diff --git a/.github/workflows/build-and-deploy-images.yaml b/.github/workflows/build-and-deploy-images.yaml
index df784f659..e60497c16 100644
--- a/.github/workflows/build-and-deploy-images.yaml
+++ b/.github/workflows/build-and-deploy-images.yaml
@@ -104,8 +104,18 @@ jobs:
with:
version: ">= 447.0.0"
+ - name: "Cache SSH Key"
+ uses: actions/cache@v3
+ with:
+ path: ~/.ssh/google_compute_engine
+ key: ${{ runner.os }}-ssh-key
+
- name: "Update API Service"
- run: gcloud compute ssh --zone us-central1-a monarch-v3-dev-manager -- sudo docker service update monarch-v3_api --with-registry-auth --update-order=start-first --force --image us-central1-docker.pkg.dev/monarch-initiative/monarch-api/monarch-api:${{ github.sha }}
+ run: |
+ gcloud compute ssh --ssh-key-expiration 60m --zone us-central1-a monarch-v3-dev-manager -- sudo docker system prune -f
+ gcloud compute ssh --ssh-key-expiration 60m --zone us-central1-a monarch-v3-dev-manager -- sudo docker service update monarch-v3_api --with-registry-auth --update-order=start-first --force --image us-central1-docker.pkg.dev/monarch-initiative/monarch-api/monarch-api:${{ github.sha }}
- name: "Update UI Service"
- run: gcloud compute ssh --zone us-central1-a monarch-v3-dev-manager -- sudo docker service update monarch-v3_nginx --with-registry-auth --update-order=start-first --force --image us-central1-docker.pkg.dev/monarch-initiative/monarch-api/monarch-ui:${{ github.sha }}
+ run: |
+ gcloud compute ssh --ssh-key-expiration 60m --zone us-central1-a monarch-v3-dev-manager -- sudo docker system prune -f
+ gcloud compute ssh --ssh-key-expiration 60m --zone us-central1-a monarch-v3-dev-manager -- sudo docker service update monarch-v3_nginx --with-registry-auth --update-order=start-first --force --image us-central1-docker.pkg.dev/monarch-initiative/monarch-api/monarch-ui:${{ github.sha }}
diff --git a/Makefile b/Makefile
index adbd08b77..008a12bda 100644
--- a/Makefile
+++ b/Makefile
@@ -77,7 +77,7 @@ install-frontend:
model: install-backend
$(RUN) gen-pydantic $(SCHEMADIR)/model.yaml > $(SCHEMADIR)/model.py
$(RUN) gen-typescript $(SCHEMADIR)/model.yaml > frontend/src/api/model.ts
- $(RUN) black $(SCHEMADIR)/model.py
+ make format
### Documentation ###
@@ -111,11 +111,20 @@ test-frontend:
.PHONY: fixtures
fixtures:
- @echo "Generating fixtures..."
+ @echo "Generating fixtures and data..."
$(RUN) python scripts/generate_fixtures.py --all-fixtures
- $(RUN) black -l 120 backend/tests/fixtures/
- cd frontend && \
- yarn lint
+ make format
+
+
+.PHONY: data
+data:
+ @echo "Generating frontpage metadata..."
+ $(RUN) python scripts/generate_fixtures.py --metadata
+ @echo "Generating publications data..."
+ $(RUN) python scripts/get_publications.py
+ @echo "Generating resources data..."
+ wget https://raw.githubusercontent.com/monarch-initiative/monarch-documentation/main/src/docs/resources/monarch-app-resources.json -O frontend/src/pages/resources/resources.json
+ make format-frontend
### Development ###
diff --git a/backend/poetry.lock b/backend/poetry.lock
index a89ae5209..bd18534a5 100644
--- a/backend/poetry.lock
+++ b/backend/poetry.lock
@@ -166,18 +166,18 @@ pyparsing = ">=2.0.3"
[[package]]
name = "bioregistry"
-version = "0.10.68"
+version = "0.10.101"
description = "Integrated registry of biological databases and nomenclatures"
optional = false
python-versions = ">=3.8"
files = [
- {file = "bioregistry-0.10.68-py3-none-any.whl", hash = "sha256:78bdff06cab90432b8b7336e997ef340dbe4d7c7148503d6ec5f4747f038a483"},
- {file = "bioregistry-0.10.68.tar.gz", hash = "sha256:1f487caf2dea2cc5eec50da33ed6c9343deffb9a27788ac4a726562efc32bf98"},
+ {file = "bioregistry-0.10.101-py3-none-any.whl", hash = "sha256:4b26748183dca2b3f9eff9fb742074c2199ec2d830f60c1dd0530271fb04187a"},
+ {file = "bioregistry-0.10.101.tar.gz", hash = "sha256:891a1178742fa166fb5209dd5cc632cfaad1540365cfb400cfbe79b03334ae28"},
]
[package.dependencies]
click = "*"
-curies = ">=0.6.0"
+curies = ">=0.7.0"
more-click = ">=0.1.2"
pydantic = "*"
pystow = ">=0.1.13"
@@ -516,13 +516,13 @@ files = [
[[package]]
name = "curies"
-version = "0.6.7"
+version = "0.7.4"
description = "Idiomatic conversion between URIs and compact URIs (CURIEs)."
optional = false
python-versions = ">=3.8"
files = [
- {file = "curies-0.6.7-py3-none-any.whl", hash = "sha256:53ade109e4b397006e2c1253680ae33e4fc533504398dacea9149c3ffcb9a4cb"},
- {file = "curies-0.6.7.tar.gz", hash = "sha256:8e441999d6abcda6530f897167f10ad1530da11f51bba58ae04ad8445bb735b5"},
+ {file = "curies-0.7.4-py3-none-any.whl", hash = "sha256:478f1818345988933d8bc6060f80a985401331f856ff8cf9bd98fa00d178ad39"},
+ {file = "curies-0.7.4.tar.gz", hash = "sha256:d3aaf16644b26ac2605ff83c565ec7df0ba0b5f7425516047666e609ec5fb718"},
]
[package.dependencies]
@@ -718,48 +718,57 @@ all = ["email-validator (>=2.0.0)", "httpx (>=0.23.0)", "itsdangerous (>=1.1.0)"
[[package]]
name = "fastobo"
-version = "0.12.2"
+version = "0.12.3"
description = "Faultless AST for Open Biomedical Ontologies in Python."
optional = false
python-versions = ">=3.7"
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[[package]]
name = "selenium"
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description = ""
optional = false
python-versions = ">=3.8"
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-networkx = ">=3.1"
-pandas = ">=2.0.3"
-pansql = ">=0.0.1"
+networkx = {version = ">=3.1", extras = ["networkx"]}
+pandas = ">1.0.3"
+pansql = {version = ">=0.0.1", extras = ["pansql"]}
pyyaml = ">=6.0.1,<7.0.0"
rdflib = ">=6.0.0"
scipy = {version = "*", extras = ["scipy"]}
@@ -4191,13 +4222,13 @@ files = [
[[package]]
name = "typing-extensions"
-version = "4.8.0"
+version = "4.9.0"
description = "Backported and Experimental Type Hints for Python 3.8+"
optional = false
python-versions = ">=3.8"
files = [
- {file = "typing_extensions-4.8.0-py3-none-any.whl", hash = "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0"},
- {file = "typing_extensions-4.8.0.tar.gz", hash = "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef"},
+ {file = "typing_extensions-4.9.0-py3-none-any.whl", hash = "sha256:af72aea155e91adfc61c3ae9e0e342dbc0cba726d6cba4b6c72c1f34e47291cd"},
+ {file = "typing_extensions-4.9.0.tar.gz", hash = "sha256:23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783"},
]
[[package]]
diff --git a/backend/src/monarch_py/datamodels/model.py b/backend/src/monarch_py/datamodels/model.py
index dbe8b7e46..1c96d4a1b 100644
--- a/backend/src/monarch_py/datamodels/model.py
+++ b/backend/src/monarch_py/datamodels/model.py
@@ -373,6 +373,10 @@ class Entity(ConfiguredBaseModel):
category: Optional[str] = Field(None)
name: Optional[str] = Field(None)
full_name: Optional[str] = Field(None, description="""The long form name of an entity""")
+ deprecated: Optional[bool] = Field(
+ None,
+ description="""A boolean flag indicating that an entity is no longer considered current or valid.""",
+ )
description: Optional[str] = Field(None)
xref: Optional[List[str]] = Field(default_factory=list)
provided_by: Optional[str] = Field(None)
@@ -474,6 +478,10 @@ class Node(Entity):
category: Optional[str] = Field(None)
name: Optional[str] = Field(None)
full_name: Optional[str] = Field(None, description="""The long form name of an entity""")
+ deprecated: Optional[bool] = Field(
+ None,
+ description="""A boolean flag indicating that an entity is no longer considered current or valid.""",
+ )
description: Optional[str] = Field(None)
xref: Optional[List[str]] = Field(default_factory=list)
provided_by: Optional[str] = Field(None)
@@ -575,6 +583,10 @@ class SearchResult(Entity):
category: str = Field(...)
name: str = Field(...)
full_name: Optional[str] = Field(None, description="""The long form name of an entity""")
+ deprecated: Optional[bool] = Field(
+ None,
+ description="""A boolean flag indicating that an entity is no longer considered current or valid.""",
+ )
description: Optional[str] = Field(None)
xref: Optional[List[str]] = Field(default_factory=list)
provided_by: Optional[str] = Field(None)
diff --git a/backend/src/monarch_py/datamodels/model.yaml b/backend/src/monarch_py/datamodels/model.yaml
index 6458fc9b3..89604d5be 100644
--- a/backend/src/monarch_py/datamodels/model.yaml
+++ b/backend/src/monarch_py/datamodels/model.yaml
@@ -166,6 +166,7 @@ classes:
- category
- name
- full_name
+ - deprecated
- description
- xref
- provided_by
@@ -304,6 +305,13 @@ slots:
The category of the counterpart entity in a given association,
eg. the category of the entity that is not the subject
range: string
+ deprecated:
+ description: >-
+ A boolean flag indicating that an entity is no longer considered current or valid.
+ range: boolean
+ exact_mappings:
+ - oboInOwl:ObsoleteClass
+
description:
range: string
direction:
diff --git a/backend/src/monarch_py/implementations/solr/solr_parsers.py b/backend/src/monarch_py/implementations/solr/solr_parsers.py
index f2dcbae2a..c56cebdc4 100644
--- a/backend/src/monarch_py/implementations/solr/solr_parsers.py
+++ b/backend/src/monarch_py/implementations/solr/solr_parsers.py
@@ -88,6 +88,7 @@ def parse_association_counts(query_result: SolrQueryResult, entity: str) -> Asso
def parse_entity(solr_document: Dict) -> Entity:
try:
entity = Entity(**solr_document)
+
entity.uri = get_uri(entity.id)
except ValidationError:
logger.error(f"Validation error for {solr_document}")
diff --git a/backend/src/monarch_py/implementations/solr/solr_query_utils.py b/backend/src/monarch_py/implementations/solr/solr_query_utils.py
index f38a835b0..51bb2a0ff 100644
--- a/backend/src/monarch_py/implementations/solr/solr_query_utils.py
+++ b/backend/src/monarch_py/implementations/solr/solr_query_utils.py
@@ -204,7 +204,8 @@ def entity_boost():
"""Shared boost function between search and autocomplete"""
disease_boost = 'if(termfreq(category,"biolink:Disease"),10.0,1)'
human_gene_boost = 'if(and(termfreq(in_taxon,"NCBITaxon:9606"),termfreq(category,"biolink:Gene")),5.0,1)'
- return f"product({disease_boost},{human_gene_boost})"
+ obsolete_unboost = 'if(termfreq(deprecated,"true"),0.1,1)'
+ return f"product({disease_boost},{human_gene_boost},{obsolete_unboost})"
def entity_query_fields():
diff --git a/backend/src/monarch_py/service/curie_service.py b/backend/src/monarch_py/service/curie_service.py
index cd62ebe22..888ac9eaa 100644
--- a/backend/src/monarch_py/service/curie_service.py
+++ b/backend/src/monarch_py/service/curie_service.py
@@ -1,7 +1,7 @@
### make a singleton class that uses prefixmap and curies to expand curies
from curies import Converter
-from prefixmaps.io.parser import load_multi_context
+from prefixmaps import load_converter
class CurieService:
@@ -17,9 +17,7 @@ def __new__(cls):
def initialize(self):
# this is a magic keyword that represents the "merged" context from Chris M's algorithm
# (https://github.com/linkml/prefixmaps/blob/main/src/prefixmaps/data/merged.csv)
- context = load_multi_context(["merged"])
- extended_prefix_map = context.as_extended_prefix_map()
- self.converter = Converter.from_extended_prefix_map(extended_prefix_map)
+ self.converter = load_converter(["merged"])
def expand(self, curie: str) -> str:
return self.converter.expand(curie)
diff --git a/backend/src/monarch_py/service/solr_service.py b/backend/src/monarch_py/service/solr_service.py
index eddb7e054..da84d45a5 100644
--- a/backend/src/monarch_py/service/solr_service.py
+++ b/backend/src/monarch_py/service/solr_service.py
@@ -18,7 +18,7 @@ def get(self, id):
response.raise_for_status()
entity = response.json()["doc"]
try:
- self._strip_json(entity, "_version_")
+ self._strip_json(entity, "_version_", "iri")
except TypeError: # if entity is None
return None
return entity
@@ -33,7 +33,7 @@ def query(self, q: SolrQuery) -> SolrQueryResult:
response.raise_for_status()
solr_query_result = SolrQueryResult.parse_obj(data)
for doc in solr_query_result.response.docs:
- self._strip_json(doc, "_version_")
+ self._strip_json(doc, "_version_", "iri")
return solr_query_result
diff --git a/backend/tests/fixtures/association_counts_response.py b/backend/tests/fixtures/association_counts_response.py
index 8878112b5..a36a793cb 100644
--- a/backend/tests/fixtures/association_counts_response.py
+++ b/backend/tests/fixtures/association_counts_response.py
@@ -5,7 +5,7 @@
def association_counts_response():
return {
"responseHeader": {
- "QTime": 0,
+ "QTime": 3,
"params": {
"facet.query": [
'(category:"biolink:DiseaseToPhenotypicFeatureAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")',
@@ -49,4214 +49,4140 @@ def association_counts_response():
"start": 0,
"docs": [
{
- "id": "uuid:c9c8bf2f-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:160500",
+ "id": "uuid:4e12a2a1-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:565899",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["PMID:17548557"],
- "frequency_qualifier": "HP:0040280",
- "has_evidence": ["ECO:0000269"],
- "subject": "MONDO:0008050",
- "object": "HP:0011399",
- "subject_label": "MYH7-related skeletal myopathy",
+ "publications": ["orphanet:565899"],
+ "frequency_qualifier": "HP:0040282",
+ "has_evidence": ["ECO:0000304"],
+ "subject": "MONDO:0035432",
+ "object": "HP:0002465",
+ "subject_label": "POMGNT2-related limb-girdle muscular dystrophy R24",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
+ "MONDO:0000001",
+ "MONDO:0020121",
"MONDO:0003847",
"BFO:0000001",
- "MONDO:0020121",
- "MONDO:0019952",
+ "MONDO:0016106",
+ "MONDO:0005336",
"BFO:0000017",
+ "MONDO:0003939",
+ "MONDO:0035432",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0016971",
+ "MONDO:0005071",
+ "BFO:0000002",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
"MONDO:0700223",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "OGMS:0000031",
],
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
"disease",
+ "realizable entity",
+ "disease",
+ "POMGNT2-related limb-girdle muscular dystrophy R24",
"muscle tissue disorder",
- "congenital nervous system disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
+ "limb-girdle muscular dystrophy",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "disposition",
+ "human disease",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
"nervous system disorder",
- "congenital myopathy",
- "realizable entity",
- "specifically dependent continuant",
+ "entity",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "muscular dystrophy",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
],
- "object_label": "Tibialis atrophy (HPO)",
+ "object_label": "Poor speech (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "UPHENO:0014121",
- "HP:0002814",
- "UPHENO:0068971",
- "UPHENO:0001005",
- "HP:0009127",
- "UPHENO:0014120",
- "UPHENO:0075195",
- "HP:0030236",
- "UPHENO:0020584",
- "UPHENO:0076692",
- "UPHENO:0003070",
- "PATO:0000001",
- "UPHENO:0012541",
- "BFO:0000004",
- "UBERON:0004708",
- "UBERON:0000154",
- "UBERON:0014892",
- "UBERON:0006058",
- "UBERON:0002529",
- "UBERON:0006067",
- "HP:0000001",
- "UPHENO:0002644",
- "UPHENO:0013936",
- "HP:0003202",
- "UPHENO:0075952",
- "UPHENO:0001002",
- "HP:0000118",
- "UPHENO:0015280",
- "UPHENO:0001003",
- "UPHENO:0076710",
- "BFO:0000001",
+ "UPHENO:0002536",
"BFO:0000001",
- "BFO:0000040",
- "UBERON:0010000",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
- "UBERON:0010709",
- "UBERON:0000366",
- "UBERON:0003661",
- "UBERON:0010890",
- "UBERON:0010538",
- "UBERON:0004466",
- "UBERON:0004256",
- "UBERON:0003823",
- "UPHENO:0075696",
- "HP:0002981",
- "HP:0003797",
- "UPHENO:0014111",
- "HP:0001430",
+ "UBERON:0000465",
+ "UPHENO:0082875",
"BFO:0000002",
- "HP:0008944",
+ "UPHENO:0004523",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UPHENO:0001002",
"BFO:0000020",
- "HP:0003011",
- "UPHENO:0002536",
- "HP:0001437",
- "UPHENO:0078056",
- "HP:0040064",
"BFO:0000002",
- "PR:000050567",
- "UBERON:0002101",
- "UBERON:0004709",
- "UBERON:0005090",
- "UBERON:0018254",
- "UBERON:0002103",
- "UBERON:0010707",
- "UBERON:0001630",
- "UBERON:0000026",
- "UBERON:0010758",
- "UBERON:0007271",
- "UBERON:0014792",
- "UBERON:0004482",
- "UBERON:0001383",
- "UBERON:0008784",
- "UBERON:0002471",
- "HP:0007210",
"UPHENO:0001001",
- "UPHENO:0075777",
- "HP:0011805",
- "HP:0003693",
- "UPHENO:0002816",
- "HP:0011399",
- "UPHENO:0081581",
- "HP:0033127",
- "UPHENO:0019778",
- "UPHENO:0002647",
- "UPHENO:0013920",
- "UPHENO:0002830",
- "UBERON:0001062",
- "UBERON:0000465",
- "RO:0002577",
+ "UPHENO:0001003",
+ "BFO:0000001",
+ "UPHENO:0075696",
+ "UPHENO:0002433",
+ "HP:0012638",
+ "BFO:0000004",
"UBERON:0000061",
- "UBERON:0015212",
- "UBERON:0000475",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "UBERON:0000978",
- "UBERON:0007270",
- "UBERON:0004480",
- "UBERON:0003663",
- "UBERON:0014795",
- "UBERON:0008230",
+ "UBERON:0000468",
+ "HP:0002167",
+ "PATO:0000001",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "HP:0000001",
+ "HP:0002465",
+ "UPHENO:0001005",
+ "HP:0000707",
+ "HP:0011446",
+ "UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0001016",
],
"object_closure_label": [
+ "abnormality of anatomical entity physiology",
+ "Neurological speech impairment (HPO)",
+ "Abnormality of higher mental function (HPO)",
+ "abnormal anatomical entity",
+ "specifically dependent continuant",
+ "phenotype by ontology source",
+ "abnormal nervous system",
+ "continuant",
+ "material anatomical entity",
+ "nervous system",
"All (HPO)",
- "abnormal musculature of lower limb",
- "Abnormality of the lower limb (HPO)",
- "decreased size of the anatomical entity",
- "Phenotypic abnormality",
+ "Poor speech (HPO)",
+ "abnormal phenotype by ontology source",
"Phenotypic abnormality (HPO)",
- "Distal amyotrophy (HPO)",
- "abnormal musculature",
- "Tibialis atrophy (HPO)",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "abnormal musculature of limb",
- "independent continuant",
- "material anatomical entity",
- "system",
- "paired limb/fin",
- "lateral structure",
- "pelvic complex",
- "appendage musculature",
- "musculature of pelvic complex",
- "musculature of leg",
- "hindlimb zeugopod muscle",
- "hindlimb zeugopod",
- "musculature of limb atrophy",
- "Limb-girdle muscle atrophy (HPO)",
- "skeletal musculature atrophy",
- "abnormal hindlimb zeugopod muscle",
- "Abnormal skeletal muscle morphology (HPO)",
- "abnormal anatomical entity morphology in the independent continuant",
- "phenotype by ontology source",
- "Abnormality of muscle size (HPO)",
- "Abnormality of the musculature of the lower limbs (HPO)",
- "tibialis atrophy",
- "Abnormality of limbs (HPO)",
+ "Abnormality of the nervous system (HPO)",
+ "entity",
+ "Phenotypic abnormality",
+ "abnormality of nervous system physiology",
"quality",
- "decreased size of the anatomical entity in the independent continuant",
- "continuant",
- "protein-containing material entity",
- "hindlimb",
- "appendage girdle complex",
- "appendage",
- "subdivision of organism along appendicular axis",
- "flexor muscle",
- "limb muscle",
- "pelvic complex muscle",
- "paired limb/fin segment",
- "musculature of lower limb",
- "muscle of leg",
- "lower limb segment",
- "zeugopod",
- "Lower limb amyotrophy (HPO)",
+ "multicellular organism",
"phenotype",
- "abnormal phenotype by ontology source",
- "Abnormality of the musculature of the limbs (HPO)",
- "musculature of lower limb atrophy",
- "abnormal size of anatomical entity",
- "abnormal muscle organ morphology",
- "abnormal muscle organ morphology",
+ "independent continuant",
"entity",
+ "Abnormal nervous system physiology (HPO)",
+ "material entity",
"anatomical entity",
"anatomical structure",
- "muscle structure",
- "skeletal musculature",
- "organism subdivision",
- "organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "leg",
- "pelvic appendage musculature",
- "musculature of limb",
- "hindlimb muscle",
- "pelvic appendage muscle",
- "tibialis",
- "abnormal anatomical entity",
- "Abnormality of the calf (HPO)",
- "anatomical entity atrophy",
- "Skeletal muscle atrophy (HPO)",
- "abnormal hindlimb zeugopod",
- "Abnormality of the calf musculature (HPO)",
"continuant",
- "Distal lower limb amyotrophy (HPO)",
- "specifically dependent continuant",
- "Abnormality of the musculature (HPO)",
+ "abnormality of anatomical entity physiology",
"abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "abnormal anatomical entity morphology",
- "abnormal leg",
- "entity",
- "muscle organ atrophy",
- "abnormal limb",
- "material entity",
- "limb",
- "pelvic appendage",
"multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "posterior region of body",
- "skeletal muscle organ",
- "multi-limb segment region",
- "limb segment",
- "musculature of hindlimb zeugopod",
],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0011399",
+ "grouping_key": "MONDO:0035432🍪🍪biolink:has_phenotype🍪HP:0002465",
},
{
- "id": "uuid:c9c8bf30-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:160500",
+ "id": "uuid:4e12a2a3-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:565899",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["PMID:17548557"],
- "frequency_qualifier": "HP:0040280",
- "has_evidence": ["ECO:0000269"],
- "subject": "MONDO:0008050",
- "object": "HP:0031295",
- "subject_label": "MYH7-related skeletal myopathy",
+ "publications": ["orphanet:565899"],
+ "frequency_qualifier": "HP:0040282",
+ "has_evidence": ["ECO:0000304"],
+ "subject": "MONDO:0035432",
+ "object": "HP:0008981",
+ "subject_label": "POMGNT2-related limb-girdle muscular dystrophy R24",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
+ "MONDO:0000001",
+ "MONDO:0020121",
"MONDO:0003847",
"BFO:0000001",
- "MONDO:0020121",
- "MONDO:0019952",
+ "MONDO:0016106",
+ "MONDO:0005336",
"BFO:0000017",
+ "MONDO:0003939",
+ "MONDO:0035432",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0016971",
+ "MONDO:0005071",
+ "BFO:0000002",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
"MONDO:0700223",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "OGMS:0000031",
],
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
"disease",
+ "realizable entity",
+ "disease",
+ "POMGNT2-related limb-girdle muscular dystrophy R24",
"muscle tissue disorder",
- "congenital nervous system disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
+ "limb-girdle muscular dystrophy",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "disposition",
+ "human disease",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
"nervous system disorder",
- "congenital myopathy",
- "realizable entity",
- "specifically dependent continuant",
+ "entity",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "muscular dystrophy",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
],
- "object_label": "Left atrial enlargement (HPO)",
+ "object_label": "Calf muscle hypertrophy (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "UPHENO:0001005",
- "BFO:0000002",
- "UPHENO:0075195",
- "UPHENO:0020584",
- "UPHENO:0076692",
- "BFO:0000004",
- "UBERON:0004535",
- "UBERON:0011676",
- "UBERON:0013701",
- "UBERON:0002081",
- "UBERON:0000915",
- "UBERON:0002100",
- "UBERON:0005181",
- "UBERON:0002075",
- "UBERON:0015228",
- "HP:0000001",
- "UPHENO:0019897",
- "HP:0030680",
- "HP:0000118",
- "HP:0001627",
- "BFO:0000020",
- "UPHENO:0019919",
- "UPHENO:0076776",
- "UPHENO:0015280",
- "UPHENO:0001020",
- "UPHENO:0001003",
- "BFO:0000001",
- "PATO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0000064",
- "UBERON:0002079",
- "UPHENO:0075696",
- "UPHENO:0015303",
- "HP:0001626",
- "UPHENO:0080362",
- "UPHENO:0065599",
- "HP:0031295",
- "UPHENO:0002536",
- "UPHENO:0076810",
+ "HP:0008981",
+ "UPHENO:0084535",
+ "UPHENO:0002816",
+ "HP:0030236",
"PR:000050567",
"UBERON:0000465",
- "UBERON:0004120",
- "UBERON:0035553",
- "UBERON:0000948",
- "UBERON:0001009",
- "UBERON:0004151",
- "UBERON:0009569",
- "UBERON:0013702",
- "UBERON:0005177",
- "UBERON:0003103",
- "UBERON:0015410",
- "UPHENO:0001001",
+ "RO:0002577",
+ "UPHENO:0015280",
+ "HP:0001437",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UBERON:0011216",
+ "UBERON:0000154",
+ "UBERON:0006067",
"UPHENO:0001002",
- "UPHENO:0015324",
- "HP:0025579",
+ "HP:0001430",
+ "UPHENO:0075195",
+ "UPHENO:0019778",
+ "UPHENO:0084489",
+ "BFO:0000002",
+ "UBERON:0002101",
+ "UBERON:0004709",
+ "UBERON:0015212",
+ "UBERON:0001630",
+ "UPHENO:0001001",
+ "UPHENO:0075777",
+ "HP:0011805",
+ "HP:0003712",
+ "UPHENO:0002647",
+ "BFO:0000001",
+ "UBERON:0004482",
+ "UBERON:0001383",
+ "UBERON:0008784",
+ "UBERON:0002471",
+ "UPHENO:0075696",
+ "UPHENO:0001005",
+ "HP:0009127",
+ "BFO:0000020",
"UPHENO:0001072",
"UPHENO:0081581",
- "HP:0005120",
- "UPHENO:0015329",
- "BFO:0000002",
- "UBERON:0001062",
- "RO:0002577",
+ "HP:0033127",
+ "UPHENO:0001003",
+ "UPHENO:0076692",
+ "UPHENO:0003070",
+ "UPHENO:0002830",
+ "BFO:0000004",
+ "UBERON:0004708",
"UBERON:0000061",
- "UBERON:0015212",
- "UBERON:0010314",
- "UBERON:0010000",
"UBERON:0000475",
"UBERON:0000062",
- "UBERON:0005178",
- "UBERON:0007100",
- ],
- "object_closure_label": [
- "All (HPO)",
- "abnormal cardiac atrium morphology",
- "abnormal cardiovascular system",
- "increased size of the anatomical entity in independent continuant",
- "Phenotypic abnormality (HPO)",
- "abnormal anatomical entity morphology in the heart",
- "Abnormal left atrium morphology (HPO)",
- "increased size of the anatomical entity",
- "abnormal multicellular organism morphology",
- "Abnormal cardiac atrium morphology (HPO)",
- "quality",
- "independent continuant",
- "system",
- "cardiovascular system",
- "lateral structure",
- "structure with developmental contribution from neural crest",
- "multicellular anatomical structure",
- "left cardiac atrium",
- "Abnormality of the cardiovascular system (HPO)",
- "Phenotypic abnormality",
- "Abnormal heart morphology (HPO)",
- "specifically dependent continuant",
- "abnormal left cardiac atrium morphology",
- "abnormal cardiovascular system morphology",
- "abnormal anatomical entity morphology in the independent continuant",
- "increased size of the left cardiac atrium",
- "phenotype by ontology source",
- "abnormal heart morphology",
- "protein-containing material entity",
- "material anatomical entity",
- "left cardiac chamber",
- "heart",
- "subdivision of trunk",
- "body proper",
- "trunk region element",
- "compound organ",
- "heart plus pericardium",
- "phenotype",
- "abnormal phenotype by ontology source",
- "continuant",
- "abnormal size of anatomical entity",
- "entity",
- "anatomical entity",
- "anatomical structure",
- "mesoderm-derived structure",
- "organism subdivision",
- "organ",
- "circulatory system",
- "cardiac chamber",
- "thoracic cavity element",
- "primary circulatory organ",
- "abnormal anatomical entity",
- "abnormal cardiac atrium morphology in the heart",
- "Abnormality of cardiovascular system morphology (HPO)",
- "Left atrial enlargement (HPO)",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "abnormal anatomical entity morphology",
- "entity",
- "abnormal cardiac atrium morphology in the independent continuant",
- "continuant",
- "material entity",
- "anatomical system",
- "multicellular organism",
- "organ part",
- "subdivision of organism along main body axis",
- "main body axis",
- "cardiac atrium",
- "thoracic segment of trunk",
- "trunk",
- "thoracic segment organ",
- "viscus",
- "circulatory organ",
- ],
- "frequency_qualifier_label": "Obligate (HPO)",
- "frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
- "evidence_count": 2,
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0031295",
- },
- {
- "id": "uuid:c9c8bf31-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:160500",
- "predicate": "biolink:has_phenotype",
- "category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "aggregator_knowledge_source": ["infores:monarchinitiative"],
- "primary_knowledge_source": "infores:hpo-annotations",
- "provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["PMID:17548557"],
- "frequency_qualifier": "HP:0040280",
- "has_evidence": ["ECO:0000269"],
- "subject": "MONDO:0008050",
- "object": "HP:0002938",
- "subject_label": "MYH7-related skeletal myopathy",
- "subject_category": "biolink:Disease",
- "subject_namespace": "MONDO",
- "subject_closure": [
+ "UBERON:0000468",
+ "UBERON:0010709",
+ "HP:0002981",
+ "UPHENO:0065599",
"BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
- "MONDO:0020121",
- "MONDO:0019952",
- "BFO:0000017",
- "BFO:0000020",
- "MONDO:0020120",
- "MONDO:0019056",
- "MONDO:0000001",
- "MONDO:0700223",
- "MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
- ],
- "subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
- "disease",
- "muscle tissue disorder",
- "congenital nervous system disorder",
- "hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
- "continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
- "myopathy",
- "hereditary disease",
- "nervous system disorder",
- "congenital myopathy",
- "realizable entity",
- "specifically dependent continuant",
- "skeletal muscle disorder",
- "neuromuscular disease",
- "entity",
- ],
- "object_label": "Lumbar hyperlordosis (HPO)",
- "object_category": "biolink:PhenotypicFeature",
- "object_namespace": "HP",
- "object_closure": [
- "UPHENO:0001005",
- "HP:0009121",
- "UPHENO:0020584",
- "UPHENO:0076692",
- "BFO:0000001",
+ "HP:0003011",
+ "UPHENO:0002536",
+ "UPHENO:0084715",
+ "UPHENO:0076710",
+ "HP:0040064",
"PATO:0000001",
- "BFO:0000004",
- "UBERON:0002204",
- "UBERON:0011676",
- "UBERON:0001137",
- "UBERON:0013701",
- "UBERON:0002100",
- "UBERON:0005462",
- "HP:0000001",
- "UPHENO:0076703",
+ "UBERON:0002103",
+ "UBERON:0010707",
+ "UBERON:0000026",
+ "UBERON:0010758",
+ "UBERON:0006058",
+ "UBERON:0004466",
+ "UBERON:0004256",
+ "UBERON:0003823",
+ "HP:0002814",
+ "UPHENO:0075952",
"HP:0000118",
- "BFO:0000020",
- "HP:0000925",
- "UPHENO:0015280",
- "UPHENO:0002964",
- "UPHENO:0001003",
- "HP:0003307",
- "UPHENO:0022529",
+ "UPHENO:0020584",
+ "HP:0008968",
+ "UBERON:0007271",
+ "UBERON:0014792",
+ "UBERON:0003661",
+ "UBERON:0010890",
+ "UBERON:0010538",
+ "HP:0000001",
+ "UPHENO:0002644",
"BFO:0000001",
- "BFO:0000040",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
- "UPHENO:0075696",
- "HP:0000924",
- "UPHENO:0002536",
- "BFO:0000002",
- "UBERON:0004288",
- "UBERON:0009569",
- "UBERON:0013702",
- "UBERON:0000075",
- "UBERON:0002417",
- "UBERON:0011137",
- "UBERON:0006077",
- "UBERON:0011138",
- "UBERON:0002090",
- "UBERON:0005944",
- "UBERON:0001130",
- "UPHENO:0001001",
- "HP:0011842",
- "UPHENO:0001002",
- "BFO:0000002",
- "HP:0010674",
- "UPHENO:0081581",
- "HP:0033127",
- "UPHENO:0002813",
- "HP:0002938",
- "UBERON:0001062",
- "UBERON:0000465",
- "UBERON:0000061",
- "UBERON:0034925",
"UBERON:0010000",
- "UBERON:0000475",
- "UBERON:0010912",
- "UBERON:0001434",
- "UBERON:0006074",
+ "UBERON:0000467",
+ "UBERON:0005090",
+ "UBERON:0018254",
+ "UBERON:0000383",
+ "UBERON:0001015",
+ "UBERON:0014892",
+ "UBERON:0000978",
+ "UBERON:0007270",
+ "UBERON:0004480",
+ "UBERON:0003663",
+ "UBERON:0014795",
+ "UBERON:0002529",
],
"object_closure_label": [
+ "increased size of the anatomical entity in independent continuant",
+ "abnormal hindlimb zeugopod muscle",
+ "Abnormal skeletal muscle morphology (HPO)",
+ "Skeletal muscle hypertrophy (HPO)",
+ "abnormal anatomical entity",
+ "musculature of hindlimb zeugopod",
+ "abnormal anatomical entity",
+ "abnormal phenotype by ontology source",
+ "Abnormality of the musculature of the limbs (HPO)",
+ "Abnormality of the musculature (HPO)",
+ "Abnormality of the musculature of the lower limbs (HPO)",
+ "abnormal musculature of limb",
+ "continuant",
+ "protein-containing material entity",
+ "material anatomical entity",
+ "system",
+ "multi-limb segment region",
"All (HPO)",
+ "abnormal musculature of lower limb",
+ "continuant",
+ "abnormal musculature",
+ "abnormal muscle organ morphology",
+ "hypertrophic multicellular anatomical structure",
+ "organ system subdivision",
+ "muscle organ",
+ "appendage",
+ "subdivision of organism along appendicular axis",
+ "Abnormality of the lower limb (HPO)",
"Phenotypic abnormality (HPO)",
- "Abnormality of the curvature of the vertebral column (HPO)",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "Hyperlordosis (HPO)",
- "abnormal postcranial axial skeleton morphology",
- "independent continuant",
- "material anatomical entity",
- "multicellular anatomical structure",
- "musculoskeletal system",
- "abdominal segment of trunk",
- "axial skeletal system",
- "subdivision of vertebral column",
- "postcranial axial skeletal system",
- "postcranial axial skeleton",
- "axial skeleton plus cranial skeleton",
- "vertebral column",
- "Abnormal skeletal morphology (HPO)",
+ "abnormal anatomical entity morphology",
+ "Muscle hypertrophy of the lower extremities (HPO)",
+ "entity",
+ "entity",
+ "leg",
+ "pelvic appendage musculature",
+ "musculature of limb",
+ "hindlimb muscle",
+ "pelvic appendage muscle",
+ "limb segment",
"Phenotypic abnormality",
- "continuant",
+ "Abnormality of the calf musculature (HPO)",
"specifically dependent continuant",
- "Abnormality of the vertebral column (HPO)",
- "abnormal anatomical entity morphology in the independent continuant",
- "abnormal skeletal system",
- "phenotype by ontology source",
+ "abnormal anatomical entity morphology",
+ "abnormal leg",
"quality",
- "continuant",
- "subdivision of trunk",
- "body proper",
- "subdivision of skeletal system",
+ "organism subdivision",
+ "organ",
+ "multicellular organism",
+ "pelvic complex",
+ "musculature of lower limb",
+ "muscle of leg",
+ "lower limb segment",
+ "zeugopod",
"phenotype",
- "abnormal phenotype by ontology source",
- "Abnormal axial skeleton morphology (HPO)",
- "abnormal vertebral column",
- "Lumbar hyperlordosis (HPO)",
- "entity",
+ "abnormal hindlimb zeugopod",
