholesterol and Abnormal Glycosylation"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Jansen-2016-TMEM199-F3-II1.json b/notebooks/LIRICAL/v1phenopackets/Jansen-2016-TMEM199-F3-II1.json
new file mode 100644
index 000000000..05698f2a6
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Jansen-2016-TMEM199-F3-II1.json
@@ -0,0 +1,267 @@
+{
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+        "description": "TMEM199 Deficiency Is a Disorder of Golgi Homeostasis Characterized by Elevated Aminotransferases, Alkaline Phosphatase, and Cholesterol and Abnormal Glycosylation"
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+    "symbol": "TMEM199"
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+    }, {
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+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
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+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
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+      "version": "2018-03-02",
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+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
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+      "name": "Online Mendelian Inheritance in Man",
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+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Janssen-2009-BSND-family-A-III3.json b/notebooks/LIRICAL/v1phenopackets/Janssen-2009-BSND-family-A-III3.json
new file mode 100644
index 000000000..552335de1
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Janssen-2009-BSND-family-A-III3.json
@@ -0,0 +1,223 @@
+{
+  "id": "PMID:18776122-Janssen-2009-BSND-family-A-III3",
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+      "age": "P2Y"
+    },
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+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
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+      "id": "HP:0003113",
+      "label": "Hypochloremia"
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+        "description": "Disease-causing dysfunctions of barttin in Bartter syndrome type IV"
+      }
+    }]
+  }, {
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+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "description": "Disease-causing dysfunctions of barttin in Bartter syndrome type IV"
+      }
+    }]
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+      "label": "Sensorineural hearing impairment"
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+        "description": "Disease-causing dysfunctions of barttin in Bartter syndrome type IV"
+      }
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+      },
+      "reference": {
+        "id": "PMID:18776122",
+        "description": "Disease-causing dysfunctions of barttin in Bartter syndrome type IV"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:7809",
+    "symbol": "BSND"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 55464998,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:602522",
+      "label": "BARTTER SYNDROME, TYPE 4A"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:18776122",
+      "description": "Disease-causing dysfunctions of barttin in Bartter syndrome type IV"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Javadiyan-2017-MAF-patient_CSA108.01.json b/notebooks/LIRICAL/v1phenopackets/Javadiyan-2017-MAF-patient_CSA108.01.json
new file mode 100644
index 000000000..07a2a89b3
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Javadiyan-2017-MAF-patient_CSA108.01.json
@@ -0,0 +1,102 @@
+{
+  "id": "PMID:28482824-Javadiyan-2017-MAF-patient_CSA108.01",
+  "subject": {
+    "id": "patient CSA108.01",
+    "ageAtCollection": {
+      "age": "P20Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0009909",
+      "label": "Uplifted earlobe"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28482824",
+        "description": "Novel missense mutation in the bZIP transcription factor, MAF, associated with congenital cataract, developmental delay, seizures and hearing loss (Aymé-Gripp syndrome)"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:4094",
+    "symbol": "MAF"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "16",
+      "pos": 79633624,
+      "ref": "G",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:601088",
+      "label": "AYME-GRIPP SYNDROME; AYGRP"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28482824",
+      "description": "Novel missense mutation in the bZIP transcription factor, MAF, associated with congenital cataract, developmental delay, seizures and hearing loss (Aymé-Gripp syndrome)"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Jeon-2014-LAMC2-patient.json b/notebooks/LIRICAL/v1phenopackets/Jeon-2014-LAMC2-patient.json
new file mode 100644
index 000000000..34eb99c72
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Jeon-2014-LAMC2-patient.json
@@ -0,0 +1,174 @@
+{
+  "id": "PMID:24533970-Jeon-2014-LAMC2-patient",
+  "subject": {
+    "id": "patient",
+    "ageAtCollection": {
+      "age": "P2W"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0100806",
+      "label": "Sepsis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24533970",
+        "description": "Novel compound heterozygous mutation in LAMC2 genes (c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0200041",
+      "label": "Skin erosion"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24533970",
+        "description": "Novel compound heterozygous mutation in LAMC2 genes (c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031446",
+      "label": "Erosion of oral mucosa"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24533970",
+        "description": "Novel compound heterozygous mutation in LAMC2 genes (c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008066",
+      "label": "Abnormal blistering of the skin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24533970",
+        "description": "Novel compound heterozygous mutation in LAMC2 genes (c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003341",
+      "label": "Junctional split"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24533970",
+        "description": "Novel compound heterozygous mutation in LAMC2 genes (c"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:3918",
+    "symbol": "LAMC2"
+  }],
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+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 183155566,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 183184700,
+      "ref": "G",
+      "alt": "GT"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:226700",
+      "label": "EPIDERMOLYSIS BULLOSA, JUNCTIONAL, HERLITZ TYPE"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:24533970",
+      "description": "Novel compound heterozygous mutation in LAMC2 genes (c"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Ji-2017-ATRX-Proband.json b/notebooks/LIRICAL/v1phenopackets/Ji-2017-ATRX-Proband.json
new file mode 100644
index 000000000..d81e2b5a2
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Ji-2017-ATRX-Proband.json
@@ -0,0 +1,222 @@
+{
+  "id": "PMID:28371217-Ji-2017-ATRX-Proband",
+  "subject": {
+    "id": "Proband",
+    "ageAtCollection": {
+      "age": "P22Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002714",
+      "label": "Downturned corners of mouth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28371217",
+        "description": "Inherited germline ATRX mutation in two brothers with ATR-X syndrome and osteosarcoma"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000252",
+      "label": "Microcephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28371217",
+        "description": "Inherited germline ATRX mutation in two brothers with ATR-X syndrome and osteosarcoma"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000316",
+      "label": "Hypertelorism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28371217",
+        "description": "Inherited germline ATRX mutation in two brothers with ATR-X syndrome and osteosarcoma"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000028",
+      "label": "Cryptorchidism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28371217",
+        "description": "Inherited germline ATRX mutation in two brothers with ATR-X syndrome and osteosarcoma"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001935",
+      "label": "Microcytic anemia"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Inherited germline ATRX mutation in two brothers with ATR-X syndrome and osteosarcoma"
+      }
+    }]
+  }, {
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+        "id": "PMID:28371217",
+        "description": "Inherited germline ATRX mutation in two brothers with ATR-X syndrome and osteosarcoma"
+      }
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+      "label": "Intellectual disability, severe"
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+        "id": "PMID:28371217",
+        "description": "Inherited germline ATRX mutation in two brothers with ATR-X syndrome and osteosarcoma"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000280",
+      "label": "Coarse facial features"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28371217",
+        "description": "Inherited germline ATRX mutation in two brothers with ATR-X syndrome and osteosarcoma"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:546",
+    "symbol": "ATRX"
+  }],
+  "variants": [{
+    "vcfAllele": {
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+      "chr": "X",
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+      "id": "GENO:0000134",
+      "label": "hemizygous"
+    }
+  }],
+  "diseases": [{
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+      "id": "OMIM:301040",
+      "label": "ALPHA-THALASSEMIA/MENTAL RETARDATION SYNDROME, X-LINKED; ATRX"
+    }
+  }],
+  "metaData": {
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+    "submittedBy": "HPO:probinson",
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+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28371217",
+      "description": "Inherited germline ATRX mutation in two brothers with ATR-X syndrome and osteosarcoma"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Jiang-2017-PPIB-second_fetus.json b/notebooks/LIRICAL/v1phenopackets/Jiang-2017-PPIB-second_fetus.json
new file mode 100644
index 000000000..f1a074f53
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Jiang-2017-PPIB-second_fetus.json
@@ -0,0 +1,172 @@
+{
+  "id": "PMID:28242392-Jiang-2017-PPIB-second_fetus",
+  "subject": {
+    "id": "second fetus",
+    "ageAtCollection": {
+      "age": "P24W"
+    },
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0006487",
+      "label": "Bowing of the long bones"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28242392",
+        "description": "Two novel mutations in the PPIB gene cause a rare pedigree of osteogenesis imperfecta type IX"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006385",
+      "label": "Short lower limbs"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28242392",
+        "description": "Two novel mutations in the PPIB gene cause a rare pedigree of osteogenesis imperfecta type IX"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005792",
+      "label": "Short humerus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28242392",
+        "description": "Two novel mutations in the PPIB gene cause a rare pedigree of osteogenesis imperfecta type IX"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005855",
+      "label": "Multiple prenatal fractures"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+      },
+      "reference": {
+        "id": "PMID:28242392",
+        "description": "Two novel mutations in the PPIB gene cause a rare pedigree of osteogenesis imperfecta type IX"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001762",
+      "label": "Talipes equinovarus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28242392",
+        "description": "Two novel mutations in the PPIB gene cause a rare pedigree of osteogenesis imperfecta type IX"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:5479",
+    "symbol": "PPIB"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "15",
+      "pos": 64455161,
+      "ref": "T",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "15",
+      "pos": 64448943,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:259440",
+      "label": "OSTEOGENESIS IMPERFECTA, TYPE IX; OI9"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28242392",
+      "description": "Two novel mutations in the PPIB gene cause a rare pedigree of osteogenesis imperfecta type IX"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Jin-2017-FBN1-patient.json b/notebooks/LIRICAL/v1phenopackets/Jin-2017-FBN1-patient.json
new file mode 100644
index 000000000..f8b02cb08
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Jin-2017-FBN1-patient.json
@@ -0,0 +1,343 @@
+{
+  "id": "PMID:27834076-Jin-2017-FBN1-patient",
+  "subject": {
+    "id": "patient",
+    "ageAtCollection": {
+      "age": "P10Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27834076",
+        "description": "Acromicric Dysplasia Caused by a Novel Heterozygous Mutation of FBN1 and Effects of Growth Hormone Treatment"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000527",
+      "label": "Long eyelashes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27834076",
+        "description": "Acromicric Dysplasia Caused by a Novel Heterozygous Mutation of FBN1 and Effects of Growth Hormone Treatment"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003180",
+      "label": "Flat acetabular roof"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27834076",
+        "description": "Acromicric Dysplasia Caused by a Novel Heterozygous Mutation of FBN1 and Effects of Growth Hormone Treatment"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002750",
+      "label": "Delayed skeletal maturation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27834076",
+        "description": "Acromicric Dysplasia Caused by a Novel Heterozygous Mutation of FBN1 and Effects of Growth Hormone Treatment"
+      }
+    }]
+  }, {
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+      "id": "HP:0000946",
+      "label": "Hypoplastic ilia"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27834076",
+        "description": "Acromicric Dysplasia Caused by a Novel Heterozygous Mutation of FBN1 and Effects of Growth Hormone Treatment"
+      }
+    }]
+  }, {
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+      "id": "HP:0000463",
+      "label": "Anteverted nares"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27834076",
+        "description": "Acromicric Dysplasia Caused by a Novel Heterozygous Mutation of FBN1 and Effects of Growth Hormone Treatment"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008807",
+      "label": "Acetabular dysplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27834076",
+        "description": "Acromicric Dysplasia Caused by a Novel Heterozygous Mutation of FBN1 and Effects of Growth Hormone Treatment"
+      }
+    }]
+  }, {
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+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27834076",
+        "description": "Acromicric Dysplasia Caused by a Novel Heterozygous Mutation of FBN1 and Effects of Growth Hormone Treatment"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012471",
+      "label": "Thick vermilion border"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27834076",
+        "description": "Acromicric Dysplasia Caused by a Novel Heterozygous Mutation of FBN1 and Effects of Growth Hormone Treatment"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003182",
+      "label": "Shallow acetabular fossae"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27834076",
+        "description": "Acromicric Dysplasia Caused by a Novel Heterozygous Mutation of FBN1 and Effects of Growth Hormone Treatment"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002673",
+      "label": "Coxa valga"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27834076",
+        "description": "Acromicric Dysplasia Caused by a Novel Heterozygous Mutation of FBN1 and Effects of Growth Hormone Treatment"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001216",
+      "label": "Delayed ossification of carpal bones"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27834076",
+        "description": "Acromicric Dysplasia Caused by a Novel Heterozygous Mutation of FBN1 and Effects of Growth Hormone Treatment"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002987",
+      "label": "Elbow flexion contracture"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27834076",
+        "description": "Acromicric Dysplasia Caused by a Novel Heterozygous Mutation of FBN1 and Effects of Growth Hormone Treatment"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000457",
+      "label": "Depressed nasal ridge"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27834076",
+        "description": "Acromicric Dysplasia Caused by a Novel Heterozygous Mutation of FBN1 and Effects of Growth Hormone Treatment"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Growth delay"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27834076",
+        "description": "Acromicric Dysplasia Caused by a Novel Heterozygous Mutation of FBN1 and Effects of Growth Hormone Treatment"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008850",
+      "label": "Severe postnatal growth retardation"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27834076",
+        "description": "Acromicric Dysplasia Caused by a Novel Heterozygous Mutation of FBN1 and Effects of Growth Hormone Treatment"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002002",
+      "label": "Deep philtrum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27834076",
+        "description": "Acromicric Dysplasia Caused by a Novel Heterozygous Mutation of FBN1 and Effects of Growth Hormone Treatment"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2200",
+    "symbol": "FBN1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "15",
+      "pos": 48752457,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:102370",
+      "label": "ACROMICRIC DYSPLASIA; ACMICD"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27834076",
+      "description": "Acromicric Dysplasia Caused by a Novel Heterozygous Mutation of FBN1 and Effects of Growth Hormone Treatment"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Jordan-2018-RERE-Subject_2.json b/notebooks/LIRICAL/v1phenopackets/Jordan-2018-RERE-Subject_2.json
new file mode 100644
index 000000000..97fa43bef
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Jordan-2018-RERE-Subject_2.json
@@ -0,0 +1,428 @@
+{
+  "id": "PMID:29330883-Jordan-2018-RERE-Subject_2",
+  "subject": {
+    "id": "Subject 2",
+    "ageAtCollection": {
+      "age": "P8M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002650",
+      "label": "Scoliosis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002194",
+      "label": "Delayed gross motor development"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000664",
+      "label": "Synophrys"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000294",
+      "label": "Low anterior hairline"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000010",
+      "label": "Recurrent urinary tract infections"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012372",
+      "label": "Abnormal eye morphology"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000476",
+      "label": "Cystic hygroma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000286",
+      "label": "Epicanthus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001276",
+      "label": "Hypertonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008589",
+      "label": "Hypoplastic helices"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001257",
+      "label": "Spasticity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030680",
+      "label": "Abnormality of cardiovascular system morphology"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000341",
+      "label": "Narrow forehead"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001290",
+      "label": "Generalized hypotonia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001270",
+      "label": "Motor delay"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001627",
+      "label": "Abnormal heart morphology"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000453",
+      "label": "Choanal atresia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005989",
+      "label": "Redundant neck skin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012443",
+      "label": "Abnormality of brain morphology"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000316",
+      "label": "Hypertelorism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000077",
+      "label": "Abnormality of the kidney"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:473",
+    "symbol": "RERE"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 8716108,
+      "ref": "C",
+      "alt": "CT"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616975",
+      "label": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29330883",
+      "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Jordan-2018-RERE-Subject_3.json b/notebooks/LIRICAL/v1phenopackets/Jordan-2018-RERE-Subject_3.json
new file mode 100644
index 000000000..ab1dc55dd
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Jordan-2018-RERE-Subject_3.json
@@ -0,0 +1,616 @@
+{
+  "id": "PMID:29330883-Jordan-2018-RERE-Subject_3",
+  "subject": {
+    "id": "Subject 3",
+    "ageAtCollection": {
+      "age": "P21Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000733",
+      "label": "Stereotypy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001631",
+      "label": "Atrial septal defect"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002363",
+      "label": "Abnormality of brainstem morphology"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000453",
+      "label": "Choanal atresia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000365",
+      "label": "Hearing impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000218",
+      "label": "High palate"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002079",
+      "label": "Hypoplasia of the corpus callosum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002463",
+      "label": "Language impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010535",
+      "label": "Sleep apnea"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000077",
+      "label": "Abnormality of the kidney"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001222",
+      "label": "Spatulate thumbs"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000478",
+      "label": "Abnormality of the eye"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001671",
+      "label": "Abnormal cardiac septum morphology"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001290",
+      "label": "Generalized hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000565",
+      "label": "Esotropia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001488",
+      "label": "Bilateral ptosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002104",
+      "label": "Apnea"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001795",
+      "label": "Hyperconvex nail"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012372",
+      "label": "Abnormal eye morphology"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001251",
+      "label": "Ataxia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000407",
+      "label": "Sensorineural hearing impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030842",
+      "label": "Choking episodes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000508",
+      "label": "Ptosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002650",
+      "label": "Scoliosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003198",
+      "label": "Myopathy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002058",
+      "label": "Myopathic facies"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000722",
+      "label": "Obsessive-compulsive behavior"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000490",
+      "label": "Deeply set eye"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002474",
+      "label": "Expressive language delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002616",
+      "label": "Aortic root aneurysm"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000961",
+      "label": "Cyanosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:473",
+    "symbol": "RERE"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 8420421,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616975",
+      "label": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29330883",
+      "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Jordan-2018-RERE-Subject_4.json b/notebooks/LIRICAL/v1phenopackets/Jordan-2018-RERE-Subject_4.json
new file mode 100644
index 000000000..f425b1174
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Jordan-2018-RERE-Subject_4.json
@@ -0,0 +1,334 @@
+{
+  "id": "PMID:29330883-Jordan-2018-RERE-Subject_4",
+  "subject": {
+    "id": "Subject 4",
+    "ageAtCollection": {
+      "age": "P13Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000478",
+      "label": "Abnormality of the eye"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001290",
+      "label": "Generalized hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002650",
+      "label": "Scoliosis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010864",
+      "label": "Intellectual disability, severe"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000365",
+      "label": "Hearing impairment"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007033",
+      "label": "Cerebellar dysplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001627",
+      "label": "Abnormal heart morphology"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000453",
+      "label": "Choanal atresia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000826",
+      "label": "Precocious puberty"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0025161",
+      "label": "Frequent temper tantrums"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011968",
+      "label": "Feeding difficulties"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001344",
+      "label": "Absent speech"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000077",
+      "label": "Abnormality of the kidney"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:473",
+    "symbol": "RERE"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 8418292,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616975",
+      "label": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29330883",
+      "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Jordan-2018-RERE-Subject_5.json b/notebooks/LIRICAL/v1phenopackets/Jordan-2018-RERE-Subject_5.json
new file mode 100644
index 000000000..6ed552950
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Jordan-2018-RERE-Subject_5.json
@@ -0,0 +1,558 @@
+{
+  "id": "PMID:29330883-Jordan-2018-RERE-Subject_5",
+  "subject": {
+    "id": "Subject 5",
+    "ageAtCollection": {
+      "age": "P25Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0030055",
+      "label": "Hyperconvex toenail"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001631",
+      "label": "Atrial septal defect"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002791",
+      "label": "Hypoventilation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100704",
+      "label": "Cerebral visual impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000486",
+      "label": "Strabismus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007110",
+      "label": "Central hypoventilation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000453",
+      "label": "Choanal atresia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000396",
+      "label": "Overfolded helix"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000540",
+      "label": "Hypermetropia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000582",
+      "label": "Upslanted palpebral fissure"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000077",
+      "label": "Abnormality of the kidney"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000478",
+      "label": "Abnormality of the eye"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001290",
+      "label": "Generalized hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002650",
+      "label": "Scoliosis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000400",
+      "label": "Macrotia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0200055",
+      "label": "Small hand"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012372",
+      "label": "Abnormal eye morphology"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004467",
+      "label": "Preauricular pit"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001513",
+      "label": "Obesity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001156",
+      "label": "Brachydactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002779",
+      "label": "Tracheomalacia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012443",
+      "label": "Abnormality of brain morphology"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001773",
+      "label": "Short foot"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000505",
+      "label": "Visual impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0400008",
+      "label": "Menometrorrhagia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002099",
+      "label": "Asthma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000878",
+      "label": "11 pairs of ribs"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:473",
+    "symbol": "RERE"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 8418291,
+      "ref": "T",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616975",
+      "label": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29330883",
+      "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Jordan-2018-RERE-Subject_6.json b/notebooks/LIRICAL/v1phenopackets/Jordan-2018-RERE-Subject_6.json
new file mode 100644
index 000000000..8f4504c4f
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Jordan-2018-RERE-Subject_6.json
@@ -0,0 +1,294 @@
+{
+  "id": "PMID:29330883-Jordan-2018-RERE-Subject_6",
+  "subject": {
+    "id": "Subject 6",
+    "ageAtCollection": {
+      "age": "P6M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004209",
+      "label": "Clinodactyly of the 5th finger"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005824",
+      "label": "Clinodactyly of the 2nd toe"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009904",
+      "label": "Prominent ear helix"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000729",
+      "label": "Autistic behavior"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000577",
+      "label": "Exotropia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000411",
+      "label": "Protruding ear"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000325",
+      "label": "Triangular face"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008619",
+      "label": "Bilateral sensorineural hearing impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100021",
+      "label": "Cerebral palsy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000378",
+      "label": "Cupped ear"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000545",
+      "label": "Myopia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:473",
+    "symbol": "RERE"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 8418292,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 8420275,
+      "ref": "G",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616975",
+      "label": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29330883",
+      "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Jordan-2018-RERE-Subject_7.json b/notebooks/LIRICAL/v1phenopackets/Jordan-2018-RERE-Subject_7.json
new file mode 100644
index 000000000..b5c79abe2
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Jordan-2018-RERE-Subject_7.json
@@ -0,0 +1,657 @@
+{
+  "id": "PMID:29330883-Jordan-2018-RERE-Subject_7",
+  "subject": {
+    "id": "Subject 7",
+    "ageAtCollection": {
+      "age": "P33D"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001561",
+      "label": "Polyhydramnios"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009800",
+      "label": "Maternal diabetes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002003",
+      "label": "Large forehead"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002094",
+      "label": "Dyspnea"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000969",
+      "label": "Edema"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001631",
+      "label": "Atrial septal defect"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011220",
+      "label": "Prominent forehead"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000819",
+      "label": "Diabetes mellitus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002119",
+      "label": "Ventriculomegaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012785",
+      "label": "Flexion contracture of finger"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002282",
+      "label": "Gray matter heterotopia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005133",
+      "label": "Right ventricular dilatation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007700",
+      "label": "Ocular anterior segment dysgenesis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004502",
+      "label": "Bilateral choanal atresia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008936",
+      "label": "Muscular hypotonia of the trunk"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000822",
+      "label": "Hypertension"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000589",
+      "label": "Coloboma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000612",
+      "label": "Iris coloboma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006610",
+      "label": "Wide intermamillary distance"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008551",
+      "label": "Microtia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001290",
+      "label": "Generalized hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001671",
+      "label": "Abnormal cardiac septum morphology"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009879",
+      "label": "Simplified gyral pattern"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002104",
+      "label": "Apnea"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001488",
+      "label": "Bilateral ptosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000369",
+      "label": "Low-set ears"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007957",
+      "label": "Corneal opacity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001629",
+      "label": "Ventricular septal defect"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001655",
+      "label": "Patent foramen ovale"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005280",
+      "label": "Depressed nasal bridge"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009062",
+      "label": "Infantile axial hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000508",
+      "label": "Ptosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000047",
+      "label": "Hypospadias"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005989",
+      "label": "Redundant neck skin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001635",
+      "label": "Congestive heart failure"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100598",
+      "label": "Pulmonary edema"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000609",
+      "label": "Optic nerve hypoplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000961",
+      "label": "Cyanosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:473",
+    "symbol": "RERE"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 8418276,
+      "ref": "T",
+      "alt": "TGGTGGA"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616975",
+      "label": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29330883",
+      "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Jordan-2018-RERE-Subject_8.json b/notebooks/LIRICAL/v1phenopackets/Jordan-2018-RERE-Subject_8.json
new file mode 100644
index 000000000..66f97e60a
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Jordan-2018-RERE-Subject_8.json
@@ -0,0 +1,649 @@
+{
+  "id": "PMID:29330883-Jordan-2018-RERE-Subject_8",
+  "subject": {
+    "id": "Subject 8",
+    "ageAtCollection": {
+      "age": "P8Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002376",
+      "label": "Developmental regression"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000453",
+      "label": "Choanal atresia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001371",
+      "label": "Flexion contracture"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001385",
+      "label": "Hip dysplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000357",
+      "label": "Abnormal location of ears"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001511",
+      "label": "Intrauterine growth retardation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001290",
+      "label": "Generalized hypotonia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004502",
+      "label": "Bilateral choanal atresia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000365",
+      "label": "Hearing impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002355",
+      "label": "Difficulty walking"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001649",
+      "label": "Tachycardia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000589",
+      "label": "Coloboma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000612",
+      "label": "Iris coloboma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000567",
+      "label": "Chorioretinal coloboma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000385",
+      "label": "Small earlobe"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001344",
+      "label": "Absent speech"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000077",
+      "label": "Abnormality of the kidney"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000431",
+      "label": "Wide nasal bridge"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011849",
+      "label": "Abnormal bone ossification"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003698",
+      "label": "Difficulty standing"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000408",
+      "label": "Progressive sensorineural hearing impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002098",
+      "label": "Respiratory distress"
+    },
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+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012803",
+      "label": "Anisometropia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002650",
+      "label": "Scoliosis"
+    },
+    "evidence": [{
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+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
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+    }]
+  }, {
+    "type": {
+      "id": "HP:0000395",
+      "label": "Prominent antihelix"
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+    "evidence": [{
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+        "id": "ECO:0000033",
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+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
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+  }, {
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+      "id": "HP:0004384",
+      "label": "Type I truncus arteriosus"
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+    "evidence": [{
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+        "id": "ECO:0000033",
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+      "reference": {
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+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
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+  }, {
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+      "id": "HP:0012368",
+      "label": "Flat face"
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+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+    }]
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+    "negated": true,
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+    }]
+  }, {
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+      "label": "Growth delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:473",
+    "symbol": "RERE"
+  }],
+  "variants": [{
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+      "chr": "1",
+      "pos": 8418276,
+      "ref": "T",
+      "alt": "TGGTGGA"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616975",
+      "label": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29330883",
+      "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Jordan-2018-RERE-Subject_9.json b/notebooks/LIRICAL/v1phenopackets/Jordan-2018-RERE-Subject_9.json
new file mode 100644
index 000000000..636689465
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Jordan-2018-RERE-Subject_9.json
@@ -0,0 +1,403 @@
+{
+  "id": "PMID:29330883-Jordan-2018-RERE-Subject_9",
+  "subject": {
+    "id": "Subject 9",
+    "ageAtCollection": {
+      "age": "P4Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000733",
+      "label": "Stereotypy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001627",
+      "label": "Abnormal heart morphology"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000077",
+      "label": "Abnormality of the kidney"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
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+      "label": "Choanal atresia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002650",
+      "label": "Scoliosis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
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+      "label": "Behavioral abnormality"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
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+      "id": "HP:0000664",
+      "label": "Synophrys"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000729",
+      "label": "Autistic behavior"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002360",
+      "label": "Sleep disturbance"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007015",
+      "label": "Poor gross motor coordination"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009889",
+      "label": "Localized hirsutism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000739",
+      "label": "Anxiety"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031468",
+      "label": "Separation insecurity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000463",
+      "label": "Anteverted nares"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012372",
+      "label": "Abnormal eye morphology"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000722",
+      "label": "Obsessive-compulsive behavior"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+    }]
+  }, {
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+      "label": "Global developmental delay"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Hypertelorism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002474",
+      "label": "Expressive language delay"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000154",
+      "label": "Wide mouth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29330883",
+        "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:473",
+    "symbol": "RERE"
+  }],
+  "variants": [{
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+      "chr": "1",
+      "pos": 8416255,
+      "ref": "T",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616975",
+      "label": "Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart"
+    }
+  }],
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+    "submittedBy": "UNC:biocuration",
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+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29330883",
+      "description": "Genotype-phenotype correlations in individuals with pathogenic RERE variants"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Kantaputra-2014-FBLN5-4-year-old_Burmese_girl_.json b/notebooks/LIRICAL/v1phenopackets/Kantaputra-2014-FBLN5-4-year-old_Burmese_girl_.json
new file mode 100644
index 000000000..2a32c7eb3
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Kantaputra-2014-FBLN5-4-year-old_Burmese_girl_.json
@@ -0,0 +1,269 @@
+{
+  "id": "PMID:24962763-Kantaputra-2014-FBLN5-4-year-old_Burmese_girl_",
+  "subject": {
+    "id": "4-year-old Burmese girl ",
+    "ageAtCollection": {
+      "age": "P4Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000579",
+      "label": "Nasolacrimal duct obstruction"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24962763",
+        "description": "Cutis laxa with pulmonary emphysema, conjunctivochalasis, nasolacrimal duct obstruction, abnormal hair, and a novel FBLN5 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000670",
+      "label": "Carious teeth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24962763",
+        "description": "Cutis laxa with pulmonary emphysema, conjunctivochalasis, nasolacrimal duct obstruction, abnormal hair, and a novel FBLN5 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000076",
+      "label": "Vesicoureteral reflux"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24962763",
+        "description": "Cutis laxa with pulmonary emphysema, conjunctivochalasis, nasolacrimal duct obstruction, abnormal hair, and a novel FBLN5 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002110",
+      "label": "Bronchiectasis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24962763",
+        "description": "Cutis laxa with pulmonary emphysema, conjunctivochalasis, nasolacrimal duct obstruction, abnormal hair, and a novel FBLN5 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000023",
+      "label": "Inguinal hernia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24962763",
+        "description": "Cutis laxa with pulmonary emphysema, conjunctivochalasis, nasolacrimal duct obstruction, abnormal hair, and a novel FBLN5 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000822",
+      "label": "Hypertension"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24962763",
+        "description": "Cutis laxa with pulmonary emphysema, conjunctivochalasis, nasolacrimal duct obstruction, abnormal hair, and a novel FBLN5 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001653",
+      "label": "Mitral regurgitation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24962763",
+        "description": "Cutis laxa with pulmonary emphysema, conjunctivochalasis, nasolacrimal duct obstruction, abnormal hair, and a novel FBLN5 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100857",
+      "label": "Flat sella turcica"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24962763",
+        "description": "Cutis laxa with pulmonary emphysema, conjunctivochalasis, nasolacrimal duct obstruction, abnormal hair, and a novel FBLN5 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002616",
+      "label": "Aortic root aneurysm"
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+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:24962763",
+        "description": "Cutis laxa with pulmonary emphysema, conjunctivochalasis, nasolacrimal duct obstruction, abnormal hair, and a novel FBLN5 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009926",
+      "label": "Epiphora"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:24962763",
+        "description": "Cutis laxa with pulmonary emphysema, conjunctivochalasis, nasolacrimal duct obstruction, abnormal hair, and a novel FBLN5 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005180",
+      "label": "Tricuspid regurgitation"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24962763",
+        "description": "Cutis laxa with pulmonary emphysema, conjunctivochalasis, nasolacrimal duct obstruction, abnormal hair, and a novel FBLN5 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000973",
+      "label": "Cutis laxa"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24962763",
+        "description": "Cutis laxa with pulmonary emphysema, conjunctivochalasis, nasolacrimal duct obstruction, abnormal hair, and a novel FBLN5 mutation"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:10516",
+    "symbol": "FBLN5"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "14",
+      "pos": 92361364,
+      "ref": "G",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:219100",
+      "label": "CUTIS LAXA, AUTOSOMAL RECESSIVE, TYPE IA; ARCL1A"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:24962763",
+      "description": "Cutis laxa with pulmonary emphysema, conjunctivochalasis, nasolacrimal duct obstruction, abnormal hair, and a novel FBLN5 mutation"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Kato-2018-HNF1B-patient.json b/notebooks/LIRICAL/v1phenopackets/Kato-2018-HNF1B-patient.json
new file mode 100644
index 000000000..7f9525cd0
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Kato-2018-HNF1B-patient.json
@@ -0,0 +1,177 @@
+{
+  "id": "PMID:29491316-Kato-2018-HNF1B-patient",
+  "subject": {
+    "id": "patient",
+    "ageAtCollection": {
+      "age": "19Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0025329",
+      "label": "Anti-glutamic acid decarboxylase antibody positivity"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29491316",
+        "description": "A Novel p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004904",
+      "label": "Maturity-onset diabetes of the young"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29491316",
+        "description": "A Novel p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012090",
+      "label": "Abnormal pancreas morphology"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29491316",
+        "description": "A Novel p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0040217",
+      "label": "Elevated hemoglobin A1c"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29491316",
+        "description": "A Novel p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003074",
+      "label": "Hyperglycemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29491316",
+        "description": "A Novel p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005562",
+      "label": "Multiple renal cysts"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29491316",
+        "description": "A Novel p"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:6928",
+    "symbol": "HNF1B"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "17",
+      "pos": 36099541,
+      "ref": "A",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:137920",
+      "label": "RENAL CYSTS AND DIABETES SYNDROME; RCAD"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29491316",
+      "description": "A Novel p"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Khan-2017-HOXC13-IV-1.json b/notebooks/LIRICAL/v1phenopackets/Khan-2017-HOXC13-IV-1.json
new file mode 100644
index 000000000..59397f437
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Khan-2017-HOXC13-IV-1.json
@@ -0,0 +1,194 @@
+{
+  "id": "PMID:28403827-Khan-2017-HOXC13-IV-1",
+  "subject": {
+    "id": "IV-1",
+    "ageAtCollection": {
+      "age": "P37Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002298",
+      "label": "Absent hair"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28403827",
+        "description": "A novel mutation in homeobox DNA binding domain of HOXC13 gene underlies pure hair and nail ectodermal dysplasia (ECTD9) in a Pakistani family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000164",
+      "label": "Abnormality of the dentition"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28403827",
+        "description": "A novel mutation in homeobox DNA binding domain of HOXC13 gene underlies pure hair and nail ectodermal dysplasia (ECTD9) in a Pakistani family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008404",
+      "label": "Nail dystrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28403827",
+        "description": "A novel mutation in homeobox DNA binding domain of HOXC13 gene underlies pure hair and nail ectodermal dysplasia (ECTD9) in a Pakistani family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000971",
+      "label": "Abnormal sweat gland morphology"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28403827",
+        "description": "A novel mutation in homeobox DNA binding domain of HOXC13 gene underlies pure hair and nail ectodermal dysplasia (ECTD9) in a Pakistani family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0040039",
+      "label": "Onycholysis of fingernails"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28403827",
+        "description": "A novel mutation in homeobox DNA binding domain of HOXC13 gene underlies pure hair and nail ectodermal dysplasia (ECTD9) in a Pakistani family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002223",
+      "label": "Absent eyebrow"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28403827",
+        "description": "A novel mutation in homeobox DNA binding domain of HOXC13 gene underlies pure hair and nail ectodermal dysplasia (ECTD9) in a Pakistani family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000561",
+      "label": "Absent eyelashes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28403827",
+        "description": "A novel mutation in homeobox DNA binding domain of HOXC13 gene underlies pure hair and nail ectodermal dysplasia (ECTD9) in a Pakistani family"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:3229",
+    "symbol": "HOXC13"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "12",
+      "pos": 54338976,
+      "ref": "A",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:614931",
+      "label": "ECTODERMAL DYSPLASIA 9, HAIR/NAIL TYPE; ECTD9"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13",
+    "submittedBy": "HP:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28403827",
+      "description": "A novel mutation in homeobox DNA binding domain of HOXC13 gene underlies pure hair and nail ectodermal dysplasia (ECTD9) in a Pakistani family"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Kim-2016-LAMB3-proband.json b/notebooks/LIRICAL/v1phenopackets/Kim-2016-LAMB3-proband.json
new file mode 100644
index 000000000..2adc1ea0a
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Kim-2016-LAMB3-proband.json
@@ -0,0 +1,117 @@
+{
+  "id": "PMID:27220909-Kim-2016-LAMB3-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P6Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0009722",
+      "label": "Dental enamel pits"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27220909",
+        "description": "A novel de novo mutation in LAMB3 causes localized hypoplastic enamel in the molar region"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006297",
+      "label": "Hypoplasia of dental enamel"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27220909",
+        "description": "A novel de novo mutation in LAMB3 causes localized hypoplastic enamel in the molar region"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:3914",
+    "symbol": "LAMB3"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 209788676,
+      "ref": "ACGCTTCT",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:104530",
+      "label": "AMELOGENESIS IMPERFECTA, TYPE IA; AI1AAMELOGENESIS IMPERFECTA, HYPOPLASTIC TYPE IA"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27220909",
+      "description": "A novel de novo mutation in LAMB3 causes localized hypoplastic enamel in the molar region"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Kinnear-2017-TTC37-index.json b/notebooks/LIRICAL/v1phenopackets/Kinnear-2017-TTC37-index.json
new file mode 100644
index 000000000..9a5110650
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Kinnear-2017-TTC37-index.json
@@ -0,0 +1,345 @@
+{
+  "id": "PMID:28292286-Kinnear-2017-TTC37-index",
+  "subject": {
+    "id": "index",
+    "ageAtCollection": {
+      "age": "P3M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0410240",
+      "label": "Abnormal IgA level"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28292286",
+        "description": "Exome sequencing identifies a novel TTC37 mutation in the first reported case of Trichohepatoenteric syndrome (THE-S) in South Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004315",
+      "label": "Decreased circulating IgG level"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28292286",
+        "description": "Exome sequencing identifies a novel TTC37 mutation in the first reported case of Trichohepatoenteric syndrome (THE-S) in South Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006579",
+      "label": "Prolonged neonatal jaundice"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28292286",
+        "description": "Exome sequencing identifies a novel TTC37 mutation in the first reported case of Trichohepatoenteric syndrome (THE-S) in South Africa"
+      }
+    }]
+  }, {
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+      "id": "HP:0011220",
+      "label": "Prominent forehead"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28292286",
+        "description": "Exome sequencing identifies a novel TTC37 mutation in the first reported case of Trichohepatoenteric syndrome (THE-S) in South Africa"
+      }
+    }]
+  }, {
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+      "label": "Failure to thrive"
+    },
+    "evidence": [{
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+        "description": "Exome sequencing identifies a novel TTC37 mutation in the first reported case of Trichohepatoenteric syndrome (THE-S) in South Africa"
+      }
+    }]
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+      "id": "HP:0040218",
+      "label": "Reduced natural killer cell count"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28292286",
+        "description": "Exome sequencing identifies a novel TTC37 mutation in the first reported case of Trichohepatoenteric syndrome (THE-S) in South Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030948",
+      "label": "Elevated gamma-glutamyltransferase activity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28292286",
+        "description": "Exome sequencing identifies a novel TTC37 mutation in the first reported case of Trichohepatoenteric syndrome (THE-S) in South Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006515",
+      "label": "Interstitial pneumonitis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28292286",
+        "description": "Exome sequencing identifies a novel TTC37 mutation in the first reported case of Trichohepatoenteric syndrome (THE-S) in South Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002090",
+      "label": "Pneumonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28292286",
+        "description": "Exome sequencing identifies a novel TTC37 mutation in the first reported case of Trichohepatoenteric syndrome (THE-S) in South Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000316",
+      "label": "Hypertelorism"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28292286",
+        "description": "Exome sequencing identifies a novel TTC37 mutation in the first reported case of Trichohepatoenteric syndrome (THE-S) in South Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0032247",
+      "label": "Persistent CMV viremia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28292286",
+        "description": "Exome sequencing identifies a novel TTC37 mutation in the first reported case of Trichohepatoenteric syndrome (THE-S) in South Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001034",
+      "label": "Hypermelanotic macule"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28292286",
+        "description": "Exome sequencing identifies a novel TTC37 mutation in the first reported case of Trichohepatoenteric syndrome (THE-S) in South Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0410243",
+      "label": "Abnormal IgM level"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28292286",
+        "description": "Exome sequencing identifies a novel TTC37 mutation in the first reported case of Trichohepatoenteric syndrome (THE-S) in South Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001019",
+      "label": "Erythroderma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28292286",
+        "description": "Exome sequencing identifies a novel TTC37 mutation in the first reported case of Trichohepatoenteric syndrome (THE-S) in South Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003073",
+      "label": "Hypoalbuminemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28292286",
+        "description": "Exome sequencing identifies a novel TTC37 mutation in the first reported case of Trichohepatoenteric syndrome (THE-S) in South Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005585",
+      "label": "Spotty hyperpigmentation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28292286",
+        "description": "Exome sequencing identifies a novel TTC37 mutation in the first reported case of Trichohepatoenteric syndrome (THE-S) in South Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002240",
+      "label": "Hepatomegaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28292286",
+        "description": "Exome sequencing identifies a novel TTC37 mutation in the first reported case of Trichohepatoenteric syndrome (THE-S) in South Africa"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:9652",
+    "symbol": "TTC37"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "5",
+      "pos": 94803683,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:222470",
+      "label": "TRICHOHEPATOENTERIC SYNDROME 1; THES1"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28292286",
+      "description": "Exome sequencing identifies a novel TTC37 mutation in the first reported case of Trichohepatoenteric syndrome (THE-S) in South Africa"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Kluijtmans-1996-CBS-patient.json b/notebooks/LIRICAL/v1phenopackets/Kluijtmans-1996-CBS-patient.json
new file mode 100644
index 000000000..c32428c39
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Kluijtmans-1996-CBS-patient.json
@@ -0,0 +1,147 @@
+{
+  "id": "PMID:8755636-Kluijtmans-1996-CBS-patient",
+  "subject": {
+    "id": "patient",
+    "ageAtCollection": {
+      "age": "20Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001166",
+      "label": "Arachnodactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:8755636",
+        "description": "Defective cystathionine beta-synthase regulation by S-adenosylmethionine in a partially pyridoxine responsive homocystinuria patient"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:8755636",
+        "description": "Defective cystathionine beta-synthase regulation by S-adenosylmethionine in a partially pyridoxine responsive homocystinuria patient"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001083",
+      "label": "Ectopia lentis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:8755636",
+        "description": "Defective cystathionine beta-synthase regulation by S-adenosylmethionine in a partially pyridoxine responsive homocystinuria patient"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001519",
+      "label": "Disproportionate tall stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:8755636",
+        "description": "Defective cystathionine beta-synthase regulation by S-adenosylmethionine in a partially pyridoxine responsive homocystinuria patient"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:875",
+    "symbol": "CBS"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "21",
+      "pos": 44478972,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:236200",
+      "label": "HOMOCYSTINURIA DUE TO CYSTATHIONINE BETA-SYNTHASE DEFICIENCY"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:8755636",
+      "description": "Defective cystathionine beta-synthase regulation by S-adenosylmethionine in a partially pyridoxine responsive homocystinuria patient"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Kocoglu-2018-CAPN1-Fam1Pat1.json b/notebooks/LIRICAL/v1phenopackets/Kocoglu-2018-CAPN1-Fam1Pat1.json
new file mode 100644
index 000000000..d5ef02cfc
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Kocoglu-2018-CAPN1-Fam1Pat1.json
@@ -0,0 +1,192 @@
+{
+  "id": "PMID:29379883-Kocoglu-2018-CAPN1-Fam1Pat1",
+  "subject": {
+    "id": "Fam1Pat1",
+    "ageAtCollection": {
+      "age": "P21Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002066",
+      "label": "Gait ataxia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29379883",
+        "description": "Homozygous CAPN1 mutations causing a spastic-ataxia phenotype in 2 families"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006986",
+      "label": "Upper limb spasticity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29379883",
+        "description": "Homozygous CAPN1 mutations causing a spastic-ataxia phenotype in 2 families"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002070",
+      "label": "Limb ataxia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29379883",
+        "description": "Homozygous CAPN1 mutations causing a spastic-ataxia phenotype in 2 families"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002061",
+      "label": "Lower limb spasticity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29379883",
+        "description": "Homozygous CAPN1 mutations causing a spastic-ataxia phenotype in 2 families"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000563",
+      "label": "Keratoconus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29379883",
+        "description": "Homozygous CAPN1 mutations causing a spastic-ataxia phenotype in 2 families"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001310",
+      "label": "Dysmetria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29379883",
+        "description": "Homozygous CAPN1 mutations causing a spastic-ataxia phenotype in 2 families"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001260",
+      "label": "Dysarthria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29379883",
+        "description": "Homozygous CAPN1 mutations causing a spastic-ataxia phenotype in 2 families"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:823",
+    "symbol": "CAPN1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "11",
+      "pos": 64955949,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616907",
+      "label": "Spastic paraplegia 76, autosomal recessive"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29379883",
+      "description": "Homozygous CAPN1 mutations causing a spastic-ataxia phenotype in 2 families"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Kocoglu-2018-CAPN1-Fam2Pat1.json b/notebooks/LIRICAL/v1phenopackets/Kocoglu-2018-CAPN1-Fam2Pat1.json
new file mode 100644
index 000000000..2232b290e
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Kocoglu-2018-CAPN1-Fam2Pat1.json
@@ -0,0 +1,192 @@
+{
+  "id": "PMID:29379883-Kocoglu-2018-CAPN1-Fam2Pat1",
+  "subject": {
+    "id": "Fam2Pat1",
+    "ageAtCollection": {
+      "age": "P15Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002066",
+      "label": "Gait ataxia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29379883",
+        "description": "Homozygous CAPN1 mutations causing a spastic-ataxia phenotype in 2 families"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006986",
+      "label": "Upper limb spasticity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29379883",
+        "description": "Homozygous CAPN1 mutations causing a spastic-ataxia phenotype in 2 families"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002070",
+      "label": "Limb ataxia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29379883",
+        "description": "Homozygous CAPN1 mutations causing a spastic-ataxia phenotype in 2 families"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002061",
+      "label": "Lower limb spasticity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29379883",
+        "description": "Homozygous CAPN1 mutations causing a spastic-ataxia phenotype in 2 families"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000563",
+      "label": "Keratoconus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29379883",
+        "description": "Homozygous CAPN1 mutations causing a spastic-ataxia phenotype in 2 families"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001310",
+      "label": "Dysmetria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29379883",
+        "description": "Homozygous CAPN1 mutations causing a spastic-ataxia phenotype in 2 families"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001260",
+      "label": "Dysarthria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29379883",
+        "description": "Homozygous CAPN1 mutations causing a spastic-ataxia phenotype in 2 families"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:823",
+    "symbol": "CAPN1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "11",
+      "pos": 64972164,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616907",
+      "label": "Spastic paraplegia 76, autosomal recessive"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29379883",
+      "description": "Homozygous CAPN1 mutations causing a spastic-ataxia phenotype in 2 families"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Konkolova-2017-GRHPR-patient.json b/notebooks/LIRICAL/v1phenopackets/Konkolova-2017-GRHPR-patient.json
new file mode 100644
index 000000000..da3697c83
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Konkolova-2017-GRHPR-patient.json
@@ -0,0 +1,255 @@
+{
+  "id": "PMID:28569194-Konkoľová-2017-GRHPR-patient",
+  "subject": {
+    "id": "patient",
+    "ageAtCollection": {
+      "age": "P11M"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000790",
+      "label": "Hematuria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28569194",
+        "description": "Severe child form of primary hyperoxaluria type 2 - a case report revealing consequence of GRHPR deficiency on metabolism"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011280",
+      "label": "Abnormality of urine calcium concentration"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28569194",
+        "description": "Severe child form of primary hyperoxaluria type 2 - a case report revealing consequence of GRHPR deficiency on metabolism"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012100",
+      "label": "Abnormal circulating creatinine level"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28569194",
+        "description": "Severe child form of primary hyperoxaluria type 2 - a case report revealing consequence of GRHPR deficiency on metabolism"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003159",
+      "label": "Hyperoxaluria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28569194",
+        "description": "Severe child form of primary hyperoxaluria type 2 - a case report revealing consequence of GRHPR deficiency on metabolism"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001903",
+      "label": "Anemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28569194",
+        "description": "Severe child form of primary hyperoxaluria type 2 - a case report revealing consequence of GRHPR deficiency on metabolism"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011227",
+      "label": "Elevated C-reactive protein level"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28569194",
+        "description": "Severe child form of primary hyperoxaluria type 2 - a case report revealing consequence of GRHPR deficiency on metabolism"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008672",
+      "label": "Calcium oxalate nephrolithiasis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28569194",
+        "description": "Severe child form of primary hyperoxaluria type 2 - a case report revealing consequence of GRHPR deficiency on metabolism"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001385",
+      "label": "Hip dysplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28569194",
+        "description": "Severe child form of primary hyperoxaluria type 2 - a case report revealing consequence of GRHPR deficiency on metabolism"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001974",
+      "label": "Leukocytosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28569194",
+        "description": "Severe child form of primary hyperoxaluria type 2 - a case report revealing consequence of GRHPR deficiency on metabolism"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001942",
+      "label": "Metabolic acidosis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28569194",
+        "description": "Severe child form of primary hyperoxaluria type 2 - a case report revealing consequence of GRHPR deficiency on metabolism"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012085",
+      "label": "Pyuria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28569194",
+        "description": "Severe child form of primary hyperoxaluria type 2 - a case report revealing consequence of GRHPR deficiency on metabolism"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:9380",
+    "symbol": "GRHPR"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "9",
+      "pos": 37428529,
+      "ref": "C",
+      "alt": "CA"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:260000",
+      "label": "HYPEROXALURIA, PRIMARY, TYPE II; HP2"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28569194",
+      "description": "Severe child form of primary hyperoxaluria type 2 - a case report revealing consequence of GRHPR deficiency on metabolism"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Kou-2018-ERCC6-index.json b/notebooks/LIRICAL/v1phenopackets/Kou-2018-ERCC6-index.json
new file mode 100644
index 000000000..58551c233
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Kou-2018-ERCC6-index.json
@@ -0,0 +1,357 @@
+{
+  "id": "PMID:30113454-Kou-2018-ERCC6-index",
+  "subject": {
+    "id": "index",
+    "ageAtCollection": {
+      "age": "P4Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001176",
+      "label": "Large hands"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30113454",
+        "description": "Novel frame shift mutation in ERCC6 leads to a severe form of Cockayne syndrome with postnatal growth failure and early death: A case report and brief literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30113454",
+        "description": "Novel frame shift mutation in ERCC6 leads to a severe form of Cockayne syndrome with postnatal growth failure and early death: A case report and brief literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000400",
+      "label": "Macrotia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30113454",
+        "description": "Novel frame shift mutation in ERCC6 leads to a severe form of Cockayne syndrome with postnatal growth failure and early death: A case report and brief literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000568",
+      "label": "Microphthalmia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30113454",
+        "description": "Novel frame shift mutation in ERCC6 leads to a severe form of Cockayne syndrome with postnatal growth failure and early death: A case report and brief literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002684",
+      "label": "Thickened calvaria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30113454",
+        "description": "Novel frame shift mutation in ERCC6 leads to a severe form of Cockayne syndrome with postnatal growth failure and early death: A case report and brief literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008897",
+      "label": "Postnatal growth retardation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30113454",
+        "description": "Novel frame shift mutation in ERCC6 leads to a severe form of Cockayne syndrome with postnatal growth failure and early death: A case report and brief literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011470",
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+    }
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+      "namespacePrefix": "NCBITaxon"
+    }, {
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+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
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+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
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+      "namespacePrefix": "OMIM"
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+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Kremer-2016-TANGO2-F1_II.2.json b/notebooks/LIRICAL/v1phenopackets/Kremer-2016-TANGO2-F1_II.2.json
new file mode 100644
index 000000000..615099ff5
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Kremer-2016-TANGO2-F1_II.2.json
@@ -0,0 +1,432 @@
+{
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+      "label": "Homo sapiens"
+    }
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+    }, {
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+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:26805782",
+      "description": "Bi-allelic Truncating Mutations in TANGO2 Cause Infancy-Onset Recurrent Metabolic Crises with Encephalocardiomyopathy"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Kretz-2011-PYCR1-Patient_4.json b/notebooks/LIRICAL/v1phenopackets/Kretz-2011-PYCR1-Patient_4.json
new file mode 100644
index 000000000..6f1e0fb89
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Kretz-2011-PYCR1-Patient_4.json
@@ -0,0 +1,329 @@
+{
+  "id": "PMID:21487760-Kretz-2011-PYCR1-Patient_4",
+  "subject": {
+    "id": "Patient 4",
+    "ageAtCollection": {
+      "age": "P5Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000369",
+      "label": "Low-set ears"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:21487760",
+        "description": "Defect in proline synthesis: pyrroline-5-carboxylate reductase 1 deficiency leads to a complex clinical phenotype with collagen and elastin abnormalities"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000460",
+      "label": "Narrow nose"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:21487760",
+        "description": "Defect in proline synthesis: pyrroline-5-carboxylate reductase 1 deficiency leads to a complex clinical phenotype with collagen and elastin abnormalities"
+      }
+    }]
+  }, {
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+      "id": "HP:0008887",
+      "label": "Adipose tissue loss"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "id": "PMID:21487760",
+        "description": "Defect in proline synthesis: pyrroline-5-carboxylate reductase 1 deficiency leads to a complex clinical phenotype with collagen and elastin abnormalities"
+      }
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+      "label": "Triangular face"
+    },
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+        "description": "Defect in proline synthesis: pyrroline-5-carboxylate reductase 1 deficiency leads to a complex clinical phenotype with collagen and elastin abnormalities"
+      }
+    }]
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+    },
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+        "description": "Defect in proline synthesis: pyrroline-5-carboxylate reductase 1 deficiency leads to a complex clinical phenotype with collagen and elastin abnormalities"
+      }
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+      "label": "Excessive wrinkled skin"
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+        "description": "Defect in proline synthesis: pyrroline-5-carboxylate reductase 1 deficiency leads to a complex clinical phenotype with collagen and elastin abnormalities"
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+    }]
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+      "label": "Delayed gross motor development"
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+        "label": "author statement supported by traceable reference"
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+        "description": "Defect in proline synthesis: pyrroline-5-carboxylate reductase 1 deficiency leads to a complex clinical phenotype with collagen and elastin abnormalities"
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+    }]
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+      "label": "Hip dysplasia"
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+    "evidence": [{
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+        "description": "Defect in proline synthesis: pyrroline-5-carboxylate reductase 1 deficiency leads to a complex clinical phenotype with collagen and elastin abnormalities"
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+      "label": "Global developmental delay"
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+        "label": "author statement supported by traceable reference"
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+        "description": "Defect in proline synthesis: pyrroline-5-carboxylate reductase 1 deficiency leads to a complex clinical phenotype with collagen and elastin abnormalities"
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+    }]
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+      "label": "Thin skin"
+    },
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+        "description": "Defect in proline synthesis: pyrroline-5-carboxylate reductase 1 deficiency leads to a complex clinical phenotype with collagen and elastin abnormalities"
+      }
+    }]
+  }, {
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+        "description": "Defect in proline synthesis: pyrroline-5-carboxylate reductase 1 deficiency leads to a complex clinical phenotype with collagen and elastin abnormalities"
+      }
+    }]
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+      "label": "Thin vermilion border"
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+    }]
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+      }
+    }]
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+      }
+    }]
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+      }
+    }]
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+        "description": "Defect in proline synthesis: pyrroline-5-carboxylate reductase 1 deficiency leads to a complex clinical phenotype with collagen and elastin abnormalities"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:5831",
+    "symbol": "PYCR1"
+  }],
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+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
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+      "label": "CUTIS LAXA, AUTOSOMAL RECESSIVE, TYPE IIB; ARCL2B"
+    }
+  }],
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+    }, {
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+      "name": "Phenotype And Trait Ontology",
