From dbd30a2b7dae0954ebd10f87a61acb4094dbde05 Mon Sep 17 00:00:00 2001 From: Peter Robinson Date: Sat, 25 Nov 2023 19:11:03 +0100 Subject: [PATCH] MAPK8IP3 --- docs/collections.md | 3 + .../Iwasawa_2019_MAPK8IP3_PMID_30945334.ipynb | 308 +++++------ notebooks/MAPK8IP3/MAPK8IP3_cases.ipynb | 485 ++++-------------- notebooks/MAPK8IP3/MAPK8IP3_summary.ipynb | 263 ++-------- .../Platzer_2019_MAPK8IP3_PMID_30612693.ipynb | 269 +++++----- .../phenopackets/PMID_30612693_1.json | 207 ++++++++ .../phenopackets/PMID_30612693_10.json | 155 ++++++ .../phenopackets/PMID_30612693_11.json | 174 +++++++ .../phenopackets/PMID_30612693_12.json | 208 ++++++++ .../phenopackets/PMID_30612693_13.json | 401 +++++++++++++++ .../phenopackets/PMID_30612693_2.json | 176 +++++++ .../phenopackets/PMID_30612693_3.json | 183 +++++++ .../phenopackets/PMID_30612693_4.json | 261 ++++++++++ .../phenopackets/PMID_30612693_5.json | 194 +++++++ .../phenopackets/PMID_30612693_6.json | 162 ++++++ .../phenopackets/PMID_30612693_7.json | 157 ++++++ .../phenopackets/PMID_30612693_8.json | 199 +++++++ .../phenopackets/PMID_30612693_9.json | 210 ++++++++ .../PMID_30945334_Individual1.json | 203 ++++++++ .../PMID_30945334_Individual2.json | 209 ++++++++ .../PMID_30945334_Individual3.json | 191 +++++++ .../PMID_30945334_Individual4.json | 195 +++++++ .../PMID_30945334_Individual5.json | 226 ++++++++ .../PMID_pending_IndividualA.json | 271 ++++++++++ .../phenopackets/PMID_pending_PatientS12.json | 139 +++++ 25 files changed, 4533 insertions(+), 916 deletions(-) create mode 100644 notebooks/MAPK8IP3/phenopackets/PMID_30612693_1.json create mode 100644 notebooks/MAPK8IP3/phenopackets/PMID_30612693_10.json create mode 100644 notebooks/MAPK8IP3/phenopackets/PMID_30612693_11.json create mode 100644 notebooks/MAPK8IP3/phenopackets/PMID_30612693_12.json create mode 100644 notebooks/MAPK8IP3/phenopackets/PMID_30612693_13.json create mode 100644 notebooks/MAPK8IP3/phenopackets/PMID_30612693_2.json create mode 100644 notebooks/MAPK8IP3/phenopackets/PMID_30612693_3.json create mode 100644 notebooks/MAPK8IP3/phenopackets/PMID_30612693_4.json create mode 100644 notebooks/MAPK8IP3/phenopackets/PMID_30612693_5.json create mode 100644 notebooks/MAPK8IP3/phenopackets/PMID_30612693_6.json create mode 100644 notebooks/MAPK8IP3/phenopackets/PMID_30612693_7.json create mode 100644 notebooks/MAPK8IP3/phenopackets/PMID_30612693_8.json create mode 100644 notebooks/MAPK8IP3/phenopackets/PMID_30612693_9.json create mode 100644 notebooks/MAPK8IP3/phenopackets/PMID_30945334_Individual1.json create mode 100644 notebooks/MAPK8IP3/phenopackets/PMID_30945334_Individual2.json create mode 100644 notebooks/MAPK8IP3/phenopackets/PMID_30945334_Individual3.json create mode 100644 notebooks/MAPK8IP3/phenopackets/PMID_30945334_Individual4.json create mode 100644 notebooks/MAPK8IP3/phenopackets/PMID_30945334_Individual5.json create mode 100644 notebooks/MAPK8IP3/phenopackets/PMID_pending_IndividualA.json create mode 100644 notebooks/MAPK8IP3/phenopackets/PMID_pending_PatientS12.json diff --git a/docs/collections.md b/docs/collections.md index 6e52ce19d..2faccb291 100644 --- a/docs/collections.md +++ b/docs/collections.md @@ -17,6 +17,9 @@ were mainly created using the Python library [pyphetools](https://github.com/mon | [GLI3](https://github.com/monarch-initiative/phenopacket-store/tree/main/notebooks/GLI3){:target="_blank"} | 77 phenopackets; [Greig cephalopolysyndactyly syndrome](https://omim.org/entry/175700){:target="_blank"}, [Pallister-Hall syndrome](https://omim.org/entry/146510){:target="_blank"}, [Polydactyly, postaxial, types A1 and B](https://omim.org/entry/174200){:target="_blank"} | | [KDM6B](https://github.com/monarch-initiative/phenopacket-store/blob/main/notebooks/KDM6B/KDM6B_PMID_37196654.ipynb){:target="_blank"} |73 phenopackets; [Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities](https://omim.org/entry/ 618505){:target="_blank"} | | [LIRICAL](https://github.com/monarch-initiative/phenopacket-store/blob/main/notebooks/LIRICAL/LIRICAL.ipynb){:target="_blank"} | 384 phenopackets, various diseases | +|[MAKP8IP3](https://github.com/monarch-initiative/phenopacket-store/blob/main/notebooks/MAPK8IP3/MAPK8IP3_summary.ipynb){:target="_blank"} | 20 phenopackets,[Neurodevelopmental disorder with or without variable brain abnormalities](https://omim.org/entry/618443){:target="_blank"}| + + diff --git a/notebooks/MAPK8IP3/Iwasawa_2019_MAPK8IP3_PMID_30945334.ipynb b/notebooks/MAPK8IP3/Iwasawa_2019_MAPK8IP3_PMID_30945334.ipynb index 02f75dbc7..1058ba780 100644 --- a/notebooks/MAPK8IP3/Iwasawa_2019_MAPK8IP3_PMID_30945334.ipynb +++ b/notebooks/MAPK8IP3/Iwasawa_2019_MAPK8IP3_PMID_30945334.ipynb @@ -23,7 +23,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Using pyphetools version 0.5.5\n" + "Using pyphetools version 0.8.28\n" ] } ], @@ -33,12 +33,12 @@ "from google.protobuf.json_format import Parse, ParseDict\n", "import pandas as pd\n", "pd.set_option('display.max_colwidth', None) # show entire column contents, important!\n", - "from collections import defaultdict\n", + "from IPython.display import display, HTML\n", "from pyphetools.creation import *\n", "from pyphetools.visualization import *\n", - "import importlib.metadata\n", - "__version__ = importlib.metadata.version(\"pyphetools\")\n", - "print(f\"Using pyphetools version {__version__}\")" + "from pyphetools.validation import *\n", + "import pyphetools\n", + "print(f\"Using pyphetools version {pyphetools.__version__}\")" ] }, { @@ -54,15 +54,25 @@ "execution_count": 2, "id": "15f56d1e-55c8-450c-9384-44159ad71994", "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "HPO version 2023-10-09\n" + ] + } + ], "source": [ + "PMID=\"PMID:30945334\"\n", + "title = \"Recurrent de novo MAPK8IP3 variants cause neurological phenotypes\"\n", "parser = HpoParser()\n", "hpo_cr = parser.get_hpo_concept_recognizer()\n", "hpo_version = parser.get_version()\n", - "pmid=\"PMID:30945334\"\n", - "title = \"Recurrent de novo MAPK8IP3 variants cause neurological phenotypes\"\n", - "metadata = MetaData(created_by=\"ORCID:0000-0002-0736-9199\", pmid=pmid, pubmed_title=title)\n", - "metadata.default_versions_with_hpo(version=hpo_version)" + "hpo_ontology = parser.get_ontology()\n", + "metadata = MetaData(created_by=\"ORCID:0000-0002-0736-9199\", pmid=PMID, pubmed_title=title)\n", + "metadata.default_versions_with_hpo(version=hpo_version)\n", + "print(f\"HPO version {hpo_version}\")" ] }, { @@ -451,17 +461,17 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 6, "id": "85176968-a6d2-4000-a768-ff9e6fdcf56e", "metadata": {}, "outputs": [], "source": [ - "column_mapper_d = defaultdict(ColumnMapper)" + "column_mapper_d = {}" ] }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 7, "id": "6297f5eb-e924-4bb9-a431-ed020af5d787", "metadata": {}, "outputs": [], @@ -476,7 +486,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 8, "id": "1cbdd929-52c2-4171-9c7f-2987c1b14888", "metadata": {}, "outputs": [], @@ -489,7 +499,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 9, "id": "1941813e-31a3-4621-83e0-a1f4faeb2dcc", "metadata": {}, "outputs": [], @@ -502,7 +512,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 10, "id": "269302e6-b01c-410d-8ac7-7e13f4aae5af", "metadata": {}, "outputs": [], @@ -516,7 +526,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 11, "id": "1974b8b0-d4b8-41e7-b78d-f5d643cce302", "metadata": {}, "outputs": [], @@ -530,7 +540,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 12, "id": "486db1b4-7c8c-4add-97bb-aba9fc6d9b39", "metadata": {}, "outputs": [ @@ -568,7 +578,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 13, "id": "b1c74190-1c95-4509-a995-7fb20951655b", "metadata": {}, "outputs": [], @@ -582,7 +592,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 14, "id": "07840aef-68dc-4772-91ef-318455b0b7cc", "metadata": {}, "outputs": [], @@ -598,7 +608,7 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 15, "id": "3ac1ed63-858d-4aa3-a90d-07f1b7a67c02", "metadata": {}, "outputs": [], @@ -615,14 +625,14 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 17, "id": "9f3d91eb-27d2-439a-9a2d-ea1ac7f85282", "metadata": {}, "outputs": [], "source": [ "# Others\n", "other_d = {'upper slanted palpebral fissures': 'Upslanted palpebral fissure'}\n", - "otherMapper = CustomColumnMapper(concept_recognizer=hpo_cr, custom_map_d=other_d)\n", + "otherMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=other_d)\n", "#otherMapper.preview_column(dft['Others'])\n", "column_mapper_d['Others'] = otherMapper" ] @@ -639,7 +649,7 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": 18, "id": "1690a779-bdd3-4996-83ff-110166e30c92", "metadata": {}, "outputs": [ @@ -654,7 +664,7 @@ "Name: NM_001318852, dtype: object" ] }, - "execution_count": 16, + "execution_count": 18, "metadata": {}, "output_type": "execute_result" } @@ -677,36 +687,23 @@ "dft['NM_001318852']" ] }, - { - "cell_type": "code", - "execution_count": 18, - "id": "67de5e99-8bcd-42c7-93f7-730e076b1227", - "metadata": {}, - "outputs": [], - "source": [ - "genome = 'hg38'\n", - "transcript='NM_001318852.2'\n", - "varMapper = VariantColumnMapper(assembly=genome,\n", - " column_name='NM_001318852', \n", - " transcript=transcript, \n", - " default_genotype='heterozygous')\n", - "#varMapper.preview_column(dft['NM_001318852'])" - ] - }, - { - "cell_type": "markdown", - "id": "8be68a08-7577-4724-a908-cf934cb44e5e", - "metadata": {}, - "source": [ - "