+ "abnormal anatomical entity morphology in the independent continuant",
+ "abnormally increased volume of anatomical entity",
+ "independent continuant",
+ "posterior region of body",
+ "Calf muscle hypertrophy (HPO)",
+ "hypertrophic pelvic complex muscle",
+ "abnormal size of anatomical entity",
+ "increased size of the anatomical entity",
+ "abnormal multicellular organism morphology",
+ "Abnormality of the musculoskeletal system (HPO)",
+ "phenotype by ontology source",
+ "abnormal limb",
+ "material entity",
"anatomical entity",
+ "paired limb/fin",
"anatomical structure",
- "anatomical collection",
- "skeleton",
- "organism subdivision",
- "subdivision of skeleton",
- "skeletal system",
- "lumbar region of vertebral column",
- "abnormal anatomical entity",
- "abnormal skeletal system morphology",
- "Abnormality of the skeletal system (HPO)",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "abnormal anatomical entity morphology",
- "entity",
- "material entity",
+ "limb",
+ "pelvic appendage",
+ "lateral structure",
+ "musculature of body",
+ "musculature",
+ "skeletal muscle organ",
+ "musculature of leg",
+ "hindlimb zeugopod muscle",
+ "hindlimb zeugopod",
+ "Abnormality of the calf (HPO)",
+ "Abnormality of muscle size (HPO)",
+ "abnormal muscle organ morphology",
+ "Abnormality of limbs (HPO)",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "subdivision of organism along main body axis",
- "dorsum",
- "main body axis",
- "trunk",
- "lower back",
+ "muscle structure",
+ "skeletal musculature",
+ "hindlimb",
+ "appendage girdle complex",
+ "appendage musculature",
+ "musculature of pelvic complex",
+ "limb muscle",
+ "pelvic complex muscle",
+ "paired limb/fin segment",
],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0002938",
+ "grouping_key": "MONDO:0035432🍪🍪biolink:has_phenotype🍪HP:0008981",
},
{
- "id": "uuid:c9c8bf38-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:160500",
+ "id": "uuid:4e12a2a4-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:565899",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["PMID:17548557"],
- "frequency_qualifier": "HP:0040280",
- "has_evidence": ["ECO:0000269"],
- "subject": "MONDO:0008050",
- "object": "HP:0001265",
- "subject_label": "MYH7-related skeletal myopathy",
+ "publications": ["orphanet:565899"],
+ "frequency_qualifier": "HP:0040282",
+ "has_evidence": ["ECO:0000304"],
+ "subject": "MONDO:0035432",
+ "object": "HP:0008994",
+ "subject_label": "POMGNT2-related limb-girdle muscular dystrophy R24",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
+ "MONDO:0000001",
+ "MONDO:0020121",
"MONDO:0003847",
"BFO:0000001",
- "MONDO:0020121",
- "MONDO:0019952",
+ "MONDO:0016106",
+ "MONDO:0005336",
"BFO:0000017",
+ "MONDO:0003939",
+ "MONDO:0035432",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0016971",
+ "MONDO:0005071",
+ "BFO:0000002",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
"MONDO:0700223",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "OGMS:0000031",
],
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
"disease",
+ "realizable entity",
+ "disease",
+ "POMGNT2-related limb-girdle muscular dystrophy R24",
"muscle tissue disorder",
- "congenital nervous system disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
+ "limb-girdle muscular dystrophy",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "disposition",
+ "human disease",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
"nervous system disorder",
- "congenital myopathy",
- "realizable entity",
- "specifically dependent continuant",
+ "entity",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "muscular dystrophy",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
],
- "object_label": "Hyporeflexia (HPO)",
+ "object_label": "Proximal muscle weakness in lower limbs (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
+ "HP:0008994",
+ "UPHENO:0002816",
+ "UPHENO:0002536",
+ "PR:000050567",
+ "UBERON:0000465",
+ "RO:0002577",
"UPHENO:0082875",
- "UPHENO:0049622",
- "UPHENO:0001005",
+ "HP:0001437",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UBERON:0011216",
+ "UBERON:0000154",
+ "UBERON:0000026",
+ "UPHENO:0001002",
+ "HP:0001324",
"BFO:0000020",
- "UPHENO:0050606",
- "HP:0012638",
- "BFO:0000015",
- "BFO:0000004",
- "GO:0050882",
- "NBO:0000338",
- "GO:0050905",
- "UBERON:0001016",
- "HP:0000001",
+ "UPHENO:0080555",
+ "HP:0011804",
+ "BFO:0000002",
+ "UBERON:0002101",
+ "UBERON:0004709",
+ "UBERON:0015212",
"UPHENO:0001001",
- "UPHENO:0080585",
- "HP:0001265",
- "HP:0031826",
- "UPHENO:0001002",
- "HP:0000118",
- "UPHENO:0052178",
- "UPHENO:0002433",
- "HP:0001315",
+ "HP:0003701",
+ "HP:0011805",
"UPHENO:0001003",
- "HP:0000708",
- "HP:0011446",
- "PATO:0000001",
+ "UPHENO:0002647",
"BFO:0000001",
- "BFO:0000040",
- "UBERON:0001062",
- "GO:0050896",
- "GO:0032501",
- "GO:0060004",
- "GO:0050881",
- "NBO:0000313",
- "GO:0050877",
- "UBERON:0000467",
- "UBERON:0000468",
- "NBO:0000403",
- "NBO:0000001",
- "NBO:0000388",
+ "UBERON:0000061",
+ "UBERON:0004482",
+ "UBERON:0008784",
"UPHENO:0075696",
- "UPHENO:0078622",
- "UPHENO:0049586",
- "UPHENO:0080377",
- "HP:0100022",
- "UPHENO:0050613",
- "UPHENO:0005433",
- "UPHENO:0002332",
- "UPHENO:0002536",
- "UPHENO:0079826",
- "UPHENO:0004523",
- "UPHENO:0049587",
- "BFO:0000003",
- "BFO:0000002",
- "GO:0008150",
- "GO:0009605",
- "GO:0050879",
- "GO:0007610",
- "GO:0003008",
- "NBO:0000389",
- "UPHENO:0052915",
+ "UPHENO:0001005",
+ "HP:0009127",
+ "UPHENO:0081581",
+ "HP:0033127",
+ "UPHENO:0076692",
+ "UPHENO:0003070",
+ "UPHENO:0002830",
+ "BFO:0000004",
+ "UBERON:0004708",
+ "UBERON:0000475",
+ "UBERON:0000062",
+ "UBERON:0000468",
+ "UBERON:0010709",
+ "HP:0003690",
"BFO:0000002",
- "UPHENO:0005625",
- "UPHENO:0050079",
- "HP:0000707",
- "UPHENO:0079833",
+ "HP:0003011",
+ "UPHENO:0076710",
+ "HP:0040064",
+ "UBERON:0002103",
+ "UBERON:0010707",
+ "UBERON:0010758",
+ "UBERON:0006058",
+ "UPHENO:0002320",
+ "HP:0002814",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "PATO:0000001",
+ "UBERON:0007271",
+ "UBERON:0014792",
+ "UBERON:0010538",
+ "HP:0000001",
+ "UPHENO:0002644",
+ "UPHENO:0080556",
"BFO:0000001",
- "UBERON:0000465",
- "UBERON:0000061",
"UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0005090",
+ "UBERON:0001630",
+ "UBERON:0000383",
+ "UBERON:0001015",
+ "UBERON:0000978",
+ "UBERON:0007270",
+ "UBERON:0004480",
+ "UBERON:0002529",
],
"object_closure_label": [
- "All (HPO)",
- "abnormal behavior",
- "Abnormality of movement (HPO)",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "decreased reflex",
- "abnormal response to external stimulus",
- "Abnormality of the nervous system (HPO)",
- "Behavioral abnormality (HPO)",
- "Abnormality of higher mental function (HPO)",
- "abnormal voluntary movement behavior",
- "entity",
- "quality",
- "process",
- "independent continuant",
- "material anatomical entity",
- "multicellular anatomical structure",
- "nervous system",
- "voluntary movement behavior",
- "body part movement",
- "reflexive behavior",
"abnormality of anatomical entity physiology",
- "phenotype",
- "continuant",
- "decreased qualitatively biological_process",
- "abnormality of nervous system physiology",
- "Reduced tendon reflexes (HPO)",
- "phenotype by ontology source",
- "abnormal behavior process",
- "abnormal nervous system",
- "abnormal biological_process",
- "Abnormal nervous system physiology (HPO)",
- "occurrent",
- "continuant",
- "biological_process",
- "response to external stimulus",
- "multicellular organismal movement",
- "behavior",
- "system process",
- "reflex",
- "musculoskeletal movement",
- "behavior process",
- "nervous system process",
- "involuntary movement behavior",
- "decreased qualitatively response to stimulus",
+ "Proximal muscle weakness (HPO)",
+ "Abnormal skeletal muscle morphology (HPO)",
+ "quality",
+ "abnormal anatomical entity",
"abnormal phenotype by ontology source",
+ "Abnormality of the musculature of the limbs (HPO)",
"specifically dependent continuant",
- "abnormal voluntary musculoskeletal movement",
+ "Abnormality of the musculature (HPO)",
+ "phenotype by ontology source",
+ "Abnormality of the musculature of the lower limbs (HPO)",
+ "abnormal musculature of limb",
+ "continuant",
+ "protein-containing material entity",
+ "material anatomical entity",
+ "system",
+ "muscle organ",
+ "multi-limb segment region",
+ "All (HPO)",
+ "abnormal musculature of lower limb",
+ "continuant",
+ "Proximal muscle weakness in lower limbs (HPO)",
+ "abnormal musculature",
+ "Abnormal muscle physiology (HPO)",
+ "organ system subdivision",
+ "subdivision of organism along appendicular axis",
+ "abnormality of muscle organ physiology",
+ "Abnormality of the lower limb (HPO)",
+ "Phenotypic abnormality (HPO)",
+ "Limb muscle weakness (HPO)",
+ "decreased muscle organ strength",
"entity",
+ "entity",
+ "leg",
+ "pelvic appendage musculature",
+ "musculature of limb",
+ "limb segment",
+ "Phenotypic abnormality",
+ "Muscle weakness (HPO)",
+ "abnormal anatomical entity morphology",
+ "abnormal leg",
"anatomical structure",
- "abnormal anatomical entity",
- "abnormal voluntary movement behavior",
- "changed biological_process rate",
- "abnormal response to stimulus",
- "abnormal behavior process",
- "Hyporeflexia (HPO)",
- "Abnormal reflex (HPO)",
- "abnormal musculoskeletal movement",
- "decreased biological_process",
- "abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
+ "organism subdivision",
+ "organ",
+ "multicellular organism",
+ "pelvic complex",
+ "musculature of lower limb",
+ "lower limb segment",
+ "phenotype",
+ "independent continuant",
+ "posterior region of body",
+ "appendage",
+ "decreased anatomical entity strength",
+ "abnormal multicellular organism morphology",
+ "Abnormality of the musculoskeletal system (HPO)",
+ "abnormal limb",
"material entity",
"anatomical entity",
- "response to stimulus",
- "multicellular organismal process",
+ "paired limb/fin",
+ "limb",
+ "pelvic appendage",
+ "lateral structure",
+ "musculature of body",
+ "musculature",
+ "abnormality of anatomical entity physiology",
+ "abnormal anatomical entity",
+ "abnormal muscle organ morphology",
+ "Abnormality of limbs (HPO)",
+ "multicellular anatomical structure",
"anatomical system",
- "voluntary musculoskeletal movement",
- "kinesthetic behavior",
- "neuromuscular process",
- "multicellular organism",
+ "muscle structure",
+ "hindlimb",
+ "appendage girdle complex",
+ "appendage musculature",
+ "musculature of pelvic complex",
+ "paired limb/fin segment",
],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0001265",
+ "grouping_key": "MONDO:0035432🍪🍪biolink:has_phenotype🍪HP:0008994",
},
{
- "id": "uuid:c9c8bf3f-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:160500",
+ "id": "uuid:4e02df81-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["PMID:17548557"],
- "frequency_qualifier": "HP:0040280",
- "has_evidence": ["ECO:0000269"],
- "subject": "MONDO:0008050",
- "object": "HP:0009053",
- "subject_label": "MYH7-related skeletal myopathy",
+ "publications": ["orphanet:589821"],
+ "frequency_qualifier": "HP:0040281",
+ "has_evidence": ["ECO:0000304"],
+ "subject": "MONDO:0035646",
+ "object": "HP:0000256",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
+ "disease",
+ "hypertrophic cardiomyopathy",
"disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Distal lower limb muscle weakness (HPO)",
+ "object_label": "Macrocephaly (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "UPHENO:0082875",
- "UPHENO:0002320",
- "HP:0002814",
- "UPHENO:0001005",
- "HP:0009127",
- "UPHENO:0076692",
- "UPHENO:0003070",
- "BFO:0000004",
- "UBERON:0004708",
- "UBERON:0000154",
- "UBERON:0000026",
- "UBERON:0014892",
- "UBERON:0006058",
- "UBERON:0002529",
- "HP:0000001",
- "HP:0000118",
- "BFO:0000002",
- "BFO:0000020",
- "UPHENO:0076710",
- "BFO:0000001",
- "PATO:0000001",
+ "HP:0000256",
+ "UPHENO:0002536",
+ "UPHENO:0081566",
+ "HP:0000240",
+ "UBERON:0000465",
+ "UPHENO:0075220",
+ "UPHENO:0001208",
+ "UPHENO:0002844",
+ "UPHENO:0015280",
"BFO:0000001",
"BFO:0000040",
- "UBERON:0000467",
- "UBERON:0000468",
+ "UBERON:0001062",
"UBERON:0011216",
- "UBERON:0010709",
- "UBERON:0010890",
- "UBERON:0010538",
- "UPHENO:0075696",
- "UPHENO:0080575",
- "HP:0001324",
- "HP:0003690",
- "HP:0003011",
- "UPHENO:0002332",
- "UPHENO:0001003",
- "UPHENO:0002536",
- "HP:0002460",
- "HP:0040064",
- "HP:0009053",
- "HP:0011804",
- "PR:000050567",
- "UBERON:0000465",
- "UBERON:0002101",
- "UBERON:0004709",
- "UBERON:0005090",
- "UBERON:0018254",
- "UBERON:0002103",
- "UBERON:0010707",
- "UBERON:0001630",
- "UBERON:0010758",
- "UBERON:0007271",
- "UBERON:0014792",
- "UBERON:0008784",
- "HP:0007340",
- "UPHENO:0001001",
- "HP:0011805",
+ "UBERON:0011676",
+ "UBERON:0013701",
+ "UPHENO:0075148",
"UPHENO:0001002",
- "UPHENO:0080555",
- "UPHENO:0002816",
- "UPHENO:0080556",
+ "UPHENO:0075195",
+ "HP:0009121",
+ "BFO:0000002",
+ "UPHENO:0001001",
+ "HP:0011842",
+ "BFO:0000020",
+ "UPHENO:0002964",
+ "UPHENO:0001003",
+ "UPHENO:0021447",
+ "BFO:0000001",
+ "UBERON:0000061",
+ "UBERON:0034925",
+ "HP:0040194",
+ "UPHENO:0075696",
+ "UPHENO:0001005",
+ "UPHENO:0002764",
+ "UPHENO:0001072",
"UPHENO:0081581",
"HP:0033127",
- "UPHENO:0002647",
- "UPHENO:0002830",
+ "UPHENO:0076692",
+ "UPHENO:0022529",
+ "BFO:0000004",
+ "UBERON:0004288",
+ "UBERON:0000475",
+ "UBERON:0000468",
+ "UBERON:0000153",
+ "UPHENO:0065599",
+ "HP:0000924",
+ "UBERON:0003129",
+ "UBERON:0007811",
+ "UBERON:0013702",
+ "UBERON:0000075",
+ "UBERON:0000033",
+ "UPHENO:0076703",
+ "HP:0000152",
+ "HP:0000118",
"BFO:0000002",
- "UBERON:0001062",
- "RO:0002577",
- "UBERON:0000061",
- "UBERON:0015212",
+ "UPHENO:0020584",
+ "PATO:0000001",
+ "UBERON:0010314",
+ "UBERON:0011137",
+ "UBERON:0010323",
+ "UBERON:0011138",
+ "UBERON:0002090",
+ "UBERON:0005944",
+ "HP:0000001",
+ "HP:0000929",
+ "HP:0000234",
"UBERON:0010000",
- "UBERON:0000475",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "UBERON:0000978",
- "UBERON:0004480",
+ "UBERON:0000467",
+ "UBERON:0002204",
+ "UBERON:0010912",
+ "UBERON:0001434",
],
"object_closure_label": [
+ "abnormal size of skull",
+ "increased size of the anatomical entity in independent continuant",
+ "Abnormal skeletal morphology (HPO)",
+ "specifically dependent continuant",
+ "abnormal skeletal system",
+ "quality",
+ "Increased head circumference (HPO)",
+ "abnormal anatomical entity",
+ "abnormal phenotype by ontology source",
+ "abnormal craniocervical region",
+ "phenotype by ontology source",
+ "abnormal head morphology",
+ "continuant",
+ "material anatomical entity",
+ "musculoskeletal system",
+ "head",
"All (HPO)",
- "abnormality of muscle organ physiology",
- "Abnormality of the lower limb (HPO)",
+ "organ system subdivision",
+ "craniocervical region",
+ "body proper",
+ "subdivision of skeletal system",
+ "Abnormality of the skeletal system (HPO)",
"Phenotypic abnormality (HPO)",
"continuant",
- "decreased anatomical entity strength",
- "abnormal musculature",
- "decreased muscle organ strength",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "abnormal musculature of limb",
- "quality",
- "independent continuant",
- "system",
- "paired limb/fin",
- "lateral structure",
- "multicellular anatomical structure",
- "pelvic complex",
- "appendage musculature",
- "musculature of pelvic complex",
- "abnormality of anatomical entity physiology",
- "Abnormal skeletal muscle morphology (HPO)",
- "Phenotypic abnormality",
- "specifically dependent continuant",
- "Distal muscle weakness (HPO)",
- "Abnormality of limbs (HPO)",
- "Distal lower limb muscle weakness (HPO)",
- "protein-containing material entity",
- "material anatomical entity",
- "hindlimb",
- "appendage girdle complex",
- "subdivision of organism along appendicular axis",
- "pelvic complex muscle",
- "paired limb/fin segment",
- "lower limb segment",
- "Lower limb muscle weakness (HPO)",
- "phenotype",
- "abnormal phenotype by ontology source",
- "Abnormality of the musculature of the limbs (HPO)",
- "abnormal muscle organ morphology",
- "Abnormal muscle physiology (HPO)",
+ "Abnormality of the head (HPO)",
+ "abnormal anatomical entity morphology",
"entity",
- "anatomical entity",
+ "structure with developmental contribution from neural crest",
+ "abnormal size of head",
+ "Phenotypic abnormality",
+ "abnormal anatomical entity morphology",
+ "Abnormality of skull size (HPO)",
"anatomical structure",
- "muscle structure",
- "skeletal musculature",
+ "anatomical collection",
+ "skeleton",
"organism subdivision",
- "organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "leg",
- "musculature of limb",
- "abnormal anatomical entity",
- "decreased pelvic complex muscle strength",
- "Muscle weakness (HPO)",
- "Limb muscle weakness (HPO)",
- "Abnormality of the musculature (HPO)",
- "abnormality of anatomical entity physiology",
- "phenotype by ontology source",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "abnormal leg",
+ "multicellular organism",
+ "anterior region of body",
+ "phenotype",
+ "abnormal skeletal system morphology",
+ "Abnormality of head or neck (HPO)",
+ "Abnormal skull morphology (HPO)",
+ "abnormal anatomical entity morphology in the independent continuant",
"entity",
- "abnormal limb",
- "continuant",
+ "independent continuant",
+ "subdivision of organism along main body axis",
+ "main body axis",
+ "Macrocephaly (HPO)",
+ "abnormal size of anatomical entity",
+ "Abnormal axial skeleton morphology (HPO)",
+ "increased size of the anatomical entity",
+ "abnormal multicellular organism morphology",
+ "Abnormality of the musculoskeletal system (HPO)",
+ "abnormal postcranial axial skeleton morphology",
"material entity",
- "limb",
- "pelvic appendage",
- "anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "posterior region of body",
- "appendage",
- "skeletal muscle organ",
- "multi-limb segment region",
- "limb segment",
+ "anatomical entity",
+ "subdivision of skeleton",
+ "skeletal system",
+ "increased size of the head",
+ "abnormal head",
+ "abnormal anatomical entity",
+ "abnormal skull morphology",
+ "multicellular anatomical structure",
+ "anatomical system",
+ "skull",
+ "axial skeletal system",
+ "cranial skeletal system",
+ "postcranial axial skeletal system",
+ "postcranial axial skeleton",
+ "axial skeleton plus cranial skeleton",
],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Very frequent (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040281", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Very frequent (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0009053",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0000256",
},
{
- "id": "uuid:c9c8bf41-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:160500",
+ "id": "uuid:4e02df82-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["PMID:17548557"],
- "frequency_qualifier": "HP:0040280",
- "has_evidence": ["ECO:0000269"],
- "subject": "MONDO:0008050",
- "object": "HP:0009077",
- "subject_label": "MYH7-related skeletal myopathy",
+ "publications": ["orphanet:589821"],
+ "frequency_qualifier": "HP:0040281",
+ "has_evidence": ["ECO:0000304"],
+ "subject": "MONDO:0035646",
+ "object": "HP:0000297",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Weakness of long finger extensor muscles (HPO)",
+ "object_label": "Facial hypotonia (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "HP:0009127",
- "BFO:0000002",
- "UPHENO:0002655",
- "UPHENO:0076692",
- "BFO:0000001",
- "PATO:0000001",
- "BFO:0000004",
- "UBERON:0004708",
- "UBERON:0000061",
- "UBERON:0000153",
- "UBERON:0000026",
- "UBERON:0006058",
- "UBERON:0002529",
- "UBERON:0002398",
- "HP:0000001",
- "UPHENO:0002649",
- "UPHENO:0001001",
- "UPHENO:0001002",
- "HP:0000118",
- "HP:0001446",
- "BFO:0000020",
- "UPHENO:0002708",
- "HP:0009077",
- "UPHENO:0076710",
+ "HP:0011799",
+ "UPHENO:0002816",
+ "UPHENO:0002536",
+ "UBERON:0000465",
+ "RO:0002577",
+ "UPHENO:0082875",
+ "UPHENO:0002910",
"BFO:0000001",
"BFO:0000040",
- "UBERON:0000467",
- "UBERON:0000468",
+ "UBERON:0001062",
"UBERON:0011216",
- "UBERON:0010708",
- "UBERON:0010538",
- "UBERON:0004489",
- "HP:0001421",
- "HP:0030237",
- "HP:0002817",
- "HP:0003011",
- "UPHENO:0002536",
- "HP:0040064",
+ "UBERON:0011676",
+ "UBERON:0013701",
+ "UPHENO:0001002",
+ "HP:0011804",
"BFO:0000002",
- "PR:000050567",
- "UBERON:0000465",
- "UBERON:0002101",
- "UBERON:0004710",
- "UBERON:0005090",
- "UBERON:0002102",
- "UBERON:0010707",
"UBERON:0001630",
- "UBERON:0010758",
- "UBERON:0007271",
- "UBERON:0014793",
- "UBERON:0004481",
- "UBERON:0002470",
- "UBERON:0008785",
- "UPHENO:0001005",
- "HP:0001155",
+ "UBERON:0002376",
+ "UBERON:0015789",
+ "UPHENO:0001001",
"HP:0011805",
- "UPHENO:0002816",
+ "BFO:0000020",
+ "UPHENO:0001003",
+ "BFO:0000001",
+ "UBERON:0000061",
+ "UPHENO:0075696",
+ "UPHENO:0001005",
+ "UPHENO:0002764",
"UPHENO:0081581",
"HP:0033127",
- "UPHENO:0001003",
- "UPHENO:0002647",
- "UPHENO:0002880",
- "UPHENO:0002830",
- "UBERON:0001062",
- "RO:0002577",
- "UBERON:0015212",
- "UBERON:0010000",
+ "UPHENO:0076692",
+ "BFO:0000004",
"UBERON:0000475",
"UBERON:0000062",
+ "UBERON:0000468",
+ "UBERON:0000153",
+ "UPHENO:0002844",
+ "BFO:0000002",
+ "HP:0003011",
+ "UPHENO:0076710",
+ "PATO:0000001",
+ "UPHENO:0002908",
+ "UBERON:0007811",
+ "UBERON:0001444",
+ "UBERON:0013702",
+ "UBERON:0000033",
+ "UPHENO:0002320",
+ "UPHENO:0082555",
+ "HP:0000152",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "HP:0001252",
+ "UPHENO:0082557",
+ "HP:0000297",
+ "HP:0000301",
+ "UBERON:0001456",
+ "UBERON:0008229",
+ "UBERON:0013700",
+ "UBERON:0010959",
+ "UBERON:0001577",
+ "HP:0000001",
+ "HP:0003808",
+ "HP:0000234",
+ "HP:0000271",
+ "UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0005090",
+ "UBERON:0018254",
+ "UBERON:0004120",
"UBERON:0000383",
"UBERON:0001015",
- "UBERON:0001460",
- "UBERON:0004480",
- "UBERON:0007269",
+ "UBERON:0014892",
+ "UBERON:0004461",
+ "UBERON:0004473",
],
"object_closure_label": [
- "All (HPO)",
- "abnormal musculature of upper limb",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "abnormal musculature",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "phenotype by ontology source",
- "abnormal musculature of limb",
- "independent continuant",
- "system",
- "paired limb/fin",
- "anatomical structure",
- "lateral structure",
- "multicellular anatomical structure",
- "pectoral complex",
- "appendage musculature",
- "musculature of pectoral complex",
- "musculature of manus",
- "phenotype",
- "Abnormality of the musculature of the hand (HPO)",
- "abnormal phenotype by ontology source",
- "Abnormality of the hand (HPO)",
+ "abnormality of anatomical entity physiology",
+ "abnormal head",
"Abnormal skeletal muscle morphology (HPO)",
- "Abnormality of the musculature of the upper limbs (HPO)",
"specifically dependent continuant",
- "abnormal manus",
- "Abnormality of limbs (HPO)",
- "quality",
+ "abnormal anatomical entity",
+ "abnormal phenotype by ontology source",
+ "abnormal craniocervical region",
+ "Abnormality of the musculature (HPO)",
+ "phenotype by ontology source",
"continuant",
- "protein-containing material entity",
"material anatomical entity",
- "forelimb",
- "appendage girdle complex",
- "subdivision of organism along appendicular axis",
- "paired limb/fin segment",
- "musculature of upper limb",
- "autopod region",
- "upper limb segment",
- "Abnormality of the musculature of the limbs (HPO)",
+ "system",
+ "cranial or facial muscle",
+ "head",
+ "All (HPO)",
+ "Abnormal muscle tone (HPO)",
"continuant",
- "abnormal musculature of manus",
- "Weakness of long finger extensor muscles (HPO)",
- "abnormal muscle organ morphology",
+ "abnormal musculature",
+ "Abnormal muscle physiology (HPO)",
+ "organ system subdivision",
+ "muscle organ",
+ "cranial muscle",
+ "craniocervical region",
+ "subdivision of head",
+ "body proper",
+ "abnormality of muscle organ physiology",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the head (HPO)",
+ "Abnormality of the face (HPO)",
+ "decreased muscle organ tone",
+ "Facial hypotonia (HPO)",
+ "Abnormality of facial musculature (HPO)",
"entity",
- "anatomical entity",
- "muscle structure",
+ "skeletal musculature of head",
+ "musculature of face",
+ "Phenotypic abnormality",
+ "abnormal anatomical entity morphology",
+ "quality",
+ "abnormal facial muscle",
+ "anatomical structure",
"organism subdivision",
"organ",
- "muscle organ",
+ "multicellular organism",
+ "anterior region of body",
+ "phenotype",
+ "decreased anatomical entity tone",
+ "Abnormality of head or neck (HPO)",
+ "entity",
+ "independent continuant",
+ "subdivision of organism along main body axis",
+ "main body axis",
+ "Abnormality of facial soft tissue (HPO)",
+ "abnormal multicellular organism morphology",
+ "Abnormality of the musculoskeletal system (HPO)",
+ "material entity",
+ "anatomical entity",
"musculature of body",
"musculature",
- "arm",
- "musculature of limb",
- "pectoral appendage musculature",
- "Hand muscle weakness (HPO)",
- "Abnormality of the upper limb (HPO)",
- "Abnormality of the musculature (HPO)",
+ "skeletal muscle organ",
+ "abnormal face",
+ "abnormality of anatomical entity physiology",
+ "Hypotonia (HPO)",
"abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "entity",
- "abnormal arm",
- "abnormal limb",
- "material entity",
- "limb",
- "pectoral appendage",
+ "abnormal muscle organ morphology",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "anterior region of body",
- "appendage",
- "multi-limb segment region",
- "limb segment",
- "manus",
+ "muscle structure",
+ "skeletal musculature",
+ "mesoderm-derived structure",
+ "face",
+ "craniocervical region musculature",
+ "axial musculature",
+ "craniocervical muscle",
+ "facial muscle",
],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Very frequent (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040281", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Very frequent (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0009077",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0000297",
},
{
- "id": "uuid:c9c8bf42-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:160500",
+ "id": "uuid:4e02df83-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["PMID:17548557"],
- "frequency_qualifier": "HP:0040280",
- "has_evidence": ["ECO:0000269"],
- "subject": "MONDO:0008050",
- "object": "HP:0030051",
- "subject_label": "MYH7-related skeletal myopathy",
+ "publications": ["orphanet:589821"],
+ "frequency_qualifier": "HP:0040281",
+ "has_evidence": ["ECO:0000304"],
+ "subject": "MONDO:0035646",
+ "object": "HP:0010804",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
+ "disease",
+ "hypertrophic cardiomyopathy",
"disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Tip-toe gait (HPO)",
+ "object_label": "Tented upper lip vermilion (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "UPHENO:0082875",
- "UPHENO:0049622",
- "UPHENO:0001005",
+ "HP:0000159",
+ "UPHENO:0076803",
+ "UBERON:0000465",
+ "UPHENO:0002910",
+ "UPHENO:0076800",
+ "UPHENO:0003064",
"BFO:0000002",
- "UPHENO:0050606",
- "HP:0001288",
- "HP:0012638",
- "BFO:0000015",
- "BFO:0000004",
- "GO:0050882",
- "NBO:0000338",
- "GO:0050905",
- "UBERON:0001016",
- "HP:0000001",
- "UPHENO:0001001",
- "UPHENO:0080585",
+ "HP:0002664",
+ "UPHENO:0015280",
+ "BFO:0000040",
+ "BFO:0000141",
+ "UBERON:0001062",
+ "UBERON:0011676",
+ "UBERON:0013701",
+ "UPHENO:0002828",
"UPHENO:0001002",
- "HP:0000118",
"BFO:0000020",
- "UPHENO:0002433",
+ "HP:0011793",
+ "UPHENO:0076786",
+ "BFO:0000002",
+ "UBERON:0000167",
+ "UPHENO:0001001",
+ "HP:0000163",
+ "HP:0000177",
+ "UPHENO:0002833",
+ "HP:0000309",
"UPHENO:0001003",
- "HP:0000708",
- "HP:0011446",
+ "UPHENO:0002536",
"BFO:0000001",
+ "UBERON:0000464",
+ "UPHENO:0075696",
+ "UPHENO:0002764",
+ "UPHENO:0081581",
+ "UPHENO:0076692",
+ "UPHENO:0020955",
+ "HP:0025031",
+ "BFO:0000004",
+ "UBERON:0000061",
+ "UBERON:0002553",
+ "UBERON:0000475",
+ "UBERON:0000062",
+ "UBERON:0004111",
+ "UBERON:0000468",
+ "UBERON:0001834",
+ "UBERON:0000153",
+ "UPHENO:0002844",
+ "HP:0025033",
+ "UBERON:0000466",
+ "UBERON:0011595",
+ "UBERON:0001709",
+ "UBERON:0001833",
+ "UBERON:0007811",
+ "UBERON:0001444",
+ "UBERON:0013702",
+ "UBERON:0000025",
+ "UBERON:0000033",
+ "UBERON:0004089",
+ "HP:0000152",
+ "UPHENO:0075998",
+ "HP:0000118",
+ "HP:0011339",
+ "HP:0010804",
+ "UPHENO:0020584",
"PATO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "GO:0032501",
- "GO:0050881",
- "NBO:0000313",
- "GO:0050877",
+ "UBERON:0010314",
+ "UBERON:0003102",
"UBERON:0010000",
+ "UBERON:0001555",
+ "UBERON:0001456",
+ "UBERON:0004921",
+ "HP:0000001",
+ "UPHENO:0001005",
+ "HP:0031816",
+ "HP:0000153",
+ "HP:0000234",
+ "HP:0000271",
+ "BFO:0000001",
"UBERON:0000467",
- "UBERON:0000468",
- "NBO:0000403",
- "NBO:0000001",
- "UPHENO:0075696",
- "UPHENO:0078622",
- "UPHENO:0049586",
- "HP:0100022",
- "UPHENO:0050613",
- "UPHENO:0002332",
- "UPHENO:0002536",
- "UPHENO:0079826",
- "UPHENO:0004523",
- "UPHENO:0049587",
- "BFO:0000003",
- "GO:0008150",
- "GO:0050879",
- "GO:0007610",
- "GO:0003008",
- "HP:0030051",
- "HP:0000707",
- "UPHENO:0079833",
- "BFO:0000002",
- "UBERON:0001062",
- "UBERON:0000465",
- "UBERON:0000061",
+ "UBERON:0000064",
+ "UBERON:0001007",
+ "UBERON:0013522",
+ "UBERON:0000165",
],
"object_closure_label": [
- "All (HPO)",
- "abnormal behavior",
- "Abnormality of movement (HPO)",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "Tip-toe gait (HPO)",
- "Abnormality of the nervous system (HPO)",
- "Behavioral abnormality (HPO)",
- "Abnormality of higher mental function (HPO)",
- "abnormal voluntary movement behavior",
+ "abnormal head",
+ "abnormal digestive system",
+ "Abnormality of the midface (HPO)",
"quality",
- "process",
- "independent continuant",
- "material anatomical entity",
- "nervous system",
- "voluntary movement behavior",
- "body part movement",
- "abnormality of anatomical entity physiology",
- "phenotype",
+ "abnormal anatomical entity",
+ "abnormal craniocervical region",
"specifically dependent continuant",
- "abnormality of nervous system physiology",
+ "Abnormality of digestive system morphology (HPO)",
"phenotype by ontology source",
- "Gait disturbance (HPO)",
- "abnormal behavior process",
- "abnormal nervous system",
- "abnormal biological_process",
- "Abnormal nervous system physiology (HPO)",
- "occurrent",
- "biological_process",
- "multicellular organismal movement",
- "behavior",
- "system process",
- "musculoskeletal movement",
- "behavior process",
- "nervous system process",
- "abnormal phenotype by ontology source",
+ "abnormal anatomical entity",
"continuant",
- "abnormal voluntary musculoskeletal movement",
+ "material anatomical entity",
+ "organ part",
+ "digestive system",
+ "head",
+ "midface",
+ "All (HPO)",
+ "abnormal phenotype by ontology source",
+ "oral cavity",
+ "craniocervical region",
+ "subdivision of head",
+ "body proper",
+ "tube",
+ "Abnormal oral cavity morphology (HPO)",
+ "Abnormality of upper lip (HPO)",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the head (HPO)",
+ "Abnormality of the face (HPO)",
+ "abnormal anatomical entity morphology",
"entity",
+ "entity",
+ "immaterial anatomical entity",
+ "structure with developmental contribution from neural crest",
+ "surface structure",
+ "multicellular anatomical structure",
+ "mouth",
+ "abnormal mouth",
+ "Phenotypic abnormality",
+ "Neoplasm by anatomical site (HPO)",
+ "abnormal oral cavity morphology",
+ "abnormal anatomical entity morphology",
+ "abnormal lip morphology",
+ "abnormal digestive system morphology",
+ "anatomical space",
+ "anatomical cavity",
+ "organism subdivision",
+ "organ",
+ "anatomical conduit",
+ "multicellular organism",
+ "upper lip",
+ "anterior region of body",
+ "phenotype",
+ "Abnormality of head or neck (HPO)",
+ "abnormal midface",
+ "Abnormal oral morphology (HPO)",
+ "Abnormality of the mouth (HPO)",
+ "Neoplasm (HPO)",
+ "abnormal anatomical entity morphology in the independent continuant",
+ "independent continuant",
+ "subdivision of organism along main body axis",
+ "main body axis",
+ "abnormal multicellular organism morphology",
+ "Abnormal lip morphology (HPO)",
+ "Abnormality of the digestive system (HPO)",
+ "material entity",
+ "immaterial entity",
"anatomical entity",
"anatomical structure",
- "abnormal anatomical entity",
- "abnormal voluntary movement behavior",
- "abnormal response to stimulus",
- "abnormal behavior process",
- "abnormal musculoskeletal movement",
- "abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
- "entity",
+ "subdivision of tube",
+ "abnormal face",
+ "abnormal mouth morphology",
+ "abnormal upper lip",
"continuant",
- "material entity",
- "multicellular organismal process",
- "multicellular anatomical structure",
+ "Abnormality of upper lip vermillion (HPO)",
+ "Tented upper lip vermilion (HPO)",
"anatomical system",
- "voluntary musculoskeletal movement",
- "kinesthetic behavior",
- "neuromuscular process",
- "multicellular organism",
+ "jaw region",
+ "upper jaw region",
+ "lip",
+ "digestive tract",
+ "face",
+ "subdivision of digestive tract",
],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Very frequent (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040281", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Very frequent (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0030051",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0010804",
},
{
- "id": "uuid:c9c8bfed-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:253600",
+ "id": "uuid:4e02df84-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["PMID:16607617"],
- "frequency_qualifier": "HP:0040282",