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+    }, {
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+      "namespacePrefix": "GENO",
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+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Kruszka-2016-FGFR3-Proband_27.json b/notebooks/LIRICAL/v1phenopackets/Kruszka-2016-FGFR3-Proband_27.json
new file mode 100644
index 000000000..d3ead078b
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Kruszka-2016-FGFR3-Proband_27.json
@@ -0,0 +1,162 @@
+{
+  "id": "PMID:26740388-Kruszka-2016-FGFR3-Proband_27",
+  "subject": {
+    "id": "Proband 27",
+    "ageAtCollection": {
+      "age": "P4Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:26740388",
+        "description": "Muenke syndrome: An international multicenter natural history study"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26740388",
+        "description": "Muenke syndrome: An international multicenter natural history study"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000365",
+      "label": "Hearing impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Muenke syndrome: An international multicenter natural history study"
+      }
+    }]
+  }, {
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+      "label": "Bicoronal synostosis"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:26740388",
+        "description": "Muenke syndrome: An international multicenter natural history study"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001250",
+      "label": "Seizures"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "description": "Muenke syndrome: An international multicenter natural history study"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2261",
+    "symbol": "FGFR3"
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+  "variants": [{
+    "vcfAllele": {
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+      "chr": "4",
+      "pos": 1803571,
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+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
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+      "id": "OMIM:602849",
+      "label": "MUENKE SYNDROME; MNKES"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
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+      "id": "hp",
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+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
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+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
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+      "namespacePrefix": "OMIM"
+    }],
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+    "externalReferences": [{
+      "id": "PMID:26740388",
+      "description": "Muenke syndrome: An international multicenter natural history study"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Kuptanon-2018-WNT1-proband.json b/notebooks/LIRICAL/v1phenopackets/Kuptanon-2018-WNT1-proband.json
new file mode 100644
index 000000000..aea842e8c
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Kuptanon-2018-WNT1-proband.json
@@ -0,0 +1,255 @@
+{
+  "id": "PMID:30012084-Kuptanon-2018-WNT1-proband",
+  "subject": {
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+    "ageAtCollection": {
+      "age": "P14Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30012084",
+        "description": "The most 5\u0027 truncating homozygous mutation of WNT1 in siblings with osteogenesis imperfecta with a variable degree of brain anomalies: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000703",
+      "label": "Dentinogenesis imperfecta"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "The most 5\u0027 truncating homozygous mutation of WNT1 in siblings with osteogenesis imperfecta with a variable degree of brain anomalies: a case report"
+      }
+    }]
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+      "label": "Premature rupture of membranes"
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+      }
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+  }, {
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+      "label": "Bowing of limbs due to multiple fractures"
+    },
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+        "description": "The most 5\u0027 truncating homozygous mutation of WNT1 in siblings with osteogenesis imperfecta with a variable degree of brain anomalies: a case report"
+      }
+    }]
+  }, {
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+      "label": "Osteopenia"
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+    "evidence": [{
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+      }
+    }]
+  }, {
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+      "label": "Platyspondyly"
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+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:30012084",
+        "description": "The most 5\u0027 truncating homozygous mutation of WNT1 in siblings with osteogenesis imperfecta with a variable degree of brain anomalies: a case report"
+      }
+    }]
+  }, {
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+      "label": "Motor delay"
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+    "evidence": [{
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+      "label": "Ptosis"
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+      "reference": {
+        "id": "PMID:30012084",
+        "description": "The most 5\u0027 truncating homozygous mutation of WNT1 in siblings with osteogenesis imperfecta with a variable degree of brain anomalies: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001510",
+      "label": "Growth delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30012084",
+        "description": "The most 5\u0027 truncating homozygous mutation of WNT1 in siblings with osteogenesis imperfecta with a variable degree of brain anomalies: a case report"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:7471",
+    "symbol": "WNT1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "12",
+      "pos": 49372435,
+      "ref": "TG",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:615220",
+      "label": "OSTEOGENESIS IMPERFECTA, TYPE XV; OI15"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30012084",
+      "description": "The most 5\u0027 truncating homozygous mutation of WNT1 in siblings with osteogenesis imperfecta with a variable degree of brain anomalies: a case report"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Kury-2017-PSMD12-Subject_1.json b/notebooks/LIRICAL/v1phenopackets/Kury-2017-PSMD12-Subject_1.json
new file mode 100644
index 000000000..63e2547c2
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Kury-2017-PSMD12-Subject_1.json
@@ -0,0 +1,597 @@
+{
+  "id": "PMID:28132691-Küry-2017-PSMD12-Subject_1",
+  "subject": {
+    "id": "Subject 1",
+    "ageAtCollection": {
+      "age": "P8Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000032",
+      "label": "Abnormality of male external genitalia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000478",
+      "label": "Abnormality of the eye"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002090",
+      "label": "Pneumonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000356",
+      "label": "Abnormality of the outer ear"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000277",
+      "label": "Abnormality of the mandible"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000708",
+      "label": "Behavioral abnormality"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009601",
+      "label": "Aplasia/Hypoplasia of the thumb"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001270",
+      "label": "Motor delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000666",
+      "label": "Horizontal nystagmus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000047",
+      "label": "Hypospadias"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001643",
+      "label": "Patent ductus arteriosus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004736",
+      "label": "Crossed fused renal ectopia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000639",
+      "label": "Nystagmus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001660",
+      "label": "Truncus arteriosus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011968",
+      "label": "Feeding difficulties"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012304",
+      "label": "Hypoplastic aortic arch"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001629",
+      "label": "Ventricular septal defect"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000085",
+      "label": "Horseshoe kidney"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
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+      "id": "HP:0002817",
+      "label": "Abnormality of the upper limb"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
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+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000358",
+      "label": "Posteriorly rotated ears"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000086",
+      "label": "Ectopic kidney"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000308",
+      "label": "Microretrognathia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
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+      "id": "HP:0001631",
+      "label": "Atrial septal defect"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000077",
+      "label": "Abnormality of the kidney"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000486",
+      "label": "Strabismus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001344",
+      "label": "Absent speech"
+    },
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+        "label": "author statement supported by traceable reference"
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+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000369",
+      "label": "Low-set ears"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
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+  }, {
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+      "label": "Recurrent pneumonia"
+    },
+    "evidence": [{
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+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
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+  }, {
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+      "id": "HP:0001626",
+      "label": "Abnormality of the cardiovascular system"
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+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
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+  }, {
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+      "label": "Generalized hypotonia"
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+    }]
+  }, {
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+      "label": "Hearing impairment"
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+    "evidence": [{
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+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:5718",
+    "symbol": "PSMD12"
+  }],
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+      "pos": 65346383,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
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+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617516",
+      "label": "Stankiewicz-Isidor syndrome"
+    }
+  }],
+  "metaData": {
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+    "submittedBy": "UNC:biocuration",
+    "resources": [{
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+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28132691",
+      "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Kury-2017-PSMD12-Subject_2.json b/notebooks/LIRICAL/v1phenopackets/Kury-2017-PSMD12-Subject_2.json
new file mode 100644
index 000000000..afdd4ae49
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Kury-2017-PSMD12-Subject_2.json
@@ -0,0 +1,539 @@
+{
+  "id": "PMID:28132691-Küry-2017-PSMD12-Subject_2",
+  "subject": {
+    "id": "Subject 2",
+    "ageAtCollection": {
+      "age": "P10Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0100704",
+      "label": "Cerebral visual impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000729",
+      "label": "Autistic behavior"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000365",
+      "label": "Hearing impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000016",
+      "label": "Urinary retention"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011968",
+      "label": "Feeding difficulties"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000077",
+      "label": "Abnormality of the kidney"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001250",
+      "label": "Seizures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012795",
+      "label": "Abnormality of the optic disc"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002817",
+      "label": "Abnormality of the upper limb"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000356",
+      "label": "Abnormality of the outer ear"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000960",
+      "label": "Sacral dimple"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001344",
+      "label": "Absent speech"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003561",
+      "label": "Birth length less than 3rd percentile"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000032",
+      "label": "Abnormality of male external genitalia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001643",
+      "label": "Patent ductus arteriosus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000054",
+      "label": "Micropenis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000369",
+      "label": "Low-set ears"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001626",
+      "label": "Abnormality of the cardiovascular system"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000308",
+      "label": "Microretrognathia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000505",
+      "label": "Visual impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009601",
+      "label": "Aplasia/Hypoplasia of the thumb"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002779",
+      "label": "Tracheomalacia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000478",
+      "label": "Abnormality of the eye"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001270",
+      "label": "Motor delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008751",
+      "label": "Laryngeal cleft"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010945",
+      "label": "Fetal pyelectasis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000073",
+      "label": "Ureteral duplication"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:5718",
+    "symbol": "PSMD12"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "17",
+      "pos": 65337056,
+      "ref": "A",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617516",
+      "label": "Stankiewicz-Isidor syndrome"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28132691",
+      "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Kury-2017-PSMD12-Subject_3.json b/notebooks/LIRICAL/v1phenopackets/Kury-2017-PSMD12-Subject_3.json
new file mode 100644
index 000000000..300e8549e
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Kury-2017-PSMD12-Subject_3.json
@@ -0,0 +1,271 @@
+{
+  "id": "PMID:28132691-Küry-2017-PSMD12-Subject_3",
+  "subject": {
+    "id": "Subject 3",
+    "ageAtCollection": {
+      "age": "P14Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030148",
+      "label": "Heart murmur"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000708",
+      "label": "Behavioral abnormality"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001270",
+      "label": "Motor delay"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011968",
+      "label": "Feeding difficulties"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000729",
+      "label": "Autistic behavior"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000032",
+      "label": "Abnormality of male external genitalia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001250",
+      "label": "Seizures"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001344",
+      "label": "Absent speech"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000365",
+      "label": "Hearing impairment"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001626",
+      "label": "Abnormality of the cardiovascular system"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:5718",
+    "symbol": "PSMD12"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "17",
+      "pos": 65343511,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617516",
+      "label": "Stankiewicz-Isidor syndrome"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28132691",
+      "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Kury-2017-PSMD12-Subject_4.json b/notebooks/LIRICAL/v1phenopackets/Kury-2017-PSMD12-Subject_4.json
new file mode 100644
index 000000000..63197f4fc
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Kury-2017-PSMD12-Subject_4.json
@@ -0,0 +1,402 @@
+{
+  "id": "PMID:28132691-Küry-2017-PSMD12-Subject_4",
+  "subject": {
+    "id": "Subject 4",
+    "ageAtCollection": {
+      "age": "P14Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000054",
+      "label": "Micropenis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007772",
+      "label": "Impaired smooth pursuit"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000729",
+      "label": "Autistic behavior"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100764",
+      "label": "Lymphangioma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000032",
+      "label": "Abnormality of male external genitalia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000478",
+      "label": "Abnormality of the eye"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000356",
+      "label": "Abnormality of the outer ear"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000324",
+      "label": "Facial asymmetry"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000271",
+      "label": "Abnormality of the face"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000358",
+      "label": "Posteriorly rotated ears"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000049",
+      "label": "Shawl scrotum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000965",
+      "label": "Cutis marmorata"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001250",
+      "label": "Seizures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000028",
+      "label": "Cryptorchidism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000708",
+      "label": "Behavioral abnormality"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000369",
+      "label": "Low-set ears"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000316",
+      "label": "Hypertelorism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012683",
+      "label": "Pineal cyst"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000448",
+      "label": "Prominent nose"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132691",
+        "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:5718",
+    "symbol": "PSMD12"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "17",
+      "pos": 65340898,
+      "ref": "T",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617516",
+      "label": "Stankiewicz-Isidor syndrome"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28132691",
+      "description": "De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Lalani-2016-TANGO2-Subject_2.json b/notebooks/LIRICAL/v1phenopackets/Lalani-2016-TANGO2-Subject_2.json
new file mode 100644
index 000000000..db1c746a6
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Lalani-2016-TANGO2-Subject_2.json
@@ -0,0 +1,583 @@
+{
+  "id": "PMID:26805781-Lalani-2016-TANGO2-Subject_2",
+  "subject": {
+    "id": "Subject 2",
+    "ageAtCollection": {
+      "age": "P6M"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001649",
+      "label": "Tachycardia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26805781",
+        "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001324",
+      "label": "Muscle weakness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26805781",
+        "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012544",
+      "label": "Elevated aldolase level"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26805781",
+        "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001942",
+      "label": "Metabolic acidosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26805781",
+        "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001941",
+      "label": "Acidosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26805781",
+        "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006956",
+      "label": "Dilation of lateral ventricles"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26805781",
+        "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001987",
+      "label": "Hyperammonemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26805781",
+        "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007340",
+      "label": "Lower limb muscle weakness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26805781",
+        "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002919",
+      "label": "Ketonuria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26805781",
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+    }
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+    }, {
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+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
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+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
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+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
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+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
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+    }],
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+    "externalReferences": [{
+      "id": "PMID:26805781",
+      "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Lalani-2016-TANGO2-Subject_4.json b/notebooks/LIRICAL/v1phenopackets/Lalani-2016-TANGO2-Subject_4.json
new file mode 100644
index 000000000..a48e62f60
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Lalani-2016-TANGO2-Subject_4.json
@@ -0,0 +1,327 @@
+{
+  "id": "PMID:26805781-Lalani-2016-TANGO2-Subject_4",
+  "subject": {
+    "id": "Subject 4",
+    "ageAtCollection": {
+      "age": "P12Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002169",
+      "label": "Clonus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:26805781",
+        "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+      }
+    }]
+  }, {
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+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:26805781",
+        "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+      }
+    }]
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+      "label": "Dysarthria"
+    },
+    "evidence": [{
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+    },
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+        "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
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+    }]
+  }, {
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+      "label": "Gait ataxia"
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+    }]
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+    }]
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+    },
+    "evidence": [{
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+    }]
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+    }]
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+      }
+    }]
+  }, {
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+      "label": "Hypothyroidism"
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:26805781",
+        "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:128989",
+    "symbol": "TANGO2"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "22",
+      "pos": 20049061,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616878",
+      "label": "Metabolic encephalomyopathic crises, recurrent, with rhabdomyolysis, cardiac arrhythmias, and neurodegeneration"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:26805781",
+      "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Lalani-2016-TANGO2-Subject_5.json b/notebooks/LIRICAL/v1phenopackets/Lalani-2016-TANGO2-Subject_5.json
new file mode 100644
index 000000000..4ca0a4d69
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Lalani-2016-TANGO2-Subject_5.json
@@ -0,0 +1,402 @@
+{
+  "id": "PMID:26805781-Lalani-2016-TANGO2-Subject_5",
+  "subject": {
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+      "age": "P7Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001649",
+      "label": "Tachycardia"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:26805781",
+        "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+      }
+    }]
+  }, {
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+      "id": "HP:0001250",
+      "label": "Seizures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26805781",
+        "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+      }
+    }]
+  }, {
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+      "id": "HP:0001324",
+      "label": "Muscle weakness"
+    },
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+        "id": "PMID:26805781",
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+      }
+    }]
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+      "label": "Torsade de pointes"
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:26805781",
+        "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+      }
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+    }]
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+      "label": "Ventricular tachycardia"
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+        "label": "author statement supported by traceable reference"
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+      }
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+      }
+    }]
+  }, {
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+      "id": "HP:0002913",
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+      }
+    }]
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+    "id": "NCBIGene:128989",
+    "symbol": "TANGO2"
+  }],
+  "variants": [{
+    "vcfAllele": {
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+      "chr": "22",
+      "pos": 20049061,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616878",
+      "label": "Metabolic encephalomyopathic crises, recurrent, with rhabdomyolysis, cardiac arrhythmias, and neurodegeneration"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:26805781",
+      "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Lalani-2016-TANGO2-Subject_6.json b/notebooks/LIRICAL/v1phenopackets/Lalani-2016-TANGO2-Subject_6.json
new file mode 100644
index 000000000..591cfac96
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Lalani-2016-TANGO2-Subject_6.json
@@ -0,0 +1,345 @@
+{
+  "id": "PMID:26805781-Lalani-2016-TANGO2-Subject_6",
+  "subject": {
+    "id": "Subject 6",
+    "ageAtCollection": {
+      "age": "P1Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002013",
+      "label": "Vomiting"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26805781",
+        "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26805781",
+        "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+      }
+    }]
+  }, {
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+      "id": "HP:0003201",
+      "label": "Rhabdomyolysis"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
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+        "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001942",
+      "label": "Metabolic acidosis"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
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+    }]
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+    },
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+    }]
+  }, {
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+      "label": "Respiratory distress"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+      }
+    }]
+  }, {
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+      "label": "Hyperammonemia"
+    },
+    "evidence": [{
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+        "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001943",
+      "label": "Hypoglycemia"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:26805781",
+        "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+      }
+    }]
+  }, {
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+    "negated": true,
+    "evidence": [{
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+      "label": "Arrhythmia"
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+      }
+    }]
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+    "id": "NCBIGene:128989",
+    "symbol": "TANGO2"
+  }],
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+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
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+    "term": {
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+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:26805781",
+      "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Lalani-2016-TANGO2-Suject_1.json b/notebooks/LIRICAL/v1phenopackets/Lalani-2016-TANGO2-Suject_1.json
new file mode 100644
index 000000000..1f425b458
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Lalani-2016-TANGO2-Suject_1.json
@@ -0,0 +1,388 @@
+{
+  "id": "PMID:26805781-Lalani-2016-TANGO2-Suject_1",
+  "subject": {
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+      "age": "P4Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002058",
+      "label": "Myopathic facies"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26805781",
+        "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+      }
+    }]
+  }, {
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+      "label": "Seizures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:26805781",
+        "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+      }
+    }]
+  }, {
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+      "label": "Focal-onset seizure"
+    },
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+        "id": "ECO:0000033",
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+        "id": "PMID:26805781",
+        "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+      }
+    }]
+  }, {
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+      "label": "Babinski sign"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:26805781",
+        "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+      }
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+        "label": "author statement supported by traceable reference"
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+        "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
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+      }
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+    }]
+  }, {
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+    }]
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+    "symbol": "TANGO2"
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+      "pos": 20049061,
+      "ref": "G",
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+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616878",
+      "label": "Metabolic encephalomyopathic crises, recurrent, with rhabdomyolysis, cardiac arrhythmias, and neurodegeneration"
+    }
+  }],
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+    "submittedBy": "UNC:biocuration",
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+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "name": "Phenotype And Trait Ontology",
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+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:26805781",
+      "description": "Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Lambe-2018-CAPN1-II-4.json b/notebooks/LIRICAL/v1phenopackets/Lambe-2018-CAPN1-II-4.json
new file mode 100644
index 000000000..e782fa65f
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Lambe-2018-CAPN1-II-4.json
@@ -0,0 +1,162 @@
+{
+  "id": "PMID:29678961-Lambe-2018-CAPN1-II-4",
+  "subject": {
+    "id": "II-4",
+    "ageAtCollection": {
+      "age": "P14Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002506",
+      "label": "Diffuse cerebral atrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29678961",
+        "description": "CAPN1 mutations broadening the hereditary spastic paraplegia/spinocerebellar ataxia phenotype"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002061",
+      "label": "Lower limb spasticity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29678961",
+        "description": "CAPN1 mutations broadening the hereditary spastic paraplegia/spinocerebellar ataxia phenotype"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002497",
+      "label": "Spastic ataxia"
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+    "evidence": [{
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+      "reference": {
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+        "description": "CAPN1 mutations broadening the hereditary spastic paraplegia/spinocerebellar ataxia phenotype"
+      }
+    }]
+  }, {
+    "type": {
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+        "description": "CAPN1 mutations broadening the hereditary spastic paraplegia/spinocerebellar ataxia phenotype"
+      }
+    }]
+  }, {
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+      "id": "HP:0011448",
+      "label": "Ankle clonus"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29678961",
+        "description": "CAPN1 mutations broadening the hereditary spastic paraplegia/spinocerebellar ataxia phenotype"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:823",
+    "symbol": "CAPN1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "11",
+      "pos": 64974114,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616907",
+      "label": "Spastic paraplegia 76, autosomal recessive"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29678961",
+      "description": "CAPN1 mutations broadening the hereditary spastic paraplegia/spinocerebellar ataxia phenotype"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Lesage-2016-VPS13C-Family_A,_V-2.json b/notebooks/LIRICAL/v1phenopackets/Lesage-2016-VPS13C-Family_A,_V-2.json
new file mode 100644
index 000000000..d19089b4c
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Lesage-2016-VPS13C-Family_A,_V-2.json
@@ -0,0 +1,360 @@
+{
+  "id": "PMID:26942284-Lesage-2016-VPS13C-Family_A,_V-2",
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+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
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+      "label": "Depressivity"
+    },
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+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:26942284",
+        "description": "Loss of VPS13C Function in Autosomal-Recessive Parkinsonism Causes Mitochondrial Dysfunction and Increases PINK1/Parkin-Dependent Mitophagy"
+      }
+    }]
+  }, {
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+      "id": "HP:0001268",
+      "label": "Mental deterioration"
+    },
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+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "id": "PMID:26942284",
+        "description": "Loss of VPS13C Function in Autosomal-Recessive Parkinsonism Causes Mitochondrial Dysfunction and Increases PINK1/Parkin-Dependent Mitophagy"
+      }
+    }]
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+      }
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+    }]
+  }, {
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+    "evidence": [{
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+      }
+    }]
+  }, {
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+    }]
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+    }, {
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+    }, {
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+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
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+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
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+    "externalReferences": [{
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+      "description": "Loss of VPS13C Function in Autosomal-Recessive Parkinsonism Causes Mitochondrial Dysfunction and Increases PINK1/Parkin-Dependent Mitophagy"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Lesage-2016-VPS13C-Family_B,_II-1.json b/notebooks/LIRICAL/v1phenopackets/Lesage-2016-VPS13C-Family_B,_II-1.json
new file mode 100644
index 000000000..afab8b137
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Lesage-2016-VPS13C-Family_B,_II-1.json
@@ -0,0 +1,174 @@
+{
+  "id": "PMID:26942284-Lesage-2016-VPS13C-Family_B,_II-1",
+  "subject": {
+    "id": "Family B, II-1",
+    "ageAtCollection": {
+      "age": "P33Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002451",
+      "label": "Limb dystonia"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:26942284",
+        "description": "Loss of VPS13C Function in Autosomal-Recessive Parkinsonism Causes Mitochondrial Dysfunction and Increases PINK1/Parkin-Dependent Mitophagy"
+      }
+    }]
+  }, {
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+      "id": "HP:0012332",
+      "label": "Abnormal autonomic nervous system physiology"
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+        "description": "Loss of VPS13C Function in Autosomal-Recessive Parkinsonism Causes Mitochondrial Dysfunction and Increases PINK1/Parkin-Dependent Mitophagy"
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+      "namespacePrefix": "GENO",
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+      "name": "NCBI organismal classification",
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+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
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+      "description": "Loss of VPS13C Function in Autosomal-Recessive Parkinsonism Causes Mitochondrial Dysfunction and Increases PINK1/Parkin-Dependent Mitophagy"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Lesage-2016-VPS13C-Family_C,_II-1.json b/notebooks/LIRICAL/v1phenopackets/Lesage-2016-VPS13C-Family_C,_II-1.json
new file mode 100644
index 000000000..8edc90a3c
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Lesage-2016-VPS13C-Family_C,_II-1.json
@@ -0,0 +1,160 @@
+{
+  "id": "PMID:26942284-Lesage-2016-VPS13C-Family_C,_II-1",
+  "subject": {
+    "id": "Family C, II-1",
+    "ageAtCollection": {
+      "age": "P25Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001350",
+      "label": "Slurred speech"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26942284",
+        "description": "Loss of VPS13C Function in Autosomal-Recessive Parkinsonism Causes Mitochondrial Dysfunction and Increases PINK1/Parkin-Dependent Mitophagy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100660",
+      "label": "Dyskinesia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26942284",
+        "description": "Loss of VPS13C Function in Autosomal-Recessive Parkinsonism Causes Mitochondrial Dysfunction and Increases PINK1/Parkin-Dependent Mitophagy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001268",
+      "label": "Mental deterioration"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26942284",
+        "description": "Loss of VPS13C Function in Autosomal-Recessive Parkinsonism Causes Mitochondrial Dysfunction and Increases PINK1/Parkin-Dependent Mitophagy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002510",
+      "label": "Spastic tetraplegia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26942284",
+        "description": "Loss of VPS13C Function in Autosomal-Recessive Parkinsonism Causes Mitochondrial Dysfunction and Increases PINK1/Parkin-Dependent Mitophagy"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:54832",
+    "symbol": "VPS13C"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "15",
+      "pos": 62250807,
+      "ref": "C",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "15",
+      "pos": 62239490,
+      "ref": "TG",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616840",
+      "label": "Parkinson disease 23, autosomal recessive, early onset"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:26942284",
+      "description": "Loss of VPS13C Function in Autosomal-Recessive Parkinsonism Causes Mitochondrial Dysfunction and Increases PINK1/Parkin-Dependent Mitophagy"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Li-2014-BBS4-4-year-old_female_patient.json b/notebooks/LIRICAL/v1phenopackets/Li-2014-BBS4-4-year-old_female_patient.json
new file mode 100644
index 000000000..7a5c4c2ce
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Li-2014-BBS4-4-year-old_female_patient.json
@@ -0,0 +1,236 @@
+{
+  "id": "PMID:25533820-Li-2014-BBS4-4-year-old_female_patient",
+  "subject": {
+    "id": "4-year-old female patient",
+    "ageAtCollection": {
+      "age": "P4Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000648",
+      "label": "Optic atrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25533820",
+        "description": "A novel nonsense mutation in BBS4 gene identified in a Chinese family with Bardet-Biedl syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030329",
+      "label": "Retinal thinning"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25533820",
+        "description": "A novel nonsense mutation in BBS4 gene identified in a Chinese family with Bardet-Biedl syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000505",
+      "label": "Visual impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25533820",
+        "description": "A novel nonsense mutation in BBS4 gene identified in a Chinese family with Bardet-Biedl syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25533820",
+        "description": "A novel nonsense mutation in BBS4 gene identified in a Chinese family with Bardet-Biedl syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25533820",
+        "description": "A novel nonsense mutation in BBS4 gene identified in a Chinese family with Bardet-Biedl syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007843",
+      "label": "Attenuation of retinal blood vessels"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25533820",
+        "description": "A novel nonsense mutation in BBS4 gene identified in a Chinese family with Bardet-Biedl syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000510",
+      "label": "Rod-cone dystrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25533820",
+        "description": "A novel nonsense mutation in BBS4 gene identified in a Chinese family with Bardet-Biedl syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001956",
+      "label": "Truncal obesity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25533820",
+        "description": "A novel nonsense mutation in BBS4 gene identified in a Chinese family with Bardet-Biedl syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010442",
+      "label": "Polydactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25533820",
+        "description": "A novel nonsense mutation in BBS4 gene identified in a Chinese family with Bardet-Biedl syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007814",
+      "label": "Retinal pigment epithelial mottling"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25533820",
+        "description": "A novel nonsense mutation in BBS4 gene identified in a Chinese family with Bardet-Biedl syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:585",
+    "symbol": "BBS4"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "15",
+      "pos": 72987563,
+      "ref": "A",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:615982",
+      "label": "BARDET-BIEDL SYNDROME 4; BBS4"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:25533820",
+      "description": "A novel nonsense mutation in BBS4 gene identified in a Chinese family with Bardet-Biedl syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Li-2018-STXBP1-P1.json b/notebooks/LIRICAL/v1phenopackets/Li-2018-STXBP1-P1.json
new file mode 100644
index 000000000..19fa834f8
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Li-2018-STXBP1-P1.json
@@ -0,0 +1,176 @@
+{
+  "id": "PMID:29896790-Li-2018-STXBP1-P1",
+  "subject": {
+    "id": "P1",
+    "ageAtCollection": {
+      "age": "P2M15D"
+    },
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001276",
+      "label": "Hypertonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29896790",
+        "description": "De novo mutations of STXBP1 in Chinese children with early onset epileptic encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010851",
+      "label": "EEG with burst suppression"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29896790",
+        "description": "De novo mutations of STXBP1 in Chinese children with early onset epileptic encephalopathy"
+      }
+    }]
+  }, {
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+      "id": "HP:0002188",
+      "label": "Delayed CNS myelination"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29896790",
+        "description": "De novo mutations of STXBP1 in Chinese children with early onset epileptic encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Global developmental delay"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29896790",
+        "description": "De novo mutations of STXBP1 in Chinese children with early onset epileptic encephalopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011167",
+      "label": "Focal tonic seizures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29896790",
+        "description": "De novo mutations of STXBP1 in Chinese children with early onset epileptic encephalopathy"
+      }
+    }]
+  }, {
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+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29896790",
+        "description": "De novo mutations of STXBP1 in Chinese children with early onset epileptic encephalopathy"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:6812",
+    "symbol": "STXBP1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "9",
+      "pos": 130438126,
+      "ref": "AC",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:612164",
+      "label": "EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 4; EIEE4"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29896790",
+      "description": "De novo mutations of STXBP1 in Chinese children with early onset epileptic encephalopathy"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Liberalesso-2017-SALL1-VMFS.json b/notebooks/LIRICAL/v1phenopackets/Liberalesso-2017-SALL1-VMFS.json
new file mode 100644
index 000000000..5306547ff
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Liberalesso-2017-SALL1-VMFS.json
@@ -0,0 +1,435 @@
+{
+  "id": "PMID:29110636-Liberalesso-2017-SALL1-VMFS",
+  "subject": {
+    "id": "VMFS",
+    "ageAtCollection": {
+      "age": "P5Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001631",
+      "label": "Atrial septal defect"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:29110636",
+        "description": "Phenotypic and genotypic aspects of Townes-Brock syndrome: case report of patient in southern Brazil with a new SALL1 hotspot region nonsense mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29110636",
+        "description": "Phenotypic and genotypic aspects of Townes-Brock syndrome: case report of patient in southern Brazil with a new SALL1 hotspot region nonsense mutation"
+      }
+    }]
+  }, {
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+      "label": "Low anterior hairline"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
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+        "description": "Phenotypic and genotypic aspects of Townes-Brock syndrome: case report of patient in southern Brazil with a new SALL1 hotspot region nonsense mutation"
+      }
+    }]
+  }, {
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+      "label": "Renal insufficiency"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:29110636",
+        "description": "Phenotypic and genotypic aspects of Townes-Brock syndrome: case report of patient in southern Brazil with a new SALL1 hotspot region nonsense mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008551",
+      "label": "Microtia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29110636",
+        "description": "Phenotypic and genotypic aspects of Townes-Brock syndrome: case report of patient in southern Brazil with a new SALL1 hotspot region nonsense mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000076",
+      "label": "Vesicoureteral reflux"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29110636",
+        "description": "Phenotypic and genotypic aspects of Townes-Brock syndrome: case report of patient in southern Brazil with a new SALL1 hotspot region nonsense mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002353",
+      "label": "EEG abnormality"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29110636",
+        "description": "Phenotypic and genotypic aspects of Townes-Brock syndrome: case report of patient in southern Brazil with a new SALL1 hotspot region nonsense mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29110636",
+        "description": "Phenotypic and genotypic aspects of Townes-Brock syndrome: case report of patient in southern Brazil with a new SALL1 hotspot region nonsense mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000384",
+      "label": "Preauricular skin tag"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29110636",
+        "description": "Phenotypic and genotypic aspects of Townes-Brock syndrome: case report of patient in southern Brazil with a new SALL1 hotspot region nonsense mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009944",
+      "label": "Partial duplication of thumb phalanx"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29110636",
+        "description": "Phenotypic and genotypic aspects of Townes-Brock syndrome: case report of patient in southern Brazil with a new SALL1 hotspot region nonsense mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012443",
+      "label": "Abnormality of brain morphology"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29110636",
+        "description": "Phenotypic and genotypic aspects of Townes-Brock syndrome: case report of patient in southern Brazil with a new SALL1 hotspot region nonsense mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000047",
+      "label": "Hypospadias"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29110636",
+        "description": "Phenotypic and genotypic aspects of Townes-Brock syndrome: case report of patient in southern Brazil with a new SALL1 hotspot region nonsense mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000470",
+      "label": "Short neck"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29110636",
+        "description": "Phenotypic and genotypic aspects of Townes-Brock syndrome: case report of patient in southern Brazil with a new SALL1 hotspot region nonsense mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29110636",
+        "description": "Phenotypic and genotypic aspects of Townes-Brock syndrome: case report of patient in southern Brazil with a new SALL1 hotspot region nonsense mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000752",
+      "label": "Hyperactivity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29110636",
+        "description": "Phenotypic and genotypic aspects of Townes-Brock syndrome: case report of patient in southern Brazil with a new SALL1 hotspot region nonsense mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007018",
+      "label": "Attention deficit hyperactivity disorder"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29110636",
+        "description": "Phenotypic and genotypic aspects of Townes-Brock syndrome: case report of patient in southern Brazil with a new SALL1 hotspot region nonsense mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001845",
+      "label": "Overlapping toe"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29110636",
+        "description": "Phenotypic and genotypic aspects of Townes-Brock syndrome: case report of patient in southern Brazil with a new SALL1 hotspot region nonsense mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000369",
+      "label": "Low-set ears"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:29110636",
+        "description": "Phenotypic and genotypic aspects of Townes-Brock syndrome: case report of patient in southern Brazil with a new SALL1 hotspot region nonsense mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002023",
+      "label": "Anal atresia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29110636",
+        "description": "Phenotypic and genotypic aspects of Townes-Brock syndrome: case report of patient in southern Brazil with a new SALL1 hotspot region nonsense mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000527",
+      "label": "Long eyelashes"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:29110636",
+        "description": "Phenotypic and genotypic aspects of Townes-Brock syndrome: case report of patient in southern Brazil with a new SALL1 hotspot region nonsense mutation"
+      }
+    }]
+  }, {
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+      "id": "HP:0000286",
+      "label": "Epicanthus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "description": "Phenotypic and genotypic aspects of Townes-Brock syndrome: case report of patient in southern Brazil with a new SALL1 hotspot region nonsense mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000718",
+      "label": "Aggressive behavior"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "id": "PMID:29110636",
+        "description": "Phenotypic and genotypic aspects of Townes-Brock syndrome: case report of patient in southern Brazil with a new SALL1 hotspot region nonsense mutation"
+      }
+    }]
+  }, {
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+      "id": "HP:0100258",
+      "label": "Preaxial polydactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29110636",
+        "description": "Phenotypic and genotypic aspects of Townes-Brock syndrome: case report of patient in southern Brazil with a new SALL1 hotspot region nonsense mutation"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:6299",
+    "symbol": "SALL1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "16",
+      "pos": 51175309,
+      "ref": "A",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:107480",
+      "label": "TOWNES-BROCKS SYNDROME; TBS"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29110636",
+      "description": "Phenotypic and genotypic aspects of Townes-Brock syndrome: case report of patient in southern Brazil with a new SALL1 hotspot region nonsense mutation"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Ling-2019-NHS-III_1.json b/notebooks/LIRICAL/v1phenopackets/Ling-2019-NHS-III_1.json
new file mode 100644
index 000000000..dc0ed17fb
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Ling-2019-NHS-III_1.json
@@ -0,0 +1,223 @@
+{
+  "id": "PMID:30642278-Ling-2019-NHS-III:1",
+  "subject": {
+    "id": "III:1",
+    "ageAtCollection": {
+      "age": "15y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0040080",
+      "label": "Anteverted ears"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30642278",
+        "description": "Whole exome sequencing identified a novel truncation mutation in the NHS gene associated with Nance-Horan syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006346",
+      "label": "Screwdriver-shaped incisors"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30642278",
+        "description": "Whole exome sequencing identified a novel truncation mutation in the NHS gene associated with Nance-Horan syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011092",
+      "label": "Mulberry molar"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30642278",
+        "description": "Whole exome sequencing identified a novel truncation mutation in the NHS gene associated with Nance-Horan syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30642278",
+        "description": "Whole exome sequencing identified a novel truncation mutation in the NHS gene associated with Nance-Horan syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000689",
+      "label": "Dental malocclusion"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "description": "Whole exome sequencing identified a novel truncation mutation in the NHS gene associated with Nance-Horan syndrome"
+      }
+    }]
+  }, {
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+      "label": "Behavioral abnormality"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30642278",
+        "description": "Whole exome sequencing identified a novel truncation mutation in the NHS gene associated with Nance-Horan syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100018",
+      "label": "Nuclear cataract"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30642278",
+        "description": "Whole exome sequencing identified a novel truncation mutation in the NHS gene associated with Nance-Horan syndrome"
+      }
+    }]
+  }, {
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+      "label": "Narrow face"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:30642278",
+        "description": "Whole exome sequencing identified a novel truncation mutation in the NHS gene associated with Nance-Horan syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000448",
+      "label": "Prominent nose"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30642278",
+        "description": "Whole exome sequencing identified a novel truncation mutation in the NHS gene associated with Nance-Horan syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:4810",
+    "symbol": "NHS"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "X",
+      "pos": 17750140,
+      "ref": "C",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000134",
+      "label": "hemizygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:302350",
+      "label": "NANCE-HORAN SYNDROME; NHS"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30642278",
+      "description": "Whole exome sequencing identified a novel truncation mutation in the NHS gene associated with Nance-Horan syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Lopez-2018-EP300-11.json b/notebooks/LIRICAL/v1phenopackets/Lopez-2018-EP300-11.json
new file mode 100644
index 000000000..5304a570a
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Lopez-2018-EP300-11.json
@@ -0,0 +1,487 @@
+{
+  "id": "PMID:29506490-López-2018-EP300-11",
+  "subject": {
+    "id": "11",
+    "ageAtCollection": {
+      "age": "P18Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000574",
+      "label": "Thick eyebrow"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29506490",
+        "description": "Rubinstein-Taybi 2 associated to novel EP300 mutations: deepening the clinical and genetic spectrum"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000252",
+      "label": "Microcephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29506490",
+        "description": "Rubinstein-Taybi 2 associated to novel EP300 mutations: deepening the clinical and genetic spectrum"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002750",
+      "label": "Delayed skeletal maturation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29506490",
+        "description": "Rubinstein-Taybi 2 associated to novel EP300 mutations: deepening the clinical and genetic spectrum"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002342",
+      "label": "Intellectual disability, moderate"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29506490",
+        "description": "Rubinstein-Taybi 2 associated to novel EP300 mutations: deepening the clinical and genetic spectrum"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001007",
+      "label": "Hirsutism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29506490",
+        "description": "Rubinstein-Taybi 2 associated to novel EP300 mutations: deepening the clinical and genetic spectrum"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008872",
+      "label": "Feeding difficulties in infancy"
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+      "label": "RUBINSTEIN-TAYBI SYNDROME 2; RSTS2"
+    }
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+  "metaData": {
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+    "submittedBy": "HPO:probinson",
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+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
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+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
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+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
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+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
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+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
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+    "externalReferences": [{
+      "id": "PMID:29506490",
+      "description": "Rubinstein-Taybi 2 associated to novel EP300 mutations: deepening the clinical and genetic spectrum"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Lopez-2018-EP300-38.json b/notebooks/LIRICAL/v1phenopackets/Lopez-2018-EP300-38.json
new file mode 100644
index 000000000..91a5388c6
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Lopez-2018-EP300-38.json
@@ -0,0 +1,484 @@
+{
+  "id": "PMID:29506490-López-2018-EP300-38",
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+      "label": "Homo sapiens"
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+      "label": "Thick eyebrow"
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+    "type": {
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+      "label": "Hydrocele testis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29506490",
+        "description": "Rubinstein-Taybi 2 associated to novel EP300 mutations: deepening the clinical and genetic spectrum"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000733",
+      "label": "Stereotypy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29506490",
+        "description": "Rubinstein-Taybi 2 associated to novel EP300 mutations: deepening the clinical and genetic spectrum"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000189",
+      "label": "Narrow palate"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29506490",
+        "description": "Rubinstein-Taybi 2 associated to novel EP300 mutations: deepening the clinical and genetic spectrum"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000448",
+      "label": "Prominent nose"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29506490",
+        "description": "Rubinstein-Taybi 2 associated to novel EP300 mutations: deepening the clinical and genetic spectrum"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29506490",
+        "description": "Rubinstein-Taybi 2 associated to novel EP300 mutations: deepening the clinical and genetic spectrum"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2033",
+    "symbol": "EP300"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "22",
+      "pos": 41551019,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:613684",
+      "label": "RUBINSTEIN-TAYBI SYNDROME 2; RSTS2"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29506490",
+      "description": "Rubinstein-Taybi 2 associated to novel EP300 mutations: deepening the clinical and genetic spectrum"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Luco-2016-DYRK1A-Patient_2.json b/notebooks/LIRICAL/v1phenopackets/Luco-2016-DYRK1A-Patient_2.json
new file mode 100644
index 000000000..d0a2c77a1
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Luco-2016-DYRK1A-Patient_2.json
@@ -0,0 +1,371 @@
+{
+  "id": "PMID:26922654-Luco-2016-DYRK1A-Patient_2",
+  "subject": {
+    "id": "Patient 2",
+    "ageAtCollection": {
+      "age": "13Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26922654",
+        "description": "Case report of novel DYRK1A mutations in 2 individuals with syndromic intellectual disability and a review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012171",
+      "label": "Stereotypical hand wringing"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26922654",
+        "description": "Case report of novel DYRK1A mutations in 2 individuals with syndromic intellectual disability and a review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000269",
+      "label": "Prominent occiput"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26922654",
+        "description": "Case report of novel DYRK1A mutations in 2 individuals with syndromic intellectual disability and a review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000426",
+      "label": "Prominent nasal bridge"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26922654",
+        "description": "Case report of novel DYRK1A mutations in 2 individuals with syndromic intellectual disability and a review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001182",
+      "label": "Tapered finger"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26922654",
+        "description": "Case report of novel DYRK1A mutations in 2 individuals with syndromic intellectual disability and a review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000276",
+      "label": "Long face"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26922654",
+        "description": "Case report of novel DYRK1A mutations in 2 individuals with syndromic intellectual disability and a review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011968",
+      "label": "Feeding difficulties"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26922654",
+        "description": "Case report of novel DYRK1A mutations in 2 individuals with syndromic intellectual disability and a review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001251",
+      "label": "Ataxia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26922654",
+        "description": "Case report of novel DYRK1A mutations in 2 individuals with syndromic intellectual disability and a review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000341",
+      "label": "Narrow forehead"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26922654",
+        "description": "Case report of novel DYRK1A mutations in 2 individuals with syndromic intellectual disability and a review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010722",
+      "label": "Asymmetry of the ears"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26922654",
+        "description": "Case report of novel DYRK1A mutations in 2 individuals with syndromic intellectual disability and a review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000414",
+      "label": "Bulbous nose"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26922654",
+        "description": "Case report of novel DYRK1A mutations in 2 individuals with syndromic intellectual disability and a review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002373",
+      "label": "Febrile seizures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26922654",
+        "description": "Case report of novel DYRK1A mutations in 2 individuals with syndromic intellectual disability and a review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002069",
+      "label": "Generalized tonic-clonic seizures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26922654",
+        "description": "Case report of novel DYRK1A mutations in 2 individuals with syndromic intellectual disability and a review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000319",
+      "label": "Smooth philtrum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26922654",
+        "description": "Case report of novel DYRK1A mutations in 2 individuals with syndromic intellectual disability and a review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100703",
+      "label": "Tongue thrusting"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26922654",
+        "description": "Case report of novel DYRK1A mutations in 2 individuals with syndromic intellectual disability and a review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000687",
+      "label": "Widely spaced teeth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26922654",
+        "description": "Case report of novel DYRK1A mutations in 2 individuals with syndromic intellectual disability and a review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000490",
+      "label": "Deeply set eye"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26922654",
+        "description": "Case report of novel DYRK1A mutations in 2 individuals with syndromic intellectual disability and a review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000767",
+      "label": "Pectus excavatum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26922654",
+        "description": "Case report of novel DYRK1A mutations in 2 individuals with syndromic intellectual disability and a review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000252",
+      "label": "Microcephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26922654",
+        "description": "Case report of novel DYRK1A mutations in 2 individuals with syndromic intellectual disability and a review of the literature"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:1859",
+    "symbol": "DYRK1A"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "21",
+      "pos": 38862599,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:614104",
+      "label": "MENTAL RETARDATION, AUTOSOMAL DOMINANT 7; MRD7"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:26922654",
+      "description": "Case report of novel DYRK1A mutations in 2 individuals with syndromic intellectual disability and a review of the literature"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Luo-2016-COMP-II-1.json b/notebooks/LIRICAL/v1phenopackets/Luo-2016-COMP-II-1.json
new file mode 100644
index 000000000..fe23d517f
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Luo-2016-COMP-II-1.json
@@ -0,0 +1,221 @@
+{
+  "id": "PMID:27330822-Luo-2016-COMP-II-1",
+  "subject": {
+    "id": "II-1",
+    "ageAtCollection": {
+      "age": "3Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002515",
+      "label": "Waddling gait"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27330822",
+        "description": "A novel deleterious mutation in the COMP gene that causes pseudoachondroplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0200055",
+      "label": "Small hand"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27330822",
+        "description": "A novel deleterious mutation in the COMP gene that causes pseudoachondroplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004568",
+      "label": "Beaking of vertebral bodies"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27330822",
+        "description": "A novel deleterious mutation in the COMP gene that causes pseudoachondroplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009381",
+      "label": "Short finger"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27330822",
+        "description": "A novel deleterious mutation in the COMP gene that causes pseudoachondroplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008802",
+      "label": "Hypoplasia of the femoral head"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27330822",
+        "description": "A novel deleterious mutation in the COMP gene that causes pseudoachondroplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003183",
+      "label": "Wide pubic symphysis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27330822",
+        "description": "A novel deleterious mutation in the COMP gene that causes pseudoachondroplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009826",
+      "label": "Limb undergrowth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27330822",
+        "description": "A novel deleterious mutation in the COMP gene that causes pseudoachondroplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003015",
+      "label": "Flared metaphysis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27330822",
+        "description": "A novel deleterious mutation in the COMP gene that causes pseudoachondroplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000926",
+      "label": "Platyspondyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27330822",
+        "description": "A novel deleterious mutation in the COMP gene that causes pseudoachondroplasia"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:1311",
+    "symbol": "COMP"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "19",
+      "pos": 18897434,
+      "ref": "GGCA",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:177170",
+      "label": "PSEUDOACHONDROPLASIA; PSACH"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27330822",
+      "description": "A novel deleterious mutation in the COMP gene that causes pseudoachondroplasia"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Lv-2016-TMEM38B-family2-patient2.json b/notebooks/LIRICAL/v1phenopackets/Lv-2016-TMEM38B-family2-patient2.json
new file mode 100644
index 000000000..1b33a42dc
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Lv-2016-TMEM38B-family2-patient2.json
@@ -0,0 +1,224 @@
+{
+  "id": "PMID:26911354-Lv-2016-TMEM38B-family2-patient2",
+  "subject": {
+    "id": "family2-patient2",
+    "ageAtCollection": {
+      "age": "P8Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002753",
+      "label": "Thin bony cortex"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26911354",
+        "description": "Two novel mutations in TMEM38B result in rare autosomal recessive osteogenesis imperfecta"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031846",
+      "label": "Femur fracture"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26911354",
+        "description": "Two novel mutations in TMEM38B result in rare autosomal recessive osteogenesis imperfecta"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002953",
+      "label": "Vertebral compression fractures"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26911354",
+        "description": "Two novel mutations in TMEM38B result in rare autosomal recessive osteogenesis imperfecta"
+      }
+    }]
+  }, {
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+      "id": "HP:0031425",
+      "label": "Increased circulating beta-C-terminal telopeptide level"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26911354",
+        "description": "Two novel mutations in TMEM38B result in rare autosomal recessive osteogenesis imperfecta"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003100",
+      "label": "Slender long bone"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:26911354",
+        "description": "Two novel mutations in TMEM38B result in rare autosomal recessive osteogenesis imperfecta"
+      }
+    }]
+  }, {
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+      "label": "Elevated alkaline phosphatase"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26911354",
+        "description": "Two novel mutations in TMEM38B result in rare autosomal recessive osteogenesis imperfecta"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002757",
+      "label": "Recurrent fractures"
+    },
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:26911354",
+        "description": "Two novel mutations in TMEM38B result in rare autosomal recessive osteogenesis imperfecta"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0040160",
+      "label": "Generalized osteoporosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26911354",
+        "description": "Two novel mutations in TMEM38B result in rare autosomal recessive osteogenesis imperfecta"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002645",
+      "label": "Wormian bones"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26911354",
+        "description": "Two novel mutations in TMEM38B result in rare autosomal recessive osteogenesis imperfecta"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:55151",
+    "symbol": "TMEM38B"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "9",
+      "pos": 108484867,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:615066",
+      "label": "OSTEOGENESIS IMPERFECTA, TYPE XIV; OI14"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:26911354",
+      "description": "Two novel mutations in TMEM38B result in rare autosomal recessive osteogenesis imperfecta"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Ma-2018-SPTA1-proband.json b/notebooks/LIRICAL/v1phenopackets/Ma-2018-SPTA1-proband.json
new file mode 100644
index 000000000..e88acbeb9
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Ma-2018-SPTA1-proband.json
@@ -0,0 +1,252 @@
+{
+  "id": "PMID:29484404-Ma-2018-SPTA1-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P3Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0004445",
+      "label": "Elliptocytosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29484404",
+        "description": "Novel compound heterozygous SPTA1 mutations in a patient with hereditary elliptocytosis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005560",
+      "label": "Imbalanced hemoglobin synthesis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29484404",
+        "description": "Novel compound heterozygous SPTA1 mutations in a patient with hereditary elliptocytosis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004844",
+      "label": "Coombs-positive hemolytic anemia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:29484404",
+        "description": "Novel compound heterozygous SPTA1 mutations in a patient with hereditary elliptocytosis"
+      }
+    }]
+  }, {
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+      "label": "Abnormal glucose-6-phosphate dehydrogenase level in blood"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29484404",
+        "description": "Novel compound heterozygous SPTA1 mutations in a patient with hereditary elliptocytosis"
+      }
+    }]
+  }, {
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+      "id": "HP:0000952",
+      "label": "Jaundice"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:29484404",
+        "description": "Novel compound heterozygous SPTA1 mutations in a patient with hereditary elliptocytosis"
+      }
+    }]
+  }, {
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+      "label": "Reticulocytosis"
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+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:29484404",
+        "description": "Novel compound heterozygous SPTA1 mutations in a patient with hereditary elliptocytosis"
+      }
+    }]
+  }, {
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+      "id": "HP:0001903",
+      "label": "Anemia"
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+    "evidence": [{
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+        "id": "ECO:0000033",
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+        "id": "PMID:29484404",
+        "description": "Novel compound heterozygous SPTA1 mutations in a patient with hereditary elliptocytosis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002240",
+      "label": "Hepatomegaly"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:29484404",
+        "description": "Novel compound heterozygous SPTA1 mutations in a patient with hereditary elliptocytosis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001744",
+      "label": "Splenomegaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29484404",
+        "description": "Novel compound heterozygous SPTA1 mutations in a patient with hereditary elliptocytosis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0032106",
+      "label": "Conjunctival icterus"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:29484404",
+        "description": "Novel compound heterozygous SPTA1 mutations in a patient with hereditary elliptocytosis"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:6708",
+    "symbol": "SPTA1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 158655001,
+      "ref": "T",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 158597507,
+      "ref": "G",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:130600",
+      "label": "ELLIPTOCYTOSIS 2; EL2"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29484404",
+      "description": "Novel compound heterozygous SPTA1 mutations in a patient with hereditary elliptocytosis"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Mackenroth-2016-ADAMTSL2-patient.json b/notebooks/LIRICAL/v1phenopackets/Mackenroth-2016-ADAMTSL2-patient.json
new file mode 100644
index 000000000..dba3bf43b
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Mackenroth-2016-ADAMTSL2-patient.json
@@ -0,0 +1,340 @@
+{
+  "id": "PMID:27057656-Mackenroth-2016-ADAMTSL2-patient",
+  "subject": {
+    "id": "patient",
+    "ageAtCollection": {
+      "age": "P1Y3M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002750",
+      "label": "Delayed skeletal maturation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27057656",
+        "description": "Novel ADAMTSL2-mutations in a patient with geleophysic dysplasia type I"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27057656",
+        "description": "Novel ADAMTSL2-mutations in a patient with geleophysic dysplasia type I"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000233",
+      "label": "Thin vermilion border"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27057656",
+        "description": "Novel ADAMTSL2-mutations in a patient with geleophysic dysplasia type I"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003097",
+      "label": "Short femur"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27057656",
+        "description": "Novel ADAMTSL2-mutations in a patient with geleophysic dysplasia type I"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001156",
+      "label": "Brachydactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27057656",
+        "description": "Novel ADAMTSL2-mutations in a patient with geleophysic dysplasia type I"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27057656",
+        "description": "Novel ADAMTSL2-mutations in a patient with geleophysic dysplasia type I"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010049",
+      "label": "Short metacarpal"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27057656",
+        "description": "Novel ADAMTSL2-mutations in a patient with geleophysic dysplasia type I"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003022",
+      "label": "Hypoplasia of the ulna"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27057656",