Demographic data

" - ] - }, { "cell_type": "code", "execution_count": 19, - "id": "59e4f966-f5cf-46d8-a3d4-cdf3d074d6e2", + "id": "67de5e99-8bcd-42c7-93f7-730e076b1227", "metadata": {}, "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.1735C>T/NM_001318852.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.1735C>T/NM_001318852.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.1735C>T/NM_001318852.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.3439C>T/NM_001318852.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.3439C>T/NM_001318852.2?content-type=application%2Fjson\n" + ] + }, { "data": { "text/html": [ @@ -728,41 +725,41 @@ " \n", " \n", " \n", - " original column contents\n", - " age\n", + " variant\n", " \n", " \n", " \n", " \n", " 0\n", - " 29\n", - " P29Y\n", + " variation_descriptor {\\n id: \"var_KIsfzFBQLRPdvRmtLteqHbcHu\"\\n gene_context {\\n value_id: \"HGNC:6884\"\\n symbol: \"MAPK8IP3\"\\n }\\n expressions {\\n syntax: \"hgvs.c\"\\n value: \"NM_001318852.2:c.1735C>T\"\\n }\\n expressions {\\n syntax: \"hgvs.g\"\\n value: \"NC_000016.10:g.1762843C>T\"\\n }\\n vcf_record {\\n genome_assembly: \"hg38\"\\n chrom: \"chr16\"\\n pos: 1762843\\n ref: \"C\"\\n alt: \"T\"\\n }\\n molecule_context: genomic\\n allelic_state {\\n id: \"GENO:0000135\"\\n label: \"heterozygous\"\\n }\\n}\\n\n", " \n", " \n", " 1\n", - " 27\n", - " P27Y\n", + " variation_descriptor {\\n id: \"var_KIsfzFBQLRPdvRmtLteqHbcHu\"\\n gene_context {\\n value_id: \"HGNC:6884\"\\n symbol: \"MAPK8IP3\"\\n }\\n expressions {\\n syntax: \"hgvs.c\"\\n value: \"NM_001318852.2:c.1735C>T\"\\n }\\n expressions {\\n syntax: \"hgvs.g\"\\n value: \"NC_000016.10:g.1762843C>T\"\\n }\\n vcf_record {\\n genome_assembly: \"hg38\"\\n chrom: \"chr16\"\\n pos: 1762843\\n ref: \"C\"\\n alt: \"T\"\\n }\\n molecule_context: genomic\\n allelic_state {\\n id: \"GENO:0000135\"\\n label: \"heterozygous\"\\n }\\n}\\n\n", " \n", " \n", " 2\n", - " 16\n", - " P16Y\n", + " variation_descriptor {\\n id: \"var_KIsfzFBQLRPdvRmtLteqHbcHu\"\\n gene_context {\\n value_id: \"HGNC:6884\"\\n symbol: \"MAPK8IP3\"\\n }\\n expressions {\\n syntax: \"hgvs.c\"\\n value: \"NM_001318852.2:c.1735C>T\"\\n }\\n expressions {\\n syntax: \"hgvs.g\"\\n value: \"NC_000016.10:g.1762843C>T\"\\n }\\n vcf_record {\\n genome_assembly: \"hg38\"\\n chrom: \"chr16\"\\n pos: 1762843\\n ref: \"C\"\\n alt: \"T\"\\n }\\n molecule_context: genomic\\n allelic_state {\\n id: \"GENO:0000135\"\\n label: \"heterozygous\"\\n }\\n}\\n\n", " \n", " \n", " 3\n", - " 5\n", - " P5Y\n", + " variation_descriptor {\\n id: \"var_vyuwdOtOlsiCylFuirVeyRrxv\"\\n gene_context {\\n value_id: \"HGNC:6884\"\\n symbol: \"MAPK8IP3\"\\n }\\n expressions {\\n syntax: \"hgvs.c\"\\n value: \"NM_001318852.2:c.3439C>T\"\\n }\\n expressions {\\n syntax: \"hgvs.g\"\\n value: \"NC_000016.10:g.1767834C>T\"\\n }\\n vcf_record {\\n genome_assembly: \"hg38\"\\n chrom: \"chr16\"\\n pos: 1767834\\n ref: \"C\"\\n alt: \"T\"\\n }\\n molecule_context: genomic\\n allelic_state {\\n id: \"GENO:0000135\"\\n label: \"heterozygous\"\\n }\\n}\\n\n", + " \n", + " \n", + " 4\n", + " variation_descriptor {\\n id: \"var_vyuwdOtOlsiCylFuirVeyRrxv\"\\n gene_context {\\n value_id: \"HGNC:6884\"\\n symbol: \"MAPK8IP3\"\\n }\\n expressions {\\n syntax: \"hgvs.c\"\\n value: \"NM_001318852.2:c.3439C>T\"\\n }\\n expressions {\\n syntax: \"hgvs.g\"\\n value: \"NC_000016.10:g.1767834C>T\"\\n }\\n vcf_record {\\n genome_assembly: \"hg38\"\\n chrom: \"chr16\"\\n pos: 1767834\\n ref: \"C\"\\n alt: \"T\"\\n }\\n molecule_context: genomic\\n allelic_state {\\n id: \"GENO:0000135\"\\n label: \"heterozygous\"\\n }\\n}\\n\n", " \n", " \n", "\n", "" ], "text/plain": [ - " original column contents age\n", - "0 29 P29Y\n", - "1 27 P27Y\n", - "2 16 P16Y\n", - "3 5 P5Y" + " variant\n", + "0 variation_descriptor {\\n id: \"var_KIsfzFBQLRPdvRmtLteqHbcHu\"\\n gene_context {\\n value_id: \"HGNC:6884\"\\n symbol: \"MAPK8IP3\"\\n }\\n expressions {\\n syntax: \"hgvs.c\"\\n value: \"NM_001318852.2:c.1735C>T\"\\n }\\n expressions {\\n syntax: \"hgvs.g\"\\n value: \"NC_000016.10:g.1762843C>T\"\\n }\\n vcf_record {\\n genome_assembly: \"hg38\"\\n chrom: \"chr16\"\\n pos: 1762843\\n ref: \"C\"\\n alt: \"T\"\\n }\\n molecule_context: genomic\\n allelic_state {\\n id: \"GENO:0000135\"\\n label: \"heterozygous\"\\n }\\n}\\n\n", + "1 variation_descriptor {\\n id: \"var_KIsfzFBQLRPdvRmtLteqHbcHu\"\\n gene_context {\\n value_id: \"HGNC:6884\"\\n symbol: \"MAPK8IP3\"\\n }\\n expressions {\\n syntax: \"hgvs.c\"\\n value: \"NM_001318852.2:c.1735C>T\"\\n }\\n expressions {\\n syntax: \"hgvs.g\"\\n value: \"NC_000016.10:g.1762843C>T\"\\n }\\n vcf_record {\\n genome_assembly: \"hg38\"\\n chrom: \"chr16\"\\n pos: 1762843\\n ref: \"C\"\\n alt: \"T\"\\n }\\n molecule_context: genomic\\n allelic_state {\\n id: \"GENO:0000135\"\\n label: \"heterozygous\"\\n }\\n}\\n\n", + "2 variation_descriptor {\\n id: \"var_KIsfzFBQLRPdvRmtLteqHbcHu\"\\n gene_context {\\n value_id: \"HGNC:6884\"\\n symbol: \"MAPK8IP3\"\\n }\\n expressions {\\n syntax: \"hgvs.c\"\\n value: \"NM_001318852.2:c.1735C>T\"\\n }\\n expressions {\\n syntax: \"hgvs.g\"\\n value: \"NC_000016.10:g.1762843C>T\"\\n }\\n vcf_record {\\n genome_assembly: \"hg38\"\\n chrom: \"chr16\"\\n pos: 1762843\\n ref: \"C\"\\n alt: \"T\"\\n }\\n molecule_context: genomic\\n allelic_state {\\n id: \"GENO:0000135\"\\n label: \"heterozygous\"\\n }\\n}\\n\n", + "3 variation_descriptor {\\n id: \"var_vyuwdOtOlsiCylFuirVeyRrxv\"\\n gene_context {\\n value_id: \"HGNC:6884\"\\n symbol: \"MAPK8IP3\"\\n }\\n expressions {\\n syntax: \"hgvs.c\"\\n value: \"NM_001318852.2:c.3439C>T\"\\n }\\n expressions {\\n syntax: \"hgvs.g\"\\n value: \"NC_000016.10:g.1767834C>T\"\\n }\\n vcf_record {\\n genome_assembly: \"hg38\"\\n chrom: \"chr16\"\\n pos: 1767834\\n ref: \"C\"\\n alt: \"T\"\\n }\\n molecule_context: genomic\\n allelic_state {\\n id: \"GENO:0000135\"\\n label: \"heterozygous\"\\n }\\n}\\n\n", + "4 variation_descriptor {\\n id: \"var_vyuwdOtOlsiCylFuirVeyRrxv\"\\n gene_context {\\n value_id: \"HGNC:6884\"\\n symbol: \"MAPK8IP3\"\\n }\\n expressions {\\n syntax: \"hgvs.c\"\\n value: \"NM_001318852.2:c.3439C>T\"\\n }\\n expressions {\\n syntax: \"hgvs.g\"\\n value: \"NC_000016.10:g.1767834C>T\"\\n }\\n vcf_record {\\n genome_assembly: \"hg38\"\\n chrom: \"chr16\"\\n pos: 1767834\\n ref: \"C\"\\n alt: \"T\"\\n }\\n molecule_context: genomic\\n allelic_state {\\n id: \"GENO:0000135\"\\n label: \"heterozygous\"\\n }\\n}\\n" ] }, "execution_count": 19, @@ -771,14 +768,31 @@ } ], "source": [ - "ageMapper = AgeColumnMapper.by_year('Age (yr)')\n", - "ageMapper.preview_column(dft['Age (yr)'])" + "transcript='NM_001318852.2'\n", + "vvalidator = VariantValidator(genome_build=\"hg38\", transcript=transcript)\n", + "var_d = {}\n", + "for v in dft['NM_001318852']:\n", + " var = vvalidator.encode_hgvs(v)\n", + " var_d[v] = var\n", + "\n", + "varMapper = VariantColumnMapper(variant_d=var_d,\n", + " variant_column_name='NM_001318852', \n", + " default_genotype='heterozygous')\n", + "#varMapper.preview_column(dft['NM_001318852'])" + ] + }, + { + "cell_type": "markdown", + "id": "8be68a08-7577-4724-a908-cf934cb44e5e", + "metadata": {}, + "source": [ + "

Demographic data

" ] }, { "cell_type": "code", "execution_count": 20, - "id": "2f3778e9-f98a-43b1-9b2b-924a7d84c7cb", + "id": "59e4f966-f5cf-46d8-a3d4-cdf3d074d6e2", "metadata": {}, "outputs": [ { @@ -803,46 +817,40 @@ " \n", " \n", " original column contents\n", - " sex\n", + " age\n", " \n", " \n", " \n", " \n", " 0\n", - " Male\n", - " MALE\n", + " 29\n", + " P29Y\n", " \n", " \n", " 1\n", - " Female\n", - " FEMALE\n", + " 27\n", + " P27Y\n", " \n", " \n", " 2\n", - " Male\n", - " MALE\n", + " 16\n", + " P16Y\n", " \n", " \n", " 3\n", - " Male\n", - " MALE\n", - " \n", - " \n", - " 4\n", - " Female\n", - " FEMALE\n", + " 5\n", + " P5Y\n", " \n", " \n", "\n", "" ], "text/plain": [ - " original column contents sex\n", - "0 Male MALE\n", - "1 Female FEMALE\n", - "2 Male MALE\n", - "3 Male MALE\n", - "4 Female FEMALE" + " original column contents age\n", + "0 29 P29Y\n", + "1 27 P27Y\n", + "2 16 P16Y\n", + "3 5 P5Y" ] }, "execution_count": 20, @@ -850,14 +858,25 @@ "output_type": "execute_result" } ], + "source": [ + "ageMapper = AgeColumnMapper.by_year('Age (yr)')\n", + "#ageMapper.preview_column(dft['Age (yr)'])" + ] + }, + { + "cell_type": "code", + "execution_count": 22, + "id": "2f3778e9-f98a-43b1-9b2b-924a7d84c7cb", + "metadata": {}, + "outputs": [], "source": [ "sexMapper = SexColumnMapper(male_symbol='Male', female_symbol='Female', column_name='Sex')\n", - "sexMapper.preview_column(dft['Sex'])\n" + "#sexMapper.preview_column(dft['Sex'])" ] }, { "cell_type": "code", - "execution_count": 21, + "execution_count": 23, "id": "c1ff6ec8-45e9-4a98-96d5-3cf42c4eaa73", "metadata": {}, "outputs": [], @@ -868,85 +887,65 @@ " sexmapper=sexMapper,\n", " metadata=metadata,\n", " variant_mapper=varMapper,\n", - " pmid=pmid)\n", + " pmid=PMID)\n", "disease_id = \"OMIM:618443\"\n", "disease_label = \"Neurodevelopmental disorder with or without variable brain abnormalities\"\n", - "encoder.set_disease(disease_id=disease_id, label=disease_label)" + "disease = Disease(disease_id=disease_id, disease_label=disease_label)\n", + "encoder.set_disease(disease=disease)" ] }, { "cell_type": "code", - "execution_count": 22, + "execution_count": 25, "id": "655399ac-9de5-421f-b6c8-05dadd26ca0c", "metadata": {}, "outputs": [ { - "name": "stdout", - "output_type": "stream", - "text": [ - "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.1735C>T/NM_001318852.2?content-type=application%2Fjson\n", - "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.1735C>T/NM_001318852.2?content-type=application%2Fjson\n", - "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.1735C>T/NM_001318852.2?content-type=application%2Fjson\n", - "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.3439C>T/NM_001318852.2?content-type=application%2Fjson\n", - "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.3439C>T/NM_001318852.2?content-type=application%2Fjson\n" - ] + "data": { + "text/html": [ + "

Cohort validation

\n", + "

Errors found with 5 of 5 phenopackets.

\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "
Error counts
LevelError categoryCount
WARNINGREDUNDANT6
INFORMATIONNOT_MEASURED30
\n", + "

A total of 36 issues were fixed and no individual was removed from the cohort.

" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" } ], "source": [ - "individuals = encoder.get_individuals()" + "individuals = encoder.get_individuals()\n", + "cvalidator = CohortValidator(cohort=individuals, ontology=hpo_ontology, min_hpo=1, allelic_requirement=AllelicRequirement.MONO_ALLELIC)\n", + "qc = QcVisualizer(ontology=hpo_ontology, cohort_validator=cvalidator)\n", + "display(HTML(qc.to_summary_html()))" ] }, { "cell_type": "code", - "execution_count": 23, + "execution_count": 27, "id": "a9cdf725-c774-4733-b328-820c0ca91bde", "metadata": {}, "outputs": [ { "data": { "text/html": [ - "\n", - "\n", + "
\n", "\n", - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "
5 phenopackets - PMID:30945334 (n=5)
IndividualDiseaseGenotypePhenotypic features
Individual 1 (MALE; P29Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.1735C>T (heterozygous)Motor delay (HP:0001270); Delayed ability to walk (HP:0031936); Spastic diplegia (HP:0001264); Cerebral atrophy (HP:0002059); Delayed CNS myelination (HP:0002188); Thin upper lip vermilion (HP:0000219); Round face (HP:0000311); Short stature (HP:0004322); Obesity (HP:0001513); Precocious puberty (HP:0000826); Intellectual disability, severe (HP:0010864); Delayed speech and language development (HP:0000750); Loss of ambulation (HP:0002505)
Individual 2 (FEMALE; P27Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.1735C>T (heterozygous)Motor delay (HP:0001270); Delayed ability to roll over (HP:0032989); Delayed ability to walk (HP:0031936); Spastic diplegia (HP:0001264); Cerebral atrophy (HP:0002059); Delayed CNS myelination (HP:0002188); Thin upper lip vermilion (HP:0000219); Round face (HP:0000311); Short stature (HP:0004322); Obesity (HP:0001513); Precocious puberty (HP:0000826); Intellectual disability, severe (HP:0010864); Delayed speech and language development (HP:0000750); Loss of ambulation (HP:0002505)
Individual 3 (MALE; P16Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.1735C>T (heterozygous)Motor delay (HP:0001270); Delayed ability to sit (HP:0025336); Delayed ability to walk (HP:0031936); Spastic diplegia (HP:0001264); Prominent nasal bridge (HP:0000426); Thin upper lip vermilion (HP:0000219); Short stature (HP:0004322); Obesity (HP:0001513); Intellectual disability, profound (HP:0002187); Delayed speech and language development (HP:0000750); Loss of ambulation (HP:0002505)
Individual 4 (MALE; P5Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.3439C>T (heterozygous)Motor delay (HP:0001270); Persistent head lag (HP:0032988); Delayed ability to roll over (HP:0032989); Delayed ability to sit (HP:0025336); Delayed ability to walk (HP:0031936); Autistic behavior (HP:0000729); Infantile muscular hypotonia (HP:0008947); Cerebral atrophy (HP:0002059); Prominent nasal bridge (HP:0000426); Thin upper lip vermilion (HP:0000219); Round face (HP:0000311); Short stature (HP:0004322); Intellectual disability, severe (HP:0010864); Absent speech (HP:0001344); Delayed gross motor development (HP:0002194)
Individual 5 (FEMALE; P5Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001374425.1:c.272G>A (heterozygous)Motor delay (HP:0001270); Persistent head lag (HP:0032988); Delayed ability to sit (HP:0025336); Delayed ability to walk (HP:0031936); Spastic diplegia (HP:0001264); Autistic behavior (HP:0000729); Infantile muscular hypotonia (HP:0008947); Cerebral atrophy (HP:0002059); Delayed CNS myelination (HP:0002188); Prominent nasal bridge (HP:0000426); Thin upper lip vermilion (HP:0000219); Round face (HP:0000311); Intellectual disability, severe (HP:0010864); Absent speech (HP:0001344); Thick eyebrow (HP:0000574); Upslanted palpebral fissure (HP:0000582); Anteverted nares (HP:0000463); Short philtrum (HP:0000322)
\n" + "IndividualDiseaseGenotypePhenotypic features\n", + "Individual 1 (MALE; P29Y)Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)NM_001318852.2:c.1735C>T (heterozygous)Delayed ability to walk (HP:0031936); Spastic diplegia (HP:0001264); Cerebral atrophy (HP:0002059); Delayed CNS myelination (HP:0002188); Thin upper lip vermilion (HP:0000219); Round face (HP:0000311); Short stature (HP:0004322); Obesity (HP:0001513); Precocious puberty (HP:0000826); Intellectual disability, severe (HP:0010864); Delayed speech and language development (HP:0000750); Loss of ambulation (HP:0002505); excluded: Persistent head lag (HP:0032988); excluded: Delayed ability to sit (HP:0025336)\n", + "Individual 2 (FEMALE; P27Y)Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)NM_001318852.2:c.1735C>T (heterozygous)Delayed ability to roll over (HP:0032989); Delayed ability to walk (HP:0031936); Spastic diplegia (HP:0001264); Cerebral atrophy (HP:0002059); Delayed CNS myelination (HP:0002188); Thin upper lip vermilion (HP:0000219); Round face (HP:0000311); Short stature (HP:0004322); Obesity (HP:0001513); Precocious puberty (HP:0000826); Intellectual disability, severe (HP:0010864); Delayed speech and language development (HP:0000750); Loss of ambulation (HP:0002505); excluded: Persistent head lag (HP:0032988); excluded: Delayed ability to sit (HP:0025336)\n", + "Individual 3 (MALE; P16Y)Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)NM_001318852.2:c.1735C>T (heterozygous)Delayed ability to sit (HP:0025336); Delayed ability to walk (HP:0031936); Spastic diplegia (HP:0001264); Prominent nasal bridge (HP:0000426); Thin upper lip vermilion (HP:0000219); Short stature (HP:0004322); Obesity (HP:0001513); Intellectual disability, profound (HP:0002187); Delayed speech and language development (HP:0000750); Loss of ambulation (HP:0002505); excluded: Persistent head lag (HP:0032988); excluded: Delayed ability to roll over (HP:0032989)\n", + "Individual 4 (MALE; P5Y)Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)NM_001318852.2:c.3439C>T (heterozygous)Persistent head lag (HP:0032988); Delayed ability to roll over (HP:0032989); Delayed ability to sit (HP:0025336); Delayed ability to walk (HP:0031936); Autistic behavior (HP:0000729); Infantile muscular hypotonia (HP:0008947); Cerebral atrophy (HP:0002059); Prominent nasal bridge (HP:0000426); Thin upper lip vermilion (HP:0000219); Round face (HP:0000311); Short stature (HP:0004322); Intellectual disability, severe (HP:0010864); Absent speech (HP:0001344)\n", + "Individual 5 (FEMALE; P5Y)Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)NM_001318852.2:c.3439C>T (heterozygous)Persistent head lag (HP:0032988); Delayed ability to sit (HP:0025336); Delayed ability to walk (HP:0031936); Spastic diplegia (HP:0001264); Autistic behavior (HP:0000729); Infantile muscular hypotonia (HP:0008947); Cerebral atrophy (HP:0002059); Delayed CNS myelination (HP:0002188); Prominent nasal bridge (HP:0000426); Thin upper lip vermilion (HP:0000219); Round face (HP:0000311); Intellectual disability, severe (HP:0010864); Absent speech (HP:0001344); Thick eyebrow (HP:0000574); Upslanted palpebral fissure (HP:0000582); Anteverted nares (HP:0000463); Short philtrum (HP:0000322); excluded: Delayed ability to roll over (HP:0032989)\n", + "" ], "text/plain": [ "" @@ -957,16 +956,14 @@ } ], "source": [ - "from IPython.display import HTML, display\n", - "\n", - "phenopackets = [i.to_ga4gh_phenopacket(metadata=metadata.to_ga4gh()) for i in individuals]\n", - "table = PhenopacketTable(phenopacket_list=phenopackets)\n", + "individuals = cvalidator.get_error_free_individual_list()\n", + "table = PhenopacketTable(individual_list=individuals, metadata=metadata)\n", "display(HTML(table.to_html()))" ] }, { "cell_type": "code", - "execution_count": 24, + "execution_count": 28, "id": "eba007c0-f07e-422f-846b-10725bf0d362", "metadata": {}, "outputs": [ @@ -979,7 +976,9 @@ } ], "source": [ - "Individual.output_individuals_as_phenopackets(individual_list=individuals, pmid=pmid, metadata=metadata.to_ga4gh(), outdir=\"phenopackets\")" + "Individual.output_individuals_as_phenopackets(individual_list=individuals, \n", + " metadata=metadata, \n", + " outdir=\"phenopackets\")" ] }, { @@ -988,7 +987,10 @@ "id": "1e6a23a7-ba87-4502-9f23-23086cf0e7c7", "metadata": {}, "outputs": [], - "source": [] + "source": [ + "# pxf validate --hpo hp.json *.json\n", + "# no errors" + ] } ], "metadata": { @@ -1007,7 +1009,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.12" + "version": "3.11.3" } }, "nbformat": 4, diff --git a/notebooks/MAPK8IP3/MAPK8IP3_cases.ipynb b/notebooks/MAPK8IP3/MAPK8IP3_cases.ipynb index 6b860c452..1f6d65f42 100644 --- a/notebooks/MAPK8IP3/MAPK8IP3_cases.ipynb +++ b/notebooks/MAPK8IP3/MAPK8IP3_cases.ipynb @@ -19,7 +19,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Using pyphetools version 0.5.5\n" + "Using pyphetools version 0.8.28\n" ] } ], @@ -29,11 +29,12 @@ "from google.protobuf.json_format import Parse, ParseDict\n", "import pandas as pd\n", "pd.set_option('display.max_colwidth', None) # show entire column contents, important!\n", - "from collections import defaultdict\n", + "from IPython.display import display, HTML\n", "from pyphetools.creation import *\n", - "import importlib.metadata\n", - "__version__ = importlib.metadata.version(\"pyphetools\")\n", - "print(f\"Using pyphetools version {__version__}\")" + "from pyphetools.visualization import *\n", + "from pyphetools.validation import *\n", + "import pyphetools\n", + "print(f\"Using pyphetools version {pyphetools.__version__}\")" ] }, { @@ -50,11 +51,21 @@ "execution_count": 2, "id": "4d08a33e-ffb7-42f0-bcb7-486de3ada9da", "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "HPO version 2023-10-09\n" + ] + } + ], "source": [ "parser = HpoParser()\n", "hpo_cr = parser.get_hpo_concept_recognizer()\n", - "hpo_version = parser.get_version()" + "hpo_version = parser.get_version()\n", + "hpo_ontology = parser.get_ontology()\n", + "print(f\"HPO version {hpo_version}\")" ] }, { @@ -66,6 +77,7 @@ "source": [ "disease_id = \"OMIM:618443\"\n", "disease_label = \"Neurodevelopmental disorder with or without variable brain abnormalities\"\n", + "disease_MAPK8IP3 = Disease(disease_id=disease_id, disease_label=disease_label)\n", "age = \"P12Y\"\n", "sex = \"MALE\"\n", "pmid = \"PMID:34321325\"\n", @@ -78,8 +90,7 @@ " metadata=metadata.to_ga4gh(),\n", " age_at_last_exam=age,\n", " sex=sex,\n", - " disease_id=disease_id,\n", - " disease_label=disease_label)" + " disease=disease_MAPK8IP3)" ] }, { @@ -255,173 +266,12 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 15, "id": "92831301-84ad-4e7b-be68-2827381853d2", "metadata": {}, "outputs": [], "source": [ - "phenopacketA = encoderA.get_phenopacket()" - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "id": "afd625b5-5feb-487f-bc65-b6373326e066", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "{\n", - " \"id\": \"PMID_34321325_Patient_S12\",\n", - " \"subject\": {\n", - " \"id\": \"Patient S12\",\n", - " \"sex\": \"MALE\"\n", - " },\n", - " \"phenotypicFeatures\": [\n", - " {\n", - " \"type\": {\n", - " \"id\": \"HP:0001249\",\n", - " \"label\": \"Intellectual