- "has_evidence": ["ECO:0000269"],
- "subject": "MONDO:0009675",
- "object": "HP:0001880",
- "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A",
+ "publications": ["orphanet:589821"],
+ "frequency_qualifier": "HP:0040281",
+ "has_evidence": ["ECO:0000304"],
+ "subject": "MONDO:0035646",
+ "object": "HP:0031843",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "MONDO:0016971",
- "MONDO:0005336",
- "MONDO:0015152",
- "MONDO:0000429",
- "MONDO:0005071",
- "MONDO:0006025",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
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+ "MONDO:0002081",
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+ "MONDO:0005217",
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],
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
- "hereditary disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
"continuant",
- "autosomal recessive disease",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
"disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "disease",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "autosomal genetic disease",
+ "myotonic dystrophy",
"nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
- "autosomal recessive limb-girdle muscular dystrophy type 2A",
"skeletal muscle disorder",
- "qualitative or quantitative defects of calpain",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Eosinophilia (HPO)",
+ "object_label": "Bradyphrenia (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "HP:0001879",
+ "UBERON:0000465",
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+ "UPHENO:0082875",
+ "UPHENO:0004523",
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+ "UBERON:0001062",
+ "GO:0003008",
+ "BFO:0000020",
+ "BFO:0000003",
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+ "UPHENO:0001002",
+ "HP:0031843",
+ "UPHENO:0001003",
+ "BFO:0000001",
+ "UBERON:0000061",
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"UPHENO:0001005",
+ "UPHENO:0002433",
+ "HP:0100543",
+ "HP:0012638",
+ "BFO:0000015",
+ "UBERON:0000468",
+ "UPHENO:0075696",
"BFO:0000002",
- "BFO:0000020",
- "HP:0002715",
- "HP:0001911",
- "HP:0001880",
+ "UPHENO:0002536",
"BFO:0000004",
- "UBERON:0000178",
- "CL:0000094",
- "CL:0002242",
- "CL:0000255",
- "CL:0000219",
- "HP:0000001",
- "HP:0032309",
- "HP:0010974",
"HP:0000118",
- "HP:0001871",
- "HP:0020064",
- "UPHENO:0001003",
- "UPHENO:0002536",
- "BFO:0000001",
+ "UPHENO:0002332",
"PATO:0000001",
+ "HP:0000001",
+ "HP:0000707",
+ "HP:0011446",
"BFO:0000001",
- "UBERON:0000467",
- "CL:0000000",
- "UBERON:0000468",
- "CL:0000738",
- "CL:0000548",
- "CL:0000763",
- "CL:0000081",
- "UPHENO:0002948",
- "UPHENO:0001002",
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- "HP:0001881",
- "HP:0020047",
- "UPHENO:0004459",
- "HP:0032251",
- "BFO:0000002",
- "BFO:0000040",
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- "CL:0000771",
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- "UBERON:0015203",
- "CL:0000003",
- "UBERON:0002193",
- "UBERON:0002390",
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- "HP:0011893",
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- "HP:0025354",
- "HP:0001974",
- "HP:0010987",
- "UBERON:0001062",
- "UBERON:0000061",
- "UBERON:0000463",
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+ "GO:0032501",
"UBERON:0010000",
- "CL:0000766",
- "CL:0002371",
+ "UBERON:0000467",
+ "UBERON:0001016",
],
"object_closure_label": [
- "All (HPO)",
- "Abnormal eosinophil morphology (HPO)",
- "Abnormal myeloid leukocyte morphology (HPO)",
- "Phenotypic abnormality (HPO)",
- "Abnormal cellular phenotype (HPO)",
- "Leukocytosis (HPO)",
- "Abnormal cellular immune system morphology (HPO)",
+ "abnormality of anatomical entity physiology",
+ "Phenotypic abnormality",
+ "Bradyphrenia (HPO)",
+ "abnormal anatomical entity",
+ "Abnormality of higher mental function (HPO)",
"quality",
- "independent continuant",
- "blood",
- "granulocyte",
- "multicellular anatomical structure",
- "myeloid cell",
- "blood cell",
- "Abnormality of blood and blood-forming tissues (HPO)",
- "Abnormal eosinophil count (HPO)",
+ "multicellular organismal process",
+ "abnormal phenotype by ontology source",
+ "specifically dependent continuant",
"phenotype by ontology source",
+ "abnormal nervous system",
+ "occurrent",
"continuant",
- "material entity",
- "protein-containing material entity",
"material anatomical entity",
- "leukocyte",
- "animal cell",
- "hematopoietic cell",
- "Abnormal leukocyte count (HPO)",
- "phenotype",
- "abnormal phenotype by ontology source",
+ "nervous system",
+ "All (HPO)",
"continuant",
- "specifically dependent continuant",
- "Abnormality of the immune system (HPO)",
- "Abnormal granulocyte morphology (HPO)",
- "Eosinophilia (HPO)",
- "abnormal anatomical entity",
- "Abnormal immune system morphology (HPO)",
+ "system process",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the nervous system (HPO)",
"entity",
- "anatomical entity",
- "anatomical structure",
- "organism substance",
- "disconnected anatomical group",
- "mesoderm-derived structure",
- "bodily fluid",
- "non-connected functional system",
- "native cell",
- "hemolymphoid system",
- "hematopoietic system",
- "haemolymphatic fluid",
- "immune system",
- "myeloid leukocyte",
- "somatic cell",
- "abnormal immune system",
- "Abnormal granulocyte count (HPO)",
- "Phenotypic abnormality",
- "Abnormal cell morphology (HPO)",
- "Abnormal leukocyte morphology (HPO)",
- "Abnormal myeloid cell morphology (HPO)",
- "abnormal hematopoietic system",
"entity",
- "eosinophil",
- "anatomical system",
- "cell",
+ "cognition",
+ "abnormality of nervous system physiology",
+ "anatomical structure",
"multicellular organism",
- "nucleate cell",
- "eukaryotic cell",
- "motile cell",
+ "phenotype",
+ "process",
+ "nervous system process",
+ "Cognitive impairment (HPO)",
+ "Abnormal nervous system physiology (HPO)",
+ "biological_process",
+ "material entity",
+ "anatomical entity",
+ "abnormal anatomical entity",
+ "abnormality of anatomical entity physiology",
+ "independent continuant",
+ "multicellular anatomical structure",
+ "anatomical system",
],
- "frequency_qualifier_label": "Frequent (HPO)",
+ "frequency_qualifier_label": "Very frequent (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Frequent (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040281", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Very frequent (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0009675🍪🍪biolink:has_phenotype🍪HP:0001880",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0031843",
},
{
- "id": "uuid:c9c8bfee-7529-11ee-b012-cbd37f5c3759",
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+ "id": "uuid:4e02df85-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
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"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["PMID:16607617"],
+ "publications": ["orphanet:589821"],
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- "has_evidence": ["ECO:0000269"],
- "subject": "MONDO:0009675",
- "object": "HP:0002312",
- "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A",
+ "has_evidence": ["ECO:0000304"],
+ "subject": "MONDO:0035646",
+ "object": "HP:0000736",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
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- "MONDO:0005071",
- "MONDO:0006025",
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],
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
- "hereditary disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
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+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
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+ "eye adnexa disorder",
+ "eyelid disorder",
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- "qualitative or quantitative protein defects in neuromuscular diseases",
- "disease",
+ "human disease",
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+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
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+ "heart disorder",
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+ "hereditary disease",
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"skeletal muscle disorder",
- "qualitative or quantitative defects of calpain",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Clumsiness (HPO)",
+ "object_label": "Short attention span (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
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+ "NBO:0000313",
+ "NBO:0000308",
"UPHENO:0082875",
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- "HP:0012638",
- "BFO:0000004",
- "UBERON:0000061",
- "UBERON:0001016",
- "HP:0000001",
- "HP:0000118",
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+ "UPHENO:0049622",
"UPHENO:0001003",
- "PATO:0000001",
"BFO:0000001",
- "BFO:0000040",
- "UBERON:0000467",
- "UBERON:0000468",
+ "NBO:0000607",
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- "HP:0011442",
- "UPHENO:0001002",
- "UPHENO:0002332",
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- "HP:0002312",
- "HP:0011443",
- "BFO:0000002",
- "UBERON:0000465",
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- "BFO:0000002",
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+ "UPHENO:0080585",
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+ "GO:0032501",
"UBERON:0010000",
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+ "UBERON:0001016",
],
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- "Abnormal central motor function (HPO)",
- "Phenotypic abnormality (HPO)",
- "Abnormality of the nervous system (HPO)",
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- "quality",
- "independent continuant",
- "anatomical structure",
- "multicellular anatomical structure",
- "nervous system",
"abnormality of anatomical entity physiology",
- "continuant",
+ "abnormal anatomical entity",
+ "Abnormality of higher mental function (HPO)",
+ "quality",
+ "multicellular organismal process",
+ "abnormal anatomical entity",
"specifically dependent continuant",
- "abnormality of nervous system physiology",
"phenotype by ontology source",
"abnormal nervous system",
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- "Abnormal nervous system physiology (HPO)",
+ "occurrent",
"continuant",
"material anatomical entity",
- "phenotype",
+ "nervous system",
+ "All (HPO)",
"abnormal phenotype by ontology source",
- "Incoordination (HPO)",
- "Abnormality of coordination (HPO)",
+ "Short attention span (HPO)",
+ "behavior",
+ "abnormal behavior",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the nervous system (HPO)",
+ "abnormal behavior process",
"entity",
- "anatomical entity",
- "abnormal anatomical entity",
+ "entity",
+ "cognitive behavior",
+ "sensation behavior",
"Phenotypic abnormality",
- "abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
+ "abnormality of nervous system physiology",
+ "multicellular organism",
+ "phenotype",
+ "abnormal behavior process",
+ "Behavioral abnormality (HPO)",
+ "abnormal biological_process",
+ "process",
+ "independent continuant",
+ "behavior process",
+ "Abnormal nervous system physiology (HPO)",
+ "biological_process",
"material entity",
+ "anatomical entity",
+ "anatomical structure",
+ "abnormal response to stimulus",
+ "continuant",
+ "abnormality of anatomical entity physiology",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
+ "attention behavior",
],
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"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Frequent (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"],
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- "grouping_key": "MONDO:0009675🍪🍪biolink:has_phenotype🍪HP:0002312",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0000736",
},
{
- "id": "uuid:c9c8bff4-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:253600",
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+ "original_subject": "Orphanet:589821",
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"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
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- "subject": "MONDO:0009675",
- "object": "HP:0032019",
- "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A",
+ "publications": ["orphanet:589821"],
+ "frequency_qualifier": "HP:0040282",
+ "has_evidence": ["ECO:0000304"],
+ "subject": "MONDO:0035646",
+ "object": "HP:0001622",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
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- "MONDO:0005071",
- "MONDO:0006025",
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],
"subject_closure_label": [
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- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
- "hereditary disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
"continuant",
- "autosomal recessive disease",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
"disposition",
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- "disease",
+ "human disease",
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+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "autosomal genetic disease",
+ "myotonic dystrophy",
"nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
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- "autosomal recessive limb-girdle muscular dystrophy type 2A",
"skeletal muscle disorder",
- "qualitative or quantitative defects of calpain",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Muscle eosinophilia (HPO)",
+ "object_label": "Premature birth (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "UPHENO:0001005",
+ "HP:0001197",
+ "UPHENO:0002536",
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+ "GO:0007567",
+ "UPHENO:0049587",
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+ "GO:0000003",
+ "GO:0044703",
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"BFO:0000002",
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- "UPHENO:0076692",
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- "BFO:0000004",
- "UBERON:0000061",
- "HP:0000001",
"UPHENO:0001001",
- "HP:0000118",
- "HP:0032019",
- "UPHENO:0001003",
- "UPHENO:0076710",
- "BFO:0000001",
+ "UPHENO:0001002",
+ "BFO:0000020",
+ "UPHENO:0001003",
"BFO:0000001",
- "BFO:0000040",
- "UBERON:0000467",
+ "UPHENO:0001005",
+ "UPHENO:0049940",
+ "BFO:0000015",
+ "UBERON:0000061",
"UBERON:0000468",
- "UBERON:0011216",
- "HP:0003011",
- "UPHENO:0002536",
"BFO:0000002",
- "UBERON:0000465",
- "UBERON:0005090",
- "UBERON:0001630",
- "HP:0011805",
- "UPHENO:0001002",
- "UPHENO:0002816",
- "UPHENO:0081581",
- "HP:0033127",
- "UBERON:0001062",
+ "UPHENO:0049440",
+ "BFO:0000004",
+ "UBERON:0000922",
+ "HP:0001622",
+ "HP:0000118",
+ "UPHENO:0049449",
+ "HP:0001787",
+ "PATO:0000001",
+ "UBERON:0000323",
+ "HP:0000001",
+ "UPHENO:0075949",
+ "GO:0032501",
+ "GO:0022414",
"UBERON:0010000",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
],
"object_closure_label": [
- "All (HPO)",
- "Phenotypic abnormality (HPO)",
- "abnormal musculature",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "independent continuant",
- "anatomical structure",
- "multicellular anatomical structure",
- "phenotype",
- "Abnormal skeletal muscle morphology (HPO)",
"Phenotypic abnormality",
- "Muscle eosinophilia (HPO)",
- "phenotype by ontology source",
+ "specifically dependent continuant",
"quality",
+ "multicellular organismal process",
+ "reproductive process",
+ "abnormal phenotype by ontology source",
+ "premature biological_process",
+ "phenotype by ontology source",
+ "occurrent",
"continuant",
"material anatomical entity",
- "abnormal phenotype by ontology source",
+ "All (HPO)",
"continuant",
- "specifically dependent continuant",
- "abnormal muscle organ morphology",
+ "multi-multicellular organism process",
+ "reproduction",
+ "multi-organism reproductive process",
+ "embryo",
+ "Phenotypic abnormality (HPO)",
+ "abnormal late embryo",
+ "Abnormal delivery (HPO)",
"entity",
- "anatomical entity",
- "muscle structure",
- "organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "Abnormality of the musculature (HPO)",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
+ "biological_process",
+ "multicellular organism",
+ "phenotype",
+ "Premature birth (HPO)",
+ "abnormal biological_process",
"entity",
+ "process",
+ "parturition",
+ "Abnormality of prenatal development or birth (HPO)",
+ "abnormal reproductive process",
"material entity",
- "anatomical system",
- "multicellular organism",
- "organ system subdivision",
+ "anatomical entity",
+ "anatomical structure",
+ "premature parturition",
+ "abnormal anatomical entity",
+ "independent continuant",
+ "multicellular anatomical structure",
+ "late embryo",
],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0009675🍪🍪biolink:has_phenotype🍪HP:0032019",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001622",
},
{
- "id": "uuid:c9c8bff5-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:253600",
+ "id": "uuid:4e02df88-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
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"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["PMID:16607617"],
+ "publications": ["orphanet:589821"],
"frequency_qualifier": "HP:0040282",
- "has_evidence": ["ECO:0000269"],
- "subject": "MONDO:0009675",
- "object": "HP:0007340",
- "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A",
+ "has_evidence": ["ECO:0000304"],
+ "subject": "MONDO:0035646",
+ "object": "HP:0001883",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "MONDO:0016971",
- "MONDO:0005336",
- "MONDO:0015152",
- "MONDO:0000429",
- "MONDO:0005071",
- "MONDO:0006025",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
"BFO:0000017",
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+ "MONDO:0035646",
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+ "MONDO:0016106",
+ "MONDO:0005336",
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+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
- "MONDO:0009675",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
- "MONDO:0016152",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
- "BFO:0000002",
- "MONDO:0016106",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003847",
- "MONDO:0003939",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
- "hereditary disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
"continuant",
- "autosomal recessive disease",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
"disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "disease",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "autosomal genetic disease",
+ "myotonic dystrophy",
"nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
- "autosomal recessive limb-girdle muscular dystrophy type 2A",
"skeletal muscle disorder",
- "qualitative or quantitative defects of calpain",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Lower limb muscle weakness (HPO)",
+ "object_label": "Talipes (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "UPHENO:0082875",
- "UPHENO:0002320",
- "UPHENO:0001005",
- "HP:0009127",
+ "PR:000050567",
+ "UBERON:0000465",
+ "RO:0002577",
+ "BFO:0000001",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UBERON:0000154",
+ "UPHENO:0001002",
"BFO:0000020",
- "UPHENO:0076692",
+ "UPHENO:0081575",
+ "BFO:0000002",
+ "UBERON:0002101",
+ "UBERON:0004709",
+ "UPHENO:0001001",
+ "UPHENO:0001003",
+ "UPHENO:0002536",
"BFO:0000001",
+ "UBERON:0000061",
+ "UBERON:0008784",
+ "UBERON:0002470",
+ "UPHENO:0001005",
+ "UPHENO:0081581",
+ "UPHENO:0076692",
+ "UPHENO:0003070",
+ "UPHENO:0002830",
"BFO:0000004",
"UBERON:0004708",
- "UBERON:0000061",
- "UBERON:0000026",
- "UBERON:0014892",
- "HP:0000001",
- "UPHENO:0001001",
- "UPHENO:0001002",
- "HP:0000118",
- "UPHENO:0076710",
- "PATO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0001062",
- "UBERON:0000467",
+ "UBERON:0000475",
"UBERON:0000468",
- "UBERON:0011216",
"UBERON:0010709",
- "UBERON:0010890",
- "UPHENO:0075696",
- "UPHENO:0080575",
- "HP:0001324",
- "HP:0003690",
- "HP:0003011",
- "UPHENO:0002332",
- "UPHENO:0001003",
- "UPHENO:0002536",
- "HP:0040064",
- "HP:0011804",
+ "HP:0001883",
"BFO:0000002",
- "PR:000050567",
- "UBERON:0002101",
- "UBERON:0005090",
- "UBERON:0018254",
+ "HP:0001760",
+ "HP:0040064",
+ "PATO:0000001",
+ "UBERON:0002103",
"UBERON:0010707",
- "UBERON:0001630",
- "UBERON:0007271",
- "UBERON:0014792",
- "HP:0007340",
- "HP:0011805",
- "BFO:0000002",
- "UPHENO:0080555",
- "UPHENO:0002816",
- "UPHENO:0080556",
- "UPHENO:0081581",
- "HP:0033127",
- "UPHENO:0002647",
- "UPHENO:0002830",
- "UBERON:0000465",
- "RO:0002577",
+ "UBERON:0000026",
+ "UBERON:0010758",
+ "UBERON:0006058",
+ "UBERON:0002387",
+ "HP:0002814",
+ "HP:0005656",
+ "HP:0000118",
"UBERON:0015212",
+ "UBERON:0010538",
+ "HP:0000001",
"UBERON:0010000",
- "UBERON:0000475",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "UBERON:0004480",
+ "UBERON:0000978",
+ "UBERON:0002529",
],
"object_closure_label": [
- "All (HPO)",
- "abnormality of muscle organ physiology",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "decreased anatomical entity strength",
- "abnormal musculature",
- "decreased muscle organ strength",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "abnormal musculature of limb",
- "quality",
- "independent continuant",
- "material anatomical entity",
- "system",
- "paired limb/fin",
- "anatomical structure",
- "lateral structure",
- "multicellular anatomical structure",
- "pelvic complex",
- "appendage musculature",
- "musculature of pelvic complex",
- "abnormality of anatomical entity physiology",
- "phenotype",
- "Abnormal skeletal muscle morphology (HPO)",
- "continuant",
- "Abnormality of limbs (HPO)",
- "continuant",
- "protein-containing material entity",
- "appendage girdle complex",
- "pelvic complex muscle",
- "Lower limb muscle weakness (HPO)",
"abnormal phenotype by ontology source",
- "Abnormality of the musculature of the limbs (HPO)",
"specifically dependent continuant",
- "abnormal muscle organ morphology",
- "Abnormal muscle physiology (HPO)",
- "entity",
- "muscle structure",
- "skeletal musculature",
- "organism subdivision",
- "organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "musculature of limb",
- "abnormal anatomical entity",
- "decreased pelvic complex muscle strength",
- "Muscle weakness (HPO)",
- "Limb muscle weakness (HPO)",
- "Abnormality of the musculature (HPO)",
- "abnormality of anatomical entity physiology",
"phenotype by ontology source",
"abnormal anatomical entity",
+ "continuant",
+ "protein-containing material entity",
+ "material anatomical entity",
+ "system",
+ "multi-limb segment region",
+ "All (HPO)",
+ "continuant",
+ "appendage",
+ "subdivision of organism along appendicular axis",
+ "Abnormality of the lower limb (HPO)",
+ "Phenotypic abnormality (HPO)",
+ "entity",
+ "lateral structure",
+ "leg",
+ "limb segment",
+ "Phenotypic abnormality",
+ "abnormal pes morphology",
"abnormal anatomical entity morphology",
+ "abnormal leg",
+ "quality",
+ "anatomical structure",
+ "organism subdivision",
+ "multicellular organism",
+ "pelvic complex",
+ "lower limb segment",
+ "autopod region",
+ "phenotype",
+ "Positional foot deformity (HPO)",
+ "Abnormal foot morphology (HPO)",
"entity",
+ "independent continuant",
+ "posterior region of body",
+ "abnormal multicellular organism morphology",
"abnormal limb",
"material entity",
"anatomical entity",
+ "paired limb/fin",
"limb",
- "anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "appendage",
- "skeletal muscle organ",
+ "pelvic appendage",
+ "pes",
+ "Talipes (HPO)",
+ "Abnormality of limbs (HPO)",
+ "multicellular anatomical structure",
+ "hindlimb",
+ "appendage girdle complex",
+ "paired limb/fin segment",
],
"frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Frequent (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0009675🍪🍪biolink:has_phenotype🍪HP:0007340",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001883",
},
{
- "id": "uuid:c9d8bdf9-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:253601",
+ "id": "uuid:4e02df8e-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
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- "has_evidence": ["ECO:0000269"],
- "subject": "MONDO:0009676",
- "object": "HP:0003701",
- "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2B",
+ "publications": ["orphanet:589821"],
+ "frequency_qualifier": "HP:0040282",
+ "has_evidence": ["ECO:0000304"],
+ "subject": "MONDO:0035646",
+ "object": "HP:0011098",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "MONDO:0016971",
- "BFO:0000002",
- "BFO:0000020",
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- "MONDO:0009676",
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- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
- "MONDO:0016145",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
"BFO:0000017",
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+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
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+ "MONDO:0000462",
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+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
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+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
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+ "MONDO:0004995",
"MONDO:0700223",
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+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
+ "disease",
+ "hypertrophic cardiomyopathy",
"disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "qualitative or quantitative defects of dysferlin",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "autosomal recessive disease",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "autosomal recessive limb-girdle muscular dystrophy type 2B",
- "disease",
"continuant",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
"specifically dependent continuant",
"myopathy",
- "hereditary disease",
- "autosomal genetic disease",
+ "myotonic dystrophy",
"nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
"skeletal muscle disorder",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Proximal muscle weakness (HPO)",
+ "object_label": "Speech apraxia (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
+ "UBERON:0000465",
"UPHENO:0082875",
- "UPHENO:0002320",
+ "HP:0011442",
+ "HP:0002186",
+ "UPHENO:0004523",
+ "BFO:0000001",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UPHENO:0001002",
"BFO:0000002",
- "BFO:0000004",
- "UBERON:0000061",
- "HP:0000001",
"UPHENO:0001001",
- "UPHENO:0001002",
- "HP:0000118",
"BFO:0000020",
"UPHENO:0001003",
+ "UPHENO:0002536",
"BFO:0000001",
- "PATO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0001062",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
+ "UBERON:0000061",
"UPHENO:0075696",
- "HP:0001324",
- "HP:0003011",
- "UPHENO:0002332",
- "UPHENO:0002536",
- "HP:0011804",
- "BFO:0000002",
- "UBERON:0000465",
- "UBERON:0005090",
- "UBERON:0001630",
"UPHENO:0001005",
- "HP:0003701",
- "UPHENO:0080555",
- "UPHENO:0002816",
- "UPHENO:0080556",
- "HP:0033127",
+ "UPHENO:0002433",
+ "HP:0012638",
+ "BFO:0000004",
+ "UBERON:0000468",
+ "BFO:0000002",
+ "HP:0011098",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "PATO:0000001",
+ "HP:0000001",
+ "HP:0000707",
+ "HP:0011446",
"UBERON:0010000",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
+ "UBERON:0000467",
+ "UBERON:0001016",
],
"object_closure_label": [
- "All (HPO)",
- "abnormality of muscle organ physiology",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "decreased anatomical entity strength",
- "abnormal musculature",
- "decreased muscle organ strength",
- "Abnormality of the musculoskeletal system (HPO)",
- "quality",
- "independent continuant",
- "anatomical structure",
- "multicellular anatomical structure",
"abnormality of anatomical entity physiology",
- "phenotype",
- "abnormal phenotype by ontology source",
- "Proximal muscle weakness (HPO)",
"specifically dependent continuant",
+ "Abnormality of higher mental function (HPO)",
+ "quality",
+ "abnormal anatomical entity",
+ "abnormal phenotype by ontology source",
"phenotype by ontology source",
+ "abnormal anatomical entity",
+ "abnormal nervous system",
"continuant",
"material anatomical entity",
+ "nervous system",
+ "All (HPO)",
"continuant",
- "Abnormal muscle physiology (HPO)",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the nervous system (HPO)",
"entity",
- "muscle structure",
- "organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "abnormal anatomical entity",
- "Muscle weakness (HPO)",
- "Abnormality of the musculature (HPO)",
- "abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
+ "Phenotypic abnormality",
+ "abnormality of nervous system physiology",
+ "anatomical structure",
+ "multicellular organism",
+ "phenotype",
+ "Speech apraxia (HPO)",
"entity",
+ "independent continuant",
+ "Abnormal nervous system physiology (HPO)",
"material entity",
"anatomical entity",
+ "Abnormal central motor function (HPO)",
+ "Apraxia (HPO)",
+ "abnormality of anatomical entity physiology",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
- "evidence_count": 3,
- "grouping_key": "MONDO:0009676🍪🍪biolink:has_phenotype🍪HP:0003701",
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"],
+ "evidence_count": 2,
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0011098",
},
{
- "id": "uuid:c9c8bf35-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:160500",
+ "id": "uuid:4e02df90-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
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"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["OMIM:160500"],
- "frequency_qualifier": "HP:0040283",
+ "publications": ["orphanet:589821"],
+ "frequency_qualifier": "HP:0040282",
"has_evidence": ["ECO:0000304"],
- "subject": "MONDO:0008050",
- "object": "HP:0003701",
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject": "MONDO:0035646",
+ "object": "HP:0011710",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
+ "disease",
+ "hypertrophic cardiomyopathy",
"disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Proximal muscle weakness (HPO)",
+ "object_label": "Bundle branch block (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
+ "UPHENO:0002536",
+ "PR:000050567",
+ "UBERON:0000465",
"UPHENO:0082875",
- "UPHENO:0002320",
+ "UPHENO:0080362",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "HP:0030956",
+ "HP:0001626",
+ "HP:0031546",
"BFO:0000002",
- "BFO:0000004",
- "UBERON:0000061",
- "HP:0000001",
"UPHENO:0001001",
"UPHENO:0001002",
- "HP:0000118",
- "BFO:0000020",
"UPHENO:0001003",
- "BFO:0000001",
- "PATO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0001062",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
"UPHENO:0075696",
- "HP:0001324",
- "HP:0003011",
- "UPHENO:0002332",
- "UPHENO:0002536",
- "HP:0011804",
- "BFO:0000002",
- "UBERON:0000465",
- "UBERON:0005090",
- "UBERON:0001630",
"UPHENO:0001005",
- "HP:0003701",
- "UPHENO:0080555",
- "UPHENO:0002816",
- "UPHENO:0080556",
- "HP:0033127",
+ "BFO:0000020",
+ "HP:0011710",
+ "UPHENO:0002406",
+ "BFO:0000004",
+ "UBERON:0004535",
+ "UBERON:0000061",
+ "UBERON:0000468",
+ "HP:0012722",
+ "HP:0000118",
+ "BFO:0000002",
+ "UPHENO:0002332",
+ "PATO:0000001",
+ "HP:0000001",
+ "HP:0011025",
+ "BFO:0000001",
+ "BFO:0000001",
"UBERON:0010000",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
+ "UBERON:0000467",
+ "UBERON:0001009",
],
"object_closure_label": [
- "All (HPO)",
- "abnormality of muscle organ physiology",
+ "abnormality of anatomical entity physiology",
"Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "decreased anatomical entity strength",
- "abnormal musculature",
- "decreased muscle organ strength",
- "Abnormality of the musculoskeletal system (HPO)",
+ "Abnormal cardiovascular system physiology (HPO)",
"quality",
- "independent continuant",
- "anatomical structure",
- "multicellular anatomical structure",
- "abnormality of anatomical entity physiology",
- "phenotype",
+ "entity",
+ "abnormal anatomical entity",
"abnormal phenotype by ontology source",
- "Proximal muscle weakness (HPO)",
- "specifically dependent continuant",
"phenotype by ontology source",
"continuant",
+ "protein-containing material entity",
"material anatomical entity",
+ "circulatory system",
+ "All (HPO)",
+ "Cardiac conduction abnormality (HPO)",
+ "Phenotypic abnormality (HPO)",
"continuant",
- "Abnormal muscle physiology (HPO)",
- "entity",
- "muscle structure",
- "organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "abnormal anatomical entity",
- "Muscle weakness (HPO)",
- "Abnormality of the musculature (HPO)",
- "abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
"entity",
+ "Abnormality of cardiovascular system electrophysiology (HPO)",
+ "Abnormality of the cardiovascular system (HPO)",
+ "specifically dependent continuant",
+ "multicellular organism",
+ "phenotype",
+ "independent continuant",
+ "Bundle branch block (HPO)",
+ "abnormality of cardiovascular system physiology",
"material entity",
"anatomical entity",
+ "cardiovascular system",
+ "anatomical structure",
+ "abnormal cardiovascular system",
+ "abnormality of anatomical entity physiology",
+ "abnormal anatomical entity",
+ "Heart block (HPO)",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
],
- "frequency_qualifier_label": "Occasional (HPO)",
+ "frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040283", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Occasional (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0003701",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0011710",