+        "description": "Novel ADAMTSL2-mutations in a patient with geleophysic dysplasia type I"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001488",
+      "label": "Bilateral ptosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27057656",
+        "description": "Novel ADAMTSL2-mutations in a patient with geleophysic dysplasia type I"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003066",
+      "label": "Limited knee extension"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27057656",
+        "description": "Novel ADAMTSL2-mutations in a patient with geleophysic dysplasia type I"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000240",
+      "label": "Abnormality of skull size"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27057656",
+        "description": "Novel ADAMTSL2-mutations in a patient with geleophysic dysplasia type I"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009803",
+      "label": "Short phalanx of finger"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27057656",
+        "description": "Novel ADAMTSL2-mutations in a patient with geleophysic dysplasia type I"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001561",
+      "label": "Polyhydramnios"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27057656",
+        "description": "Novel ADAMTSL2-mutations in a patient with geleophysic dysplasia type I"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002205",
+      "label": "Recurrent respiratory infections"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27057656",
+        "description": "Novel ADAMTSL2-mutations in a patient with geleophysic dysplasia type I"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001377",
+      "label": "Limited elbow extension"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27057656",
+        "description": "Novel ADAMTSL2-mutations in a patient with geleophysic dysplasia type I"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000343",
+      "label": "Long philtrum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27057656",
+        "description": "Novel ADAMTSL2-mutations in a patient with geleophysic dysplasia type I"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:9719",
+    "symbol": "ADAMTSL2"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "9",
+      "pos": 136435570,
+      "ref": "G",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "9",
+      "pos": 136412195,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:231050",
+      "label": "GELEOPHYSIC DYSPLASIA 1; GPHYSD1"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27057656",
+      "description": "Novel ADAMTSL2-mutations in a patient with geleophysic dysplasia type I"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Magerus-Chatinet-2013-FASLG-patient.json b/notebooks/LIRICAL/v1phenopackets/Magerus-Chatinet-2013-FASLG-patient.json
new file mode 100644
index 000000000..c3e1adfbb
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Magerus-Chatinet-2013-FASLG-patient.json
@@ -0,0 +1,297 @@
+{
+  "id": "PMID:22857792-Magerus-Chatinet-2013-FASLG-patient",
+  "subject": {
+    "id": "patient",
+    "ageAtCollection": {
+      "age": "P11M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0012311",
+      "label": "Monocytosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:22857792",
+        "description": "Autoimmune lymphoproliferative syndrome caused by a homozygous null FAS ligand (FASLG) mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003496",
+      "label": "Increased circulating IgM level"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:22857792",
+        "description": "Autoimmune lymphoproliferative syndrome caused by a homozygous null FAS ligand (FASLG) mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001433",
+      "label": "Hepatosplenomegaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:22857792",
+        "description": "Autoimmune lymphoproliferative syndrome caused by a homozygous null FAS ligand (FASLG) mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002851",
+      "label": "Elevated proportion of CD4-negative, CD8-negative, alpha-beta regulatory T cells"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:22857792",
+        "description": "Autoimmune lymphoproliferative syndrome caused by a homozygous null FAS ligand (FASLG) mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003270",
+      "label": "Abdominal distention"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+      "reference": {
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+        "description": "Autoimmune lymphoproliferative syndrome caused by a homozygous null FAS ligand (FASLG) mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001945",
+      "label": "Fever"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:22857792",
+        "description": "Autoimmune lymphoproliferative syndrome caused by a homozygous null FAS ligand (FASLG) mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001903",
+      "label": "Anemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:22857792",
+        "description": "Autoimmune lymphoproliferative syndrome caused by a homozygous null FAS ligand (FASLG) mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011897",
+      "label": "Neutrophilia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
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+        "description": "Autoimmune lymphoproliferative syndrome caused by a homozygous null FAS ligand (FASLG) mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003237",
+      "label": "Increased circulating IgG level"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:22857792",
+        "description": "Autoimmune lymphoproliferative syndrome caused by a homozygous null FAS ligand (FASLG) mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100827",
+      "label": "Lymphocytosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:22857792",
+        "description": "Autoimmune lymphoproliferative syndrome caused by a homozygous null FAS ligand (FASLG) mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003261",
+      "label": "Increased circulating IgA level"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:22857792",
+        "description": "Autoimmune lymphoproliferative syndrome caused by a homozygous null FAS ligand (FASLG) mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002113",
+      "label": "Pulmonary infiltrates"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:22857792",
+        "description": "Autoimmune lymphoproliferative syndrome caused by a homozygous null FAS ligand (FASLG) mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002788",
+      "label": "Recurrent upper respiratory tract infections"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:22857792",
+        "description": "Autoimmune lymphoproliferative syndrome caused by a homozygous null FAS ligand (FASLG) mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002716",
+      "label": "Lymphadenopathy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:22857792",
+        "description": "Autoimmune lymphoproliferative syndrome caused by a homozygous null FAS ligand (FASLG) mutation"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:356",
+    "symbol": "FASLG"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 172628599,
+      "ref": "GT",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:601859",
+      "label": "AUTOIMMUNE LYMPHOPROLIFERATIVE SYNDROME; ALPS"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:22857792",
+      "description": "Autoimmune lymphoproliferative syndrome caused by a homozygous null FAS ligand (FASLG) mutation"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Maghami-2018-FKBP10-proband.json b/notebooks/LIRICAL/v1phenopackets/Maghami-2018-FKBP10-proband.json
new file mode 100644
index 000000000..f1fad1058
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Maghami-2018-FKBP10-proband.json
@@ -0,0 +1,228 @@
+{
+  "id": "PMID:29801479-Maghami-2018-FKBP10-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P8Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0003155",
+      "label": "Elevated alkaline phosphatase"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29801479",
+        "description": "Splicing defect in FKBP10 gene causes autosomal recessive osteogenesis imperfecta disease: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001433",
+      "label": "Hepatosplenomegaly"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29801479",
+        "description": "Splicing defect in FKBP10 gene causes autosomal recessive osteogenesis imperfecta disease: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001371",
+      "label": "Flexion contracture"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29801479",
+        "description": "Splicing defect in FKBP10 gene causes autosomal recessive osteogenesis imperfecta disease: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003116",
+      "label": "Abnormal echocardiogram"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29801479",
+        "description": "Splicing defect in FKBP10 gene causes autosomal recessive osteogenesis imperfecta disease: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004349",
+      "label": "Reduced bone mineral density"
+    },
+    "evidence": [{
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+      },
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+        "id": "PMID:29801479",
+        "description": "Splicing defect in FKBP10 gene causes autosomal recessive osteogenesis imperfecta disease: a case report"
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+    }]
+  }, {
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+      "label": "Blue sclerae"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:29801479",
+        "description": "Splicing defect in FKBP10 gene causes autosomal recessive osteogenesis imperfecta disease: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29801479",
+        "description": "Splicing defect in FKBP10 gene causes autosomal recessive osteogenesis imperfecta disease: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002757",
+      "label": "Recurrent fractures"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:29801479",
+        "description": "Splicing defect in FKBP10 gene causes autosomal recessive osteogenesis imperfecta disease: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000365",
+      "label": "Hearing impairment"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:29801479",
+        "description": "Splicing defect in FKBP10 gene causes autosomal recessive osteogenesis imperfecta disease: a case report"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:60681",
+    "symbol": "FKBP10"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "17",
+      "pos": 39977197,
+      "ref": "A",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:610968",
+      "label": "OSTEOGENESIS IMPERFECTA, TYPE XI; OI11"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
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+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29801479",
+      "description": "Splicing defect in FKBP10 gene causes autosomal recessive osteogenesis imperfecta disease: a case report"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Mattioli-2017-BRPF1-Individual_11_Family_F.json b/notebooks/LIRICAL/v1phenopackets/Mattioli-2017-BRPF1-Individual_11_Family_F.json
new file mode 100644
index 000000000..886cfb68d
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Mattioli-2017-BRPF1-Individual_11_Family_F.json
@@ -0,0 +1,253 @@
+{
+  "id": "PMID:27939639-Mattioli-2017-BRPF1-Individual_11/Family_F",
+  "subject": {
+    "id": "Individual 11/Family F",
+    "ageAtCollection": {
+      "age": "12"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0010631",
+      "label": "Abnormality of the epiphyses of the feet"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27939639",
+        "description": "Mutations in Histone Acetylase Modifier BRPF1 Cause an Autosomal-Dominant Form of Intellectual Disability with Associated Ptosis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000545",
+      "label": "Myopia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27939639",
+        "description": "Mutations in Histone Acetylase Modifier BRPF1 Cause an Autosomal-Dominant Form of Intellectual Disability with Associated Ptosis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005617",
+      "label": "Bilateral camptodactyly"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
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+        "id": "PMID:27939639",
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+    }]
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+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
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+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27939639",
+        "description": "Mutations in Histone Acetylase Modifier BRPF1 Cause an Autosomal-Dominant Form of Intellectual Disability with Associated Ptosis"
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+    }]
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+      "id": "HP:0000252",
+      "label": "Microcephaly"
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+        "id": "PMID:27939639",
+        "description": "Mutations in Histone Acetylase Modifier BRPF1 Cause an Autosomal-Dominant Form of Intellectual Disability with Associated Ptosis"
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+      "label": "Autism"
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+      "label": "Hyperactivity"
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+  }, {
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+      "id": "HP:0004322",
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+      "label": "Delayed ability to walk"
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+        "description": "Mutations in Histone Acetylase Modifier BRPF1 Cause an Autosomal-Dominant Form of Intellectual Disability with Associated Ptosis"
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+      "id": "HP:0000508",
+      "label": "Ptosis"
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+        "description": "Mutations in Histone Acetylase Modifier BRPF1 Cause an Autosomal-Dominant Form of Intellectual Disability with Associated Ptosis"
+      }
+    }]
+  }],
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+    "id": "NCBIGene:7862",
+    "symbol": "BRPF1"
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+      "id": "GENO:0000135",
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+  }],
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+    "term": {
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+      "label": "Intellectual developmental disorder with dysmorphic facies and ptosis"
+    }
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+  "metaData": {
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+    "submittedBy": "HPO:probinson",
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+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "name": "Phenotype And Trait Ontology",
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+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27939639",
+      "description": "Mutations in Histone Acetylase Modifier BRPF1 Cause an Autosomal-Dominant Form of Intellectual Disability with Associated Ptosis"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Mazzucchelli-2011-LAMA3-Proband.json b/notebooks/LIRICAL/v1phenopackets/Mazzucchelli-2011-LAMA3-Proband.json
new file mode 100644
index 000000000..5e662fbe1
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Mazzucchelli-2011-LAMA3-Proband.json
@@ -0,0 +1,117 @@
+{
+  "id": "PMID:20881434-Mazzucchelli-2011-LAMA3-Proband",
+  "subject": {
+    "id": "Proband",
+    "ageAtCollection": {
+      "age": "8M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0031538",
+      "label": "Abnormal dermoepidermal junction morphology"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20881434",
+        "description": "A novel LAMA3 mutation in a newborn with junctional epidermolysis bullosa herlitz type"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008066",
+      "label": "Abnormal blistering of the skin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20881434",
+        "description": "A novel LAMA3 mutation in a newborn with junctional epidermolysis bullosa herlitz type"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:3909",
+    "symbol": "LAMA3"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "18",
+      "pos": 21487603,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:226700",
+      "label": "EPIDERMOLYSIS BULLOSA, JUNCTIONAL, HERLITZ TYPE"
+    }
+  }],
+  "metaData": {
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+    "submittedBy": "HPO:probinson",
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+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:20881434",
+      "description": "A novel LAMA3 mutation in a newborn with junctional epidermolysis bullosa herlitz type"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Mei-2015-NIPBL-Patient_1.json b/notebooks/LIRICAL/v1phenopackets/Mei-2015-NIPBL-Patient_1.json
new file mode 100644
index 000000000..0ab89905a
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Mei-2015-NIPBL-Patient_1.json
@@ -0,0 +1,297 @@
+{
+  "id": "PMID:25447906-Mei-2015-NIPBL-Patient_1",
+  "subject": {
+    "id": "Patient 1",
+    "ageAtCollection": {
+      "age": "P7Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000175",
+      "label": "Cleft palate"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25447906",
+        "description": "Two novel NIPBL gene mutations in Chinese patients with Cornelia de Lange syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25447906",
+        "description": "Two novel NIPBL gene mutations in Chinese patients with Cornelia de Lange syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000219",
+      "label": "Thin upper lip vermilion"
+    },
+    "evidence": [{
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+  }, {
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+      }
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+  }, {
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+      }
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+      }
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+  }, {
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+    "evidence": [{
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+        "description": "Two novel NIPBL gene mutations in Chinese patients with Cornelia de Lange syndrome"
+      }
+    }]
+  }, {
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+      "id": "HP:0000252",
+      "label": "Microcephaly"
+    },
+    "evidence": [{
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+        "description": "Two novel NIPBL gene mutations in Chinese patients with Cornelia de Lange syndrome"
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+  }, {
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+      "id": "HP:0005280",
+      "label": "Depressed nasal bridge"
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+    "evidence": [{
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+        "id": "ECO:0000033",
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+      "reference": {
+        "id": "PMID:25447906",
+        "description": "Two novel NIPBL gene mutations in Chinese patients with Cornelia de Lange syndrome"
+      }
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+  }, {
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+      "label": "Long philtrum"
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+    "evidence": [{
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+  }, {
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+      }
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+  }, {
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+    }]
+  }, {
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+      "label": "Curly eyelashes"
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+        "description": "Two novel NIPBL gene mutations in Chinese patients with Cornelia de Lange syndrome"
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+  }, {
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+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:25447906",
+        "description": "Two novel NIPBL gene mutations in Chinese patients with Cornelia de Lange syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:25836",
+    "symbol": "NIPBL"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "5",
+      "pos": 36985760,
+      "ref": "CA",
+      "alt": "C"
+    },
+    "zygosity": {
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+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:122470",
+      "label": "CORNELIA DE LANGE SYNDROME 1; CDLS1"
+    }
+  }],
+  "metaData": {
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+    "submittedBy": "HPO:probinson",
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+      "id": "hp",
+      "name": "human phenotype ontology",
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+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:25447906",
+      "description": "Two novel NIPBL gene mutations in Chinese patients with Cornelia de Lange syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Mei-2015-NIPBL-Patient_2.json b/notebooks/LIRICAL/v1phenopackets/Mei-2015-NIPBL-Patient_2.json
new file mode 100644
index 000000000..10d405eee
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Mei-2015-NIPBL-Patient_2.json
@@ -0,0 +1,237 @@
+{
+  "id": "PMID:25447906-Mei-2015-NIPBL-Patient_2",
+  "subject": {
+    "id": "Patient 2",
+    "ageAtCollection": {
+      "age": "P6Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25447906",
+        "description": "Two novel NIPBL gene mutations in Chinese patients with Cornelia de Lange syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000219",
+      "label": "Thin upper lip vermilion"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25447906",
+        "description": "Two novel NIPBL gene mutations in Chinese patients with Cornelia de Lange syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000252",
+      "label": "Microcephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25447906",
+        "description": "Two novel NIPBL gene mutations in Chinese patients with Cornelia de Lange syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005280",
+      "label": "Depressed nasal bridge"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25447906",
+        "description": "Two novel NIPBL gene mutations in Chinese patients with Cornelia de Lange syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008897",
+      "label": "Postnatal growth retardation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "description": "Two novel NIPBL gene mutations in Chinese patients with Cornelia de Lange syndrome"
+      }
+    }]
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+      "label": "Low anterior hairline"
+    },
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+        "id": "PMID:25447906",
+        "description": "Two novel NIPBL gene mutations in Chinese patients with Cornelia de Lange syndrome"
+      }
+    }]
+  }, {
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+      "id": "HP:0002342",
+      "label": "Intellectual disability, moderate"
+    },
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:25447906",
+        "description": "Two novel NIPBL gene mutations in Chinese patients with Cornelia de Lange syndrome"
+      }
+    }]
+  }, {
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+      "id": "HP:0000664",
+      "label": "Synophrys"
+    },
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25447906",
+        "description": "Two novel NIPBL gene mutations in Chinese patients with Cornelia de Lange syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007665",
+      "label": "Curly eyelashes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25447906",
+        "description": "Two novel NIPBL gene mutations in Chinese patients with Cornelia de Lange syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:25836",
+    "symbol": "NIPBL"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "5",
+      "pos": 37044760,
+      "ref": "G",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:122470",
+      "label": "CORNELIA DE LANGE SYNDROME 1; CDLS1"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:25447906",
+      "description": "Two novel NIPBL gene mutations in Chinese patients with Cornelia de Lange syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Metodiev-2016-TRMT10C-Subject_1.json b/notebooks/LIRICAL/v1phenopackets/Metodiev-2016-TRMT10C-Subject_1.json
new file mode 100644
index 000000000..ca9f19049
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Metodiev-2016-TRMT10C-Subject_1.json
@@ -0,0 +1,370 @@
+{
+  "id": "PMID:27132592-Metodiev-2016-TRMT10C-Subject_1",
+  "subject": {
+    "id": "Subject 1",
+    "ageAtCollection": {
+      "age": "P5M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002151",
+      "label": "Increased serum lactate"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011950",
+      "label": "Bronchiolitis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003348",
+      "label": "Hyperalaninemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008872",
+      "label": "Feeding difficulties in infancy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003688",
+      "label": "Cytochrome C oxidase-negative muscle fibers"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0045045",
+      "label": "Elevated plasma acylcarnitine levels"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001531",
+      "label": "Failure to thrive in infancy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001319",
+      "label": "Neonatal hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001324",
+      "label": "Muscle weakness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003198",
+      "label": "Myopathy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000407",
+      "label": "Sensorineural hearing impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003324",
+      "label": "Generalized muscle weakness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001363",
+      "label": "Craniosynostosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003200",
+      "label": "Ragged-red muscle fibers"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002910",
+      "label": "Elevated hepatic transaminase"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002490",
+      "label": "Increased CSF lactate"
+    },
+    "evidence": [{
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+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002020",
+      "label": "Gastroesophageal reflux"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002098",
+      "label": "Respiratory distress"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:54931",
+    "symbol": "TRMT10C"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "3",
+      "pos": 101284167,
+      "ref": "G",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "3",
+      "pos": 101284439,
+      "ref": "A",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616974",
+      "label": "Combined oxidative phosphorylation deficiency 30"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27132592",
+      "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Metodiev-2016-TRMT10C-Subject_2.json b/notebooks/LIRICAL/v1phenopackets/Metodiev-2016-TRMT10C-Subject_2.json
new file mode 100644
index 000000000..314278e6a
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Metodiev-2016-TRMT10C-Subject_2.json
@@ -0,0 +1,312 @@
+{
+  "id": "PMID:27132592-Metodiev-2016-TRMT10C-Subject_2",
+  "subject": {
+    "id": "Subject 2",
+    "ageAtCollection": {
+      "age": "P5Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002151",
+      "label": "Increased serum lactate"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002126",
+      "label": "Polymicrogyria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001941",
+      "label": "Acidosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008872",
+      "label": "Feeding difficulties in infancy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002033",
+      "label": "Poor suck"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001531",
+      "label": "Failure to thrive in infancy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000365",
+      "label": "Hearing impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001319",
+      "label": "Neonatal hypotonia"
+    },
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+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
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+      "id": "HP:0040288",
+      "label": "Nasogastric tube feeding"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001712",
+      "label": "Left ventricular hypertrophy"
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+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002910",
+      "label": "Elevated hepatic transaminase"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+      },
+      "reference": {
+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
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+      "id": "HP:0002490",
+      "label": "Increased CSF lactate"
+    },
+    "evidence": [{
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+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002098",
+      "label": "Respiratory distress"
+    },
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Lactic acidosis"
+    },
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+        "id": "ECO:0000033",
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+      },
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+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001410",
+      "label": "Decreased liver function"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27132592",
+        "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:54931",
+    "symbol": "TRMT10C"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "3",
+      "pos": 101284167,
+      "ref": "G",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616974",
+      "label": "Combined oxidative phosphorylation deficiency 30"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27132592",
+      "description": "Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Miao-2018-CLCN1-man.json b/notebooks/LIRICAL/v1phenopackets/Miao-2018-CLCN1-man.json
new file mode 100644
index 000000000..f1c559c6c
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Miao-2018-CLCN1-man.json
@@ -0,0 +1,194 @@
+{
+  "id": "PMID:30243293-Miao-2018-CLCN1-man",
+  "subject": {
+    "id": "man",
+    "ageAtCollection": {
+      "age": "P21Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0003688",
+      "label": "Cytochrome C oxidase-negative muscle fibers"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30243293",
+        "description": "A case report: autosomal recessive Myotonia congenita caused by a novel splice mutation (c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003720",
+      "label": "Generalized muscle hypertrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30243293",
+        "description": "A case report: autosomal recessive Myotonia congenita caused by a novel splice mutation (c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002486",
+      "label": "Myotonia"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "description": "A case report: autosomal recessive Myotonia congenita caused by a novel splice mutation (c"
+      }
+    }]
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+      "label": "Muscle weakness"
+    },
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+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:30243293",
+        "description": "A case report: autosomal recessive Myotonia congenita caused by a novel splice mutation (c"
+      }
+    }]
+  }, {
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+      "id": "HP:0003236",
+      "label": "Elevated serum creatine kinase"
+    },
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+      "label": "Hyporeflexia"
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+        "id": "PMID:30243293",
+        "description": "A case report: autosomal recessive Myotonia congenita caused by a novel splice mutation (c"
+      }
+    }]
+  }, {
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+      "id": "HP:0003552",
+      "label": "Muscle stiffness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:30243293",
+        "description": "A case report: autosomal recessive Myotonia congenita caused by a novel splice mutation (c"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:1180",
+    "symbol": "CLCN1"
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+    "vcfAllele": {
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+      "chr": "7",
+      "pos": 143029967,
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+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:160800",
+      "label": "MYOTONIA CONGENITA, AUTOSOMAL DOMINANT"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13",
+    "submittedBy": "HP:probinson",
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+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30243293",
+      "description": "A case report: autosomal recessive Myotonia congenita caused by a novel splice mutation (c"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Micaglio-2019-SCN5A-proband.json b/notebooks/LIRICAL/v1phenopackets/Micaglio-2019-SCN5A-proband.json
new file mode 100644
index 000000000..91fbb7df2
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Micaglio-2019-SCN5A-proband.json
@@ -0,0 +1,132 @@
+{
+  "id": "PMID:31590245-Micaglio-2019-SCN5A-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P30Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001279",
+      "label": "Syncope"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31590245",
+        "description": "Novel SCN5A p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012251",
+      "label": "ST segment elevation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31590245",
+        "description": "Novel SCN5A p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001962",
+      "label": "Palpitations"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31590245",
+        "description": "Novel SCN5A p"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:6331",
+    "symbol": "SCN5A"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "3",
+      "pos": 38639391,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:601144",
+      "label": "BRUGADA SYNDROME 1; BRGDA1"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:31590245",
+      "description": "Novel SCN5A p"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Michalska-2018-GTF2H5-male_infant.json b/notebooks/LIRICAL/v1phenopackets/Michalska-2018-GTF2H5-male_infant.json
new file mode 100644
index 000000000..cefa449e1
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Michalska-2018-GTF2H5-male_infant.json
@@ -0,0 +1,504 @@
+{
+  "id": "PMID:30359777-Michalska-2018-GTF2H5-male_infant",
+  "subject": {
+    "id": "male infant",
+    "ageAtCollection": {
+      "age": "P6M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001788",
+      "label": "Premature rupture of membranes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30359777",
+        "description": "A case of severe trichothiodystrophy 3 in a neonate due to mutation in the GTF2H5 gene: Clinical report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000656",
+      "label": "Ectropion"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30359777",
+        "description": "A case of severe trichothiodystrophy 3 in a neonate due to mutation in the GTF2H5 gene: Clinical report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001763",
+      "label": "Pes planus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30359777",
+        "description": "A case of severe trichothiodystrophy 3 in a neonate due to mutation in the GTF2H5 gene: Clinical report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000695",
+      "label": "Natal tooth"
+    },
+    "evidence": [{
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+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Mokbel-2013-TPM2-1A.json b/notebooks/LIRICAL/v1phenopackets/Mokbel-2013-TPM2-1A.json
new file mode 100644
index 000000000..c3e8d76cd
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Mokbel-2013-TPM2-1A.json
@@ -0,0 +1,162 @@
+{
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+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Montgomery-2015-AMN-III_1.json b/notebooks/LIRICAL/v1phenopackets/Montgomery-2015-AMN-III_1.json
new file mode 100644
index 000000000..83ef51f0f
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Montgomery-2015-AMN-III_1.json
@@ -0,0 +1,143 @@
+{
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+      "label": "Anemia"
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+      }
+    }]
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+        "description": "Novel compound heterozygous mutations in AMN cause Imerslund-Gräsbeck syndrome in two half-sisters: a case report"
+      }
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+      "label": "Vitamin B12 deficiency"
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+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "14",
+      "pos": 103390315,
+      "ref": "T",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:261100",
+      "label": "MEGALOBLASTIC ANEMIA 1"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:26040326",
+      "description": "Novel compound heterozygous mutations in AMN cause Imerslund-Gräsbeck syndrome in two half-sisters: a case report"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Moosa-1799-MTOR-index.json b/notebooks/LIRICAL/v1phenopackets/Moosa-1799-MTOR-index.json
new file mode 100644
index 000000000..f7c5a489c
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Moosa-1799-MTOR-index.json
@@ -0,0 +1,222 @@
+{
+  "id": "PMID:27753196-Moosa-1799-MTOR-index",
+  "subject": {
+    "id": "index",
+    "ageAtCollection": {
+      "age": "P7Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002573",
+      "label": "Hematochezia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27753196",
+        "description": "Smith-Kingsmore syndrome: A third family with the MTOR mutation c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011220",
+      "label": "Prominent forehead"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27753196",
+        "description": "Smith-Kingsmore syndrome: A third family with the MTOR mutation c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009882",
+      "label": "Short distal phalanx of finger"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27753196",
+        "description": "Smith-Kingsmore syndrome: A third family with the MTOR mutation c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002119",
+      "label": "Ventriculomegaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27753196",
+        "description": "Smith-Kingsmore syndrome: A third family with the MTOR mutation c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000774",
+      "label": "Narrow chest"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27753196",
+        "description": "Smith-Kingsmore syndrome: A third family with the MTOR mutation c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030255",
+      "label": "Large intestinal polyposis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27753196",
+        "description": "Smith-Kingsmore syndrome: A third family with the MTOR mutation c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001328",
+      "label": "Specific learning disability"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27753196",
+        "description": "Smith-Kingsmore syndrome: A third family with the MTOR mutation c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000107",
+      "label": "Renal cyst"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27753196",
+        "description": "Smith-Kingsmore syndrome: A third family with the MTOR mutation c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000256",
+      "label": "Macrocephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27753196",
+        "description": "Smith-Kingsmore syndrome: A third family with the MTOR mutation c"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2475",
+    "symbol": "MTOR"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 11190804,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616638",
+      "label": "SMITH-KINGSMORE SYNDROME; SKS"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27753196",
+      "description": "Smith-Kingsmore syndrome: A third family with the MTOR mutation c"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Moreau-Le_Lan-2018-ACTA1-Patient_5.json b/notebooks/LIRICAL/v1phenopackets/Moreau-Le_Lan-2018-ACTA1-Patient_5.json
new file mode 100644
index 000000000..48fd62b65
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Moreau-Le_Lan-2018-ACTA1-Patient_5.json
@@ -0,0 +1,243 @@
+{
+  "id": "PMID:30517146-Moreau-Le_Lan-2018-ACTA1-Patient_5",
+  "subject": {
+    "id": "Patient 5",
+    "ageAtCollection": {
+      "age": "n/a"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30517146",
+        "description": "New mutations found by Next-Generation Sequencing screening of Spanish patients with Nemaline Myopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002650",
+      "label": "Scoliosis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30517146",
+        "description": "New mutations found by Next-Generation Sequencing screening of Spanish patients with Nemaline Myopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30517146",
+        "description": "New mutations found by Next-Generation Sequencing screening of Spanish patients with Nemaline Myopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000602",
+      "label": "Ophthalmoplegia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30517146",
+        "description": "New mutations found by Next-Generation Sequencing screening of Spanish patients with Nemaline Myopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002093",
+      "label": "Respiratory insufficiency"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30517146",
+        "description": "New mutations found by Next-Generation Sequencing screening of Spanish patients with Nemaline Myopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006466",
+      "label": "Ankle contracture"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30517146",
+        "description": "New mutations found by Next-Generation Sequencing screening of Spanish patients with Nemaline Myopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001284",
+      "label": "Areflexia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30517146",
+        "description": "New mutations found by Next-Generation Sequencing screening of Spanish patients with Nemaline Myopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003701",
+      "label": "Proximal muscle weakness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30517146",
+        "description": "New mutations found by Next-Generation Sequencing screening of Spanish patients with Nemaline Myopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002307",
+      "label": "Drooling"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30517146",
+        "description": "New mutations found by Next-Generation Sequencing screening of Spanish patients with Nemaline Myopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001283",
+      "label": "Bulbar palsy"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30517146",
+        "description": "New mutations found by Next-Generation Sequencing screening of Spanish patients with Nemaline Myopathy"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:58",
+    "symbol": "ACTA1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 229567587,
+      "ref": "T",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:161800",
+      "label": "NEMALINE MYOPATHY 3; NEM3MYOPATHY, ACTIN, CONGENITAL, WITH EXCESS OF THIN MYOFILAMENTS, INCLUDED"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30517146",
+      "description": "New mutations found by Next-Generation Sequencing screening of Spanish patients with Nemaline Myopathy"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Mundhofir-2013-FGFR2-Patient_1.json b/notebooks/LIRICAL/v1phenopackets/Mundhofir-2013-FGFR2-Patient_1.json
new file mode 100644
index 000000000..d09387f2f
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Mundhofir-2013-FGFR2-Patient_1.json
@@ -0,0 +1,297 @@
+{
+  "id": "PMID:23546041-Mundhofir-2013-FGFR2-Patient_1",
+  "subject": {
+    "id": "Patient 1",
+    "ageAtCollection": {
+      "age": "P11M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001561",
+      "label": "Polyhydramnios"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006610",
+      "label": "Wide intermamillary distance"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000520",
+      "label": "Proptosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000028",
+      "label": "Cryptorchidism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000368",
+      "label": "Low-set, posteriorly rotated ears"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001631",
+      "label": "Atrial septal defect"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011220",
+      "label": "Prominent forehead"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000494",
+      "label": "Downslanted palpebral fissures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000239",
+      "label": "Large fontanelles"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011800",
+      "label": "Midface retrusion"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000248",
+      "label": "Brachycephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010709",
+      "label": "2-4 finger syndactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010713",
+      "label": "1-5 toe syndactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000218",
+      "label": "High palate"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2263",
+    "symbol": "FGFR2"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "10",
+      "pos": 123279677,
+      "ref": "G",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:101200",
+      "label": "APERT SYNDROME"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:23546041",
+      "description": "p"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Mundhofir-2013-FGFR2-Patient_2.json b/notebooks/LIRICAL/v1phenopackets/Mundhofir-2013-FGFR2-Patient_2.json
new file mode 100644
index 000000000..d04dd3a62
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Mundhofir-2013-FGFR2-Patient_2.json
@@ -0,0 +1,327 @@
+{
+  "id": "PMID:23546041-Mundhofir-2013-FGFR2-Patient_2",
+  "subject": {
+    "id": "Patient 2",
+    "ageAtCollection": {
+      "age": "P1Y6M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000219",
+      "label": "Thin upper lip vermilion"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000237",
+      "label": "Small anterior fontanelle"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010708",
+      "label": "1-5 finger syndactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001522",
+      "label": "Death in infancy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000463",
+      "label": "Anteverted nares"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005280",
+      "label": "Depressed nasal bridge"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000508",
+      "label": "Ptosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011330",
+      "label": "Metopic synostosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011800",
+      "label": "Midface retrusion"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010713",
+      "label": "1-5 toe syndactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000316",
+      "label": "Hypertelorism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011318",
+      "label": "Bicoronal synostosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000400",
+      "label": "Macrotia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002007",
+      "label": "Frontal bossing"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010109",
+      "label": "Short hallux"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000218",
+      "label": "High palate"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23546041",
+        "description": "p"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2263",
+    "symbol": "FGFR2"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "10",
+      "pos": 123279674,
+      "ref": "G",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:101200",
+      "label": "APERT SYNDROME"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:23546041",
+      "description": "p"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Mwasamwaja-2018-TGFB1-patient.json b/notebooks/LIRICAL/v1phenopackets/Mwasamwaja-2018-TGFB1-patient.json
new file mode 100644
index 000000000..d8522b9c5
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Mwasamwaja-2018-TGFB1-patient.json
@@ -0,0 +1,284 @@
+{
+  "id": "PMID:30034812-Mwasamwaja-2018-TGFB1-patient",
+  "subject": {
+    "id": "patient",
+    "ageAtCollection": {
+      "age": "35Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0003202",
+      "label": "Skeletal muscle atrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30034812",
+        "description": "Camurati-Engelmann disease: a case report from sub-Saharan Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011220",
+      "label": "Prominent forehead"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30034812",
+        "description": "Camurati-Engelmann disease: a case report from sub-Saharan Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012100",
+      "label": "Abnormal circulating creatinine level"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30034812",
+        "description": "Camurati-Engelmann disease: a case report from sub-Saharan Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002653",
+      "label": "Bone pain"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30034812",
+        "description": "Camurati-Engelmann disease: a case report from sub-Saharan Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003155",
+      "label": "Elevated alkaline phosphatase"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30034812",
+        "description": "Camurati-Engelmann disease: a case report from sub-Saharan Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100543",
+      "label": "Cognitive impairment"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30034812",
+        "description": "Camurati-Engelmann disease: a case report from sub-Saharan Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003115",
+      "label": "Abnormal EKG"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30034812",
+        "description": "Camurati-Engelmann disease: a case report from sub-Saharan Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002829",
+      "label": "Arthralgia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30034812",
+        "description": "Camurati-Engelmann disease: a case report from sub-Saharan Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000508",
+      "label": "Ptosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30034812",
+        "description": "Camurati-Engelmann disease: a case report from sub-Saharan Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002515",
+      "label": "Waddling gait"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30034812",
+        "description": "Camurati-Engelmann disease: a case report from sub-Saharan Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003868",
+      "label": "Humeral cortical thickening"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30034812",
+        "description": "Camurati-Engelmann disease: a case report from sub-Saharan Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000520",
+      "label": "Proptosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30034812",
+        "description": "Camurati-Engelmann disease: a case report from sub-Saharan Africa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100774",
+      "label": "Hyperostosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30034812",
+        "description": "Camurati-Engelmann disease: a case report from sub-Saharan Africa"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:7040",
+    "symbol": "TGFB1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "19",
+      "pos": 41848135,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:131300",
+      "label": "CAMURATI-ENGELMANN DISEASE; CAEND"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30034812",
+      "description": "Camurati-Engelmann disease: a case report from sub-Saharan Africa"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Nakajima-2013-B3GALT6-P7_F6.json b/notebooks/LIRICAL/v1phenopackets/Nakajima-2013-B3GALT6-P7_F6.json
new file mode 100644
index 000000000..ca1b9b8d2
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Nakajima-2013-B3GALT6-P7_F6.json
@@ -0,0 +1,545 @@
+{
+  "id": "PMID:23664117-Nakajima-2013-B3GALT6-P7/F6",
+  "subject": {
+    "id": "P7/F6",
+    "ageAtCollection": {
+      "age": "2"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0012368",
+      "label": "Flat face"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23664117",
+        "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002656",
+      "label": "Epiphyseal dysplasia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23664117",
+        "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009811",
+      "label": "Abnormality of the elbow"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23664117",
+        "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000175",
+      "label": "Cleft palate"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23664117",
+        "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+      }
+    }]
+  }, {
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+      "label": "Joint hypermobility"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23664117",
+        "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011341",
+      "label": "Long upper lip"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23664117",
+        "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000973",
+      "label": "Cutis laxa"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23664117",
+        "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100866",
+      "label": "Short iliac bones"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:23664117",
+        "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:23664117",
+        "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006187",
+      "label": "Fusion of midphalangeal joints"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23664117",
+        "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001027",
+      "label": "Soft, doughy skin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23664117",
+        "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011300",
+      "label": "Broad fingertip"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23664117",
+        "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001239",
+      "label": "Wrist flexion contracture"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23664117",
+        "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002822",
+      "label": "Hyperplasia of the femoral trochanters"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23664117",
+        "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001388",
+      "label": "Joint laxity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23664117",
+        "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000520",
+      "label": "Proptosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23664117",
+        "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000592",
+      "label": "Blue sclerae"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23664117",
+        "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004233",
+      "label": "Advanced ossification of carpal bones"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23664117",
+        "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004568",
+      "label": "Beaking of vertebral bodies"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:23664117",
+        "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006149",
+      "label": "Increased laxity of fingers"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+      }
+    }]
+  }, {
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+      "label": "Talipes"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Platyspondyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002996",
+      "label": "Limited elbow movement"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000347",
+      "label": "Micrognathia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23664117",
+        "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008070",
+      "label": "Sparse hair"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:23664117",
+        "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006391",
+      "label": "Overtubulated long bones"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003015",
+      "label": "Flared metaphysis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23664117",
+        "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011220",
+      "label": "Prominent forehead"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23664117",
+        "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002827",
+      "label": "Hip dislocation"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:23664117",
+        "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:126792",
+    "symbol": "B3GALT6"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 1167851,
+      "ref": "A",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 1167659,
+      "ref": "A",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:271640",
+      "label": "SPONDYLOEPIMETAPHYSEAL DYSPLASIA WITH JOINT LAXITY, TYPE 1, WITH ORWITHOUT FRACTURES; SEMDJL1"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:lccarmody",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:23664117",
+      "description": "Mutations in B3GALT6, which encodes a glycosaminoglycan linker region enzyme, cause a spectrum of skeletal and connective tissue disorders"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Naz_Villalba-2016-NLRP3-proband.json b/notebooks/LIRICAL/v1phenopackets/Naz_Villalba-2016-NLRP3-proband.json
new file mode 100644
index 000000000..be518aa94
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Naz_Villalba-2016-NLRP3-proband.json
@@ -0,0 +1,224 @@
+{
+  "id": "PMID:27435956-Naz_Villalba-2016-NLRP3-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P5Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0011227",
+      "label": "Elevated C-reactive protein level"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27435956",
+        "description": "Muckle-Wells Syndrome: A Case Report with an NLRP3 T348M Mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000509",
+      "label": "Conjunctivitis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27435956",
+        "description": "Muckle-Wells Syndrome: A Case Report with an NLRP3 T348M Mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002516",
+      "label": "Increased intracranial pressure"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27435956",
+        "description": "Muckle-Wells Syndrome: A Case Report with an NLRP3 T348M Mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002633",
+      "label": "Vasculitis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27435956",
+        "description": "Muckle-Wells Syndrome: A Case Report with an NLRP3 T348M Mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011897",
+      "label": "Neutrophilia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27435956",
+        "description": "Muckle-Wells Syndrome: A Case Report with an NLRP3 T348M Mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003565",
+      "label": "Elevated erythrocyte sedimentation rate"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27435956",
+        "description": "Muckle-Wells Syndrome: A Case Report with an NLRP3 T348M Mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002315",
+      "label": "Headache"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27435956",
+        "description": "Muckle-Wells Syndrome: A Case Report with an NLRP3 T348M Mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001085",
+      "label": "Papilledema"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27435956",
+        "description": "Muckle-Wells Syndrome: A Case Report with an NLRP3 T348M Mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001025",
+      "label": "Urticaria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27435956",
+        "description": "Muckle-Wells Syndrome: A Case Report with an NLRP3 T348M Mutation"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:114548",
+    "symbol": "NLRP3"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 247587794,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:191900",
+      "label": "MUCKLE-WELLS SYNDROME; MWS"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27435956",
+      "description": "Muckle-Wells Syndrome: A Case Report with an NLRP3 T348M Mutation"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Nellist-2009-TSC1-II_3_Family_2.json b/notebooks/LIRICAL/v1phenopackets/Nellist-2009-TSC1-II_3_Family_2.json
new file mode 100644
index 000000000..220f467bf
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Nellist-2009-TSC1-II_3_Family_2.json
@@ -0,0 +1,202 @@
+{
+  "id": "PMID:18830229-Nellist-2009-TSC1-II:3/Family_2",
+  "subject": {
+    "id": "II:3/Family 2",
+    "ageAtCollection": {
+      "age": "N/A"
+    },
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0009719",
+      "label": "Hypomelanotic macule"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18830229",
+        "description": "Missense mutations to the TSC1 gene cause tuberous sclerosis complex"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010614",
+      "label": "Fibroma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18830229",
+        "description": "Missense mutations to the TSC1 gene cause tuberous sclerosis complex"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012736",
+      "label": "Profound global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18830229",
+        "description": "Missense mutations to the TSC1 gene cause tuberous sclerosis complex"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001250",
+      "label": "Seizures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18830229",
+        "description": "Missense mutations to the TSC1 gene cause tuberous sclerosis complex"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100804",
+      "label": "Ungual fibroma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18830229",
+        "description": "Missense mutations to the TSC1 gene cause tuberous sclerosis complex"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009721",
+      "label": "Shagreen patch"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18830229",
+        "description": "Missense mutations to the TSC1 gene cause tuberous sclerosis complex"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012733",
+      "label": "Macule"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18830229",
+        "description": "Missense mutations to the TSC1 gene cause tuberous sclerosis complex"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:7248",
+    "symbol": "TSC1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "9",
+      "pos": 135796816,
+      "ref": "A",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "9",
+      "pos": 135772014,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:191100",
+      "label": "TUBEROUS SCLEROSIS 1; TSC1"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:lccarmody",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:18830229",
+      "description": "Missense mutations to the TSC1 gene cause tuberous sclerosis complex"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Nevidomskyte-2017-SMAD3-54-year_old_woman.json b/notebooks/LIRICAL/v1phenopackets/Nevidomskyte-2017-SMAD3-54-year_old_woman.json
new file mode 100644
index 000000000..b31936d0a
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Nevidomskyte-2017-SMAD3-54-year_old_woman.json
@@ -0,0 +1,116 @@
+{
+  "id": "PMID:28286188-Nevidomskyte-2017-SMAD3-54-year_old_woman",
+  "subject": {
+    "id": "54-year old woman",
+    "ageAtCollection": {
+      "age": "P54Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002616",
+      "label": "Aortic root aneurysm"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28286188",
+        "description": "Endovascular Repair of Internal Mammary Artery Aneurysms in 2 Sisters with SMAD3 Mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005302",
+      "label": "Carotid artery tortuosity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28286188",
+        "description": "Endovascular Repair of Internal Mammary Artery Aneurysms in 2 Sisters with SMAD3 Mutation"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:4088",
+    "symbol": "SMAD3"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "15",
+      "pos": 67473653,
+      "ref": "G",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:613795",
+      "label": "LOEYS-DIETZ SYNDROME 3; LDS3"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28286188",
+      "description": "Endovascular Repair of Internal Mammary Artery Aneurysms in 2 Sisters with SMAD3 Mutation"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Nguyen-2017-NPHS1-patient_1.json b/notebooks/LIRICAL/v1phenopackets/Nguyen-2017-NPHS1-patient_1.json
new file mode 100644
index 000000000..d80a9c990
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Nguyen-2017-NPHS1-patient_1.json
@@ -0,0 +1,246 @@
+{
+  "id": "PMID:28392951-Nguyen-2017-NPHS1-patient_1",
+  "subject": {
+    "id": "patient 1",
+    "ageAtCollection": {
+      "age": "40"
+    },
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0008360",
+      "label": "Neonatal hypoproteinemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28392951",
+        "description": "Three Novel Mutations in the NPHS1 Gene in Vietnamese Patients with Congenital Nephrotic Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000093",
+      "label": "Proteinuria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28392951",
+        "description": "Three Novel Mutations in the NPHS1 Gene in Vietnamese Patients with Congenital Nephrotic Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008677",
+      "label": "Congenital nephrotic syndrome"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28392951",
+        "description": "Three Novel Mutations in the NPHS1 Gene in Vietnamese Patients with Congenital Nephrotic Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003124",
+      "label": "Hypercholesterolemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28392951",
+        "description": "Three Novel Mutations in the NPHS1 Gene in Vietnamese Patients with Congenital Nephrotic Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000969",
+      "label": "Edema"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28392951",
+        "description": "Three Novel Mutations in the NPHS1 Gene in Vietnamese Patients with Congenital Nephrotic Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002202",
+      "label": "Pleural effusion"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28392951",
+        "description": "Three Novel Mutations in the NPHS1 Gene in Vietnamese Patients with Congenital Nephrotic Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002090",
+      "label": "Pneumonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28392951",
+        "description": "Three Novel Mutations in the NPHS1 Gene in Vietnamese Patients with Congenital Nephrotic Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001518",
+      "label": "Small for gestational age"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28392951",
+        "description": "Three Novel Mutations in the NPHS1 Gene in Vietnamese Patients with Congenital Nephrotic Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003073",
+      "label": "Hypoalbuminemia"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28392951",
+        "description": "Three Novel Mutations in the NPHS1 Gene in Vietnamese Patients with Congenital Nephrotic Syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:4868",
+    "symbol": "NPHS1"
+  }],
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+      "ref": "C",
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+    },
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+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "19",
+      "pos": 36339962,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
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+      "pos": 36322580,
+      "ref": "A",
+      "alt": "AC"
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+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:256300",
+      "label": "NEPHROTIC SYNDROME, TYPE 1; NPHS1"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28392951",
+      "description": "Three Novel Mutations in the NPHS1 Gene in Vietnamese Patients with Congenital Nephrotic Syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Nicole-2014-AGRN-Patient_3_Kinship_2.json b/notebooks/LIRICAL/v1phenopackets/Nicole-2014-AGRN-Patient_3_Kinship_2.json
new file mode 100644
index 000000000..c1592bb1a
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Nicole-2014-AGRN-Patient_3_Kinship_2.json
@@ -0,0 +1,324 @@
+{
+  "id": "PMID:24951643-Nicole-2014-AGRN-Patient_3/Kinship_2",
+  "subject": {
+    "id": "Patient 3/Kinship 2",
+    "ageAtCollection": {
+      "age": "36"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0010307",
+      "label": "Stridor"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24951643",
+        "description": "Agrin mutations lead to a congenital myasthenic syndrome with distal muscle weakness and atrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003691",
+      "label": "Scapular winging"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:24951643",
+        "description": "Agrin mutations lead to a congenital myasthenic syndrome with distal muscle weakness and atrophy"
+      }
+    }]
+  }, {
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+      "id": "HP:0001371",
+      "label": "Flexion contracture"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:24951643",
+        "description": "Agrin mutations lead to a congenital myasthenic syndrome with distal muscle weakness and atrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008959",
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+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24951643",
+        "description": "Agrin mutations lead to a congenital myasthenic syndrome with distal muscle weakness and atrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002793",
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+    },
+    "evidence": [{
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+        "id": "PMID:24951643",
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+        "description": "Agrin mutations lead to a congenital myasthenic syndrome with distal muscle weakness and atrophy"
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+        "description": "Agrin mutations lead to a congenital myasthenic syndrome with distal muscle weakness and atrophy"
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+    }]
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+      "id": "HP:0009027",
+      "label": "Foot dorsiflexor weakness"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:24951643",
+        "description": "Agrin mutations lead to a congenital myasthenic syndrome with distal muscle weakness and atrophy"
+      }
+    }]
+  }, {
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+      "id": "HP:0010535",
+      "label": "Sleep apnea"
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+        "id": "PMID:24951643",
+        "description": "Agrin mutations lead to a congenital myasthenic syndrome with distal muscle weakness and atrophy"
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+      "label": "Distal lower limb muscle weakness"
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+        "id": "ECO:0000033",
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+        "description": "Agrin mutations lead to a congenital myasthenic syndrome with distal muscle weakness and atrophy"
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+    }]
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+      "label": "Easy fatigability"
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+  }, {
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+      "label": "Apnea"
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:24951643",
+        "description": "Agrin mutations lead to a congenital myasthenic syndrome with distal muscle weakness and atrophy"
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+    }]
+  }, {
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+      "id": "HP:0002792",
+      "label": "Reduced vital capacity"
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+        "description": "Agrin mutations lead to a congenital myasthenic syndrome with distal muscle weakness and atrophy"
+      }
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+      "id": "HP:0002878",
+      "label": "Respiratory failure"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+      },
+      "reference": {
+        "id": "PMID:24951643",
+        "description": "Agrin mutations lead to a congenital myasthenic syndrome with distal muscle weakness and atrophy"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:375790",
+    "symbol": "AGRN"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 957693,
+      "ref": "A",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 977517,
+      "ref": "C",
+      "alt": "CC"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:615120",
+      "label": "MYASTHENIC SYNDROME, CONGENITAL, 8; CMS8"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:lccarmody",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:24951643",
+      "description": "Agrin mutations lead to a congenital myasthenic syndrome with distal muscle weakness and atrophy"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Niihori-2006-BRAF-CFC16.json b/notebooks/LIRICAL/v1phenopackets/Niihori-2006-BRAF-CFC16.json
new file mode 100644
index 000000000..08aa1de11
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Niihori-2006-BRAF-CFC16.json
@@ -0,0 +1,329 @@
+{
+  "id": "PMID:16474404-Niihori-2006-BRAF-CFC16",
+  "subject": {
+    "id": "CFC16",
+    "ageAtCollection": {
+      "age": "P7Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0005280",
+      "label": "Depressed nasal bridge"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:16474404",
+        "description": "Germline KRAS and BRAF mutations in cardio-facio-cutaneous syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004482",
+      "label": "Relative macrocephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:16474404",
+        "description": "Germline KRAS and BRAF mutations in cardio-facio-cutaneous syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009891",
+      "label": "Underdeveloped supraorbital ridges"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:16474404",
+        "description": "Germline KRAS and BRAF mutations in cardio-facio-cutaneous syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000218",
+      "label": "High palate"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:16474404",
+        "description": "Germline KRAS and BRAF mutations in cardio-facio-cutaneous syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008070",
+      "label": "Sparse hair"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:16474404",
+        "description": "Germline KRAS and BRAF mutations in cardio-facio-cutaneous syndrome"
+      }
+    }]
+  }, {
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+      "id": "HP:0000463",
+      "label": "Anteverted nares"
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+    "evidence": [{
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+        "id": "ECO:0000033",
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+      "reference": {
+        "id": "PMID:16474404",
+        "description": "Germline KRAS and BRAF mutations in cardio-facio-cutaneous syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000962",
+      "label": "Hyperkeratosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:16474404",
+        "description": "Germline KRAS and BRAF mutations in cardio-facio-cutaneous syndrome"
+      }
+    }]
+  }, {
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+      "id": "HP:0001250",
+      "label": "Seizures"
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+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:16474404",
+        "description": "Germline KRAS and BRAF mutations in cardio-facio-cutaneous syndrome"
+      }
+    }]
+  }, {
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+      "id": "HP:0008064",
+      "label": "Ichthyosis"
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+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:16474404",
+        "description": "Germline KRAS and BRAF mutations in cardio-facio-cutaneous syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000508",
+      "label": "Ptosis"
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+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:16474404",
+        "description": "Germline KRAS and BRAF mutations in cardio-facio-cutaneous syndrome"
+      }
+    }]
+  }, {
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+      "label": "Pulmonic stenosis"
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+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:16474404",
+        "description": "Germline KRAS and BRAF mutations in cardio-facio-cutaneous syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000470",
+      "label": "Short neck"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:16474404",
+        "description": "Germline KRAS and BRAF mutations in cardio-facio-cutaneous syndrome"
+      }
+    }]
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+      "id": "HP:0001631",
+      "label": "Atrial septal defect"
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+        "description": "Germline KRAS and BRAF mutations in cardio-facio-cutaneous syndrome"
+      }
+    }]
+  }, {
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+      "label": "Webbed neck"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:16474404",
+        "description": "Germline KRAS and BRAF mutations in cardio-facio-cutaneous syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000494",
+      "label": "Downslanted palpebral fissures"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:16474404",
+        "description": "Germline KRAS and BRAF mutations in cardio-facio-cutaneous syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010864",
+      "label": "Intellectual disability, severe"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:16474404",
+        "description": "Germline KRAS and BRAF mutations in cardio-facio-cutaneous syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:673",
+    "symbol": "BRAF"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "7",
+      "pos": 140501302,
+      "ref": "T",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:115150",
+      "label": "CARDIOFACIOCUTANEOUS SYNDROME 1; CFC1"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:16474404",
+      "description": "Germline KRAS and BRAF mutations in cardio-facio-cutaneous syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Ning-2015-MEN1-III-3.json b/notebooks/LIRICAL/v1phenopackets/Ning-2015-MEN1-III-3.json
new file mode 100644
index 000000000..4fed8f718
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Ning-2015-MEN1-III-3.json
@@ -0,0 +1,313 @@
+{
+  "id": "PMID:26239674-Ning-2015-MEN1-III-3",
+  "subject": {
+    "id": "III-3",
+    "ageAtCollection": {
+      "age": "P54Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0011748",
+      "label": "Adrenocorticotropic hormone deficiency"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26239674",
+        "description": "MEN1 c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012587",
+      "label": "Macroscopic hematuria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26239674",
+        "description": "MEN1 c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100829",
+      "label": "Galactorrhea"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26239674",
+        "description": "MEN1 c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002315",
+      "label": "Headache"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26239674",
+        "description": "MEN1 c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002588",
+      "label": "Duodenal ulcer"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26239674",
+        "description": "MEN1 c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100522",
+      "label": "Thymoma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26239674",
+        "description": "MEN1 c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0500167",
+      "label": "Hypergastrinemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26239674",
+        "description": "MEN1 c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003418",
+      "label": "Back pain"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26239674",
+        "description": "MEN1 c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000869",
+      "label": "Secondary amenorrhea"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26239674",
+        "description": "MEN1 c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002893",
+      "label": "Pituitary adenoma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26239674",
+        "description": "MEN1 c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000787",
+      "label": "Nephrolithiasis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26239674",
+        "description": "MEN1 c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003165",
+      "label": "Elevated circulating parathyroid hormone level"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26239674",
+        "description": "MEN1 c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100634",
+      "label": "Neuroendocrine neoplasm"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26239674",
+        "description": "MEN1 c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008200",
+      "label": "Primary hyperparathyroidism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26239674",