disability\"\n", - " }\n", - " },\n", - " {\n", - " \"type\": {\n", - " \"id\": \"HP:0034183\",\n", - " \"label\": \"Spastic triplegia\"\n", - " }\n", - " }\n", - " ],\n", - " \"interpretations\": [\n", - " {\n", - " \"id\": \"Patient S12\",\n", - " \"progressStatus\": \"SOLVED\",\n", - " \"diagnosis\": {\n", - " \"disease\": {\n", - " \"id\": \"OMIM:618443\",\n", - " \"label\": \"Neurodevelopmental disorder with or without variable brain abnormalities\"\n", - " },\n", - " \"genomicInterpretations\": [\n", - " {\n", - " \"subjectOrBiosampleId\": \"Patient S12\",\n", - " \"interpretationStatus\": \"CAUSATIVE\",\n", - " \"variantInterpretation\": {\n", - " \"variationDescriptor\": {\n", - " \"id\": \"var_BfixpjeiCzVKEAETORjegMQLk\",\n", - " \"geneContext\": {\n", - " \"valueId\": \"HGNC:6884\",\n", - " \"symbol\": \"MAPK8IP3\"\n", - " },\n", - " \"expressions\": [\n", - " {\n", - " \"syntax\": \"hgvs.c\",\n", - " \"value\": \"NM_001318852.2:c.45C>G\"\n", - " },\n", - " {\n", - " \"syntax\": \"hgvs.g\",\n", - " \"value\": \"NC_000016.10:g.1706384C>G\"\n", - " }\n", - " ],\n", - " \"vcfRecord\": {\n", - " \"genomeAssembly\": \"hg38\",\n", - " \"chrom\": \"chr16\",\n", - " \"pos\": \"1706384\",\n", - " \"ref\": \"C\",\n", - " \"alt\": \"G\"\n", - " },\n", - " \"moleculeContext\": \"genomic\",\n", - " \"allelicState\": {\n", - " \"id\": \"GENO:0000135\",\n", - " \"label\": \"heterozygous\"\n", - " }\n", - " }\n", - " }\n", - " }\n", - " ]\n", - " }\n", - " }\n", - " ],\n", - " \"metaData\": {\n", - " \"created\": \"2023-09-19T16:54:49.641586065Z\",\n", - " \"createdBy\": \"ORCID:0000-0002-0736-9199\",\n", - " \"resources\": [\n", - " {\n", - " \"id\": \"geno\",\n", - " \"name\": \"Genotype Ontology\",\n", - " \"url\": \"http://purl.obolibrary.org/obo/geno.owl\",\n", - " \"version\": \"2022-03-05\",\n", - " \"namespacePrefix\": \"GENO\",\n", - " \"iriPrefix\": \"http://purl.obolibrary.org/obo/GENO_\"\n", - " },\n", - " {\n", - " \"id\": \"hgnc\",\n", - " \"name\": \"HUGO Gene Nomenclature Committee\",\n", - " \"url\": \"https://www.genenames.org\",\n", - " \"version\": \"06/01/23\",\n", - " \"namespacePrefix\": \"HGNC\",\n", - " \"iriPrefix\": \"https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/\"\n", - " },\n", - " {\n", - " \"id\": \"omim\",\n", - " \"name\": \"An Online Catalog of Human Genes and Genetic Disorders\",\n", - " \"url\": \"https://www.omim.org\",\n", - " \"version\": \"January 4, 2023\",\n", - " \"namespacePrefix\": \"OMIM\",\n", - " \"iriPrefix\": \"https://www.omim.org/entry/\"\n", - " },\n", - " {\n", - " \"id\": \"so\",\n", - " \"name\": \"Sequence types and features ontology\",\n", - " \"url\": \"http://purl.obolibrary.org/obo/so.obo\",\n", - " \"version\": \"2021-11-22\",\n", - " \"namespacePrefix\": \"SO\",\n", - " \"iriPrefix\": \"http://purl.obolibrary.org/obo/SO_\"\n", - " },\n", - " {\n", - " \"id\": \"hp\",\n", - " \"name\": \"human phenotype ontology\",\n", - " \"url\": \"http://purl.obolibrary.org/obo/hp.owl\",\n", - " \"version\": \"2023-09-01\",\n", - " \"namespacePrefix\": \"HP\",\n", - " \"iriPrefix\": \"http://purl.obolibrary.org/obo/HP_\"\n", - " }\n", - " ],\n", - " \"phenopacketSchemaVersion\": \"2.0\",\n", - " \"externalReferences\": [\n", - " {\n", - " \"id\": \"PMID:34321325\",\n", - " \"reference\": \"https://pubmed.ncbi.nlm.nih.gov/34321325\",\n", - " \"description\": \"Diagnostic yield of chromosomal microarray and trio whole exome sequencing in cryptogenic cerebral palsy\"\n", - " }\n", - " ]\n", - " }\n", - "}\n" - ] - } - ], - "source": [ - "json_string = MessageToJson(phenopacketA)\n", - "print(json_string)" - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "id": "5c23ef39-87fc-4036-a9be-7ae04cc2edd0", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Wrote phenopacket to phenopackets/PMID_34321325_Patient_S12.json\n" - ] - } - ], - "source": [ - "output_directory = \"phenopackets\"\n", - "encoderA.output_phenopacket(outdir=output_directory)" + "individual_A = encoderA.get_individual()" ] }, { @@ -435,13 +285,11 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 9, "id": "0dfa7cdf-82ba-4399-8dd2-2609b40f9e0b", "metadata": {}, "outputs": [], "source": [ - "disease_id = \"OMIM:618443\"\n", - "disease_label = \"Neurodevelopmental disorder with or without variable brain abnormalities\"\n", "age = \"P5Y\"\n", "sex = \"FEMALE\"\n", "pmid = \"PMID:pending\"\n", @@ -454,13 +302,12 @@ " metadata=metadata.to_ga4gh(),\n", " age_at_last_exam=age,\n", " sex=sex,\n", - " disease_id=disease_id,\n", - " disease_label=disease_label)" + " disease=disease_MAPK8IP3)" ] }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 10, "id": "ef39baf2-b088-4f36-b40b-e050b2c1b65f", "metadata": {}, "outputs": [ @@ -508,7 +355,7 @@ "0 HP:0100021 Cerebral palsy True True" ] }, - "execution_count": 12, + "execution_count": 10, "metadata": {}, "output_type": "execute_result" } @@ -532,7 +379,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 11, "id": "e995ad38-a3f8-46fa-b8a5-f8406d56af15", "metadata": {}, "outputs": [ @@ -549,7 +396,7 @@ "'chr16:1762843C>T'" ] }, - "execution_count": 13, + "execution_count": 11, "metadata": {}, "output_type": "execute_result" } @@ -562,7 +409,7 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 12, "id": "833a8175-c548-4b91-8a1d-803f2acf3885", "metadata": {}, "outputs": [], @@ -572,241 +419,95 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 13, "id": "0aaf47fe-2ce8-4eba-9618-f192e354f74e", "metadata": {}, + "outputs": [], + "source": [ + "individual_B = encoderB.get_individual()" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "id": "934ae2e9-72a8-4659-aa76-9d905f2f1494", + "metadata": {}, "outputs": [ { - "name": "stdout", - "output_type": "stream", - "text": [ - "{\n", - " \"id\": \"PMID_pending_Individual_A\",\n", - " \"subject\": {\n", - " \"id\": \"Individual A\",\n", - " \"sex\": \"FEMALE\"\n", - " },\n", - " \"phenotypicFeatures\": [\n", - " {\n", - " \"type\": {\n", - " \"id\": \"HP:0012498\",\n", - " \"label\": \"Nuchal cord\"\n", - " }\n", - " },\n", - " {\n", - " \"type\": {\n", - " \"id\": \"HP:0002333\",\n", - " \"label\": \"Motor deterioration\"\n", - " }\n", - " },\n", - " {\n", - " \"type\": {\n", - " \"id\": \"HP:0000252\",\n", - " \"label\": \"Microcephaly\"\n", - " }\n", - " },\n", - " {\n", - " \"type\": {\n", - " \"id\": \"HP:0001264\",\n", - " \"label\": \"Spastic diplegia\"\n", - " }\n", - " },\n", - " {\n", - " \"type\": {\n", - " \"id\": \"HP:0100021\",\n", - " \"label\": \"Cerebral palsy\"\n", - " }\n", - " },\n", - " {\n", - " \"type\": {\n", - " \"id\": \"HP:0001263\",\n", - " \"label\": \"Global developmental delay\"\n", - " }\n", - " },\n", - " {\n", - " \"type\": {\n", - " \"id\": \"HP:0031936\",\n", - " \"label\": \"Delayed ability to walk\"\n", - " }\n", - " },\n", - " {\n", - " \"type\": {\n", - " \"id\": \"HP:0000750\",\n", - " \"label\": \"Delayed speech and language development\"\n", - " }\n", - " },\n", - " {\n", - " \"type\": {\n", - " \"id\": \"HP:0001321\",\n", - " \"label\": \"Cerebellar hypoplasia\"\n", - " }\n", - " },\n", - " {\n", - " \"type\": {\n", - " \"id\": \"HP:0006872\",\n", - " \"label\": \"Cerebral hypoplasia\"\n", - " }\n", - " },\n", - " {\n", - " \"type\": {\n", - " \"id\": \"HP:0033725\",\n", - " \"label\": \"Thin corpus callosum\"\n", - " }\n", - " },\n", - " {\n", - " \"type\": {\n", - " \"id\": \"HP:0012110\",\n", - " \"label\": \"Hypoplasia of the pons\"\n", - " }\n", - " },\n", - " {\n", - " \"type\": {\n", - " \"id\": \"HP:0034295\",\n", - " \"label\": \"Reduced cerebral white matter volume\"\n", - " }\n", - " },\n", - " {\n", - " \"type\": {\n", - " \"id\": \"HP:0006970\",\n", - " \"label\": \"Periventricular leukomalacia\"\n", - " }\n", - " }\n", - " ],\n", - " \"interpretations\": [\n", - " {\n", - " \"id\": \"Individual A\",\n", - " \"progressStatus\": \"SOLVED\",\n", - " \"diagnosis\": {\n", - " \"disease\": {\n", - " \"id\": \"OMIM:618443\",\n", - " \"label\": \"Neurodevelopmental disorder with or without variable brain abnormalities\"\n", - " },\n", - " \"genomicInterpretations\": [\n", - " {\n", - " \"subjectOrBiosampleId\": \"Individual A\",\n", - " \"interpretationStatus\": \"CAUSATIVE\",\n", - " \"variantInterpretation\": {\n", - " \"variationDescriptor\": {\n", - " \"id\": \"var_dEqaQhEIdjYadVhQrzydwwalj\",\n", - " \"geneContext\": {\n", - " \"valueId\": \"HGNC:6884\",\n", - " \"symbol\": \"MAPK8IP3\"\n", - " },\n", - " \"expressions\": [\n", - " {\n", - " \"syntax\": \"hgvs.c\",\n", - " \"value\": \"NM_001318852.2:c.1735C>T\"\n", - " },\n", - " {\n", - " \"syntax\": \"hgvs.g\",\n", - " \"value\": \"NC_000016.10:g.1762843C>T\"\n", - " }\n", - " ],\n", - " \"vcfRecord\": {\n", - " \"genomeAssembly\": \"hg38\",\n", - " \"chrom\": \"chr16\",\n", - " \"pos\": \"1762843\",\n", - " \"ref\": \"C\",\n", - " \"alt\": \"T\"\n", - " },\n", - " \"moleculeContext\": \"genomic\",\n", - " \"allelicState\": {\n", - " \"id\": \"GENO:0000135\",\n", - " \"label\": \"heterozygous\"\n", - " }\n", - " }\n", - " }\n", - " }\n", - " ]\n", - " }\n", - " }\n", - " ],\n", - " \"metaData\": {\n", - " \"created\": \"2023-09-19T16:54:50.415200948Z\",\n", - " \"createdBy\": \"ORCID:0000-0002-0736-9199\",\n", - " \"resources\": [\n", - " {\n", - " \"id\": \"geno\",\n", - " \"name\": \"Genotype Ontology\",\n", - " \"url\": \"http://purl.obolibrary.org/obo/geno.owl\",\n", - " \"version\": \"2022-03-05\",\n", - " \"namespacePrefix\": \"GENO\",\n", - " \"iriPrefix\": \"http://purl.obolibrary.org/obo/GENO_\"\n", - " },\n", - " {\n", - " \"id\": \"hgnc\",\n", - " \"name\": \"HUGO Gene Nomenclature Committee\",\n", - " \"url\": \"https://www.genenames.org\",\n", - " \"version\": \"06/01/23\",\n", - " \"namespacePrefix\": \"HGNC\",\n", - " \"iriPrefix\": \"https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/\"\n", - " },\n", - " {\n", - " \"id\": \"omim\",\n", - " \"name\": \"An Online Catalog of Human Genes and Genetic Disorders\",\n", - " \"url\": \"https://www.omim.org\",\n", - " \"version\": \"January 4, 2023\",\n", - " \"namespacePrefix\": \"OMIM\",\n", - " \"iriPrefix\": \"https://www.omim.org/entry/\"\n", - " },\n", - " {\n", - " \"id\": \"so\",\n", - " \"name\": \"Sequence types and features ontology\",\n", - " \"url\": \"http://purl.obolibrary.org/obo/so.obo\",\n", - " \"version\": \"2021-11-22\",\n", - " \"namespacePrefix\": \"SO\",\n", - " \"iriPrefix\": \"http://purl.obolibrary.org/obo/SO_\"\n", - " },\n", - " {\n", - " \"id\": \"hp\",\n", - " \"name\": \"human phenotype ontology\",\n", - " \"url\": \"http://purl.obolibrary.org/obo/hp.owl\",\n", - " \"version\": \"2023-09-01\",\n", - " \"namespacePrefix\": \"HP\",\n", - " \"iriPrefix\": \"http://purl.obolibrary.org/obo/HP_\"\n", - " }\n", - " ],\n", - " \"phenopacketSchemaVersion\": \"2.0\",\n", - " \"externalReferences\": [\n", - " {\n", - " \"id\": \"PMID:pending\",\n", - " \"reference\": \"https://pubmed.ncbi.nlm.nih.gov/pending\",\n", - " \"description\": \"in preparation\"\n", - " }\n", - " ]\n", - " }\n", - "}\n" - ] + "data": { + "text/html": [ + "