},
{
- "id": "uuid:c9c8bf37-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:160500",
+ "id": "uuid:4e02dfa2-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["OMIM:160500"],
- "frequency_qualifier": "HP:0040283",
+ "publications": ["orphanet:589821"],
+ "frequency_qualifier": "HP:0040284",
"has_evidence": ["ECO:0000304"],
- "subject": "MONDO:0008050",
- "object": "HP:0001644",
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject": "MONDO:0035646",
+ "object": "HP:0001513",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Dilated cardiomyopathy (HPO)",
+ "object_label": "Obesity (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "UPHENO:0082875",
- "HP:0001637",
- "UPHENO:0001005",
- "BFO:0000020",
- "UPHENO:0077800",
- "UPHENO:0066927",
- "UPHENO:0076692",
- "PATO:0000001",
- "BFO:0000004",
- "UBERON:0004535",
- "UBERON:0011676",
- "UBERON:0013701",
- "UBERON:0002349",
- "UBERON:0000915",
- "UBERON:0002100",
- "UBERON:0005181",
- "UBERON:0002075",
- "UBERON:0015228",
- "HP:0000001",
+ "UPHENO:0049587",
+ "GO:0008150",
+ "UBERON:0000465",
+ "HP:0001513",
+ "BFO:0000001",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UBERON:0000468",
+ "UPHENO:0008273",
+ "UPHENO:0049874",
+ "BFO:0000003",
+ "BFO:0000002",
"UPHENO:0001001",
- "HP:0001644",
- "HP:0030680",
"UPHENO:0001002",
- "HP:0000118",
- "HP:0001627",
- "UPHENO:0076776",
"UPHENO:0001003",
- "UPHENO:0024906",
"BFO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0010000",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
- "UBERON:0000064",
+ "UBERON:0000061",
"UPHENO:0075696",
- "HP:0001626",
- "UPHENO:0080362",
- "HP:0001638",
+ "UPHENO:0001005",
+ "BFO:0000020",
+ "BFO:0000015",
+ "BFO:0000004",
+ "HP:0001507",
"BFO:0000002",
- "UPHENO:0002332",
"UPHENO:0002536",
- "UPHENO:0076810",
- "BFO:0000002",
- "PR:000050567",
- "UBERON:0004120",
- "UBERON:0000948",
- "UBERON:0001009",
- "UBERON:0005983",
- "UBERON:0009569",
- "UBERON:0013702",
- "UBERON:0005177",
- "UBERON:0003103",
- "UBERON:0018260",
- "UBERON:0015410",
- "UPHENO:0076781",
- "UPHENO:0081581",
- "UBERON:0001062",
- "UBERON:0000465",
- "UBERON:0000061",
- "UBERON:0010314",
- "UBERON:0000475",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0000060",
- "UBERON:0004923",
- "UBERON:0005178",
- "UBERON:0007100",
+ "HP:0000118",
+ "UPHENO:0010795",
+ "HP:0004323",
+ "UPHENO:0010763",
+ "PATO:0000001",
+ "HP:0000001",
+ "HP:0004324",
+ "UPHENO:0008312",
+ "GO:0040007",
+ "UBERON:0010000",
],
"object_closure_label": [
- "All (HPO)",
- "abnormal cardiovascular system",
- "Cardiomyopathy (HPO)",
"Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "abnormal myocardium morphology",
- "abnormal multicellular organism morphology",
- "independent continuant",
- "material anatomical entity",
- "cardiovascular system",
- "structure with developmental contribution from neural crest",
- "layer of muscle tissue",
- "abnormality of anatomical entity physiology",
- "Abnormal myocardium morphology (HPO)",
- "phenotype",
- "Abnormality of the cardiovascular system (HPO)",
- "Abnormal heart morphology (HPO)",
- "abnormal cardiovascular system morphology",
- "phenotype by ontology source",
- "abnormally decreased functionality of the anatomical entity",
- "abnormal heart morphology",
+ "abnormal anatomical entity",
+ "increased multicellular organism mass",
"quality",
- "continuant",
- "protein-containing material entity",
- "heart",
- "subdivision of trunk",
- "body proper",
- "trunk region element",
- "compound organ",
- "heart plus pericardium",
+ "growth",
+ "abnormal anatomical entity",
"abnormal phenotype by ontology source",
- "specifically dependent continuant",
- "abnormally decreased functionality of the myocardium",
- "anatomical entity dysfunction in independent continuant",
+ "phenotype by ontology source",
+ "Obesity (HPO)",
+ "occurrent",
+ "continuant",
+ "material anatomical entity",
+ "All (HPO)",
+ "continuant",
+ "abnormal growth",
+ "multicellular organism",
+ "Phenotypic abnormality (HPO)",
+ "abnormality of anatomical entity mass",
"entity",
- "anatomical entity",
+ "biological_process",
+ "increased anatomical entity mass",
+ "specifically dependent continuant",
"anatomical structure",
- "mesoderm-derived structure",
- "organism subdivision",
- "organ",
- "circulatory system",
- "heart layer",
- "musculature of body",
- "anatomical wall",
- "organ component layer",
- "thoracic cavity element",
- "primary circulatory organ",
- "abnormal anatomical entity",
- "Dilated cardiomyopathy (HPO)",
- "Abnormality of cardiovascular system morphology (HPO)",
- "continuant",
- "abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
+ "phenotype",
+ "Increased body weight (HPO)",
"entity",
+ "process",
+ "independent continuant",
+ "abnormal biological_process",
"material entity",
+ "anatomical entity",
+ "Growth abnormality (HPO)",
+ "abnormality of multicellular organism mass",
+ "Abnormality of body weight (HPO)",
"multicellular anatomical structure",
- "anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "organ part",
- "subdivision of organism along main body axis",
- "main body axis",
- "myocardium",
- "thoracic segment of trunk",
- "trunk",
- "thoracic segment organ",
- "viscus",
- "circulatory organ",
],
- "frequency_qualifier_label": "Occasional (HPO)",
+ "frequency_qualifier_label": "Very rare (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040283", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Occasional (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0000001", "HP:0040284"],
+ "frequency_qualifier_closure_label": ["Very rare (HPO)", "Frequency (HPO)", "All (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0001644",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001513",
},
{
- "id": "uuid:c9c8bff0-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:253600",
+ "id": "uuid:4e02df92-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["OMIM:253600"],
+ "publications": ["orphanet:589821"],
"frequency_qualifier": "HP:0040283",
"has_evidence": ["ECO:0000304"],
- "subject": "MONDO:0009675",
- "object": "HP:0010628",
- "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A",
+ "subject": "MONDO:0035646",
+ "object": "HP:0000729",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "MONDO:0016971",
- "MONDO:0005336",
- "MONDO:0015152",
- "MONDO:0000429",
- "MONDO:0005071",
- "MONDO:0006025",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
- "MONDO:0009675",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
- "MONDO:0016152",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
- "BFO:0000002",
- "MONDO:0016106",
- "MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003847",
- "MONDO:0003939",
+ "MONDO:0003382",
+ "BFO:0000016",
+ "MONDO:0700096",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
- "hereditary disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
"continuant",
- "autosomal recessive disease",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
"disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "disease",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "autosomal genetic disease",
+ "myotonic dystrophy",
"nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
- "autosomal recessive limb-girdle muscular dystrophy type 2A",
"skeletal muscle disorder",
- "qualitative or quantitative defects of calpain",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Facial palsy (HPO)",
+ "object_label": "Autistic behavior (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "UPHENO:0082875",
- "UPHENO:0076772",
- "UPHENO:0002320",
- "UPHENO:0005116",
- "HP:0031910",
- "HP:0011799",
- "HP:0410008",
- "UPHENO:0076692",
- "BFO:0000001",
- "PATO:0000001",
- "HP:0012638",
- "BFO:0000004",
- "UBERON:0001016",
- "UBERON:0001021",
- "UBERON:0000153",
- "UBERON:0011676",
- "UBERON:0013701",
- "UBERON:0014892",
- "UBERON:0015789",
- "UBERON:0011779",
- "UBERON:0000033",
- "HP:0000001",
- "HP:0000152",
- "UPHENO:0002764",
- "UPHENO:0001002",
- "HP:0000118",
- "BFO:0000020",
- "UPHENO:0002433",
- "HP:0000234",
- "HP:0000271",
- "HP:0010827",
- "UPHENO:0001003",
- "HP:0012639",
- "UPHENO:0076710",
- "UPHENO:0002908",
+ "UPHENO:0002536",
"BFO:0000001",
+ "GO:0008150",
+ "UBERON:0000465",
+ "NBO:0000313",
+ "UPHENO:0082875",
+ "UPHENO:0004523",
+ "UPHENO:0049587",
"BFO:0000040",
- "UBERON:0000467",
+ "GO:0007610",
"UBERON:0000468",
- "UBERON:0011216",
- "UBERON:0001785",
- "UBERON:0010959",
- "UBERON:0001577",
- "UPHENO:0075696",
- "HP:0045010",
- "UPHENO:0002844",
- "HP:0001291",
- "HP:0001324",
- "HP:0030319",
- "HP:0000759",
- "UPHENO:0081700",
- "HP:0003011",
- "UPHENO:0002332",
- "UPHENO:0078730",
- "UPHENO:0002536",
- "UPHENO:0081709",
- "HP:0000301",
- "UPHENO:0004523",
- "UPHENO:0004508",
- "HP:0011804",
+ "BFO:0000020",
+ "BFO:0000003",
"BFO:0000002",
- "UBERON:0000465",
- "UBERON:0005090",
- "UBERON:0018254",
- "UBERON:0004120",
- "UBERON:0034713",
- "UBERON:0001647",
- "UBERON:0000122",
- "UBERON:0001630",
- "UBERON:0001033",
- "UBERON:0002376",
- "UBERON:0007811",
- "UBERON:0001444",
- "UBERON:0013702",
- "UBERON:0001456",
- "UBERON:0008229",
- "UBERON:0013700",
"UPHENO:0001001",
- "UPHENO:0002910",
- "HP:0010628",
+ "UPHENO:0049622",
+ "UPHENO:0001002",
+ "UPHENO:0001003",
+ "BFO:0000001",
+ "UBERON:0001062",
+ "UBERON:0000061",
+ "UPHENO:0075696",
"UPHENO:0001005",
- "HP:0011805",
+ "UPHENO:0002433",
+ "HP:0012638",
+ "BFO:0000015",
+ "UPHENO:0049586",
+ "HP:0000729",
"BFO:0000002",
- "UPHENO:0076722",
- "UPHENO:0080555",
- "UPHENO:0003587",
- "UPHENO:0002816",
- "UPHENO:0080556",
+ "HP:0000708",
+ "BFO:0000004",
+ "UPHENO:0080585",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "UPHENO:0079826",
+ "PATO:0000001",
+ "HP:0000001",
"HP:0000707",
- "HP:0006824",
- "UPHENO:0081581",
- "HP:0033127",
- "UPHENO:0076702",
- "UBERON:0001062",
- "RO:0002577",
- "UBERON:0000061",
- "UBERON:0015212",
- "UBERON:0010314",
- "UBERON:0005162",
+ "HP:0011446",
+ "GO:0032501",
"UBERON:0010000",
- "UBERON:0000475",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "UBERON:0000010",
- "UBERON:0004461",
- "UBERON:0004473",
+ "UBERON:0000467",
+ "UBERON:0001016",
],
"object_closure_label": [
- "All (HPO)",
- "abnormality of muscle organ physiology",
- "abnormal peripheral nervous system",
- "Abnormal cranial nerve physiology (HPO)",
- "Abnormality of facial soft tissue (HPO)",
- "abnormal head",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "abnormal peripheral nervous system morphology",
- "decreased anatomical entity strength",
- "abnormal facial nerve",
- "abnormal musculature",
- "decreased muscle organ strength",
- "Abnormality of the nervous system (HPO)",
- "Cranial nerve paralysis (HPO)",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "Abnormal nervous system morphology (HPO)",
- "abnormal facial muscle",
- "independent continuant",
- "system",
- "lateral structure",
- "structure with developmental contribution from neural crest",
- "multi cell part structure",
- "multicellular anatomical structure",
- "nervous system",
- "cranial nerve",
- "face",
- "craniocervical region musculature",
- "axial musculature",
"abnormality of anatomical entity physiology",
- "abnormal cranial nerve morphology",
- "Abnormality of peripheral nerves (HPO)",
- "Facial palsy (HPO)",
+ "Phenotypic abnormality",
+ "Abnormality of higher mental function (HPO)",
+ "quality",
+ "multicellular organismal process",
+ "abnormal anatomical entity",
"abnormal phenotype by ontology source",
- "Abnormal skeletal muscle morphology (HPO)",
- "continuant",
"specifically dependent continuant",
- "abnormality of nervous system physiology",
- "Abnormality of the head (HPO)",
- "Abnormality of the face (HPO)",
- "Abnormality of the seventh cranial nerve (HPO)",
"phenotype by ontology source",
- "Abnormality of the peripheral nervous system (HPO)",
- "paralysed cranial nerve",
- "Abnormality of facial musculature (HPO)",
"abnormal nervous system",
- "abnormal nerve",
- "quality",
- "Abnormal nervous system physiology (HPO)",
+ "occurrent",
"continuant",
"material anatomical entity",
- "cranial neuron projection bundle",
- "facial nerve",
- "neuron projection bundle",
- "craniocervical region",
- "subdivision of head",
- "body proper",
- "craniocervical muscle",
- "facial muscle",
- "phenotype",
- "abnormal face",
- "abnormal muscle organ morphology",
- "Abnormal muscle physiology (HPO)",
+ "nervous system",
+ "All (HPO)",
+ "continuant",
+ "behavior",
+ "multicellular organism",
+ "abnormal behavior",
+ "Autistic behavior (HPO)",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the nervous system (HPO)",
+ "abnormal behavior process",
"entity",
+ "biological_process",
+ "abnormality of nervous system physiology",
"anatomical entity",
"anatomical structure",
- "muscle structure",
- "skeletal musculature",
- "mesoderm-derived structure",
- "organism subdivision",
- "organ",
- "muscle organ",
- "gustatory system",
- "cranial muscle",
- "musculature of body",
- "musculature",
- "peripheral nervous system",
- "skeletal musculature of head",
- "musculature of face",
- "abnormal anatomical entity",
- "Abnormality of head or neck (HPO)",
- "abnormal craniocervical region",
- "Abnormal cranial nerve morphology (HPO)",
- "Muscle weakness (HPO)",
- "Weakness of facial musculature (HPO)",
- "Abnormal peripheral nervous system morphology (HPO)",
- "paralysed anatomical entity",
- "Abnormality of the musculature (HPO)",
- "abnormality of anatomical entity physiology",
- "abnormality of cranial nerve physiology",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
+ "phenotype",
+ "abnormal behavior process",
+ "Behavioral abnormality (HPO)",
+ "abnormal biological_process",
+ "process",
+ "behavior process",
"entity",
- "abnormal nervous system morphology",
+ "Abnormal nervous system physiology (HPO)",
"material entity",
+ "abnormal response to stimulus",
+ "abnormality of anatomical entity physiology",
+ "abnormal anatomical entity",
+ "independent continuant",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "nerve",
- "anterior region of body",
- "subdivision of organism along main body axis",
- "main body axis",
- "skeletal muscle organ",
- "cranial or facial muscle",
- "nerve of head region",
- "head",
],
"frequency_qualifier_label": "Occasional (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040283", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Occasional (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Occasional (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0009675🍪🍪biolink:has_phenotype🍪HP:0010628",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0000729",
},
{
- "id": "uuid:c9d8bdf7-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:253601",
+ "id": "uuid:4e02df94-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["PMID:9731527"],
+ "publications": ["orphanet:589821"],
"frequency_qualifier": "HP:0040283",
- "has_evidence": ["ECO:0000269"],
- "subject": "MONDO:0009676",
- "object": "HP:0002505",
- "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2B",
+ "has_evidence": ["ECO:0000304"],
+ "subject": "MONDO:0035646",
+ "object": "HP:0000752",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "MONDO:0016971",
- "BFO:0000002",
- "BFO:0000020",
- "MONDO:0005336",
- "MONDO:0009676",
- "MONDO:0015152",
- "MONDO:0000429",
- "MONDO:0005071",
- "MONDO:0006025",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
- "MONDO:0016145",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
+ "BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
- "MONDO:0016106",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "qualitative or quantitative defects of dysferlin",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "autosomal recessive disease",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "autosomal recessive limb-girdle muscular dystrophy type 2B",
- "disease",
"continuant",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
"specifically dependent continuant",
"myopathy",
- "hereditary disease",
- "autosomal genetic disease",
+ "myotonic dystrophy",
"nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
"skeletal muscle disorder",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Loss of ambulation (HPO)",
+ "object_label": "Hyperactivity (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
+ "UPHENO:0049587",
+ "NBO:0000030",
+ "GO:0008150",
+ "UBERON:0000465",
+ "NBO:0000313",
"UPHENO:0082875",
- "UPHENO:0049622",
- "UPHENO:0001005",
+ "UPHENO:0004523",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "GO:0007610",
+ "NBO:0000568",
+ "BFO:0000003",
"BFO:0000002",
- "HP:0002540",
- "UPHENO:0050606",
- "HP:0001288",
- "HP:0012638",
- "BFO:0000015",
- "UBERON:0000061",
- "GO:0050882",
- "NBO:0000338",
- "GO:0050905",
- "UBERON:0001016",
- "HP:0000001",
"UPHENO:0001001",
- "UPHENO:0080585",
- "HP:0000118",
- "BFO:0000020",
- "UPHENO:0002433",
+ "UPHENO:0049622",
+ "UPHENO:0001002",
"UPHENO:0001003",
- "HP:0000708",
- "HP:0011446",
- "BFO:0000001",
- "PATO:0000001",
"BFO:0000001",
+ "UBERON:0000061",
+ "HP:0000752",
+ "UPHENO:0075696",
+ "UPHENO:0001005",
+ "BFO:0000020",
+ "UPHENO:0002433",
+ "HP:0012638",
+ "NBO:0000644",
+ "BFO:0000015",
"BFO:0000004",
- "GO:0032501",
- "GO:0050881",
- "NBO:0000313",
- "GO:0050877",
- "UBERON:0000467",
"UBERON:0000468",
- "NBO:0000403",
- "NBO:0000001",
- "UPHENO:0075696",
- "UPHENO:0078622",
- "HP:0002505",
"UPHENO:0049586",
- "HP:0100022",
- "UPHENO:0001002",
- "UPHENO:0050613",
- "UPHENO:0002332",
+ "BFO:0000002",
"UPHENO:0002536",
+ "HP:0000708",
+ "NBO:0000243",
+ "UPHENO:0080585",
+ "HP:0000118",
+ "UPHENO:0002332",
"UPHENO:0079826",
- "UPHENO:0004523",
- "UPHENO:0049587",
- "BFO:0000003",
- "BFO:0000002",
- "GO:0008150",
- "BFO:0000040",
- "GO:0050879",
- "GO:0007610",
- "GO:0003008",
+ "PATO:0000001",
+ "HP:0000001",
"HP:0000707",
- "UPHENO:0079833",
- "UBERON:0001062",
- "UBERON:0000465",
+ "HP:0011446",
+ "BFO:0000001",
+ "GO:0032501",
"UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0001016",
],
"object_closure_label": [
- "All (HPO)",
- "abnormal behavior",
- "Abnormality of movement (HPO)",
- "Phenotypic abnormality (HPO)",
- "Abnormality of the nervous system (HPO)",
- "Behavioral abnormality (HPO)",
+ "abnormality of anatomical entity physiology",
+ "Phenotypic abnormality",
+ "abnormal anatomical entity",
"Abnormality of higher mental function (HPO)",
- "abnormal voluntary movement behavior",
"quality",
- "process",
+ "multicellular organismal process",
+ "Hyperactivity (HPO)",
+ "abnormal anatomical entity",
+ "abnormal phenotype by ontology source",
+ "phenotype by ontology source",
+ "abnormal nervous system",
+ "kinesthetic behavior phenotype",
+ "occurrent",
+ "continuant",
"material anatomical entity",
- "anatomical structure",
- "multicellular anatomical structure",
"nervous system",
- "voluntary movement behavior",
- "body part movement",
- "abnormality of anatomical entity physiology",
- "phenotype",
+ "All (HPO)",
+ "continuant",
+ "behavior",
+ "abnormal behavior",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the nervous system (HPO)",
+ "abnormal behavior process",
+ "entity",
+ "entity",
+ "hyperactivity",
+ "biological_process",
"specifically dependent continuant",
"abnormality of nervous system physiology",
- "phenotype by ontology source",
- "Gait disturbance (HPO)",
+ "anatomical structure",
+ "multicellular organism",
+ "phenotype",
"abnormal behavior process",
- "abnormal nervous system",
+ "Behavioral abnormality (HPO)",
+ "voluntary movement behavior phenotype",
+ "process",
+ "independent continuant",
+ "behavior process",
"abnormal biological_process",
"Abnormal nervous system physiology (HPO)",
- "occurrent",
- "continuant",
- "biological_process",
"material entity",
- "multicellular organismal movement",
- "behavior",
- "system process",
- "musculoskeletal movement",
- "behavior process",
- "nervous system process",
- "abnormal phenotype by ontology source",
- "continuant",
- "Inability to walk (HPO)",
- "abnormal voluntary musculoskeletal movement",
- "entity",
- "independent continuant",
"anatomical entity",
- "abnormal anatomical entity",
- "abnormal voluntary movement behavior",
- "Loss of ambulation (HPO)",
"abnormal response to stimulus",
- "abnormal behavior process",
- "Phenotypic abnormality",
- "abnormal musculoskeletal movement",
"abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
- "entity",
- "multicellular organismal process",
+ "behavioral phenotype",
+ "multicellular anatomical structure",
"anatomical system",
- "voluntary musculoskeletal movement",
- "kinesthetic behavior",
- "neuromuscular process",
- "multicellular organism",
],
"frequency_qualifier_label": "Occasional (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040283", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Occasional (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Occasional (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0009676🍪🍪biolink:has_phenotype🍪HP:0002505",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0000752",
},
{
- "id": "uuid:c9c8bf2b-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:160500",
+ "id": "uuid:4e02df96-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["OMIM:160500"],
+ "publications": ["orphanet:589821"],
+ "frequency_qualifier": "HP:0040283",
"has_evidence": ["ECO:0000304"],
- "subject": "MONDO:0008050",
- "object": "HP:0010628",
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject": "MONDO:0035646",
+ "object": "HP:0001558",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
+ "disease",
+ "hypertrophic cardiomyopathy",
"disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Facial palsy (HPO)",
+ "object_label": "Decreased fetal movement (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "UPHENO:0082875",
- "UPHENO:0076772",
- "UPHENO:0002320",
- "UPHENO:0005116",
- "HP:0031910",
- "HP:0011799",
- "HP:0410008",
- "UPHENO:0076692",
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- "PATO:0000001",
- "HP:0012638",
- "BFO:0000004",
- "UBERON:0001016",
- "UBERON:0001021",
- "UBERON:0000153",
- "UBERON:0011676",
- "UBERON:0013701",
- "UBERON:0014892",
- "UBERON:0015789",
- "UBERON:0011779",
- "UBERON:0000033",
- "HP:0000001",
- "HP:0000152",
- "UPHENO:0002764",
+ "HP:0001197",
+ "UBERON:0000465",
+ "HP:0034059",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "BFO:0000002",
+ "UPHENO:0001001",
"UPHENO:0001002",
- "HP:0000118",
"BFO:0000020",
- "UPHENO:0002433",
- "HP:0000234",
- "HP:0000271",
- "HP:0010827",
"UPHENO:0001003",
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- "UPHENO:0076710",
- "UPHENO:0002908",
"BFO:0000001",
- "BFO:0000040",
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- "UBERON:0000468",
- "UBERON:0011216",
- "UBERON:0001785",
- "UBERON:0010959",
- "UBERON:0001577",
- "UPHENO:0075696",
- "HP:0045010",
- "UPHENO:0002844",
- "HP:0001291",
- "HP:0001324",
- "HP:0030319",
- "HP:0000759",
- "UPHENO:0081700",
- "HP:0003011",
- "UPHENO:0002332",
- "UPHENO:0078730",
- "UPHENO:0002536",
- "UPHENO:0081709",
- "HP:0000301",
- "UPHENO:0004523",
- "UPHENO:0004508",
- "HP:0011804",
- "BFO:0000002",
- "UBERON:0000465",
- "UBERON:0005090",
- "UBERON:0018254",
- "UBERON:0004120",
- "UBERON:0034713",
- "UBERON:0001647",
- "UBERON:0000122",
- "UBERON:0001630",
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- "UBERON:0002376",
- "UBERON:0007811",
- "UBERON:0001444",
- "UBERON:0013702",
- "UBERON:0001456",
- "UBERON:0008229",
- "UBERON:0013700",
- "UPHENO:0001001",
- "UPHENO:0002910",
- "HP:0010628",
"UPHENO:0001005",
- "HP:0011805",
- "BFO:0000002",
- "UPHENO:0076722",
- "UPHENO:0080555",
- "UPHENO:0003587",
- "UPHENO:0002816",
- "UPHENO:0080556",
- "HP:0000707",
- "HP:0006824",
- "UPHENO:0081581",
- "HP:0033127",
- "UPHENO:0076702",
- "UBERON:0001062",
- "RO:0002577",
+ "HP:0001558",
+ "BFO:0000004",
"UBERON:0000061",
- "UBERON:0015212",
- "UBERON:0010314",
- "UBERON:0005162",
+ "UBERON:0000468",
+ "BFO:0000002",
+ "UPHENO:0002536",
+ "HP:0001557",
+ "UBERON:0000922",
+ "HP:0000118",
+ "HP:0034057",
+ "PATO:0000001",
+ "UBERON:0000323",
+ "HP:0000001",
+ "UPHENO:0075949",
+ "BFO:0000001",
"UBERON:0010000",
- "UBERON:0000475",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "UBERON:0000010",
- "UBERON:0004461",
- "UBERON:0004473",
- ],
- "object_closure_label": [
- "All (HPO)",
- "abnormality of muscle organ physiology",
- "abnormal peripheral nervous system",
- "Abnormal cranial nerve physiology (HPO)",
- "Abnormality of facial soft tissue (HPO)",
- "abnormal head",
+ ],
+ "object_closure_label": [
"Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "abnormal peripheral nervous system morphology",
- "decreased anatomical entity strength",
- "abnormal facial nerve",
- "abnormal musculature",
- "decreased muscle organ strength",
- "Abnormality of the nervous system (HPO)",
- "Cranial nerve paralysis (HPO)",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "Abnormal nervous system morphology (HPO)",
- "abnormal facial muscle",
- "independent continuant",
- "system",
- "lateral structure",
- "structure with developmental contribution from neural crest",
- "multi cell part structure",
- "multicellular anatomical structure",
- "nervous system",
- "cranial nerve",
- "face",
- "craniocervical region musculature",
- "axial musculature",
- "abnormality of anatomical entity physiology",
- "abnormal cranial nerve morphology",
- "Abnormality of peripheral nerves (HPO)",
- "Facial palsy (HPO)",
- "abnormal phenotype by ontology source",
- "Abnormal skeletal muscle morphology (HPO)",
- "continuant",
"specifically dependent continuant",
- "abnormality of nervous system physiology",
- "Abnormality of the head (HPO)",
- "Abnormality of the face (HPO)",
- "Abnormality of the seventh cranial nerve (HPO)",
- "phenotype by ontology source",
- "Abnormality of the peripheral nervous system (HPO)",
- "paralysed cranial nerve",
- "Abnormality of facial musculature (HPO)",
- "abnormal nervous system",
- "abnormal nerve",
+ "abnormal anatomical entity",
"quality",
- "Abnormal nervous system physiology (HPO)",
+ "abnormal phenotype by ontology source",
+ "phenotype by ontology source",
"continuant",
"material anatomical entity",
- "cranial neuron projection bundle",
- "facial nerve",
- "neuron projection bundle",
- "craniocervical region",
- "subdivision of head",
- "body proper",
- "craniocervical muscle",
- "facial muscle",
- "phenotype",
- "abnormal face",
- "abnormal muscle organ morphology",
- "Abnormal muscle physiology (HPO)",
+ "All (HPO)",
+ "continuant",
+ "embryo",
+ "Phenotypic abnormality (HPO)",
+ "abnormal late embryo",
+ "Fetal anomaly (HPO)",
"entity",
- "anatomical entity",
- "anatomical structure",
- "muscle structure",
- "skeletal musculature",
- "mesoderm-derived structure",
- "organism subdivision",
- "organ",
- "muscle organ",
- "gustatory system",
- "cranial muscle",
- "musculature of body",
- "musculature",
- "peripheral nervous system",
- "skeletal musculature of head",
- "musculature of face",
- "abnormal anatomical entity",
- "Abnormality of head or neck (HPO)",
- "abnormal craniocervical region",
- "Abnormal cranial nerve morphology (HPO)",
- "Muscle weakness (HPO)",
- "Weakness of facial musculature (HPO)",
- "Abnormal peripheral nervous system morphology (HPO)",
- "paralysed anatomical entity",
- "Abnormality of the musculature (HPO)",
- "abnormality of anatomical entity physiology",
- "abnormality of cranial nerve physiology",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
"entity",
- "abnormal nervous system morphology",
- "material entity",
- "anatomical system",
+ "Decreased fetal movement (HPO)",
"multicellular organism",
- "organ system subdivision",
- "nerve",
- "anterior region of body",
- "subdivision of organism along main body axis",
- "main body axis",
- "skeletal muscle organ",
- "cranial or facial muscle",
- "nerve of head region",
- "head",
+ "phenotype",
+ "Prenatal movement abnormality (HPO)",
+ "independent continuant",
+ "Abnormality of prenatal development or birth (HPO)",
+ "material entity",
+ "anatomical entity",
+ "anatomical structure",
+ "Abnormal fetal physiology (HPO)",
+ "multicellular anatomical structure",
+ "late embryo",
],
+ "frequency_qualifier_label": "Occasional (HPO)",
+ "frequency_qualifier_category": "biolink:PhenotypicFeature",
+ "frequency_qualifier_namespace": "HP",
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Occasional (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0010628",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001558",
},
{
- "id": "uuid:c9c8bf2d-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:160500",
+ "id": "uuid:4e02df97-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["OMIM:160500"],
+ "publications": ["orphanet:589821"],
+ "frequency_qualifier": "HP:0040283",
"has_evidence": ["ECO:0000304"],
- "subject": "MONDO:0008050",
- "object": "HP:0011916",
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject": "MONDO:0035646",
+ "object": "HP:0001561",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
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+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
+ "disease",
+ "hypertrophic cardiomyopathy",
"disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Toe extensor amyotrophy (HPO)",
+ "object_label": "Polyhydramnios (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "HP:0002814",
- "HP:0009127",
- "UPHENO:0076692",
- "UPHENO:0003070",
- "PATO:0000001",
- "BFO:0000004",
- "UBERON:0004708",
- "UBERON:0000154",
- "UBERON:0006058",
- "UBERON:0002529",
- "UBERON:0002387",
- "HP:0000001",
- "UPHENO:0002644",
+ "HP:0001197",
+ "UPHENO:0075852",
+ "UPHENO:0002536",
+ "UBERON:0000465",
+ "BFO:0000001",
+ "BFO:0000040",
+ "BFO:0000002",
"UPHENO:0001001",
"UPHENO:0001002",
- "HP:0000118",
- "BFO:0000020",
"UPHENO:0001003",
- "UPHENO:0076710",
- "HP:0011916",
"BFO:0000001",
- "BFO:0000040",
"UBERON:0001062",
- "UBERON:0010000",
- "UBERON:0000467",
+ "UBERON:0000061",
+ "UBERON:0000463",
+ "UPHENO:0001005",
+ "BFO:0000020",
+ "BFO:0000004",
+ "UBERON:0000173",
"UBERON:0000468",
- "UBERON:0011216",
- "UBERON:0010709",
- "UBERON:0010538",
- "UBERON:0004488",
- "HP:0001436",
- "UPHENO:0002653",
- "HP:0003011",
- "UPHENO:0002536",
- "HP:0001437",
- "HP:0040064",
+ "HP:0001561",
+ "UBERON:0000922",
+ "HP:0000118",
+ "PATO:0000001",
+ "UBERON:0000323",
+ "HP:0000001",
"BFO:0000002",
- "PR:000050567",
- "UBERON:0000465",
- "UBERON:0002101",
- "UBERON:0004709",
- "UBERON:0005090",
- "UBERON:0002103",
- "UBERON:0010707",
- "UBERON:0001630",
- "UBERON:0000026",
- "UBERON:0010758",
- "UBERON:0007271",
- "UBERON:0014792",
- "UBERON:0004482",
- "UBERON:0008784",
- "UBERON:0002470",
- "UPHENO:0001005",
- "HP:0011805",
+ "UPHENO:0075949",
+ "HP:0001560",
+ "UBERON:0010000",
+ ],
+ "object_closure_label": [
+ "Phenotypic abnormality",
+ "Abnormality of the amniotic fluid (HPO)",
+ "quality",
+ "abnormal phenotype by ontology source",
+ "phenotype by ontology source",
+ "continuant",
+ "material anatomical entity",
+ "All (HPO)",
+ "embryo",
+ "Phenotypic abnormality (HPO)",
+ "abnormal late embryo",
+ "entity",
+ "specifically dependent continuant",
+ "anatomical entity",
+ "anatomical structure",
+ "organism substance",
+ "amniotic fluid",
+ "multicellular organism",
+ "phenotype",
+ "continuant",
+ "entity",
+ "independent continuant",
+ "Abnormality of prenatal development or birth (HPO)",
+ "abnormal amniotic fluid",
+ "material entity",
+ "Polyhydramnios (HPO)",
+ "abnormal anatomical entity",
+ "multicellular anatomical structure",
+ "late embryo",
+ ],
+ "frequency_qualifier_label": "Occasional (HPO)",
+ "frequency_qualifier_category": "biolink:PhenotypicFeature",
+ "frequency_qualifier_namespace": "HP",
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Occasional (HPO)"],
+ "evidence_count": 2,
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001561",
+ },
+ {
+ "id": "uuid:4e02df98-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
+ "predicate": "biolink:has_phenotype",
+ "category": "biolink:DiseaseToPhenotypicFeatureAssociation",
+ "aggregator_knowledge_source": ["infores:monarchinitiative"],
+ "primary_knowledge_source": "infores:hpo-annotations",
+ "provided_by": "hpoa_disease_to_phenotype_edges",
+ "publications": ["orphanet:589821"],
+ "frequency_qualifier": "HP:0040283",
+ "has_evidence": ["ECO:0000304"],
+ "subject": "MONDO:0035646",
+ "object": "HP:0001643",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
+ "subject_category": "biolink:Disease",
+ "subject_namespace": "MONDO",
+ "subject_closure": [
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
+ "MONDO:0020121",
+ "BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
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+ "MONDO:0003939",
+ "MONDO:0002022",
+ "BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
+ "MONDO:0020120",
+ "MONDO:0019056",
+ "MONDO:0004994",
+ "MONDO:0004995",
+ "MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
+ "MONDO:0700096",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
+ ],
+ "subject_closure_label": [
+ "eyelids malposition disorder",
+ "disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
+ "muscle tissue disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
+ "hereditary skeletal muscle disorder",
+ "continuant",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
+ "myopathy",
+ "myotonic dystrophy",
+ "nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
+ "realizable entity",
+ "skeletal muscle disorder",
+ "neuromuscular disease",
+ "myotonic syndrome",
+ ],
+ "object_label": "Patent ductus arteriosus (HPO)",
+ "object_category": "biolink:PhenotypicFeature",
+ "object_namespace": "HP",
+ "object_closure": [
+ "HP:0030962",
+ "UPHENO:0019771",