+        "description": "MEN1 c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100570",
+      "label": "Carcinoid tumor"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26239674",
+        "description": "MEN1 c"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:4221",
+    "symbol": "MEN1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "11",
+      "pos": 64574571,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:131100",
+      "label": "MULTIPLE ENDOCRINE NEOPLASIA, TYPE I; MEN1"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:26239674",
+      "description": "MEN1 c"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Noch-2017-ATP13A2-Case_1.json b/notebooks/LIRICAL/v1phenopackets/Noch-2017-ATP13A2-Case_1.json
new file mode 100644
index 000000000..81ebadd27
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Noch-2017-ATP13A2-Case_1.json
@@ -0,0 +1,268 @@
+{
+  "id": "PMID:30746398-Noch-2017-ATP13A2-Case_1",
+  "subject": {
+    "id": "Case 1",
+    "ageAtCollection": {
+      "age": "P30Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001347",
+      "label": "Hyperreflexia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30746398",
+        "description": "Kufor-Rakeb Syndrome Due to a Novel ATP13A2 Mutation in 2 Chinese-American Brothers"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001288",
+      "label": "Gait disturbance"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30746398",
+        "description": "Kufor-Rakeb Syndrome Due to a Novel ATP13A2 Mutation in 2 Chinese-American Brothers"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001260",
+      "label": "Dysarthria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30746398",
+        "description": "Kufor-Rakeb Syndrome Due to a Novel ATP13A2 Mutation in 2 Chinese-American Brothers"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000338",
+      "label": "Hypomimic face"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30746398",
+        "description": "Kufor-Rakeb Syndrome Due to a Novel ATP13A2 Mutation in 2 Chinese-American Brothers"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30746398",
+        "description": "Kufor-Rakeb Syndrome Due to a Novel ATP13A2 Mutation in 2 Chinese-American Brothers"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000278",
+      "label": "Retrognathia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30746398",
+        "description": "Kufor-Rakeb Syndrome Due to a Novel ATP13A2 Mutation in 2 Chinese-American Brothers"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0025331",
+      "label": "Upgaze palsy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30746398",
+        "description": "Kufor-Rakeb Syndrome Due to a Novel ATP13A2 Mutation in 2 Chinese-American Brothers"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002064",
+      "label": "Spastic gait"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30746398",
+        "description": "Kufor-Rakeb Syndrome Due to a Novel ATP13A2 Mutation in 2 Chinese-American Brothers"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000369",
+      "label": "Low-set ears"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30746398",
+        "description": "Kufor-Rakeb Syndrome Due to a Novel ATP13A2 Mutation in 2 Chinese-American Brothers"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002067",
+      "label": "Bradykinesia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30746398",
+        "description": "Kufor-Rakeb Syndrome Due to a Novel ATP13A2 Mutation in 2 Chinese-American Brothers"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100660",
+      "label": "Dyskinesia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30746398",
+        "description": "Kufor-Rakeb Syndrome Due to a Novel ATP13A2 Mutation in 2 Chinese-American Brothers"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002063",
+      "label": "Rigidity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30746398",
+        "description": "Kufor-Rakeb Syndrome Due to a Novel ATP13A2 Mutation in 2 Chinese-American Brothers"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:23400",
+    "symbol": "ATP13A2"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 17322554,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:606693",
+      "label": "KUFOR-RAKEB SYNDROME; KRS"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30746398",
+      "description": "Kufor-Rakeb Syndrome Due to a Novel ATP13A2 Mutation in 2 Chinese-American Brothers"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Ockeloen-2012-CFL2-_Patient_1.json b/notebooks/LIRICAL/v1phenopackets/Ockeloen-2012-CFL2-_Patient_1.json
new file mode 100644
index 000000000..19315ad75
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Ockeloen-2012-CFL2-_Patient_1.json
@@ -0,0 +1,269 @@
+{
+  "id": "PMID:22560515-Ockeloen-2012-CFL2-_Patient_1",
+  "subject": {
+    "id": " Patient 1",
+    "ageAtCollection": {
+      "age": "P21Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002751",
+      "label": "Kyphoscoliosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:22560515",
+        "description": "Congenital myopathy caused by a novel missense mutation in the CFL2 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001324",
+      "label": "Muscle weakness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:22560515",
+        "description": "Congenital myopathy caused by a novel missense mutation in the CFL2 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000467",
+      "label": "Neck muscle weakness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:22560515",
+        "description": "Congenital myopathy caused by a novel missense mutation in the CFL2 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000218",
+      "label": "High palate"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:22560515",
+        "description": "Congenital myopathy caused by a novel missense mutation in the CFL2 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003391",
+      "label": "Gowers sign"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:22560515",
+        "description": "Congenital myopathy caused by a novel missense mutation in the CFL2 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001623",
+      "label": "Breech presentation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:22560515",
+        "description": "Congenital myopathy caused by a novel missense mutation in the CFL2 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031936",
+      "label": "Delayed ability to walk"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:22560515",
+        "description": "Congenital myopathy caused by a novel missense mutation in the CFL2 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0040129",
+      "label": "Abnormal nerve conduction velocity"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:22560515",
+        "description": "Congenital myopathy caused by a novel missense mutation in the CFL2 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006380",
+      "label": "Knee flexion contracture"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:22560515",
+        "description": "Congenital myopathy caused by a novel missense mutation in the CFL2 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010546",
+      "label": "Muscle fibrillation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:22560515",
+        "description": "Congenital myopathy caused by a novel missense mutation in the CFL2 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:22560515",
+        "description": "Congenital myopathy caused by a novel missense mutation in the CFL2 gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002747",
+      "label": "Respiratory insufficiency due to muscle weakness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:22560515",
+        "description": "Congenital myopathy caused by a novel missense mutation in the CFL2 gene"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:1073",
+    "symbol": "CFL2"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "14",
+      "pos": 35182752,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:610687",
+      "label": "NEMALINE MYOPATHY 7; NEM7"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:22560515",
+      "description": "Congenital myopathy caused by a novel missense mutation in the CFL2 gene"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Okamoto-2018-ASPM-patient.json b/notebooks/LIRICAL/v1phenopackets/Okamoto-2018-ASPM-patient.json
new file mode 100644
index 000000000..dbbf42184
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Okamoto-2018-ASPM-patient.json
@@ -0,0 +1,249 @@
+{
+  "id": "PMID:29644084-Okamoto-2018-ASPM-patient",
+  "subject": {
+    "id": "patient",
+    "ageAtCollection": {
+      "age": "P5Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001270",
+      "label": "Motor delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29644084",
+        "description": "Primary microcephaly caused by novel compound heterozygous mutations in ASPM"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000347",
+      "label": "Micrognathia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29644084",
+        "description": "Primary microcephaly caused by novel compound heterozygous mutations in ASPM"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009879",
+      "label": "Simplified gyral pattern"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29644084",
+        "description": "Primary microcephaly caused by novel compound heterozygous mutations in ASPM"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29644084",
+        "description": "Primary microcephaly caused by novel compound heterozygous mutations in ASPM"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001276",
+      "label": "Hypertonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29644084",
+        "description": "Primary microcephaly caused by novel compound heterozygous mutations in ASPM"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000252",
+      "label": "Microcephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29644084",
+        "description": "Primary microcephaly caused by novel compound heterozygous mutations in ASPM"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000286",
+      "label": "Epicanthus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29644084",
+        "description": "Primary microcephaly caused by novel compound heterozygous mutations in ASPM"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002360",
+      "label": "Sleep disturbance"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29644084",
+        "description": "Primary microcephaly caused by novel compound heterozygous mutations in ASPM"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006956",
+      "label": "Dilation of lateral ventricles"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29644084",
+        "description": "Primary microcephaly caused by novel compound heterozygous mutations in ASPM"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000218",
+      "label": "High palate"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29644084",
+        "description": "Primary microcephaly caused by novel compound heterozygous mutations in ASPM"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:259266",
+    "symbol": "ASPM"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 197059409,
+      "ref": "AGTTT",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 197070597,
+      "ref": "TTC",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:608716",
+      "label": "MICROCEPHALY 5, PRIMARY, AUTOSOMAL RECESSIVE; MCPH5"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29644084",
+      "description": "Primary microcephaly caused by novel compound heterozygous mutations in ASPM"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Oud-2017-EXTL3-AII-1.json b/notebooks/LIRICAL/v1phenopackets/Oud-2017-EXTL3-AII-1.json
new file mode 100644
index 000000000..c65f39353
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Oud-2017-EXTL3-AII-1.json
@@ -0,0 +1,297 @@
+{
+  "id": "PMID:28132690-Oud-2017-EXTL3-AII-1",
+  "subject": {
+    "id": "AII-1",
+    "ageAtCollection": {
+      "age": "P1M3W"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000926",
+      "label": "Platyspondyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002652",
+      "label": "Skeletal dysplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009826",
+      "label": "Limb undergrowth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002079",
+      "label": "Hypoplasia of the corpus callosum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005562",
+      "label": "Multiple renal cysts"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001999",
+      "label": "Abnormal facial shape"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002789",
+      "label": "Tachypnea"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001156",
+      "label": "Brachydactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011839",
+      "label": "Abnormal T cell count"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001407",
+      "label": "Hepatic cysts"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000083",
+      "label": "Renal insufficiency"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030747",
+      "label": "Preterm intraventricular hemorrhage"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002119",
+      "label": "Ventriculomegaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000085",
+      "label": "Horseshoe kidney"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2137",
+    "symbol": "EXTL3"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "8",
+      "pos": 28575113,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617425",
+      "label": "Immunoskeletal dysplasia with neurodevelopmental abnormalities"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28132690",
+      "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Oud-2017-EXTL3-BII-1.json b/notebooks/LIRICAL/v1phenopackets/Oud-2017-EXTL3-BII-1.json
new file mode 100644
index 000000000..67cdd4b77
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Oud-2017-EXTL3-BII-1.json
@@ -0,0 +1,477 @@
+{
+  "id": "PMID:28132690-Oud-2017-EXTL3-BII-1",
+  "subject": {
+    "id": "BII-1",
+    "ageAtCollection": {
+      "age": "P8Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0005407",
+      "label": "Decreased proportion of CD4-positive T cells"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002987",
+      "label": "Elbow flexion contracture"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004313",
+      "label": "Decreased antibody level in blood"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009826",
+      "label": "Limb undergrowth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000252",
+      "label": "Microcephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003799",
+      "label": "Marked delay in bone age"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002750",
+      "label": "Delayed skeletal maturation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005415",
+      "label": "Decreased proportion of CD8-positive T cells"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001276",
+      "label": "Hypertonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002655",
+      "label": "Spondyloepiphyseal dysplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031141",
+      "label": "Increased hepatic echogenicity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002788",
+      "label": "Recurrent upper respiratory tract infections"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011849",
+      "label": "Abnormal bone ossification"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000470",
+      "label": "Short neck"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001508",
+      "label": "Failure to thrive"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011344",
+      "label": "Severe global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004209",
+      "label": "Clinodactyly of the 5th finger"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001999",
+      "label": "Abnormal facial shape"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009237",
+      "label": "Short 5th finger"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005930",
+      "label": "Abnormality of epiphysis morphology"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011097",
+      "label": "Epileptic spasms"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0025502",
+      "label": "Overweight"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000914",
+      "label": "Shield chest"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001518",
+      "label": "Small for gestational age"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2137",
+    "symbol": "EXTL3"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "8",
+      "pos": 28575584,
+      "ref": "T",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617425",
+      "label": "Immunoskeletal dysplasia with neurodevelopmental abnormalities"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28132690",
+      "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Oud-2017-EXTL3-B_II-2.json b/notebooks/LIRICAL/v1phenopackets/Oud-2017-EXTL3-B_II-2.json
new file mode 100644
index 000000000..bcddbbc53
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Oud-2017-EXTL3-B_II-2.json
@@ -0,0 +1,507 @@
+{
+  "id": "PMID:28132690-Oud-2017-EXTL3-B:II-2",
+  "subject": {
+    "id": "B:II-2",
+    "ageAtCollection": {
+      "age": "P3M"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001631",
+      "label": "Atrial septal defect"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001830",
+      "label": "Postaxial foot polydactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002652",
+      "label": "Skeletal dysplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002987",
+      "label": "Elbow flexion contracture"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002509",
+      "label": "Limb hypertonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000252",
+      "label": "Microcephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000160",
+      "label": "Narrow mouth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004554",
+      "label": "Generalized hypertrichosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002194",
+      "label": "Delayed gross motor development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0040089",
+      "label": "Abnormal natural killer cell count"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008936",
+      "label": "Muscular hypotonia of the trunk"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002521",
+      "label": "Hypsarrhythmia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001250",
+      "label": "Seizures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002655",
+      "label": "Spondyloepiphyseal dysplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001276",
+      "label": "Hypertonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005387",
+      "label": "Combined immunodeficiency"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001671",
+      "label": "Abnormal cardiac septum morphology"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012736",
+      "label": "Profound global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001177",
+      "label": "Preaxial hand polydactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100878",
+      "label": "Enlarged uterus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001880",
+      "label": "Eosinophilia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000998",
+      "label": "Hypertrichosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001999",
+      "label": "Abnormal facial shape"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001156",
+      "label": "Brachydactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005422",
+      "label": "Absence of CD8-positive T cells"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004430",
+      "label": "Severe combined immunodeficiency"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001019",
+      "label": "Erythroderma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000639",
+      "label": "Nystagmus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2137",
+    "symbol": "EXTL3"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "8",
+      "pos": 28575584,
+      "ref": "T",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617425",
+      "label": "Immunoskeletal dysplasia with neurodevelopmental abnormalities"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28132690",
+      "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Oud-2017-EXTL3-C_II-1.json b/notebooks/LIRICAL/v1phenopackets/Oud-2017-EXTL3-C_II-1.json
new file mode 100644
index 000000000..7d987d74c
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Oud-2017-EXTL3-C_II-1.json
@@ -0,0 +1,267 @@
+{
+  "id": "PMID:28132690-Oud-2017-EXTL3-C:II-1",
+  "subject": {
+    "id": "C:II-1",
+    "ageAtCollection": {
+      "age": "P12Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0011569",
+      "label": "Cleft anterior mitral valve leaflet"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001363",
+      "label": "Craniosynostosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000193",
+      "label": "Bifid uvula"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002652",
+      "label": "Skeletal dysplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002904",
+      "label": "Hyperbilirubinemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008454",
+      "label": "Lumbar kyphosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001888",
+      "label": "Lymphopenia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001655",
+      "label": "Patent foramen ovale"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
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+      "id": "HP:0001999",
+      "label": "Abnormal facial shape"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002205",
+      "label": "Recurrent respiratory infections"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001943",
+      "label": "Hypoglycemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000158",
+      "label": "Macroglossia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2137",
+    "symbol": "EXTL3"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "8",
+      "pos": 28574958,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617425",
+      "label": "Immunoskeletal dysplasia with neurodevelopmental abnormalities"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28132690",
+      "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Oud-2017-EXTL3-D_IV-1.json b/notebooks/LIRICAL/v1phenopackets/Oud-2017-EXTL3-D_IV-1.json
new file mode 100644
index 000000000..a43551823
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Oud-2017-EXTL3-D_IV-1.json
@@ -0,0 +1,432 @@
+{
+  "id": "PMID:28132690-Oud-2017-EXTL3-D:IV-1",
+  "subject": {
+    "id": "D:IV-1",
+    "ageAtCollection": {
+      "age": "P12Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0003090",
+      "label": "Hypoplasia of the capital femoral epiphysis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001539",
+      "label": "Omphalocele"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002673",
+      "label": "Coxa valga"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001270",
+      "label": "Motor delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002651",
+      "label": "Spondyloepimetaphyseal dysplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003048",
+      "label": "Radial head subluxation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001653",
+      "label": "Mitral regurgitation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000886",
+      "label": "Deformed rib cage"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003265",
+      "label": "Neonatal hyperbilirubinemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003319",
+      "label": "Abnormality of the cervical spine"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001582",
+      "label": "Redundant skin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001999",
+      "label": "Abnormal facial shape"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0040163",
+      "label": "Abnormal pelvis bone morphology"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000767",
+      "label": "Pectus excavatum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000280",
+      "label": "Coarse facial features"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004565",
+      "label": "Severe platyspondyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001407",
+      "label": "Hepatic cysts"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000486",
+      "label": "Strabismus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002176",
+      "label": "Spinal cord compression"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002751",
+      "label": "Kyphoscoliosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008462",
+      "label": "Cervical instability"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2137",
+    "symbol": "EXTL3"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "8",
+      "pos": 28574958,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617425",
+      "label": "Immunoskeletal dysplasia with neurodevelopmental abnormalities"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28132690",
+      "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Oud-2017-EXTL3-E_II-1.json b/notebooks/LIRICAL/v1phenopackets/Oud-2017-EXTL3-E_II-1.json
new file mode 100644
index 000000000..a7cfec900
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Oud-2017-EXTL3-E_II-1.json
@@ -0,0 +1,387 @@
+{
+  "id": "PMID:28132690-Oud-2017-EXTL3-E:II-1",
+  "subject": {
+    "id": "E:II-1",
+    "ageAtCollection": {
+      "age": "P6M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000961",
+      "label": "Cyanosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002878",
+      "label": "Respiratory failure"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000110",
+      "label": "Renal dysplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002104",
+      "label": "Apnea"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005352",
+      "label": "Severe T-cell immunodeficiency"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
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+      "id": "HP:0001336",
+      "label": "Myoclonus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012211",
+      "label": "Abnormal renal physiology"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000976",
+      "label": "Eczematoid dermatitis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000252",
+      "label": "Microcephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010881",
+      "label": "Abnormality of the umbilical cord"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005484",
+      "label": "Postnatal microcephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005943",
+      "label": "Respiratory arrest"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003121",
+      "label": "Limb joint contracture"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001999",
+      "label": "Abnormal facial shape"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011123",
+      "label": "Inflammatory abnormality of the skin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
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+      "id": "HP:0002925",
+      "label": "Increased thyroid-stimulating hormone level"
+    },
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+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
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+      "id": "HP:0031430",
+      "label": "Oligoclonal T cell expansion"
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008936",
+      "label": "Muscular hypotonia of the trunk"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
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+      "id": "HP:0000821",
+      "label": "Hypothyroidism"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002721",
+      "label": "Immunodeficiency"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28132690",
+        "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2137",
+    "symbol": "EXTL3"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "8",
+      "pos": 28575546,
+      "ref": "A",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617425",
+      "label": "Immunoskeletal dysplasia with neurodevelopmental abnormalities"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28132690",
+      "description": "Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Papanastasiou-2010-STAT3-12_year_old_girl.json b/notebooks/LIRICAL/v1phenopackets/Papanastasiou-2010-STAT3-12_year_old_girl.json
new file mode 100644
index 000000000..817456471
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Papanastasiou-2010-STAT3-12_year_old_girl.json
@@ -0,0 +1,269 @@
+{
+  "id": "PMID:20149460-Papanastasiou-2010-STAT3-12_year_old_girl",
+  "subject": {
+    "id": "12 year old girl",
+    "ageAtCollection": {
+      "age": "P12Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000976",
+      "label": "Eczematoid dermatitis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20149460",
+        "description": "A novel mutation in the signal transducer and activator of transcription 3 (STAT3) gene, in hyper-IgE syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031292",
+      "label": "Cutaneous abscess"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20149460",
+        "description": "A novel mutation in the signal transducer and activator of transcription 3 (STAT3) gene, in hyper-IgE syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011220",
+      "label": "Prominent forehead"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20149460",
+        "description": "A novel mutation in the signal transducer and activator of transcription 3 (STAT3) gene, in hyper-IgE syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031393",
+      "label": "Abnormal proportion of CD8 T cells"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20149460",
+        "description": "A novel mutation in the signal transducer and activator of transcription 3 (STAT3) gene, in hyper-IgE syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003212",
+      "label": "Increased IgE level"
+    },
+    "evidence": [{
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+    }]
+  }, {
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+      "label": "Recurrent pneumonia"
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+        "description": "A novel mutation in the signal transducer and activator of transcription 3 (STAT3) gene, in hyper-IgE syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002726",
+      "label": "Recurrent Staphylococcus aureus infections"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "description": "A novel mutation in the signal transducer and activator of transcription 3 (STAT3) gene, in hyper-IgE syndrome"
+      }
+    }]
+  }, {
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+      "id": "HP:0025419",
+      "label": "Pulmonary pneumatocele"
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+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:20149460",
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+      }
+    }]
+  }, {
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+      "label": "Abnormal proportion of CD4 T cells"
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+    "negated": true,
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+        "description": "A novel mutation in the signal transducer and activator of transcription 3 (STAT3) gene, in hyper-IgE syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001880",
+      "label": "Eosinophilia"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:20149460",
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+      }
+    }]
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+        "description": "A novel mutation in the signal transducer and activator of transcription 3 (STAT3) gene, in hyper-IgE syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000280",
+      "label": "Coarse facial features"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20149460",
+        "description": "A novel mutation in the signal transducer and activator of transcription 3 (STAT3) gene, in hyper-IgE syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:6774",
+    "symbol": "STAT3"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "17",
+      "pos": 40485715,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:147060",
+      "label": "HYPER-IgE RECURRENT INFECTION SYNDROME, AUTOSOMAL DOMINANT"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:20149460",
+      "description": "A novel mutation in the signal transducer and activator of transcription 3 (STAT3) gene, in hyper-IgE syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Park-2014-DNM2-Patient_1.json b/notebooks/LIRICAL/v1phenopackets/Park-2014-DNM2-Patient_1.json
new file mode 100644
index 000000000..85be628fd
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Park-2014-DNM2-Patient_1.json
@@ -0,0 +1,268 @@
+{
+  "id": "PMID:24465259-Park-2014-DNM2-Patient_1",
+  "subject": {
+    "id": "Patient 1",
+    "ageAtCollection": {
+      "age": "35"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0003749",
+      "label": "Pelvic girdle muscle weakness"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24465259",
+        "description": "Clinical and Pathological Features of Korean Patients with DNM2-Related Centronuclear Myopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003722",
+      "label": "Neck flexor weakness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24465259",
+        "description": "Clinical and Pathological Features of Korean Patients with DNM2-Related Centronuclear Myopathy"
+      }
+    }]
+  }, {
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+      "id": "HP:0040129",
+      "label": "Abnormal nerve conduction velocity"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
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+      }
+    }]
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+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:24465259",
+        "description": "Clinical and Pathological Features of Korean Patients with DNM2-Related Centronuclear Myopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003693",
+      "label": "Distal amyotrophy"
+    },
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+        "id": "PMID:24465259",
+        "description": "Clinical and Pathological Features of Korean Patients with DNM2-Related Centronuclear Myopathy"
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+    }]
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+      "label": "External ophthalmoplegia"
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:24465259",
+        "description": "Clinical and Pathological Features of Korean Patients with DNM2-Related Centronuclear Myopathy"
+      }
+    }]
+  }, {
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+      "id": "HP:0000277",
+      "label": "Abnormality of the mandible"
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+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:24465259",
+        "description": "Clinical and Pathological Features of Korean Patients with DNM2-Related Centronuclear Myopathy"
+      }
+    }]
+  }, {
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+      "id": "HP:0002486",
+      "label": "Myotonia"
+    },
+    "evidence": [{
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+        "description": "Clinical and Pathological Features of Korean Patients with DNM2-Related Centronuclear Myopathy"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Distal lower limb muscle weakness"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:24465259",
+        "description": "Clinical and Pathological Features of Korean Patients with DNM2-Related Centronuclear Myopathy"
+      }
+    }]
+  }, {
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+      "id": "HP:0007209",
+      "label": "Facial paralysis"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Clinical and Pathological Features of Korean Patients with DNM2-Related Centronuclear Myopathy"
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+    }]
+  }, {
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+      "label": "Achilles tendon contracture"
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:24465259",
+        "description": "Clinical and Pathological Features of Korean Patients with DNM2-Related Centronuclear Myopathy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000508",
+      "label": "Ptosis"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:24465259",
+        "description": "Clinical and Pathological Features of Korean Patients with DNM2-Related Centronuclear Myopathy"
+      }
+    }]
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+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:160150",
+      "label": "MYOPATHY, CENTRONUCLEAR, 1; CNM1"
+    }
+  }],
+  "metaData": {
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+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:24465259",
+      "description": "Clinical and Pathological Features of Korean Patients with DNM2-Related Centronuclear Myopathy"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Park-2016-GSN-III_5.json b/notebooks/LIRICAL/v1phenopackets/Park-2016-GSN-III_5.json
new file mode 100644
index 000000000..4df34a51a
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Park-2016-GSN-III_5.json
@@ -0,0 +1,177 @@
+{
+  "id": "PMID:26915616-Park-2016-GSN-III:5",
+  "subject": {
+    "id": "III:5",
+    "ageAtCollection": {
+      "age": "P58Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0007089",
+      "label": "Facial-lingual fasciculations"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26915616",
+        "description": "The First Korean Family With Hereditary Gelsolin Amyloidosis Caused by p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000966",
+      "label": "Hypohidrosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:26915616",
+        "description": "The First Korean Family With Hereditary Gelsolin Amyloidosis Caused by p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000221",
+      "label": "Furrowed tongue"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "The First Korean Family With Hereditary Gelsolin Amyloidosis Caused by p"
+      }
+    }]
+  }, {
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+      "label": "EMG: decremental response of compound muscle action potential to repetitive nerve stimulation"
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:26915616",
+        "description": "The First Korean Family With Hereditary Gelsolin Amyloidosis Caused by p"
+      }
+    }]
+  }, {
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+      "id": "HP:0000973",
+      "label": "Cutis laxa"
+    },
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+        "label": "author statement supported by traceable reference"
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+    }]
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+      "label": "Paresthesia"
+    },
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+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:26915616",
+        "description": "The First Korean Family With Hereditary Gelsolin Amyloidosis Caused by p"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2934",
+    "symbol": "GSN"
+  }],
+  "variants": [{
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+      "chr": "9",
+      "pos": 124073097,
+      "ref": "G",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:105120",
+      "label": "AMYLOIDOSIS, FINNISH TYPE"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:26915616",
+      "description": "The First Korean Family With Hereditary Gelsolin Amyloidosis Caused by p"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Pasic-2013-NBN-12-year-old_girl.json b/notebooks/LIRICAL/v1phenopackets/Pasic-2013-NBN-12-year-old_girl.json
new file mode 100644
index 000000000..34af43276
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Pasic-2013-NBN-12-year-old_girl.json
@@ -0,0 +1,357 @@
+{
+  "id": "PMID:24044622-Pasic-2013-NBN-12-year-old_girl",
+  "subject": {
+    "id": "12-year-old girl",
+    "ageAtCollection": {
+      "age": "P12T"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000320",
+      "label": "Bird-like facies"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24044622",
+        "description": "Nijmegen breakage syndrome and chronic polyarthritis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002110",
+      "label": "Bronchiectasis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24044622",
+        "description": "Nijmegen breakage syndrome and chronic polyarthritis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003347",
+      "label": "Impaired lymphocyte transformation with phytohemagglutinin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24044622",
+        "description": "Nijmegen breakage syndrome and chronic polyarthritis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011227",
+      "label": "Elevated C-reactive protein level"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24044622",
+        "description": "Nijmegen breakage syndrome and chronic polyarthritis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000582",
+      "label": "Upslanted palpebral fissure"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24044622",
+        "description": "Nijmegen breakage syndrome and chronic polyarthritis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030084",
+      "label": "Clinodactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24044622",
+        "description": "Nijmegen breakage syndrome and chronic polyarthritis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003565",
+      "label": "Elevated erythrocyte sedimentation rate"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24044622",
+        "description": "Nijmegen breakage syndrome and chronic polyarthritis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001010",
+      "label": "Hypopigmentation of the skin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24044622",
+        "description": "Nijmegen breakage syndrome and chronic polyarthritis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004315",
+      "label": "Decreased circulating IgG level"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24044622",
+        "description": "Nijmegen breakage syndrome and chronic polyarthritis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000403",
+      "label": "Recurrent otitis media"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24044622",
+        "description": "Nijmegen breakage syndrome and chronic polyarthritis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002720",
+      "label": "Decreased circulating IgA level"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24044622",
+        "description": "Nijmegen breakage syndrome and chronic polyarthritis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002850",
+      "label": "Decreased circulating total IgM"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24044622",
+        "description": "Nijmegen breakage syndrome and chronic polyarthritis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006532",
+      "label": "Recurrent pneumonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24044622",
+        "description": "Nijmegen breakage syndrome and chronic polyarthritis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002265",
+      "label": "Large fleshy ears"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24044622",
+        "description": "Nijmegen breakage syndrome and chronic polyarthritis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000316",
+      "label": "Hypertelorism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24044622",
+        "description": "Nijmegen breakage syndrome and chronic polyarthritis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000252",
+      "label": "Microcephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24044622",
+        "description": "Nijmegen breakage syndrome and chronic polyarthritis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001511",
+      "label": "Intrauterine growth retardation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24044622",
+        "description": "Nijmegen breakage syndrome and chronic polyarthritis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0032170",
+      "label": "Severe varicella zoster infection"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24044622",
+        "description": "Nijmegen breakage syndrome and chronic polyarthritis"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:4683",
+    "symbol": "NBN"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "8",
+      "pos": 90983441,
+      "ref": "ATTTGT",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:251260",
+      "label": "NIJMEGEN BREAKAGE SYNDROME"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:24044622",
+      "description": "Nijmegen breakage syndrome and chronic polyarthritis"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Pastor-2018-SAMD9L-P5.json b/notebooks/LIRICAL/v1phenopackets/Pastor-2018-SAMD9L-P5.json
new file mode 100644
index 000000000..0fa0767ec
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Pastor-2018-SAMD9L-P5.json
@@ -0,0 +1,117 @@
+{
+  "id": "PMID:29217778-Pastor-2018-SAMD9L-P5",
+  "subject": {
+    "id": "P5",
+    "ageAtCollection": {
+      "age": "P7Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0005528",
+      "label": "Bone marrow hypocellularity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29217778",
+        "description": "Constitutional SAMD9L mutations cause familial myelodysplastic syndrome and transient monosomy 7"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001873",
+      "label": "Thrombocytopenia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29217778",
+        "description": "Constitutional SAMD9L mutations cause familial myelodysplastic syndrome and transient monosomy 7"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:219285",
+    "symbol": "SAMD9L"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "7",
+      "pos": 92762329,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:159550",
+      "label": "Ataxia-pancytopenia syndrome"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29217778",
+      "description": "Constitutional SAMD9L mutations cause familial myelodysplastic syndrome and transient monosomy 7"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Pastor-2018-SAMD9L-P7.json b/notebooks/LIRICAL/v1phenopackets/Pastor-2018-SAMD9L-P7.json
new file mode 100644
index 000000000..9b0319be0
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Pastor-2018-SAMD9L-P7.json
@@ -0,0 +1,117 @@
+{
+  "id": "PMID:29217778-Pastor-2018-SAMD9L-P7",
+  "subject": {
+    "id": "P7",
+    "ageAtCollection": {
+      "age": "P2Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0005528",
+      "label": "Bone marrow hypocellularity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29217778",
+        "description": "Constitutional SAMD9L mutations cause familial myelodysplastic syndrome and transient monosomy 7"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001873",
+      "label": "Thrombocytopenia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29217778",
+        "description": "Constitutional SAMD9L mutations cause familial myelodysplastic syndrome and transient monosomy 7"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:219285",
+    "symbol": "SAMD9L"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "7",
+      "pos": 92762645,
+      "ref": "G",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:159550",
+      "label": "Ataxia-pancytopenia syndrome"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29217778",
+      "description": "Constitutional SAMD9L mutations cause familial myelodysplastic syndrome and transient monosomy 7"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Patsi-2018-PNPLA6-18_year-old_female.json b/notebooks/LIRICAL/v1phenopackets/Patsi-2018-PNPLA6-18_year-old_female.json
new file mode 100644
index 000000000..b114ffa7e
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Patsi-2018-PNPLA6-18_year-old_female.json
@@ -0,0 +1,341 @@
+{
+  "id": "PMID:30097146-Patsi-2018-PNPLA6-18_year-old_female",
+  "subject": {
+    "id": "18 year-old female",
+    "ageAtCollection": {
+      "age": "18Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002317",
+      "label": "Unsteady gait"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30097146",
+        "description": "A new PNPLA6 mutation presenting as Oliver McFarlane syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000533",
+      "label": "Chorioretinal atrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30097146",
+        "description": "A new PNPLA6 mutation presenting as Oliver McFarlane syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003477",
+      "label": "Peripheral axonal neuropathy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30097146",
+        "description": "A new PNPLA6 mutation presenting as Oliver McFarlane syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008070",
+      "label": "Sparse hair"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30097146",
+        "description": "A new PNPLA6 mutation presenting as Oliver McFarlane syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000821",
+      "label": "Hypothyroidism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30097146",
+        "description": "A new PNPLA6 mutation presenting as Oliver McFarlane syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002080",
+      "label": "Intention tremor"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30097146",
+        "description": "A new PNPLA6 mutation presenting as Oliver McFarlane syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000824",
+      "label": "Growth hormone deficiency"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30097146",
+        "description": "A new PNPLA6 mutation presenting as Oliver McFarlane syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002066",
+      "label": "Gait ataxia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30097146",
+        "description": "A new PNPLA6 mutation presenting as Oliver McFarlane syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001260",
+      "label": "Dysarthria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30097146",
+        "description": "A new PNPLA6 mutation presenting as Oliver McFarlane syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000639",
+      "label": "Nystagmus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30097146",
+        "description": "A new PNPLA6 mutation presenting as Oliver McFarlane syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001265",
+      "label": "Hyporeflexia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30097146",
+        "description": "A new PNPLA6 mutation presenting as Oliver McFarlane syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000527",
+      "label": "Long eyelashes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30097146",
+        "description": "A new PNPLA6 mutation presenting as Oliver McFarlane syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006855",
+      "label": "Cerebellar vermis atrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30097146",
+        "description": "A new PNPLA6 mutation presenting as Oliver McFarlane syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001761",
+      "label": "Pes cavus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30097146",
+        "description": "A new PNPLA6 mutation presenting as Oliver McFarlane syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011003",
+      "label": "High myopia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30097146",
+        "description": "A new PNPLA6 mutation presenting as Oliver McFarlane syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30097146",
+        "description": "A new PNPLA6 mutation presenting as Oliver McFarlane syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001643",
+      "label": "Patent ductus arteriosus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30097146",
+        "description": "A new PNPLA6 mutation presenting as Oliver McFarlane syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:10908",
+    "symbol": "PNPLA6"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "19",
+      "pos": 7623928,
+      "ref": "C",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:275400",
+      "label": "OLIVER-MCFARLANE SYNDROME; OMCS"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30097146",
+      "description": "A new PNPLA6 mutation presenting as Oliver McFarlane syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Paun-2013-RET-DM_patient.json b/notebooks/LIRICAL/v1phenopackets/Paun-2013-RET-DM_patient.json
new file mode 100644
index 000000000..ca01ad2d7
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Paun-2013-RET-DM_patient.json
@@ -0,0 +1,131 @@
+{
+  "id": "PMID:24331334-Păun-2013-RET-DM_patient",
+  "subject": {
+    "id": "DM  patient",
+    "ageAtCollection": {
+      "age": "19Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0025388",
+      "label": "Thyroid nodule"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24331334",
+        "description": "Multiple endocrine neoplasia type 2A: case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003528",
+      "label": "Elevated calcitonin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24331334",
+        "description": "Multiple endocrine neoplasia type 2A: case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002666",
+      "label": "Pheochromocytoma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24331334",
+        "description": "Multiple endocrine neoplasia type 2A: case report"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:5979",
+    "symbol": "RET"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "10",
+      "pos": 43609950,
+      "ref": "C",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:171400",
+      "label": "MULTIPLE ENDOCRINE NEOPLASIA, TYPE IIA; MEN2A"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:24331334",
+      "description": "Multiple endocrine neoplasia type 2A: case report"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Pipilas-2016-CALM1-Case_2.json b/notebooks/LIRICAL/v1phenopackets/Pipilas-2016-CALM1-Case_2.json
new file mode 100644
index 000000000..180be4522
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Pipilas-2016-CALM1-Case_2.json
@@ -0,0 +1,148 @@
+{
+  "id": "PMID:27374306-Pipilas-2016-CALM1-Case_2",
+  "subject": {
+    "id": "Case 2",
+    "ageAtCollection": {
+      "age": "P3Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0005184",
+      "label": "Prolonged QTc interval"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27374306",
+        "description": "Novel calmodulin mutations associated with congenital long QT syndrome affect calcium current in human cardiomyocytes"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001663",
+      "label": "Ventricular fibrillation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27374306",
+        "description": "Novel calmodulin mutations associated with congenital long QT syndrome affect calcium current in human cardiomyocytes"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012819",
+      "label": "Myocarditis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27374306",
+        "description": "Novel calmodulin mutations associated with congenital long QT syndrome affect calcium current in human cardiomyocytes"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031677",
+      "label": "Polymorphic ventricular tachycardia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27374306",
+        "description": "Novel calmodulin mutations associated with congenital long QT syndrome affect calcium current in human cardiomyocytes"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:801",
+    "symbol": "CALM1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "14",
+      "pos": 90870832,
+      "ref": "A",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616247",
+      "label": "LONG QT SYNDROME 14; LQT14"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27374306",
+      "description": "Novel calmodulin mutations associated with congenital long QT syndrome affect calcium current in human cardiomyocytes"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Pipilas-2016-CALM2-Case_1.json b/notebooks/LIRICAL/v1phenopackets/Pipilas-2016-CALM2-Case_1.json
new file mode 100644
index 000000000..47a2da6f0
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Pipilas-2016-CALM2-Case_1.json
@@ -0,0 +1,147 @@
+{
+  "id": "PMID:27374306-Pipilas-2016-CALM2-Case_1",
+  "subject": {
+    "id": "Case 1",
+    "ageAtCollection": {
+      "age": "P1Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0005184",
+      "label": "Prolonged QTc interval"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27374306",
+        "description": "Novel calmodulin mutations associated with congenital long QT syndrome affect calcium current in human cardiomyocytes"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001678",
+      "label": "Atrioventricular block"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27374306",
+        "description": "Novel calmodulin mutations associated with congenital long QT syndrome affect calcium current in human cardiomyocytes"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030682",
+      "label": "Left ventricular noncompaction"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27374306",
+        "description": "Novel calmodulin mutations associated with congenital long QT syndrome affect calcium current in human cardiomyocytes"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001688",
+      "label": "Sinus bradycardia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27374306",
+        "description": "Novel calmodulin mutations associated with congenital long QT syndrome affect calcium current in human cardiomyocytes"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:805",
+    "symbol": "CALM2"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "2",
+      "pos": 47388889,
+      "ref": "C",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616249",
+      "label": "LONG QT SYNDROME 15; LQT15"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27374306",
+      "description": "Novel calmodulin mutations associated with congenital long QT syndrome affect calcium current in human cardiomyocytes"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Prada-2014-CTSA-BAB3767.json b/notebooks/LIRICAL/v1phenopackets/Prada-2014-CTSA-BAB3767.json
new file mode 100644
index 000000000..94d280eb1
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Prada-2014-CTSA-BAB3767.json
@@ -0,0 +1,299 @@
+{
+  "id": "PMID:24769197-Prada-2014-CTSA-BAB3767",
+  "subject": {
+    "id": "BAB3767",
+    "ageAtCollection": {
+      "age": "24Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000405",
+      "label": "Conductive hearing impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24769197",
+        "description": "Clinical utility of whole-exome sequencing in rare diseases: Galactosialidosis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010729",
+      "label": "Cherry red spot of the macula"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24769197",
+        "description": "Clinical utility of whole-exome sequencing in rare diseases: Galactosialidosis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24769197",
+        "description": "Clinical utility of whole-exome sequencing in rare diseases: Galactosialidosis"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000470",
+      "label": "Short neck"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24769197",
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+  }, {
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+      "ref": "CTA",
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+    "zygosity": {
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+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
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+      "label": "GALACTOSIALIDOSIS; GSL"
+    }
+  }],
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+      "id": "hp",
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+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
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+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
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+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
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+    }, {
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+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
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+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
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+    "externalReferences": [{
+      "id": "PMID:24769197",
+      "description": "Clinical utility of whole-exome sequencing in rare diseases: Galactosialidosis"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Qin-2017-NRL-II_2.json b/notebooks/LIRICAL/v1phenopackets/Qin-2017-NRL-II_2.json
new file mode 100644
index 000000000..0794f3afb
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Qin-2017-NRL-II_2.json
@@ -0,0 +1,147 @@
+{
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+      "label": "Visual field defect"
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+      }
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+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
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+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
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+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
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+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Rejeb-2017-VPS13B-proposita.json b/notebooks/LIRICAL/v1phenopackets/Rejeb-2017-VPS13B-proposita.json
new file mode 100644
index 000000000..40602651e
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Rejeb-2017-VPS13B-proposita.json
@@ -0,0 +1,371 @@
+{
+  "id": "PMID:29149870-Rejeb-2017-VPS13B-proposita",
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+      "age": "P12Y"
+    },
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+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000580",
+      "label": "Pigmentary retinopathy"
+    },
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:29149870",
+        "description": "First case report of Cohen syndrome in the Tunisian population caused by VPS13B mutations"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:29149870",
+        "description": "First case report of Cohen syndrome in the Tunisian population caused by VPS13B mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001382",
+      "label": "Joint hypermobility"
+    },
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+      "label": "Tapered finger"
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+        "description": "First case report of Cohen syndrome in the Tunisian population caused by VPS13B mutations"
+      }
+    }]
+  }, {
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+      "id": "HP:0000253",
+      "label": "Progressive microcephaly"
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+    "evidence": [{
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+    }]
+  }, {
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+      "label": "Thick hair"
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+  "genes": [{
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+    "zygosity": {
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+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29149870",
+      "description": "First case report of Cohen syndrome in the Tunisian population caused by VPS13B mutations"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Reyes-de_la_Rosa-2018-JAG1-Proband.json b/notebooks/LIRICAL/v1phenopackets/Reyes-de_la_Rosa-2018-JAG1-Proband.json
new file mode 100644
index 000000000..62900af33
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Reyes-de_la_Rosa-2018-JAG1-Proband.json
@@ -0,0 +1,358 @@
+{
+  "id": "PMID:30046498-Reyes-de_la_Rosa-2018-JAG1-Proband",
+  "subject": {
+    "id": "Proband",
+    "ageAtCollection": {
+      "age": "P2Y7M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000958",
+      "label": "Dry skin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30046498",
+        "description": "A Novel c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000411",
+      "label": "Protruding ear"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30046498",
+        "description": "A Novel c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003316",
+      "label": "Butterfly vertebrae"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30046498",
+        "description": "A Novel c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30046498",
+        "description": "A Novel c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001114",
+      "label": "Xanthelasma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30046498",
+        "description": "A Novel c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000325",
+      "label": "Triangular face"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30046498",
+        "description": "A Novel c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002240",
+      "label": "Hepatomegaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30046498",
+        "description": "A Novel c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002089",
+      "label": "Pulmonary hypoplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30046498",
+        "description": "A Novel c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012704",
+      "label": "Widened subarachnoid space"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30046498",
+        "description": "A Novel c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001396",
+      "label": "Cholestasis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30046498",
+        "description": "A Novel c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0045075",
+      "label": "Sparse eyebrow"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30046498",
+        "description": "A Novel c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000490",
+      "label": "Deeply set eye"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30046498",
+        "description": "A Novel c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030148",
+      "label": "Heart murmur"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30046498",
+        "description": "A Novel c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000952",
+      "label": "Jaundice"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30046498",
+        "description": "A Novel c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011985",
+      "label": "Acholic stools"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30046498",
+        "description": "A Novel c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000627",
+      "label": "Posterior embryotoxon"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30046498",
+        "description": "A Novel c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000337",
+      "label": "Broad forehead"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30046498",
+        "description": "A Novel c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000303",
+      "label": "Mandibular prognathia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30046498",
+        "description": "A Novel c"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:182",
+    "symbol": "JAG1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "20",
+      "pos": 10653644,
+      "ref": "G",
+      "alt": "GC"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:118450",
+      "label": "ALAGILLE SYNDROME 1; ALGS1"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30046498",
+      "description": "A Novel c"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Rincon-2019-WRN-48-year-old_male.json b/notebooks/LIRICAL/v1phenopackets/Rincon-2019-WRN-48-year-old_male.json
new file mode 100644
index 000000000..385238ed9
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Rincon-2019-WRN-48-year-old_male.json
@@ -0,0 +1,360 @@
+{
+  "id": "PMID:30891318-Rincón-2019-WRN-48-year-old_male",
+  "subject": {
+    "id": "48-year-old male",
+    "ageAtCollection": {
+      "age": "P48Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000939",
+      "label": "Osteoporosis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30891318",
+        "description": "Werner\u0027s Syndrome: Understanding the Phenotype of Premature Aging-First Case Described in Colombia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001763",
+      "label": "Pes planus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30891318",
+        "description": "Werner\u0027s Syndrome: Understanding the Phenotype of Premature Aging-First Case Described in Colombia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003758",
+      "label": "Reduced subcutaneous adipose tissue"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30891318",
+        "description": "Werner\u0027s Syndrome: Understanding the Phenotype of Premature Aging-First Case Described in Colombia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012804",
+      "label": "Corneal ulceration"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30891318",
+        "description": "Werner\u0027s Syndrome: Understanding the Phenotype of Premature Aging-First Case Described in Colombia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001956",
+      "label": "Truncal obesity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30891318",
+        "description": "Werner\u0027s Syndrome: Understanding the Phenotype of Premature Aging-First Case Described in Colombia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000518",
+      "label": "Cataract"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30891318",
+        "description": "Werner\u0027s Syndrome: Understanding the Phenotype of Premature Aging-First Case Described in Colombia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000962",
+      "label": "Hyperkeratosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30891318",
+        "description": "Werner\u0027s Syndrome: Understanding the Phenotype of Premature Aging-First Case Described in Colombia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000822",
+      "label": "Hypertension"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30891318",
+        "description": "Werner\u0027s Syndrome: Understanding the Phenotype of Premature Aging-First Case Described in Colombia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002216",
+      "label": "Premature graying of hair"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30891318",
+        "description": "Werner\u0027s Syndrome: Understanding the Phenotype of Premature Aging-First Case Described in Colombia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002155",
+      "label": "Hypertriglyceridemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30891318",
+        "description": "Werner\u0027s Syndrome: Understanding the Phenotype of Premature Aging-First Case Described in Colombia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001620",
+      "label": "High pitched voice"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30891318",
+        "description": "Werner\u0027s Syndrome: Understanding the Phenotype of Premature Aging-First Case Described in Colombia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005978",
+      "label": "Type II diabetes mellitus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30891318",
+        "description": "Werner\u0027s Syndrome: Understanding the Phenotype of Premature Aging-First Case Described in Colombia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000320",
+      "label": "Bird-like facies"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30891318",
+        "description": "Werner\u0027s Syndrome: Understanding the Phenotype of Premature Aging-First Case Described in Colombia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000819",
+      "label": "Diabetes mellitus"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30891318",
+        "description": "Werner\u0027s Syndrome: Understanding the Phenotype of Premature Aging-First Case Described in Colombia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30891318",
+        "description": "Werner\u0027s Syndrome: Understanding the Phenotype of Premature Aging-First Case Described in Colombia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000821",
+      "label": "Hypothyroidism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30891318",
+        "description": "Werner\u0027s Syndrome: Understanding the Phenotype of Premature Aging-First Case Described in Colombia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0025441",
+      "label": "Achilles tendon calcification"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30891318",
+        "description": "Werner\u0027s Syndrome: Understanding the Phenotype of Premature Aging-First Case Described in Colombia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003241",
+      "label": "External genital hypoplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30891318",
+        "description": "Werner\u0027s Syndrome: Understanding the Phenotype of Premature Aging-First Case Described in Colombia"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:7486",
+    "symbol": "WRN"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "8",
+      "pos": 30977891,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:277700",
+      "label": "WERNER SYNDROME; WRN"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
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+      "namespacePrefix": "OMIM"
+    }],
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+    "externalReferences": [{
+      "id": "PMID:30891318",
+      "description": "Werner\u0027s Syndrome: Understanding the Phenotype of Premature Aging-First Case Described in Colombia"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Ritelli-2013-COL5A1-AN_002501.json b/notebooks/LIRICAL/v1phenopackets/Ritelli-2013-COL5A1-AN_002501.json
new file mode 100644
index 000000000..47b6aae88
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Ritelli-2013-COL5A1-AN_002501.json
@@ -0,0 +1,222 @@
+{
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+      "name": "NCBI organismal classification",
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+      "namespacePrefix": "NCBITaxon"
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+    }, {
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+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Ritelli-2014-TGFB2-proposita.json b/notebooks/LIRICAL/v1phenopackets/Ritelli-2014-TGFB2-proposita.json
new file mode 100644
index 000000000..83db83e99
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Ritelli-2014-TGFB2-proposita.json
@@ -0,0 +1,313 @@
+{
+  "id": "PMID:25163805-Ritelli-2014-TGFB2-proposita",
+  "subject": {
+    "id": "proposita",
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+      "age": "P57Y"
+    },
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+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
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+      "id": "HP:0012532",
+      "label": "Chronic pain"
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+      "label": "Scoliosis"
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+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Ritelli-2019-AEBP1-AN_006205.json b/notebooks/LIRICAL/v1phenopackets/Ritelli-2019-AEBP1-AN_006205.json
new file mode 100644
index 000000000..360bf7a90
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Ritelli-2019-AEBP1-AN_006205.json
@@ -0,0 +1,433 @@
+{
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+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
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+      "label": "Scoliosis"
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+  }, {
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+  }, {
+    "type": {
+      "id": "HP:0012432",
+      "label": "Chronic fatigue"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30759870",
+        "description": "Expanding the Clinical and Mutational Spectrum of Recessive AEBP1-Related Classical-Like Ehlers-Danlos Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001319",
+      "label": "Neonatal hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30759870",
+        "description": "Expanding the Clinical and Mutational Spectrum of Recessive AEBP1-Related Classical-Like Ehlers-Danlos Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000974",
+      "label": "Hyperextensible skin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30759870",
+        "description": "Expanding the Clinical and Mutational Spectrum of Recessive AEBP1-Related Classical-Like Ehlers-Danlos Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004417",
+      "label": "Intermittent claudication"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30759870",
+        "description": "Expanding the Clinical and Mutational Spectrum of Recessive AEBP1-Related Classical-Like Ehlers-Danlos Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031158",
+      "label": "Widened atrophic scar"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30759870",
+        "description": "Expanding the Clinical and Mutational Spectrum of Recessive AEBP1-Related Classical-Like Ehlers-Danlos Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004976",
+      "label": "Knee dislocation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30759870",
+        "description": "Expanding the Clinical and Mutational Spectrum of Recessive AEBP1-Related Classical-Like Ehlers-Danlos Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001582",
+      "label": "Redundant skin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30759870",
+        "description": "Expanding the Clinical and Mutational Spectrum of Recessive AEBP1-Related Classical-Like Ehlers-Danlos Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001270",
+      "label": "Motor delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30759870",
+        "description": "Expanding the Clinical and Mutational Spectrum of Recessive AEBP1-Related Classical-Like Ehlers-Danlos Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002619",
+      "label": "Varicose veins"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30759870",
+        "description": "Expanding the Clinical and Mutational Spectrum of Recessive AEBP1-Related Classical-Like Ehlers-Danlos Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000993",
+      "label": "Molluscoid pseudotumors"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30759870",
+        "description": "Expanding the Clinical and Mutational Spectrum of Recessive AEBP1-Related Classical-Like Ehlers-Danlos Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000978",
+      "label": "Bruising susceptibility"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30759870",
+        "description": "Expanding the Clinical and Mutational Spectrum of Recessive AEBP1-Related Classical-Like Ehlers-Danlos Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30759870",
+        "description": "Expanding the Clinical and Mutational Spectrum of Recessive AEBP1-Related Classical-Like Ehlers-Danlos Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001058",
+      "label": "Poor wound healing"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30759870",
+        "description": "Expanding the Clinical and Mutational Spectrum of Recessive AEBP1-Related Classical-Like Ehlers-Danlos Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003419",
+      "label": "Low back pain"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30759870",
+        "description": "Expanding the Clinical and Mutational Spectrum of Recessive AEBP1-Related Classical-Like Ehlers-Danlos Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000218",
+      "label": "High palate"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30759870",
+        "description": "Expanding the Clinical and Mutational Spectrum of Recessive AEBP1-Related Classical-Like Ehlers-Danlos Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001027",
+      "label": "Soft, doughy skin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30759870",
+        "description": "Expanding the Clinical and Mutational Spectrum of Recessive AEBP1-Related Classical-Like Ehlers-Danlos Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004419",
+      "label": "Recurrent thrombophlebitis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30759870",
+        "description": "Expanding the Clinical and Mutational Spectrum of Recessive AEBP1-Related Classical-Like Ehlers-Danlos Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000704",
+      "label": "Periodontitis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30759870",
+        "description": "Expanding the Clinical and Mutational Spectrum of Recessive AEBP1-Related Classical-Like Ehlers-Danlos Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001030",
+      "label": "Fragile skin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30759870",
+        "description": "Expanding the Clinical and Mutational Spectrum of Recessive AEBP1-Related Classical-Like Ehlers-Danlos Syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:165",
+    "symbol": "AEBP1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "7",
+      "pos": 44151537,
+      "ref": "T",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:618000",
+      "label": "Ehlers-Danlos syndrome, classic-like, 2"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30759870",
+      "description": "Expanding the Clinical and Mutational Spectrum of Recessive AEBP1-Related Classical-Like Ehlers-Danlos Syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Rohanizadegan-2018-DHCR24-proband.json b/notebooks/LIRICAL/v1phenopackets/Rohanizadegan-2018-DHCR24-proband.json
new file mode 100644
index 000000000..094a56656
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Rohanizadegan-2018-DHCR24-proband.json
@@ -0,0 +1,598 @@
+{
+  "id": "PMID:29175559-Rohanizadegan-2018-DHCR24-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P1Y8M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000403",
+      "label": "Recurrent otitis media"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002007",
+      "label": "Frontal bossing"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100807",
+      "label": "Long fingers"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002099",