Cohort validation

\n", + "

No errors found for the cohort with 2 individuals

" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" } ], "source": [ - "phenopacketB = encoderB.get_phenopacket()\n", - "json_string = MessageToJson(phenopacketB)\n", - "print(json_string)" + "individuals = [individual_A, individual_B]\n", + "cvalidator = CohortValidator(cohort=individuals, ontology=hpo_ontology, min_hpo=1, allelic_requirement=AllelicRequirement.MONO_ALLELIC)\n", + "qc = QcVisualizer(ontology=hpo_ontology, cohort_validator=cvalidator)\n", + "display(HTML(qc.to_summary_html()))" ] }, { "cell_type": "code", - "execution_count": 16, - "id": "934ae2e9-72a8-4659-aa76-9d905f2f1494", + "execution_count": 17, + "id": "e68f2ffe-872f-408d-95bd-1b9e166358a4", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "
2 phenopackets - PMID:pending (n=2)
IndividualDiseaseGenotypePhenotypic features
Patient S12 (MALE; P12Y)Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)NM_001318852.2:c.45C>G (heterozygous)P12Y: Intellectual disability (HP:0001249); Spastic triplegia (HP:0034183)
Individual A (FEMALE; P5Y)Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)NM_001318852.2:c.1735C>T (heterozygous)P1Y: Cerebellar hypoplasia (HP:0001321); Cerebral hypoplasia (HP:0006872); Thin corpus callosum (HP:0033725); Hypoplasia of the pons (HP:0012110); Reduced cerebral white matter volume (HP:0034295); Periventricular leukomalacia (HP:0006970)
P1Y4M: Global developmental delay (HP:0001263)
P2Y: Delayed ability to walk (HP:0031936); Delayed speech and language development (HP:0000750)
P5Y: Nuchal cord (HP:0012498); Motor deterioration (HP:0002333); Microcephaly (HP:0000252); Spastic diplegia (HP:0001264); Cerebral palsy (HP:0100021)
" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "individuals = cvalidator.get_error_free_individual_list()\n", + "table = PhenopacketTable(individual_list=individuals, metadata=metadata)\n", + "display(HTML(table.to_html()))" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "id": "595222f1-eee3-44ed-8ea8-91c7b1e437a0", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "Wrote phenopacket to phenopackets/PMID_pending_Individual_A.json\n" + "We output 2 GA4GH phenopackets to the directory phenopackets\n" ] } ], "source": [ - "encoderB.output_phenopacket(outdir=output_directory)" + "Individual.output_individuals_as_phenopackets(individual_list=individuals,\n", + " metadata=metadata,\n", + " outdir=\"phenopackets\")" ] }, { "cell_type": "code", "execution_count": null, - "id": "e68f2ffe-872f-408d-95bd-1b9e166358a4", + "id": "85c43010-bd2c-41ac-9895-4c32c4e72825", "metadata": {}, "outputs": [], "source": [] @@ -828,7 +529,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.12" + "version": "3.11.3" } }, "nbformat": 4, diff --git a/notebooks/MAPK8IP3/MAPK8IP3_summary.ipynb b/notebooks/MAPK8IP3/MAPK8IP3_summary.ipynb index c4bfe06a3..fc307933f 100644 --- a/notebooks/MAPK8IP3/MAPK8IP3_summary.ipynb +++ b/notebooks/MAPK8IP3/MAPK8IP3_summary.ipynb @@ -19,7 +19,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Using pyphetools version 0.5.8\n" + "Using pyphetools version 0.8.28\n" ] } ], @@ -30,6 +30,7 @@ "import pandas as pd\n", "pd.set_option('display.max_colwidth', None) # show entire column contents, important!\n", "from collections import defaultdict\n", + "from IPython.display import HTML, display\n", "import hpotk\n", "from hpotk.ontology import Ontology\n", "from hpotk.ontology.load.obographs import load_ontology\n", @@ -64,182 +65,8 @@ } ], "source": [ - "ingestor = PhenopacketIngestor(indir=\"phenopackets\")" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "id": "f9ba84a2-4b73-4473-b993-95c97439ac28", - "metadata": {}, - "outputs": [], - "source": [ - "ppkt_d = ingestor.get_phenopacket_dictionary()\n", - "ppkt_list = list(ppkt_d.values())\n", - "table = PhenopacketTable(phenopacket_list=ppkt_list)" - ] - }, - { - "cell_type": "markdown", - "id": "17dcdbc4-38c7-4f1d-856b-aa78eaae02bf", - "metadata": {}, - "source": [ - "