+ "PR:000050567",
+ "UBERON:0000465",
+ "UPHENO:0020542",
+ "UPHENO:0076729",
+ "UPHENO:0080362",
+ "HP:0001627",
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+ "UPHENO:0001002",
+ "UPHENO:0033572",
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+ "UPHENO:0015324",
+ "UPHENO:0015290",
"BFO:0000002",
- "UPHENO:0002816",
- "UPHENO:0081581",
- "HP:0033127",
- "UPHENO:0002647",
+ "UBERON:0013768",
+ "UBERON:0003509",
+ "UBERON:0003513",
+ "UBERON:0011695",
+ "UBERON:0004716",
+ "UBERON:0004145",
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+ "UBERON:0002201",
+ "UBERON:0006876",
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+ "UPHENO:0001003",
+ "UPHENO:0002536",
"BFO:0000001",
- "UPHENO:0002830",
- "RO:0002577",
+ "UBERON:0034923",
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+ "UPHENO:0075696",
+ "HP:0001643",
+ "UPHENO:0076776",
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+ "UBERON:0004572",
+ "UBERON:0004535",
"UBERON:0000061",
- "UBERON:0015212",
+ "UBERON:0000477",
"UBERON:0000475",
"UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "UBERON:0000978",
- "UBERON:0007270",
- "UBERON:0004480",
+ "UBERON:0004111",
+ "UBERON:0004573",
+ "UBERON:0003498",
+ "HP:0011603",
+ "UPHENO:0020351",
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+ "UPHENO:0076765",
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+ "HP:0025015",
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+ "UBERON:0000467",
+ "UBERON:0004120",
+ "UBERON:0007798",
+ "UBERON:0001009",
+ "UBERON:0004571",
+ "UBERON:0005178",
+ "UBERON:0007100",
],
"object_closure_label": [
- "All (HPO)",
- "abnormal musculature of lower limb",
- "Abnormality of the lower limb (HPO)",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "abnormal musculature",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "abnormal musculature of limb",
- "entity",
- "independent continuant",
- "system",
- "paired limb/fin",
- "lateral structure",
- "pelvic complex",
- "appendage musculature",
- "musculature of pelvic complex",
- "musculature of pes",
- "phenotype",
- "Abnormality of the foot musculature (HPO)",
- "abnormal phenotype by ontology source",
- "Abnormal skeletal muscle morphology (HPO)",
- "continuant",
+ "abnormal blood vessel morphology",
+ "abnormal anatomical entity",
"specifically dependent continuant",
"phenotype by ontology source",
- "Abnormality of the musculature of the lower limbs (HPO)",
- "Abnormality of limbs (HPO)",
- "quality",
+ "abnormal anatomical entity",
"continuant",
"protein-containing material entity",
"material anatomical entity",
- "hindlimb",
- "appendage girdle complex",
- "appendage",
- "subdivision of organism along appendicular axis",
- "paired limb/fin segment",
- "musculature of lower limb",
- "lower limb segment",
- "autopod region",
- "Abnormality of the musculature of the limbs (HPO)",
- "abnormal muscle organ morphology",
- "Toe extensor amyotrophy (HPO)",
+ "vascular system",
+ "circulatory system",
+ "vasculature of trunk",
+ "vasculature of organ",
+ "ductus arteriosus",
+ "thoracic segment of trunk",
+ "trunk",
+ "thoracic segment organ",
+ "viscus",
+ "circulatory organ",
+ "All (HPO)",
+ "abnormal vasculature",
+ "abnormal phenotype by ontology source",
+ "continuant",
+ "abnormal artery morphology in the independent continuant",
+ "multicellular organism",
+ "outflow tract",
+ "coronary vessel",
+ "vasculature",
+ "subdivision of trunk",
+ "body proper",
+ "trunk region element",
+ "compound organ",
+ "vessel",
+ "Abnormality of cardiovascular system morphology (HPO)",
+ "abnormal great vessel of heart morphology",
+ "Phenotypic abnormality (HPO)",
+ "abnormal opening of the anatomical entity",
+ "abnormal anatomical entity morphology",
+ "abnormal systemic artery morphology",
"entity",
- "anatomical structure",
- "muscle structure",
+ "structure with developmental contribution from neural crest",
+ "thoracic cavity element",
+ "primary circulatory organ",
+ "abnormal coronary vessel morphology",
+ "Abnormality of the cardiovascular system (HPO)",
+ "Phenotypic abnormality",
+ "abnormal incomplete closing of the anatomical entity",
+ "Patent ductus arteriosus (HPO)",
+ "abnormal cardiovascular system morphology",
+ "abnormal anatomical entity morphology",
+ "quality",
+ "disconnected anatomical group",
+ "anatomical cluster",
"organism subdivision",
"organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "leg",
- "pelvic appendage musculature",
- "musculature of limb",
- "abnormal musculature of pes",
- "Abnormality of the musculature (HPO)",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "abnormal leg",
- "abnormal limb",
+ "anatomical conduit",
+ "systemic artery",
+ "heart blood vessel",
+ "heart plus pericardium",
+ "phenotype",
+ "abnormal incomplete closing of the ductus arteriosus",
+ "abnormal anatomical entity morphology in the independent continuant",
+ "Abnormal vascular morphology (HPO)",
+ "entity",
+ "independent continuant",
+ "subdivision of organism along main body axis",
+ "main body axis",
+ "abnormal anatomical entity morphology in the heart",
+ "abnormal multicellular organism morphology",
"material entity",
"anatomical entity",
- "limb",
- "pelvic appendage",
+ "blood vessel",
+ "arterial system",
+ "blood vasculature",
+ "cardiovascular system",
+ "anatomical structure",
+ "great vessel of heart",
+ "arterial blood vessel",
+ "trunk blood vessel",
+ "embryonic cardiovascular system",
+ "conceptus",
+ "systemic arterial system",
+ "Congenital malformation of the great arteries (HPO)",
+ "abnormal ductus arteriosus morphology",
+ "abnormal vascular system morphology",
+ "abnormal cardiovascular system",
+ "Abnormal heart morphology (HPO)",
+ "Abnormal morphology of the great vessels (HPO)",
+ "abnormal artery morphology",
+ "Abnormality of the vasculature (HPO)",
+ "abnormal heart morphology",
+ "Abnormal blood vessel morphology (HPO)",
"multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "posterior region of body",
- "multi-limb segment region",
- "limb segment",
- "pes",
+ "mesoderm-derived structure",
+ "artery",
+ "thoracic segment blood vessel",
+ "heart",
+ "heart vasculature",
],
+ "frequency_qualifier_label": "Occasional (HPO)",
+ "frequency_qualifier_category": "biolink:PhenotypicFeature",
+ "frequency_qualifier_namespace": "HP",
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Occasional (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0011916",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001643",
},
{
- "id": "uuid:c9c8bf2e-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:160500",
+ "id": "uuid:4e02df99-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["OMIM:160500"],
+ "publications": ["orphanet:589821"],
+ "frequency_qualifier": "HP:0040283",
"has_evidence": ["ECO:0000304"],
- "subject": "MONDO:0008050",
- "object": "HP:0002460",
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject": "MONDO:0035646",
+ "object": "HP:0001671",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Distal muscle weakness (HPO)",
+ "object_label": "Abnormal cardiac septum morphology (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "UPHENO:0082875",
- "UPHENO:0002320",
- "UPHENO:0001005",
+ "PR:000050567",
+ "UBERON:0000465",
+ "UPHENO:0019888",
+ "UPHENO:0080362",
+ "HP:0001627",
+ "UPHENO:0015280",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UBERON:0000468",
+ "UBERON:0011676",
+ "UBERON:0013701",
+ "HP:0001626",
+ "UPHENO:0001002",
"BFO:0000020",
+ "UPHENO:0015324",
+ "HP:0001671",
+ "BFO:0000002",
+ "UPHENO:0001001",
+ "UPHENO:0001003",
+ "BFO:0000001",
+ "UBERON:0015410",
+ "UPHENO:0076776",
+ "UPHENO:0081581",
+ "UPHENO:0076692",
+ "BFO:0000004",
+ "UBERON:0004535",
+ "UBERON:0000061",
+ "UBERON:0000475",
+ "UBERON:0000062",
+ "UPHENO:0075696",
+ "HP:0030680",
+ "BFO:0000002",
+ "UPHENO:0002536",
+ "UPHENO:0076810",
+ "UBERON:0002099",
+ "UBERON:0000948",
+ "UBERON:0009569",
+ "UBERON:0013702",
+ "UBERON:0005177",
+ "UBERON:0003103",
+ "UBERON:0000915",
+ "UBERON:0002100",
+ "UBERON:0005181",
+ "UBERON:0002075",
+ "UBERON:0015228",
+ "HP:0000118",
+ "UPHENO:0020584",
"PATO:0000001",
- "BFO:0000004",
- "UBERON:0000061",
+ "UBERON:0003037",
+ "UBERON:0010314",
"HP:0000001",
- "UPHENO:0001001",
- "HP:0000118",
- "BFO:0000001",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
- "UPHENO:0075696",
- "HP:0001324",
- "HP:0003011",
- "UPHENO:0002332",
- "UPHENO:0001003",
- "UPHENO:0002536",
- "HP:0002460",
- "HP:0011804",
- "BFO:0000002",
- "BFO:0000040",
- "UBERON:0005090",
- "UBERON:0001630",
- "UPHENO:0001002",
- "BFO:0000002",
- "UPHENO:0080555",
- "UPHENO:0002816",
- "UPHENO:0080556",
- "HP:0033127",
+ "UPHENO:0001005",
"BFO:0000001",
- "UBERON:0001062",
- "UBERON:0000465",
"UBERON:0010000",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
+ "UBERON:0000467",
+ "UBERON:0004120",
+ "UBERON:0001009",
+ "UBERON:0005178",
+ "UBERON:0007100",
],
"object_closure_label": [
+ "abnormal anatomical entity",
+ "quality",
+ "specifically dependent continuant",
+ "phenotype by ontology source",
+ "continuant",
+ "protein-containing material entity",
+ "material anatomical entity",
+ "circulatory system",
+ "thoracic segment of trunk",
+ "trunk",
+ "thoracic segment organ",
+ "viscus",
+ "circulatory organ",
"All (HPO)",
- "abnormality of muscle organ physiology",
+ "abnormal phenotype by ontology source",
+ "continuant",
+ "Abnormal cardiac septum morphology (HPO)",
+ "multicellular organism",
+ "subdivision of trunk",
+ "body proper",
+ "trunk region element",
+ "compound organ",
+ "Abnormality of cardiovascular system morphology (HPO)",
"Phenotypic abnormality (HPO)",
- "decreased anatomical entity strength",
- "abnormal musculature",
- "decreased muscle organ strength",
- "Abnormality of the musculoskeletal system (HPO)",
+ "abnormal anatomical entity morphology",
"entity",
- "independent continuant",
- "material anatomical entity",
- "anatomical structure",
- "multicellular anatomical structure",
- "abnormality of anatomical entity physiology",
- "phenotype",
+ "entity",
+ "septum",
+ "structure with developmental contribution from neural crest",
+ "thoracic cavity element",
+ "primary circulatory organ",
+ "Abnormality of the cardiovascular system (HPO)",
"Phenotypic abnormality",
- "continuant",
- "Distal muscle weakness (HPO)",
- "quality",
- "continuant",
+ "abnormal cardiovascular system morphology",
+ "abnormal anatomical entity morphology",
+ "organism subdivision",
+ "organ",
+ "heart plus pericardium",
+ "phenotype",
+ "abnormal anatomical entity morphology in the independent continuant",
+ "independent continuant",
+ "subdivision of organism along main body axis",
+ "main body axis",
+ "abnormal anatomical entity morphology in the heart",
+ "abnormal multicellular organism morphology",
"material entity",
- "abnormal phenotype by ontology source",
- "specifically dependent continuant",
- "Abnormal muscle physiology (HPO)",
- "entity",
"anatomical entity",
- "muscle structure",
- "organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "abnormal anatomical entity",
- "Muscle weakness (HPO)",
- "Abnormality of the musculature (HPO)",
- "abnormality of anatomical entity physiology",
- "phenotype by ontology source",
+ "cardiovascular system",
+ "anatomical structure",
"abnormal anatomical entity",
+ "abnormal cardiac septum morphology",
+ "abnormal cardiovascular system",
+ "Abnormal heart morphology (HPO)",
+ "abnormal heart morphology",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
+ "mesoderm-derived structure",
+ "cardiac septum",
+ "heart",
],
+ "frequency_qualifier_label": "Occasional (HPO)",
+ "frequency_qualifier_category": "biolink:PhenotypicFeature",
+ "frequency_qualifier_namespace": "HP",
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Occasional (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0002460",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001671",
},
{
- "id": "uuid:c9c8bf32-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:160500",
+ "id": "uuid:4e02df9a-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["OMIM:160500"],
- "has_evidence": ["ECO:0000501"],
- "subject": "MONDO:0008050",
- "object": "HP:0003805",
- "subject_label": "MYH7-related skeletal myopathy",
+ "publications": ["orphanet:589821"],
+ "frequency_qualifier": "HP:0040283",
+ "has_evidence": ["ECO:0000304"],
+ "subject": "MONDO:0035646",
+ "object": "HP:0002014",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
+ "disease",
+ "hypertrophic cardiomyopathy",
"disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Rimmed vacuoles (HPO)",
+ "object_label": "Diarrhea (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "BFO:0000002",
- "BFO:0000020",
- "UPHENO:0076692",
+ "UPHENO:0002443",
+ "UPHENO:0002536",
+ "UBERON:0000465",
+ "UPHENO:0082875",
+ "HP:0002664",
"BFO:0000001",
- "BFO:0000004",
- "CL:0000255",
- "UBERON:0014892",
- "UBERON:0002036",
- "HP:0000001",
- "HP:0004303",
- "UPHENO:0001001",
+ "BFO:0000040",
+ "UBERON:0001062",
"UPHENO:0001002",
- "HP:0000118",
+ "BFO:0000020",
+ "HP:0011793",
+ "HP:0011458",
+ "BFO:0000002",
+ "UBERON:0001988",
+ "UPHENO:0001001",
+ "UPHENO:0002833",
"UPHENO:0001003",
- "UPHENO:0076710",
- "PATO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0000467",
- "CL:0000000",
+ "UBERON:0000463",
+ "UPHENO:0075696",
+ "HP:0002014",
+ "HP:0025031",
+ "BFO:0000004",
+ "UBERON:0000061",
+ "UBERON:0000174",
"UBERON:0000468",
- "UBERON:0011216",
- "CL:0000548",
- "UBERON:0001134",
- "HP:0003011",
- "UPHENO:0002536",
- "HP:0003805",
- "UBERON:0005090",
- "UBERON:0018254",
- "UBERON:0004120",
- "UBERON:0000479",
- "CL:0000003",
- "UBERON:0001630",
- "UBERON:0002385",
- "CL:0000188",
- "UPHENO:0001005",
- "HP:0011805",
- "HP:0025354",
- "UPHENO:0002816",
- "UPHENO:0081581",
- "HP:0033127",
"BFO:0000002",
- "UBERON:0001062",
- "UBERON:0000465",
- "RO:0002577",
- "UBERON:0000061",
+ "HP:0025032",
+ "PATO:0000001",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "HP:0000001",
+ "UPHENO:0001005",
+ "BFO:0000001",
"UBERON:0010000",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "CL:0002371",
+ "UBERON:0000467",
+ "UBERON:0001007",
],
"object_closure_label": [
+ "abnormality of anatomical entity physiology",
+ "abnormal digestive system",
+ "entity",
+ "abnormal anatomical entity",
+ "Diarrhea (HPO)",
+ "specifically dependent continuant",
+ "Abnormality of digestive system physiology (HPO)",
+ "phenotype by ontology source",
+ "continuant",
+ "material anatomical entity",
+ "digestive system",
"All (HPO)",
- "Abnormal muscle fiber morphology (HPO)",
- "Phenotypic abnormality",
+ "abnormal phenotype by ontology source",
+ "continuant",
+ "feces",
"Phenotypic abnormality (HPO)",
- "Abnormal cellular phenotype (HPO)",
- "abnormal musculature",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
+ "Phenotypic abnormality",
+ "Neoplasm by anatomical site (HPO)",
+ "Abdominal symptom (HPO)",
"quality",
- "independent continuant",
- "material anatomical entity",
- "system",
- "multicellular anatomical structure",
+ "organism substance",
+ "excreta",
+ "multicellular organism",
"phenotype",
- "abnormal phenotype by ontology source",
- "Abnormal skeletal muscle morphology (HPO)",
- "phenotype by ontology source",
- "tissue",
- "animal cell",
- "skeletal muscle tissue",
- "cell of skeletal muscle",
- "continuant",
- "specifically dependent continuant",
- "abnormal muscle organ morphology",
- "Rimmed vacuoles (HPO)",
+ "Neoplasm (HPO)",
"entity",
+ "independent continuant",
+ "abnormality of digestive system physiology",
+ "Abnormality of the digestive system (HPO)",
+ "material entity",
"anatomical entity",
"anatomical structure",
- "muscle structure",
- "skeletal musculature",
- "mesoderm-derived structure",
- "organ",
- "native cell",
- "muscle organ",
- "muscle tissue",
- "musculature of body",
- "musculature",
- "somatic cell",
- "Abnormality of the musculature (HPO)",
+ "abnormality of anatomical entity physiology",
"abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "entity",
- "continuant",
- "material entity",
+ "multicellular anatomical structure",
"anatomical system",
- "cell",
- "multicellular organism",
- "organ system subdivision",
- "eukaryotic cell",
- "skeletal muscle organ",
- "striated muscle tissue",
],
+ "frequency_qualifier_label": "Occasional (HPO)",
+ "frequency_qualifier_category": "biolink:PhenotypicFeature",
+ "frequency_qualifier_namespace": "HP",
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Occasional (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0003805",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0002014",
},
],
},
diff --git a/backend/tests/fixtures/association_response.py b/backend/tests/fixtures/association_response.py
index 77bedbfd1..04c1e96f6 100644
--- a/backend/tests/fixtures/association_response.py
+++ b/backend/tests/fixtures/association_response.py
@@ -23,4214 +23,4140 @@ def association_response():
"start": 0,
"docs": [
{
- "id": "uuid:c9c8bf2f-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:160500",
+ "id": "uuid:4e12a2a1-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:565899",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["PMID:17548557"],
- "frequency_qualifier": "HP:0040280",
- "has_evidence": ["ECO:0000269"],
- "subject": "MONDO:0008050",
- "object": "HP:0011399",
- "subject_label": "MYH7-related skeletal myopathy",
+ "publications": ["orphanet:565899"],
+ "frequency_qualifier": "HP:0040282",
+ "has_evidence": ["ECO:0000304"],
+ "subject": "MONDO:0035432",
+ "object": "HP:0002465",
+ "subject_label": "POMGNT2-related limb-girdle muscular dystrophy R24",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
+ "MONDO:0000001",
+ "MONDO:0020121",
"MONDO:0003847",
"BFO:0000001",
- "MONDO:0020121",
- "MONDO:0019952",
+ "MONDO:0016106",
+ "MONDO:0005336",
"BFO:0000017",
+ "MONDO:0003939",
+ "MONDO:0035432",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0016971",
+ "MONDO:0005071",
+ "BFO:0000002",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
"MONDO:0700223",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "OGMS:0000031",
],
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
"disease",
+ "realizable entity",
+ "disease",
+ "POMGNT2-related limb-girdle muscular dystrophy R24",
"muscle tissue disorder",
- "congenital nervous system disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
+ "limb-girdle muscular dystrophy",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "disposition",
+ "human disease",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
"nervous system disorder",
- "congenital myopathy",
- "realizable entity",
- "specifically dependent continuant",
+ "entity",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "muscular dystrophy",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
],
- "object_label": "Tibialis atrophy (HPO)",
+ "object_label": "Poor speech (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "UPHENO:0014121",
- "HP:0002814",
- "UPHENO:0068971",
- "UPHENO:0001005",
- "HP:0009127",
- "UPHENO:0014120",
- "UPHENO:0075195",
- "HP:0030236",
- "UPHENO:0020584",
- "UPHENO:0076692",
- "UPHENO:0003070",
- "PATO:0000001",
- "UPHENO:0012541",
- "BFO:0000004",
- "UBERON:0004708",
- "UBERON:0000154",
- "UBERON:0014892",
- "UBERON:0006058",
- "UBERON:0002529",
- "UBERON:0006067",
- "HP:0000001",
- "UPHENO:0002644",
- "UPHENO:0013936",
- "HP:0003202",
- "UPHENO:0075952",
- "UPHENO:0001002",
- "HP:0000118",
- "UPHENO:0015280",
- "UPHENO:0001003",
- "UPHENO:0076710",
- "BFO:0000001",
+ "UPHENO:0002536",
"BFO:0000001",
- "BFO:0000040",
- "UBERON:0010000",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
- "UBERON:0010709",
- "UBERON:0000366",
- "UBERON:0003661",
- "UBERON:0010890",
- "UBERON:0010538",
- "UBERON:0004466",
- "UBERON:0004256",
- "UBERON:0003823",
- "UPHENO:0075696",
- "HP:0002981",
- "HP:0003797",
- "UPHENO:0014111",
- "HP:0001430",
+ "UBERON:0000465",
+ "UPHENO:0082875",
"BFO:0000002",
- "HP:0008944",
+ "UPHENO:0004523",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UPHENO:0001002",
"BFO:0000020",
- "HP:0003011",
- "UPHENO:0002536",
- "HP:0001437",
- "UPHENO:0078056",
- "HP:0040064",
"BFO:0000002",
- "PR:000050567",
- "UBERON:0002101",
- "UBERON:0004709",
- "UBERON:0005090",
- "UBERON:0018254",
- "UBERON:0002103",
- "UBERON:0010707",
- "UBERON:0001630",
- "UBERON:0000026",
- "UBERON:0010758",
- "UBERON:0007271",
- "UBERON:0014792",
- "UBERON:0004482",
- "UBERON:0001383",
- "UBERON:0008784",
- "UBERON:0002471",
- "HP:0007210",
"UPHENO:0001001",
- "UPHENO:0075777",
- "HP:0011805",
- "HP:0003693",
- "UPHENO:0002816",
- "HP:0011399",
- "UPHENO:0081581",
- "HP:0033127",
- "UPHENO:0019778",
- "UPHENO:0002647",
- "UPHENO:0013920",
- "UPHENO:0002830",
- "UBERON:0001062",
- "UBERON:0000465",
- "RO:0002577",
+ "UPHENO:0001003",
+ "BFO:0000001",
+ "UPHENO:0075696",
+ "UPHENO:0002433",
+ "HP:0012638",
+ "BFO:0000004",
"UBERON:0000061",
- "UBERON:0015212",
- "UBERON:0000475",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "UBERON:0000978",
- "UBERON:0007270",
- "UBERON:0004480",
- "UBERON:0003663",
- "UBERON:0014795",
- "UBERON:0008230",
+ "UBERON:0000468",
+ "HP:0002167",
+ "PATO:0000001",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "HP:0000001",
+ "HP:0002465",
+ "UPHENO:0001005",
+ "HP:0000707",
+ "HP:0011446",
+ "UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0001016",
],
"object_closure_label": [
+ "abnormality of anatomical entity physiology",
+ "Neurological speech impairment (HPO)",
+ "Abnormality of higher mental function (HPO)",
+ "abnormal anatomical entity",
+ "specifically dependent continuant",
+ "phenotype by ontology source",
+ "abnormal nervous system",
+ "continuant",
+ "material anatomical entity",
+ "nervous system",
"All (HPO)",
- "abnormal musculature of lower limb",
- "Abnormality of the lower limb (HPO)",
- "decreased size of the anatomical entity",
- "Phenotypic abnormality",
+ "Poor speech (HPO)",
+ "abnormal phenotype by ontology source",
"Phenotypic abnormality (HPO)",
- "Distal amyotrophy (HPO)",
- "abnormal musculature",
- "Tibialis atrophy (HPO)",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "abnormal musculature of limb",
- "independent continuant",
- "material anatomical entity",
- "system",
- "paired limb/fin",
- "lateral structure",
- "pelvic complex",
- "appendage musculature",
- "musculature of pelvic complex",
- "musculature of leg",
- "hindlimb zeugopod muscle",
- "hindlimb zeugopod",
- "musculature of limb atrophy",
- "Limb-girdle muscle atrophy (HPO)",
- "skeletal musculature atrophy",
- "abnormal hindlimb zeugopod muscle",
- "Abnormal skeletal muscle morphology (HPO)",
- "abnormal anatomical entity morphology in the independent continuant",
- "phenotype by ontology source",
- "Abnormality of muscle size (HPO)",
- "Abnormality of the musculature of the lower limbs (HPO)",
- "tibialis atrophy",
- "Abnormality of limbs (HPO)",
+ "Abnormality of the nervous system (HPO)",
+ "entity",
+ "Phenotypic abnormality",
+ "abnormality of nervous system physiology",
"quality",
- "decreased size of the anatomical entity in the independent continuant",
- "continuant",
- "protein-containing material entity",
- "hindlimb",
- "appendage girdle complex",
- "appendage",
- "subdivision of organism along appendicular axis",
- "flexor muscle",
- "limb muscle",
- "pelvic complex muscle",
- "paired limb/fin segment",
- "musculature of lower limb",
- "muscle of leg",
- "lower limb segment",
- "zeugopod",
- "Lower limb amyotrophy (HPO)",
+ "multicellular organism",
"phenotype",
- "abnormal phenotype by ontology source",
- "Abnormality of the musculature of the limbs (HPO)",
- "musculature of lower limb atrophy",
- "abnormal size of anatomical entity",
- "abnormal muscle organ morphology",
- "abnormal muscle organ morphology",
+ "independent continuant",
"entity",
+ "Abnormal nervous system physiology (HPO)",
+ "material entity",
"anatomical entity",
"anatomical structure",
- "muscle structure",
- "skeletal musculature",
- "organism subdivision",
- "organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "leg",
- "pelvic appendage musculature",
- "musculature of limb",
- "hindlimb muscle",
- "pelvic appendage muscle",
- "tibialis",
- "abnormal anatomical entity",
- "Abnormality of the calf (HPO)",
- "anatomical entity atrophy",
- "Skeletal muscle atrophy (HPO)",
- "abnormal hindlimb zeugopod",
- "Abnormality of the calf musculature (HPO)",
"continuant",
- "Distal lower limb amyotrophy (HPO)",
- "specifically dependent continuant",
- "Abnormality of the musculature (HPO)",
+ "abnormality of anatomical entity physiology",
"abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "abnormal anatomical entity morphology",
- "abnormal leg",
- "entity",
- "muscle organ atrophy",
- "abnormal limb",
- "material entity",
- "limb",
- "pelvic appendage",
"multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "posterior region of body",
- "skeletal muscle organ",
- "multi-limb segment region",
- "limb segment",
- "musculature of hindlimb zeugopod",
],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0011399",
+ "grouping_key": "MONDO:0035432🍪🍪biolink:has_phenotype🍪HP:0002465",
},
{
- "id": "uuid:c9c8bf30-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:160500",
+ "id": "uuid:4e12a2a3-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:565899",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["PMID:17548557"],
- "frequency_qualifier": "HP:0040280",
- "has_evidence": ["ECO:0000269"],
- "subject": "MONDO:0008050",
- "object": "HP:0031295",
- "subject_label": "MYH7-related skeletal myopathy",
+ "publications": ["orphanet:565899"],
+ "frequency_qualifier": "HP:0040282",
+ "has_evidence": ["ECO:0000304"],
+ "subject": "MONDO:0035432",
+ "object": "HP:0008981",
+ "subject_label": "POMGNT2-related limb-girdle muscular dystrophy R24",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
+ "MONDO:0000001",
+ "MONDO:0020121",
"MONDO:0003847",
"BFO:0000001",
- "MONDO:0020121",
- "MONDO:0019952",
+ "MONDO:0016106",
+ "MONDO:0005336",
"BFO:0000017",
+ "MONDO:0003939",
+ "MONDO:0035432",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0016971",
+ "MONDO:0005071",
+ "BFO:0000002",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
"MONDO:0700223",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "OGMS:0000031",
],
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
"disease",
+ "realizable entity",
+ "disease",
+ "POMGNT2-related limb-girdle muscular dystrophy R24",
"muscle tissue disorder",
- "congenital nervous system disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
+ "limb-girdle muscular dystrophy",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "disposition",
+ "human disease",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
"nervous system disorder",
- "congenital myopathy",
- "realizable entity",
- "specifically dependent continuant",
+ "entity",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "muscular dystrophy",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
],
- "object_label": "Left atrial enlargement (HPO)",
+ "object_label": "Calf muscle hypertrophy (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "UPHENO:0001005",
- "BFO:0000002",
- "UPHENO:0075195",
- "UPHENO:0020584",
- "UPHENO:0076692",
- "BFO:0000004",
- "UBERON:0004535",
- "UBERON:0011676",
- "UBERON:0013701",
- "UBERON:0002081",
- "UBERON:0000915",
- "UBERON:0002100",
- "UBERON:0005181",
- "UBERON:0002075",
- "UBERON:0015228",
- "HP:0000001",
- "UPHENO:0019897",
- "HP:0030680",
- "HP:0000118",
- "HP:0001627",
- "BFO:0000020",
- "UPHENO:0019919",
- "UPHENO:0076776",
- "UPHENO:0015280",
- "UPHENO:0001020",
- "UPHENO:0001003",
- "BFO:0000001",
- "PATO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0000064",
- "UBERON:0002079",
- "UPHENO:0075696",
- "UPHENO:0015303",
- "HP:0001626",
- "UPHENO:0080362",
- "UPHENO:0065599",
- "HP:0031295",
- "UPHENO:0002536",
- "UPHENO:0076810",
+ "HP:0008981",
+ "UPHENO:0084535",
+ "UPHENO:0002816",
+ "HP:0030236",
"PR:000050567",
"UBERON:0000465",
- "UBERON:0004120",
- "UBERON:0035553",
- "UBERON:0000948",
- "UBERON:0001009",
- "UBERON:0004151",
- "UBERON:0009569",
- "UBERON:0013702",
- "UBERON:0005177",
- "UBERON:0003103",
- "UBERON:0015410",
- "UPHENO:0001001",
+ "RO:0002577",
+ "UPHENO:0015280",
+ "HP:0001437",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UBERON:0011216",
+ "UBERON:0000154",
+ "UBERON:0006067",
"UPHENO:0001002",
- "UPHENO:0015324",
- "HP:0025579",
+ "HP:0001430",
+ "UPHENO:0075195",
+ "UPHENO:0019778",
+ "UPHENO:0084489",
+ "BFO:0000002",
+ "UBERON:0002101",
+ "UBERON:0004709",
+ "UBERON:0015212",
+ "UBERON:0001630",
+ "UPHENO:0001001",
+ "UPHENO:0075777",
+ "HP:0011805",
+ "HP:0003712",
+ "UPHENO:0002647",
+ "BFO:0000001",
+ "UBERON:0004482",
+ "UBERON:0001383",
+ "UBERON:0008784",
+ "UBERON:0002471",
+ "UPHENO:0075696",
+ "UPHENO:0001005",
+ "HP:0009127",
+ "BFO:0000020",
"UPHENO:0001072",
"UPHENO:0081581",
- "HP:0005120",
- "UPHENO:0015329",
- "BFO:0000002",
- "UBERON:0001062",
- "RO:0002577",
+ "HP:0033127",
+ "UPHENO:0001003",
+ "UPHENO:0076692",
+ "UPHENO:0003070",
+ "UPHENO:0002830",
+ "BFO:0000004",
+ "UBERON:0004708",
"UBERON:0000061",
- "UBERON:0015212",
- "UBERON:0010314",
- "UBERON:0010000",
"UBERON:0000475",
"UBERON:0000062",
- "UBERON:0005178",
- "UBERON:0007100",
- ],
- "object_closure_label": [
- "All (HPO)",
- "abnormal cardiac atrium morphology",
- "abnormal cardiovascular system",
- "increased size of the anatomical entity in independent continuant",
- "Phenotypic abnormality (HPO)",
- "abnormal anatomical entity morphology in the heart",
- "Abnormal left atrium morphology (HPO)",
- "increased size of the anatomical entity",
- "abnormal multicellular organism morphology",
- "Abnormal cardiac atrium morphology (HPO)",
- "quality",
- "independent continuant",
- "system",
- "cardiovascular system",
- "lateral structure",
- "structure with developmental contribution from neural crest",
- "multicellular anatomical structure",
- "left cardiac atrium",
- "Abnormality of the cardiovascular system (HPO)",
- "Phenotypic abnormality",
- "Abnormal heart morphology (HPO)",
- "specifically dependent continuant",
- "abnormal left cardiac atrium morphology",
- "abnormal cardiovascular system morphology",
- "abnormal anatomical entity morphology in the independent continuant",
- "increased size of the left cardiac atrium",
- "phenotype by ontology source",
- "abnormal heart morphology",
- "protein-containing material entity",
- "material anatomical entity",
- "left cardiac chamber",
- "heart",
- "subdivision of trunk",
- "body proper",
- "trunk region element",
- "compound organ",
- "heart plus pericardium",
- "phenotype",
- "abnormal phenotype by ontology source",
- "continuant",
- "abnormal size of anatomical entity",
- "entity",
- "anatomical entity",
- "anatomical structure",
- "mesoderm-derived structure",
- "organism subdivision",
- "organ",
- "circulatory system",
- "cardiac chamber",
- "thoracic cavity element",
- "primary circulatory organ",
- "abnormal anatomical entity",
- "abnormal cardiac atrium morphology in the heart",
- "Abnormality of cardiovascular system morphology (HPO)",
- "Left atrial enlargement (HPO)",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "abnormal anatomical entity morphology",
- "entity",
- "abnormal cardiac atrium morphology in the independent continuant",
- "continuant",
- "material entity",
- "anatomical system",
- "multicellular organism",
- "organ part",
- "subdivision of organism along main body axis",
- "main body axis",
- "cardiac atrium",
- "thoracic segment of trunk",
- "trunk",
- "thoracic segment organ",
- "viscus",
- "circulatory organ",
- ],
- "frequency_qualifier_label": "Obligate (HPO)",
- "frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
- "evidence_count": 2,
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0031295",
- },
- {
- "id": "uuid:c9c8bf31-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:160500",
- "predicate": "biolink:has_phenotype",
- "category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "aggregator_knowledge_source": ["infores:monarchinitiative"],
- "primary_knowledge_source": "infores:hpo-annotations",
- "provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["PMID:17548557"],
- "frequency_qualifier": "HP:0040280",
- "has_evidence": ["ECO:0000269"],
- "subject": "MONDO:0008050",
- "object": "HP:0002938",
- "subject_label": "MYH7-related skeletal myopathy",
- "subject_category": "biolink:Disease",
- "subject_namespace": "MONDO",
- "subject_closure": [
+ "UBERON:0000468",
+ "UBERON:0010709",
+ "HP:0002981",
+ "UPHENO:0065599",
"BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
- "MONDO:0020121",
- "MONDO:0019952",
- "BFO:0000017",
- "BFO:0000020",
- "MONDO:0020120",
- "MONDO:0019056",
- "MONDO:0000001",
- "MONDO:0700223",
- "MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
- ],
- "subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
- "disease",
- "muscle tissue disorder",
- "congenital nervous system disorder",
- "hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
- "continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
- "myopathy",
- "hereditary disease",
- "nervous system disorder",
- "congenital myopathy",
- "realizable entity",
- "specifically dependent continuant",
- "skeletal muscle disorder",
- "neuromuscular disease",
- "entity",
- ],
- "object_label": "Lumbar hyperlordosis (HPO)",
- "object_category": "biolink:PhenotypicFeature",
- "object_namespace": "HP",
- "object_closure": [
- "UPHENO:0001005",
- "HP:0009121",
- "UPHENO:0020584",
- "UPHENO:0076692",
- "BFO:0000001",
+ "HP:0003011",
+ "UPHENO:0002536",
+ "UPHENO:0084715",
+ "UPHENO:0076710",
+ "HP:0040064",
"PATO:0000001",
- "BFO:0000004",