+      "label": "Asthma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002019",
+      "label": "Constipation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001558",
+      "label": "Decreased fetal movement"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002208",
+      "label": "Coarse hair"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000426",
+      "label": "Prominent nasal bridge"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003487",
+      "label": "Babinski sign"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006610",
+      "label": "Wide intermamillary distance"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002307",
+      "label": "Drooling"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000475",
+      "label": "Broad neck"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001762",
+      "label": "Talipes equinovarus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000369",
+      "label": "Low-set ears"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000914",
+      "label": "Shield chest"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007665",
+      "label": "Curly eyelashes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000494",
+      "label": "Downslanted palpebral fissures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000238",
+      "label": "Hydrocephalus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000577",
+      "label": "Exotropia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000358",
+      "label": "Posteriorly rotated ears"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000252",
+      "label": "Microcephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000347",
+      "label": "Micrognathia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001845",
+      "label": "Overlapping toe"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000341",
+      "label": "Narrow forehead"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001181",
+      "label": "Adducted thumb"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000175",
+      "label": "Cleft palate"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000767",
+      "label": "Pectus excavatum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001510",
+      "label": "Growth delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000470",
+      "label": "Short neck"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005487",
+      "label": "Prominent metopic ridge"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
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+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Long eyelashes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031910",
+      "label": "Abnormal cranial nerve physiology"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29175559",
+        "description": "Desmosterolosis presenting with multiple congenital anomalies"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:1718",
+    "symbol": "DHCR24"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 55340807,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:602398",
+      "label": "DESMOSTEROLOSIS"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29175559",
+      "description": "Desmosterolosis presenting with multiple congenital anomalies"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Romero-Quintana-2013-CTSC-Case_1P1.json b/notebooks/LIRICAL/v1phenopackets/Romero-Quintana-2013-CTSC-Case_1P1.json
new file mode 100644
index 000000000..447ff7c39
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Romero-Quintana-2013-CTSC-Case_1P1.json
@@ -0,0 +1,177 @@
+{
+  "id": "PMID:23311634-Romero-Quintana-2013-CTSC-Case_1P1",
+  "subject": {
+    "id": "Case 1P1",
+    "ageAtCollection": {
+      "age": "P7Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0011132",
+      "label": "Chronic furunculosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23311634",
+        "description": "Identification of novel mutation in cathepsin C gene causing Papillon-Lefèvre Syndrome in Mexican patients"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000972",
+      "label": "Palmoplantar hyperkeratosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23311634",
+        "description": "Identification of novel mutation in cathepsin C gene causing Papillon-Lefèvre Syndrome in Mexican patients"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006323",
+      "label": "Premature loss of primary teeth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:23311634",
+        "description": "Identification of novel mutation in cathepsin C gene causing Papillon-Lefèvre Syndrome in Mexican patients"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0410027",
+      "label": "Alveolar bone loss around teeth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23311634",
+        "description": "Identification of novel mutation in cathepsin C gene causing Papillon-Lefèvre Syndrome in Mexican patients"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000166",
+      "label": "Severe periodontitis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:23311634",
+        "description": "Identification of novel mutation in cathepsin C gene causing Papillon-Lefèvre Syndrome in Mexican patients"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0025084",
+      "label": "Folliculitis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23311634",
+        "description": "Identification of novel mutation in cathepsin C gene causing Papillon-Lefèvre Syndrome in Mexican patients"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:1075",
+    "symbol": "CTSC"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "11",
+      "pos": 88068220,
+      "ref": "A",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:245000",
+      "label": "PAPILLON-LEFEVRE SYNDROME; PALS"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:23311634",
+      "description": "Identification of novel mutation in cathepsin C gene causing Papillon-Lefèvre Syndrome in Mexican patients"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Salas-Alanis-2016-ANTXR1-14_year_old_brother.json b/notebooks/LIRICAL/v1phenopackets/Salas-Alanis-2016-ANTXR1-14_year_old_brother.json
new file mode 100644
index 000000000..b0afc7cad
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Salas-Alanis-2016-ANTXR1-14_year_old_brother.json
@@ -0,0 +1,252 @@
+{
+  "id": "PMID:27587992-Salas-Alanís-2016-ANTXR1-14_year_old_brother",
+  "subject": {
+    "id": "14 year old brother",
+    "ageAtCollection": {
+      "age": "P14Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000586",
+      "label": "Shallow orbits"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27587992",
+        "description": "New ANTXR1 Gene Mutation for GAPO Syndrome: A Case Report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000706",
+      "label": "Unerupted tooth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27587992",
+        "description": "New ANTXR1 Gene Mutation for GAPO Syndrome: A Case Report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011120",
+      "label": "Concave nasal ridge"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27587992",
+        "description": "New ANTXR1 Gene Mutation for GAPO Syndrome: A Case Report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012471",
+      "label": "Thick vermilion border"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27587992",
+        "description": "New ANTXR1 Gene Mutation for GAPO Syndrome: A Case Report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001006",
+      "label": "Hypotrichosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27587992",
+        "description": "New ANTXR1 Gene Mutation for GAPO Syndrome: A Case Report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003510",
+      "label": "Severe short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27587992",
+        "description": "New ANTXR1 Gene Mutation for GAPO Syndrome: A Case Report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000486",
+      "label": "Strabismus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27587992",
+        "description": "New ANTXR1 Gene Mutation for GAPO Syndrome: A Case Report"
+      }
+    }]
+  }, {
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+      "id": "HP:0000274",
+      "label": "Small face"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27587992",
+        "description": "New ANTXR1 Gene Mutation for GAPO Syndrome: A Case Report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001596",
+      "label": "Alopecia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27587992",
+        "description": "New ANTXR1 Gene Mutation for GAPO Syndrome: A Case Report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002007",
+      "label": "Frontal bossing"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27587992",
+        "description": "New ANTXR1 Gene Mutation for GAPO Syndrome: A Case Report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000336",
+      "label": "Prominent supraorbital ridges"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27587992",
+        "description": "New ANTXR1 Gene Mutation for GAPO Syndrome: A Case Report"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:84168",
+    "symbol": "ANTXR1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "2",
+      "pos": 69298917,
+      "ref": "A",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:230740",
+      "label": "GAPO SYNDROME"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27587992",
+      "description": "New ANTXR1 Gene Mutation for GAPO Syndrome: A Case Report"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Salpietro-2018-DDX59-Patient_1.json b/notebooks/LIRICAL/v1phenopackets/Salpietro-2018-DDX59-Patient_1.json
new file mode 100644
index 000000000..b01284f98
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Salpietro-2018-DDX59-Patient_1.json
@@ -0,0 +1,252 @@
+{
+  "id": "PMID:29127725-Salpietro-2018-DDX59-Patient_1",
+  "subject": {
+    "id": "Patient 1",
+    "ageAtCollection": {
+      "age": "adult"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0010554",
+      "label": "Cutaneous finger syndactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29127725",
+        "description": "A loss-of-function homozygous mutation in DDX59 implicates a conserved DEAD-box RNA helicase in nervous system development and function"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001162",
+      "label": "Postaxial hand polydactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29127725",
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+  }, {
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+      "label": "Prominent fingertip pads"
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+        "id": "ECO:0000033",
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+        "description": "A loss-of-function homozygous mutation in DDX59 implicates a conserved DEAD-box RNA helicase in nervous system development and function"
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+      "id": "HP:0007236",
+      "label": "Recurrent subcortical infarcts"
+    },
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+        "id": "ECO:0000033",
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+      "label": "Seizures"
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+      "evidenceCode": {
+        "id": "ECO:0000033",
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+    }]
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+      "label": "Dental malocclusion"
+    },
+    "evidence": [{
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+        "description": "A loss-of-function homozygous mutation in DDX59 implicates a conserved DEAD-box RNA helicase in nervous system development and function"
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+      "label": "High palate"
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+  }, {
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+      "label": "Intrauterine growth retardation"
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+  }, {
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+      "label": "Thick eyebrow"
+    },
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+        "description": "A loss-of-function homozygous mutation in DDX59 implicates a conserved DEAD-box RNA helicase in nervous system development and function"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:83479",
+    "symbol": "DDX59"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
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+      "pos": 200635683,
+      "ref": "GA",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:174300",
+      "label": "OROFACIODIGITAL SYNDROME V; OFD5"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29127725",
+      "description": "A loss-of-function homozygous mutation in DDX59 implicates a conserved DEAD-box RNA helicase in nervous system development and function"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Sandal-2018-CHST14-3-year_old_boy.json b/notebooks/LIRICAL/v1phenopackets/Sandal-2018-CHST14-3-year_old_boy.json
new file mode 100644
index 000000000..28e1f98e1
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Sandal-2018-CHST14-3-year_old_boy.json
@@ -0,0 +1,327 @@
+{
+  "id": "PMID:30249733-Sandal-2018-CHST14-3-year_old_boy",
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+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001762",
+      "label": "Talipes equinovarus"
+    },
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30249733",
+        "description": "Novel mutation in the CHST14 gene causing musculocontractural type of Ehlers-Danlos syndrome"
+      }
+    }]
+  }, {
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+      "id": "HP:0000316",
+      "label": "Hypertelorism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:30249733",
+        "description": "Novel mutation in the CHST14 gene causing musculocontractural type of Ehlers-Danlos syndrome"
+      }
+    }]
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+      }
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+    }]
+  }, {
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+      "label": "Arthrogryposis multiplex congenita"
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+        "description": "Novel mutation in the CHST14 gene causing musculocontractural type of Ehlers-Danlos syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:113189",
+    "symbol": "CHST14"
+  }],
+  "variants": [{
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+      "ref": "T",
+      "alt": "TA"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:601776",
+      "label": "EHLERS-DANLOS SYNDROME, MUSCULOCONTRACTURAL TYPE 1; EDSMC1"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
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+    "externalReferences": [{
+      "id": "PMID:30249733",
+      "description": "Novel mutation in the CHST14 gene causing musculocontractural type of Ehlers-Danlos syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Savage-2016-FANCI-NCI-309-1.json b/notebooks/LIRICAL/v1phenopackets/Savage-2016-FANCI-NCI-309-1.json
new file mode 100644
index 000000000..b5165f1d9
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Savage-2016-FANCI-NCI-309-1.json
@@ -0,0 +1,233 @@
+{
+  "id": "PMID:26590883-Savage-2016-FANCI-NCI-309-1",
+  "subject": {
+    "id": "NCI-309-1",
+    "ageAtCollection": {
+      "age": "P8Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002308",
+      "label": "Arnold-Chiari malformation"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26590883",
+        "description": "Novel FANCI mutations in Fanconi anemia with VACTERL association"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001631",
+      "label": "Atrial septal defect"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26590883",
+        "description": "Novel FANCI mutations in Fanconi anemia with VACTERL association"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0040012",
+      "label": "Chromosome breakage"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Novel FANCI mutations in Fanconi anemia with VACTERL association"
+      }
+    }]
+  }, {
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+      "label": "Ventricular septal defect"
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:26590883",
+        "description": "Novel FANCI mutations in Fanconi anemia with VACTERL association"
+      }
+    }]
+  }, {
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+      "id": "HP:0001643",
+      "label": "Patent ductus arteriosus"
+    },
+    "evidence": [{
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+      "label": "Small pituitary gland"
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+        "description": "Novel FANCI mutations in Fanconi anemia with VACTERL association"
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+      "label": "Short thumb"
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+        "description": "Novel FANCI mutations in Fanconi anemia with VACTERL association"
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+    }]
+  }, {
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+        "description": "Novel FANCI mutations in Fanconi anemia with VACTERL association"
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+      "reference": {
+        "id": "PMID:26590883",
+        "description": "Novel FANCI mutations in Fanconi anemia with VACTERL association"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:55215",
+    "symbol": "FANCI"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "15",
+      "pos": 89817462,
+      "ref": "T",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "15",
+      "pos": 89820029,
+      "ref": "TG",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:609053",
+      "label": "FANCONI ANEMIA, COMPLEMENTATION GROUP I; FANCI"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:26590883",
+      "description": "Novel FANCI mutations in Fanconi anemia with VACTERL association"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Sawal-2018-ADGRG1-Family_A,_II_2.json b/notebooks/LIRICAL/v1phenopackets/Sawal-2018-ADGRG1-Family_A,_II_2.json
new file mode 100644
index 000000000..fed84d60a
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Sawal-2018-ADGRG1-Family_A,_II_2.json
@@ -0,0 +1,146 @@
+{
+  "id": "PMID:29707406-Sawal-2018-ADGRG1-Family_A,_II:2",
+  "subject": {
+    "id": "Family A, II:2",
+    "ageAtCollection": {
+      "age": "7Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0006821",
+      "label": "Polymicrogyria, anterior to posterior gradient"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29707406",
+        "description": "Three Mutations in the Bilateral Frontoparietal Polymicrogyria Gene GPR56 in Pakistani Intellectual Disability Families"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29707406",
+        "description": "Three Mutations in the Bilateral Frontoparietal Polymicrogyria Gene GPR56 in Pakistani Intellectual Disability Families"
+      }
+    }]
+  }, {
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+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:29707406",
+        "description": "Three Mutations in the Bilateral Frontoparietal Polymicrogyria Gene GPR56 in Pakistani Intellectual Disability Families"
+      }
+    }]
+  }, {
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+      "id": "HP:0002069",
+      "label": "Generalized tonic-clonic seizures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29707406",
+        "description": "Three Mutations in the Bilateral Frontoparietal Polymicrogyria Gene GPR56 in Pakistani Intellectual Disability Families"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:9289",
+    "symbol": "ADGRG1"
+  }],
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+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:606854",
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+    }
+  }],
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+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
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+    }, {
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+      "name": "NCBI organismal classification",
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+    }, {
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+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
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+      "namespacePrefix": "OMIM"
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+      "description": "Three Mutations in the Bilateral Frontoparietal Polymicrogyria Gene GPR56 in Pakistani Intellectual Disability Families"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Schaefer-2014-POLR1D-family_1_patient.json b/notebooks/LIRICAL/v1phenopackets/Schaefer-2014-POLR1D-family_1_patient.json
new file mode 100644
index 000000000..f60660070
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Schaefer-2014-POLR1D-family_1_patient.json
@@ -0,0 +1,147 @@
+{
+  "id": "PMID:24603435-Schaefer-2014-POLR1D-family_1:patient",
+  "subject": {
+    "id": "family 1:patient",
+    "ageAtCollection": {
+      "age": "P7Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000494",
+      "label": "Downslanted palpebral fissures"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24603435",
+        "description": "Autosomal recessive POLR1D mutation with decrease of TCOF1 mRNA is responsible for Treacher Collins syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000308",
+      "label": "Microretrognathia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24603435",
+        "description": "Autosomal recessive POLR1D mutation with decrease of TCOF1 mRNA is responsible for Treacher Collins syndrome"
+      }
+    }]
+  }, {
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+      "id": "HP:0000272",
+      "label": "Malar flattening"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:24603435",
+        "description": "Autosomal recessive POLR1D mutation with decrease of TCOF1 mRNA is responsible for Treacher Collins syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000365",
+      "label": "Hearing impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24603435",
+        "description": "Autosomal recessive POLR1D mutation with decrease of TCOF1 mRNA is responsible for Treacher Collins syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:51082",
+    "symbol": "POLR1D"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "13",
+      "pos": 28239968,
+      "ref": "C",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:613717",
+      "label": "TREACHER COLLINS SYNDROME 2; TCS2"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
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+      "id": "hp",
+      "name": "human phenotype ontology",
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+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
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+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
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+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
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+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
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+      "name": "Online Mendelian Inheritance in Man",
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+    }],
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+      "id": "PMID:24603435",
+      "description": "Autosomal recessive POLR1D mutation with decrease of TCOF1 mRNA is responsible for Treacher Collins syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Schormair-2018-VPS13C-VPS13C_case.json b/notebooks/LIRICAL/v1phenopackets/Schormair-2018-VPS13C-VPS13C_case.json
new file mode 100644
index 000000000..5ca64828a
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Schormair-2018-VPS13C-VPS13C_case.json
@@ -0,0 +1,264 @@
+{
+  "id": "PMID:28862745-Schormair-2018-VPS13C-VPS13C_case",
+  "subject": {
+    "id": "VPS13C case",
+    "ageAtCollection": {
+      "age": "P39Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000726",
+      "label": "Dementia"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28862745",
+        "description": "Diagnostic exome sequencing in early-onset Parkinson\u0027s disease confirms VPS13C as a rare cause of autosomal-recessive Parkinson\u0027s disease"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100660",
+      "label": "Dyskinesia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28862745",
+        "description": "Diagnostic exome sequencing in early-onset Parkinson\u0027s disease confirms VPS13C as a rare cause of autosomal-recessive Parkinson\u0027s disease"
+      }
+    }]
+  }, {
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+      "id": "HP:0031908",
+      "label": "Micrographia"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28862745",
+        "description": "Diagnostic exome sequencing in early-onset Parkinson\u0027s disease confirms VPS13C as a rare cause of autosomal-recessive Parkinson\u0027s disease"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000738",
+      "label": "Hallucinations"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28862745",
+        "description": "Diagnostic exome sequencing in early-onset Parkinson\u0027s disease confirms VPS13C as a rare cause of autosomal-recessive Parkinson\u0027s disease"
+      }
+    }]
+  }, {
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+      "id": "HP:0000746",
+      "label": "Delusions"
+    },
+    "evidence": [{
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+        "description": "Diagnostic exome sequencing in early-onset Parkinson\u0027s disease confirms VPS13C as a rare cause of autosomal-recessive Parkinson\u0027s disease"
+      }
+    }]
+  }, {
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+      "id": "HP:0001337",
+      "label": "Tremor"
+    },
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28862745",
+        "description": "Diagnostic exome sequencing in early-onset Parkinson\u0027s disease confirms VPS13C as a rare cause of autosomal-recessive Parkinson\u0027s disease"
+      }
+    }]
+  }, {
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+      "id": "HP:0001260",
+      "label": "Dysarthria"
+    },
+    "evidence": [{
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+      "reference": {
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+        "description": "Diagnostic exome sequencing in early-onset Parkinson\u0027s disease confirms VPS13C as a rare cause of autosomal-recessive Parkinson\u0027s disease"
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+      "id": "HP:0002063",
+      "label": "Rigidity"
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+      "label": "Dystonia"
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+      "label": "heterozygous"
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+  }, {
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+    },
+    "zygosity": {
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+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616840",
+      "label": "Parkinson disease 23, autosomal recessive, early onset"
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+  }],
+  "metaData": {
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+      "name": "Evidence and Conclusion Ontology",
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+      "version": "2018-11-10",
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+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28862745",
+      "description": "Diagnostic exome sequencing in early-onset Parkinson\u0027s disease confirms VPS13C as a rare cause of autosomal-recessive Parkinson\u0027s disease"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Schreckenbach-2014-TPM3-II.2.json b/notebooks/LIRICAL/v1phenopackets/Schreckenbach-2014-TPM3-II.2.json
new file mode 100644
index 000000000..96a13fbe6
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Schreckenbach-2014-TPM3-II.2.json
@@ -0,0 +1,396 @@
+{
+  "id": "PMID:24239060-Schreckenbach-2014-TPM3-II.2",
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+    "ageAtCollection": {
+      "age": "P45Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002527",
+      "label": "Falls"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24239060",
+        "description": "Novel TPM3 mutation in a family with cap myopathy and review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001260",
+      "label": "Dysarthria"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24239060",
+        "description": "Novel TPM3 mutation in a family with cap myopathy and review of the literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003391",
+      "label": "Gowers sign"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:24239060",
+        "description": "Novel TPM3 mutation in a family with cap myopathy and review of the literature"
+      }
+    }]
+  }, {
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+      "label": "Difficulty running"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24239060",
+        "description": "Novel TPM3 mutation in a family with cap myopathy and review of the literature"
+      }
+    }]
+  }, {
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+        "label": "author statement supported by traceable reference"
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+        "description": "Novel TPM3 mutation in a family with cap myopathy and review of the literature"
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+        "description": "Novel TPM3 mutation in a family with cap myopathy and review of the literature"
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+    }]
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+      "id": "HP:0000275",
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:24239060",
+        "description": "Novel TPM3 mutation in a family with cap myopathy and review of the literature"
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+    }]
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+      "id": "HP:0002650",
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+    }]
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+    "evidence": [{
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+        "description": "Novel TPM3 mutation in a family with cap myopathy and review of the literature"
+      }
+    }]
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:24239060",
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+    }]
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+    "evidence": [{
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+        "description": "Novel TPM3 mutation in a family with cap myopathy and review of the literature"
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+    }]
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+      "id": "HP:0010830",
+      "label": "Impaired tactile sensation"
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+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:24239060",
+        "description": "Novel TPM3 mutation in a family with cap myopathy and review of the literature"
+      }
+    }]
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+      }
+    }]
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+      "label": "Abnormal nerve conduction velocity"
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+    "negated": true,
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+        "description": "Novel TPM3 mutation in a family with cap myopathy and review of the literature"
+      }
+    }]
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+      "id": "HP:0003701",
+      "label": "Proximal muscle weakness"
+    },
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+        "id": "PMID:24239060",
+        "description": "Novel TPM3 mutation in a family with cap myopathy and review of the literature"
+      }
+    }]
+  }, {
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+      "id": "HP:0000508",
+      "label": "Ptosis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24239060",
+        "description": "Novel TPM3 mutation in a family with cap myopathy and review of the literature"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:7170",
+    "symbol": "TPM3"
+  }],
+  "variants": [{
+    "vcfAllele": {
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+      "chr": "1",
+      "pos": 154145610,
+      "ref": "G",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:609284",
+      "label": "NEMALINE MYOPATHY 1; NEM1CAP MYOPATHY 1, INCLUDED; CAPM1, INCLUDED"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:24239060",
+      "description": "Novel TPM3 mutation in a family with cap myopathy and review of the literature"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Schussler-2018-ANTXR2-II-3_.json b/notebooks/LIRICAL/v1phenopackets/Schussler-2018-ANTXR2-II-3_.json
new file mode 100644
index 000000000..65aaae9c7
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Schussler-2018-ANTXR2-II-3_.json
@@ -0,0 +1,282 @@
+{
+  "id": "PMID:30050362-Schussler-2018-ANTXR2-II-3_",
+  "subject": {
+    "id": "II-3 ",
+    "ageAtCollection": {
+      "age": "P10M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0012531",
+      "label": "Pain"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30050362",
+        "description": "Protein-losing enteropathy and joint contractures caused by a novel homozygous ANTXR2 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003073",
+      "label": "Hypoalbuminemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30050362",
+        "description": "Protein-losing enteropathy and joint contractures caused by a novel homozygous ANTXR2 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030350",
+      "label": "Erythematous papule"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:30050362",
+        "description": "Protein-losing enteropathy and joint contractures caused by a novel homozygous ANTXR2 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000737",
+      "label": "Irritability"
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+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:30050362",
+        "description": "Protein-losing enteropathy and joint contractures caused by a novel homozygous ANTXR2 mutation"
+      }
+    }]
+  }, {
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+    },
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+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Weight loss"
+    },
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+      "label": "Malnutrition"
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+        "id": "PMID:30050362",
+        "description": "Protein-losing enteropathy and joint contractures caused by a novel homozygous ANTXR2 mutation"
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+        "description": "Protein-losing enteropathy and joint contractures caused by a novel homozygous ANTXR2 mutation"
+      }
+    }]
+  }, {
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+      "label": "Gingival overgrowth"
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:30050362",
+        "description": "Protein-losing enteropathy and joint contractures caused by a novel homozygous ANTXR2 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002902",
+      "label": "Hyponatremia"
+    },
+    "evidence": [{
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+        "description": "Protein-losing enteropathy and joint contractures caused by a novel homozygous ANTXR2 mutation"
+      }
+    }]
+  }, {
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+      "label": "Hyperkalemia"
+    },
+    "evidence": [{
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+        "id": "PMID:30050362",
+        "description": "Protein-losing enteropathy and joint contractures caused by a novel homozygous ANTXR2 mutation"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:118429",
+    "symbol": "ANTXR2"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "4",
+      "pos": 80905082,
+      "ref": "CCA",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:228600",
+      "label": "HYALINE FIBROMATOSIS SYNDROME; HFS"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30050362",
+      "description": "Protein-losing enteropathy and joint contractures caused by a novel homozygous ANTXR2 mutation"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Schweizer-2014-HCN4-family_A_II_1.json b/notebooks/LIRICAL/v1phenopackets/Schweizer-2014-HCN4-family_A_II_1.json
new file mode 100644
index 000000000..05b07370d
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Schweizer-2014-HCN4-family_A_II_1.json
@@ -0,0 +1,132 @@
+{
+  "id": "PMID:25145518-Schweizer-2014-HCN4-family_A/II:1",
+  "subject": {
+    "id": "family A/II:1",
+    "ageAtCollection": {
+      "age": "P57Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0030682",
+      "label": "Left ventricular noncompaction"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25145518",
+        "description": "The symptom complex of familial sinus node dysfunction and myocardial noncompaction is associated with mutations in the HCN4 channel"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001663",
+      "label": "Ventricular fibrillation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25145518",
+        "description": "The symptom complex of familial sinus node dysfunction and myocardial noncompaction is associated with mutations in the HCN4 channel"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001688",
+      "label": "Sinus bradycardia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25145518",
+        "description": "The symptom complex of familial sinus node dysfunction and myocardial noncompaction is associated with mutations in the HCN4 channel"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:10021",
+    "symbol": "HCN4"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "15",
+      "pos": 73622060,
+      "ref": "C",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:163800",
+      "label": "SICK SINUS SYNDROME 2, AUTOSOMAL DOMINANT; SSS2"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:25145518",
+      "description": "The symptom complex of familial sinus node dysfunction and myocardial noncompaction is associated with mutations in the HCN4 channel"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Seidlmayer-2018-RYR2-proband.json b/notebooks/LIRICAL/v1phenopackets/Seidlmayer-2018-RYR2-proband.json
new file mode 100644
index 000000000..5abf25848
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Seidlmayer-2018-RYR2-proband.json
@@ -0,0 +1,179 @@
+{
+  "id": "PMID:30296944-Seidlmayer-2018-RYR2-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P17Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0011712",
+      "label": "Right bundle branch block"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30296944",
+        "description": "Description of a novel RyR2 mutation in a juvenile patient with symptomatic catecholaminergic polymorphic ventricular tachycardia in sleep and during exercise: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001695",
+      "label": "Cardiac arrest"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30296944",
+        "description": "Description of a novel RyR2 mutation in a juvenile patient with symptomatic catecholaminergic polymorphic ventricular tachycardia in sleep and during exercise: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012819",
+      "label": "Myocarditis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30296944",
+        "description": "Description of a novel RyR2 mutation in a juvenile patient with symptomatic catecholaminergic polymorphic ventricular tachycardia in sleep and during exercise: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001638",
+      "label": "Cardiomyopathy"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30296944",
+        "description": "Description of a novel RyR2 mutation in a juvenile patient with symptomatic catecholaminergic polymorphic ventricular tachycardia in sleep and during exercise: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001279",
+      "label": "Syncope"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30296944",
+        "description": "Description of a novel RyR2 mutation in a juvenile patient with symptomatic catecholaminergic polymorphic ventricular tachycardia in sleep and during exercise: a case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001663",
+      "label": "Ventricular fibrillation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30296944",
+        "description": "Description of a novel RyR2 mutation in a juvenile patient with symptomatic catecholaminergic polymorphic ventricular tachycardia in sleep and during exercise: a case report"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:6262",
+    "symbol": "RYR2"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 237947532,
+      "ref": "T",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:604772",
+      "label": "VENTRICULAR TACHYCARDIA, CATECHOLAMINERGIC POLYMORPHIC, 1, WITH ORWITHOUT ATRIAL DYSFUNCTION AND/OR DILATED CARDIOMYOPATHY; CPVT1"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30296944",
+      "description": "Description of a novel RyR2 mutation in a juvenile patient with symptomatic catecholaminergic polymorphic ventricular tachycardia in sleep and during exercise: a case report"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Sekelska-2017-SPRED1-P62.json b/notebooks/LIRICAL/v1phenopackets/Sekelska-2017-SPRED1-P62.json
new file mode 100644
index 000000000..1e90f0886
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Sekelska-2017-SPRED1-P62.json
@@ -0,0 +1,117 @@
+{
+  "id": "PMID:28150585-Sekelska-2017-SPRED1-P62",
+  "subject": {
+    "id": "P62",
+    "ageAtCollection": {
+      "age": "P21Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001328",
+      "label": "Specific learning disability"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28150585",
+        "description": "The first Slovak Legius syndrome patient carrying the SPRED1 gene mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007565",
+      "label": "Multiple cafe-au-lait spots"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28150585",
+        "description": "The first Slovak Legius syndrome patient carrying the SPRED1 gene mutation"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:161742",
+    "symbol": "SPRED1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "15",
+      "pos": 38591587,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:611431",
+      "label": "LEGIUS SYNDROME"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28150585",
+      "description": "The first Slovak Legius syndrome patient carrying the SPRED1 gene mutation"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Servian-Morilla-2016-POGLUT1-Patient_II.1.json b/notebooks/LIRICAL/v1phenopackets/Servian-Morilla-2016-POGLUT1-Patient_II.1.json
new file mode 100644
index 000000000..d42cd2b9b
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Servian-Morilla-2016-POGLUT1-Patient_II.1.json
@@ -0,0 +1,288 @@
+{
+  "id": "PMID:27807076-Servián-Morilla-2016-POGLUT1-Patient_II.1",
+  "subject": {
+    "id": "Patient II.1",
+    "ageAtCollection": {
+      "age": "39"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0032178",
+      "label": "Flaky paint dermatosis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27807076",
+        "description": "A POGLUT1 mutation causes a muscular dystrophy with reduced Notch signaling and satellite cell loss"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002505",
+      "label": "Progressive inability to walk"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27807076",
+        "description": "A POGLUT1 mutation causes a muscular dystrophy with reduced Notch signaling and satellite cell loss"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003691",
+      "label": "Scapular winging"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27807076",
+        "description": "A POGLUT1 mutation causes a muscular dystrophy with reduced Notch signaling and satellite cell loss"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001371",
+      "label": "Flexion contracture"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27807076",
+        "description": "A POGLUT1 mutation causes a muscular dystrophy with reduced Notch signaling and satellite cell loss"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003749",
+      "label": "Pelvic girdle muscle weakness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27807076",
+        "description": "A POGLUT1 mutation causes a muscular dystrophy with reduced Notch signaling and satellite cell loss"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001388",
+      "label": "Joint laxity"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27807076",
+        "description": "A POGLUT1 mutation causes a muscular dystrophy with reduced Notch signaling and satellite cell loss"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000301",
+      "label": "Abnormality of facial musculature"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27807076",
+        "description": "A POGLUT1 mutation causes a muscular dystrophy with reduced Notch signaling and satellite cell loss"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003236",
+      "label": "Elevated serum creatine kinase"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27807076",
+        "description": "A POGLUT1 mutation causes a muscular dystrophy with reduced Notch signaling and satellite cell loss"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100851",
+      "label": "Abnormal emotion/affect behavior"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27807076",
+        "description": "A POGLUT1 mutation causes a muscular dystrophy with reduced Notch signaling and satellite cell loss"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003720",
+      "label": "Generalized muscle hypertrophy"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27807076",
+        "description": "A POGLUT1 mutation causes a muscular dystrophy with reduced Notch signaling and satellite cell loss"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006520",
+      "label": "Progressive pulmonary function impairment"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27807076",
+        "description": "A POGLUT1 mutation causes a muscular dystrophy with reduced Notch signaling and satellite cell loss"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008994",
+      "label": "Proximal muscle weakness in lower limbs"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27807076",
+        "description": "A POGLUT1 mutation causes a muscular dystrophy with reduced Notch signaling and satellite cell loss"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001283",
+      "label": "Bulbar palsy"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27807076",
+        "description": "A POGLUT1 mutation causes a muscular dystrophy with reduced Notch signaling and satellite cell loss"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:56983",
+    "symbol": "POGLUT1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "3",
+      "pos": 119205740,
+      "ref": "T",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617232",
+      "label": "MUSCULAR DYSTROPHY, LIMB-GIRDLE, TYPE 2Z"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:lccarmody",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27807076",
+      "description": "A POGLUT1 mutation causes a muscular dystrophy with reduced Notch signaling and satellite cell loss"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Seven-2014-DYM-Patient_2.json b/notebooks/LIRICAL/v1phenopackets/Seven-2014-DYM-Patient_2.json
new file mode 100644
index 000000000..94ed37afc
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Seven-2014-DYM-Patient_2.json
@@ -0,0 +1,191 @@
+{
+  "id": "PMID:24300288-Seven-2014-DYM-Patient_2",
+  "subject": {
+    "id": "Patient 2",
+    "ageAtCollection": {
+      "age": "3Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002035",
+      "label": "Rectal prolapse"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24300288",
+        "description": "A novel frameshift mutation and infrequent clinical findings in two cases with Dyggve-Melchior-Clausen syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001256",
+      "label": "Intellectual disability, mild"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24300288",
+        "description": "A novel frameshift mutation and infrequent clinical findings in two cases with Dyggve-Melchior-Clausen syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003183",
+      "label": "Wide pubic symphysis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24300288",
+        "description": "A novel frameshift mutation and infrequent clinical findings in two cases with Dyggve-Melchior-Clausen syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010049",
+      "label": "Short metacarpal"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24300288",
+        "description": "A novel frameshift mutation and infrequent clinical findings in two cases with Dyggve-Melchior-Clausen syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008905",
+      "label": "Rhizomelia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24300288",
+        "description": "A novel frameshift mutation and infrequent clinical findings in two cases with Dyggve-Melchior-Clausen syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010743",
+      "label": "Short metatarsal"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24300288",
+        "description": "A novel frameshift mutation and infrequent clinical findings in two cases with Dyggve-Melchior-Clausen syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003796",
+      "label": "Irregular iliac crest"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24300288",
+        "description": "A novel frameshift mutation and infrequent clinical findings in two cases with Dyggve-Melchior-Clausen syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:54808",
+    "symbol": "DYM"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "18",
+      "pos": 46860138,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:223800",
+      "label": "DYGGVE-MELCHIOR-CLAUSEN DISEASE; DMC"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:24300288",
+      "description": "A novel frameshift mutation and infrequent clinical findings in two cases with Dyggve-Melchior-Clausen syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Shahid-2019-FERMT3-index.json b/notebooks/LIRICAL/v1phenopackets/Shahid-2019-FERMT3-index.json
new file mode 100644
index 000000000..66fa5ea46
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Shahid-2019-FERMT3-index.json
@@ -0,0 +1,149 @@
+{
+  "id": "PMID:31068971-Shahid-2019-FERMT3-index",
+  "subject": {
+    "id": "index",
+    "ageAtCollection": {
+      "age": "P7M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002716",
+      "label": "Lymphadenopathy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31068971",
+        "description": "A Novel Nonsense Mutation in FERMT3 Causes LAD-III in a Pakistani Family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0032455",
+      "label": "Reduced granulocyte CD18 level"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31068971",
+        "description": "A Novel Nonsense Mutation in FERMT3 Causes LAD-III in a Pakistani Family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001433",
+      "label": "Hepatosplenomegaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31068971",
+        "description": "A Novel Nonsense Mutation in FERMT3 Causes LAD-III in a Pakistani Family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010701",
+      "label": "Abnormal immunoglobulin level"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31068971",
+        "description": "A Novel Nonsense Mutation in FERMT3 Causes LAD-III in a Pakistani Family"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:83706",
+    "symbol": "FERMT3"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "11",
+      "pos": 63978208,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:612840",
+      "label": "LEUKOCYTE ADHESION DEFICIENCY, TYPE III; LAD3"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:31068971",
+      "description": "A Novel Nonsense Mutation in FERMT3 Causes LAD-III in a Pakistani Family"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Shalaby-2009-MYOT-patient.json b/notebooks/LIRICAL/v1phenopackets/Shalaby-2009-MYOT-patient.json
new file mode 100644
index 000000000..614a5cd75
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Shalaby-2009-MYOT-patient.json
@@ -0,0 +1,163 @@
+{
+  "id": "PMID:19458539-Shalaby-2009-MYOT-patient",
+  "subject": {
+    "id": "patient",
+    "ageAtCollection": {
+      "age": "P57Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0003557",
+      "label": "Increased variability in muscle fiber diameter"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:19458539",
+        "description": "Defective myotilin homodimerization caused by a novel mutation in MYOT exon 9 in the first Japanese limb girdle muscular dystrophy 1A patient"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030319",
+      "label": "Weakness of facial musculature"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:19458539",
+        "description": "Defective myotilin homodimerization caused by a novel mutation in MYOT exon 9 in the first Japanese limb girdle muscular dystrophy 1A patient"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031237",
+      "label": "Internally nucleated skeletal muscle fibers"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:19458539",
+        "description": "Defective myotilin homodimerization caused by a novel mutation in MYOT exon 9 in the first Japanese limb girdle muscular dystrophy 1A patient"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008180",
+      "label": "Mildly elevated creatine kinase"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:19458539",
+        "description": "Defective myotilin homodimerization caused by a novel mutation in MYOT exon 9 in the first Japanese limb girdle muscular dystrophy 1A patient"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003701",
+      "label": "Proximal muscle weakness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:19458539",
+        "description": "Defective myotilin homodimerization caused by a novel mutation in MYOT exon 9 in the first Japanese limb girdle muscular dystrophy 1A patient"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:9499",
+    "symbol": "MYOT"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "5",
+      "pos": 137222576,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:609200",
+      "label": "MYOPATHY, MYOFIBRILLAR, 3; MFM3"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:19458539",
+      "description": "Defective myotilin homodimerization caused by a novel mutation in MYOT exon 9 in the first Japanese limb girdle muscular dystrophy 1A patient"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Shen-2017-VPS13A-Patient-2.json b/notebooks/LIRICAL/v1phenopackets/Shen-2017-VPS13A-Patient-2.json
new file mode 100644
index 000000000..924b25204
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Shen-2017-VPS13A-Patient-2.json
@@ -0,0 +1,234 @@
+{
+  "id": "PMID:28446873-Shen-2017-VPS13A-Patient-2",
+  "subject": {
+    "id": "Patient-2",
+    "ageAtCollection": {
+      "age": "P45Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002072",
+      "label": "Chorea"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28446873",
+        "description": "Novel VPS13A Gene Mutations Identified in Patients Diagnosed with Chorea-acanthocytosis (ChAc): Case Presentation and Literature Review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28446873",
+        "description": "Novel VPS13A Gene Mutations Identified in Patients Diagnosed with Chorea-acanthocytosis (ChAc): Case Presentation and Literature Review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001260",
+      "label": "Dysarthria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28446873",
+        "description": "Novel VPS13A Gene Mutations Identified in Patients Diagnosed with Chorea-acanthocytosis (ChAc): Case Presentation and Literature Review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003763",
+      "label": "Bruxism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28446873",
+        "description": "Novel VPS13A Gene Mutations Identified in Patients Diagnosed with Chorea-acanthocytosis (ChAc): Case Presentation and Literature Review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001927",
+      "label": "Acanthocytosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28446873",
+        "description": "Novel VPS13A Gene Mutations Identified in Patients Diagnosed with Chorea-acanthocytosis (ChAc): Case Presentation and Literature Review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006956",
+      "label": "Dilation of lateral ventricles"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28446873",
+        "description": "Novel VPS13A Gene Mutations Identified in Patients Diagnosed with Chorea-acanthocytosis (ChAc): Case Presentation and Literature Review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002015",
+      "label": "Dysphagia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28446873",
+        "description": "Novel VPS13A Gene Mutations Identified in Patients Diagnosed with Chorea-acanthocytosis (ChAc): Case Presentation and Literature Review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000742",
+      "label": "Self-mutilation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28446873",
+        "description": "Novel VPS13A Gene Mutations Identified in Patients Diagnosed with Chorea-acanthocytosis (ChAc): Case Presentation and Literature Review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001265",
+      "label": "Hyporeflexia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28446873",
+        "description": "Novel VPS13A Gene Mutations Identified in Patients Diagnosed with Chorea-acanthocytosis (ChAc): Case Presentation and Literature Review"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:23230",
+    "symbol": "VPS13A"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "9",
+      "pos": 79980446,
+      "ref": "C",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "9",
+      "pos": 80020779,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:200150",
+      "label": "CHOREOACANTHOCYTOSIS; CHAC"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28446873",
+      "description": "Novel VPS13A Gene Mutations Identified in Patients Diagnosed with Chorea-acanthocytosis (ChAc): Case Presentation and Literature Review"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Sher-2014-CHSY1-IV-1.json b/notebooks/LIRICAL/v1phenopackets/Sher-2014-CHSY1-IV-1.json
new file mode 100644
index 000000000..561928a01
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Sher-2014-CHSY1-IV-1.json
@@ -0,0 +1,329 @@
+{
+  "id": "PMID:24269551-Sher-2014-CHSY1-IV-1",
+  "subject": {
+    "id": "IV-1",
+    "ageAtCollection": {
+      "age": "P21Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002308",
+      "label": "Arnold-Chiari malformation"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24269551",
+        "description": "A novel CHSY1 gene mutation underlies Temtamy preaxial brachydactyly syndrome in a Pakistani family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000691",
+      "label": "Microdontia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24269551",
+        "description": "A novel CHSY1 gene mutation underlies Temtamy preaxial brachydactyly syndrome in a Pakistani family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030084",
+      "label": "Clinodactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24269551",
+        "description": "A novel CHSY1 gene mutation underlies Temtamy preaxial brachydactyly syndrome in a Pakistani family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24269551",
+        "description": "A novel CHSY1 gene mutation underlies Temtamy preaxial brachydactyly syndrome in a Pakistani family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000347",
+      "label": "Micrognathia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24269551",
+        "description": "A novel CHSY1 gene mutation underlies Temtamy preaxial brachydactyly syndrome in a Pakistani family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003196",
+      "label": "Short nose"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24269551",
+        "description": "A novel CHSY1 gene mutation underlies Temtamy preaxial brachydactyly syndrome in a Pakistani family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002751",
+      "label": "Kyphoscoliosis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24269551",
+        "description": "A novel CHSY1 gene mutation underlies Temtamy preaxial brachydactyly syndrome in a Pakistani family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010109",
+      "label": "Short hallux"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24269551",
+        "description": "A novel CHSY1 gene mutation underlies Temtamy preaxial brachydactyly syndrome in a Pakistani family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000767",
+      "label": "Pectus excavatum"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24269551",
+        "description": "A novel CHSY1 gene mutation underlies Temtamy preaxial brachydactyly syndrome in a Pakistani family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001234",
+      "label": "Hitchhiker thumb"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24269551",
+        "description": "A novel CHSY1 gene mutation underlies Temtamy preaxial brachydactyly syndrome in a Pakistani family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001449",
+      "label": "Duplication of metatarsal bones"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24269551",
+        "description": "A novel CHSY1 gene mutation underlies Temtamy preaxial brachydactyly syndrome in a Pakistani family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000369",
+      "label": "Low-set ears"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24269551",
+        "description": "A novel CHSY1 gene mutation underlies Temtamy preaxial brachydactyly syndrome in a Pakistani family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012725",
+      "label": "Cutaneous syndactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24269551",
+        "description": "A novel CHSY1 gene mutation underlies Temtamy preaxial brachydactyly syndrome in a Pakistani family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000677",
+      "label": "Oligodontia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24269551",
+        "description": "A novel CHSY1 gene mutation underlies Temtamy preaxial brachydactyly syndrome in a Pakistani family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000316",
+      "label": "Hypertelorism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24269551",
+        "description": "A novel CHSY1 gene mutation underlies Temtamy preaxial brachydactyly syndrome in a Pakistani family"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011087",
+      "label": "Talon cusp"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24269551",
+        "description": "A novel CHSY1 gene mutation underlies Temtamy preaxial brachydactyly syndrome in a Pakistani family"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:22856",
+    "symbol": "CHSY1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "15",
+      "pos": 101718105,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:605282",
+      "label": "TEMTAMY PREAXIAL BRACHYDACTYLY SYNDROME; TPBS"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:24269551",
+      "description": "A novel CHSY1 gene mutation underlies Temtamy preaxial brachydactyly syndrome in a Pakistani family"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Shervin_Badv-2019-ASAH1-patient.json b/notebooks/LIRICAL/v1phenopackets/Shervin_Badv-2019-ASAH1-patient.json
new file mode 100644
index 000000000..8fa83ef0f
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Shervin_Badv-2019-ASAH1-patient.json
@@ -0,0 +1,284 @@
+{
+  "id": "PMID:31213928-Shervin_Badv-2019-ASAH1-patient",
+  "subject": {
+    "id": "patient",
+    "ageAtCollection": {
+      "age": "P15Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0010819",
+      "label": "Atonic seizures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31213928",
+        "description": "A novel case report of spinal muscular atrophy with progressive myoclonic epilepsy from Iran"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0045040",
+      "label": "Abnormal lactate dehydrogenase activity"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31213928",
+        "description": "A novel case report of spinal muscular atrophy with progressive myoclonic epilepsy from Iran"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0040081",
+      "label": "Abnormal circulating creatine kinase concentration"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31213928",
+        "description": "A novel case report of spinal muscular atrophy with progressive myoclonic epilepsy from Iran"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001308",
+      "label": "Tongue fasciculations"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31213928",
+        "description": "A novel case report of spinal muscular atrophy with progressive myoclonic epilepsy from Iran"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012473",
+      "label": "Tongue atrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
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+    }]
+  }, {
+    "type": {
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+      "label": "Seizures"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
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+        "description": "A novel case report of spinal muscular atrophy with progressive myoclonic epilepsy from Iran"
+      }
+    }]
+  }, {
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+      "id": "HP:0002322",
+      "label": "Resting tremor"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:31213928",
+        "description": "A novel case report of spinal muscular atrophy with progressive myoclonic epilepsy from Iran"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Gowers sign"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:31213928",
+        "description": "A novel case report of spinal muscular atrophy with progressive myoclonic epilepsy from Iran"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001336",
+      "label": "Myoclonus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "A novel case report of spinal muscular atrophy with progressive myoclonic epilepsy from Iran"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003701",
+      "label": "Proximal muscle weakness"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "A novel case report of spinal muscular atrophy with progressive myoclonic epilepsy from Iran"
+      }
+    }]
+  }, {
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+      "id": "HP:0002069",
+      "label": "Generalized tonic-clonic seizures"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31213928",
+        "description": "A novel case report of spinal muscular atrophy with progressive myoclonic epilepsy from Iran"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002515",
+      "label": "Waddling gait"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31213928",
+        "description": "A novel case report of spinal muscular atrophy with progressive myoclonic epilepsy from Iran"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003690",
+      "label": "Limb muscle weakness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31213928",
+        "description": "A novel case report of spinal muscular atrophy with progressive myoclonic epilepsy from Iran"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:427",
+    "symbol": "ASAH1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "8",
+      "pos": 17933050,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:159950",
+      "label": "SPINAL MUSCULAR ATROPHY WITH PROGRESSIVE MYOCLONIC EPILEPSY; SMAPME"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13",
+    "submittedBy": "HP:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:31213928",
+      "description": "A novel case report of spinal muscular atrophy with progressive myoclonic epilepsy from Iran"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Shlebak-2015-GP1BA-Patient_3.json b/notebooks/LIRICAL/v1phenopackets/Shlebak-2015-GP1BA-Patient_3.json
new file mode 100644
index 000000000..3571d46c7
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Shlebak-2015-GP1BA-Patient_3.json
@@ -0,0 +1,239 @@
+{
+  "id": "PMID:26044173-Shlebak-2015-GP1BA-Patient_3",
+  "subject": {
+    "id": "Patient 3",
+    "ageAtCollection": {
+      "age": "P10Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0008148",
+      "label": "Impaired epinephrine-induced platelet aggregation"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26044173",
+        "description": "A Novel Homozygous c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011877",
+      "label": "Increased mean platelet volume"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26044173",
+        "description": "A Novel Homozygous c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004866",
+      "label": "Impaired ADP-induced platelet aggregation"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26044173",
+        "description": "A Novel Homozygous c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011870",
+      "label": "Impaired arachidonic acid-induced platelet aggregation"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26044173",
+        "description": "A Novel Homozygous c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001873",
+      "label": "Thrombocytopenia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26044173",
+        "description": "A Novel Homozygous c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000967",
+      "label": "Petechiae"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26044173",
+        "description": "A Novel Homozygous c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000421",
+      "label": "Epistaxis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26044173",
+        "description": "A Novel Homozygous c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012343",
+      "label": "Decreased serum ferritin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26044173",
+        "description": "A Novel Homozygous c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000225",
+      "label": "Gingival bleeding"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26044173",
+        "description": "A Novel Homozygous c"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011871",
+      "label": "Impaired ristocetin-induced platelet aggregation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26044173",
+        "description": "A Novel Homozygous c"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2811",
+    "symbol": "GP1BA"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "17",
+      "pos": 4836699,
+      "ref": "C",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:231200",
+      "label": "BERNARD-SOULIER SYNDROME; BSS"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:26044173",
+      "description": "A Novel Homozygous c"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Silva-2018-PREPL-proband.json b/notebooks/LIRICAL/v1phenopackets/Silva-2018-PREPL-proband.json
new file mode 100644
index 000000000..d726e23ba
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Silva-2018-PREPL-proband.json
@@ -0,0 +1,357 @@
+{
+  "id": "PMID:29483676-Silva-2018-PREPL-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P10Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000218",
+      "label": "High palate"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29483676",
+        "description": "The second point mutation in PREPL: a case report and literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000508",
+      "label": "Ptosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29483676",
+        "description": "The second point mutation in PREPL: a case report and literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000268",
+      "label": "Dolichocephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29483676",
+        "description": "The second point mutation in PREPL: a case report and literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000194",
+      "label": "Open mouth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29483676",
+        "description": "The second point mutation in PREPL: a case report and literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000637",
+      "label": "Long palpebral fissure"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29483676",
+        "description": "The second point mutation in PREPL: a case report and literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002650",
+      "label": "Scoliosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29483676",
+        "description": "The second point mutation in PREPL: a case report and literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001319",
+      "label": "Neonatal hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29483676",
+        "description": "The second point mutation in PREPL: a case report and literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000411",
+      "label": "Protruding ear"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29483676",
+        "description": "The second point mutation in PREPL: a case report and literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001611",
+      "label": "Nasal speech"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29483676",
+        "description": "The second point mutation in PREPL: a case report and literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000639",
+      "label": "Nystagmus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29483676",
+        "description": "The second point mutation in PREPL: a case report and literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010804",
+      "label": "Tented upper lip vermilion"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29483676",
+        "description": "The second point mutation in PREPL: a case report and literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29483676",
+        "description": "The second point mutation in PREPL: a case report and literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003391",
+      "label": "Gowers sign"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29483676",
+        "description": "The second point mutation in PREPL: a case report and literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001270",
+      "label": "Motor delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29483676",
+        "description": "The second point mutation in PREPL: a case report and literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002591",
+      "label": "Polyphagia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29483676",
+        "description": "The second point mutation in PREPL: a case report and literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030319",
+      "label": "Weakness of facial musculature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29483676",
+        "description": "The second point mutation in PREPL: a case report and literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001324",
+      "label": "Muscle weakness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29483676",
+        "description": "The second point mutation in PREPL: a case report and literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001525",
+      "label": "Severe failure to thrive"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29483676",
+        "description": "The second point mutation in PREPL: a case report and literature review"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:9581",
+    "symbol": "PREPL"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "2",
+      "pos": 44573406,
+      "ref": "CT",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616224",
+      "label": "Myasthenic syndrome, congenital, 22"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29483676",
+      "description": "The second point mutation in PREPL: a case report and literature review"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Skraban-2017-WDR26-Individual_1,_PPMD01P,_GEA055P.json b/notebooks/LIRICAL/v1phenopackets/Skraban-2017-WDR26-Individual_1,_PPMD01P,_GEA055P.json
new file mode 100644
index 000000000..c7f882214
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Skraban-2017-WDR26-Individual_1,_PPMD01P,_GEA055P.json
@@ -0,0 +1,894 @@
+{
+  "id": "PMID:28686853-Skraban-2017-WDR26-Individual_1,_PPMD01P,_GEA055P",
+  "subject": {
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+    "ageAtCollection": {
+      "age": "P4Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
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+      "id": "HP:0001773",
+      "label": "Short foot"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
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+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
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+      "label": "Broad nasal tip"
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+    "evidence": [{
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+        "id": "ECO:0000033",
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+      "reference": {
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+      }
+    }]
+  }, {
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+      "id": "HP:0000545",
+      "label": "Myopia"
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+    "evidence": [{
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+    }]
+  }, {
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+      "label": "Short stature"
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+    "evidence": [{
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+      }
+    }]
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+      }
+    }]
+  }, {
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+      "label": "Otitis media"
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+    }]
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+      "label": "Absent cupid\u0027s bow"
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+      }
+    }]
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+      "label": "Bruxism"
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+      }
+    }]
+  }, {
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+      "label": "Thin upper lip vermilion"
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+    "evidence": [{
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+    }]
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+      "label": "Hypertelorism"
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+    }]
+  }, {
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+      "label": "Abnormality of the gingiva"
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+      }
+    }]
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+      "label": "Micrognathia"
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+      }
+    }]
+  }, {
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+      "id": "HP:0002020",
+      "label": "Gastroesophageal reflux"
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+    "evidence": [{
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+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Widely spaced teeth"
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+    "evidence": [{
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+      }
+    }]
+  }, {
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+      "label": "Hypertonia"
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+    "evidence": [{
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+      }
+    }]
+  }, {
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+      "label": "Proptosis"
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+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
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+      "label": "Short philtrum"
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+      }
+    }]
+  }, {
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+      "id": "HP:0001357",
+      "label": "Plagiocephaly"
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+    "evidence": [{
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+        "id": "ECO:0000033",
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+      }
+    }]
+  }, {
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+      "id": "HP:0007269",
+      "label": "Spinal muscular atrophy"
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+    "evidence": [{
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+      }
+    }]
+  }, {
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+      "id": "HP:0000336",
+      "label": "Prominent supraorbital ridges"
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+    "negated": true,
+    "evidence": [{
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+      }
+    }]
+  }, {
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+      "id": "HP:0003202",
+      "label": "Skeletal muscle atrophy"
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+    "evidence": [{
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+      }
+    }]
+  }, {
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+      "id": "HP:0000463",
+      "label": "Anteverted nares"
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+    "evidence": [{
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+        "id": "ECO:0000033",
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+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001090",
+      "label": "Abnormally large globe"
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+    "evidence": [{
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+        "id": "ECO:0000033",
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+      },
+      "reference": {
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+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
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+    "evidence": [{
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+        "id": "ECO:0000033",
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+      "reference": {
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+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002019",
+      "label": "Constipation"
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+    "evidence": [{
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+        "id": "ECO:0000033",
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+      "reference": {