Individuals included in the cohort

" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "id": "df752aaa-60da-422c-b417-2fe81476198d", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "\n", - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "
20 phenopackets - PMID:30612693 (n=13); PMID:pending (n=1); PMID:30945334 (n=5); PMID:34321325 (n=1)
IndividualDiseaseGenotypePhenotypic features
11 (FEMALE; P11Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.3439C>T (heterozygous)Spasticity (HP:0001257); Intellectual disability, moderate (HP:0002342); Thin corpus callosum (HP:0033725); Lateral ventricle dilatation (HP:0006956); Cerebral visual impairment (HP:0100704); Global developmental delay (HP:0001263)
3 (MALE; P4Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.111C>G (heterozygous)Intellectual disability, moderate (HP:0002342); Nystagmus (HP:0000639); Hypotonia (HP:0001252); Global developmental delay (HP:0001263)
12 (FEMALE; P4Y6M)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.3439C>T (heterozygous)Cerebral palsy (HP:0100021); Spastic diplegia (HP:0001264); Intellectual disability, severe (HP:0010864); Periventricular leukomalacia (HP:0006970); Dysplastic corpus callosum (HP:0006989); Myopic astigmatism (HP:0500041); Global developmental delay (HP:0001263)
Individual A (FEMALE; )\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.1735C>T (heterozygous)Nuchal cord (HP:0012498); Motor deterioration (HP:0002333); Microcephaly (HP:0000252); Spastic diplegia (HP:0001264); Cerebral palsy (HP:0100021); Global developmental delay (HP:0001263); Delayed ability to walk (HP:0031936); Delayed speech and language development (HP:0000750); Cerebellar hypoplasia (HP:0001321); Cerebral hypoplasia (HP:0006872); Thin corpus callosum (HP:0033725); Hypoplasia of the pons (HP:0012110); Reduced cerebral white matter volume (HP:0034295); Periventricular leukomalacia (HP:0006970)
2 (MALE; P4Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.79G>T (heterozygous)Ataxia (HP:0001251); Intellectual disability, severe (HP:0010864); Hypotonia (HP:0001252); Global developmental delay (HP:0001263)
Individual 1 (MALE; P29Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.1735C>T (heterozygous)Motor delay (HP:0001270); Delayed ability to walk (HP:0031936); Spastic diplegia (HP:0001264); Cerebral atrophy (HP:0002059); Delayed CNS myelination (HP:0002188); Thin upper lip vermilion (HP:0000219); Round face (HP:0000311); Short stature (HP:0004322); Obesity (HP:0001513); Precocious puberty (HP:0000826); Intellectual disability, severe (HP:0010864); Delayed speech and language development (HP:0000750); Loss of ambulation (HP:0002505)
6 (FEMALE; P9Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.1334T>C (heterozygous)Intellectual disability, mild (HP:0001256); Perisylvian polymicrogyria (HP:0012650); Hypotonia (HP:0001252); Global developmental delay (HP:0001263)
4 (MALE; P7Y6M)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.1201G>A (heterozygous)Intellectual disability, mild (HP:0001256); Hearing impairment (HP:0000365); Hypertelorism (HP:0000316); Protruding ear (HP:0000411); Hypodontia (HP:0000668); Finger clinodactyly (HP:0040019); Synophrys (HP:0000664); Encopresis (HP:0040183); Autism (HP:0000717); Global developmental delay (HP:0001263)
Patient S12 (MALE; )\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.45C>G (heterozygous)Intellectual disability (HP:0001249); Spastic triplegia (HP:0034183)
Individual 5 (FEMALE; P5Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001374425.1:c.272G>A (heterozygous)Motor delay (HP:0001270); Persistent head lag (HP:0032988); Delayed ability to sit (HP:0025336); Delayed ability to walk (HP:0031936); Spastic diplegia (HP:0001264); Autistic behavior (HP:0000729); Infantile muscular hypotonia (HP:0008947); Cerebral atrophy (HP:0002059); Delayed CNS myelination (HP:0002188); Prominent nasal bridge (HP:0000426); Thin upper lip vermilion (HP:0000219); Round face (HP:0000311); Intellectual disability, severe (HP:0010864); Absent speech (HP:0001344); Thick eyebrow (HP:0000574); Upslanted palpebral fissure (HP:0000582); Anteverted nares (HP:0000463); Short philtrum (HP:0000322)
9 (FEMALE; P6Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.1735C>T (heterozygous)Spasticity (HP:0001257); Upper motor neuron dysfunction (HP:0002493); Lower limb muscle weakness (HP:0007340); Intellectual disability, moderate (HP:0002342); Thin corpus callosum (HP:0033725); Hypoplasia of the brainstem (HP:0002365); Polymicrogyria (HP:0002126); Reduced cerebral white matter volume (HP:0034295); Pica (HP:0011856); Syringomyelia (HP:0003396); Small hand (HP:0200055); Hypotonia (HP:0001252); Seizure (HP:0001250); Global developmental delay (HP:0001263)
1 (MALE; P14Y8M)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.65del (heterozygous)Ataxia (HP:0001251); Intellectual disability, moderate (HP:0002342); Cerebellar atrophy (HP:0001272); Emotional lability (HP:0000712); Scoliosis (HP:0002650); Autism (HP:0000717); Hypotonia (HP:0001252); Global developmental delay (HP:0001263)
Individual 3 (MALE; P16Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.1735C>T (heterozygous)Motor delay (HP:0001270); Delayed ability to sit (HP:0025336); Delayed ability to walk (HP:0031936); Spastic diplegia (HP:0001264); Prominent nasal bridge (HP:0000426); Thin upper lip vermilion (HP:0000219); Short stature (HP:0004322); Obesity (HP:0001513); Intellectual disability, profound (HP:0002187); Delayed speech and language development (HP:0000750); Loss of ambulation (HP:0002505)
Individual 2 (FEMALE; P27Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.1735C>T (heterozygous)Motor delay (HP:0001270); Delayed ability to roll over (HP:0032989); Delayed ability to walk (HP:0031936); Spastic diplegia (HP:0001264); Cerebral atrophy (HP:0002059); Delayed CNS myelination (HP:0002188); Thin upper lip vermilion (HP:0000219); Round face (HP:0000311); Short stature (HP:0004322); Obesity (HP:0001513); Precocious puberty (HP:0000826); Intellectual disability, severe (HP:0010864); Delayed speech and language development (HP:0000750); Loss of ambulation (HP:0002505)
5 (MALE; P10Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.1334T>C (heterozygous)Intellectual disability, moderate (HP:0002342); Perisylvian polymicrogyria (HP:0012650); Microdontia (HP:0000691); Scoliosis (HP:0002650); Hypotonia (HP:0001252); Seizure (HP:0001250); Global developmental delay (HP:0001263)
7 (FEMALE; P3Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.1577G>A (heterozygous)Intellectual disability, mild (HP:0001256); Global developmental delay (HP:0001263)
Individual 4 (MALE; P5Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.3439C>T (heterozygous)Motor delay (HP:0001270); Persistent head lag (HP:0032988); Delayed ability to roll over (HP:0032989); Delayed ability to sit (HP:0025336); Delayed ability to walk (HP:0031936); Autistic behavior (HP:0000729); Infantile muscular hypotonia (HP:0008947); Cerebral atrophy (HP:0002059); Prominent nasal bridge (HP:0000426); Thin upper lip vermilion (HP:0000219); Round face (HP:0000311); Short stature (HP:0004322); Intellectual disability, severe (HP:0010864); Absent speech (HP:0001344); Delayed gross motor development (HP:0002194)
13 (FEMALE; P19Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.3439C>T (heterozygous)Oromotor apraxia (HP:0007301); Poor coordination (HP:0002370); Unsteady gait (HP:0002317); Intellectual disability, moderate (HP:0002342); Gastroesophageal reflux (HP:0002020); Hepatomegaly (HP:0002240); Long face (HP:0000276); Thick eyebrow (HP:0000574); Narrow palpebral fissure (HP:0045025); Strabismus (HP:0000486); Prominent nasal bridge (HP:0000426); Anteverted nares (HP:0000463); Short philtrum (HP:0000322); Narrow mouth (HP:0000160); High palate (HP:0000218); Truncal obesity (HP:0001956); Slender finger (HP:0001238); Kyphosis (HP:0002808); Hyperlordosis (HP:0003307); Scoliosis (HP:0002650); Genu valgum (HP:0002857); Hypotonia (HP:0001252); Cerebral visual impairment (HP:0100704); Global developmental delay (HP:0001263)
8 (FEMALE; P5Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.1735C>T (heterozygous)Spastic paraplegia (HP:0001258); Intellectual disability, severe (HP:0010864); CNS hypomyelination (HP:0003429); Thin corpus callosum (HP:0033725); Full cheeks (HP:0000293); Long philtrum (HP:0000343); Hypotonia (HP:0001252); Seizure (HP:0001250); Global developmental delay (HP:0001263)
10 (MALE; P4Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.2985C>G (heterozygous)Intellectual disability, moderate (HP:0002342); Hypotonia (HP:0001252); Seizure (HP:0001250); Global developmental delay (HP:0001263)
\n" - ], - "text/plain": [ - "" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "from IPython.display import HTML, display\n", - "display(HTML(table.to_html()))" + "ingestor = PhenopacketIngestor(indir=\"phenopackets\")\n", + "ppkt_d = ingestor.get_phenopacket_dictionary()" ] }, { @@ -253,7 +80,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 4, "id": "e6f38064-8c3b-4cf1-8408-15329b770571", "metadata": {}, "outputs": [], @@ -263,7 +90,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 5, "id": "003ac056-05d5-48b4-bc8d-6b6e46aa4d4d", "metadata": {}, "outputs": [ @@ -272,82 +99,80 @@ "text/html": [ "\n", "\n", - "\n", - "\n", - "\n", - "\n", + "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", - "\n", + "\n", "\n", "
HPO termPMID:30612693PMID:30945334PMID:pendingPMID:34321325
Global developmental delay (HP:0001263)13/13 (100.0%)0/5 (0.0%)1/1 (100.0%)0/1 (0.0%)
Hypotonia (HP:0001252)9/13 (69.2%)0/5 (0.0%)0/1 (0.0%)0/1 (0.0%)
HPO termPMID:30612693PMID:30945334PMID:pending
Global developmental delay (HP:0001263)13/13 (100.0%)0/5 (0.0%)1/2 (50.0%)
Intellectual disability, moderate (HP:0002342)7/13 (53.8%)0/5 (0.0%)0/1 (0.0%)0/1 (0.0%)
Hypotonia (HP:0001252)9/13 (69.2%)0/5 (0.0%)0/2 (0.0%)
Intellectual disability, severe (HP:0010864)3/13 (23.1%)4/5 (80.0%)0/1 (0.0%)0/1 (0.0%)
Intellectual disability, severe (HP:0010864)3/13 (23.1%)4/5 (80.0%)0/2 (0.0%)
Spastic diplegia (HP:0001264)1/13 (7.7%)4/5 (80.0%)1/1 (100.0%)0/1 (0.0%)
Intellectual disability, moderate (HP:0002342)7/13 (53.8%)0/5 (0.0%)0/2 (0.0%)
Delayed ability to walk (HP:0031936)0/13 (0.0%)5/5 (100.0%)1/1 (100.0%)0/1 (0.0%)
Delayed ability to walk (HP:0031936)0/13 (0.0%)5/5 (100.0%)1/2 (50.0%)
Motor delay (HP:0001270)0/13 (0.0%)5/5 (100.0%)0/1 (0.0%)0/1 (0.0%)
Spastic diplegia (HP:0001264)1/13 (7.7%)4/5 (80.0%)1/2 (50.0%)
Thin upper lip vermilion (HP:0000219)0/13 (0.0%)5/5 (100.0%)0/1 (0.0%)0/1 (0.0%)
Thin upper lip vermilion (HP:0000219)0/13 (0.0%)5/5 (100.0%)0/2 (0.0%)
Thin corpus callosum (HP:0033725)3/13 (23.1%)0/5 (0.0%)1/1 (100.0%)0/1 (0.0%)
Cerebral atrophy (HP:0002059)0/13 (0.0%)4/5 (80.0%)0/2 (0.0%)
Delayed speech and language development (HP:0000750)0/13 (0.0%)3/5 (60.0%)1/1 (100.0%)0/1 (0.0%)
Round face (HP:0000311)0/13 (0.0%)4/5 (80.0%)0/2 (0.0%)
Cerebral atrophy (HP:0002059)0/13 (0.0%)4/5 (80.0%)0/1 (0.0%)0/1 (0.0%)
Short stature (HP:0004322)0/13 (0.0%)4/5 (80.0%)0/2 (0.0%)
Round face (HP:0000311)0/13 (0.0%)4/5 (80.0%)0/1 (0.0%)0/1 (0.0%)
Delayed speech and language development (HP:0000750)0/13 (0.0%)3/5 (60.0%)1/2 (50.0%)
Short stature (HP:0004322)0/13 (0.0%)4/5 (80.0%)0/1 (0.0%)0/1 (0.0%)
Prominent nasal bridge (HP:0000426)1/13 (7.7%)3/5 (60.0%)0/2 (0.0%)
Prominent nasal bridge (HP:0000426)1/13 (7.7%)3/5 (60.0%)0/1 (0.0%)0/1 (0.0%)
Thin corpus callosum (HP:0033725)3/13 (23.1%)0/5 (0.0%)1/2 (50.0%)
Seizure (HP:0001250)4/13 (30.8%)0/5 (0.0%)0/1 (0.0%)0/1 (0.0%)
Seizure (HP:0001250)4/13 (30.8%)0/5 (0.0%)0/2 (0.0%)
Delayed CNS myelination (HP:0002188)0/13 (0.0%)3/5 (60.0%)0/1 (0.0%)0/1 (0.0%)
Delayed CNS myelination (HP:0002188)0/13 (0.0%)3/5 (60.0%)0/2 (0.0%)
Obesity (HP:0001513)0/13 (0.0%)3/5 (60.0%)0/1 (0.0%)0/1 (0.0%)
Obesity (HP:0001513)0/13 (0.0%)3/5 (60.0%)0/2 (0.0%)
Loss of ambulation (HP:0002505)0/13 (0.0%)3/5 (60.0%)0/1 (0.0%)0/1 (0.0%)
Loss of ambulation (HP:0002505)0/13 (0.0%)3/5 (60.0%)0/2 (0.0%)
Intellectual disability, mild (HP:0001256)3/13 (23.1%)0/5 (0.0%)0/1 (0.0%)0/1 (0.0%)