- "UBERON:0002204",
- "UBERON:0011676",
- "UBERON:0001137",
- "UBERON:0013701",
- "UBERON:0002100",
- "UBERON:0005462",
- "HP:0000001",
- "UPHENO:0076703",
+ "UBERON:0002103",
+ "UBERON:0010707",
+ "UBERON:0000026",
+ "UBERON:0010758",
+ "UBERON:0006058",
+ "UBERON:0004466",
+ "UBERON:0004256",
+ "UBERON:0003823",
+ "HP:0002814",
+ "UPHENO:0075952",
"HP:0000118",
- "BFO:0000020",
- "HP:0000925",
- "UPHENO:0015280",
- "UPHENO:0002964",
- "UPHENO:0001003",
- "HP:0003307",
- "UPHENO:0022529",
+ "UPHENO:0020584",
+ "HP:0008968",
+ "UBERON:0007271",
+ "UBERON:0014792",
+ "UBERON:0003661",
+ "UBERON:0010890",
+ "UBERON:0010538",
+ "HP:0000001",
+ "UPHENO:0002644",
"BFO:0000001",
- "BFO:0000040",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
- "UPHENO:0075696",
- "HP:0000924",
- "UPHENO:0002536",
- "BFO:0000002",
- "UBERON:0004288",
- "UBERON:0009569",
- "UBERON:0013702",
- "UBERON:0000075",
- "UBERON:0002417",
- "UBERON:0011137",
- "UBERON:0006077",
- "UBERON:0011138",
- "UBERON:0002090",
- "UBERON:0005944",
- "UBERON:0001130",
- "UPHENO:0001001",
- "HP:0011842",
- "UPHENO:0001002",
- "BFO:0000002",
- "HP:0010674",
- "UPHENO:0081581",
- "HP:0033127",
- "UPHENO:0002813",
- "HP:0002938",
- "UBERON:0001062",
- "UBERON:0000465",
- "UBERON:0000061",
- "UBERON:0034925",
"UBERON:0010000",
- "UBERON:0000475",
- "UBERON:0010912",
- "UBERON:0001434",
- "UBERON:0006074",
+ "UBERON:0000467",
+ "UBERON:0005090",
+ "UBERON:0018254",
+ "UBERON:0000383",
+ "UBERON:0001015",
+ "UBERON:0014892",
+ "UBERON:0000978",
+ "UBERON:0007270",
+ "UBERON:0004480",
+ "UBERON:0003663",
+ "UBERON:0014795",
+ "UBERON:0002529",
],
"object_closure_label": [
+ "increased size of the anatomical entity in independent continuant",
+ "abnormal hindlimb zeugopod muscle",
+ "Abnormal skeletal muscle morphology (HPO)",
+ "Skeletal muscle hypertrophy (HPO)",
+ "abnormal anatomical entity",
+ "musculature of hindlimb zeugopod",
+ "abnormal anatomical entity",
+ "abnormal phenotype by ontology source",
+ "Abnormality of the musculature of the limbs (HPO)",
+ "Abnormality of the musculature (HPO)",
+ "Abnormality of the musculature of the lower limbs (HPO)",
+ "abnormal musculature of limb",
+ "continuant",
+ "protein-containing material entity",
+ "material anatomical entity",
+ "system",
+ "multi-limb segment region",
"All (HPO)",
+ "abnormal musculature of lower limb",
+ "continuant",
+ "abnormal musculature",
+ "abnormal muscle organ morphology",
+ "hypertrophic multicellular anatomical structure",
+ "organ system subdivision",
+ "muscle organ",
+ "appendage",
+ "subdivision of organism along appendicular axis",
+ "Abnormality of the lower limb (HPO)",
"Phenotypic abnormality (HPO)",
- "Abnormality of the curvature of the vertebral column (HPO)",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "Hyperlordosis (HPO)",
- "abnormal postcranial axial skeleton morphology",
- "independent continuant",
- "material anatomical entity",
- "multicellular anatomical structure",
- "musculoskeletal system",
- "abdominal segment of trunk",
- "axial skeletal system",
- "subdivision of vertebral column",
- "postcranial axial skeletal system",
- "postcranial axial skeleton",
- "axial skeleton plus cranial skeleton",
- "vertebral column",
- "Abnormal skeletal morphology (HPO)",
+ "abnormal anatomical entity morphology",
+ "Muscle hypertrophy of the lower extremities (HPO)",
+ "entity",
+ "entity",
+ "leg",
+ "pelvic appendage musculature",
+ "musculature of limb",
+ "hindlimb muscle",
+ "pelvic appendage muscle",
+ "limb segment",
"Phenotypic abnormality",
- "continuant",
+ "Abnormality of the calf musculature (HPO)",
"specifically dependent continuant",
- "Abnormality of the vertebral column (HPO)",
- "abnormal anatomical entity morphology in the independent continuant",
- "abnormal skeletal system",
- "phenotype by ontology source",
+ "abnormal anatomical entity morphology",
+ "abnormal leg",
"quality",
- "continuant",
- "subdivision of trunk",
- "body proper",
- "subdivision of skeletal system",
+ "organism subdivision",
+ "organ",
+ "multicellular organism",
+ "pelvic complex",
+ "musculature of lower limb",
+ "muscle of leg",
+ "lower limb segment",
+ "zeugopod",
"phenotype",
- "abnormal phenotype by ontology source",
- "Abnormal axial skeleton morphology (HPO)",
- "abnormal vertebral column",
- "Lumbar hyperlordosis (HPO)",
- "entity",
+ "abnormal hindlimb zeugopod",
+ "abnormal anatomical entity morphology in the independent continuant",
+ "abnormally increased volume of anatomical entity",
+ "independent continuant",
+ "posterior region of body",
+ "Calf muscle hypertrophy (HPO)",
+ "hypertrophic pelvic complex muscle",
+ "abnormal size of anatomical entity",
+ "increased size of the anatomical entity",
+ "abnormal multicellular organism morphology",
+ "Abnormality of the musculoskeletal system (HPO)",
+ "phenotype by ontology source",
+ "abnormal limb",
+ "material entity",
"anatomical entity",
+ "paired limb/fin",
"anatomical structure",
- "anatomical collection",
- "skeleton",
- "organism subdivision",
- "subdivision of skeleton",
- "skeletal system",
- "lumbar region of vertebral column",
- "abnormal anatomical entity",
- "abnormal skeletal system morphology",
- "Abnormality of the skeletal system (HPO)",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "abnormal anatomical entity morphology",
- "entity",
- "material entity",
+ "limb",
+ "pelvic appendage",
+ "lateral structure",
+ "musculature of body",
+ "musculature",
+ "skeletal muscle organ",
+ "musculature of leg",
+ "hindlimb zeugopod muscle",
+ "hindlimb zeugopod",
+ "Abnormality of the calf (HPO)",
+ "Abnormality of muscle size (HPO)",
+ "abnormal muscle organ morphology",
+ "Abnormality of limbs (HPO)",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "subdivision of organism along main body axis",
- "dorsum",
- "main body axis",
- "trunk",
- "lower back",
+ "muscle structure",
+ "skeletal musculature",
+ "hindlimb",
+ "appendage girdle complex",
+ "appendage musculature",
+ "musculature of pelvic complex",
+ "limb muscle",
+ "pelvic complex muscle",
+ "paired limb/fin segment",
],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0002938",
+ "grouping_key": "MONDO:0035432🍪🍪biolink:has_phenotype🍪HP:0008981",
},
{
- "id": "uuid:c9c8bf38-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:160500",
+ "id": "uuid:4e12a2a4-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:565899",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["PMID:17548557"],
- "frequency_qualifier": "HP:0040280",
- "has_evidence": ["ECO:0000269"],
- "subject": "MONDO:0008050",
- "object": "HP:0001265",
- "subject_label": "MYH7-related skeletal myopathy",
+ "publications": ["orphanet:565899"],
+ "frequency_qualifier": "HP:0040282",
+ "has_evidence": ["ECO:0000304"],
+ "subject": "MONDO:0035432",
+ "object": "HP:0008994",
+ "subject_label": "POMGNT2-related limb-girdle muscular dystrophy R24",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
+ "MONDO:0000001",
+ "MONDO:0020121",
"MONDO:0003847",
"BFO:0000001",
- "MONDO:0020121",
- "MONDO:0019952",
+ "MONDO:0016106",
+ "MONDO:0005336",
"BFO:0000017",
+ "MONDO:0003939",
+ "MONDO:0035432",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0016971",
+ "MONDO:0005071",
+ "BFO:0000002",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
"MONDO:0700223",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "OGMS:0000031",
],
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
"disease",
+ "realizable entity",
+ "disease",
+ "POMGNT2-related limb-girdle muscular dystrophy R24",
"muscle tissue disorder",
- "congenital nervous system disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
+ "limb-girdle muscular dystrophy",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "disposition",
+ "human disease",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
"nervous system disorder",
- "congenital myopathy",
- "realizable entity",
- "specifically dependent continuant",
+ "entity",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "muscular dystrophy",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
],
- "object_label": "Hyporeflexia (HPO)",
+ "object_label": "Proximal muscle weakness in lower limbs (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
+ "HP:0008994",
+ "UPHENO:0002816",
+ "UPHENO:0002536",
+ "PR:000050567",
+ "UBERON:0000465",
+ "RO:0002577",
"UPHENO:0082875",
- "UPHENO:0049622",
- "UPHENO:0001005",
+ "HP:0001437",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UBERON:0011216",
+ "UBERON:0000154",
+ "UBERON:0000026",
+ "UPHENO:0001002",
+ "HP:0001324",
"BFO:0000020",
- "UPHENO:0050606",
- "HP:0012638",
- "BFO:0000015",
- "BFO:0000004",
- "GO:0050882",
- "NBO:0000338",
- "GO:0050905",
- "UBERON:0001016",
- "HP:0000001",
+ "UPHENO:0080555",
+ "HP:0011804",
+ "BFO:0000002",
+ "UBERON:0002101",
+ "UBERON:0004709",
+ "UBERON:0015212",
"UPHENO:0001001",
- "UPHENO:0080585",
- "HP:0001265",
- "HP:0031826",
- "UPHENO:0001002",
- "HP:0000118",
- "UPHENO:0052178",
- "UPHENO:0002433",
- "HP:0001315",
+ "HP:0003701",
+ "HP:0011805",
"UPHENO:0001003",
- "HP:0000708",
- "HP:0011446",
- "PATO:0000001",
+ "UPHENO:0002647",
"BFO:0000001",
- "BFO:0000040",
- "UBERON:0001062",
- "GO:0050896",
- "GO:0032501",
- "GO:0060004",
- "GO:0050881",
- "NBO:0000313",
- "GO:0050877",
- "UBERON:0000467",
- "UBERON:0000468",
- "NBO:0000403",
- "NBO:0000001",
- "NBO:0000388",
+ "UBERON:0000061",
+ "UBERON:0004482",
+ "UBERON:0008784",
"UPHENO:0075696",
- "UPHENO:0078622",
- "UPHENO:0049586",
- "UPHENO:0080377",
- "HP:0100022",
- "UPHENO:0050613",
- "UPHENO:0005433",
- "UPHENO:0002332",
- "UPHENO:0002536",
- "UPHENO:0079826",
- "UPHENO:0004523",
- "UPHENO:0049587",
- "BFO:0000003",
- "BFO:0000002",
- "GO:0008150",
- "GO:0009605",
- "GO:0050879",
- "GO:0007610",
- "GO:0003008",
- "NBO:0000389",
- "UPHENO:0052915",
+ "UPHENO:0001005",
+ "HP:0009127",
+ "UPHENO:0081581",
+ "HP:0033127",
+ "UPHENO:0076692",
+ "UPHENO:0003070",
+ "UPHENO:0002830",
+ "BFO:0000004",
+ "UBERON:0004708",
+ "UBERON:0000475",
+ "UBERON:0000062",
+ "UBERON:0000468",
+ "UBERON:0010709",
+ "HP:0003690",
"BFO:0000002",
- "UPHENO:0005625",
- "UPHENO:0050079",
- "HP:0000707",
- "UPHENO:0079833",
+ "HP:0003011",
+ "UPHENO:0076710",
+ "HP:0040064",
+ "UBERON:0002103",
+ "UBERON:0010707",
+ "UBERON:0010758",
+ "UBERON:0006058",
+ "UPHENO:0002320",
+ "HP:0002814",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "PATO:0000001",
+ "UBERON:0007271",
+ "UBERON:0014792",
+ "UBERON:0010538",
+ "HP:0000001",
+ "UPHENO:0002644",
+ "UPHENO:0080556",
"BFO:0000001",
- "UBERON:0000465",
- "UBERON:0000061",
"UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0005090",
+ "UBERON:0001630",
+ "UBERON:0000383",
+ "UBERON:0001015",
+ "UBERON:0000978",
+ "UBERON:0007270",
+ "UBERON:0004480",
+ "UBERON:0002529",
],
"object_closure_label": [
- "All (HPO)",
- "abnormal behavior",
- "Abnormality of movement (HPO)",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "decreased reflex",
- "abnormal response to external stimulus",
- "Abnormality of the nervous system (HPO)",
- "Behavioral abnormality (HPO)",
- "Abnormality of higher mental function (HPO)",
- "abnormal voluntary movement behavior",
- "entity",
- "quality",
- "process",
- "independent continuant",
- "material anatomical entity",
- "multicellular anatomical structure",
- "nervous system",
- "voluntary movement behavior",
- "body part movement",
- "reflexive behavior",
"abnormality of anatomical entity physiology",
- "phenotype",
- "continuant",
- "decreased qualitatively biological_process",
- "abnormality of nervous system physiology",
- "Reduced tendon reflexes (HPO)",
- "phenotype by ontology source",
- "abnormal behavior process",
- "abnormal nervous system",
- "abnormal biological_process",
- "Abnormal nervous system physiology (HPO)",
- "occurrent",
- "continuant",
- "biological_process",
- "response to external stimulus",
- "multicellular organismal movement",
- "behavior",
- "system process",
- "reflex",
- "musculoskeletal movement",
- "behavior process",
- "nervous system process",
- "involuntary movement behavior",
- "decreased qualitatively response to stimulus",
+ "Proximal muscle weakness (HPO)",
+ "Abnormal skeletal muscle morphology (HPO)",
+ "quality",
+ "abnormal anatomical entity",
"abnormal phenotype by ontology source",
+ "Abnormality of the musculature of the limbs (HPO)",
"specifically dependent continuant",
- "abnormal voluntary musculoskeletal movement",
+ "Abnormality of the musculature (HPO)",
+ "phenotype by ontology source",
+ "Abnormality of the musculature of the lower limbs (HPO)",
+ "abnormal musculature of limb",
+ "continuant",
+ "protein-containing material entity",
+ "material anatomical entity",
+ "system",
+ "muscle organ",
+ "multi-limb segment region",
+ "All (HPO)",
+ "abnormal musculature of lower limb",
+ "continuant",
+ "Proximal muscle weakness in lower limbs (HPO)",
+ "abnormal musculature",
+ "Abnormal muscle physiology (HPO)",
+ "organ system subdivision",
+ "subdivision of organism along appendicular axis",
+ "abnormality of muscle organ physiology",
+ "Abnormality of the lower limb (HPO)",
+ "Phenotypic abnormality (HPO)",
+ "Limb muscle weakness (HPO)",
+ "decreased muscle organ strength",
"entity",
+ "entity",
+ "leg",
+ "pelvic appendage musculature",
+ "musculature of limb",
+ "limb segment",
+ "Phenotypic abnormality",
+ "Muscle weakness (HPO)",
+ "abnormal anatomical entity morphology",
+ "abnormal leg",
"anatomical structure",
- "abnormal anatomical entity",
- "abnormal voluntary movement behavior",
- "changed biological_process rate",
- "abnormal response to stimulus",
- "abnormal behavior process",
- "Hyporeflexia (HPO)",
- "Abnormal reflex (HPO)",
- "abnormal musculoskeletal movement",
- "decreased biological_process",
- "abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
+ "organism subdivision",
+ "organ",
+ "multicellular organism",
+ "pelvic complex",
+ "musculature of lower limb",
+ "lower limb segment",
+ "phenotype",
+ "independent continuant",
+ "posterior region of body",
+ "appendage",
+ "decreased anatomical entity strength",
+ "abnormal multicellular organism morphology",
+ "Abnormality of the musculoskeletal system (HPO)",
+ "abnormal limb",
"material entity",
"anatomical entity",
- "response to stimulus",
- "multicellular organismal process",
+ "paired limb/fin",
+ "limb",
+ "pelvic appendage",
+ "lateral structure",
+ "musculature of body",
+ "musculature",
+ "abnormality of anatomical entity physiology",
+ "abnormal anatomical entity",
+ "abnormal muscle organ morphology",
+ "Abnormality of limbs (HPO)",
+ "multicellular anatomical structure",
"anatomical system",
- "voluntary musculoskeletal movement",
- "kinesthetic behavior",
- "neuromuscular process",
- "multicellular organism",
+ "muscle structure",
+ "hindlimb",
+ "appendage girdle complex",
+ "appendage musculature",
+ "musculature of pelvic complex",
+ "paired limb/fin segment",
],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0001265",
+ "grouping_key": "MONDO:0035432🍪🍪biolink:has_phenotype🍪HP:0008994",
},
{
- "id": "uuid:c9c8bf3f-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:160500",
+ "id": "uuid:4e02df81-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["PMID:17548557"],
- "frequency_qualifier": "HP:0040280",
- "has_evidence": ["ECO:0000269"],
- "subject": "MONDO:0008050",
- "object": "HP:0009053",
- "subject_label": "MYH7-related skeletal myopathy",
+ "publications": ["orphanet:589821"],
+ "frequency_qualifier": "HP:0040281",
+ "has_evidence": ["ECO:0000304"],
+ "subject": "MONDO:0035646",
+ "object": "HP:0000256",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
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+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
+ "disease",
+ "hypertrophic cardiomyopathy",
"disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Distal lower limb muscle weakness (HPO)",
+ "object_label": "Macrocephaly (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "UPHENO:0082875",
- "UPHENO:0002320",
- "HP:0002814",
- "UPHENO:0001005",
- "HP:0009127",
- "UPHENO:0076692",
- "UPHENO:0003070",
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- "UBERON:0000154",
- "UBERON:0000026",
- "UBERON:0014892",
- "UBERON:0006058",
- "UBERON:0002529",
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- "HP:0000118",
- "BFO:0000002",
- "BFO:0000020",
- "UPHENO:0076710",
- "BFO:0000001",
- "PATO:0000001",
+ "HP:0000256",
+ "UPHENO:0002536",
+ "UPHENO:0081566",
+ "HP:0000240",
+ "UBERON:0000465",
+ "UPHENO:0075220",
+ "UPHENO:0001208",
+ "UPHENO:0002844",
+ "UPHENO:0015280",
"BFO:0000001",
"BFO:0000040",
- "UBERON:0000467",
- "UBERON:0000468",
+ "UBERON:0001062",
"UBERON:0011216",
- "UBERON:0010709",
- "UBERON:0010890",
- "UBERON:0010538",
- "UPHENO:0075696",
- "UPHENO:0080575",
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- "HP:0003690",
- "HP:0003011",
- "UPHENO:0002332",
- "UPHENO:0001003",
- "UPHENO:0002536",
- "HP:0002460",
- "HP:0040064",
- "HP:0009053",
- "HP:0011804",
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- "UBERON:0000465",
- "UBERON:0002101",
- "UBERON:0004709",
- "UBERON:0005090",
- "UBERON:0018254",
- "UBERON:0002103",
- "UBERON:0010707",
- "UBERON:0001630",
- "UBERON:0010758",
- "UBERON:0007271",
- "UBERON:0014792",
- "UBERON:0008784",
- "HP:0007340",
- "UPHENO:0001001",
- "HP:0011805",
+ "UBERON:0011676",
+ "UBERON:0013701",
+ "UPHENO:0075148",
"UPHENO:0001002",
- "UPHENO:0080555",
- "UPHENO:0002816",
- "UPHENO:0080556",
+ "UPHENO:0075195",
+ "HP:0009121",
+ "BFO:0000002",
+ "UPHENO:0001001",
+ "HP:0011842",
+ "BFO:0000020",
+ "UPHENO:0002964",
+ "UPHENO:0001003",
+ "UPHENO:0021447",
+ "BFO:0000001",
+ "UBERON:0000061",
+ "UBERON:0034925",
+ "HP:0040194",
+ "UPHENO:0075696",
+ "UPHENO:0001005",
+ "UPHENO:0002764",
+ "UPHENO:0001072",
"UPHENO:0081581",
"HP:0033127",
- "UPHENO:0002647",
- "UPHENO:0002830",
+ "UPHENO:0076692",
+ "UPHENO:0022529",
+ "BFO:0000004",
+ "UBERON:0004288",
+ "UBERON:0000475",
+ "UBERON:0000468",
+ "UBERON:0000153",
+ "UPHENO:0065599",
+ "HP:0000924",
+ "UBERON:0003129",
+ "UBERON:0007811",
+ "UBERON:0013702",
+ "UBERON:0000075",
+ "UBERON:0000033",
+ "UPHENO:0076703",
+ "HP:0000152",
+ "HP:0000118",
"BFO:0000002",
- "UBERON:0001062",
- "RO:0002577",
- "UBERON:0000061",
- "UBERON:0015212",
+ "UPHENO:0020584",
+ "PATO:0000001",
+ "UBERON:0010314",
+ "UBERON:0011137",
+ "UBERON:0010323",
+ "UBERON:0011138",
+ "UBERON:0002090",
+ "UBERON:0005944",
+ "HP:0000001",
+ "HP:0000929",
+ "HP:0000234",
"UBERON:0010000",
- "UBERON:0000475",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "UBERON:0000978",
- "UBERON:0004480",
+ "UBERON:0000467",
+ "UBERON:0002204",
+ "UBERON:0010912",
+ "UBERON:0001434",
],
"object_closure_label": [
+ "abnormal size of skull",
+ "increased size of the anatomical entity in independent continuant",
+ "Abnormal skeletal morphology (HPO)",
+ "specifically dependent continuant",
+ "abnormal skeletal system",
+ "quality",
+ "Increased head circumference (HPO)",
+ "abnormal anatomical entity",
+ "abnormal phenotype by ontology source",
+ "abnormal craniocervical region",
+ "phenotype by ontology source",
+ "abnormal head morphology",
+ "continuant",
+ "material anatomical entity",
+ "musculoskeletal system",
+ "head",
"All (HPO)",
- "abnormality of muscle organ physiology",
- "Abnormality of the lower limb (HPO)",
+ "organ system subdivision",
+ "craniocervical region",
+ "body proper",
+ "subdivision of skeletal system",
+ "Abnormality of the skeletal system (HPO)",
"Phenotypic abnormality (HPO)",
"continuant",
- "decreased anatomical entity strength",
- "abnormal musculature",
- "decreased muscle organ strength",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "abnormal musculature of limb",
- "quality",
- "independent continuant",
- "system",
- "paired limb/fin",
- "lateral structure",
- "multicellular anatomical structure",
- "pelvic complex",
- "appendage musculature",
- "musculature of pelvic complex",
- "abnormality of anatomical entity physiology",
- "Abnormal skeletal muscle morphology (HPO)",
- "Phenotypic abnormality",
- "specifically dependent continuant",
- "Distal muscle weakness (HPO)",
- "Abnormality of limbs (HPO)",
- "Distal lower limb muscle weakness (HPO)",
- "protein-containing material entity",
- "material anatomical entity",
- "hindlimb",
- "appendage girdle complex",
- "subdivision of organism along appendicular axis",
- "pelvic complex muscle",
- "paired limb/fin segment",
- "lower limb segment",
- "Lower limb muscle weakness (HPO)",
- "phenotype",
- "abnormal phenotype by ontology source",
- "Abnormality of the musculature of the limbs (HPO)",
- "abnormal muscle organ morphology",
- "Abnormal muscle physiology (HPO)",
+ "Abnormality of the head (HPO)",
+ "abnormal anatomical entity morphology",
"entity",
- "anatomical entity",
+ "structure with developmental contribution from neural crest",
+ "abnormal size of head",
+ "Phenotypic abnormality",
+ "abnormal anatomical entity morphology",
+ "Abnormality of skull size (HPO)",
"anatomical structure",
- "muscle structure",
- "skeletal musculature",
+ "anatomical collection",
+ "skeleton",
"organism subdivision",
- "organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "leg",
- "musculature of limb",
- "abnormal anatomical entity",
- "decreased pelvic complex muscle strength",
- "Muscle weakness (HPO)",
- "Limb muscle weakness (HPO)",
- "Abnormality of the musculature (HPO)",
- "abnormality of anatomical entity physiology",
- "phenotype by ontology source",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "abnormal leg",
+ "multicellular organism",
+ "anterior region of body",
+ "phenotype",
+ "abnormal skeletal system morphology",
+ "Abnormality of head or neck (HPO)",
+ "Abnormal skull morphology (HPO)",
+ "abnormal anatomical entity morphology in the independent continuant",
"entity",
- "abnormal limb",
- "continuant",
+ "independent continuant",
+ "subdivision of organism along main body axis",
+ "main body axis",
+ "Macrocephaly (HPO)",
+ "abnormal size of anatomical entity",
+ "Abnormal axial skeleton morphology (HPO)",
+ "increased size of the anatomical entity",
+ "abnormal multicellular organism morphology",
+ "Abnormality of the musculoskeletal system (HPO)",
+ "abnormal postcranial axial skeleton morphology",
"material entity",
- "limb",
- "pelvic appendage",
- "anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "posterior region of body",
- "appendage",
- "skeletal muscle organ",
- "multi-limb segment region",
- "limb segment",
+ "anatomical entity",
+ "subdivision of skeleton",
+ "skeletal system",
+ "increased size of the head",
+ "abnormal head",
+ "abnormal anatomical entity",
+ "abnormal skull morphology",
+ "multicellular anatomical structure",
+ "anatomical system",
+ "skull",
+ "axial skeletal system",
+ "cranial skeletal system",
+ "postcranial axial skeletal system",
+ "postcranial axial skeleton",
+ "axial skeleton plus cranial skeleton",
],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Very frequent (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040281", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Very frequent (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0009053",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0000256",
},
{
- "id": "uuid:c9c8bf41-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:160500",
+ "id": "uuid:4e02df82-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["PMID:17548557"],
- "frequency_qualifier": "HP:0040280",
- "has_evidence": ["ECO:0000269"],
- "subject": "MONDO:0008050",
- "object": "HP:0009077",
- "subject_label": "MYH7-related skeletal myopathy",
+ "publications": ["orphanet:589821"],
+ "frequency_qualifier": "HP:0040281",
+ "has_evidence": ["ECO:0000304"],
+ "subject": "MONDO:0035646",
+ "object": "HP:0000297",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Weakness of long finger extensor muscles (HPO)",
+ "object_label": "Facial hypotonia (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "HP:0009127",
- "BFO:0000002",
- "UPHENO:0002655",
- "UPHENO:0076692",
- "BFO:0000001",
- "PATO:0000001",
- "BFO:0000004",
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- "UBERON:0000061",
- "UBERON:0000153",
- "UBERON:0000026",
- "UBERON:0006058",
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- "UBERON:0002398",
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- "UPHENO:0001001",
- "UPHENO:0001002",
- "HP:0000118",
- "HP:0001446",
- "BFO:0000020",
- "UPHENO:0002708",
- "HP:0009077",
- "UPHENO:0076710",
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+ "UPHENO:0002816",
+ "UPHENO:0002536",
+ "UBERON:0000465",
+ "RO:0002577",
+ "UPHENO:0082875",
+ "UPHENO:0002910",
"BFO:0000001",
"BFO:0000040",
- "UBERON:0000467",
- "UBERON:0000468",
+ "UBERON:0001062",
"UBERON:0011216",
- "UBERON:0010708",
- "UBERON:0010538",
- "UBERON:0004489",
- "HP:0001421",
- "HP:0030237",
- "HP:0002817",
- "HP:0003011",
- "UPHENO:0002536",
- "HP:0040064",
+ "UBERON:0011676",
+ "UBERON:0013701",
+ "UPHENO:0001002",
+ "HP:0011804",
"BFO:0000002",
- "PR:000050567",
- "UBERON:0000465",
- "UBERON:0002101",
- "UBERON:0004710",
- "UBERON:0005090",
- "UBERON:0002102",
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"UBERON:0001630",
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- "UBERON:0004481",
- "UBERON:0002470",
- "UBERON:0008785",
- "UPHENO:0001005",
- "HP:0001155",
+ "UBERON:0002376",
+ "UBERON:0015789",
+ "UPHENO:0001001",
"HP:0011805",
- "UPHENO:0002816",
+ "BFO:0000020",
+ "UPHENO:0001003",
+ "BFO:0000001",
+ "UBERON:0000061",
+ "UPHENO:0075696",
+ "UPHENO:0001005",
+ "UPHENO:0002764",
"UPHENO:0081581",
"HP:0033127",
- "UPHENO:0001003",
- "UPHENO:0002647",
- "UPHENO:0002880",
- "UPHENO:0002830",
- "UBERON:0001062",
- "RO:0002577",
- "UBERON:0015212",
- "UBERON:0010000",
+ "UPHENO:0076692",
+ "BFO:0000004",
"UBERON:0000475",
"UBERON:0000062",
+ "UBERON:0000468",
+ "UBERON:0000153",
+ "UPHENO:0002844",
+ "BFO:0000002",
+ "HP:0003011",
+ "UPHENO:0076710",
+ "PATO:0000001",
+ "UPHENO:0002908",
+ "UBERON:0007811",
+ "UBERON:0001444",
+ "UBERON:0013702",
+ "UBERON:0000033",
+ "UPHENO:0002320",
+ "UPHENO:0082555",
+ "HP:0000152",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "HP:0001252",
+ "UPHENO:0082557",
+ "HP:0000297",
+ "HP:0000301",
+ "UBERON:0001456",
+ "UBERON:0008229",
+ "UBERON:0013700",
+ "UBERON:0010959",
+ "UBERON:0001577",
+ "HP:0000001",
+ "HP:0003808",
+ "HP:0000234",
+ "HP:0000271",
+ "UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0005090",
+ "UBERON:0018254",
+ "UBERON:0004120",
"UBERON:0000383",
"UBERON:0001015",
- "UBERON:0001460",
- "UBERON:0004480",
- "UBERON:0007269",
+ "UBERON:0014892",
+ "UBERON:0004461",
+ "UBERON:0004473",
],
"object_closure_label": [
- "All (HPO)",
- "abnormal musculature of upper limb",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "abnormal musculature",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "phenotype by ontology source",
- "abnormal musculature of limb",
- "independent continuant",
- "system",
- "paired limb/fin",
- "anatomical structure",
- "lateral structure",
- "multicellular anatomical structure",
- "pectoral complex",
- "appendage musculature",
- "musculature of pectoral complex",
- "musculature of manus",
- "phenotype",
- "Abnormality of the musculature of the hand (HPO)",
- "abnormal phenotype by ontology source",
- "Abnormality of the hand (HPO)",
+ "abnormality of anatomical entity physiology",
+ "abnormal head",
"Abnormal skeletal muscle morphology (HPO)",
- "Abnormality of the musculature of the upper limbs (HPO)",
"specifically dependent continuant",
- "abnormal manus",
- "Abnormality of limbs (HPO)",
- "quality",
+ "abnormal anatomical entity",
+ "abnormal phenotype by ontology source",
+ "abnormal craniocervical region",
+ "Abnormality of the musculature (HPO)",
+ "phenotype by ontology source",
"continuant",
- "protein-containing material entity",
"material anatomical entity",
- "forelimb",
- "appendage girdle complex",
- "subdivision of organism along appendicular axis",
- "paired limb/fin segment",
- "musculature of upper limb",
- "autopod region",
- "upper limb segment",
- "Abnormality of the musculature of the limbs (HPO)",
+ "system",
+ "cranial or facial muscle",
+ "head",
+ "All (HPO)",
+ "Abnormal muscle tone (HPO)",
"continuant",
- "abnormal musculature of manus",
- "Weakness of long finger extensor muscles (HPO)",
- "abnormal muscle organ morphology",
+ "abnormal musculature",
+ "Abnormal muscle physiology (HPO)",
+ "organ system subdivision",
+ "muscle organ",
+ "cranial muscle",
+ "craniocervical region",
+ "subdivision of head",
+ "body proper",
+ "abnormality of muscle organ physiology",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the head (HPO)",
+ "Abnormality of the face (HPO)",
+ "decreased muscle organ tone",
+ "Facial hypotonia (HPO)",
+ "Abnormality of facial musculature (HPO)",
"entity",
- "anatomical entity",
- "muscle structure",
+ "skeletal musculature of head",
+ "musculature of face",
+ "Phenotypic abnormality",
+ "abnormal anatomical entity morphology",
+ "quality",
+ "abnormal facial muscle",
+ "anatomical structure",
"organism subdivision",
"organ",
- "muscle organ",
+ "multicellular organism",
+ "anterior region of body",
+ "phenotype",
+ "decreased anatomical entity tone",
+ "Abnormality of head or neck (HPO)",
+ "entity",
+ "independent continuant",
+ "subdivision of organism along main body axis",
+ "main body axis",
+ "Abnormality of facial soft tissue (HPO)",
+ "abnormal multicellular organism morphology",
+ "Abnormality of the musculoskeletal system (HPO)",
+ "material entity",
+ "anatomical entity",
"musculature of body",
"musculature",
- "arm",
- "musculature of limb",
- "pectoral appendage musculature",
- "Hand muscle weakness (HPO)",
- "Abnormality of the upper limb (HPO)",
- "Abnormality of the musculature (HPO)",
+ "skeletal muscle organ",
+ "abnormal face",
+ "abnormality of anatomical entity physiology",
+ "Hypotonia (HPO)",
"abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "entity",
- "abnormal arm",
- "abnormal limb",
- "material entity",
- "limb",
- "pectoral appendage",
+ "abnormal muscle organ morphology",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "anterior region of body",
- "appendage",
- "multi-limb segment region",
- "limb segment",
- "manus",
+ "muscle structure",
+ "skeletal musculature",
+ "mesoderm-derived structure",
+ "face",
+ "craniocervical region musculature",
+ "axial musculature",
+ "craniocervical muscle",
+ "facial muscle",
],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Very frequent (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040281", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Very frequent (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0009077",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0000297",
},
{
- "id": "uuid:c9c8bf42-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:160500",
+ "id": "uuid:4e02df83-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["PMID:17548557"],
- "frequency_qualifier": "HP:0040280",
- "has_evidence": ["ECO:0000269"],
- "subject": "MONDO:0008050",
- "object": "HP:0030051",
- "subject_label": "MYH7-related skeletal myopathy",
+ "publications": ["orphanet:589821"],
+ "frequency_qualifier": "HP:0040281",
+ "has_evidence": ["ECO:0000304"],
+ "subject": "MONDO:0035646",
+ "object": "HP:0010804",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
+ "disease",
+ "hypertrophic cardiomyopathy",
"disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Tip-toe gait (HPO)",
+ "object_label": "Tented upper lip vermilion (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "UPHENO:0082875",
- "UPHENO:0049622",
- "UPHENO:0001005",
+ "HP:0000159",
+ "UPHENO:0076803",
+ "UBERON:0000465",
+ "UPHENO:0002910",
+ "UPHENO:0076800",
+ "UPHENO:0003064",
"BFO:0000002",
- "UPHENO:0050606",
- "HP:0001288",
- "HP:0012638",
- "BFO:0000015",
- "BFO:0000004",
- "GO:0050882",
- "NBO:0000338",
- "GO:0050905",
- "UBERON:0001016",
- "HP:0000001",
- "UPHENO:0001001",
- "UPHENO:0080585",
+ "HP:0002664",
+ "UPHENO:0015280",
+ "BFO:0000040",
+ "BFO:0000141",
+ "UBERON:0001062",
+ "UBERON:0011676",
+ "UBERON:0013701",
+ "UPHENO:0002828",
"UPHENO:0001002",
- "HP:0000118",
"BFO:0000020",
- "UPHENO:0002433",
+ "HP:0011793",
+ "UPHENO:0076786",
+ "BFO:0000002",
+ "UBERON:0000167",
+ "UPHENO:0001001",
+ "HP:0000163",
+ "HP:0000177",
+ "UPHENO:0002833",
+ "HP:0000309",
"UPHENO:0001003",
- "HP:0000708",
- "HP:0011446",
+ "UPHENO:0002536",
"BFO:0000001",
+ "UBERON:0000464",
+ "UPHENO:0075696",
+ "UPHENO:0002764",
+ "UPHENO:0081581",
+ "UPHENO:0076692",
+ "UPHENO:0020955",
+ "HP:0025031",
+ "BFO:0000004",
+ "UBERON:0000061",
+ "UBERON:0002553",
+ "UBERON:0000475",
+ "UBERON:0000062",
+ "UBERON:0004111",
+ "UBERON:0000468",
+ "UBERON:0001834",
+ "UBERON:0000153",
+ "UPHENO:0002844",
+ "HP:0025033",
+ "UBERON:0000466",
+ "UBERON:0011595",
+ "UBERON:0001709",
+ "UBERON:0001833",
+ "UBERON:0007811",
+ "UBERON:0001444",
+ "UBERON:0013702",
+ "UBERON:0000025",
+ "UBERON:0000033",
+ "UBERON:0004089",
+ "HP:0000152",
+ "UPHENO:0075998",
+ "HP:0000118",
+ "HP:0011339",
+ "HP:0010804",
+ "UPHENO:0020584",
"PATO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "GO:0032501",
- "GO:0050881",
- "NBO:0000313",
- "GO:0050877",
+ "UBERON:0010314",
+ "UBERON:0003102",
"UBERON:0010000",
+ "UBERON:0001555",
+ "UBERON:0001456",
+ "UBERON:0004921",
+ "HP:0000001",
+ "UPHENO:0001005",
+ "HP:0031816",
+ "HP:0000153",
+ "HP:0000234",
+ "HP:0000271",
+ "BFO:0000001",
"UBERON:0000467",
- "UBERON:0000468",
- "NBO:0000403",
- "NBO:0000001",
- "UPHENO:0075696",
- "UPHENO:0078622",
- "UPHENO:0049586",
- "HP:0100022",
- "UPHENO:0050613",