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+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001508",
+      "label": "Failure to thrive"
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+    "evidence": [{
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+        "id": "ECO:0000033",
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+      "reference": {
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+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004209",
+      "label": "Clinodactyly of the 5th finger"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
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+      "reference": {
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+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000473",
+      "label": "Torticollis"
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+    "evidence": [{
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+        "id": "ECO:0000033",
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+      "reference": {
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+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012471",
+      "label": "Thick vermilion border"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
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+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002373",
+      "label": "Febrile seizures"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
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+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009933",
+      "label": "Narrow naris"
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+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+      "reference": {
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+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000341",
+      "label": "Narrow forehead"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
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+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000486",
+      "label": "Strabismus"
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+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
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+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002064",
+      "label": "Spastic gait"
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+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
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+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001007",
+      "label": "Hirsutism"
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+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
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+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009623",
+      "label": "Proximal placement of thumb"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
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+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000154",
+      "label": "Wide mouth"
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+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
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+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005338",
+      "label": "Sparse lateral eyebrow"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
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+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000343",
+      "label": "Long philtrum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28686853",
+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000490",
+      "label": "Deeply set eye"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
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+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0200055",
+      "label": "Small hand"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28686853",
+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005280",
+      "label": "Depressed nasal bridge"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28686853",
+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000280",
+      "label": "Coarse facial features"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28686853",
+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000540",
+      "label": "Hypermetropia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
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+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0430028",
+      "label": "Hyperplasia of the maxilla"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28686853",
+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002779",
+      "label": "Tracheomalacia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28686853",
+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000768",
+      "label": "Pectus carinatum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28686853",
+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001250",
+      "label": "Seizures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28686853",
+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002007",
+      "label": "Frontal bossing"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28686853",
+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002500",
+      "label": "Abnormality of the cerebral white matter"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28686853",
+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000293",
+      "label": "Full cheeks"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28686853",
+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012171",
+      "label": "Stereotypical hand wringing"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28686853",
+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003194",
+      "label": "Short nasal bridge"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28686853",
+        "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:80232",
+    "symbol": "WDR26"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 224592155,
+      "ref": "C",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617616",
+      "label": "Skraban-Deardorff syndrome"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28686853",
+      "description": "WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Skrabl-Baumgartner-2017-ADA2-patient_1.json b/notebooks/LIRICAL/v1phenopackets/Skrabl-Baumgartner-2017-ADA2-patient_1.json
new file mode 100644
index 000000000..923b4ef3d
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Skrabl-Baumgartner-2017-ADA2-patient_1.json
@@ -0,0 +1,293 @@
+{
+  "id": "PMID:28830446-Skrabl-Baumgartner-2017-ADA2-patient_1",
+  "subject": {
+    "id": "patient 1",
+    "ageAtCollection": {
+      "age": "10Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001269",
+      "label": "Hemiparesis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28830446",
+        "description": "Autoimmune phenotype with type I interferon signature in two brothers with ADA2 deficiency carrying a novel CECR1 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010702",
+      "label": "Increased antibody level in blood"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28830446",
+        "description": "Autoimmune phenotype with type I interferon signature in two brothers with ADA2 deficiency carrying a novel CECR1 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002829",
+      "label": "Arthralgia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28830446",
+        "description": "Autoimmune phenotype with type I interferon signature in two brothers with ADA2 deficiency carrying a novel CECR1 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000155",
+      "label": "Oral ulcer"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28830446",
+        "description": "Autoimmune phenotype with type I interferon signature in two brothers with ADA2 deficiency carrying a novel CECR1 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002321",
+      "label": "Vertigo"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28830446",
+        "description": "Autoimmune phenotype with type I interferon signature in two brothers with ADA2 deficiency carrying a novel CECR1 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003493",
+      "label": "Antinuclear antibody positivity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28830446",
+        "description": "Autoimmune phenotype with type I interferon signature in two brothers with ADA2 deficiency carrying a novel CECR1 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002140",
+      "label": "Ischemic stroke"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28830446",
+        "description": "Autoimmune phenotype with type I interferon signature in two brothers with ADA2 deficiency carrying a novel CECR1 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000965",
+      "label": "Cutis marmorata"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28830446",
+        "description": "Autoimmune phenotype with type I interferon signature in two brothers with ADA2 deficiency carrying a novel CECR1 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001945",
+      "label": "Fever"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28830446",
+        "description": "Autoimmune phenotype with type I interferon signature in two brothers with ADA2 deficiency carrying a novel CECR1 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011227",
+      "label": "Elevated C-reactive protein level"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28830446",
+        "description": "Autoimmune phenotype with type I interferon signature in two brothers with ADA2 deficiency carrying a novel CECR1 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012246",
+      "label": "Oculomotor nerve palsy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28830446",
+        "description": "Autoimmune phenotype with type I interferon signature in two brothers with ADA2 deficiency carrying a novel CECR1 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002027",
+      "label": "Abdominal pain"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28830446",
+        "description": "Autoimmune phenotype with type I interferon signature in two brothers with ADA2 deficiency carrying a novel CECR1 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002315",
+      "label": "Headache"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28830446",
+        "description": "Autoimmune phenotype with type I interferon signature in two brothers with ADA2 deficiency carrying a novel CECR1 mutation"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:51816",
+    "symbol": "ADA2"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "22",
+      "pos": 17690429,
+      "ref": "C",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "22",
+      "pos": 17663510,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:615688",
+      "label": "POLYARTERITIS NODOSA, CHILDHOOD-ONSET; PAN"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28830446",
+      "description": "Autoimmune phenotype with type I interferon signature in two brothers with ADA2 deficiency carrying a novel CECR1 mutation"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Slavotinek-2017-TBL1XR1-seven_year_old_male.json b/notebooks/LIRICAL/v1phenopackets/Slavotinek-2017-TBL1XR1-seven_year_old_male.json
new file mode 100644
index 000000000..4960690a2
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Slavotinek-2017-TBL1XR1-seven_year_old_male.json
@@ -0,0 +1,522 @@
+{
+  "id": "PMID:28687524-Slavotinek-2017-TBL1XR1-seven_year_old_male",
+  "subject": {
+    "id": "seven year old male",
+    "ageAtCollection": {
+      "age": "7Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0012385",
+      "label": "Camptodactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012523",
+      "label": "Oral aversion"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000252",
+      "label": "Microcephaly"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000486",
+      "label": "Strabismus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000107",
+      "label": "Renal cyst"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011819",
+      "label": "Submucous cleft soft palate"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000126",
+      "label": "Hydronephrosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012450",
+      "label": "Chronic constipation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001591",
+      "label": "Bell-shaped thorax"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000414",
+      "label": "Bulbous nose"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008689",
+      "label": "Bilateral cryptorchidism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100730",
+      "label": "Bronchogenic cyst"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009890",
+      "label": "High anterior hairline"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000331",
+      "label": "Short chin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007099",
+      "label": "Arnold-Chiari type I malformation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002236",
+      "label": "Frontal upsweep of hair"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002000",
+      "label": "Short columella"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000582",
+      "label": "Upslanted palpebral fissure"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002098",
+      "label": "Respiratory distress"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000400",
+      "label": "Macrotia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001792",
+      "label": "Small nail"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001558",
+      "label": "Decreased fetal movement"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0410018",
+      "label": "Recurrent ear infections"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002944",
+      "label": "Thoracolumbar scoliosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001883",
+      "label": "Talipes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000154",
+      "label": "Wide mouth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000952",
+      "label": "Jaundice"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28687524",
+        "description": "Pierpont syndrome associated with the p"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:79718",
+    "symbol": "TBL1XR1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "3",
+      "pos": 176750838,
+      "ref": "T",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:602342",
+      "label": "Pierpont syndrome"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28687524",
+      "description": "Pierpont syndrome associated with the p"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Smith-2000-MITF-family_815.json b/notebooks/LIRICAL/v1phenopackets/Smith-2000-MITF-family_815.json
new file mode 100644
index 000000000..95afa4524
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Smith-2000-MITF-family_815.json
@@ -0,0 +1,177 @@
+{
+  "id": "PMID:10851256-Smith-2000-MITF-family_815",
+  "subject": {
+    "id": "family 815",
+    "ageAtCollection": {
+      "age": "n/a"
+    },
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001100",
+      "label": "Heterochromia iridis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:10851256",
+        "description": "Tietz syndrome (hypopigmentation/deafness) caused by mutation of MITF"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002226",
+      "label": "White eyebrow"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:10851256",
+        "description": "Tietz syndrome (hypopigmentation/deafness) caused by mutation of MITF"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008527",
+      "label": "Congenital sensorineural hearing impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:10851256",
+        "description": "Tietz syndrome (hypopigmentation/deafness) caused by mutation of MITF"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000635",
+      "label": "Blue irides"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:10851256",
+        "description": "Tietz syndrome (hypopigmentation/deafness) caused by mutation of MITF"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002227",
+      "label": "White eyelashes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:10851256",
+        "description": "Tietz syndrome (hypopigmentation/deafness) caused by mutation of MITF"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007894",
+      "label": "Hypopigmentation of the fundus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:10851256",
+        "description": "Tietz syndrome (hypopigmentation/deafness) caused by mutation of MITF"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:4286",
+    "symbol": "MITF"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "3",
+      "pos": 70001033,
+      "ref": "C",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:103500",
+      "label": "TIETZ SYNDROME"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:10851256",
+      "description": "Tietz syndrome (hypopigmentation/deafness) caused by mutation of MITF"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Smith-2017-ACP4-Family_1-IV_3.json b/notebooks/LIRICAL/v1phenopackets/Smith-2017-ACP4-Family_1-IV_3.json
new file mode 100644
index 000000000..a31de12da
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Smith-2017-ACP4-Family_1-IV_3.json
@@ -0,0 +1,117 @@
+{
+  "id": "PMID:28513613-Smith-2017-ACP4-Family_1-IV:3",
+  "subject": {
+    "id": "Family 1-IV:3",
+    "ageAtCollection": {
+      "age": "n/a"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000685",
+      "label": "Hypoplasia of teeth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28513613",
+        "description": "Defects in the acid phosphatase ACPT cause recessive hypoplastic amelogenesis imperfecta"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000705",
+      "label": "Amelogenesis imperfecta"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28513613",
+        "description": "Defects in the acid phosphatase ACPT cause recessive hypoplastic amelogenesis imperfecta"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:93650",
+    "symbol": "ACP4"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "19",
+      "pos": 51297041,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617297",
+      "label": "Amelogenesis imperfecta, type IJ"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28513613",
+      "description": "Defects in the acid phosphatase ACPT cause recessive hypoplastic amelogenesis imperfecta"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Snanoudj-2019-SERAC1-proband.json b/notebooks/LIRICAL/v1phenopackets/Snanoudj-2019-SERAC1-proband.json
new file mode 100644
index 000000000..35b6946bb
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Snanoudj-2019-SERAC1-proband.json
@@ -0,0 +1,446 @@
+{
+  "id": "PMID:31251474-Snanoudj-2019-SERAC1-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P8Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001508",
+      "label": "Failure to thrive"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31251474",
+        "description": "Identification of a novel splice site mutation in the SERAC1 gene responsible for the MEGDHEL syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003200",
+      "label": "Ragged-red muscle fibers"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31251474",
+        "description": "Identification of a novel splice site mutation in the SERAC1 gene responsible for the MEGDHEL syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000648",
+      "label": "Optic atrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31251474",
+        "description": "Identification of a novel splice site mutation in the SERAC1 gene responsible for the MEGDHEL syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012751",
+      "label": "Abnormal basal ganglia MRI signal intensity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:31251474",
+        "description": "Identification of a novel splice site mutation in the SERAC1 gene responsible for the MEGDHEL syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001943",
+      "label": "Hypoglycemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+      }
+    }]
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+      "label": "Hearing impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:31251474",
+        "description": "Identification of a novel splice site mutation in the SERAC1 gene responsible for the MEGDHEL syndrome"
+      }
+    }]
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+      "id": "HP:0012708",
+      "label": "Reduced brain N-acetyl aspartate level by MRS"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "id": "PMID:31251474",
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+      }
+    }]
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+      "id": "HP:0008947",
+      "label": "Infantile muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+      "label": "Microcephaly"
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+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+      }
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+      "label": "Subcortical cerebral atrophy"
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+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+    "evidence": [{
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+    },
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+  }, {
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+    "zygosity": {
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+      "label": "heterozygous"
+    }
+  }],
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+      "label": "3-@METHYLGLUTACONIC ACIDURIA WITH DEAFNESS, ENCEPHALOPATHY, AND LEIGH-LIKESYNDROME; MEGDEL"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
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+    }, {
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+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
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+      "url": "http://purl.obolibrary.org/obo/eco.owl",
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+    }, {
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+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Soumittra-2014-SLC4A11-Patient_1.json b/notebooks/LIRICAL/v1phenopackets/Soumittra-2014-SLC4A11-Patient_1.json
new file mode 100644
index 000000000..0ca45ca7c
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Soumittra-2014-SLC4A11-Patient_1.json
@@ -0,0 +1,115 @@
+{
+  "id": "PMID:25007886-Soumittra-2014-SLC4A11-Patient_1",
+  "subject": {
+    "id": "Patient 1",
+    "ageAtCollection": {
+      "age": "P46Y"
+    },
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0012038",
+      "label": "Corneal guttata"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25007886",
+        "description": "Biosynthetic and functional defects in newly identified SLC4A11 mutants and absence of COL8A2 mutations in Fuchs endothelial corneal dystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011487",
+      "label": "Increased corneal thickness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25007886",
+        "description": "Biosynthetic and functional defects in newly identified SLC4A11 mutants and absence of COL8A2 mutations in Fuchs endothelial corneal dystrophy"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:83959",
+    "symbol": "SLC4A11"
+  }],
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+      "chr": "20",
+      "pos": 3214218,
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+      "alt": "G"
+    },
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+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:613268",
+      "label": "CORNEAL DYSTROPHY, FUCHS ENDOTHELIAL, 4; FECD4"
+    }
+  }],
+  "metaData": {
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+    "resources": [{
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+      "name": "human phenotype ontology",
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+      "namespacePrefix": "HP",
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+      "name": "Phenotype And Trait Ontology",
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+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
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+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
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+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:25007886",
+      "description": "Biosynthetic and functional defects in newly identified SLC4A11 mutants and absence of COL8A2 mutations in Fuchs endothelial corneal dystrophy"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Steinkellner-2015-ADAMTS10-18-year-old_woman.json b/notebooks/LIRICAL/v1phenopackets/Steinkellner-2015-ADAMTS10-18-year-old_woman.json
new file mode 100644
index 000000000..b9c562d7a
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Steinkellner-2015-ADAMTS10-18-year-old_woman.json
@@ -0,0 +1,221 @@
+{
+  "id": "PMID:25469541-Steinkellner-2015-ADAMTS10-18-year-old_woman",
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+      "age": "18Y"
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+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
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+      "label": "High myopia"
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:25469541",
+        "description": "Identification and molecular characterisation of a homozygous missense mutation in the ADAMTS10 gene in a patient with Weill-Marchesani syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011623",
+      "label": "Muscular ventricular septal defect"
+    },
+    "evidence": [{
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+        "description": "Identification and molecular characterisation of a homozygous missense mutation in the ADAMTS10 gene in a patient with Weill-Marchesani syndrome"
+      }
+    }]
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+      "label": "Short stature"
+    },
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+      "label": "Microspherophakia"
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+    "evidence": [{
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+      "label": "Brachydactyly"
+    },
+    "evidence": [{
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+  }],
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+  }],
+  "metaData": {
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+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
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+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:25469541",
+      "description": "Identification and molecular characterisation of a homozygous missense mutation in the ADAMTS10 gene in a patient with Weill-Marchesani syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Stouffs-2018-RTTN-Patient_3.json b/notebooks/LIRICAL/v1phenopackets/Stouffs-2018-RTTN-Patient_3.json
new file mode 100644
index 000000000..471854e17
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Stouffs-2018-RTTN-Patient_3.json
@@ -0,0 +1,236 @@
+{
+  "id": "PMID:29883675-Stouffs-2018-RTTN-Patient_3",
+  "subject": {
+    "id": "Patient 3",
+    "ageAtCollection": {
+      "age": "6Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29883675",
+        "description": "Biallelic mutations in RTTN are associated with microcephaly, short stature and a wide range of brain malformations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002126",
+      "label": "Polymicrogyria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29883675",
+        "description": "Biallelic mutations in RTTN are associated with microcephaly, short stature and a wide range of brain malformations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000712",
+      "label": "Emotional lability"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29883675",
+        "description": "Biallelic mutations in RTTN are associated with microcephaly, short stature and a wide range of brain malformations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29883675",
+        "description": "Biallelic mutations in RTTN are associated with microcephaly, short stature and a wide range of brain malformations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000252",
+      "label": "Microcephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29883675",
+        "description": "Biallelic mutations in RTTN are associated with microcephaly, short stature and a wide range of brain malformations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002079",
+      "label": "Hypoplasia of the corpus callosum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29883675",
+        "description": "Biallelic mutations in RTTN are associated with microcephaly, short stature and a wide range of brain malformations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004325",
+      "label": "Decreased body weight"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29883675",
+        "description": "Biallelic mutations in RTTN are associated with microcephaly, short stature and a wide range of brain malformations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012758",
+      "label": "Neurodevelopmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29883675",
+        "description": "Biallelic mutations in RTTN are associated with microcephaly, short stature and a wide range of brain malformations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001320",
+      "label": "Cerebellar vermis hypoplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29883675",
+        "description": "Biallelic mutations in RTTN are associated with microcephaly, short stature and a wide range of brain malformations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001845",
+      "label": "Overlapping toe"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29883675",
+        "description": "Biallelic mutations in RTTN are associated with microcephaly, short stature and a wide range of brain malformations"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:25914",
+    "symbol": "RTTN"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "18",
+      "pos": 67834203,
+      "ref": "T",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:614833",
+      "label": "POLYMICROGYRIA WITH SEIZURES; PMGYS"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29883675",
+      "description": "Biallelic mutations in RTTN are associated with microcephaly, short stature and a wide range of brain malformations"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Straniero-2018-OTUD6B-proband.json b/notebooks/LIRICAL/v1phenopackets/Straniero-2018-OTUD6B-proband.json
new file mode 100644
index 000000000..0e4451e85
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Straniero-2018-OTUD6B-proband.json
@@ -0,0 +1,309 @@
+{
+  "id": "PMID:30364145-Straniero-2018-OTUD6B-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P6Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0012758",
+      "label": "Neurodevelopmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30364145",
+        "description": "First Replication of the Involvement of OTUD6B in Intellectual Disability Syndrome With Seizures and Dysmorphic Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002020",
+      "label": "Gastroesophageal reflux"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30364145",
+        "description": "First Replication of the Involvement of OTUD6B in Intellectual Disability Syndrome With Seizures and Dysmorphic Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001636",
+      "label": "Tetralogy of Fallot"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30364145",
+        "description": "First Replication of the Involvement of OTUD6B in Intellectual Disability Syndrome With Seizures and Dysmorphic Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000218",
+      "label": "High palate"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30364145",
+        "description": "First Replication of the Involvement of OTUD6B in Intellectual Disability Syndrome With Seizures and Dysmorphic Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000337",
+      "label": "Broad forehead"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30364145",
+        "description": "First Replication of the Involvement of OTUD6B in Intellectual Disability Syndrome With Seizures and Dysmorphic Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000319",
+      "label": "Smooth philtrum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30364145",
+        "description": "First Replication of the Involvement of OTUD6B in Intellectual Disability Syndrome With Seizures and Dysmorphic Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000400",
+      "label": "Macrotia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30364145",
+        "description": "First Replication of the Involvement of OTUD6B in Intellectual Disability Syndrome With Seizures and Dysmorphic Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001511",
+      "label": "Intrauterine growth retardation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30364145",
+        "description": "First Replication of the Involvement of OTUD6B in Intellectual Disability Syndrome With Seizures and Dysmorphic Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000490",
+      "label": "Deeply set eye"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30364145",
+        "description": "First Replication of the Involvement of OTUD6B in Intellectual Disability Syndrome With Seizures and Dysmorphic Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000276",
+      "label": "Long face"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30364145",
+        "description": "First Replication of the Involvement of OTUD6B in Intellectual Disability Syndrome With Seizures and Dysmorphic Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000601",
+      "label": "Hypotelorism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30364145",
+        "description": "First Replication of the Involvement of OTUD6B in Intellectual Disability Syndrome With Seizures and Dysmorphic Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011968",
+      "label": "Feeding difficulties"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:30364145",
+        "description": "First Replication of the Involvement of OTUD6B in Intellectual Disability Syndrome With Seizures and Dysmorphic Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000508",
+      "label": "Ptosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30364145",
+        "description": "First Replication of the Involvement of OTUD6B in Intellectual Disability Syndrome With Seizures and Dysmorphic Features"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000219",
+      "label": "Thin upper lip vermilion"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30364145",
+        "description": "First Replication of the Involvement of OTUD6B in Intellectual Disability Syndrome With Seizures and Dysmorphic Features"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:51633",
+    "symbol": "OTUD6B"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "8",
+      "pos": 92083518,
+      "ref": "G",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "8",
+      "pos": 92086140,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617452",
+      "label": " Intellectual developmental disorder with dysmorphic facies, seizures, and distal limb anomalies"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30364145",
+      "description": "First Replication of the Involvement of OTUD6B in Intellectual Disability Syndrome With Seizures and Dysmorphic Features"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Suarez-Artiles-2018-OCRL-Patient_1.json b/notebooks/LIRICAL/v1phenopackets/Suarez-Artiles-2018-OCRL-Patient_1.json
new file mode 100644
index 000000000..78769774e
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Suarez-Artiles-2018-OCRL-Patient_1.json
@@ -0,0 +1,208 @@
+{
+  "id": "PMID:29300302-Suarez-Artiles-2018-OCRL-Patient_1",
+  "subject": {
+    "id": "Patient 1",
+    "ageAtCollection": {
+      "age": "P27Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000501",
+      "label": "Glaucoma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29300302",
+        "description": "Splicing Analysis of Exonic OCRL Mutations Causing Lowe Syndrome or Dent-2 Disease"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003126",
+      "label": "Low-molecular-weight proteinuria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29300302",
+        "description": "Splicing Analysis of Exonic OCRL Mutations Causing Lowe Syndrome or Dent-2 Disease"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003076",
+      "label": "Glycosuria"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29300302",
+        "description": "Splicing Analysis of Exonic OCRL Mutations Causing Lowe Syndrome or Dent-2 Disease"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012592",
+      "label": "Albuminuria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29300302",
+        "description": "Splicing Analysis of Exonic OCRL Mutations Causing Lowe Syndrome or Dent-2 Disease"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000518",
+      "label": "Cataract"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29300302",
+        "description": "Splicing Analysis of Exonic OCRL Mutations Causing Lowe Syndrome or Dent-2 Disease"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:29300302",
+        "description": "Splicing Analysis of Exonic OCRL Mutations Causing Lowe Syndrome or Dent-2 Disease"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
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+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "description": "Splicing Analysis of Exonic OCRL Mutations Causing Lowe Syndrome or Dent-2 Disease"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003355",
+      "label": "Aminoaciduria"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29300302",
+        "description": "Splicing Analysis of Exonic OCRL Mutations Causing Lowe Syndrome or Dent-2 Disease"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:4952",
+    "symbol": "OCRL"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "X",
+      "pos": 128723933,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000134",
+      "label": "hemizygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:309000",
+      "label": "LOWE OCULOCEREBRORENAL SYNDROME; OCRL"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
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+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29300302",
+      "description": "Splicing Analysis of Exonic OCRL Mutations Causing Lowe Syndrome or Dent-2 Disease"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Suter-2016-USB1-patient.json b/notebooks/LIRICAL/v1phenopackets/Suter-2016-USB1-patient.json
new file mode 100644
index 000000000..598e0ba00
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Suter-2016-USB1-patient.json
@@ -0,0 +1,191 @@
+{
+  "id": "PMID:27247962-Suter-2016-USB1-patient",
+  "subject": {
+    "id": "patient",
+    "ageAtCollection": {
+      "age": "n/a"
+    },
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27247962",
+        "description": "Rothmund-Thomson Syndrome: novel pathogenic mutations and frequencies of variants in the RECQL4 and USB1 (C16orf57) gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006530",
+      "label": "Interstitial pulmonary abnormality"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27247962",
+        "description": "Rothmund-Thomson Syndrome: novel pathogenic mutations and frequencies of variants in the RECQL4 and USB1 (C16orf57) gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0032252",
+      "label": "Granuloma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Rothmund-Thomson Syndrome: novel pathogenic mutations and frequencies of variants in the RECQL4 and USB1 (C16orf57) gene"
+      }
+    }]
+  }, {
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+      "label": "Neutropenia"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27247962",
+        "description": "Rothmund-Thomson Syndrome: novel pathogenic mutations and frequencies of variants in the RECQL4 and USB1 (C16orf57) gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002110",
+      "label": "Bronchiectasis"
+    },
+    "evidence": [{
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+        "description": "Rothmund-Thomson Syndrome: novel pathogenic mutations and frequencies of variants in the RECQL4 and USB1 (C16orf57) gene"
+      }
+    }]
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+      "label": "Poikiloderma"
+    },
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+      "reference": {
+        "id": "PMID:27247962",
+        "description": "Rothmund-Thomson Syndrome: novel pathogenic mutations and frequencies of variants in the RECQL4 and USB1 (C16orf57) gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000044",
+      "label": "Hypogonadotrophic hypogonadism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27247962",
+        "description": "Rothmund-Thomson Syndrome: novel pathogenic mutations and frequencies of variants in the RECQL4 and USB1 (C16orf57) gene"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:79650",
+    "symbol": "USB1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "16",
+      "pos": 58043896,
+      "ref": "T",
+      "alt": "TC"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:604173",
+      "label": "POIKILODERMA WITH NEUTROPENIA; PN"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
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+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
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+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27247962",
+      "description": "Rothmund-Thomson Syndrome: novel pathogenic mutations and frequencies of variants in the RECQL4 and USB1 (C16orf57) gene"
+    }]
+  }
+}
\ No newline at end of file
diff --git "a/notebooks/LIRICAL/v1phenopackets/Szcza\305\202uba-2018-GNB1-proband.json" "b/notebooks/LIRICAL/v1phenopackets/Szcza\305\202uba-2018-GNB1-proband.json"
new file mode 100644
index 000000000..3a4e462ed
--- /dev/null
+++ "b/notebooks/LIRICAL/v1phenopackets/Szcza\305\202uba-2018-GNB1-proband.json"
@@ -0,0 +1,238 @@
+{
+  "id": "PMID:29174093-Szczałuba-2018-GNB1-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P4Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000308",
+      "label": "Microretrognathia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29174093",
+        "description": "Novel GNB1 de novo mutation in a patient with neurodevelopmental disorder and cutaneous mastocytosis: Clinical report and literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29174093",
+        "description": "Novel GNB1 de novo mutation in a patient with neurodevelopmental disorder and cutaneous mastocytosis: Clinical report and literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000076",
+      "label": "Vesicoureteral reflux"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:29174093",
+        "description": "Novel GNB1 de novo mutation in a patient with neurodevelopmental disorder and cutaneous mastocytosis: Clinical report and literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001266",
+      "label": "Choreoathetosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:29174093",
+        "description": "Novel GNB1 de novo mutation in a patient with neurodevelopmental disorder and cutaneous mastocytosis: Clinical report and literature review"
+      }
+    }]
+  }, {
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+      "label": "Global developmental delay"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
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+      "label": "Clinodactyly of the 5th finger"
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+    "evidence": [{
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+        "description": "Novel GNB1 de novo mutation in a patient with neurodevelopmental disorder and cutaneous mastocytosis: Clinical report and literature review"
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+    "negated": true,
+    "evidence": [{
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+        "description": "Novel GNB1 de novo mutation in a patient with neurodevelopmental disorder and cutaneous mastocytosis: Clinical report and literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005709",
+      "label": "2-3 toe cutaneous syndactyly"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
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+        "id": "PMID:29174093",
+        "description": "Novel GNB1 de novo mutation in a patient with neurodevelopmental disorder and cutaneous mastocytosis: Clinical report and literature review"
+      }
+    }]
+  }, {
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+      "label": "Broad-based gait"
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+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "id": "PMID:29174093",
+        "description": "Novel GNB1 de novo mutation in a patient with neurodevelopmental disorder and cutaneous mastocytosis: Clinical report and literature review"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000733",
+      "label": "Stereotypy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29174093",
+        "description": "Novel GNB1 de novo mutation in a patient with neurodevelopmental disorder and cutaneous mastocytosis: Clinical report and literature review"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2782",
+    "symbol": "GNB1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 1737951,
+      "ref": "C",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616973",
+      "label": "Mental retardation, autosomal dominant 42"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
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+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29174093",
+      "description": "Novel GNB1 de novo mutation in a patient with neurodevelopmental disorder and cutaneous mastocytosis: Clinical report and literature review"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Ta-Shma-2017-TMEM260-1-II-1.json b/notebooks/LIRICAL/v1phenopackets/Ta-Shma-2017-TMEM260-1-II-1.json
new file mode 100644
index 000000000..92454bb0e
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Ta-Shma-2017-TMEM260-1-II-1.json
@@ -0,0 +1,441 @@
+{
+  "id": "PMID:28318500-Ta-Shma-2017-TMEM260-1-II-1",
+  "subject": {
+    "id": "1-II-1",
+    "ageAtCollection": {
+      "age": "P1Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001629",
+      "label": "Ventricular septal defect"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28318500",
+        "description": "Mutations in TMEM260 Cause a Pediatric Neurodevelopmental, Cardiac, and Renal Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031664",
+      "label": "Systolic heart murmur"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28318500",
+        "description": "Mutations in TMEM260 Cause a Pediatric Neurodevelopmental, Cardiac, and Renal Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001660",
+      "label": "Truncus arteriosus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28318500",
+        "description": "Mutations in TMEM260 Cause a Pediatric Neurodevelopmental, Cardiac, and Renal Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010773",
+      "label": "Partial anomalous pulmonary venous return"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28318500",
+        "description": "Mutations in TMEM260 Cause a Pediatric Neurodevelopmental, Cardiac, and Renal Syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100520",
+      "label": "Oliguria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28318500",
+        "description": "Mutations in TMEM260 Cause a Pediatric Neurodevelopmental, Cardiac, and Renal Syndrome"
+      }
+    }]
+  }, {
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+      "id": "HP:0010442",
+      "label": "Polydactyly"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28318500",
+        "description": "Mutations in TMEM260 Cause a Pediatric Neurodevelopmental, Cardiac, and Renal Syndrome"
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+      "namespacePrefix": "PATO",
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+      "namespacePrefix": "NCBITaxon"
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+      "name": "Evidence and Conclusion Ontology",
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+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
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+    "externalReferences": [{
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+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Ta-Shma-2017-TMEM260-2-II-4.json b/notebooks/LIRICAL/v1phenopackets/Ta-Shma-2017-TMEM260-2-II-4.json
new file mode 100644
index 000000000..7119d13b4
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Ta-Shma-2017-TMEM260-2-II-4.json
@@ -0,0 +1,378 @@
+{
+  "id": "PMID:28318500-Ta-Shma-2017-TMEM260-2-II-4",
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+      "label": "Homo sapiens"
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+    "externalReferences": [{
+      "id": "PMID:28318500",
+      "description": "Mutations in TMEM260 Cause a Pediatric Neurodevelopmental, Cardiac, and Renal Syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Tadic-2017-CAPN1-Index.json b/notebooks/LIRICAL/v1phenopackets/Tadic-2017-CAPN1-Index.json
new file mode 100644
index 000000000..b4cd10691
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Tadic-2017-CAPN1-Index.json
@@ -0,0 +1,192 @@
+{
+  "id": "PMID:28321562-Tadic-2017-CAPN1-Index",
+  "subject": {
+    "id": "Index",
+    "ageAtCollection": {
+      "age": "P39Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002317",
+      "label": "Unsteady gait"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28321562",
+        "description": "CAPN1 mutations are associated with a syndrome of combined spasticity and ataxia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002070",
+      "label": "Limb ataxia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28321562",
+        "description": "CAPN1 mutations are associated with a syndrome of combined spasticity and ataxia"
+      }
+    }]
+  }, {
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+      "id": "HP:0001285",
+      "label": "Spastic tetraparesis"
+    },
+    "evidence": [{
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+    }]
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+        "description": "CAPN1 mutations are associated with a syndrome of combined spasticity and ataxia"
+      }
+    }]
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+      "label": "Hypertonia"
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+      "namespacePrefix": "GENO",
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+      "namespacePrefix": "NCBITaxon"
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+      "namespacePrefix": "ECO",
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+    }, {
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+      "id": "PMID:28321562",
+      "description": "CAPN1 mutations are associated with a syndrome of combined spasticity and ataxia"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Taghizade_Mortezaee-2015-ITGB2-P1.json b/notebooks/LIRICAL/v1phenopackets/Taghizade_Mortezaee-2015-ITGB2-P1.json
new file mode 100644
index 000000000..03c222b91
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Taghizade_Mortezaee-2015-ITGB2-P1.json
@@ -0,0 +1,147 @@
+{
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+      "label": "Homo sapiens"
+    }
+  },
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+    "type": {
+      "id": "HP:0011897",
+      "label": "Neutrophilia"
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+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0032435",
+      "label": "Neonatal omphalitis"
+    },
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+        "description": "Investigation of ITGB2 gene in 12 new cases of leukocyte adhesion deficiency-type I revealed four novel mutations from Iran"
+      }
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+      "id": "HP:0200042",
+      "label": "Skin ulcer"
+    },
+    "evidence": [{
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+      }
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+      "id": "HP:0032434",
+      "label": "Delayed umbilical cord separation"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:26497373",
+        "description": "Investigation of ITGB2 gene in 12 new cases of leukocyte adhesion deficiency-type I revealed four novel mutations from Iran"
+      }
+    }]
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+    "id": "NCBIGene:3689",
+    "symbol": "ITGB2"
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+      "id": "OMIM:116920",
+      "label": "LEUKOCYTE ADHESION DEFICIENCY, TYPE I; LAD"
+    }
+  }],
+  "metaData": {
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+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
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+    "externalReferences": [{
+      "id": "PMID:26497373",
+      "description": "Investigation of ITGB2 gene in 12 new cases of leukocyte adhesion deficiency-type I revealed four novel mutations from Iran"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Takagi-2006-WNK1-Patient.json b/notebooks/LIRICAL/v1phenopackets/Takagi-2006-WNK1-Patient.json
new file mode 100644
index 000000000..e6853b4a1
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Takagi-2006-WNK1-Patient.json
@@ -0,0 +1,298 @@
+{
+  "id": "PMID:16636245-Takagi-2006-WNK1-Patient",
+  "subject": {
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+    "ageAtCollection": {
+      "age": "28"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001265",
+      "label": "Hyporeflexia"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:16636245",
+        "description": "New HSN2 mutation in Japanese patient with hereditary sensory and autonomic neuropathy type 2"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003400",
+      "label": "Basal lamina onion bulb formation"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:16636245",
+        "description": "New HSN2 mutation in Japanese patient with hereditary sensory and autonomic neuropathy type 2"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031860",
+      "label": "Abnormal heart rate variability"
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+    "negated": true,
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+    }]
+  }, {
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+      "label": "Recurrent bacterial skin infections"
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+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+      }
+    }]
+  }, {
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+      "id": "HP:0007021",
+      "label": "Pain insensitivity"
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+    "evidence": [{
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+      "label": "Abnormal systemic blood pressure"
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+    }]
+  }, {
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+      }
+    }]
+  }, {
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+      "label": "Hyporeflexia"
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+    "evidence": [{
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+        "description": "New HSN2 mutation in Japanese patient with hereditary sensory and autonomic neuropathy type 2"
+      }
+    }]
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+      "id": "HP:0040132",
+      "label": "Abnormal sensory nerve conduction velocity"
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+    }]
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+      "label": "Abnormal autonomic nervous system physiology"
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+    "negated": true,
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+        "description": "New HSN2 mutation in Japanese patient with hereditary sensory and autonomic neuropathy type 2"
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+  }, {
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+      "label": "Polyneuropathy"
+    },
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+        "id": "PMID:16636245",
+        "description": "New HSN2 mutation in Japanese patient with hereditary sensory and autonomic neuropathy type 2"
+      }
+    }]
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+  "genes": [{
+    "id": "NCBIGene:65125",
+    "symbol": "WNK1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "12",
+      "pos": 977212,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
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+      "genomeAssembly": "GRCh37",
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+      "pos": 936408,
+      "ref": "C",
+      "alt": "CT"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:201300",
+      "label": "NEUROPATHY, HEREDITARY SENSORY AND AUTONOMIC, TYPE IIA; HSAN2A"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:lccarmody",
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+      "id": "hp",
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+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
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+      "description": "New HSN2 mutation in Japanese patient with hereditary sensory and autonomic neuropathy type 2"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Tamhankar-2014-ROR2-Patient_1.json b/notebooks/LIRICAL/v1phenopackets/Tamhankar-2014-ROR2-Patient_1.json
new file mode 100644
index 000000000..ea150b0e0
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Tamhankar-2014-ROR2-Patient_1.json
@@ -0,0 +1,387 @@
+{
+  "id": "PMID:24932600-Tamhankar-2014-ROR2-Patient_1",
+  "subject": {
+    "id": "Patient 1",
+    "ageAtCollection": {
+      "age": "P2Y6M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000054",
+      "label": "Micropenis"
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+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003022",
+      "label": "Hypoplasia of the ulna"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000256",
+      "label": "Macrocephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002007",
+      "label": "Frontal bossing"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008439",
+      "label": "Lumbar hemivertebrae"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000369",
+      "label": "Low-set ears"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002984",
+      "label": "Hypoplasia of the radius"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000921",
+      "label": "Missing ribs"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003086",
+      "label": "Acromesomelia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012646",
+      "label": "Retractile testis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000520",
+      "label": "Proptosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000212",
+      "label": "Gingival overgrowth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0200055",
+      "label": "Small hand"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000316",
+      "label": "Hypertelorism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
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+      "id": "HP:0000463",
+      "label": "Anteverted nares"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
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+      "id": "HP:0002944",
+      "label": "Thoracolumbar scoliosis"
+    },
+    "evidence": [{
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+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Wide mouth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010804",
+      "label": "Tented upper lip vermilion"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
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+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005280",
+      "label": "Depressed nasal bridge"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:4920",
+    "symbol": "ROR2"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "9",
+      "pos": 94499750,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:268310",
+      "label": "ROBINOW SYNDROME, AUTOSOMAL RECESSIVE; RRS"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:24932600",
+      "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Tamhankar-2014-ROR2-Patient_2.json b/notebooks/LIRICAL/v1phenopackets/Tamhankar-2014-ROR2-Patient_2.json
new file mode 100644
index 000000000..3e206afa6
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Tamhankar-2014-ROR2-Patient_2.json
@@ -0,0 +1,372 @@
+{
+  "id": "PMID:24932600-Tamhankar-2014-ROR2-Patient_2",
+  "subject": {
+    "id": "Patient 2",
+    "ageAtCollection": {
+      "age": "P2Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000054",
+      "label": "Micropenis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010281",
+      "label": "Cleft lower lip"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002007",
+      "label": "Frontal bossing"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001647",
+      "label": "Bicuspid aortic valve"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000343",
+      "label": "Long philtrum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
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+      "label": "Micrognathia"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
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+      "id": "HP:0003086",
+      "label": "Acromesomelia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
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+      "label": "Elbow dislocation"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008551",
+      "label": "Microtia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000520",
+      "label": "Proptosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
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+      "id": "HP:0000212",
+      "label": "Gingival overgrowth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009381",
+      "label": "Short finger"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007655",
+      "label": "Eversion of lateral third of lower eyelids"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
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+    },
+    "evidence": [{
+      "evidenceCode": {
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+      },
+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009826",
+      "label": "Limb undergrowth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002937",
+      "label": "Hemivertebrae"
+    },
+    "evidence": [{
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+      },
+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005280",
+      "label": "Depressed nasal bridge"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
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+      "id": "HP:0000892",
+      "label": "Bifid ribs"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:24932600",
+        "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:4920",
+    "symbol": "ROR2"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "9",
+      "pos": 94519790,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:268310",
+      "label": "ROBINOW SYNDROME, AUTOSOMAL RECESSIVE; RRS"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:24932600",
+      "description": "Identification of novel ROR2 gene mutations in Indian children with Robinow syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Tamura-2017-DHCR7-patient.json b/notebooks/LIRICAL/v1phenopackets/Tamura-2017-DHCR7-patient.json
new file mode 100644
index 000000000..80e704876
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Tamura-2017-DHCR7-patient.json
@@ -0,0 +1,295 @@
+{
+  "id": "PMID:28503313-Tamura-2017-DHCR7-patient",
+  "subject": {
+    "id": "patient",
+    "ageAtCollection": {
+      "age": "P2M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0004691",
+      "label": "2-3 toe syndactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28503313",
+        "description": "Novel DHCR7 mutation in a case of Smith-Lemli-Opitz syndrome showing 46,XY disorder of sex development"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003196",
+      "label": "Short nose"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28503313",
+        "description": "Novel DHCR7 mutation in a case of Smith-Lemli-Opitz syndrome showing 46,XY disorder of sex development"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030087",
+      "label": "Abnormal serum testosterone level"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28503313",
+        "description": "Novel DHCR7 mutation in a case of Smith-Lemli-Opitz syndrome showing 46,XY disorder of sex development"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000062",
+      "label": "Ambiguous genitalia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28503313",
+        "description": "Novel DHCR7 mutation in a case of Smith-Lemli-Opitz syndrome showing 46,XY disorder of sex development"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000048",
+      "label": "Bifid scrotum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28503313",
+        "description": "Novel DHCR7 mutation in a case of Smith-Lemli-Opitz syndrome showing 46,XY disorder of sex development"
+      }
+    }]
+  }, {
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+      "id": "HP:0008734",
+      "label": "Decreased testicular size"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28503313",
+        "description": "Novel DHCR7 mutation in a case of Smith-Lemli-Opitz syndrome showing 46,XY disorder of sex development"
+      }
+    }]
+  }, {
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+      "id": "HP:0001047",
+      "label": "Atopic dermatitis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28503313",
+        "description": "Novel DHCR7 mutation in a case of Smith-Lemli-Opitz syndrome showing 46,XY disorder of sex development"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003146",
+      "label": "Hypocholesterolemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28503313",
+        "description": "Novel DHCR7 mutation in a case of Smith-Lemli-Opitz syndrome showing 46,XY disorder of sex development"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010569",
+      "label": "Elevated 7-dehydrocholesterol"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28503313",
+        "description": "Novel DHCR7 mutation in a case of Smith-Lemli-Opitz syndrome showing 46,XY disorder of sex development"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000047",
+      "label": "Hypospadias"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28503313",
+        "description": "Novel DHCR7 mutation in a case of Smith-Lemli-Opitz syndrome showing 46,XY disorder of sex development"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000369",
+      "label": "Low-set ears"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28503313",
+        "description": "Novel DHCR7 mutation in a case of Smith-Lemli-Opitz syndrome showing 46,XY disorder of sex development"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003462",
+      "label": "Elevated 8-dehydrocholesterol"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28503313",
+        "description": "Novel DHCR7 mutation in a case of Smith-Lemli-Opitz syndrome showing 46,XY disorder of sex development"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000054",
+      "label": "Micropenis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28503313",
+        "description": "Novel DHCR7 mutation in a case of Smith-Lemli-Opitz syndrome showing 46,XY disorder of sex development"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:1717",
+    "symbol": "DHCR7"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "11",
+      "pos": 71148914,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "11",
+      "pos": 71146524,
+      "ref": "T",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:270400",
+      "label": "SMITH-LEMLI-OPITZ SYNDROME; SLOS"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
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+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28503313",
+      "description": "Novel DHCR7 mutation in a case of Smith-Lemli-Opitz syndrome showing 46,XY disorder of sex development"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Tan-2014-CDK5RAP2-patient.json b/notebooks/LIRICAL/v1phenopackets/Tan-2014-CDK5RAP2-patient.json
new file mode 100644
index 000000000..9cd13ebfd
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Tan-2014-CDK5RAP2-patient.json
@@ -0,0 +1,189 @@
+{
+  "id": "PMID:23726037-Tan-2014-CDK5RAP2-patient",
+  "subject": {
+    "id": "patient",
+    "ageAtCollection": {
+      "age": "P6Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002099",
+      "label": "Asthma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23726037",
+        "description": "The first case of CDK5RAP2-related primary microcephaly in a non-consanguineous patient identified by next generation sequencing"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23726037",
+        "description": "The first case of CDK5RAP2-related primary microcephaly in a non-consanguineous patient identified by next generation sequencing"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010862",
+      "label": "Delayed fine motor development"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:23726037",
+        "description": "The first case of CDK5RAP2-related primary microcephaly in a non-consanguineous patient identified by next generation sequencing"
+      }
+    }]
+  }, {
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+      "id": "HP:0010535",
+      "label": "Sleep apnea"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:23726037",
+        "description": "The first case of CDK5RAP2-related primary microcephaly in a non-consanguineous patient identified by next generation sequencing"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
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+      "label": "Delayed skeletal maturation"
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:23726037",
+        "description": "The first case of CDK5RAP2-related primary microcephaly in a non-consanguineous patient identified by next generation sequencing"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:55755",
+    "symbol": "CDK5RAP2"
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+      "genomeAssembly": "GRCh37",
+      "chr": "9",
+      "pos": 123298783,
+      "ref": "CTGCCT",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "9",
+      "pos": 123182239,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:604804",
+      "label": "MICROCEPHALY 3, PRIMARY, AUTOSOMAL RECESSIVE; MCPH3"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:23726037",
+      "description": "The first case of CDK5RAP2-related primary microcephaly in a non-consanguineous patient identified by next generation sequencing"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Tesi-2017-SAMD9L-II-4.json b/notebooks/LIRICAL/v1phenopackets/Tesi-2017-SAMD9L-II-4.json
new file mode 100644
index 000000000..f36907f92
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Tesi-2017-SAMD9L-II-4.json
@@ -0,0 +1,282 @@
+{
+  "id": "PMID:28202457-Tesi-2017-SAMD9L-II-4",
+  "subject": {
+    "id": "II-4",
+    "ageAtCollection": {
+      "age": "P1Y6M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0011950",
+      "label": "Bronchiolitis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28202457",
+        "description": "Gain-of-function SAMD9L mutations cause a syndrome of cytopenia, immunodeficiency, MDS, and neurological symptoms"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001875",
+      "label": "Neutropenia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28202457",
+        "description": "Gain-of-function SAMD9L mutations cause a syndrome of cytopenia, immunodeficiency, MDS, and neurological symptoms"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007018",
+      "label": "Attention deficit hyperactivity disorder"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28202457",
+        "description": "Gain-of-function SAMD9L mutations cause a syndrome of cytopenia, immunodeficiency, MDS, and neurological symptoms"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000752",
+      "label": "Hyperactivity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28202457",
+        "description": "Gain-of-function SAMD9L mutations cause a syndrome of cytopenia, immunodeficiency, MDS, and neurological symptoms"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001310",
+      "label": "Dysmetria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28202457",
+        "description": "Gain-of-function SAMD9L mutations cause a syndrome of cytopenia, immunodeficiency, MDS, and neurological symptoms"
+      }
+    }]
+  }, {
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+      "id": "HP:0002863",
+      "label": "Myelodysplasia"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28202457",
+        "description": "Gain-of-function SAMD9L mutations cause a syndrome of cytopenia, immunodeficiency, MDS, and neurological symptoms"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001387",
+      "label": "Joint stiffness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28202457",
+        "description": "Gain-of-function SAMD9L mutations cause a syndrome of cytopenia, immunodeficiency, MDS, and neurological symptoms"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002172",
+      "label": "Postural instability"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28202457",
+        "description": "Gain-of-function SAMD9L mutations cause a syndrome of cytopenia, immunodeficiency, MDS, and neurological symptoms"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001873",
+      "label": "Thrombocytopenia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28202457",
+        "description": "Gain-of-function SAMD9L mutations cause a syndrome of cytopenia, immunodeficiency, MDS, and neurological symptoms"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002141",
+      "label": "Gait imbalance"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28202457",
+        "description": "Gain-of-function SAMD9L mutations cause a syndrome of cytopenia, immunodeficiency, MDS, and neurological symptoms"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002395",
+      "label": "Lower limb hyperreflexia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Tesi-2017-SAMD9L-III-1.json b/notebooks/LIRICAL/v1phenopackets/Tesi-2017-SAMD9L-III-1.json
new file mode 100644
index 000000000..e0db117a0
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Tesi-2017-SAMD9L-III-1.json
@@ -0,0 +1,237 @@
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+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Tian-2018-ACVR1-patient.json b/notebooks/LIRICAL/v1phenopackets/Tian-2018-ACVR1-patient.json
new file mode 100644
index 000000000..191bd5609
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Tian-2018-ACVR1-patient.json
@@ -0,0 +1,241 @@
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+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Tiecke-2001-FBN1-B15.json b/notebooks/LIRICAL/v1phenopackets/Tiecke-2001-FBN1-B15.json
new file mode 100644
index 000000000..1b0e29119
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Tiecke-2001-FBN1-B15.json
@@ -0,0 +1,251 @@
+{
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+      "label": "Decreased body weight"
+    },
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      }
+    }]
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+        "description": "Classic, atypically severe and neonatal Marfan syndrome: twelve mutations and genotype-phenotype correlations in FBN1 exons 24-40"
+      }
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+    "id": "NCBIGene:2200",
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+    }
+  }],
+  "diseases": [{
+    "term": {
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+      "label": "MARFAN SYNDROME; MFS"
+    }
+  }],
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+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
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+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
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+    "externalReferences": [{
+      "id": "PMID:11175294",
+      "description": "Classic, atypically severe and neonatal Marfan syndrome: twelve mutations and genotype-phenotype correlations in FBN1 exons 24-40"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Tran-2015-GALT-FKT118.json b/notebooks/LIRICAL/v1phenopackets/Tran-2015-GALT-FKT118.json
new file mode 100644
index 000000000..62f2173b5
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Tran-2015-GALT-FKT118.json
@@ -0,0 +1,204 @@
+{
+  "id": "PMID:25681079-Tran-2015-GALT-FKT118",
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+    "id": "FKT118",
+    "ageAtCollection": {
+      "age": "P6Y"
+    },
+    "sex": "FEMALE",
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+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
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+    "type": {
+      "id": "HP:0000952",
+      "label": "Jaundice"
+    },
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:25681079",
+        "description": "A De Novo Variant in Galactose-1-P Uridylyltransferase (GALT) Leading to Classic Galactosemia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012024",
+      "label": "Hypergalactosemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+    }]
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+      "id": "OMIM:230400",
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+      "description": "A De Novo Variant in Galactose-1-P Uridylyltransferase (GALT) Leading to Classic Galactosemia"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Travaglini-2017-CAPN1-index.json b/notebooks/LIRICAL/v1phenopackets/Travaglini-2017-CAPN1-index.json
new file mode 100644
index 000000000..9b24ee9bf
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Travaglini-2017-CAPN1-index.json
@@ -0,0 +1,159 @@
+{
+  "id": "PMID:28566166-Travaglini-2017-CAPN1-index",
+  "subject": {
+    "id": "index",
+    "ageAtCollection": {
+      "age": "P16Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0003487",
+      "label": "Babinski sign"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28566166",
+        "description": "Expanding the clinical phenotype of CAPN1-associated mutations: A new case with congenital-onset pure spastic paraplegia"
+      }
+    }]
+  }, {
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+      "label": "Toe walking"
+    },
+    "evidence": [{
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+        "description": "Expanding the clinical phenotype of CAPN1-associated mutations: A new case with congenital-onset pure spastic paraplegia"
+      }
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+  }, {
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+      "label": "Lower limb hypertonia"
+    },
+    "evidence": [{
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+      }
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+    "id": "NCBIGene:823",
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+      "label": "heterozygous"
+    }
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+      "id": "OMIM:616907",
+      "label": "Spastic paraplegia 76, autosomal recessive"
+    }
+  }],
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+      "name": "human phenotype ontology",
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+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
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+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
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+      "version": "2018-03-02",
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+    }, {
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+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
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+    "externalReferences": [{
+      "id": "PMID:28566166",
+      "description": "Expanding the clinical phenotype of CAPN1-associated mutations: A new case with congenital-onset pure spastic paraplegia"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Truong-2010-RAI1-SMS324.json b/notebooks/LIRICAL/v1phenopackets/Truong-2010-RAI1-SMS324.json
new file mode 100644
index 000000000..54c563019
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Truong-2010-RAI1-SMS324.json
@@ -0,0 +1,462 @@
+{
+  "id": "PMID:20932317-Truong-2010-RAI1-SMS324",
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+    },
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+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002020",
+      "label": "Gastroesophageal reflux"
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+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000739",
+      "label": "Anxiety"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
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+      "id": "HP:0100716",
+      "label": "Self-injurious behavior"
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+    "evidence": [{
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+    }]
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+    }]
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+    "type": {
+      "id": "HP:0000582",
+      "label": "Upslanted palpebral fissure"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000664",
+      "label": "Synophrys"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002360",
+      "label": "Sleep disturbance"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000545",
+      "label": "Myopia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004220",
+      "label": "Short middle phalanx of the 5th finger"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002121",
+      "label": "Absence seizure"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001156",
+      "label": "Brachydactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012168",
+      "label": "Head-banging"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011342",
+      "label": "Mild global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001763",
+      "label": "Pes planus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001956",
+      "label": "Truncal obesity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002714",
+      "label": "Downturned corners of mouth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001250",
+      "label": "Seizures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004209",
+      "label": "Clinodactyly of the 5th finger"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:10743",