Scoliosis (HP:0002650)3/13 (23.1%)0/5 (0.0%)0/2 (0.0%)
Delayed ability to sit (HP:0025336)0/13 (0.0%)3/5 (60.0%)0/1 (0.0%)0/1 (0.0%)
Intellectual disability, mild (HP:0001256)3/13 (23.1%)0/5 (0.0%)0/2 (0.0%)
Scoliosis (HP:0002650)3/13 (23.1%)0/5 (0.0%)0/1 (0.0%)0/1 (0.0%)
Delayed ability to sit (HP:0025336)0/13 (0.0%)3/5 (60.0%)0/2 (0.0%)
Spasticity (HP:0001257)2/13 (15.4%)0/5 (0.0%)0/1 (0.0%)0/1 (0.0%)
Precocious puberty (HP:0000826)0/13 (0.0%)2/5 (40.0%)0/2 (0.0%)
Cerebral visual impairment (HP:0100704)2/13 (15.4%)0/5 (0.0%)0/1 (0.0%)0/1 (0.0%)
Cerebral palsy (HP:0100021)1/13 (7.7%)0/5 (0.0%)1/2 (50.0%)
Cerebral palsy (HP:0100021)1/13 (7.7%)0/5 (0.0%)1/1 (100.0%)0/1 (0.0%)
Periventricular leukomalacia (HP:0006970)1/13 (7.7%)0/5 (0.0%)1/2 (50.0%)
Periventricular leukomalacia (HP:0006970)1/13 (7.7%)0/5 (0.0%)1/1 (100.0%)0/1 (0.0%)
Ataxia (HP:0001251)2/13 (15.4%)0/5 (0.0%)0/2 (0.0%)
Reduced cerebral white matter volume (HP:0034295)1/13 (7.7%)0/5 (0.0%)1/1 (100.0%)0/1 (0.0%)
Thick eyebrow (HP:0000574)1/13 (7.7%)1/5 (20.0%)0/2 (0.0%)
Ataxia (HP:0001251)2/13 (15.4%)0/5 (0.0%)0/1 (0.0%)0/1 (0.0%)
Anteverted nares (HP:0000463)1/13 (7.7%)1/5 (20.0%)0/2 (0.0%)
Precocious puberty (HP:0000826)0/13 (0.0%)2/5 (40.0%)0/1 (0.0%)0/1 (0.0%)
Short philtrum (HP:0000322)1/13 (7.7%)1/5 (20.0%)0/2 (0.0%)
Perisylvian polymicrogyria (HP:0012650)2/13 (15.4%)0/5 (0.0%)0/1 (0.0%)0/1 (0.0%)
Cerebral visual impairment (HP:0100704)2/13 (15.4%)0/5 (0.0%)0/2 (0.0%)
Autism (HP:0000717)2/13 (15.4%)0/5 (0.0%)0/1 (0.0%)0/1 (0.0%)
Autism (HP:0000717)2/13 (15.4%)0/5 (0.0%)0/2 (0.0%)
Persistent head lag (HP:0032988)0/13 (0.0%)2/5 (40.0%)0/1 (0.0%)0/1 (0.0%)
Spasticity (HP:0001257)2/13 (15.4%)0/5 (0.0%)0/2 (0.0%)
Autistic behavior (HP:0000729)0/13 (0.0%)2/5 (40.0%)0/1 (0.0%)0/1 (0.0%)
Reduced cerebral white matter volume (HP:0034295)1/13 (7.7%)0/5 (0.0%)1/2 (50.0%)
Infantile muscular hypotonia (HP:0008947)0/13 (0.0%)2/5 (40.0%)0/1 (0.0%)0/1 (0.0%)
Perisylvian polymicrogyria (HP:0012650)2/13 (15.4%)0/5 (0.0%)0/2 (0.0%)
Absent speech (HP:0001344)0/13 (0.0%)2/5 (40.0%)0/1 (0.0%)0/1 (0.0%)
Persistent head lag (HP:0032988)0/13 (0.0%)2/5 (40.0%)0/2 (0.0%)
Thick eyebrow (HP:0000574)1/13 (7.7%)1/5 (20.0%)0/1 (0.0%)0/1 (0.0%)
Autistic behavior (HP:0000729)0/13 (0.0%)2/5 (40.0%)0/2 (0.0%)
Anteverted nares (HP:0000463)1/13 (7.7%)1/5 (20.0%)0/1 (0.0%)0/1 (0.0%)
Infantile muscular hypotonia (HP:0008947)0/13 (0.0%)2/5 (40.0%)0/2 (0.0%)
Short philtrum (HP:0000322)1/13 (7.7%)1/5 (20.0%)0/1 (0.0%)0/1 (0.0%)
Absent speech (HP:0001344)0/13 (0.0%)2/5 (40.0%)0/2 (0.0%)
Delayed ability to roll over (HP:0032989)0/13 (0.0%)2/5 (40.0%)0/1 (0.0%)0/1 (0.0%)
Delayed ability to roll over (HP:0032989)0/13 (0.0%)2/5 (40.0%)0/2 (0.0%)
\n" ], diff --git a/notebooks/MAPK8IP3/Platzer_2019_MAPK8IP3_PMID_30612693.ipynb b/notebooks/MAPK8IP3/Platzer_2019_MAPK8IP3_PMID_30612693.ipynb index 1b9f2ee93..7ef7feb3c 100644 --- a/notebooks/MAPK8IP3/Platzer_2019_MAPK8IP3_PMID_30612693.ipynb +++ b/notebooks/MAPK8IP3/Platzer_2019_MAPK8IP3_PMID_30612693.ipynb @@ -22,7 +22,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Using pyphetools version 0.5.5\n" + "Using pyphetools version 0.8.28\n" ] } ], @@ -32,12 +32,12 @@ "from google.protobuf.json_format import Parse, ParseDict\n", "import pandas as pd\n", "pd.set_option('display.max_colwidth', None) # show entire column contents, important!\n", - "from collections import defaultdict\n", + "from IPython.display import display, HTML\n", "from pyphetools.creation import *\n", "from pyphetools.visualization import *\n", - "import importlib.metadata\n", - "__version__ = importlib.metadata.version(\"pyphetools\")\n", - "print(f\"Using pyphetools version {__version__}\")" + "from pyphetools.validation import *\n", + "import pyphetools\n", + "print(f\"Using pyphetools version {pyphetools.__version__}\")" ] }, { @@ -53,15 +53,25 @@ "execution_count": 2, "id": "feefba63-c315-4cf6-b9d9-d414eb2b86cb", "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "HPO version 2023-10-09\n" + ] + } + ], "source": [ "parser = HpoParser()\n", "hpo_cr = parser.get_hpo_concept_recognizer()\n", "hpo_version = parser.get_version()\n", - "pmid = \"PMID:30612693\"\n", + "hpo_ontology = parser.get_ontology()\n", + "PMID = \"PMID:30612693\"\n", "title = \"De Novo Variants in MAPK8IP3 Cause Intellectual Disability with Variable Brain Anomalies\"\n", - "metadata = MetaData(created_by=\"ORCID:0000-0002-0736-9199\", pmid=pmid, pubmed_title=title)\n", - "metadata.default_versions_with_hpo(version=hpo_version)" + "metadata = MetaData(created_by=\"ORCID:0000-0002-0736-9199\", pmid=PMID, pubmed_title=title)\n", + "metadata.default_versions_with_hpo(version=hpo_version)\n", + "print(f\"HPO version {hpo_version}\")" ] }, { @@ -354,7 +364,7 @@ "metadata": {}, "outputs": [], "source": [ - "column_mapper_d = defaultdict(ColumnMapper)" + "column_mapper_d = {}" ] }, { @@ -371,8 +381,8 @@ " 'orobuccal dyspraxia': 'Oromotor apraxia',\n", " 'difficulty in coordination':'Poor coordination'\n", " }\n", - "neuroMapper = CustomColumnMapper(concept_recognizer=hpo_cr, custom_map_d=neuro_exam_custom_map, )\n", - "#neuroMapper.preview_column(df['neurological examination'])\n", + "neuroMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=neuro_exam_custom_map, )\n", + "neuroMapper.preview_column(df['neurological examination'])\n", "column_mapper_d['neurological examination'] = neuroMapper" ] }, @@ -407,7 +417,7 @@ " 'dysgenesis of corpus callosum': 'Dysplastic corpus callosum',\n", " 'hypoplasia of mesencephalon and brainstem': 'Hypoplasia of the brainstem'\n", " }\n", - "mriMapper = CustomColumnMapper(concept_recognizer=hpo_cr, custom_map_d=mri_custom_map, )\n", + "mriMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=mri_custom_map, )\n", "#mriMapper.preview_column(df['result of external MRI'])\n", "column_mapper_d['result of external MRI'] = mriMapper" ] @@ -426,10 +436,10 @@ " 'dysgenesis of corpus callosum': 'Dysplastic corpus callosum',\n", " 'dramatic increased weight': 'Obesity'\n", " }\n", - "excluded = {'pseudostrabismus'}\n", - "additionalFeaturesMapper = CustomColumnMapper(concept_recognizer=hpo_cr, \n", - " custom_map_d=mri_custom_map, \n", - " excluded_set=excluded)\n", + "excluded = {'pseudostrabismus': \"Strabismus\"}\n", + "additionalFeaturesMapper = OptionColumnMapper(concept_recognizer=hpo_cr, \n", + " option_d=mri_custom_map, \n", + " excluded_d=excluded)\n", "additionalFeaturesMapper.preview_column(df['Additional symptoms'])\n", "column_mapper_d['Additional symptoms'] = additionalFeaturesMapper" ] @@ -513,7 +523,7 @@ " 'dysgenesis of corpus callosum': 'Dysplastic corpus callosum',\n", " 'hypoplasia of mesencephalon and brainstem': 'Hypoplasia of the brainstem'\n", " }\n", - "mriMapper = CustomColumnMapper(concept_recognizer=hpo_cr, custom_map_d=mri_custom_map, )\n", + "mriMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=mri_custom_map, )\n", "mriMapper.preview_column(df['result of external MRI'])\n", "column_mapper_d['result of external MRI'] = mriMapper" ] @@ -532,10 +542,10 @@ " 'dysgenesis of corpus callosum': 'Dysplastic corpus callosum',\n", " 'dramatic increased weight': 'Obesity'\n", " }\n", - "excluded = {'pseudostrabismus'}\n", - "additionalFeaturesMapper = CustomColumnMapper(concept_recognizer=hpo_cr, \n", - " custom_map_d=mri_custom_map, \n", - " excluded_set=excluded)\n", + "excluded = {'pseudostrabismus': \"Strabismus\"}\n", + "additionalFeaturesMapper = OptionColumnMapper(concept_recognizer=hpo_cr, \n", + " option_d=mri_custom_map, \n", + " excluded_d=excluded)\n", "additionalFeaturesMapper.preview_column(df['Additional symptoms'])\n", "column_mapper_d['Additional symptoms'] = additionalFeaturesMapper" ] @@ -612,13 +622,38 @@ "execution_count": 15, "id": "4b92a142-63fa-4636-bfb9-f3b45ab3a77a", "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.65del/NM_001318852.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.79G>T/NM_001318852.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.111C>G/NM_001318852.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.1201G>A/NM_001318852.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.1334T>C/NM_001318852.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.1334T>C/NM_001318852.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.1577G>A/NM_001318852.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.1735C>T/NM_001318852.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.1735C>T/NM_001318852.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.2985C>G/NM_001318852.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.3439C>T/NM_001318852.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.3439C>T/NM_001318852.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.3439C>T/NM_001318852.2?content-type=application%2Fjson\n" + ] + } + ], "source": [ - "genome = 'hg38'\n", "transcript='NM_001318852.2'\n", - "varMapper = VariantColumnMapper(assembly=genome,\n", - " column_name='NM_001318852', \n", - " transcript=transcript, \n", + "vvalidator = VariantValidator(genome_build=\"hg38\", transcript=transcript)\n", + "\n", + "var_d = {}\n", + "for v in df['NM_001318852']:\n", + " var = vvalidator.encode_hgvs(v)\n", + " var_d[v] = var\n", + "\n", + "varMapper = VariantColumnMapper(variant_d=var_d,\n", + " variant_column_name='NM_001318852', \n", " default_genotype='heterozygous')\n", "# varMapper.preview_column(df['NM_001318852'])" ] @@ -631,14 +666,12 @@ "outputs": [], "source": [ "ageMapper = AgeColumnMapper.by_year_and_month('age at last assesment')\n", - "ageMapper.preview_column(df['age at last assesment'])\n", - "\n", + "#ageMapper.preview_column(df['age at last assesment'])\n", "sexMapper = SexColumnMapper(male_symbol='M', female_symbol='F', column_name='Sex')\n", - "sexMapper.preview_column(df['Sex'])\n", + "#sexMapper.preview_column(df['Sex'])\n", "\n", "individual_column_name = 'Indvidual\\nin\\nmanuscript'\n", "\n", - "\n", "encoder = CohortEncoder(df=df, \n", " hpo_cr=hpo_cr, \n", " column_mapper_d=column_mapper_d, \n", @@ -647,11 +680,11 @@ " sexmapper=sexMapper,\n", " variant_mapper=varMapper,\n", " metadata=metadata,\n", - " pmid=pmid)\n", + " pmid=PMID)\n", "disease_id = 'OMIM:618443'\n", "disease_name = 'Neurodevelopmental disorder with or without variable brain abnormalities'\n", - "\n", - "encoder.set_disease(disease_id=disease_id, label=disease_name)" + "disease = Disease(disease_id=disease_id, disease_label=disease_name)\n", + "encoder.set_disease(disease=disease)" ] }, { @@ -669,27 +702,32 @@ "metadata": {}, "outputs": [ { - "name": "stdout", - "output_type": "stream", - "text": [ - "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.65del/NM_001318852.2?content-type=application%2Fjson\n", - "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.79G>T/NM_001318852.2?content-type=application%2Fjson\n", - "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.111C>G/NM_001318852.2?content-type=application%2Fjson\n", - "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.1201G>A/NM_001318852.2?content-type=application%2Fjson\n", - "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.1334T>C/NM_001318852.2?content-type=application%2Fjson\n", - "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.1334T>C/NM_001318852.2?content-type=application%2Fjson\n", - "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.1577G>A/NM_001318852.2?content-type=application%2Fjson\n", - "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.1735C>T/NM_001318852.2?content-type=application%2Fjson\n", - "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.1735C>T/NM_001318852.2?content-type=application%2Fjson\n", - "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.2985C>G/NM_001318852.2?content-type=application%2Fjson\n", - "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.3439C>T/NM_001318852.2?content-type=application%2Fjson\n", - "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.3439C>T/NM_001318852.2?content-type=application%2Fjson\n", - "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001318852.2%3Ac.3439C>T/NM_001318852.2?content-type=application%2Fjson\n" - ] + "data": { + "text/html": [ + "