- "UPHENO:0002332",
- "UPHENO:0002536",
- "UPHENO:0079826",
- "UPHENO:0004523",
- "UPHENO:0049587",
- "BFO:0000003",
- "GO:0008150",
- "GO:0050879",
- "GO:0007610",
- "GO:0003008",
- "HP:0030051",
- "HP:0000707",
- "UPHENO:0079833",
- "BFO:0000002",
- "UBERON:0001062",
- "UBERON:0000465",
- "UBERON:0000061",
+ "UBERON:0000064",
+ "UBERON:0001007",
+ "UBERON:0013522",
+ "UBERON:0000165",
],
"object_closure_label": [
- "All (HPO)",
- "abnormal behavior",
- "Abnormality of movement (HPO)",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "Tip-toe gait (HPO)",
- "Abnormality of the nervous system (HPO)",
- "Behavioral abnormality (HPO)",
- "Abnormality of higher mental function (HPO)",
- "abnormal voluntary movement behavior",
+ "abnormal head",
+ "abnormal digestive system",
+ "Abnormality of the midface (HPO)",
"quality",
- "process",
- "independent continuant",
- "material anatomical entity",
- "nervous system",
- "voluntary movement behavior",
- "body part movement",
- "abnormality of anatomical entity physiology",
- "phenotype",
+ "abnormal anatomical entity",
+ "abnormal craniocervical region",
"specifically dependent continuant",
- "abnormality of nervous system physiology",
+ "Abnormality of digestive system morphology (HPO)",
"phenotype by ontology source",
- "Gait disturbance (HPO)",
- "abnormal behavior process",
- "abnormal nervous system",
- "abnormal biological_process",
- "Abnormal nervous system physiology (HPO)",
- "occurrent",
- "biological_process",
- "multicellular organismal movement",
- "behavior",
- "system process",
- "musculoskeletal movement",
- "behavior process",
- "nervous system process",
- "abnormal phenotype by ontology source",
+ "abnormal anatomical entity",
"continuant",
- "abnormal voluntary musculoskeletal movement",
+ "material anatomical entity",
+ "organ part",
+ "digestive system",
+ "head",
+ "midface",
+ "All (HPO)",
+ "abnormal phenotype by ontology source",
+ "oral cavity",
+ "craniocervical region",
+ "subdivision of head",
+ "body proper",
+ "tube",
+ "Abnormal oral cavity morphology (HPO)",
+ "Abnormality of upper lip (HPO)",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the head (HPO)",
+ "Abnormality of the face (HPO)",
+ "abnormal anatomical entity morphology",
"entity",
+ "entity",
+ "immaterial anatomical entity",
+ "structure with developmental contribution from neural crest",
+ "surface structure",
+ "multicellular anatomical structure",
+ "mouth",
+ "abnormal mouth",
+ "Phenotypic abnormality",
+ "Neoplasm by anatomical site (HPO)",
+ "abnormal oral cavity morphology",
+ "abnormal anatomical entity morphology",
+ "abnormal lip morphology",
+ "abnormal digestive system morphology",
+ "anatomical space",
+ "anatomical cavity",
+ "organism subdivision",
+ "organ",
+ "anatomical conduit",
+ "multicellular organism",
+ "upper lip",
+ "anterior region of body",
+ "phenotype",
+ "Abnormality of head or neck (HPO)",
+ "abnormal midface",
+ "Abnormal oral morphology (HPO)",
+ "Abnormality of the mouth (HPO)",
+ "Neoplasm (HPO)",
+ "abnormal anatomical entity morphology in the independent continuant",
+ "independent continuant",
+ "subdivision of organism along main body axis",
+ "main body axis",
+ "abnormal multicellular organism morphology",
+ "Abnormal lip morphology (HPO)",
+ "Abnormality of the digestive system (HPO)",
+ "material entity",
+ "immaterial entity",
"anatomical entity",
"anatomical structure",
- "abnormal anatomical entity",
- "abnormal voluntary movement behavior",
- "abnormal response to stimulus",
- "abnormal behavior process",
- "abnormal musculoskeletal movement",
- "abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
- "entity",
+ "subdivision of tube",
+ "abnormal face",
+ "abnormal mouth morphology",
+ "abnormal upper lip",
"continuant",
- "material entity",
- "multicellular organismal process",
- "multicellular anatomical structure",
+ "Abnormality of upper lip vermillion (HPO)",
+ "Tented upper lip vermilion (HPO)",
"anatomical system",
- "voluntary musculoskeletal movement",
- "kinesthetic behavior",
- "neuromuscular process",
- "multicellular organism",
+ "jaw region",
+ "upper jaw region",
+ "lip",
+ "digestive tract",
+ "face",
+ "subdivision of digestive tract",
],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Very frequent (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040281", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Very frequent (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0030051",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0010804",
},
{
- "id": "uuid:c9c8bfed-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:253600",
+ "id": "uuid:4e02df84-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["PMID:16607617"],
- "frequency_qualifier": "HP:0040282",
- "has_evidence": ["ECO:0000269"],
- "subject": "MONDO:0009675",
- "object": "HP:0001880",
- "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A",
+ "publications": ["orphanet:589821"],
+ "frequency_qualifier": "HP:0040281",
+ "has_evidence": ["ECO:0000304"],
+ "subject": "MONDO:0035646",
+ "object": "HP:0031843",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "MONDO:0016971",
- "MONDO:0005336",
- "MONDO:0015152",
- "MONDO:0000429",
- "MONDO:0005071",
- "MONDO:0006025",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
- "MONDO:0009675",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
- "MONDO:0016152",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
- "BFO:0000002",
- "MONDO:0016106",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003847",
- "MONDO:0003939",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
- "hereditary disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
"continuant",
- "autosomal recessive disease",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
"disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "disease",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "autosomal genetic disease",
+ "myotonic dystrophy",
"nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
- "autosomal recessive limb-girdle muscular dystrophy type 2A",
"skeletal muscle disorder",
- "qualitative or quantitative defects of calpain",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Eosinophilia (HPO)",
+ "object_label": "Bradyphrenia (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "HP:0001879",
+ "UBERON:0000465",
+ "GO:0050877",
+ "UPHENO:0082875",
+ "UPHENO:0004523",
+ "GO:0008150",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "GO:0003008",
+ "BFO:0000020",
+ "BFO:0000003",
+ "BFO:0000002",
+ "UPHENO:0001001",
+ "UPHENO:0001002",
+ "HP:0031843",
+ "UPHENO:0001003",
+ "BFO:0000001",
+ "UBERON:0000061",
+ "GO:0050890",
"UPHENO:0001005",
+ "UPHENO:0002433",
+ "HP:0100543",
+ "HP:0012638",
+ "BFO:0000015",
+ "UBERON:0000468",
+ "UPHENO:0075696",
"BFO:0000002",
- "BFO:0000020",
- "HP:0002715",
- "HP:0001911",
- "HP:0001880",
+ "UPHENO:0002536",
"BFO:0000004",
- "UBERON:0000178",
- "CL:0000094",
- "CL:0002242",
- "CL:0000255",
- "CL:0000219",
- "HP:0000001",
- "HP:0032309",
- "HP:0010974",
"HP:0000118",
- "HP:0001871",
- "HP:0020064",
- "UPHENO:0001003",
- "UPHENO:0002536",
- "BFO:0000001",
+ "UPHENO:0002332",
"PATO:0000001",
+ "HP:0000001",
+ "HP:0000707",
+ "HP:0011446",
"BFO:0000001",
- "UBERON:0000467",
- "CL:0000000",
- "UBERON:0000468",
- "CL:0000738",
- "CL:0000548",
- "CL:0000763",
- "CL:0000081",
- "UPHENO:0002948",
- "UPHENO:0001002",
- "HP:0025461",
- "HP:0001881",
- "HP:0020047",
- "UPHENO:0004459",
- "HP:0032251",
- "BFO:0000002",
- "BFO:0000040",
- "PR:000050567",
- "UBERON:0000465",
- "CL:0000771",
- "UBERON:0004120",
- "UBERON:0006314",
- "UBERON:0015203",
- "CL:0000003",
- "UBERON:0002193",
- "UBERON:0002390",
- "UBERON:0000179",
- "UBERON:0002405",
- "CL:0000988",
- "HP:0011893",
- "UPHENO:0001001",
- "HP:0025354",
- "HP:0001974",
- "HP:0010987",
- "UBERON:0001062",
- "UBERON:0000061",
- "UBERON:0000463",
- "UBERON:0034923",
+ "GO:0032501",
"UBERON:0010000",
- "CL:0000766",
- "CL:0002371",
+ "UBERON:0000467",
+ "UBERON:0001016",
],
"object_closure_label": [
- "All (HPO)",
- "Abnormal eosinophil morphology (HPO)",
- "Abnormal myeloid leukocyte morphology (HPO)",
- "Phenotypic abnormality (HPO)",
- "Abnormal cellular phenotype (HPO)",
- "Leukocytosis (HPO)",
- "Abnormal cellular immune system morphology (HPO)",
+ "abnormality of anatomical entity physiology",
+ "Phenotypic abnormality",
+ "Bradyphrenia (HPO)",
+ "abnormal anatomical entity",
+ "Abnormality of higher mental function (HPO)",
"quality",
- "independent continuant",
- "blood",
- "granulocyte",
- "multicellular anatomical structure",
- "myeloid cell",
- "blood cell",
- "Abnormality of blood and blood-forming tissues (HPO)",
- "Abnormal eosinophil count (HPO)",
+ "multicellular organismal process",
+ "abnormal phenotype by ontology source",
+ "specifically dependent continuant",
"phenotype by ontology source",
+ "abnormal nervous system",
+ "occurrent",
"continuant",
- "material entity",
- "protein-containing material entity",
"material anatomical entity",
- "leukocyte",
- "animal cell",
- "hematopoietic cell",
- "Abnormal leukocyte count (HPO)",
- "phenotype",
- "abnormal phenotype by ontology source",
+ "nervous system",
+ "All (HPO)",
"continuant",
- "specifically dependent continuant",
- "Abnormality of the immune system (HPO)",
- "Abnormal granulocyte morphology (HPO)",
- "Eosinophilia (HPO)",
- "abnormal anatomical entity",
- "Abnormal immune system morphology (HPO)",
+ "system process",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the nervous system (HPO)",
"entity",
- "anatomical entity",
- "anatomical structure",
- "organism substance",
- "disconnected anatomical group",
- "mesoderm-derived structure",
- "bodily fluid",
- "non-connected functional system",
- "native cell",
- "hemolymphoid system",
- "hematopoietic system",
- "haemolymphatic fluid",
- "immune system",
- "myeloid leukocyte",
- "somatic cell",
- "abnormal immune system",
- "Abnormal granulocyte count (HPO)",
- "Phenotypic abnormality",
- "Abnormal cell morphology (HPO)",
- "Abnormal leukocyte morphology (HPO)",
- "Abnormal myeloid cell morphology (HPO)",
- "abnormal hematopoietic system",
"entity",
- "eosinophil",
- "anatomical system",
- "cell",
+ "cognition",
+ "abnormality of nervous system physiology",
+ "anatomical structure",
"multicellular organism",
- "nucleate cell",
- "eukaryotic cell",
- "motile cell",
+ "phenotype",
+ "process",
+ "nervous system process",
+ "Cognitive impairment (HPO)",
+ "Abnormal nervous system physiology (HPO)",
+ "biological_process",
+ "material entity",
+ "anatomical entity",
+ "abnormal anatomical entity",
+ "abnormality of anatomical entity physiology",
+ "independent continuant",
+ "multicellular anatomical structure",
+ "anatomical system",
],
- "frequency_qualifier_label": "Frequent (HPO)",
+ "frequency_qualifier_label": "Very frequent (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Frequent (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040281", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Very frequent (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0009675🍪🍪biolink:has_phenotype🍪HP:0001880",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0031843",
},
{
- "id": "uuid:c9c8bfee-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:253600",
+ "id": "uuid:4e02df85-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["PMID:16607617"],
+ "publications": ["orphanet:589821"],
"frequency_qualifier": "HP:0040282",
- "has_evidence": ["ECO:0000269"],
- "subject": "MONDO:0009675",
- "object": "HP:0002312",
- "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A",
+ "has_evidence": ["ECO:0000304"],
+ "subject": "MONDO:0035646",
+ "object": "HP:0000736",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "MONDO:0016971",
- "MONDO:0005336",
- "MONDO:0015152",
- "MONDO:0000429",
- "MONDO:0005071",
- "MONDO:0006025",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
- "MONDO:0009675",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
- "MONDO:0016152",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
- "BFO:0000002",
- "MONDO:0016106",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003847",
- "MONDO:0003939",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
- "hereditary disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
"continuant",
- "autosomal recessive disease",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
"disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "disease",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "autosomal genetic disease",
+ "myotonic dystrophy",
"nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
- "autosomal recessive limb-girdle muscular dystrophy type 2A",
"skeletal muscle disorder",
- "qualitative or quantitative defects of calpain",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Clumsiness (HPO)",
+ "object_label": "Short attention span (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
+ "UBERON:0000465",
+ "NBO:0000313",
+ "NBO:0000308",
"UPHENO:0082875",
- "UPHENO:0001005",
- "HP:0012638",
- "BFO:0000004",
- "UBERON:0000061",
- "UBERON:0001016",
- "HP:0000001",
- "HP:0000118",
+ "BFO:0000002",
+ "UPHENO:0004523",
+ "UPHENO:0049587",
+ "GO:0008150",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "GO:0007610",
+ "UPHENO:0001002",
"BFO:0000020",
- "UPHENO:0002433",
+ "HP:0000736",
+ "BFO:0000003",
+ "BFO:0000002",
+ "UPHENO:0001001",
+ "UPHENO:0049622",
"UPHENO:0001003",
- "PATO:0000001",
"BFO:0000001",
- "BFO:0000040",
- "UBERON:0000467",
- "UBERON:0000468",
+ "NBO:0000607",
"UPHENO:0075696",
- "HP:0011442",
- "UPHENO:0001002",
- "UPHENO:0002332",
+ "UPHENO:0002433",
+ "HP:0012638",
+ "BFO:0000015",
+ "BFO:0000004",
+ "UBERON:0000061",
+ "UBERON:0000468",
+ "NBO:0000455",
+ "UPHENO:0049586",
"UPHENO:0002536",
- "UPHENO:0004523",
- "HP:0002312",
- "HP:0011443",
- "BFO:0000002",
- "UBERON:0000465",
- "UPHENO:0001001",
- "BFO:0000002",
+ "HP:0000708",
+ "UPHENO:0080585",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "UPHENO:0079826",
+ "PATO:0000001",
+ "HP:0000001",
+ "UPHENO:0001005",
"HP:0000707",
- "HP:0002311",
+ "HP:0011446",
"BFO:0000001",
- "UBERON:0001062",
+ "GO:0032501",
"UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0001016",
],
"object_closure_label": [
- "All (HPO)",
- "Abnormal central motor function (HPO)",
- "Phenotypic abnormality (HPO)",
- "Abnormality of the nervous system (HPO)",
- "entity",
- "quality",
- "independent continuant",
- "anatomical structure",
- "multicellular anatomical structure",
- "nervous system",
"abnormality of anatomical entity physiology",
- "continuant",
+ "abnormal anatomical entity",
+ "Abnormality of higher mental function (HPO)",
+ "quality",
+ "multicellular organismal process",
+ "abnormal anatomical entity",
"specifically dependent continuant",
- "abnormality of nervous system physiology",
"phenotype by ontology source",
"abnormal nervous system",
- "Clumsiness (HPO)",
- "Abnormal nervous system physiology (HPO)",
+ "occurrent",
"continuant",
"material anatomical entity",
- "phenotype",
+ "nervous system",
+ "All (HPO)",
"abnormal phenotype by ontology source",
- "Incoordination (HPO)",
- "Abnormality of coordination (HPO)",
+ "Short attention span (HPO)",
+ "behavior",
+ "abnormal behavior",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the nervous system (HPO)",
+ "abnormal behavior process",
"entity",
- "anatomical entity",
- "abnormal anatomical entity",
+ "entity",
+ "cognitive behavior",
+ "sensation behavior",
"Phenotypic abnormality",
- "abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
+ "abnormality of nervous system physiology",
+ "multicellular organism",
+ "phenotype",
+ "abnormal behavior process",
+ "Behavioral abnormality (HPO)",
+ "abnormal biological_process",
+ "process",
+ "independent continuant",
+ "behavior process",
+ "Abnormal nervous system physiology (HPO)",
+ "biological_process",
"material entity",
+ "anatomical entity",
+ "anatomical structure",
+ "abnormal response to stimulus",
+ "continuant",
+ "abnormality of anatomical entity physiology",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
+ "attention behavior",
],
"frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Frequent (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0009675🍪🍪biolink:has_phenotype🍪HP:0002312",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0000736",
},
{
- "id": "uuid:c9c8bff4-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:253600",
+ "id": "uuid:4e02df87-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["PMID:16607617"],
- "frequency_qualifier": "HP:0040280",
- "has_evidence": ["ECO:0000269"],
- "subject": "MONDO:0009675",
- "object": "HP:0032019",
- "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A",
+ "publications": ["orphanet:589821"],
+ "frequency_qualifier": "HP:0040282",
+ "has_evidence": ["ECO:0000304"],
+ "subject": "MONDO:0035646",
+ "object": "HP:0001622",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "MONDO:0016971",
- "MONDO:0005336",
- "MONDO:0015152",
- "MONDO:0000429",
- "MONDO:0005071",
- "MONDO:0006025",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
- "MONDO:0009675",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
- "MONDO:0016152",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
- "BFO:0000002",
- "MONDO:0016106",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003847",
- "MONDO:0003939",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
- "hereditary disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
"continuant",
- "autosomal recessive disease",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
"disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "disease",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "autosomal genetic disease",
+ "myotonic dystrophy",
"nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
- "autosomal recessive limb-girdle muscular dystrophy type 2A",
"skeletal muscle disorder",
- "qualitative or quantitative defects of calpain",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Muscle eosinophilia (HPO)",
+ "object_label": "Premature birth (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "UPHENO:0001005",
+ "HP:0001197",
+ "UPHENO:0002536",
+ "GO:0008150",
+ "UBERON:0000465",
+ "GO:0007567",
+ "UPHENO:0049587",
+ "BFO:0000001",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "GO:0044706",
+ "GO:0000003",
+ "GO:0044703",
+ "BFO:0000003",
"BFO:0000002",
- "BFO:0000020",
- "UPHENO:0076692",
- "PATO:0000001",
- "BFO:0000004",
- "UBERON:0000061",
- "HP:0000001",
"UPHENO:0001001",
- "HP:0000118",
- "HP:0032019",
- "UPHENO:0001003",
- "UPHENO:0076710",
- "BFO:0000001",
+ "UPHENO:0001002",
+ "BFO:0000020",
+ "UPHENO:0001003",
"BFO:0000001",
- "BFO:0000040",
- "UBERON:0000467",
+ "UPHENO:0001005",
+ "UPHENO:0049940",
+ "BFO:0000015",
+ "UBERON:0000061",
"UBERON:0000468",
- "UBERON:0011216",
- "HP:0003011",
- "UPHENO:0002536",
"BFO:0000002",
- "UBERON:0000465",
- "UBERON:0005090",
- "UBERON:0001630",
- "HP:0011805",
- "UPHENO:0001002",
- "UPHENO:0002816",
- "UPHENO:0081581",
- "HP:0033127",
- "UBERON:0001062",
+ "UPHENO:0049440",
+ "BFO:0000004",
+ "UBERON:0000922",
+ "HP:0001622",
+ "HP:0000118",
+ "UPHENO:0049449",
+ "HP:0001787",
+ "PATO:0000001",
+ "UBERON:0000323",
+ "HP:0000001",
+ "UPHENO:0075949",
+ "GO:0032501",
+ "GO:0022414",
"UBERON:0010000",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
],
"object_closure_label": [
- "All (HPO)",
- "Phenotypic abnormality (HPO)",
- "abnormal musculature",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "independent continuant",
- "anatomical structure",
- "multicellular anatomical structure",
- "phenotype",
- "Abnormal skeletal muscle morphology (HPO)",
"Phenotypic abnormality",
- "Muscle eosinophilia (HPO)",
- "phenotype by ontology source",
+ "specifically dependent continuant",
"quality",
+ "multicellular organismal process",
+ "reproductive process",
+ "abnormal phenotype by ontology source",
+ "premature biological_process",
+ "phenotype by ontology source",
+ "occurrent",
"continuant",
"material anatomical entity",
- "abnormal phenotype by ontology source",
+ "All (HPO)",
"continuant",
- "specifically dependent continuant",
- "abnormal muscle organ morphology",
+ "multi-multicellular organism process",
+ "reproduction",
+ "multi-organism reproductive process",
+ "embryo",
+ "Phenotypic abnormality (HPO)",
+ "abnormal late embryo",
+ "Abnormal delivery (HPO)",
"entity",
- "anatomical entity",
- "muscle structure",
- "organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "Abnormality of the musculature (HPO)",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
+ "biological_process",
+ "multicellular organism",
+ "phenotype",
+ "Premature birth (HPO)",
+ "abnormal biological_process",
"entity",
+ "process",
+ "parturition",
+ "Abnormality of prenatal development or birth (HPO)",
+ "abnormal reproductive process",
"material entity",
- "anatomical system",
- "multicellular organism",
- "organ system subdivision",
+ "anatomical entity",
+ "anatomical structure",
+ "premature parturition",
+ "abnormal anatomical entity",
+ "independent continuant",
+ "multicellular anatomical structure",
+ "late embryo",
],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0009675🍪🍪biolink:has_phenotype🍪HP:0032019",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001622",
},
{
- "id": "uuid:c9c8bff5-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:253600",
+ "id": "uuid:4e02df88-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["PMID:16607617"],
+ "publications": ["orphanet:589821"],
"frequency_qualifier": "HP:0040282",
- "has_evidence": ["ECO:0000269"],
- "subject": "MONDO:0009675",
- "object": "HP:0007340",
- "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A",
+ "has_evidence": ["ECO:0000304"],
+ "subject": "MONDO:0035646",
+ "object": "HP:0001883",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "MONDO:0016971",
- "MONDO:0005336",
- "MONDO:0015152",
- "MONDO:0000429",
- "MONDO:0005071",
- "MONDO:0006025",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
"BFO:0000017",
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+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
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+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
- "MONDO:0009675",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
- "MONDO:0016152",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
- "BFO:0000002",
- "MONDO:0016106",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003847",
- "MONDO:0003939",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
- "hereditary disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
"continuant",
- "autosomal recessive disease",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
"disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "disease",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "autosomal genetic disease",
+ "myotonic dystrophy",
"nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
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- "specifically dependent continuant",
- "autosomal recessive limb-girdle muscular dystrophy type 2A",
"skeletal muscle disorder",
- "qualitative or quantitative defects of calpain",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Lower limb muscle weakness (HPO)",
+ "object_label": "Talipes (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "UPHENO:0082875",
- "UPHENO:0002320",
- "UPHENO:0001005",
- "HP:0009127",
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- "PATO:0000001",
- "BFO:0000001",
- "BFO:0000040",
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- "HP:0003011",
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- "UPHENO:0002536",
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- "UBERON:0005090",
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"UBERON:0010707",
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- "HP:0033127",
- "UPHENO:0002647",
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+ "UBERON:0010758",
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- "UBERON:0000475",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "UBERON:0004480",
+ "UBERON:0000978",
+ "UBERON:0002529",
],
"object_closure_label": [
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- "paired limb/fin",
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- "muscle structure",
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- "organism subdivision",
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- "muscle organ",
- "musculature of body",
- "musculature",
- "musculature of limb",
- "abnormal anatomical entity",
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- "Limb muscle weakness (HPO)",
- "Abnormality of the musculature (HPO)",
- "abnormality of anatomical entity physiology",
"phenotype by ontology source",
"abnormal anatomical entity",
+ "continuant",
+ "protein-containing material entity",
+ "material anatomical entity",
+ "system",
+ "multi-limb segment region",
+ "All (HPO)",
+ "continuant",
+ "appendage",
+ "subdivision of organism along appendicular axis",
+ "Abnormality of the lower limb (HPO)",
+ "Phenotypic abnormality (HPO)",
+ "entity",
+ "lateral structure",
+ "leg",
+ "limb segment",
+ "Phenotypic abnormality",
+ "abnormal pes morphology",
"abnormal anatomical entity morphology",
+ "abnormal leg",
+ "quality",
+ "anatomical structure",
+ "organism subdivision",
+ "multicellular organism",
+ "pelvic complex",
+ "lower limb segment",
+ "autopod region",
+ "phenotype",
+ "Positional foot deformity (HPO)",
+ "Abnormal foot morphology (HPO)",
"entity",
+ "independent continuant",
+ "posterior region of body",
+ "abnormal multicellular organism morphology",
"abnormal limb",
"material entity",
"anatomical entity",
+ "paired limb/fin",
"limb",
- "anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "appendage",
- "skeletal muscle organ",
+ "pelvic appendage",
+ "pes",
+ "Talipes (HPO)",
+ "Abnormality of limbs (HPO)",
+ "multicellular anatomical structure",
+ "hindlimb",
+ "appendage girdle complex",
+ "paired limb/fin segment",
],
"frequency_qualifier_label": "Frequent (HPO)",
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"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Frequent (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0009675🍪🍪biolink:has_phenotype🍪HP:0007340",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001883",
},
{
- "id": "uuid:c9d8bdf9-7529-11ee-b012-cbd37f5c3759",
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- "subject": "MONDO:0009676",
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+ "subject": "MONDO:0035646",
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- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "autosomal recessive limb-girdle muscular dystrophy type 2B",
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"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
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+ "myotonic syndrome",
],
- "object_label": "Proximal muscle weakness (HPO)",
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"object_closure": [
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- "multicellular anatomical structure",
"abnormality of anatomical entity physiology",
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+ "abnormal nervous system",
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- "abnormal anatomical entity",
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- "Abnormality of the musculature (HPO)",
- "abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
+ "Phenotypic abnormality",
+ "abnormality of nervous system physiology",
+ "anatomical structure",
+ "multicellular organism",
+ "phenotype",
+ "Speech apraxia (HPO)",
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+ "independent continuant",
+ "Abnormal nervous system physiology (HPO)",
"material entity",
"anatomical entity",
+ "Abnormal central motor function (HPO)",
+ "Apraxia (HPO)",
+ "abnormality of anatomical entity physiology",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
],
- "frequency_qualifier_label": "Obligate (HPO)",
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},
{
- "id": "uuid:c9c8bf35-7529-11ee-b012-cbd37f5c3759",
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"has_evidence": ["ECO:0000304"],
- "subject": "MONDO:0008050",
- "object": "HP:0003701",
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject": "MONDO:0035646",
+ "object": "HP:0011710",
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+ "disposition",
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+ "myotonic syndrome",
],
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- "All (HPO)",
- "abnormality of muscle organ physiology",
+ "abnormality of anatomical entity physiology",
"Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "decreased anatomical entity strength",
- "abnormal musculature",
- "decreased muscle organ strength",
- "Abnormality of the musculoskeletal system (HPO)",
+ "Abnormal cardiovascular system physiology (HPO)",
"quality",
- "independent continuant",
- "anatomical structure",
- "multicellular anatomical structure",
- "abnormality of anatomical entity physiology",
- "phenotype",
+ "entity",
+ "abnormal anatomical entity",
"abnormal phenotype by ontology source",
- "Proximal muscle weakness (HPO)",
- "specifically dependent continuant",
"phenotype by ontology source",
"continuant",
+ "protein-containing material entity",
"material anatomical entity",
+ "circulatory system",
+ "All (HPO)",
+ "Cardiac conduction abnormality (HPO)",
+ "Phenotypic abnormality (HPO)",
"continuant",
- "Abnormal muscle physiology (HPO)",
- "entity",
- "muscle structure",
- "organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "abnormal anatomical entity",
- "Muscle weakness (HPO)",
- "Abnormality of the musculature (HPO)",
- "abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
"entity",
+ "Abnormality of cardiovascular system electrophysiology (HPO)",
+ "Abnormality of the cardiovascular system (HPO)",
+ "specifically dependent continuant",
+ "multicellular organism",
+ "phenotype",
+ "independent continuant",
+ "Bundle branch block (HPO)",
+ "abnormality of cardiovascular system physiology",
"material entity",
"anatomical entity",
+ "cardiovascular system",
+ "anatomical structure",
+ "abnormal cardiovascular system",
+ "abnormality of anatomical entity physiology",
+ "abnormal anatomical entity",
+ "Heart block (HPO)",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
],
- "frequency_qualifier_label": "Occasional (HPO)",
+ "frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040283", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Occasional (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0003701",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0011710",
},
{
- "id": "uuid:c9c8bf37-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:160500",
+ "id": "uuid:4e02dfa2-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["OMIM:160500"],
- "frequency_qualifier": "HP:0040283",
+ "publications": ["orphanet:589821"],
+ "frequency_qualifier": "HP:0040284",
"has_evidence": ["ECO:0000304"],
- "subject": "MONDO:0008050",
- "object": "HP:0001644",
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject": "MONDO:0035646",
+ "object": "HP:0001513",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Dilated cardiomyopathy (HPO)",
+ "object_label": "Obesity (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "UPHENO:0082875",
- "HP:0001637",
- "UPHENO:0001005",
- "BFO:0000020",
- "UPHENO:0077800",
- "UPHENO:0066927",
- "UPHENO:0076692",
- "PATO:0000001",
- "BFO:0000004",
- "UBERON:0004535",
- "UBERON:0011676",
- "UBERON:0013701",
- "UBERON:0002349",
- "UBERON:0000915",
- "UBERON:0002100",
- "UBERON:0005181",
- "UBERON:0002075",
- "UBERON:0015228",
- "HP:0000001",
+ "UPHENO:0049587",
+ "GO:0008150",
+ "UBERON:0000465",
+ "HP:0001513",
+ "BFO:0000001",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UBERON:0000468",
+ "UPHENO:0008273",
+ "UPHENO:0049874",
+ "BFO:0000003",
+ "BFO:0000002",
"UPHENO:0001001",
- "HP:0001644",
- "HP:0030680",
"UPHENO:0001002",
- "HP:0000118",
- "HP:0001627",
- "UPHENO:0076776",
"UPHENO:0001003",
- "UPHENO:0024906",
"BFO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0010000",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
- "UBERON:0000064",
+ "UBERON:0000061",
"UPHENO:0075696",
- "HP:0001626",
- "UPHENO:0080362",
- "HP:0001638",
+ "UPHENO:0001005",
+ "BFO:0000020",
+ "BFO:0000015",
+ "BFO:0000004",
+ "HP:0001507",
"BFO:0000002",
- "UPHENO:0002332",
"UPHENO:0002536",
- "UPHENO:0076810",
- "BFO:0000002",
- "PR:000050567",
- "UBERON:0004120",
- "UBERON:0000948",
- "UBERON:0001009",
- "UBERON:0005983",
- "UBERON:0009569",
- "UBERON:0013702",
- "UBERON:0005177",
- "UBERON:0003103",
- "UBERON:0018260",
- "UBERON:0015410",
- "UPHENO:0076781",
- "UPHENO:0081581",
- "UBERON:0001062",
- "UBERON:0000465",
- "UBERON:0000061",
- "UBERON:0010314",
- "UBERON:0000475",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0000060",
- "UBERON:0004923",
- "UBERON:0005178",
- "UBERON:0007100",
+ "HP:0000118",
+ "UPHENO:0010795",
+ "HP:0004323",
+ "UPHENO:0010763",
+ "PATO:0000001",
+ "HP:0000001",
+ "HP:0004324",
+ "UPHENO:0008312",
+ "GO:0040007",
+ "UBERON:0010000",
],
"object_closure_label": [
- "All (HPO)",
- "abnormal cardiovascular system",
- "Cardiomyopathy (HPO)",
"Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "abnormal myocardium morphology",
- "abnormal multicellular organism morphology",
- "independent continuant",
- "material anatomical entity",
- "cardiovascular system",
- "structure with developmental contribution from neural crest",
- "layer of muscle tissue",