+    "symbol": "RAI1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "17",
+      "pos": 17699358,
+      "ref": "GC",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:182290",
+      "label": "SMITH-MAGENIS SYNDROME; SMS"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:20932317",
+      "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Truong-2010-RAI1-SMS335.json b/notebooks/LIRICAL/v1phenopackets/Truong-2010-RAI1-SMS335.json
new file mode 100644
index 000000000..c1e3f8711
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Truong-2010-RAI1-SMS335.json
@@ -0,0 +1,312 @@
+{
+  "id": "PMID:20932317-Truong-2010-RAI1-SMS335",
+  "subject": {
+    "id": "SMS335",
+    "ageAtCollection": {
+      "age": "P16Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0011800",
+      "label": "Midface retrusion"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000365",
+      "label": "Hearing impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000248",
+      "label": "Brachycephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001270",
+      "label": "Motor delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000403",
+      "label": "Recurrent otitis media"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100716",
+      "label": "Self-injurious behavior"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
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+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000486",
+      "label": "Strabismus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001956",
+      "label": "Truncal obesity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002650",
+      "label": "Scoliosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001290",
+      "label": "Generalized hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002360",
+      "label": "Sleep disturbance"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:20932317",
+        "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:10743",
+    "symbol": "RAI1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "17",
+      "pos": 17699358,
+      "ref": "G",
+      "alt": "GC"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:182290",
+      "label": "SMITH-MAGENIS SYNDROME; SMS"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:20932317",
+      "description": "Frameshift mutation hotspot identified in Smith-Magenis syndrome: case report and review of literature"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Twigg-2013-EFNB1-3269.json b/notebooks/LIRICAL/v1phenopackets/Twigg-2013-EFNB1-3269.json
new file mode 100644
index 000000000..145a7c36f
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Twigg-2013-EFNB1-3269.json
@@ -0,0 +1,341 @@
+{
+  "id": "PMID:23335590-Twigg-2013-EFNB1-3269",
+  "subject": {
+    "id": "3269",
+    "ageAtCollection": {
+      "age": "n/a"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000164",
+      "label": "Abnormality of the dentition"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23335590",
+        "description": "Cellular interference in craniofrontonasal syndrome: males mosaic for mutations in the X-linked EFNB1 gene are more severely affected than true hemizygotes"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001274",
+      "label": "Agenesis of corpus callosum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23335590",
+        "description": "Cellular interference in craniofrontonasal syndrome: males mosaic for mutations in the X-linked EFNB1 gene are more severely affected than true hemizygotes"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000369",
+      "label": "Low-set ears"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23335590",
+        "description": "Cellular interference in craniofrontonasal syndrome: males mosaic for mutations in the X-linked EFNB1 gene are more severely affected than true hemizygotes"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000508",
+      "label": "Ptosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23335590",
+        "description": "Cellular interference in craniofrontonasal syndrome: males mosaic for mutations in the X-linked EFNB1 gene are more severely affected than true hemizygotes"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100874",
+      "label": "Thick hair"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23335590",
+        "description": "Cellular interference in craniofrontonasal syndrome: males mosaic for mutations in the X-linked EFNB1 gene are more severely affected than true hemizygotes"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004440",
+      "label": "Coronal craniosynostosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:23335590",
+        "description": "Cellular interference in craniofrontonasal syndrome: males mosaic for mutations in the X-linked EFNB1 gene are more severely affected than true hemizygotes"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000316",
+      "label": "Hypertelorism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:23335590",
+        "description": "Cellular interference in craniofrontonasal syndrome: males mosaic for mutations in the X-linked EFNB1 gene are more severely affected than true hemizygotes"
+      }
+    }]
+  }, {
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+      "label": "2-3 finger syndactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Cellular interference in craniofrontonasal syndrome: males mosaic for mutations in the X-linked EFNB1 gene are more severely affected than true hemizygotes"
+      }
+    }]
+  }, {
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+      "label": "Ridged nail"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:23335590",
+        "description": "Cellular interference in craniofrontonasal syndrome: males mosaic for mutations in the X-linked EFNB1 gene are more severely affected than true hemizygotes"
+      }
+    }]
+  }, {
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+      "label": "Clinodactyly of the 5th finger"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "description": "Cellular interference in craniofrontonasal syndrome: males mosaic for mutations in the X-linked EFNB1 gene are more severely affected than true hemizygotes"
+      }
+    }]
+  }, {
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+      "id": "HP:0000912",
+      "label": "Sprengel anomaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:23335590",
+        "description": "Cellular interference in craniofrontonasal syndrome: males mosaic for mutations in the X-linked EFNB1 gene are more severely affected than true hemizygotes"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000494",
+      "label": "Downslanted palpebral fissures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:23335590",
+        "description": "Cellular interference in craniofrontonasal syndrome: males mosaic for mutations in the X-linked EFNB1 gene are more severely affected than true hemizygotes"
+      }
+    }]
+  }, {
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+      "id": "HP:0001363",
+      "label": "Craniosynostosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:23335590",
+        "description": "Cellular interference in craniofrontonasal syndrome: males mosaic for mutations in the X-linked EFNB1 gene are more severely affected than true hemizygotes"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Brachydactyly"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:23335590",
+        "description": "Cellular interference in craniofrontonasal syndrome: males mosaic for mutations in the X-linked EFNB1 gene are more severely affected than true hemizygotes"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000456",
+      "label": "Bifid nasal tip"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23335590",
+        "description": "Cellular interference in craniofrontonasal syndrome: males mosaic for mutations in the X-linked EFNB1 gene are more severely affected than true hemizygotes"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012741",
+      "label": "Unilateral cryptorchidism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23335590",
+        "description": "Cellular interference in craniofrontonasal syndrome: males mosaic for mutations in the X-linked EFNB1 gene are more severely affected than true hemizygotes"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001328",
+      "label": "Specific learning disability"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23335590",
+        "description": "Cellular interference in craniofrontonasal syndrome: males mosaic for mutations in the X-linked EFNB1 gene are more severely affected than true hemizygotes"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:1947",
+    "symbol": "EFNB1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "X",
+      "pos": 68059596,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000134",
+      "label": "hemizygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:304110",
+      "label": "CRANIOFRONTONASAL SYNDROME; CFNS"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:23335590",
+      "description": "Cellular interference in craniofrontonasal syndrome: males mosaic for mutations in the X-linked EFNB1 gene are more severely affected than true hemizygotes"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Unger-2008-CCNQ-Case_2.json b/notebooks/LIRICAL/v1phenopackets/Unger-2008-CCNQ-Case_2.json
new file mode 100644
index 000000000..2bc83dd10
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Unger-2008-CCNQ-Case_2.json
@@ -0,0 +1,296 @@
+{
+  "id": "PMID:18297069-Unger-2008-CCNQ-Case_2",
+  "subject": {
+    "id": "Case 2",
+    "ageAtCollection": {
+      "age": "n/a"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0004442",
+      "label": "Sagittal craniosynostosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18297069",
+        "description": "Mutations in the cyclin family member FAM58A cause an X-linked dominant disorder characterized by syndactyly, telecanthus and anogenital and renal malformations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001153",
+      "label": "Septate vagina"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18297069",
+        "description": "Mutations in the cyclin family member FAM58A cause an X-linked dominant disorder characterized by syndactyly, telecanthus and anogenital and renal malformations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000813",
+      "label": "Bicornuate uterus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18297069",
+        "description": "Mutations in the cyclin family member FAM58A cause an X-linked dominant disorder characterized by syndactyly, telecanthus and anogenital and renal malformations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000556",
+      "label": "Retinal dystrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18297069",
+        "description": "Mutations in the cyclin family member FAM58A cause an X-linked dominant disorder characterized by syndactyly, telecanthus and anogenital and renal malformations"
+      }
+    }]
+  }, {
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+      "label": "Clinodactyly of the 5th finger"
+    },
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:18297069",
+        "description": "Mutations in the cyclin family member FAM58A cause an X-linked dominant disorder characterized by syndactyly, telecanthus and anogenital and renal malformations"
+      }
+    }]
+  }, {
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+      "id": "HP:0000394",
+      "label": "Lop ear"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18297069",
+        "description": "Mutations in the cyclin family member FAM58A cause an X-linked dominant disorder characterized by syndactyly, telecanthus and anogenital and renal malformations"
+      }
+    }]
+  }, {
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+      "id": "HP:0001647",
+      "label": "Bicuspid aortic valve"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:18297069",
+        "description": "Mutations in the cyclin family member FAM58A cause an X-linked dominant disorder characterized by syndactyly, telecanthus and anogenital and renal malformations"
+      }
+    }]
+  }, {
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+      "id": "HP:0002023",
+      "label": "Anal atresia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18297069",
+        "description": "Mutations in the cyclin family member FAM58A cause an X-linked dominant disorder characterized by syndactyly, telecanthus and anogenital and renal malformations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0410049",
+      "label": "Abnormality of radial ray"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18297069",
+        "description": "Mutations in the cyclin family member FAM58A cause an X-linked dominant disorder characterized by syndactyly, telecanthus and anogenital and renal malformations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18297069",
+        "description": "Mutations in the cyclin family member FAM58A cause an X-linked dominant disorder characterized by syndactyly, telecanthus and anogenital and renal malformations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001642",
+      "label": "Pulmonic stenosis"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Mutations in the cyclin family member FAM58A cause an X-linked dominant disorder characterized by syndactyly, telecanthus and anogenital and renal malformations"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Telecanthus"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18297069",
+        "description": "Mutations in the cyclin family member FAM58A cause an X-linked dominant disorder characterized by syndactyly, telecanthus and anogenital and renal malformations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001770",
+      "label": "Toe syndactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18297069",
+        "description": "Mutations in the cyclin family member FAM58A cause an X-linked dominant disorder characterized by syndactyly, telecanthus and anogenital and renal malformations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031624",
+      "label": "Moderate myopia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18297069",
+        "description": "Mutations in the cyclin family member FAM58A cause an X-linked dominant disorder characterized by syndactyly, telecanthus and anogenital and renal malformations"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:92002",
+    "symbol": "CCNQ"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "X",
+      "pos": 152860129,
+      "ref": "T",
+      "alt": "TA"
+    },
+    "zygosity": {
+      "id": "GENO:0000134",
+      "label": "hemizygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:300707",
+      "label": "TOE SYNDACTYLY, TELECANTHUS, AND ANOGENITAL AND RENAL MALFORMATIONS;STAR"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:18297069",
+      "description": "Mutations in the cyclin family member FAM58A cause an X-linked dominant disorder characterized by syndactyly, telecanthus and anogenital and renal malformations"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Uysal-2017-KCNQ1-family_III-IV-5.json b/notebooks/LIRICAL/v1phenopackets/Uysal-2017-KCNQ1-family_III-IV-5.json
new file mode 100644
index 000000000..4e965a24d
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Uysal-2017-KCNQ1-family_III-IV-5.json
@@ -0,0 +1,147 @@
+{
+  "id": "PMID:29037160-Uysal-2017-KCNQ1-family_III-IV-5",
+  "subject": {
+    "id": "family III-IV-5",
+    "ageAtCollection": {
+      "age": "5Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002789",
+      "label": "Tachypnea"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29037160",
+        "description": "\"Homozygous, and compound heterozygous mutation in 3 Turkish family with Jervell and Lange-Nielsen syndrome: case reports\""
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000365",
+      "label": "Hearing impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29037160",
+        "description": "\"Homozygous, and compound heterozygous mutation in 3 Turkish family with Jervell and Lange-Nielsen syndrome: case reports\""
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001662",
+      "label": "Bradycardia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29037160",
+        "description": "\"Homozygous, and compound heterozygous mutation in 3 Turkish family with Jervell and Lange-Nielsen syndrome: case reports\""
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005184",
+      "label": "Prolonged QTc interval"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29037160",
+        "description": "\"Homozygous, and compound heterozygous mutation in 3 Turkish family with Jervell and Lange-Nielsen syndrome: case reports\""
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:3784",
+    "symbol": "KCNQ1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "11",
+      "pos": 2606506,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:220400",
+      "label": "JERVELL AND LANGE-NIELSEN SYNDROME 1; JLNS1"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29037160",
+      "description": "\"Homozygous, and compound heterozygous mutation in 3 Turkish family with Jervell and Lange-Nielsen syndrome: case reports\""
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Vajro-2018-TMEM199-Patient_1.json b/notebooks/LIRICAL/v1phenopackets/Vajro-2018-TMEM199-Patient_1.json
new file mode 100644
index 000000000..ea8ab4979
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Vajro-2018-TMEM199-Patient_1.json
@@ -0,0 +1,204 @@
+{
+  "id": "PMID:29321044-Vajro-2018-TMEM199-Patient_1",
+  "subject": {
+    "id": "Patient 1",
+    "ageAtCollection": {
+      "age": "P2Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0011967",
+      "label": "Decreased circulating copper concentration"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29321044",
+        "description": "Three unreported cases of TMEM199-CDG, a rare genetic liver disease with abnormal glycosylation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001397",
+      "label": "Hepatic steatosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29321044",
+        "description": "Three unreported cases of TMEM199-CDG, a rare genetic liver disease with abnormal glycosylation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003124",
+      "label": "Hypercholesterolemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29321044",
+        "description": "Three unreported cases of TMEM199-CDG, a rare genetic liver disease with abnormal glycosylation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003155",
+      "label": "Elevated alkaline phosphatase"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29321044",
+        "description": "Three unreported cases of TMEM199-CDG, a rare genetic liver disease with abnormal glycosylation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010837",
+      "label": "Decreased serum ceruloplasmin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29321044",
+        "description": "Three unreported cases of TMEM199-CDG, a rare genetic liver disease with abnormal glycosylation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003236",
+      "label": "Elevated serum creatine kinase"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29321044",
+        "description": "Three unreported cases of TMEM199-CDG, a rare genetic liver disease with abnormal glycosylation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001405",
+      "label": "Periportal fibrosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29321044",
+        "description": "Three unreported cases of TMEM199-CDG, a rare genetic liver disease with abnormal glycosylation"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:147007",
+    "symbol": "TMEM199"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "17",
+      "pos": 26684704,
+      "ref": "CTT",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "17",
+      "pos": 26684785,
+      "ref": "G",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616829",
+      "label": "Congenital disorder of glycosylation, type IIp "
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13",
+    "submittedBy": "HP:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29321044",
+      "description": "Three unreported cases of TMEM199-CDG, a rare genetic liver disease with abnormal glycosylation"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Vajro-2018-TMEM199-Patient_2.json b/notebooks/LIRICAL/v1phenopackets/Vajro-2018-TMEM199-Patient_2.json
new file mode 100644
index 000000000..74f630e24
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Vajro-2018-TMEM199-Patient_2.json
@@ -0,0 +1,204 @@
+{
+  "id": "PMID:29321044-Vajro-2018-TMEM199-Patient_2",
+  "subject": {
+    "id": "Patient 2",
+    "ageAtCollection": {
+      "age": "P2Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0011967",
+      "label": "Decreased circulating copper concentration"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29321044",
+        "description": "Three unreported cases of TMEM199-CDG, a rare genetic liver disease with abnormal glycosylation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003124",
+      "label": "Hypercholesterolemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29321044",
+        "description": "Three unreported cases of TMEM199-CDG, a rare genetic liver disease with abnormal glycosylation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001397",
+      "label": "Hepatic steatosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29321044",
+        "description": "Three unreported cases of TMEM199-CDG, a rare genetic liver disease with abnormal glycosylation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003155",
+      "label": "Elevated alkaline phosphatase"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29321044",
+        "description": "Three unreported cases of TMEM199-CDG, a rare genetic liver disease with abnormal glycosylation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010837",
+      "label": "Decreased serum ceruloplasmin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29321044",
+        "description": "Three unreported cases of TMEM199-CDG, a rare genetic liver disease with abnormal glycosylation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003236",
+      "label": "Elevated serum creatine kinase"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29321044",
+        "description": "Three unreported cases of TMEM199-CDG, a rare genetic liver disease with abnormal glycosylation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001405",
+      "label": "Periportal fibrosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29321044",
+        "description": "Three unreported cases of TMEM199-CDG, a rare genetic liver disease with abnormal glycosylation"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:147007",
+    "symbol": "TMEM199"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "17",
+      "pos": 26684704,
+      "ref": "CTT",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "17",
+      "pos": 26684785,
+      "ref": "G",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616829",
+      "label": "Congenital disorder of glycosylation, type IIp"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13",
+    "submittedBy": "HP:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29321044",
+      "description": "Three unreported cases of TMEM199-CDG, a rare genetic liver disease with abnormal glycosylation"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Vajro-2018-TMEM199-Patient_3.json b/notebooks/LIRICAL/v1phenopackets/Vajro-2018-TMEM199-Patient_3.json
new file mode 100644
index 000000000..df26eadf0
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Vajro-2018-TMEM199-Patient_3.json
@@ -0,0 +1,189 @@
+{
+  "id": "PMID:29321044-Vajro-2018-TMEM199-Patient_3",
+  "subject": {
+    "id": "Patient 3",
+    "ageAtCollection": {
+      "age": "P2Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0011967",
+      "label": "Decreased circulating copper concentration"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29321044",
+        "description": "Three unreported cases of TMEM199-CDG, a rare genetic liver disease with abnormal glycosylation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001397",
+      "label": "Hepatic steatosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29321044",
+        "description": "Three unreported cases of TMEM199-CDG, a rare genetic liver disease with abnormal glycosylation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003155",
+      "label": "Elevated alkaline phosphatase"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29321044",
+        "description": "Three unreported cases of TMEM199-CDG, a rare genetic liver disease with abnormal glycosylation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010837",
+      "label": "Decreased serum ceruloplasmin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29321044",
+        "description": "Three unreported cases of TMEM199-CDG, a rare genetic liver disease with abnormal glycosylation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001976",
+      "label": "Reduced antithrombin III activity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29321044",
+        "description": "Three unreported cases of TMEM199-CDG, a rare genetic liver disease with abnormal glycosylation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002240",
+      "label": "Hepatomegaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:29321044",
+        "description": "Three unreported cases of TMEM199-CDG, a rare genetic liver disease with abnormal glycosylation"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:147007",
+    "symbol": "TMEM199"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "17",
+      "pos": 26684704,
+      "ref": "CTT",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "17",
+      "pos": 26684785,
+      "ref": "G",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616829",
+      "label": "Congenital disorder of glycosylation, type IIp"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13",
+    "submittedBy": "HP:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29321044",
+      "description": "Three unreported cases of TMEM199-CDG, a rare genetic liver disease with abnormal glycosylation"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Van_Damme-2017-ATP6V1A-PIII_1.json b/notebooks/LIRICAL/v1phenopackets/Van_Damme-2017-ATP6V1A-PIII_1.json
new file mode 100644
index 000000000..e6f71249a
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Van_Damme-2017-ATP6V1A-PIII_1.json
@@ -0,0 +1,302 @@
+{
+  "id": "PMID:28065471-Van_Damme-2017-ATP6V1A-PIII:1",
+  "subject": {
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+    "ageAtCollection": {
+      "age": "P15Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000973",
+      "label": "Cutis laxa"
+    },
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+      }
+    }]
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+      "label": "Abnormal heart morphology"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:28065471",
+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
+  }, {
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+      "label": "Generalized hypotonia"
+    },
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+    },
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+    }]
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+      "id": "HP:0002119",
+      "label": "Ventriculomegaly"
+    },
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+      }
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+    "symbol": "ATP6V1A"
+  }],
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+    },
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+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
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+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
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+      "id": "hp",
+      "name": "human phenotype ontology",
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+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28065471",
+      "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Van_Damme-2017-ATP6V1A-PIV_1.json b/notebooks/LIRICAL/v1phenopackets/Van_Damme-2017-ATP6V1A-PIV_1.json
new file mode 100644
index 000000000..f385ef3a5
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Van_Damme-2017-ATP6V1A-PIV_1.json
@@ -0,0 +1,376 @@
+{
+  "id": "PMID:28065471-Van_Damme-2017-ATP6V1A-PIV:1",
+  "subject": {
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+    "ageAtCollection": {
+      "age": "P3M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0007552",
+      "label": "Abnormal subcutaneous fat tissue distribution"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28065471",
+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000973",
+      "label": "Cutis laxa"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:28065471",
+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001627",
+      "label": "Abnormal heart morphology"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
+  }, {
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+      "label": "Death in infancy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
+  }, {
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+      "label": "Cryptorchidism"
+    },
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+      "label": "Inguinal hernia"
+    },
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+      }
+    }]
+  }],
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+    },
+    "zygosity": {
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+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
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+      "label": "Cutis laxa, autosomal recessive, type IID"
+    }
+  }],
+  "metaData": {
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+    "submittedBy": "UNC:biocuration",
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+      "name": "Phenotype And Trait Ontology",
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+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
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+      "version": "19-03-2018",
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+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28065471",
+      "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Van_Damme-2017-ATP6V1A-PV_1.json b/notebooks/LIRICAL/v1phenopackets/Van_Damme-2017-ATP6V1A-PV_1.json
new file mode 100644
index 000000000..9d1b823b5
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Van_Damme-2017-ATP6V1A-PV_1.json
@@ -0,0 +1,256 @@
+{
+  "id": "PMID:28065471-Van_Damme-2017-ATP6V1A-PV:1",
+  "subject": {
+    "id": "PV:1",
+    "ageAtCollection": {
+      "age": "n/a"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0007552",
+      "label": "Abnormal subcutaneous fat tissue distribution"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28065471",
+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000973",
+      "label": "Cutis laxa"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28065471",
+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001627",
+      "label": "Abnormal heart morphology"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28065471",
+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
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+    }]
+  }, {
+    "type": {
+      "id": "HP:0001671",
+      "label": "Abnormal cardiac septum morphology"
+    },
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28065471",
+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
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+      "label": "Generalized hypotonia"
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+        "id": "PMID:28065471",
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+    },
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+        "id": "PMID:28065471",
+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
+  }, {
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+      "id": "HP:0000621",
+      "label": "Entropion"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28065471",
+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
+  }, {
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+      "id": "HP:0001519",
+      "label": "Disproportionate tall stature"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001385",
+      "label": "Hip dysplasia"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28065471",
+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
+  }, {
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+      "id": "HP:0001999",
+      "label": "Abnormal facial shape"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28065471",
+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002751",
+      "label": "Kyphoscoliosis"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28065471",
+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:523",
+    "symbol": "ATP6V1A"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "3",
+      "pos": 113503074,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617403",
+      "label": "Cutis laxa, autosomal recessive, type IID"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28065471",
+      "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Van_Damme-2017-ATP6V1E1-PII_1.json b/notebooks/LIRICAL/v1phenopackets/Van_Damme-2017-ATP6V1E1-PII_1.json
new file mode 100644
index 000000000..923da751a
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Van_Damme-2017-ATP6V1E1-PII_1.json
@@ -0,0 +1,286 @@
+{
+  "id": "PMID:28065471-Van_Damme-2017-ATP6V1E1-PII:1",
+  "subject": {
+    "id": "PII:1",
+    "ageAtCollection": {
+      "age": "P10Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002107",
+      "label": "Pneumothorax"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28065471",
+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000973",
+      "label": "Cutis laxa"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28065471",
+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001627",
+      "label": "Abnormal heart morphology"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28065471",
+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
+  }, {
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+      "id": "HP:0001290",
+      "label": "Generalized hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28065471",
+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
+  }, {
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+      "label": "Abnormality of the genitourinary system"
+    },
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+    "evidence": [{
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+  }, {
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+      "label": "Abnormal facial shape"
+    },
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+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:28065471",
+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001519",
+      "label": "Disproportionate tall stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28065471",
+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001371",
+      "label": "Flexion contracture"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28065471",
+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001385",
+      "label": "Hip dysplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+      "label": "Aortic aneurysm"
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+        "id": "PMID:28065471",
+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
+  }, {
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+      "id": "HP:0000621",
+      "label": "Entropion"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28065471",
+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
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+      "label": "Dilatation"
+    },
+    "negated": true,
+    "evidence": [{
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+      }
+    }]
+  }, {
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+      "id": "HP:0002751",
+      "label": "Kyphoscoliosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28065471",
+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:529",
+    "symbol": "ATP6V1E1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "22",
+      "pos": 18075487,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617402",
+      "label": "Cutis laxa, autosomal recessive, type IIC"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28065471",
+      "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Van_Damme-2017-ATP6V1E1-PI_1.json b/notebooks/LIRICAL/v1phenopackets/Van_Damme-2017-ATP6V1E1-PI_1.json
new file mode 100644
index 000000000..287f64101
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Van_Damme-2017-ATP6V1E1-PI_1.json
@@ -0,0 +1,286 @@
+{
+  "id": "PMID:28065471-Van_Damme-2017-ATP6V1E1-PI:1",
+  "subject": {
+    "id": "PI:1",
+    "ageAtCollection": {
+      "age": "P5M"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001627",
+      "label": "Abnormal heart morphology"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28065471",
+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001290",
+      "label": "Generalized hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28065471",
+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001522",
+      "label": "Death in infancy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28065471",
+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001371",
+      "label": "Flexion contracture"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28065471",
+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000119",
+      "label": "Abnormality of the genitourinary system"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28065471",
+        "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
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+    }]
+  }, {
+    "type": {
+      "id": "HP:0001999",
+      "label": "Abnormal facial shape"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+    }
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+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "namespacePrefix": "PATO",
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+    }, {
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+      "namespacePrefix": "GENO",
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+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
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+      "namespacePrefix": "OMIM"
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+      "id": "PMID:28065471",
+      "description": "Mutations in ATP6V1E1 or ATP6V1A Cause Autosomal-Recessive Cutis Laxa"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Van_De_Weghe-2017-ARMC9-UW132-3.json b/notebooks/LIRICAL/v1phenopackets/Van_De_Weghe-2017-ARMC9-UW132-3.json
new file mode 100644
index 000000000..9e3d5c6da
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Van_De_Weghe-2017-ARMC9-UW132-3.json
@@ -0,0 +1,174 @@
+{
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+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Van_Zwieten-2013-SLC4A1-c.1432-2A_T.json b/notebooks/LIRICAL/v1phenopackets/Van_Zwieten-2013-SLC4A1-c.1432-2A_T.json
new file mode 100644
index 000000000..3b0d9e5aa
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Van_Zwieten-2013-SLC4A1-c.1432-2A_T.json
@@ -0,0 +1,130 @@
+{
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+      "label": "Hemolytic anemia"
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+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
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+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Vogiatzi-2018-COL11A1-proband.json b/notebooks/LIRICAL/v1phenopackets/Vogiatzi-2018-COL11A1-proband.json
new file mode 100644
index 000000000..8d8c69dab
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Vogiatzi-2018-COL11A1-proband.json
@@ -0,0 +1,222 @@
+{
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+      "label": "Homo sapiens"
+    }
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+      "id": "HP:0030840",
+      "label": "Ankle pain"
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+      }
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+      "label": "Muscular hypotonia"
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+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:604841",
+      "label": "STICKLER SYNDROME, TYPE II; STL2"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28971234",
+      "description": "A novel dominant COL11A1 mutation in a child with Stickler syndrome type II is associated with recurrent fractures"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Volpi-2017-EXTL3-Patient_1.json b/notebooks/LIRICAL/v1phenopackets/Volpi-2017-EXTL3-Patient_1.json
new file mode 100644
index 000000000..f1bd9caef
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Volpi-2017-EXTL3-Patient_1.json
@@ -0,0 +1,237 @@
+{
+  "id": "PMID:28148688-Volpi-2017-EXTL3-Patient_1",
+  "subject": {
+    "id": "Patient 1",
+    "ageAtCollection": {
+      "age": "P11M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0100806",
+      "label": "Sepsis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0025116",
+      "label": "Fetal distress"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001347",
+      "label": "Hyperreflexia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001019",
+      "label": "Erythroderma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031430",
+      "label": "Oligoclonal T cell expansion"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002197",
+      "label": "Generalized-onset seizure"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008873",
+      "label": "Disproportionate short-limb short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002179",
+      "label": "Opisthotonus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2137",
+    "symbol": "EXTL3"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "8",
+      "pos": 28574591,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617425",
+      "label": "Immunoskeletal dysplasia with neurodevelopmental abnormalities"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28148688",
+      "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Volpi-2017-EXTL3-Patient_2.json b/notebooks/LIRICAL/v1phenopackets/Volpi-2017-EXTL3-Patient_2.json
new file mode 100644
index 000000000..de63bd0a2
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Volpi-2017-EXTL3-Patient_2.json
@@ -0,0 +1,207 @@
+{
+  "id": "PMID:28148688-Volpi-2017-EXTL3-Patient_2",
+  "subject": {
+    "id": "Patient 2",
+    "ageAtCollection": {
+      "age": "P7M"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0007281",
+      "label": "Developmental stagnation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002169",
+      "label": "Clonus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002676",
+      "label": "Cloverleaf skull"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000639",
+      "label": "Nystagmus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0025116",
+      "label": "Fetal distress"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002266",
+      "label": "Focal clonic seizures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004430",
+      "label": "Severe combined immunodeficiency"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002023",
+      "label": "Anal atresia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2137",
+    "symbol": "EXTL3"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "8",
+      "pos": 28574591,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617425",
+      "label": "Immunoskeletal dysplasia with neurodevelopmental abnormalities"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28148688",
+      "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Volpi-2017-EXTL3-Patient_3.json b/notebooks/LIRICAL/v1phenopackets/Volpi-2017-EXTL3-Patient_3.json
new file mode 100644
index 000000000..fdbd27e09
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Volpi-2017-EXTL3-Patient_3.json
@@ -0,0 +1,507 @@
+{
+  "id": "PMID:28148688-Volpi-2017-EXTL3-Patient_3",
+  "subject": {
+    "id": "Patient 3",
+    "ageAtCollection": {
+      "age": "P2Y5M"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001880",
+      "label": "Eosinophilia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001508",
+      "label": "Failure to thrive"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008947",
+      "label": "Infantile muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008445",
+      "label": "Cervical spinal canal stenosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001385",
+      "label": "Hip dysplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006610",
+      "label": "Wide intermamillary distance"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002652",
+      "label": "Skeletal dysplasia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000767",
+      "label": "Pectus excavatum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002155",
+      "label": "Hypertriglyceridemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000577",
+      "label": "Exotropia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030043",
+      "label": "Hip subluxation"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000377",
+      "label": "Abnormality of the pinna"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030320",
+      "label": "Increased intervertebral space"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003416",
+      "label": "Spinal canal stenosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004430",
+      "label": "Severe combined immunodeficiency"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010605",
+      "label": "Chalazion"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005352",
+      "label": "Severe T-cell immunodeficiency"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002812",
+      "label": "Coxa vara"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009826",
+      "label": "Limb undergrowth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002943",
+      "label": "Thoracic scoliosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000331",
+      "label": "Short chin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000582",
+      "label": "Upslanted palpebral fissure"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004565",
+      "label": "Severe platyspondyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001363",
+      "label": "Craniosynostosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000498",
+      "label": "Blepharitis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004566",
+      "label": "Pear-shaped vertebrae"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002938",
+      "label": "Lumbar hyperlordosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28148688",
+        "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2137",
+    "symbol": "EXTL3"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "8",
+      "pos": 28574958,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617425",
+      "label": "Immunoskeletal dysplasia with neurodevelopmental abnormalities"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28148688",
+      "description": "EXTL3 mutations cause skeletal dysplasia, immune deficiency, and developmental delay"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Vrtel-1996-TSC2-III-1.json b/notebooks/LIRICAL/v1phenopackets/Vrtel-1996-TSC2-III-1.json
new file mode 100644
index 000000000..cfc585903
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Vrtel-1996-TSC2-III-1.json
@@ -0,0 +1,146 @@
+{
+  "id": "PMID:8825048-Vrtel-1996-TSC2-III-1",
+  "subject": {
+    "id": "III-1",
+    "ageAtCollection": {
+      "age": "3M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0009719",
+      "label": "Hypomelanotic macule"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:8825048",
+        "description": "Identification of a nonsense mutation at the 5\u0027 end of the TSC2 gene in a family with a presumptive diagnosis of tuberous sclerosis complex"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009730",
+      "label": "Rhabdomyoma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:8825048",
+        "description": "Identification of a nonsense mutation at the 5\u0027 end of the TSC2 gene in a family with a presumptive diagnosis of tuberous sclerosis complex"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009722",
+      "label": "Dental enamel pits"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:8825048",
+        "description": "Identification of a nonsense mutation at the 5\u0027 end of the TSC2 gene in a family with a presumptive diagnosis of tuberous sclerosis complex"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000169",
+      "label": "Gingival fibromatosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:8825048",
+        "description": "Identification of a nonsense mutation at the 5\u0027 end of the TSC2 gene in a family with a presumptive diagnosis of tuberous sclerosis complex"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:7249",
+    "symbol": "TSC2"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "16",
+      "pos": 2098650,
+      "ref": "A",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:613254",
+      "label": "TUBEROUS SCLEROSIS 2; TSC2TSC2 ANGIOMYOLIPOMAS, RENAL, MODIFIER OF, INCLUDED"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:8825048",
+      "description": "Identification of a nonsense mutation at the 5\u0027 end of the TSC2 gene in a family with a presumptive diagnosis of tuberous sclerosis complex"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Wakil-2018-RETREG1-F2_IV_1.json b/notebooks/LIRICAL/v1phenopackets/Wakil-2018-RETREG1-F2_IV_1.json
new file mode 100644
index 000000000..825b646b1
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Wakil-2018-RETREG1-F2_IV_1.json
@@ -0,0 +1,209 @@
+{
+  "id": "PMID:30643655-Wakil-2018-RETREG1-F2:IV:1",
+  "subject": {
+    "id": "F2:IV:1",
+    "ageAtCollection": {
+      "age": "P15Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001257",
+      "label": "Spasticity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30643655",
+        "description": "Exome Sequencing: Mutilating Sensory Neuropathy with Spastic Paraplegia due to a Mutation in FAM134B Gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002359",
+      "label": "Frequent falls"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30643655",
+        "description": "Exome Sequencing: Mutilating Sensory Neuropathy with Spastic Paraplegia due to a Mutation in FAM134B Gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0200042",
+      "label": "Skin ulcer"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30643655",
+        "description": "Exome Sequencing: Mutilating Sensory Neuropathy with Spastic Paraplegia due to a Mutation in FAM134B Gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006801",
+      "label": "Hyperactive deep tendon reflexes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30643655",
+        "description": "Exome Sequencing: Mutilating Sensory Neuropathy with Spastic Paraplegia due to a Mutation in FAM134B Gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002754",
+      "label": "Osteomyelitis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30643655",
+        "description": "Exome Sequencing: Mutilating Sensory Neuropathy with Spastic Paraplegia due to a Mutation in FAM134B Gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002011",
+      "label": "Morphological abnormality of the central nervous system"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30643655",
+        "description": "Exome Sequencing: Mutilating Sensory Neuropathy with Spastic Paraplegia due to a Mutation in FAM134B Gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007021",
+      "label": "Pain insensitivity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30643655",
+        "description": "Exome Sequencing: Mutilating Sensory Neuropathy with Spastic Paraplegia due to a Mutation in FAM134B Gene"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003487",
+      "label": "Babinski sign"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30643655",
+        "description": "Exome Sequencing: Mutilating Sensory Neuropathy with Spastic Paraplegia due to a Mutation in FAM134B Gene"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:54463",
+    "symbol": "RETREG1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "5",
+      "pos": 16477845,
+      "ref": "G",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:613115",
+      "label": "NEUROPATHY, HEREDITARY SENSORY AND AUTONOMIC, TYPE IIB; HSAN2B"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30643655",
+      "description": "Exome Sequencing: Mutilating Sensory Neuropathy with Spastic Paraplegia due to a Mutation in FAM134B Gene"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Wang-2016-CAPN1-R-III_1.json b/notebooks/LIRICAL/v1phenopackets/Wang-2016-CAPN1-R-III_1.json
new file mode 100644
index 000000000..ed82122cf
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Wang-2016-CAPN1-R-III_1.json
@@ -0,0 +1,162 @@
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+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Wang-2016-CAPN1-SAL-399-073.json b/notebooks/LIRICAL/v1phenopackets/Wang-2016-CAPN1-SAL-399-073.json
new file mode 100644
index 000000000..9d0cbbf8f
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Wang-2016-CAPN1-SAL-399-073.json
@@ -0,0 +1,204 @@
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+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Wang-2016-CAPN1-SAL-584-005.json b/notebooks/LIRICAL/v1phenopackets/Wang-2016-CAPN1-SAL-584-005.json
new file mode 100644
index 000000000..767f468a0
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Wang-2016-CAPN1-SAL-584-005.json
@@ -0,0 +1,147 @@
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\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Wang-2016-CAPN1-Tun66275.json b/notebooks/LIRICAL/v1phenopackets/Wang-2016-CAPN1-Tun66275.json
new file mode 100644
index 000000000..f9d2d05f1
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Wang-2016-CAPN1-Tun66275.json
@@ -0,0 +1,132 @@
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+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27320912",
+      "description": "Defects in the CAPN1 Gene Result in Alterations in Cerebellar Development and Cerebellar Ataxia in Mice and Humans"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Wang-2017-OCA2-B.json b/notebooks/LIRICAL/v1phenopackets/Wang-2017-OCA2-B.json
new file mode 100644
index 000000000..36b0e750e
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Wang-2017-OCA2-B.json
@@ -0,0 +1,159 @@
+{
+  "id": "PMID:29050284-Wang-2017-OCA2-B",
+  "subject": {
+    "id": "B",
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+      "age": "P8Y"
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+    "sex": "FEMALE",
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+      "label": "Homo sapiens"
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+      "label": "Hypopigmentation of hair"
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+      "label": "Nystagmus"
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+      "version": "2018-03-28",
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+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
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+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
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+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
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+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:29050284",
+      "description": "Mutational analysis of a Chinese family with oculocutaneous albinism type 2"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Wang-2018-CRX-IV_5.json b/notebooks/LIRICAL/v1phenopackets/Wang-2018-CRX-IV_5.json
new file mode 100644
index 000000000..67e8bfc84
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Wang-2018-CRX-IV_5.json
@@ -0,0 +1,146 @@
+{
+  "id": "PMID:30095615-Wang-2018-CRX-IV:5",
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+      "label": "Homo sapiens"
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+      "label": "Nyctalopia"
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+        "id": "PMID:30095615",
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+      }
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+      "label": "Visual impairment"
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+        "label": "author statement supported by traceable reference"
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+        "description": "A novel CRX frameshift mutation causing cone-rod dystrophy in a Chinese family: A case report"
+      }
+    }]
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+      "label": "Visual field defect"
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+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
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+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
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+      "version": "19-03-2018",
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+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Wang-2018-SLC6A8-proband.json b/notebooks/LIRICAL/v1phenopackets/Wang-2018-SLC6A8-proband.json
new file mode 100644
index 000000000..1a2888464
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Wang-2018-SLC6A8-proband.json
@@ -0,0 +1,192 @@
+{
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+    },
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+      "label": "Homo sapiens"
+    }
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+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Warnecke-2007-SPG7-II-3.json b/notebooks/LIRICAL/v1phenopackets/Warnecke-2007-SPG7-II-3.json
new file mode 100644
index 000000000..2abea3bf6
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Warnecke-2007-SPG7-II-3.json
@@ -0,0 +1,285 @@
+{
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+    },
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+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002353",
+      "label": "EEG abnormality"
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+    "negated": true,
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:17646629",
+        "description": "A novel form of autosomal recessive hereditary spastic paraplegia caused by a new SPG7 mutation"
+      }
+    }]
+  }, {
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+      "id": "HP:0001260",
+      "label": "Dysarthria"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "description": "A novel form of autosomal recessive hereditary spastic paraplegia caused by a new SPG7 mutation"
+      }
+    }]
+  }, {
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+      "label": "Cognitive impairment"
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+    "negated": true,
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+      "reference": {
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+        "description": "A novel form of autosomal recessive hereditary spastic paraplegia caused by a new SPG7 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012896",
+      "label": "Abnormal motor evoked potentials"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:17646629",
+        "description": "A novel form of autosomal recessive hereditary spastic paraplegia caused by a new SPG7 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000639",
+      "label": "Nystagmus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:17646629",
+        "description": "A novel form of autosomal recessive hereditary spastic paraplegia caused by a new SPG7 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002061",
+      "label": "Lower limb spasticity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:17646629",
+        "description": "A novel form of autosomal recessive hereditary spastic paraplegia caused by a new SPG7 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007377",
+      "label": "Abnormality of somatosensory evoked potentials"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:17646629",
+        "description": "A novel form of autosomal recessive hereditary spastic paraplegia caused by a new SPG7 mutation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002355",
+      "label": "Difficulty walking"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:17646629",
+        "description": "A novel form of autosomal recessive hereditary spastic paraplegia caused by a new SPG7 mutation"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:6687",
+    "symbol": "SPG7"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "16",
+      "pos": 89620340,
+      "ref": "G",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:607259",
+      "label": "SPASTIC PARAPLEGIA 7, AUTOSOMAL RECESSIVE; SPG7"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:17646629",
+      "description": "A novel form of autosomal recessive hereditary spastic paraplegia caused by a new SPG7 mutation"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Watanabe-2016-COL5A2-patient.json b/notebooks/LIRICAL/v1phenopackets/Watanabe-2016-COL5A2-patient.json
new file mode 100644
index 000000000..f22691570
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Watanabe-2016-COL5A2-patient.json
@@ -0,0 +1,208 @@
+{
+  "id": "PMID:27656288-Watanabe-2016-COL5A2-patient",
+  "subject": {
+    "id": "patient",
+    "ageAtCollection": {
+      "age": "P9Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000977",
+      "label": "Soft skin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27656288",
+        "description": "A novel missense mutation of COL5A2 in a patient with Ehlers-Danlos syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000974",
+      "label": "Hyperextensible skin"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27656288",
+        "description": "A novel missense mutation of COL5A2 in a patient with Ehlers-Danlos syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001382",
+      "label": "Joint hypermobility"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27656288",
+        "description": "A novel missense mutation of COL5A2 in a patient with Ehlers-Danlos syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0031158",
+      "label": "Widened atrophic scar"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27656288",
+        "description": "A novel missense mutation of COL5A2 in a patient with Ehlers-Danlos syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001324",
+      "label": "Muscle weakness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27656288",
+        "description": "A novel missense mutation of COL5A2 in a patient with Ehlers-Danlos syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002751",
+      "label": "Kyphoscoliosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27656288",
+        "description": "A novel missense mutation of COL5A2 in a patient with Ehlers-Danlos syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002194",
+      "label": "Delayed gross motor development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27656288",
+        "description": "A novel missense mutation of COL5A2 in a patient with Ehlers-Danlos syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001290",
+      "label": "Generalized hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27656288",
+        "description": "A novel missense mutation of COL5A2 in a patient with Ehlers-Danlos syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:1290",
+    "symbol": "COL5A2"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "2",
+      "pos": 189951460,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:130010",
+      "label": "Ehlers-Danlos syndrome, classic type, 2"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27656288",
+      "description": "A novel missense mutation of COL5A2 in a patient with Ehlers-Danlos syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Whittock-2004-DLL3-II.6.json b/notebooks/LIRICAL/v1phenopackets/Whittock-2004-DLL3-II.6.json
new file mode 100644
index 000000000..bdcddc683
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Whittock-2004-DLL3-II.6.json
@@ -0,0 +1,189 @@
+{
+  "id": "PMID:15200511-Whittock-2004-DLL3-II.6",
+  "subject": {
+    "id": "II.6",
+    "ageAtCollection": {
+      "age": "40Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0003521",
+      "label": "Disproportionate short-trunk short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:15200511",
+        "description": "Pseudodominant inheritance of spondylocostal dysostosis type 1 caused by two familial delta-like 3 mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000470",
+      "label": "Short neck"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:15200511",
+        "description": "Pseudodominant inheritance of spondylocostal dysostosis type 1 caused by two familial delta-like 3 mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:15200511",
+        "description": "Pseudodominant inheritance of spondylocostal dysostosis type 1 caused by two familial delta-like 3 mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003422",
+      "label": "Vertebral segmentation defect"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:15200511",
+        "description": "Pseudodominant inheritance of spondylocostal dysostosis type 1 caused by two familial delta-like 3 mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003418",
+      "label": "Back pain"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:15200511",
+        "description": "Pseudodominant inheritance of spondylocostal dysostosis type 1 caused by two familial delta-like 3 mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002751",
+      "label": "Kyphoscoliosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:15200511",
+        "description": "Pseudodominant inheritance of spondylocostal dysostosis type 1 caused by two familial delta-like 3 mutations"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:10683",
+    "symbol": "DLL3"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "19",
+      "pos": 39998096,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "19",
+      "pos": 39998024,
+      "ref": "CG",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:277300",
+      "label": "SPONDYLOCOSTAL DYSOSTOSIS 1, AUTOSOMAL RECESSIVE; SCDO1"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:15200511",
+      "description": "Pseudodominant inheritance of spondylocostal dysostosis type 1 caused by two familial delta-like 3 mutations"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Wiltshire-2013-LMNA-II3.json b/notebooks/LIRICAL/v1phenopackets/Wiltshire-2013-LMNA-II3.json
new file mode 100644
index 000000000..481736a1d
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Wiltshire-2013-LMNA-II3.json
@@ -0,0 +1,267 @@
+{
+  "id": "PMID:23313286-Wiltshire-2013-LMNA-II3",
+  "subject": {
+    "id": "II3",
+    "ageAtCollection": {
+      "age": "P30Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0007495",
+      "label": "Prematurely aged appearance"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23313286",
+        "description": "Homozygous lamin A/C familial lipodystrophy R482Q mutation in autosomal recessive Emery Dreifuss muscular dystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000822",
+      "label": "Hypertension"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23313286",
+        "description": "Homozygous lamin A/C familial lipodystrophy R482Q mutation in autosomal recessive Emery Dreifuss muscular dystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007485",
+      "label": "Absence of subcutaneous fat"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23313286",
+        "description": "Homozygous lamin A/C familial lipodystrophy R482Q mutation in autosomal recessive Emery Dreifuss muscular dystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009046",
+      "label": "Difficulty running"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23313286",
+        "description": "Homozygous lamin A/C familial lipodystrophy R482Q mutation in autosomal recessive Emery Dreifuss muscular dystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000347",
+      "label": "Micrognathia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23313286",
+        "description": "Homozygous lamin A/C familial lipodystrophy R482Q mutation in autosomal recessive Emery Dreifuss muscular dystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003077",
+      "label": "Hyperlipidemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23313286",
+        "description": "Homozygous lamin A/C familial lipodystrophy R482Q mutation in autosomal recessive Emery Dreifuss muscular dystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002938",
+      "label": "Lumbar hyperlordosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23313286",
+        "description": "Homozygous lamin A/C familial lipodystrophy R482Q mutation in autosomal recessive Emery Dreifuss muscular dystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001284",
+      "label": "Areflexia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23313286",
+        "description": "Homozygous lamin A/C familial lipodystrophy R482Q mutation in autosomal recessive Emery Dreifuss muscular dystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000508",
+      "label": "Ptosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23313286",
+        "description": "Homozygous lamin A/C familial lipodystrophy R482Q mutation in autosomal recessive Emery Dreifuss muscular dystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008994",
+      "label": "Proximal muscle weakness in lower limbs"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:23313286",
+        "description": "Homozygous lamin A/C familial lipodystrophy R482Q mutation in autosomal recessive Emery Dreifuss muscular dystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002987",
+      "label": "Elbow flexion contracture"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23313286",
+        "description": "Homozygous lamin A/C familial lipodystrophy R482Q mutation in autosomal recessive Emery Dreifuss muscular dystrophy"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008112",
+      "label": "Plantar flexion contractures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23313286",
+        "description": "Homozygous lamin A/C familial lipodystrophy R482Q mutation in autosomal recessive Emery Dreifuss muscular dystrophy"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:4000",
+    "symbol": "LMNA"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "1",
+      "pos": 156106776,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616516",
+      "label": "EMERY-DREIFUSS MUSCULAR DYSTROPHY 3, AUTOSOMAL RECESSIVE; EDMD3"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:23313286",
+      "description": "Homozygous lamin A/C familial lipodystrophy R482Q mutation in autosomal recessive Emery Dreifuss muscular dystrophy"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Windpassinger-2017-CDK10-F1-II_1.json b/notebooks/LIRICAL/v1phenopackets/Windpassinger-2017-CDK10-F1-II_1.json
new file mode 100644
index 000000000..f6d6a046a
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Windpassinger-2017-CDK10-F1-II_1.json
@@ -0,0 +1,387 @@
+{
+  "id": "PMID:28886341-Windpassinger-2017-CDK10-F1-II:1",
+  "subject": {
+    "id": "F1-II:1",
+    "ageAtCollection": {
+      "age": "P9Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000369",
+      "label": "Low-set ears"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28886341",
+        "description": "CDK10 Mutations in Humans and Mice Cause Severe Growth Retardation, Spine Malformations, and Developmental Delays"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000939",
+      "label": "Osteoporosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28886341",
+        "description": "CDK10 Mutations in Humans and Mice Cause Severe Growth Retardation, Spine Malformations, and Developmental Delays"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000343",
+      "label": "Long philtrum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28886341",
+        "description": "CDK10 Mutations in Humans and Mice Cause Severe Growth Retardation, Spine Malformations, and Developmental Delays"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000473",
+      "label": "Torticollis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28886341",
+        "description": "CDK10 Mutations in Humans and Mice Cause Severe Growth Retardation, Spine Malformations, and Developmental Delays"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0200055",
+      "label": "Small hand"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:28886341",
+        "description": "CDK10 Mutations in Humans and Mice Cause Severe Growth Retardation, Spine Malformations, and Developmental Delays"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000325",
+      "label": "Triangular face"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28886341",
+        "description": "CDK10 Mutations in Humans and Mice Cause Severe Growth Retardation, Spine Malformations, and Developmental Delays"
+      }
+    }]
+  }, {
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+      "id": "HP:0000494",
+      "label": "Downslanted palpebral fissures"
+    },
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+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:28886341",
+        "description": "CDK10 Mutations in Humans and Mice Cause Severe Growth Retardation, Spine Malformations, and Developmental Delays"
+      }
+    }]
+  }, {
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+      "label": "Kyphosis"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28886341",
+        "description": "CDK10 Mutations in Humans and Mice Cause Severe Growth Retardation, Spine Malformations, and Developmental Delays"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001371",
+      "label": "Flexion contracture"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28886341",
+        "description": "CDK10 Mutations in Humans and Mice Cause Severe Growth Retardation, Spine Malformations, and Developmental Delays"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000286",
+      "label": "Epicanthus"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28886341",
+        "description": "CDK10 Mutations in Humans and Mice Cause Severe Growth Retardation, Spine Malformations, and Developmental Delays"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000331",
+      "label": "Short chin"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "description": "CDK10 Mutations in Humans and Mice Cause Severe Growth Retardation, Spine Malformations, and Developmental Delays"
+      }
+    }]
+  }, {
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+      "id": "HP:0001572",
+      "label": "Macrodontia"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "CDK10 Mutations in Humans and Mice Cause Severe Growth Retardation, Spine Malformations, and Developmental Delays"
+      }
+    }]
+  }, {
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+      "id": "HP:0011344",
+      "label": "Severe global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
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+        "description": "CDK10 Mutations in Humans and Mice Cause Severe Growth Retardation, Spine Malformations, and Developmental Delays"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000358",
+      "label": "Posteriorly rotated ears"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28886341",
+        "description": "CDK10 Mutations in Humans and Mice Cause Severe Growth Retardation, Spine Malformations, and Developmental Delays"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005280",
+      "label": "Depressed nasal bridge"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28886341",
+        "description": "CDK10 Mutations in Humans and Mice Cause Severe Growth Retardation, Spine Malformations, and Developmental Delays"
+      }
+    }]
+  }, {
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+      "id": "HP:0000455",
+      "label": "Broad nasal tip"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "CDK10 Mutations in Humans and Mice Cause Severe Growth Retardation, Spine Malformations, and Developmental Delays"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Language impairment"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "CDK10 Mutations in Humans and Mice Cause Severe Growth Retardation, Spine Malformations, and Developmental Delays"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000506",
+      "label": "Telecanthus"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28886341",
+        "description": "CDK10 Mutations in Humans and Mice Cause Severe Growth Retardation, Spine Malformations, and Developmental Delays"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100543",
+      "label": "Cognitive impairment"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:28886341",
+        "description": "CDK10 Mutations in Humans and Mice Cause Severe Growth Retardation, Spine Malformations, and Developmental Delays"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006191",
+      "label": "Deep palmar crease"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28886341",
+        "description": "CDK10 Mutations in Humans and Mice Cause Severe Growth Retardation, Spine Malformations, and Developmental Delays"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:8558",
+    "symbol": "CDK10"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "16",
+      "pos": 89760580,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:617694",
+      "label": "Al Kaissi syndrome"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28886341",
+      "description": "CDK10 Mutations in Humans and Mice Cause Severe Growth Retardation, Spine Malformations, and Developmental Delays"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Wollnik-2003-PAX3-proposita.json b/notebooks/LIRICAL/v1phenopackets/Wollnik-2003-PAX3-proposita.json
new file mode 100644
index 000000000..9ce389346
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Wollnik-2003-PAX3-proposita.json
@@ -0,0 +1,207 @@
+{
+  "id": "PMID:12949970-Wollnik-2003-PAX3-proposita",
+  "subject": {
+    "id": "proposita",
+    "ageAtCollection": {
+      "age": "P1Y1M"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0012453",
+      "label": "Bilateral wrist flexion contracture"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:12949970",
+        "description": "Homozygous and heterozygous inheritance of PAX3 mutations causes different types of Waardenburg syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000635",
+      "label": "Blue irides"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:12949970",
+        "description": "Homozygous and heterozygous inheritance of PAX3 mutations causes different types of Waardenburg syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000537",
+      "label": "Epicanthus inversus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:12949970",
+        "description": "Homozygous and heterozygous inheritance of PAX3 mutations causes different types of Waardenburg syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010862",
+      "label": "Delayed fine motor development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:12949970",
+        "description": "Homozygous and heterozygous inheritance of PAX3 mutations causes different types of Waardenburg syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012785",
+      "label": "Flexion contracture of finger"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:12949970",
+        "description": "Homozygous and heterozygous inheritance of PAX3 mutations causes different types of Waardenburg syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002226",
+      "label": "White eyebrow"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:12949970",
+        "description": "Homozygous and heterozygous inheritance of PAX3 mutations causes different types of Waardenburg syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012745",
+      "label": "Short palpebral fissure"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:12949970",
+        "description": "Homozygous and heterozygous inheritance of PAX3 mutations causes different types of Waardenburg syndrome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002227",
+      "label": "White eyelashes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:12949970",
+        "description": "Homozygous and heterozygous inheritance of PAX3 mutations causes different types of Waardenburg syndrome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:5077",
+    "symbol": "PAX3"
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+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "2",
+      "pos": 223161750,
+      "ref": "A",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:148820",
+      "label": "WAARDENBURG SYNDROME, TYPE 3; WS3"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:12949970",
+      "description": "Homozygous and heterozygous inheritance of PAX3 mutations causes different types of Waardenburg syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Woo-2013-ASS1-5.json b/notebooks/LIRICAL/v1phenopackets/Woo-2013-ASS1-5.json
new file mode 100644
index 000000000..59cb603a3
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Woo-2013-ASS1-5.json
@@ -0,0 +1,207 @@
+{
+  "id": "PMID:23099195-Woo-2013-ASS1-5",
+  "subject": {
+    "id": "5",
+    "ageAtCollection": {
+      "age": "P3M"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001250",
+      "label": "Seizures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23099195",
+        "description": "Mutation spectrum of the ASS1 gene in Korean patients with citrullinemia type I"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005961",
+      "label": "Hypoargininemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23099195",
+        "description": "Mutation spectrum of the ASS1 gene in Korean patients with citrullinemia type I"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003218",
+      "label": "Oroticaciduria"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23099195",
+        "description": "Mutation spectrum of the ASS1 gene in Korean patients with citrullinemia type I"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002181",
+      "label": "Cerebral edema"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23099195",
+        "description": "Mutation spectrum of the ASS1 gene in Korean patients with citrullinemia type I"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008358",
+      "label": "Hyperprolinemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23099195",
+        "description": "Mutation spectrum of the ASS1 gene in Korean patients with citrullinemia type I"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011966",
+      "label": "Elevated plasma citrulline"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23099195",