Cohort validation

\n", + "

Errors found with 9 of 13 phenopackets.

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Error counts
LevelError categoryCount
ERRORCONFLICT1
WARNINGREDUNDANT3
INFORMATIONNOT_MEASURED14
\n", + "

A total of 18 issues were fixed and no individual was removed from the cohort.

" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" } ], "source": [ - "individuals = encoder.get_individuals()" + "individuals = encoder.get_individuals()\n", + "cvalidator = CohortValidator(cohort=individuals, ontology=hpo_ontology, min_hpo=1, allelic_requirement=AllelicRequirement.MONO_ALLELIC)\n", + "qc = QcVisualizer(ontology=hpo_ontology, cohort_validator=cvalidator)\n", + "display(HTML(qc.to_summary_html()))" ] }, { @@ -701,96 +739,23 @@ { "data": { "text/html": [ - "\n", - "\n", + "
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13 phenopackets - PMID:30612693 (n=13)
IndividualDiseaseGenotypePhenotypic features
1 (MALE; P14Y8M)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.65del (heterozygous)Ataxia (HP:0001251); Intellectual disability, moderate (HP:0002342); Cerebellar atrophy (HP:0001272); Emotional lability (HP:0000712); Scoliosis (HP:0002650); Autism (HP:0000717); Hypotonia (HP:0001252); Global developmental delay (HP:0001263)
2 (MALE; P4Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.79G>T (heterozygous)Ataxia (HP:0001251); Intellectual disability, severe (HP:0010864); Hypotonia (HP:0001252); Global developmental delay (HP:0001263)
3 (MALE; P4Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.111C>G (heterozygous)Intellectual disability, moderate (HP:0002342); Nystagmus (HP:0000639); Hypotonia (HP:0001252); Global developmental delay (HP:0001263)
4 (MALE; P7Y6M)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.1201G>A (heterozygous)Intellectual disability, mild (HP:0001256); Hearing impairment (HP:0000365); Hypertelorism (HP:0000316); Protruding ear (HP:0000411); Hypodontia (HP:0000668); Finger clinodactyly (HP:0040019); Synophrys (HP:0000664); Encopresis (HP:0040183); Autism (HP:0000717); Global developmental delay (HP:0001263)
5 (MALE; P10Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.1334T>C (heterozygous)Intellectual disability, moderate (HP:0002342); Perisylvian polymicrogyria (HP:0012650); Microdontia (HP:0000691); Scoliosis (HP:0002650); Hypotonia (HP:0001252); Seizure (HP:0001250); Global developmental delay (HP:0001263)
6 (FEMALE; P9Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.1334T>C (heterozygous)Intellectual disability, mild (HP:0001256); Perisylvian polymicrogyria (HP:0012650); Hypotonia (HP:0001252); Global developmental delay (HP:0001263)
7 (FEMALE; P3Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.1577G>A (heterozygous)Intellectual disability, mild (HP:0001256); Global developmental delay (HP:0001263)
8 (FEMALE; P5Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.1735C>T (heterozygous)Spastic paraplegia (HP:0001258); Intellectual disability, severe (HP:0010864); CNS hypomyelination (HP:0003429); Thin corpus callosum (HP:0033725); Full cheeks (HP:0000293); Long philtrum (HP:0000343); Hypotonia (HP:0001252); Seizure (HP:0001250); Global developmental delay (HP:0001263)
9 (FEMALE; P6Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.1735C>T (heterozygous)Spasticity (HP:0001257); Upper motor neuron dysfunction (HP:0002493); Lower limb muscle weakness (HP:0007340); Intellectual disability, moderate (HP:0002342); Thin corpus callosum (HP:0033725); Hypoplasia of the brainstem (HP:0002365); Polymicrogyria (HP:0002126); Reduced cerebral white matter volume (HP:0034295); Pica (HP:0011856); Syringomyelia (HP:0003396); Small hand (HP:0200055); Hypotonia (HP:0001252); Seizure (HP:0001250); Global developmental delay (HP:0001263)
10 (MALE; P4Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.2985C>G (heterozygous)Intellectual disability, moderate (HP:0002342); Hypotonia (HP:0001252); Seizure (HP:0001250); Global developmental delay (HP:0001263)
11 (FEMALE; P11Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.3439C>T (heterozygous)Spasticity (HP:0001257); Intellectual disability, moderate (HP:0002342); Thin corpus callosum (HP:0033725); Lateral ventricle dilatation (HP:0006956); Cerebral visual impairment (HP:0100704); Global developmental delay (HP:0001263)
12 (FEMALE; P4Y6M)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.3439C>T (heterozygous)Cerebral palsy (HP:0100021); Spastic diplegia (HP:0001264); Intellectual disability, severe (HP:0010864); Periventricular leukomalacia (HP:0006970); Dysplastic corpus callosum (HP:0006989); Myopic astigmatism (HP:0500041); Global developmental delay (HP:0001263)
13 (FEMALE; P19Y)\n", - "Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)\n", - "NM_001318852.2:c.3439C>T (heterozygous)Oromotor apraxia (HP:0007301); Poor coordination (HP:0002370); Unsteady gait (HP:0002317); Intellectual disability, moderate (HP:0002342); Gastroesophageal reflux (HP:0002020); Hepatomegaly (HP:0002240); Long face (HP:0000276); Thick eyebrow (HP:0000574); Narrow palpebral fissure (HP:0045025); Strabismus (HP:0000486); Prominent nasal bridge (HP:0000426); Anteverted nares (HP:0000463); Short philtrum (HP:0000322); Narrow mouth (HP:0000160); High palate (HP:0000218); Truncal obesity (HP:0001956); Slender finger (HP:0001238); Kyphosis (HP:0002808); Hyperlordosis (HP:0003307); Scoliosis (HP:0002650); Genu valgum (HP:0002857); Hypotonia (HP:0001252); Cerebral visual impairment (HP:0100704); Global developmental delay (HP:0001263)
\n" + "IndividualDiseaseGenotypePhenotypic features\n", + "1 (MALE; P14Y8M)Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)NM_001318852.2:c.65del (heterozygous)Ataxia (HP:0001251); Intellectual disability, moderate (HP:0002342); Cerebellar atrophy (HP:0001272); Emotional lability (HP:0000712); Scoliosis (HP:0002650); Autism (HP:0000717); Hypotonia (HP:0001252); Global developmental delay (HP:0001263); excluded: Emotional lability (HP:0000712); excluded: Scoliosis (HP:0002650); excluded: Developmental regression (HP:0002376); excluded: Abnormality of movement (HP:0100022); excluded: Cerebral visual impairment (HP:0100704); excluded: Seizure (HP:0001250)\n", + "2 (MALE; P4Y)Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)NM_001318852.2:c.79G>T (heterozygous)Ataxia (HP:0001251); Intellectual disability, severe (HP:0010864); Hypotonia (HP:0001252); Global developmental delay (HP:0001263); excluded: Developmental regression (HP:0002376); excluded: Autism (HP:0000717); excluded: Abnormality of movement (HP:0100022); excluded: Cerebral visual impairment (HP:0100704); excluded: Seizure (HP:0001250)\n", + "3 (MALE; P4Y)Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)NM_001318852.2:c.111C>G (heterozygous)Intellectual disability, moderate (HP:0002342); Nystagmus (HP:0000639); Hypotonia (HP:0001252); Global developmental delay (HP:0001263); excluded: Nystagmus (HP:0000639); excluded: Developmental regression (HP:0002376); excluded: Autism (HP:0000717); excluded: Abnormality of movement (HP:0100022); excluded: Cerebral visual impairment (HP:0100704); excluded: Seizure (HP:0001250)\n", + "4 (MALE; P7Y6M)Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)NM_001318852.2:c.1201G>A (heterozygous)Intellectual disability, mild (HP:0001256); Hearing impairment (HP:0000365); Hypertelorism (HP:0000316); Protruding ear (HP:0000411); Hypodontia (HP:0000668); Finger clinodactyly (HP:0040019); Synophrys (HP:0000664); Encopresis (HP:0040183); Autism (HP:0000717); Global developmental delay (HP:0001263); excluded: Hearing impairment (HP:0000365); excluded: Hypertelorism (HP:0000316); excluded: Protruding ear (HP:0000411); excluded: Hypodontia (HP:0000668); excluded: Finger clinodactyly (HP:0040019); excluded: Synophrys (HP:0000664); excluded: Encopresis (HP:0040183); excluded: Developmental regression (HP:0002376); excluded: Hypotonia (HP:0001252); excluded: Abnormality of movement (HP:0100022); excluded: Cerebral visual impairment (HP:0100704); excluded: Seizure (HP:0001250)\n", + "5 (MALE; P10Y)Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)NM_001318852.2:c.1334T>C (heterozygous)Intellectual disability, moderate (HP:0002342); Perisylvian polymicrogyria (HP:0012650); Microdontia (HP:0000691); Scoliosis (HP:0002650); Hypotonia (HP:0001252); Seizure (HP:0001250); Global developmental delay (HP:0001263); excluded: Microdontia (HP:0000691); excluded: Scoliosis (HP:0002650); excluded: Developmental regression (HP:0002376); excluded: Autism (HP:0000717); excluded: Abnormality of movement (HP:0100022)\n", + "6 (FEMALE; P9Y)Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)NM_001318852.2:c.1334T>C (heterozygous)Intellectual disability, mild (HP:0001256); Perisylvian polymicrogyria (HP:0012650); Hypotonia (HP:0001252); Global developmental delay (HP:0001263); excluded: Developmental regression (HP:0002376); excluded: Autism (HP:0000717); excluded: Seizure (HP:0001250)\n", + "7 (FEMALE; P3Y)Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)NM_001318852.2:c.1577G>A (heterozygous)Intellectual disability, mild (HP:0001256); Global developmental delay (HP:0001263); excluded: Developmental regression (HP:0002376); excluded: Autism (HP:0000717); excluded: Hypotonia (HP:0001252); excluded: Seizure (HP:0001250)\n", + "8 (FEMALE; P5Y)Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)NM_001318852.2:c.1735C>T (heterozygous)Spastic paraplegia (HP:0001258); Intellectual disability, severe (HP:0010864); Thin corpus callosum (HP:0033725); CNS hypomyelination (HP:0003429); Full cheeks (HP:0000293); Long philtrum (HP:0000343); Hypotonia (HP:0001252); Seizure (HP:0001250); Global developmental delay (HP:0001263); excluded: Full cheeks (HP:0000293); excluded: Long philtrum (HP:0000343); excluded: Developmental regression (HP:0002376); excluded: Autism (HP:0000717)\n", + "9 (FEMALE; P6Y)Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)NM_001318852.2:c.1735C>T (heterozygous)Spasticity (HP:0001257); Lower limb muscle weakness (HP:0007340); Intellectual disability, moderate (HP:0002342); Hypoplasia of the brainstem (HP:0002365); Polymicrogyria (HP:0002126); Thin corpus callosum (HP:0033725); Reduced cerebral white matter volume (HP:0034295); Syringomyelia (HP:0003396); Small hand (HP:0200055); Hypotonia (HP:0001252); Seizure (HP:0001250); Global developmental delay (HP:0001263); excluded: Small hand (HP:0200055); excluded: Developmental regression (HP:0002376); excluded: Autism (HP:0000717)\n", + "10 (MALE; P4Y)Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)NM_001318852.2:c.2985C>G (heterozygous)Intellectual disability, moderate (HP:0002342); Hypotonia (HP:0001252); Seizure (HP:0001250); Global developmental delay (HP:0001263); excluded: Developmental regression (HP:0002376); excluded: Autism (HP:0000717)\n", + "11 (FEMALE; P11Y)Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)NM_001318852.2:c.3439C>T (heterozygous)Spasticity (HP:0001257); Intellectual disability, moderate (HP:0002342); Thin corpus callosum (HP:0033725); Lateral ventricle dilatation (HP:0006956); Cerebral visual impairment (HP:0100704); Global developmental delay (HP:0001263); excluded: Hypotonia (HP:0001252); excluded: Abnormality of movement (HP:0100022); excluded: Seizure (HP:0001250)\n", + "12 (FEMALE; P4Y6M)Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)NM_001318852.2:c.3439C>T (heterozygous)Spastic diplegia (HP:0001264); Cerebral palsy (HP:0100021); Intellectual disability, severe (HP:0010864); Periventricular leukomalacia (HP:0006970); Dysplastic corpus callosum (HP:0006989); Myopic astigmatism (HP:0500041); Global developmental delay (HP:0001263); excluded: Strabismus (HP:0000486); excluded: Myopic astigmatism (HP:0500041); excluded: Developmental regression (HP:0002376); excluded: Autism (HP:0000717); excluded: Hypotonia (HP:0001252); excluded: Cerebral visual impairment (HP:0100704); excluded: Seizure (HP:0001250)\n", + "13 (FEMALE; P19Y)Neurodevelopmental disorder with or without variable brain abnormalities (OMIM:618443)NM_001318852.2:c.3439C>T (heterozygous)Oromotor apraxia (HP:0007301); Poor coordination (HP:0002370); Unsteady gait (HP:0002317); Intellectual disability, moderate (HP:0002342); Gastroesophageal reflux (HP:0002020); Hepatomegaly (HP:0002240); Long face (HP:0000276); Thick eyebrow (HP:0000574); Narrow palpebral fissure (HP:0045025); Strabismus (HP:0000486); Prominent nasal bridge (HP:0000426); Anteverted nares (HP:0000463); Short philtrum (HP:0000322); Narrow mouth (HP:0000160); High palate (HP:0000218); Truncal obesity (HP:0001956); Slender finger (HP:0001238); Kyphosis (HP:0002808); Hyperlordosis (HP:0003307); Scoliosis (HP:0002650); Genu valgum (HP:0002857); Hypotonia (HP:0001252); Cerebral visual impairment (HP:0100704); Global developmental delay (HP:0001263); excluded: Gastroesophageal reflux (HP:0002020); excluded: Hepatomegaly (HP:0002240); excluded: Long face (HP:0000276); excluded: Thick eyebrow (HP:0000574); excluded: Narrow palpebral fissure (HP:0045025); excluded: Strabismus (HP:0000486); excluded: Prominent nasal bridge (HP:0000426); excluded: Anteverted nares (HP:0000463); excluded: Short philtrum (HP:0000322); excluded: Narrow mouth (HP:0000160); excluded: High palate (HP:0000218); excluded: Truncal obesity (HP:0001956); excluded: Slender finger (HP:0001238); excluded: Kyphosis (HP:0002808); excluded: Hyperlordosis (HP:0003307); excluded: Scoliosis (HP:0002650); excluded: Genu valgum (HP:0002857); excluded: Developmental regression (HP:0002376); excluded: Autism (HP:0000717); excluded: Seizure (HP:0001250)\n", + "" ], "text/plain": [ "" @@ -801,10 +766,8 @@ } ], "source": [ - "from IPython.display import HTML, display\n", - "\n", - "phenopackets = [i.to_ga4gh_phenopacket(metadata=metadata.to_ga4gh()) for i in individuals]\n", - "table = PhenopacketTable(phenopacket_list=phenopackets)\n", + "individuals = cvalidator.get_error_free_individual_list()\n", + "table = PhenopacketTable(individual_list=individuals, metadata=metadata)\n", "display(HTML(table.to_html()))" ] }, @@ -832,25 +795,27 @@ ], "source": [ "Individual.output_individuals_as_phenopackets(individual_list=individuals, \n", - " pmid=pmid, \n", - " metadata=metadata.to_ga4gh(), \n", + " metadata=metadata, \n", " outdir=\"phenopackets\")" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 20, "id": "2ee8143c-7ea5-41f1-9bf8-2450d7fb98a6", "metadata": {}, "outputs": [], - "source": [] + "source": [ + "# pxf validate --hpo hp.json *.json\n", + "# no errors" + ] } ], "metadata": { "kernelspec": { - "display_name": "ps_venv", + "display_name": "pstore_env", "language": "python", - "name": "ps_venv" + "name": "pstore_env" }, "language_info": { "codemirror_mode": { @@ -862,7 +827,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.12" + "version": "3.11.3" } }, "nbformat": 4, diff --git a/notebooks/MAPK8IP3/phenopackets/PMID_30612693_1.json b/notebooks/MAPK8IP3/phenopackets/PMID_30612693_1.json new file mode 100644 index 000000000..bc3b24637 --- 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