+        "description": "Mutation spectrum of the ASS1 gene in Korean patients with citrullinemia type I"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0032397",
+      "label": "Citrullinuria"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23099195",
+        "description": "Mutation spectrum of the ASS1 gene in Korean patients with citrullinemia type I"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001987",
+      "label": "Hyperammonemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23099195",
+        "description": "Mutation spectrum of the ASS1 gene in Korean patients with citrullinemia type I"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:445",
+    "symbol": "ASS1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "9",
+      "pos": 133342110,
+      "ref": "A",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:215700",
+      "label": "CITRULLINEMIA, CLASSIC"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:23099195",
+      "description": "Mutation spectrum of the ASS1 gene in Korean patients with citrullinemia type I"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Xie-2013-COMP-patient.json b/notebooks/LIRICAL/v1phenopackets/Xie-2013-COMP-patient.json
new file mode 100644
index 000000000..107796a8c
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Xie-2013-COMP-patient.json
@@ -0,0 +1,343 @@
+{
+  "id": "PMID:23562786-Xie-2013-COMP-patient",
+  "subject": {
+    "id": "patient",
+    "ageAtCollection": {
+      "age": "2Y9M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0003026",
+      "label": "Short long bone"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23562786",
+        "description": "A novel COMP mutation in a Chinese patient with pseudoachondroplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010582",
+      "label": "Irregular epiphyses"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23562786",
+        "description": "A novel COMP mutation in a Chinese patient with pseudoachondroplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002970",
+      "label": "Genu varum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23562786",
+        "description": "A novel COMP mutation in a Chinese patient with pseudoachondroplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23562786",
+        "description": "A novel COMP mutation in a Chinese patient with pseudoachondroplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002834",
+      "label": "Flared femoral metaphysis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23562786",
+        "description": "A novel COMP mutation in a Chinese patient with pseudoachondroplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012514",
+      "label": "Lower limb pain"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23562786",
+        "description": "A novel COMP mutation in a Chinese patient with pseudoachondroplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003180",
+      "label": "Flat acetabular roof"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23562786",
+        "description": "A novel COMP mutation in a Chinese patient with pseudoachondroplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003025",
+      "label": "Metaphyseal irregularity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23562786",
+        "description": "A novel COMP mutation in a Chinese patient with pseudoachondroplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008155",
+      "label": "Mucopolysacchariduria"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23562786",
+        "description": "A novel COMP mutation in a Chinese patient with pseudoachondroplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001999",
+      "label": "Abnormal facial shape"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23562786",
+        "description": "A novel COMP mutation in a Chinese patient with pseudoachondroplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001216",
+      "label": "Delayed ossification of carpal bones"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23562786",
+        "description": "A novel COMP mutation in a Chinese patient with pseudoachondroplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008833",
+      "label": "Irregular acetabular roof"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23562786",
+        "description": "A novel COMP mutation in a Chinese patient with pseudoachondroplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004568",
+      "label": "Beaking of vertebral bodies"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23562786",
+        "description": "A novel COMP mutation in a Chinese patient with pseudoachondroplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008873",
+      "label": "Disproportionate short-limb short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23562786",
+        "description": "A novel COMP mutation in a Chinese patient with pseudoachondroplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003090",
+      "label": "Hypoplasia of the capital femoral epiphysis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23562786",
+        "description": "A novel COMP mutation in a Chinese patient with pseudoachondroplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002515",
+      "label": "Waddling gait"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23562786",
+        "description": "A novel COMP mutation in a Chinese patient with pseudoachondroplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001156",
+      "label": "Brachydactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:23562786",
+        "description": "A novel COMP mutation in a Chinese patient with pseudoachondroplasia"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:1311",
+    "symbol": "COMP"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "19",
+      "pos": 18896640,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:177170",
+      "label": "PSEUDOACHONDROPLASIA; PSACH"
+    }
+  }],
+  "metaData": {
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:23562786",
+      "description": "A novel COMP mutation in a Chinese patient with pseudoachondroplasia"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Xiong-2019-ZIC2-proband.json b/notebooks/LIRICAL/v1phenopackets/Xiong-2019-ZIC2-proband.json
new file mode 100644
index 000000000..7f0498fbb
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Xiong-2019-ZIC2-proband.json
@@ -0,0 +1,132 @@
+{
+  "id": "PMID:30855487-Xiong-2019-ZIC2-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P9M"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000238",
+      "label": "Hydrocephalus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30855487",
+        "description": "Case report: a novel mutation in ZIC2 in an infant with microcephaly, holoprosencephaly, and arachnoid cyst"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002507",
+      "label": "Semilobar holoprosencephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30855487",
+        "description": "Case report: a novel mutation in ZIC2 in an infant with microcephaly, holoprosencephaly, and arachnoid cyst"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002119",
+      "label": "Ventriculomegaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30855487",
+        "description": "Case report: a novel mutation in ZIC2 in an infant with microcephaly, holoprosencephaly, and arachnoid cyst"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:7546",
+    "symbol": "ZIC2"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "13",
+      "pos": 100635387,
+      "ref": "C",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:609637",
+      "label": "HOLOPROSENCEPHALY 5; HPE5"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30855487",
+      "description": "Case report: a novel mutation in ZIC2 in an infant with microcephaly, holoprosencephaly, and arachnoid cyst"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Xu-2017-CWC27-1_II-3.json b/notebooks/LIRICAL/v1phenopackets/Xu-2017-CWC27-1_II-3.json
new file mode 100644
index 000000000..d9e67881a
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Xu-2017-CWC27-1_II-3.json
@@ -0,0 +1,267 @@
+{
+  "id": "PMID:28285769-Xu-2017-CWC27-1:II-3",
+  "subject": {
+    "id": "1:II-3",
+    "ageAtCollection": {
+      "age": "P20Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0031936",
+      "label": "Delayed ability to walk"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000369",
+      "label": "Low-set ears"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000653",
+      "label": "Sparse eyelashes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009890",
+      "label": "High anterior hairline"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0045075",
+      "label": "Sparse eyebrow"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012471",
+      "label": "Thick vermilion border"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001156",
+      "label": "Brachydactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000510",
+      "label": "Rod-cone dystrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000957",
+      "label": "Cafe-au-lait spot"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008070",
+      "label": "Sparse hair"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:10283",
+    "symbol": "CWC27"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "5",
+      "pos": 64181274,
+      "ref": "G",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:250410",
+      "label": "Retinitis pigmentosa with or without skeletal anomalies"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28285769",
+      "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Xu-2017-CWC27-3_II-1.json b/notebooks/LIRICAL/v1phenopackets/Xu-2017-CWC27-3_II-1.json
new file mode 100644
index 000000000..a8b417c2a
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Xu-2017-CWC27-3_II-1.json
@@ -0,0 +1,117 @@
+{
+  "id": "PMID:28285769-Xu-2017-CWC27-3:II-1",
+  "subject": {
+    "id": "3:II-1",
+    "ageAtCollection": {
+      "age": "P9Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0007675",
+      "label": "Progressive night blindness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000510",
+      "label": "Rod-cone dystrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:10283",
+    "symbol": "CWC27"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "5",
+      "pos": 64181325,
+      "ref": "C",
+      "alt": "CA"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:250410",
+      "label": "Retinitis pigmentosa with or without skeletal anomalies"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28285769",
+      "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Xu-2017-CWC27-4_II-3.json b/notebooks/LIRICAL/v1phenopackets/Xu-2017-CWC27-4_II-3.json
new file mode 100644
index 000000000..8059454d9
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Xu-2017-CWC27-4_II-3.json
@@ -0,0 +1,297 @@
+{
+  "id": "PMID:28285769-Xu-2017-CWC27-4:II-3",
+  "subject": {
+    "id": "4:II-3",
+    "ageAtCollection": {
+      "age": "P17Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001363",
+      "label": "Craniosynostosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011968",
+      "label": "Feeding difficulties"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000107",
+      "label": "Renal cyst"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001156",
+      "label": "Brachydactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000510",
+      "label": "Rod-cone dystrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011344",
+      "label": "Severe global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001596",
+      "label": "Alopecia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002223",
+      "label": "Absent eyebrow"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001249",
+      "label": "Intellectual disability"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000512",
+      "label": "Abnormal electroretinogram"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000649",
+      "label": "Abnormality of visual evoked potentials"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000561",
+      "label": "Absent eyelashes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008064",
+      "label": "Ichthyosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:10283",
+    "symbol": "CWC27"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "5",
+      "pos": 64082455,
+      "ref": "G",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:250410",
+      "label": "Retinitis pigmentosa with or without skeletal anomalies"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28285769",
+      "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Xu-2017-CWC27-II-4.json b/notebooks/LIRICAL/v1phenopackets/Xu-2017-CWC27-II-4.json
new file mode 100644
index 000000000..079d24aa7
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Xu-2017-CWC27-II-4.json
@@ -0,0 +1,252 @@
+{
+  "id": "PMID:28285769-Xu-2017-CWC27-II-4",
+  "subject": {
+    "id": "II-4",
+    "ageAtCollection": {
+      "age": "P18Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001363",
+      "label": "Craniosynostosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000957",
+      "label": "Cafe-au-lait spot"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001763",
+      "label": "Pes planus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002194",
+      "label": "Delayed gross motor development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001156",
+      "label": "Brachydactyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007565",
+      "label": "Multiple cafe-au-lait spots"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000510",
+      "label": "Rod-cone dystrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001344",
+      "label": "Absent speech"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001822",
+      "label": "Hallux valgus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28285769",
+        "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:10283",
+    "symbol": "CWC27"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "5",
+      "pos": 64181274,
+      "ref": "G",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:250410",
+      "label": "Retinitis pigmentosa with or without skeletal anomalies"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28285769",
+      "description": "Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Yalcin-Cakmakli-2014-FBXO7-ANK-07.json b/notebooks/LIRICAL/v1phenopackets/Yalcin-Cakmakli-2014-FBXO7-ANK-07.json
new file mode 100644
index 000000000..de80db043
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Yalcin-Cakmakli-2014-FBXO7-ANK-07.json
@@ -0,0 +1,193 @@
+{
+  "id": "PMID:25085748-Yalcin-Cakmakli-2014-FBXO7-ANK-07",
+  "subject": {
+    "id": "ANK-07",
+    "ageAtCollection": {
+      "age": "21Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002067",
+      "label": "Bradykinesia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25085748",
+        "description": "A new Turkish family with homozygous FBXO7 truncating mutation and juvenile atypical parkinsonism"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001300",
+      "label": "Parkinsonism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25085748",
+        "description": "A new Turkish family with homozygous FBXO7 truncating mutation and juvenile atypical parkinsonism"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002063",
+      "label": "Rigidity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25085748",
+        "description": "A new Turkish family with homozygous FBXO7 truncating mutation and juvenile atypical parkinsonism"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002172",
+      "label": "Postural instability"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25085748",
+        "description": "A new Turkish family with homozygous FBXO7 truncating mutation and juvenile atypical parkinsonism"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002353",
+      "label": "EEG abnormality"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25085748",
+        "description": "A new Turkish family with homozygous FBXO7 truncating mutation and juvenile atypical parkinsonism"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002527",
+      "label": "Falls"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25085748",
+        "description": "A new Turkish family with homozygous FBXO7 truncating mutation and juvenile atypical parkinsonism"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002141",
+      "label": "Gait imbalance"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25085748",
+        "description": "A new Turkish family with homozygous FBXO7 truncating mutation and juvenile atypical parkinsonism"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:25793",
+    "symbol": "FBXO7"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "22",
+      "pos": 32894440,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:260300",
+      "label": "PARKINSON DISEASE 15, AUTOSOMAL RECESSIVE EARLY-ONSET; PARK15"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:25085748",
+      "description": "A new Turkish family with homozygous FBXO7 truncating mutation and juvenile atypical parkinsonism"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Yang-2016-MFN2-patient.json b/notebooks/LIRICAL/v1phenopackets/Yang-2016-MFN2-patient.json
new file mode 100644
index 000000000..626651f38
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Yang-2016-MFN2-patient.json
@@ -0,0 +1,256 @@
+{
+  "id": "PMID:26956144-Yang-2016-MFN2-patient",
+  "subject": {
+    "id": "patient",
+    "ageAtCollection": {
+      "age": "P4Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0003448",
+      "label": "Decreased sensory nerve conduction velocity"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26956144",
+        "description": "A novel p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030180",
+      "label": "Oppenheim reflex"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26956144",
+        "description": "A novel p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001761",
+      "label": "Pes cavus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26956144",
+        "description": "A novel p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006970",
+      "label": "Periventricular leukomalacia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26956144",
+        "description": "A novel p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0009072",
+      "label": "Decreased Achilles reflex"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26956144",
+        "description": "A novel p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0030181",
+      "label": "Gordon reflex"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26956144",
+        "description": "A novel p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011808",
+      "label": "Decreased patellar reflex"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26956144",
+        "description": "A novel p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007340",
+      "label": "Lower limb muscle weakness"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26956144",
+        "description": "A novel p"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003487",
+      "label": "Babinski sign"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26956144",
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+      }
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+        "id": "PMID:26956144",
+        "description": "A novel p"
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+      "id": "HP:0002527",
+      "label": "Falls"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26956144",
+        "description": "A novel p"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:9927",
+    "symbol": "MFN2"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
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+      "pos": 12059066,
+      "ref": "G",
+      "alt": "C"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:609260",
+      "label": "CHARCOT-MARIE-TOOTH DISEASE, AXONAL, TYPE 2A2; CMT2A2"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
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+      "id": "hp",
+      "name": "human phenotype ontology",
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+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:26956144",
+      "description": "A novel p"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Yao-2019-FGFR3-VI-5.json b/notebooks/LIRICAL/v1phenopackets/Yao-2019-FGFR3-VI-5.json
new file mode 100644
index 000000000..b4d03fc64
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Yao-2019-FGFR3-VI-5.json
@@ -0,0 +1,226 @@
+{
+  "id": "PMID:30681580-Yao-2019-FGFR3-VI-5",
+  "subject": {
+    "id": "VI-5",
+    "ageAtCollection": {
+      "age": "P7Y8M"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0004379",
+      "label": "Abnormality of alkaline phosphatase activity"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Identification of a novel mutation of FGFR3 gene in a large Chinese pedigree with hypochondroplasia by next-generation sequencing: A case report and brief literature review"
+      }
+    }]
+  }, {
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+      "label": "Abnormal thyroid hormone level"
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+    "negated": true,
+    "evidence": [{
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+        "id": "PMID:30681580",
+        "description": "Identification of a novel mutation of FGFR3 gene in a large Chinese pedigree with hypochondroplasia by next-generation sequencing: A case report and brief literature review"
+      }
+    }]
+  }, {
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+    },
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+      }
+    }]
+  }, {
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+      "id": "HP:0002970",
+      "label": "Genu varum"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:30681580",
+        "description": "Identification of a novel mutation of FGFR3 gene in a large Chinese pedigree with hypochondroplasia by next-generation sequencing: A case report and brief literature review"
+      }
+    }]
+  }, {
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+      "label": "Short femoral neck"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
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+      }
+    }]
+  }, {
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+      "label": "Narrow vertebral interpedicular distance"
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+        "description": "Identification of a novel mutation of FGFR3 gene in a large Chinese pedigree with hypochondroplasia by next-generation sequencing: A case report and brief literature review"
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+      "label": "Brachydactyly"
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+    "evidence": [{
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+        "description": "Identification of a novel mutation of FGFR3 gene in a large Chinese pedigree with hypochondroplasia by next-generation sequencing: A case report and brief literature review"
+      }
+    }]
+  }, {
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+      "id": "HP:0100866",
+      "label": "Short iliac bones"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:30681580",
+        "description": "Identification of a novel mutation of FGFR3 gene in a large Chinese pedigree with hypochondroplasia by next-generation sequencing: A case report and brief literature review"
+      }
+    }]
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+    "id": "NCBIGene:2261",
+    "symbol": "FGFR3"
+  }],
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+  }],
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+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30681580",
+      "description": "Identification of a novel mutation of FGFR3 gene in a large Chinese pedigree with hypochondroplasia by next-generation sequencing: A case report and brief literature review"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Yoshida-1991-GLB1-KT.json b/notebooks/LIRICAL/v1phenopackets/Yoshida-1991-GLB1-KT.json
new file mode 100644
index 000000000..ea5012016
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Yoshida-1991-GLB1-KT.json
@@ -0,0 +1,179 @@
+{
+  "id": "PMID:1907800-Yoshida-1991-GLB1-KT",
+  "subject": {
+    "id": "KT",
+    "ageAtCollection": {
+      "age": "P13Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0010729",
+      "label": "Cherry red spot of the macula"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:1907800",
+        "description": "Human beta-galactosidase gene mutations in GM1-gangliosidosis: a common mutation among Japanese adult/chronic cases"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000926",
+      "label": "Platyspondyly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:1907800",
+        "description": "Human beta-galactosidase gene mutations in GM1-gangliosidosis: a common mutation among Japanese adult/chronic cases"
+      }
+    }]
+  }, {
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+      "label": "Decreased beta-galactosidase activity"
+    },
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+        "label": "author statement supported by traceable reference"
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+        "description": "Human beta-galactosidase gene mutations in GM1-gangliosidosis: a common mutation among Japanese adult/chronic cases"
+      }
+    }]
+  }, {
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+      "label": "Abnormality of extrapyramidal motor function"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:1907800",
+        "description": "Human beta-galactosidase gene mutations in GM1-gangliosidosis: a common mutation among Japanese adult/chronic cases"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001256",
+      "label": "Intellectual disability, mild"
+    },
+    "evidence": [{
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+        "description": "Human beta-galactosidase gene mutations in GM1-gangliosidosis: a common mutation among Japanese adult/chronic cases"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001433",
+      "label": "Hepatosplenomegaly"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:1907800",
+        "description": "Human beta-galactosidase gene mutations in GM1-gangliosidosis: a common mutation among Japanese adult/chronic cases"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2720",
+    "symbol": "GLB1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "3",
+      "pos": 33114129,
+      "ref": "A",
+      "alt": "G"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:230650",
+      "label": "GM1-GANGLIOSIDOSIS, TYPE III"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13",
+    "submittedBy": "HP:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:1907800",
+      "description": "Human beta-galactosidase gene mutations in GM1-gangliosidosis: a common mutation among Japanese adult/chronic cases"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Zapata-Aldana-2019-TBCK-Patient_1.json b/notebooks/LIRICAL/v1phenopackets/Zapata-Aldana-2019-TBCK-Patient_1.json
new file mode 100644
index 000000000..c8d70b683
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Zapata-Aldana-2019-TBCK-Patient_1.json
@@ -0,0 +1,538 @@
+{
+  "id": "PMID:30103036-Zapata-Aldana-2019-TBCK-Patient_1",
+  "subject": {
+    "id": "Patient 1",
+    "ageAtCollection": {
+      "age": "P5Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002133",
+      "label": "Status epilepticus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012032",
+      "label": "Lipoma"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002069",
+      "label": "Generalized tonic-clonic seizures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007305",
+      "label": "CNS demyelination"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001284",
+      "label": "Areflexia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100288",
+      "label": "EMG: myokymic discharges"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001344",
+      "label": "Absent speech"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001331",
+      "label": "Absent septum pellucidum"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
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+      "id": "HP:0002280",
+      "label": "Enlarged cisterna magna"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011344",
+      "label": "Severe global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001272",
+      "label": "Cerebellar atrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005667",
+      "label": "Os odontoideum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000194",
+      "label": "Open mouth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012444",
+      "label": "Brain atrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001935",
+      "label": "Microcytic anemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002079",
+      "label": "Hypoplasia of the corpus callosum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Brachycephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Long philtrum"
+    },
+    "evidence": [{
+      "evidenceCode": {
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+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
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+    },
+    "evidence": [{
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+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
+    "type": {
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+      "label": "Global brain atrophy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
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+      }
+    }]
+  }, {
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+      "label": "Severe muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
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+      "label": "Tented upper lip vermilion"
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+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
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+  }, {
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+      "id": "HP:0002119",
+      "label": "Ventriculomegaly"
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+    "evidence": [{
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+    }]
+  }, {
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+    "evidence": [{
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+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002375",
+      "label": "Hypokinesia"
+    },
+    "evidence": [{
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+    }]
+  }, {
+    "type": {
+      "id": "HP:0001347",
+      "label": "Hyperreflexia"
+    },
+    "evidence": [{
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+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
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+    }]
+  }, {
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+    },
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+      }
+    }]
+  }, {
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+    },
+    "evidence": [{
+      "evidenceCode": {
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+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:93627",
+    "symbol": "TBCK"
+  }],
+  "variants": [{
+    "vcfAllele": {
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+      "chr": "4",
+      "pos": 107169430,
+      "ref": "T",
+      "alt": "TA"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616900",
+      "label": "Hypotonia, infantile, with psychomotor retardation and characteristic facies 3"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30103036",
+      "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Zapata-Aldana-2019-TBCK-Patient_2.json b/notebooks/LIRICAL/v1phenopackets/Zapata-Aldana-2019-TBCK-Patient_2.json
new file mode 100644
index 000000000..ead79f9ef
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Zapata-Aldana-2019-TBCK-Patient_2.json
@@ -0,0 +1,327 @@
+{
+  "id": "PMID:30103036-Zapata-Aldana-2019-TBCK-Patient_2",
+  "subject": {
+    "id": "Patient 2",
+    "ageAtCollection": {
+      "age": "P3Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000194",
+      "label": "Open mouth"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0100716",
+      "label": "Self-injurious behavior"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002421",
+      "label": "Poor head control"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000248",
+      "label": "Brachycephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000343",
+      "label": "Long philtrum"
+    },
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+      "evidenceCode": {
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+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
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+      "label": "Deeply set eye"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
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+      "id": "HP:0001270",
+      "label": "Motor delay"
+    },
+    "evidence": [{
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+      "reference": {
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+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
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+      "label": "Absent speech"
+    },
+    "evidence": [{
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+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
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+      "label": "Poor eye contact"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000565",
+      "label": "Esotropia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0006829",
+      "label": "Severe muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+      },
+      "reference": {
+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010804",
+      "label": "Tented upper lip vermilion"
+    },
+    "evidence": [{
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+      "reference": {
+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
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+      "label": "Sloping forehead"
+    },
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+      "evidenceCode": {
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+      "reference": {
+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001347",
+      "label": "Hyperreflexia"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000586",
+      "label": "Shallow orbits"
+    },
+    "evidence": [{
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+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }, {
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+      "label": "Respiratory failure"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30103036",
+        "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:93627",
+    "symbol": "TBCK"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "4",
+      "pos": 107169430,
+      "ref": "T",
+      "alt": "TA"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:616900",
+      "label": "Hypotonia, infantile, with psychomotor retardation and characteristic facies 3"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.14-SNAPSHOT",
+    "submittedBy": "UNC:biocuration",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30103036",
+      "description": "Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Zemojtel-2014-KMT2A-P1.json b/notebooks/LIRICAL/v1phenopackets/Zemojtel-2014-KMT2A-P1.json
new file mode 100644
index 000000000..7d27c5c06
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Zemojtel-2014-KMT2A-P1.json
@@ -0,0 +1,327 @@
+{
+  "id": "PMID:25186178-Zemojtel-2014-KMT2A-P1",
+  "subject": {
+    "id": "P1",
+    "ageAtCollection": {
+      "age": "P3Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0003508",
+      "label": "Proportionate short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25186178",
+        "description": "Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007441",
+      "label": "Hyperpigmented/hypopigmented macules"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25186178",
+        "description": "Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000470",
+      "label": "Short neck"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25186178",
+        "description": "Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010230",
+      "label": "Cone-shaped epiphyses of the phalanges of the hand"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25186178",
+        "description": "Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008676",
+      "label": "Congenital megaureter"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:25186178",
+        "description": "Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome"
+      }
+    }]
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+      "id": "HP:0000252",
+      "label": "Microcephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25186178",
+        "description": "Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000179",
+      "label": "Thick lower lip vermilion"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25186178",
+        "description": "Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome"
+      }
+    }]
+  }, {
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+      "id": "HP:0001270",
+      "label": "Motor delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25186178",
+        "description": "Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000960",
+      "label": "Sacral dimple"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25186178",
+        "description": "Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011968",
+      "label": "Feeding difficulties"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25186178",
+        "description": "Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001263",
+      "label": "Global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25186178",
+        "description": "Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000457",
+      "label": "Depressed nasal ridge"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25186178",
+        "description": "Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000215",
+      "label": "Thick upper lip vermilion"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25186178",
+        "description": "Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25186178",
+        "description": "Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000309",
+      "label": "Abnormality of the midface"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25186178",
+        "description": "Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000293",
+      "label": "Full cheeks"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:25186178",
+        "description": "Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:4297",
+    "symbol": "KMT2A"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "11",
+      "pos": 118373871,
+      "ref": "G",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:605130",
+      "label": "WIEDEMANN-STEINER SYNDROME; WDSTS"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:25186178",
+      "description": "Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Zenker-2007-KRAS-Patient_2.json b/notebooks/LIRICAL/v1phenopackets/Zenker-2007-KRAS-Patient_2.json
new file mode 100644
index 000000000..ab6eb4d66
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Zenker-2007-KRAS-Patient_2.json
@@ -0,0 +1,297 @@
+{
+  "id": "PMID:17056636-Zenker-2007-KRAS-Patient_2",
+  "subject": {
+    "id": "Patient 2",
+    "ageAtCollection": {
+      "age": "P16Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0004482",
+      "label": "Relative macrocephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:17056636",
+        "description": "Expansion of the genotypic and phenotypic spectrum in patients with KRAS germline mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0004322",
+      "label": "Short stature"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:17056636",
+        "description": "Expansion of the genotypic and phenotypic spectrum in patients with KRAS germline mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008070",
+      "label": "Sparse hair"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:17056636",
+        "description": "Expansion of the genotypic and phenotypic spectrum in patients with KRAS germline mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000316",
+      "label": "Hypertelorism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:17056636",
+        "description": "Expansion of the genotypic and phenotypic spectrum in patients with KRAS germline mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002967",
+      "label": "Cubitus valgus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:17056636",
+        "description": "Expansion of the genotypic and phenotypic spectrum in patients with KRAS germline mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000767",
+      "label": "Pectus excavatum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:17056636",
+        "description": "Expansion of the genotypic and phenotypic spectrum in patients with KRAS germline mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000508",
+      "label": "Ptosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:17056636",
+        "description": "Expansion of the genotypic and phenotypic spectrum in patients with KRAS germline mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000470",
+      "label": "Short neck"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:17056636",
+        "description": "Expansion of the genotypic and phenotypic spectrum in patients with KRAS germline mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001250",
+      "label": "Seizures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:17056636",
+        "description": "Expansion of the genotypic and phenotypic spectrum in patients with KRAS germline mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000486",
+      "label": "Strabismus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:17056636",
+        "description": "Expansion of the genotypic and phenotypic spectrum in patients with KRAS germline mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000238",
+      "label": "Hydrocephalus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:17056636",
+        "description": "Expansion of the genotypic and phenotypic spectrum in patients with KRAS germline mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000369",
+      "label": "Low-set ears"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:17056636",
+        "description": "Expansion of the genotypic and phenotypic spectrum in patients with KRAS germline mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011342",
+      "label": "Mild global developmental delay"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:17056636",
+        "description": "Expansion of the genotypic and phenotypic spectrum in patients with KRAS germline mutations"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000256",
+      "label": "Macrocephaly"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:17056636",
+        "description": "Expansion of the genotypic and phenotypic spectrum in patients with KRAS germline mutations"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:3845",
+    "symbol": "KRAS"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "12",
+      "pos": 25398279,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:609942",
+      "label": "NOONAN SYNDROME 3; NS3"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:17056636",
+      "description": "Expansion of the genotypic and phenotypic spectrum in patients with KRAS germline mutations"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Zerkaoui-2015-GALC-child.json b/notebooks/LIRICAL/v1phenopackets/Zerkaoui-2015-GALC-child.json
new file mode 100644
index 000000000..f5ef0482e
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Zerkaoui-2015-GALC-child.json
@@ -0,0 +1,189 @@
+{
+  "id": "PMID:26567009-Zerkaoui-2015-GALC-child",
+  "subject": {
+    "id": "child",
+    "ageAtCollection": {
+      "age": "P11M"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001290",
+      "label": "Generalized hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26567009",
+        "description": "Clinical and molecular report of novel GALC mutations in Moroccan patient with Krabbe disease: case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001945",
+      "label": "Fever"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:26567009",
+        "description": "Clinical and molecular report of novel GALC mutations in Moroccan patient with Krabbe disease: case report"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001276",
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+    "id": "NCBIGene:2581",
+    "symbol": "GALC"
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+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "14",
+      "pos": 88434727,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
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+    "vcfAllele": {
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+      "chr": "14",
+      "pos": 88411945,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:245200",
+      "label": "KRABBE DISEASE"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
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+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:26567009",
+      "description": "Clinical and molecular report of novel GALC mutations in Moroccan patient with Krabbe disease: case report"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Zhang-2009-EDA-proband.json b/notebooks/LIRICAL/v1phenopackets/Zhang-2009-EDA-proband.json
new file mode 100644
index 000000000..7dd6967fd
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Zhang-2009-EDA-proband.json
@@ -0,0 +1,222 @@
+{
+  "id": "PMID:18702659-Zhang-2009-EDA-proband",
+  "subject": {
+    "id": "proband",
+    "ageAtCollection": {
+      "age": "P23Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0000966",
+      "label": "Hypohidrosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18702659",
+        "description": "A novel frameshift mutation of the EDA1 gene in a Chinese Han family with X-linked hypohidrotic ectodermal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005280",
+      "label": "Depressed nasal bridge"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18702659",
+        "description": "A novel frameshift mutation of the EDA1 gene in a Chinese Han family with X-linked hypohidrotic ectodermal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011220",
+      "label": "Prominent forehead"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:18702659",
+        "description": "A novel frameshift mutation of the EDA1 gene in a Chinese Han family with X-linked hypohidrotic ectodermal dysplasia"
+      }
+    }]
+  }, {
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+      "id": "HP:0001006",
+      "label": "Hypotrichosis"
+    },
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "A novel frameshift mutation of the EDA1 gene in a Chinese Han family with X-linked hypohidrotic ectodermal dysplasia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001954",
+      "label": "Recurrent fever"
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+      "label": "Pointed chin"
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+        "description": "A novel frameshift mutation of the EDA1 gene in a Chinese Han family with X-linked hypohidrotic ectodermal dysplasia"
+      }
+    }]
+  }, {
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+      "id": "HP:0012471",
+      "label": "Thick vermilion border"
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+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:18702659",
+        "description": "A novel frameshift mutation of the EDA1 gene in a Chinese Han family with X-linked hypohidrotic ectodermal dysplasia"
+      }
+    }]
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+    "id": "NCBIGene:1896",
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+    }, {
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+      "name": "Genotype Ontology",
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+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
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+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
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+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
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+    "externalReferences": [{
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+      "description": "A novel frameshift mutation of the EDA1 gene in a Chinese Han family with X-linked hypohidrotic ectodermal dysplasia"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Zhang-2011-TYRP1-patient_2.json b/notebooks/LIRICAL/v1phenopackets/Zhang-2011-TYRP1-patient_2.json
new file mode 100644
index 000000000..e2609fad2
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Zhang-2011-TYRP1-patient_2.json
@@ -0,0 +1,144 @@
+{
+  "id": "PMID:21739261-Zhang-2011-TYRP1-patient_2",
+  "subject": {
+    "id": "patient 2",
+    "ageAtCollection": {
+      "age": "P1Y9M"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0005599",
+      "label": "Hypopigmentation of hair"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:21739261",
+        "description": "Oculocutaneous albinism type 3 (OCA3): analysis of two novel mutations in TYRP1 gene in two Chinese patients"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000639",
+      "label": "Nystagmus"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:21739261",
+        "description": "Oculocutaneous albinism type 3 (OCA3): analysis of two novel mutations in TYRP1 gene in two Chinese patients"
+      }
+    }]
+  }, {
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+      "id": "HP:0001010",
+      "label": "Hypopigmentation of the skin"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "description": "Oculocutaneous albinism type 3 (OCA3): analysis of two novel mutations in TYRP1 gene in two Chinese patients"
+      }
+    }]
+  }],
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+    "id": "NCBIGene:7306",
+    "symbol": "TYRP1"
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+      "pos": 12695754,
+      "ref": "G",
+      "alt": "TT"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }, {
+    "vcfAllele": {
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+      "pos": 12695772,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:203290",
+      "label": "ALBINISM, OCULOCUTANEOUS, TYPE III; OCA3"
+    }
+  }],
+  "metaData": {
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+    "submittedBy": "HPO:probinson",
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+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
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+    "externalReferences": [{
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+      "description": "Oculocutaneous albinism type 3 (OCA3): analysis of two novel mutations in TYRP1 gene in two Chinese patients"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Zhang-2016-RPS19-patient.json b/notebooks/LIRICAL/v1phenopackets/Zhang-2016-RPS19-patient.json
new file mode 100644
index 000000000..da8d163a0
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Zhang-2016-RPS19-patient.json
@@ -0,0 +1,166 @@
+{
+  "id": "PMID:27732904-Zhang-2016-RPS19-patient",
+  "subject": {
+    "id": "patient",
+    "ageAtCollection": {
+      "age": "P2M"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0011873",
+      "label": "Abnormal platelet count"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27732904",
+        "description": "A new in-frame deletion in ribosomal protein S19 in a Chinese infant with Diamond-Blackfan anemia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001627",
+      "label": "Abnormal heart morphology"
+    },
+    "negated": true,
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:27732904",
+        "description": "A new in-frame deletion in ribosomal protein S19 in a Chinese infant with Diamond-Blackfan anemia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001972",
+      "label": "Macrocytic anemia"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
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+        "description": "A new in-frame deletion in ribosomal protein S19 in a Chinese infant with Diamond-Blackfan anemia"
+      }
+    }]
+  }, {
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+      "id": "HP:0011893",
+      "label": "Abnormal leukocyte count"
+    },
+    "negated": true,
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:27732904",
+        "description": "A new in-frame deletion in ribosomal protein S19 in a Chinese infant with Diamond-Blackfan anemia"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002011",
+      "label": "Morphological abnormality of the central nervous system"
+    },
+    "negated": true,
+    "evidence": [{
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+        "description": "A new in-frame deletion in ribosomal protein S19 in a Chinese infant with Diamond-Blackfan anemia"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:6223",
+    "symbol": "RPS19"
+  }],
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+      "chr": "19",
+      "pos": 42373178,
+      "ref": "AG",
+      "alt": "A"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:105650",
+      "label": "DIAMOND-BLACKFAN ANEMIA 1; DBA1"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
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+      "name": "human phenotype ontology",
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+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
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+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27732904",
+      "description": "A new in-frame deletion in ribosomal protein S19 in a Chinese infant with Diamond-Blackfan anemia"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Zhang-2017-FOXG1-Patient_1.json b/notebooks/LIRICAL/v1phenopackets/Zhang-2017-FOXG1-Patient_1.json
new file mode 100644
index 000000000..40111761f
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Zhang-2017-FOXG1-Patient_1.json
@@ -0,0 +1,267 @@
+{
+  "id": "PMID:28851325-Zhang-2017-FOXG1-Patient_1",
+  "subject": {
+    "id": "Patient 1",
+    "ageAtCollection": {
+      "age": "P1Y8M"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002079",
+      "label": "Hypoplasia of the corpus callosum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001250",
+      "label": "Seizures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002188",
+      "label": "Delayed CNS myelination"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003763",
+      "label": "Bruxism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
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+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000733",
+      "label": "Stereotypy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002353",
+      "label": "EEG abnormality"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
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+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007333",
+      "label": "Hypoplasia of the frontal lobes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005484",
+      "label": "Postnatal microcephaly"
+    },
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002376",
+      "label": "Developmental regression"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002540",
+      "label": "Inability to walk"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2290",
+    "symbol": "FOXG1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "14",
+      "pos": 29237342,
+      "ref": "T",
+      "alt": "TC"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:613454",
+      "label": "RETT SYNDROME, CONGENITAL VARIANT"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28851325",
+      "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Zhang-2017-FOXG1-Patient_2.json b/notebooks/LIRICAL/v1phenopackets/Zhang-2017-FOXG1-Patient_2.json
new file mode 100644
index 000000000..a55aeb811
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Zhang-2017-FOXG1-Patient_2.json
@@ -0,0 +1,252 @@
+{
+  "id": "PMID:28851325-Zhang-2017-FOXG1-Patient_2",
+  "subject": {
+    "id": "Patient 2",
+    "ageAtCollection": {
+      "age": "P4Y6M"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002360",
+      "label": "Sleep disturbance"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002079",
+      "label": "Hypoplasia of the corpus callosum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011968",
+      "label": "Feeding difficulties"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000750",
+      "label": "Delayed speech and language development"
+    },
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+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
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+      "id": "HP:0003763",
+      "label": "Bruxism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000817",
+      "label": "Poor eye contact"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000733",
+      "label": "Stereotypy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001250",
+      "label": "Seizures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002353",
+      "label": "EEG abnormality"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007333",
+      "label": "Hypoplasia of the frontal lobes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2290",
+    "symbol": "FOXG1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "14",
+      "pos": 29237179,
+      "ref": "A",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:613454",
+      "label": "RETT SYNDROME, CONGENITAL VARIANT"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:28851325",
+      "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Zhang-2017-FOXG1-Patient_3.json b/notebooks/LIRICAL/v1phenopackets/Zhang-2017-FOXG1-Patient_3.json
new file mode 100644
index 000000000..2c6403d00
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Zhang-2017-FOXG1-Patient_3.json
@@ -0,0 +1,222 @@
+{
+  "id": "PMID:28851325-Zhang-2017-FOXG1-Patient_3",
+  "subject": {
+    "id": "Patient 3",
+    "ageAtCollection": {
+      "age": "P1Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0002360",
+      "label": "Sleep disturbance"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002079",
+      "label": "Hypoplasia of the corpus callosum"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0008872",
+      "label": "Feeding difficulties in infancy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0003763",
+      "label": "Bruxism"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000733",
+      "label": "Stereotypy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001250",
+      "label": "Seizures"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007333",
+      "label": "Hypoplasia of the frontal lobes"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005484",
+      "label": "Postnatal microcephaly"
+    },
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2290",
+    "symbol": "FOXG1"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "14",
+      "pos": 29236938,
+      "ref": "C",
+      "alt": "CG"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:613454",
+      "label": "RETT SYNDROME, CONGENITAL VARIANT"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
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+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
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+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
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+    "externalReferences": [{
+      "id": "PMID:28851325",
+      "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Zhang-2017-FOXG1-Patient_4.json b/notebooks/LIRICAL/v1phenopackets/Zhang-2017-FOXG1-Patient_4.json
new file mode 100644
index 000000000..aa4904ac7
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Zhang-2017-FOXG1-Patient_4.json
@@ -0,0 +1,223 @@
+{
+  "id": "PMID:28851325-Zhang-2017-FOXG1-Patient_4",
+  "subject": {
+    "id": "Patient 4",
+    "ageAtCollection": {
+      "age": "P2Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
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+    "type": {
+      "id": "HP:0002360",
+      "label": "Sleep disturbance"
+    },
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
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+      "id": "HP:0008872",
+      "label": "Feeding difficulties in infancy"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }, {
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+      "id": "HP:0001252",
+      "label": "Muscular hypotonia"
+    },
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+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
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+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
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+  }, {
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+      "id": "HP:0005484",
+      "label": "Postnatal microcephaly"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:28851325",
+        "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2290",
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+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
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+      "url": "http://purl.obolibrary.org/obo/geno.owl",
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+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
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+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
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+    }, {
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+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
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+      "namespacePrefix": "OMIM"
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+    "externalReferences": [{
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+      "description": "Novel FOXG1 mutations in Chinese patients with Rett syndrome or Rett-like mental retardation"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Zhao-2008-KRT9-III_4.json b/notebooks/LIRICAL/v1phenopackets/Zhao-2008-KRT9-III_4.json
new file mode 100644
index 000000000..6c6d81547
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Zhao-2008-KRT9-III_4.json
@@ -0,0 +1,131 @@
+{
+  "id": "PMID:18477167-Zhao-2008-KRT9-III:4",
+  "subject": {
+    "id": "III:4",
+    "ageAtCollection": {
+      "age": "32Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0007559",
+      "label": "Localized epidermolytic hyperkeratosis"
+    },
+    "evidence": [{
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+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18477167",
+        "description": "Mutation M157R of keratin 9 in a Chinese family with epidermolytic palmoplantar keratoderma"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0010765",
+      "label": "Palmar hyperkeratosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:18477167",
+        "description": "Mutation M157R of keratin 9 in a Chinese family with epidermolytic palmoplantar keratoderma"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0007556",
+      "label": "Plantar hyperkeratosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
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+      },
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+        "description": "Mutation M157R of keratin 9 in a Chinese family with epidermolytic palmoplantar keratoderma"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:3857",
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+      "pos": 39727775,
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+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:144200",
+      "label": "PALMOPLANTAR KERATODERMA, EPIDERMOLYTIC; EPPK"
+    }
+  }],
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+    }, {
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+    }, {
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+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
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+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
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+    "externalReferences": [{
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+      "description": "Mutation M157R of keratin 9 in a Chinese family with epidermolytic palmoplantar keratoderma"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Zheng-2018-PNPLA6-II.2.json b/notebooks/LIRICAL/v1phenopackets/Zheng-2018-PNPLA6-II.2.json
new file mode 100644
index 000000000..1a6b87c04
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Zheng-2018-PNPLA6-II.2.json
@@ -0,0 +1,218 @@
+{
+  "id": "PMID:29749493-Zheng-2018-PNPLA6-II.2",
+  "subject": {
+    "id": "II.2",
+    "ageAtCollection": {
+      "age": "50Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0040171",
+      "label": "Decreased serum testosterone level"
+    },
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+        "label": "author statement supported by traceable reference"
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+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0002075",
+      "label": "Dysdiadochokinesis"
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+    "evidence": [{
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+      }
+    }]
+  }, {
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+      "id": "HP:0001265",
+      "label": "Hyporeflexia"
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+    "zygosity": {
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+    }, {
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+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
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+    "externalReferences": [{
+      "id": "PMID:29749493",
+      "description": "A novel PNPLA6 compound heterozygous mutation identified in a Chinese patient with Boucher‑Neuhäuser syndrome"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Zhong-2016-PRPF3-020001-II_4.json b/notebooks/LIRICAL/v1phenopackets/Zhong-2016-PRPF3-020001-II_4.json
new file mode 100644
index 000000000..480d7017e
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Zhong-2016-PRPF3-020001-II_4.json
@@ -0,0 +1,147 @@
+{
+  "id": "PMID:27886254-Zhong-2016-PRPF3-020001-II:4",
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+    "id": "020001-II:4",
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+    },
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+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
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+      "label": "Nyctalopia"
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+    }]
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+        "id": "ECO:0000033",
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+      }
+    }]
+  }, {
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+    }]
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+      }
+    }]
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+    "id": "NCBIGene:9129",
+    "symbol": "PRPF3"
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+    }
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+  "diseases": [{
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+  }],
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+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:27886254",
+      "description": "Two novel mutations in PRPF3 causing autosomal dominant retinitis pigmentosa"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Zhou-2018-FBN2-IV_7.json b/notebooks/LIRICAL/v1phenopackets/Zhou-2018-FBN2-IV_7.json
new file mode 100644
index 000000000..24c35c6da
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Zhou-2018-FBN2-IV_7.json
@@ -0,0 +1,181 @@
+{
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+    },
+    "sex": "FEMALE",
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+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
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+      "id": "HP:0000098",
+      "label": "Tall stature"
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+    "negated": true,
+    "evidence": [{
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+      }
+    }]
+  }, {
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+      "id": "HP:0012372",
+      "label": "Abnormal eye morphology"
+    },
+    "negated": true,
+    "evidence": [{
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+      }
+    }]
+  }, {
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+    }]
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+    "evidence": [{
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+        "description": "A novel FBN2 mutation cosegregates with congenital contractural arachnodactyly in a five-generation Chinese family"
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+    }]
+  }],
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+    "id": "NCBIGene:2201",
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+  }],
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+    },
+    "zygosity": {
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+      "label": "heterozygous"
+    }
+  }],
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+      "label": "ARTHROGRYPOSIS, DISTAL, TYPE 9; DA9"
+    }
+  }],
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+      "url": "http://purl.obolibrary.org/obo/hp.owl",
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+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
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+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
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+      "url": "http://purl.obolibrary.org/obo/geno.owl",
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+      "namespacePrefix": "GENO",
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+    }, {
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+      "namespacePrefix": "NCBITaxon"
+    }, {
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+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
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+    "externalReferences": [{
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+      "description": "A novel FBN2 mutation cosegregates with congenital contractural arachnodactyly in a five-generation Chinese family"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/Zhu-2017-AIRE-V-1.json b/notebooks/LIRICAL/v1phenopackets/Zhu-2017-AIRE-V-1.json
new file mode 100644
index 000000000..d4cccd757
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/Zhu-2017-AIRE-V-1.json
@@ -0,0 +1,236 @@
+{
+  "id": "PMID:28540407-Zhu-2017-AIRE-V-1",
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+      "age": "19Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
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+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0006297",
+      "label": "Hypoplasia of dental enamel"
+    },
+    "evidence": [{
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+        "description": "A new mutation site in the AIRE gene causes autoimmune polyendocrine syndrome type 1"
+      }
+    }]
+  }, {
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+      "label": "Hypocalcemia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+        "id": "PMID:28540407",
+        "description": "A new mutation site in the AIRE gene causes autoimmune polyendocrine syndrome type 1"
+      }
+    }]
+  }, {
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+      "id": "HP:0002024",
+      "label": "Malabsorption"
+    },
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+        "description": "A new mutation site in the AIRE gene causes autoimmune polyendocrine syndrome type 1"
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+      "label": "Chronic mucocutaneous candidiasis"
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+      }
+    }]
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+      "label": "Tetany"
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+        "description": "A new mutation site in the AIRE gene causes autoimmune polyendocrine syndrome type 1"
+      }
+    }]
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+      "label": "homozygous"
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+  "diseases": [{
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+      "label": "AUTOIMMUNE POLYENDOCRINE SYNDROME, TYPE I, WITH OR WITHOUT REVERSIBLEMETAPHYSEAL DYSPLASIA; APS1"
+    }
+  }],
+  "metaData": {
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+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
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+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
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+    "externalReferences": [{
+      "id": "PMID:28540407",
+      "description": "A new mutation site in the AIRE gene causes autoimmune polyendocrine syndrome type 1"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/de_Vries-2012-FANCC-proband.json b/notebooks/LIRICAL/v1phenopackets/de_Vries-2012-FANCC-proband.json
new file mode 100644
index 000000000..cc3486d5d
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/de_Vries-2012-FANCC-proband.json
@@ -0,0 +1,192 @@
+{
+  "id": "PMID:22701786-de_Vries-2012-FANCC-proband",
+  "subject": {
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+    "ageAtCollection": {
+      "age": "P6Y"
+    },
+    "sex": "FEMALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
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+      "id": "HP:0001511",
+      "label": "Intrauterine growth retardation"
+    },
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:22701786",
+        "description": "A Dutch Fanconi Anemia FANCC Founder Mutation in Canadian Manitoba Mennonites"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001629",
+      "label": "Ventricular septal defect"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
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+      "reference": {
+        "id": "PMID:22701786",
+        "description": "A Dutch Fanconi Anemia FANCC Founder Mutation in Canadian Manitoba Mennonites"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005528",
+      "label": "Bone marrow hypocellularity"
+    },
+    "evidence": [{
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+        "label": "author statement supported by traceable reference"
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+        "description": "A Dutch Fanconi Anemia FANCC Founder Mutation in Canadian Manitoba Mennonites"
+      }
+    }]
+  }, {
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+      "label": "Short stature"
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+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:22701786",
+        "description": "A Dutch Fanconi Anemia FANCC Founder Mutation in Canadian Manitoba Mennonites"
+      }
+    }]
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+      "id": "HP:0001371",
+      "label": "Flexion contracture"
+    },
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+    }]
+  }, {
+    "type": {
+      "id": "HP:0000325",
+      "label": "Triangular face"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:22701786",
+        "description": "A Dutch Fanconi Anemia FANCC Founder Mutation in Canadian Manitoba Mennonites"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0000957",
+      "label": "Cafe-au-lait spot"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:22701786",
+        "description": "A Dutch Fanconi Anemia FANCC Founder Mutation in Canadian Manitoba Mennonites"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:2176",
+    "symbol": "FANCC"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "9",
+      "pos": 98011506,
+      "ref": "TC",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000136",
+      "label": "homozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:227645",
+      "label": "FANCONI ANEMIA, COMPLEMENTATION GROUP C; FANCC"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:22701786",
+      "description": "A Dutch Fanconi Anemia FANCC Founder Mutation in Canadian Manitoba Mennonites"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/LIRICAL/v1phenopackets/van_Oorschot-2019-GFI1B-II_6.json b/notebooks/LIRICAL/v1phenopackets/van_Oorschot-2019-GFI1B-II_6.json
new file mode 100644
index 000000000..a083f6d29
--- /dev/null
+++ b/notebooks/LIRICAL/v1phenopackets/van_Oorschot-2019-GFI1B-II_6.json
@@ -0,0 +1,162 @@
+{
+  "id": "PMID:30655368-van_Oorschot-2019-GFI1B-II:6",
+  "subject": {
+    "id": "II:6",
+    "ageAtCollection": {
+      "age": "P42Y"
+    },
+    "sex": "MALE",
+    "taxonomy": {
+      "id": "NCBITaxon:9606",
+      "label": "Homo sapiens"
+    }
+  },
+  "phenotypicFeatures": [{
+    "type": {
+      "id": "HP:0001873",
+      "label": "Thrombocytopenia"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30655368",
+        "description": "Molecular mechanisms of bleeding disorder-associated GFI1BQ287* mutation and its affected pathways in megakaryocytes and platelets"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0011974",
+      "label": "Myelofibrosis"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30655368",
+        "description": "Molecular mechanisms of bleeding disorder-associated GFI1BQ287* mutation and its affected pathways in megakaryocytes and platelets"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0012528",
+      "label": "Abnormal number of alpha granules"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30655368",
+        "description": "Molecular mechanisms of bleeding disorder-associated GFI1BQ287* mutation and its affected pathways in megakaryocytes and platelets"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0001892",
+      "label": "Abnormal bleeding"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30655368",
+        "description": "Molecular mechanisms of bleeding disorder-associated GFI1BQ287* mutation and its affected pathways in megakaryocytes and platelets"
+      }
+    }]
+  }, {
+    "type": {
+      "id": "HP:0005513",
+      "label": "Increased megakaryocyte count"
+    },
+    "evidence": [{
+      "evidenceCode": {
+        "id": "ECO:0000033",
+        "label": "author statement supported by traceable reference"
+      },
+      "reference": {
+        "id": "PMID:30655368",
+        "description": "Molecular mechanisms of bleeding disorder-associated GFI1BQ287* mutation and its affected pathways in megakaryocytes and platelets"
+      }
+    }]
+  }],
+  "genes": [{
+    "id": "NCBIGene:8328",
+    "symbol": "GFI1B"
+  }],
+  "variants": [{
+    "vcfAllele": {
+      "genomeAssembly": "GRCh37",
+      "chr": "9",
+      "pos": 135866303,
+      "ref": "C",
+      "alt": "T"
+    },
+    "zygosity": {
+      "id": "GENO:0000135",
+      "label": "heterozygous"
+    }
+  }],
+  "diseases": [{
+    "term": {
+      "id": "OMIM:187900",
+      "label": "BLEEDING DISORDER, PLATELET-TYPE, 17; BDPLT17"
+    }
+  }],
+  "metaData": {
+    "createdBy": "Hpo Case Annotator : 1.0.13-SNAPSHOT",
+    "submittedBy": "HPO:probinson",
+    "resources": [{
+      "id": "hp",
+      "name": "human phenotype ontology",
+      "url": "http://purl.obolibrary.org/obo/hp.owl",
+      "version": "2018-03-08",
+      "namespacePrefix": "HP",
+      "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+    }, {
+      "id": "pato",
+      "name": "Phenotype And Trait Ontology",
+      "url": "http://purl.obolibrary.org/obo/pato.owl",
+      "version": "2018-03-28",
+      "namespacePrefix": "PATO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/PATO_"
+    }, {
+      "id": "geno",
+      "name": "Genotype Ontology",
+      "url": "http://purl.obolibrary.org/obo/geno.owl",
+      "version": "19-03-2018",
+      "namespacePrefix": "GENO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+    }, {
+      "id": "ncbitaxon",
+      "name": "NCBI organismal classification",
+      "url": "http://purl.obolibrary.org/obo/ncbitaxon.owl",
+      "version": "2018-03-02",
+      "namespacePrefix": "NCBITaxon"
+    }, {
+      "id": "eco",
+      "name": "Evidence and Conclusion Ontology",
+      "url": "http://purl.obolibrary.org/obo/eco.owl",
+      "version": "2018-11-10",
+      "namespacePrefix": "ECO",
+      "iriPrefix": "http://purl.obolibrary.org/obo/ECO_"
+    }, {
+      "id": "omim",
+      "name": "Online Mendelian Inheritance in Man",
+      "url": "https://www.omim.org",
+      "namespacePrefix": "OMIM"
+    }],
+    "phenopacketSchemaVersion": "1.0.0-RC3",
+    "externalReferences": [{
+      "id": "PMID:30655368",
+      "description": "Molecular mechanisms of bleeding disorder-associated GFI1BQ287* mutation and its affected pathways in megakaryocytes and platelets"
+    }]
+  }
+}
\ No newline at end of file
diff --git a/notebooks/PRIORIT/input/Supplementary1_PRIORIT.xlsx b/notebooks/PRIORIT/input/Supplementary1_PRIORIT.xlsx
index 6b69fddf0..1a29926f9 100644
Binary files a/notebooks/PRIORIT/input/Supplementary1_PRIORIT.xlsx and b/notebooks/PRIORIT/input/Supplementary1_PRIORIT.xlsx differ
diff --git a/notebooks/PRIORIT/priori-t.ipynb b/notebooks/PRIORIT/priori-t.ipynb
index 15b8031aa..9013f6c81 100644
--- a/notebooks/PRIORIT/priori-t.ipynb
+++ b/notebooks/PRIORIT/priori-t.ipynb
@@ -26,6 +26,23 @@
     "- Lee H, et al. (2014) Clinical exome sequencing for genetic identification of rare Mendelian disorders. JAMA 312:1880-7.  PMID:25326637"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "c1c7804b-7ad7-40c7-ad94-029a34b46611",
+   "metadata": {},
+   "source": [
+    "## Probands\n",
+    "Some probands were excluded because it was npot possible to determine the specific (genetic) diagnosis from the available input data or because the diagnosis was not unambiguous. Cases with mixed diagnoses were excluded because cosegregation data was not presented that would allow an unambiguous diagnosis\n",
+    "- TCS021 (mixed phenotype)\n",
+    "- TCS022 (unclear disease-level diagnosis)\n",
+    "- TCS024 (mixed phenotype)\n",
+    "- TCS025 (mixed phenotype)\n",
+    "- TCS041 (Systemic capillary leak syndrome and TLN1 association not confirmed)\n",
+    "- TCS051\n",
+    "- TCS053\n",
+    "- TCS056"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 8,
@@ -427,9 +444,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "pstore_env",
+   "display_name": "ps_venv",
    "language": "python",
-   "name": "pstore_env"
+   "name": "ps_venv"
   },
   "language_info": {
    "codemirror_mode": {
@@ -441,7 +458,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.3"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,