- "abnormality of anatomical entity physiology",
- "Abnormal myocardium morphology (HPO)",
- "phenotype",
- "Abnormality of the cardiovascular system (HPO)",
- "Abnormal heart morphology (HPO)",
- "abnormal cardiovascular system morphology",
- "phenotype by ontology source",
- "abnormally decreased functionality of the anatomical entity",
- "abnormal heart morphology",
+ "abnormal anatomical entity",
+ "increased multicellular organism mass",
"quality",
- "continuant",
- "protein-containing material entity",
- "heart",
- "subdivision of trunk",
- "body proper",
- "trunk region element",
- "compound organ",
- "heart plus pericardium",
+ "growth",
+ "abnormal anatomical entity",
"abnormal phenotype by ontology source",
- "specifically dependent continuant",
- "abnormally decreased functionality of the myocardium",
- "anatomical entity dysfunction in independent continuant",
+ "phenotype by ontology source",
+ "Obesity (HPO)",
+ "occurrent",
+ "continuant",
+ "material anatomical entity",
+ "All (HPO)",
+ "continuant",
+ "abnormal growth",
+ "multicellular organism",
+ "Phenotypic abnormality (HPO)",
+ "abnormality of anatomical entity mass",
"entity",
- "anatomical entity",
+ "biological_process",
+ "increased anatomical entity mass",
+ "specifically dependent continuant",
"anatomical structure",
- "mesoderm-derived structure",
- "organism subdivision",
- "organ",
- "circulatory system",
- "heart layer",
- "musculature of body",
- "anatomical wall",
- "organ component layer",
- "thoracic cavity element",
- "primary circulatory organ",
- "abnormal anatomical entity",
- "Dilated cardiomyopathy (HPO)",
- "Abnormality of cardiovascular system morphology (HPO)",
- "continuant",
- "abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
+ "phenotype",
+ "Increased body weight (HPO)",
"entity",
+ "process",
+ "independent continuant",
+ "abnormal biological_process",
"material entity",
+ "anatomical entity",
+ "Growth abnormality (HPO)",
+ "abnormality of multicellular organism mass",
+ "Abnormality of body weight (HPO)",
"multicellular anatomical structure",
- "anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "organ part",
- "subdivision of organism along main body axis",
- "main body axis",
- "myocardium",
- "thoracic segment of trunk",
- "trunk",
- "thoracic segment organ",
- "viscus",
- "circulatory organ",
],
- "frequency_qualifier_label": "Occasional (HPO)",
+ "frequency_qualifier_label": "Very rare (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040283", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Occasional (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0000001", "HP:0040284"],
+ "frequency_qualifier_closure_label": ["Very rare (HPO)", "Frequency (HPO)", "All (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0001644",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001513",
},
{
- "id": "uuid:c9c8bff0-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:253600",
+ "id": "uuid:4e02df92-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["OMIM:253600"],
+ "publications": ["orphanet:589821"],
"frequency_qualifier": "HP:0040283",
"has_evidence": ["ECO:0000304"],
- "subject": "MONDO:0009675",
- "object": "HP:0010628",
- "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A",
+ "subject": "MONDO:0035646",
+ "object": "HP:0000729",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "MONDO:0016971",
- "MONDO:0005336",
- "MONDO:0015152",
- "MONDO:0000429",
- "MONDO:0005071",
- "MONDO:0006025",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
- "MONDO:0009675",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
- "MONDO:0016152",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
- "BFO:0000002",
- "MONDO:0016106",
- "MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003847",
- "MONDO:0003939",
+ "MONDO:0003382",
+ "BFO:0000016",
+ "MONDO:0700096",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
- "hereditary disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
"continuant",
- "autosomal recessive disease",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
"disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "disease",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "autosomal genetic disease",
+ "myotonic dystrophy",
"nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
- "autosomal recessive limb-girdle muscular dystrophy type 2A",
"skeletal muscle disorder",
- "qualitative or quantitative defects of calpain",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Facial palsy (HPO)",
+ "object_label": "Autistic behavior (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "UPHENO:0082875",
- "UPHENO:0076772",
- "UPHENO:0002320",
- "UPHENO:0005116",
- "HP:0031910",
- "HP:0011799",
- "HP:0410008",
- "UPHENO:0076692",
- "BFO:0000001",
- "PATO:0000001",
- "HP:0012638",
- "BFO:0000004",
- "UBERON:0001016",
- "UBERON:0001021",
- "UBERON:0000153",
- "UBERON:0011676",
- "UBERON:0013701",
- "UBERON:0014892",
- "UBERON:0015789",
- "UBERON:0011779",
- "UBERON:0000033",
- "HP:0000001",
- "HP:0000152",
- "UPHENO:0002764",
- "UPHENO:0001002",
- "HP:0000118",
- "BFO:0000020",
- "UPHENO:0002433",
- "HP:0000234",
- "HP:0000271",
- "HP:0010827",
- "UPHENO:0001003",
- "HP:0012639",
- "UPHENO:0076710",
- "UPHENO:0002908",
+ "UPHENO:0002536",
"BFO:0000001",
+ "GO:0008150",
+ "UBERON:0000465",
+ "NBO:0000313",
+ "UPHENO:0082875",
+ "UPHENO:0004523",
+ "UPHENO:0049587",
"BFO:0000040",
- "UBERON:0000467",
+ "GO:0007610",
"UBERON:0000468",
- "UBERON:0011216",
- "UBERON:0001785",
- "UBERON:0010959",
- "UBERON:0001577",
- "UPHENO:0075696",
- "HP:0045010",
- "UPHENO:0002844",
- "HP:0001291",
- "HP:0001324",
- "HP:0030319",
- "HP:0000759",
- "UPHENO:0081700",
- "HP:0003011",
- "UPHENO:0002332",
- "UPHENO:0078730",
- "UPHENO:0002536",
- "UPHENO:0081709",
- "HP:0000301",
- "UPHENO:0004523",
- "UPHENO:0004508",
- "HP:0011804",
+ "BFO:0000020",
+ "BFO:0000003",
"BFO:0000002",
- "UBERON:0000465",
- "UBERON:0005090",
- "UBERON:0018254",
- "UBERON:0004120",
- "UBERON:0034713",
- "UBERON:0001647",
- "UBERON:0000122",
- "UBERON:0001630",
- "UBERON:0001033",
- "UBERON:0002376",
- "UBERON:0007811",
- "UBERON:0001444",
- "UBERON:0013702",
- "UBERON:0001456",
- "UBERON:0008229",
- "UBERON:0013700",
"UPHENO:0001001",
- "UPHENO:0002910",
- "HP:0010628",
+ "UPHENO:0049622",
+ "UPHENO:0001002",
+ "UPHENO:0001003",
+ "BFO:0000001",
+ "UBERON:0001062",
+ "UBERON:0000061",
+ "UPHENO:0075696",
"UPHENO:0001005",
- "HP:0011805",
+ "UPHENO:0002433",
+ "HP:0012638",
+ "BFO:0000015",
+ "UPHENO:0049586",
+ "HP:0000729",
"BFO:0000002",
- "UPHENO:0076722",
- "UPHENO:0080555",
- "UPHENO:0003587",
- "UPHENO:0002816",
- "UPHENO:0080556",
+ "HP:0000708",
+ "BFO:0000004",
+ "UPHENO:0080585",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "UPHENO:0079826",
+ "PATO:0000001",
+ "HP:0000001",
"HP:0000707",
- "HP:0006824",
- "UPHENO:0081581",
- "HP:0033127",
- "UPHENO:0076702",
- "UBERON:0001062",
- "RO:0002577",
- "UBERON:0000061",
- "UBERON:0015212",
- "UBERON:0010314",
- "UBERON:0005162",
+ "HP:0011446",
+ "GO:0032501",
"UBERON:0010000",
- "UBERON:0000475",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "UBERON:0000010",
- "UBERON:0004461",
- "UBERON:0004473",
+ "UBERON:0000467",
+ "UBERON:0001016",
],
"object_closure_label": [
- "All (HPO)",
- "abnormality of muscle organ physiology",
- "abnormal peripheral nervous system",
- "Abnormal cranial nerve physiology (HPO)",
- "Abnormality of facial soft tissue (HPO)",
- "abnormal head",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "abnormal peripheral nervous system morphology",
- "decreased anatomical entity strength",
- "abnormal facial nerve",
- "abnormal musculature",
- "decreased muscle organ strength",
- "Abnormality of the nervous system (HPO)",
- "Cranial nerve paralysis (HPO)",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "Abnormal nervous system morphology (HPO)",
- "abnormal facial muscle",
- "independent continuant",
- "system",
- "lateral structure",
- "structure with developmental contribution from neural crest",
- "multi cell part structure",
- "multicellular anatomical structure",
- "nervous system",
- "cranial nerve",
- "face",
- "craniocervical region musculature",
- "axial musculature",
"abnormality of anatomical entity physiology",
- "abnormal cranial nerve morphology",
- "Abnormality of peripheral nerves (HPO)",
- "Facial palsy (HPO)",
+ "Phenotypic abnormality",
+ "Abnormality of higher mental function (HPO)",
+ "quality",
+ "multicellular organismal process",
+ "abnormal anatomical entity",
"abnormal phenotype by ontology source",
- "Abnormal skeletal muscle morphology (HPO)",
- "continuant",
"specifically dependent continuant",
- "abnormality of nervous system physiology",
- "Abnormality of the head (HPO)",
- "Abnormality of the face (HPO)",
- "Abnormality of the seventh cranial nerve (HPO)",
"phenotype by ontology source",
- "Abnormality of the peripheral nervous system (HPO)",
- "paralysed cranial nerve",
- "Abnormality of facial musculature (HPO)",
"abnormal nervous system",
- "abnormal nerve",
- "quality",
- "Abnormal nervous system physiology (HPO)",
+ "occurrent",
"continuant",
"material anatomical entity",
- "cranial neuron projection bundle",
- "facial nerve",
- "neuron projection bundle",
- "craniocervical region",
- "subdivision of head",
- "body proper",
- "craniocervical muscle",
- "facial muscle",
- "phenotype",
- "abnormal face",
- "abnormal muscle organ morphology",
- "Abnormal muscle physiology (HPO)",
+ "nervous system",
+ "All (HPO)",
+ "continuant",
+ "behavior",
+ "multicellular organism",
+ "abnormal behavior",
+ "Autistic behavior (HPO)",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the nervous system (HPO)",
+ "abnormal behavior process",
"entity",
+ "biological_process",
+ "abnormality of nervous system physiology",
"anatomical entity",
"anatomical structure",
- "muscle structure",
- "skeletal musculature",
- "mesoderm-derived structure",
- "organism subdivision",
- "organ",
- "muscle organ",
- "gustatory system",
- "cranial muscle",
- "musculature of body",
- "musculature",
- "peripheral nervous system",
- "skeletal musculature of head",
- "musculature of face",
- "abnormal anatomical entity",
- "Abnormality of head or neck (HPO)",
- "abnormal craniocervical region",
- "Abnormal cranial nerve morphology (HPO)",
- "Muscle weakness (HPO)",
- "Weakness of facial musculature (HPO)",
- "Abnormal peripheral nervous system morphology (HPO)",
- "paralysed anatomical entity",
- "Abnormality of the musculature (HPO)",
- "abnormality of anatomical entity physiology",
- "abnormality of cranial nerve physiology",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
+ "phenotype",
+ "abnormal behavior process",
+ "Behavioral abnormality (HPO)",
+ "abnormal biological_process",
+ "process",
+ "behavior process",
"entity",
- "abnormal nervous system morphology",
+ "Abnormal nervous system physiology (HPO)",
"material entity",
+ "abnormal response to stimulus",
+ "abnormality of anatomical entity physiology",
+ "abnormal anatomical entity",
+ "independent continuant",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "nerve",
- "anterior region of body",
- "subdivision of organism along main body axis",
- "main body axis",
- "skeletal muscle organ",
- "cranial or facial muscle",
- "nerve of head region",
- "head",
],
"frequency_qualifier_label": "Occasional (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040283", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Occasional (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Occasional (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0009675🍪🍪biolink:has_phenotype🍪HP:0010628",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0000729",
},
{
- "id": "uuid:c9d8bdf7-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:253601",
+ "id": "uuid:4e02df94-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["PMID:9731527"],
+ "publications": ["orphanet:589821"],
"frequency_qualifier": "HP:0040283",
- "has_evidence": ["ECO:0000269"],
- "subject": "MONDO:0009676",
- "object": "HP:0002505",
- "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2B",
+ "has_evidence": ["ECO:0000304"],
+ "subject": "MONDO:0035646",
+ "object": "HP:0000752",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "MONDO:0016971",
- "BFO:0000002",
- "BFO:0000020",
- "MONDO:0005336",
- "MONDO:0009676",
- "MONDO:0015152",
- "MONDO:0000429",
- "MONDO:0005071",
- "MONDO:0006025",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
- "MONDO:0016145",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
+ "BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
- "MONDO:0016106",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "qualitative or quantitative defects of dysferlin",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "autosomal recessive disease",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "autosomal recessive limb-girdle muscular dystrophy type 2B",
- "disease",
"continuant",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
"specifically dependent continuant",
"myopathy",
- "hereditary disease",
- "autosomal genetic disease",
+ "myotonic dystrophy",
"nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
"skeletal muscle disorder",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Loss of ambulation (HPO)",
+ "object_label": "Hyperactivity (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
+ "UPHENO:0049587",
+ "NBO:0000030",
+ "GO:0008150",
+ "UBERON:0000465",
+ "NBO:0000313",
"UPHENO:0082875",
- "UPHENO:0049622",
- "UPHENO:0001005",
+ "UPHENO:0004523",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "GO:0007610",
+ "NBO:0000568",
+ "BFO:0000003",
"BFO:0000002",
- "HP:0002540",
- "UPHENO:0050606",
- "HP:0001288",
- "HP:0012638",
- "BFO:0000015",
- "UBERON:0000061",
- "GO:0050882",
- "NBO:0000338",
- "GO:0050905",
- "UBERON:0001016",
- "HP:0000001",
"UPHENO:0001001",
- "UPHENO:0080585",
- "HP:0000118",
- "BFO:0000020",
- "UPHENO:0002433",
+ "UPHENO:0049622",
+ "UPHENO:0001002",
"UPHENO:0001003",
- "HP:0000708",
- "HP:0011446",
- "BFO:0000001",
- "PATO:0000001",
"BFO:0000001",
+ "UBERON:0000061",
+ "HP:0000752",
+ "UPHENO:0075696",
+ "UPHENO:0001005",
+ "BFO:0000020",
+ "UPHENO:0002433",
+ "HP:0012638",
+ "NBO:0000644",
+ "BFO:0000015",
"BFO:0000004",
- "GO:0032501",
- "GO:0050881",
- "NBO:0000313",
- "GO:0050877",
- "UBERON:0000467",
"UBERON:0000468",
- "NBO:0000403",
- "NBO:0000001",
- "UPHENO:0075696",
- "UPHENO:0078622",
- "HP:0002505",
"UPHENO:0049586",
- "HP:0100022",
- "UPHENO:0001002",
- "UPHENO:0050613",
- "UPHENO:0002332",
+ "BFO:0000002",
"UPHENO:0002536",
+ "HP:0000708",
+ "NBO:0000243",
+ "UPHENO:0080585",
+ "HP:0000118",
+ "UPHENO:0002332",
"UPHENO:0079826",
- "UPHENO:0004523",
- "UPHENO:0049587",
- "BFO:0000003",
- "BFO:0000002",
- "GO:0008150",
- "BFO:0000040",
- "GO:0050879",
- "GO:0007610",
- "GO:0003008",
+ "PATO:0000001",
+ "HP:0000001",
"HP:0000707",
- "UPHENO:0079833",
- "UBERON:0001062",
- "UBERON:0000465",
+ "HP:0011446",
+ "BFO:0000001",
+ "GO:0032501",
"UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0001016",
],
"object_closure_label": [
- "All (HPO)",
- "abnormal behavior",
- "Abnormality of movement (HPO)",
- "Phenotypic abnormality (HPO)",
- "Abnormality of the nervous system (HPO)",
- "Behavioral abnormality (HPO)",
+ "abnormality of anatomical entity physiology",
+ "Phenotypic abnormality",
+ "abnormal anatomical entity",
"Abnormality of higher mental function (HPO)",
- "abnormal voluntary movement behavior",
"quality",
- "process",
+ "multicellular organismal process",
+ "Hyperactivity (HPO)",
+ "abnormal anatomical entity",
+ "abnormal phenotype by ontology source",
+ "phenotype by ontology source",
+ "abnormal nervous system",
+ "kinesthetic behavior phenotype",
+ "occurrent",
+ "continuant",
"material anatomical entity",
- "anatomical structure",
- "multicellular anatomical structure",
"nervous system",
- "voluntary movement behavior",
- "body part movement",
- "abnormality of anatomical entity physiology",
- "phenotype",
+ "All (HPO)",
+ "continuant",
+ "behavior",
+ "abnormal behavior",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the nervous system (HPO)",
+ "abnormal behavior process",
+ "entity",
+ "entity",
+ "hyperactivity",
+ "biological_process",
"specifically dependent continuant",
"abnormality of nervous system physiology",
- "phenotype by ontology source",
- "Gait disturbance (HPO)",
+ "anatomical structure",
+ "multicellular organism",
+ "phenotype",
"abnormal behavior process",
- "abnormal nervous system",
+ "Behavioral abnormality (HPO)",
+ "voluntary movement behavior phenotype",
+ "process",
+ "independent continuant",
+ "behavior process",
"abnormal biological_process",
"Abnormal nervous system physiology (HPO)",
- "occurrent",
- "continuant",
- "biological_process",
"material entity",
- "multicellular organismal movement",
- "behavior",
- "system process",
- "musculoskeletal movement",
- "behavior process",
- "nervous system process",
- "abnormal phenotype by ontology source",
- "continuant",
- "Inability to walk (HPO)",
- "abnormal voluntary musculoskeletal movement",
- "entity",
- "independent continuant",
"anatomical entity",
- "abnormal anatomical entity",
- "abnormal voluntary movement behavior",
- "Loss of ambulation (HPO)",
"abnormal response to stimulus",
- "abnormal behavior process",
- "Phenotypic abnormality",
- "abnormal musculoskeletal movement",
"abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
- "entity",
- "multicellular organismal process",
+ "behavioral phenotype",
+ "multicellular anatomical structure",
"anatomical system",
- "voluntary musculoskeletal movement",
- "kinesthetic behavior",
- "neuromuscular process",
- "multicellular organism",
],
"frequency_qualifier_label": "Occasional (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040283", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Occasional (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Occasional (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0009676🍪🍪biolink:has_phenotype🍪HP:0002505",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0000752",
},
{
- "id": "uuid:c9c8bf2b-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:160500",
+ "id": "uuid:4e02df96-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["OMIM:160500"],
+ "publications": ["orphanet:589821"],
+ "frequency_qualifier": "HP:0040283",
"has_evidence": ["ECO:0000304"],
- "subject": "MONDO:0008050",
- "object": "HP:0010628",
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject": "MONDO:0035646",
+ "object": "HP:0001558",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
+ "disease",
+ "hypertrophic cardiomyopathy",
"disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Facial palsy (HPO)",
+ "object_label": "Decreased fetal movement (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "UPHENO:0082875",
- "UPHENO:0076772",
- "UPHENO:0002320",
- "UPHENO:0005116",
- "HP:0031910",
- "HP:0011799",
- "HP:0410008",
- "UPHENO:0076692",
- "BFO:0000001",
- "PATO:0000001",
- "HP:0012638",
- "BFO:0000004",
- "UBERON:0001016",
- "UBERON:0001021",
- "UBERON:0000153",
- "UBERON:0011676",
- "UBERON:0013701",
- "UBERON:0014892",
- "UBERON:0015789",
- "UBERON:0011779",
- "UBERON:0000033",
- "HP:0000001",
- "HP:0000152",
- "UPHENO:0002764",
+ "HP:0001197",
+ "UBERON:0000465",
+ "HP:0034059",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "BFO:0000002",
+ "UPHENO:0001001",
"UPHENO:0001002",
- "HP:0000118",
"BFO:0000020",
- "UPHENO:0002433",
- "HP:0000234",
- "HP:0000271",
- "HP:0010827",
"UPHENO:0001003",
- "HP:0012639",
- "UPHENO:0076710",
- "UPHENO:0002908",
"BFO:0000001",
- "BFO:0000040",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
- "UBERON:0001785",
- "UBERON:0010959",
- "UBERON:0001577",
- "UPHENO:0075696",
- "HP:0045010",
- "UPHENO:0002844",
- "HP:0001291",
- "HP:0001324",
- "HP:0030319",
- "HP:0000759",
- "UPHENO:0081700",
- "HP:0003011",
- "UPHENO:0002332",
- "UPHENO:0078730",
- "UPHENO:0002536",
- "UPHENO:0081709",
- "HP:0000301",
- "UPHENO:0004523",
- "UPHENO:0004508",
- "HP:0011804",
- "BFO:0000002",
- "UBERON:0000465",
- "UBERON:0005090",
- "UBERON:0018254",
- "UBERON:0004120",
- "UBERON:0034713",
- "UBERON:0001647",
- "UBERON:0000122",
- "UBERON:0001630",
- "UBERON:0001033",
- "UBERON:0002376",
- "UBERON:0007811",
- "UBERON:0001444",
- "UBERON:0013702",
- "UBERON:0001456",
- "UBERON:0008229",
- "UBERON:0013700",
- "UPHENO:0001001",
- "UPHENO:0002910",
- "HP:0010628",
"UPHENO:0001005",
- "HP:0011805",
- "BFO:0000002",
- "UPHENO:0076722",
- "UPHENO:0080555",
- "UPHENO:0003587",
- "UPHENO:0002816",
- "UPHENO:0080556",
- "HP:0000707",
- "HP:0006824",
- "UPHENO:0081581",
- "HP:0033127",
- "UPHENO:0076702",
- "UBERON:0001062",
- "RO:0002577",
+ "HP:0001558",
+ "BFO:0000004",
"UBERON:0000061",
- "UBERON:0015212",
- "UBERON:0010314",
- "UBERON:0005162",
+ "UBERON:0000468",
+ "BFO:0000002",
+ "UPHENO:0002536",
+ "HP:0001557",
+ "UBERON:0000922",
+ "HP:0000118",
+ "HP:0034057",
+ "PATO:0000001",
+ "UBERON:0000323",
+ "HP:0000001",
+ "UPHENO:0075949",
+ "BFO:0000001",
"UBERON:0010000",
- "UBERON:0000475",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "UBERON:0000010",
- "UBERON:0004461",
- "UBERON:0004473",
- ],
- "object_closure_label": [
- "All (HPO)",
- "abnormality of muscle organ physiology",
- "abnormal peripheral nervous system",
- "Abnormal cranial nerve physiology (HPO)",
- "Abnormality of facial soft tissue (HPO)",
- "abnormal head",
+ ],
+ "object_closure_label": [
"Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "abnormal peripheral nervous system morphology",
- "decreased anatomical entity strength",
- "abnormal facial nerve",
- "abnormal musculature",
- "decreased muscle organ strength",
- "Abnormality of the nervous system (HPO)",
- "Cranial nerve paralysis (HPO)",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "Abnormal nervous system morphology (HPO)",
- "abnormal facial muscle",
- "independent continuant",
- "system",
- "lateral structure",
- "structure with developmental contribution from neural crest",
- "multi cell part structure",
- "multicellular anatomical structure",
- "nervous system",
- "cranial nerve",
- "face",
- "craniocervical region musculature",
- "axial musculature",
- "abnormality of anatomical entity physiology",
- "abnormal cranial nerve morphology",
- "Abnormality of peripheral nerves (HPO)",
- "Facial palsy (HPO)",
- "abnormal phenotype by ontology source",
- "Abnormal skeletal muscle morphology (HPO)",
- "continuant",
"specifically dependent continuant",
- "abnormality of nervous system physiology",
- "Abnormality of the head (HPO)",
- "Abnormality of the face (HPO)",
- "Abnormality of the seventh cranial nerve (HPO)",
- "phenotype by ontology source",
- "Abnormality of the peripheral nervous system (HPO)",
- "paralysed cranial nerve",
- "Abnormality of facial musculature (HPO)",
- "abnormal nervous system",
- "abnormal nerve",
+ "abnormal anatomical entity",
"quality",
- "Abnormal nervous system physiology (HPO)",
+ "abnormal phenotype by ontology source",
+ "phenotype by ontology source",
"continuant",
"material anatomical entity",
- "cranial neuron projection bundle",
- "facial nerve",
- "neuron projection bundle",
- "craniocervical region",
- "subdivision of head",
- "body proper",
- "craniocervical muscle",
- "facial muscle",
- "phenotype",
- "abnormal face",
- "abnormal muscle organ morphology",
- "Abnormal muscle physiology (HPO)",
+ "All (HPO)",
+ "continuant",
+ "embryo",
+ "Phenotypic abnormality (HPO)",
+ "abnormal late embryo",
+ "Fetal anomaly (HPO)",
"entity",
- "anatomical entity",
- "anatomical structure",
- "muscle structure",
- "skeletal musculature",
- "mesoderm-derived structure",
- "organism subdivision",
- "organ",
- "muscle organ",
- "gustatory system",
- "cranial muscle",
- "musculature of body",
- "musculature",
- "peripheral nervous system",
- "skeletal musculature of head",
- "musculature of face",
- "abnormal anatomical entity",
- "Abnormality of head or neck (HPO)",
- "abnormal craniocervical region",
- "Abnormal cranial nerve morphology (HPO)",
- "Muscle weakness (HPO)",
- "Weakness of facial musculature (HPO)",
- "Abnormal peripheral nervous system morphology (HPO)",
- "paralysed anatomical entity",
- "Abnormality of the musculature (HPO)",
- "abnormality of anatomical entity physiology",
- "abnormality of cranial nerve physiology",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
"entity",
- "abnormal nervous system morphology",
- "material entity",
- "anatomical system",
+ "Decreased fetal movement (HPO)",
"multicellular organism",
- "organ system subdivision",
- "nerve",
- "anterior region of body",
- "subdivision of organism along main body axis",
- "main body axis",
- "skeletal muscle organ",
- "cranial or facial muscle",
- "nerve of head region",
- "head",
+ "phenotype",
+ "Prenatal movement abnormality (HPO)",
+ "independent continuant",
+ "Abnormality of prenatal development or birth (HPO)",
+ "material entity",
+ "anatomical entity",
+ "anatomical structure",
+ "Abnormal fetal physiology (HPO)",
+ "multicellular anatomical structure",
+ "late embryo",
],
+ "frequency_qualifier_label": "Occasional (HPO)",
+ "frequency_qualifier_category": "biolink:PhenotypicFeature",
+ "frequency_qualifier_namespace": "HP",
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Occasional (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0010628",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001558",
},
{
- "id": "uuid:c9c8bf2d-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:160500",
+ "id": "uuid:4e02df97-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["OMIM:160500"],
+ "publications": ["orphanet:589821"],
+ "frequency_qualifier": "HP:0040283",
"has_evidence": ["ECO:0000304"],
- "subject": "MONDO:0008050",
- "object": "HP:0011916",
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject": "MONDO:0035646",
+ "object": "HP:0001561",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
+ "disease",
+ "hypertrophic cardiomyopathy",
"disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Toe extensor amyotrophy (HPO)",
+ "object_label": "Polyhydramnios (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "HP:0002814",
- "HP:0009127",
- "UPHENO:0076692",
- "UPHENO:0003070",
- "PATO:0000001",
- "BFO:0000004",
- "UBERON:0004708",
- "UBERON:0000154",
- "UBERON:0006058",
- "UBERON:0002529",
- "UBERON:0002387",
- "HP:0000001",
- "UPHENO:0002644",
+ "HP:0001197",
+ "UPHENO:0075852",
+ "UPHENO:0002536",
+ "UBERON:0000465",
+ "BFO:0000001",
+ "BFO:0000040",
+ "BFO:0000002",
"UPHENO:0001001",
"UPHENO:0001002",
- "HP:0000118",
- "BFO:0000020",
"UPHENO:0001003",
- "UPHENO:0076710",
- "HP:0011916",
"BFO:0000001",
- "BFO:0000040",
"UBERON:0001062",
- "UBERON:0010000",
- "UBERON:0000467",
+ "UBERON:0000061",
+ "UBERON:0000463",
+ "UPHENO:0001005",
+ "BFO:0000020",
+ "BFO:0000004",
+ "UBERON:0000173",
"UBERON:0000468",
- "UBERON:0011216",
- "UBERON:0010709",
- "UBERON:0010538",
- "UBERON:0004488",
- "HP:0001436",
- "UPHENO:0002653",
- "HP:0003011",
- "UPHENO:0002536",
- "HP:0001437",
- "HP:0040064",
+ "HP:0001561",
+ "UBERON:0000922",
+ "HP:0000118",
+ "PATO:0000001",
+ "UBERON:0000323",
+ "HP:0000001",
"BFO:0000002",
- "PR:000050567",
- "UBERON:0000465",
- "UBERON:0002101",
- "UBERON:0004709",
- "UBERON:0005090",
- "UBERON:0002103",
- "UBERON:0010707",
- "UBERON:0001630",
- "UBERON:0000026",
- "UBERON:0010758",
- "UBERON:0007271",
- "UBERON:0014792",
- "UBERON:0004482",
- "UBERON:0008784",
- "UBERON:0002470",
- "UPHENO:0001005",
- "HP:0011805",
+ "UPHENO:0075949",
+ "HP:0001560",
+ "UBERON:0010000",
+ ],
+ "object_closure_label": [
+ "Phenotypic abnormality",
+ "Abnormality of the amniotic fluid (HPO)",
+ "quality",
+ "abnormal phenotype by ontology source",
+ "phenotype by ontology source",
+ "continuant",
+ "material anatomical entity",
+ "All (HPO)",
+ "embryo",
+ "Phenotypic abnormality (HPO)",
+ "abnormal late embryo",
+ "entity",
+ "specifically dependent continuant",
+ "anatomical entity",
+ "anatomical structure",
+ "organism substance",
+ "amniotic fluid",
+ "multicellular organism",
+ "phenotype",
+ "continuant",
+ "entity",
+ "independent continuant",
+ "Abnormality of prenatal development or birth (HPO)",
+ "abnormal amniotic fluid",
+ "material entity",
+ "Polyhydramnios (HPO)",
+ "abnormal anatomical entity",
+ "multicellular anatomical structure",
+ "late embryo",
+ ],
+ "frequency_qualifier_label": "Occasional (HPO)",
+ "frequency_qualifier_category": "biolink:PhenotypicFeature",
+ "frequency_qualifier_namespace": "HP",
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Occasional (HPO)"],
+ "evidence_count": 2,
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001561",
+ },
+ {
+ "id": "uuid:4e02df98-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
+ "predicate": "biolink:has_phenotype",
+ "category": "biolink:DiseaseToPhenotypicFeatureAssociation",
+ "aggregator_knowledge_source": ["infores:monarchinitiative"],
+ "primary_knowledge_source": "infores:hpo-annotations",
+ "provided_by": "hpoa_disease_to_phenotype_edges",
+ "publications": ["orphanet:589821"],
+ "frequency_qualifier": "HP:0040283",
+ "has_evidence": ["ECO:0000304"],
+ "subject": "MONDO:0035646",
+ "object": "HP:0001643",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
+ "subject_category": "biolink:Disease",
+ "subject_namespace": "MONDO",
+ "subject_closure": [
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
+ "MONDO:0020121",
+ "BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
+ "BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
+ "MONDO:0020120",
+ "MONDO:0019056",
+ "MONDO:0004994",
+ "MONDO:0004995",
+ "MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
+ "MONDO:0700096",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
+ ],
+ "subject_closure_label": [
+ "eyelids malposition disorder",
+ "disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
+ "muscle tissue disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
+ "hereditary skeletal muscle disorder",
+ "continuant",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
+ "myopathy",
+ "myotonic dystrophy",
+ "nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
+ "realizable entity",
+ "skeletal muscle disorder",
+ "neuromuscular disease",
+ "myotonic syndrome",
+ ],
+ "object_label": "Patent ductus arteriosus (HPO)",
+ "object_category": "biolink:PhenotypicFeature",
+ "object_namespace": "HP",
+ "object_closure": [
+ "HP:0030962",
+ "UPHENO:0019771",
+ "PR:000050567",
+ "UBERON:0000465",
+ "UPHENO:0020542",
+ "UPHENO:0076729",
+ "UPHENO:0080362",
+ "HP:0001627",
+ "UPHENO:0015280",
+ "BFO:0000001",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UBERON:0000468",
+ "UBERON:0011676",
+ "UBERON:0013701",
+ "UPHENO:0020119",
+ "HP:0001626",
+ "UPHENO:0001002",
+ "UPHENO:0033572",
+ "BFO:0000020",
+ "UPHENO:0015324",
+ "UPHENO:0015290",
"BFO:0000002",
- "UPHENO:0002816",
- "UPHENO:0081581",
- "HP:0033127",
- "UPHENO:0002647",
+ "UBERON:0013768",
+ "UBERON:0003509",
+ "UBERON:0003513",
+ "UBERON:0011695",
+ "UBERON:0004716",
+ "UBERON:0004145",
+ "UBERON:0005985",
+ "UBERON:0002049",
+ "UBERON:0002201",
+ "UBERON:0006876",
+ "UPHENO:0001001",
+ "UPHENO:0001003",
+ "UPHENO:0002536",
"BFO:0000001",
- "UPHENO:0002830",
- "RO:0002577",
+ "UBERON:0034923",
+ "UBERON:0015410",
+ "UPHENO:0075696",
+ "HP:0001643",
+ "UPHENO:0076776",
+ "UPHENO:0081581",
+ "UPHENO:0076692",
+ "BFO:0000004",
+ "UBERON:0001981",
+ "UBERON:0004537",
+ "UBERON:0004572",
+ "UBERON:0004535",
"UBERON:0000061",
- "UBERON:0015212",
+ "UBERON:0000477",
"UBERON:0000475",
"UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "UBERON:0000978",
- "UBERON:0007270",
- "UBERON:0004480",
+ "UBERON:0004111",
+ "UBERON:0004573",
+ "UBERON:0003498",
+ "HP:0011603",
+ "UPHENO:0020351",
+ "HP:0030680",
+ "UPHENO:0076765",
+ "BFO:0000002",
+ "HP:0025015",
+ "HP:0002597",
+ "UPHENO:0076810",
+ "HP:0033353",
+ "PATO:0000001",
+ "UBERON:0001637",
+ "UBERON:0003834",
+ "UBERON:0000948",
+ "UBERON:0009569",
+ "UBERON:0013702",
+ "UBERON:0005177",
+ "UBERON:0003103",
+ "UBERON:0000055",
+ "UBERON:0005440",
+ "UBERON:0000915",
+ "UBERON:0002100",
+ "UBERON:0005181",
+ "UBERON:0002075",
+ "UBERON:0015228",
+ "HP:0000118",
+ "UPHENO:0075655",
+ "UPHENO:0020584",
+ "UPHENO:0020587",
+ "UBERON:0010314",
+ "UBERON:0018674",
+ "HP:0000001",
+ "UPHENO:0002678",
+ "UPHENO:0001005",
+ "UPHENO:0033603",
+ "UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0004120",
+ "UBERON:0007798",
+ "UBERON:0001009",
+ "UBERON:0004571",
+ "UBERON:0005178",
+ "UBERON:0007100",
],
"object_closure_label": [
- "All (HPO)",
- "abnormal musculature of lower limb",
- "Abnormality of the lower limb (HPO)",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "abnormal musculature",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "abnormal musculature of limb",
- "entity",
- "independent continuant",
- "system",
- "paired limb/fin",
- "lateral structure",
- "pelvic complex",
- "appendage musculature",
- "musculature of pelvic complex",
- "musculature of pes",
- "phenotype",
- "Abnormality of the foot musculature (HPO)",
- "abnormal phenotype by ontology source",
- "Abnormal skeletal muscle morphology (HPO)",
- "continuant",
+ "abnormal blood vessel morphology",
+ "abnormal anatomical entity",
"specifically dependent continuant",
"phenotype by ontology source",
- "Abnormality of the musculature of the lower limbs (HPO)",
- "Abnormality of limbs (HPO)",
- "quality",
+ "abnormal anatomical entity",
"continuant",
"protein-containing material entity",
"material anatomical entity",
- "hindlimb",
- "appendage girdle complex",
- "appendage",
- "subdivision of organism along appendicular axis",
- "paired limb/fin segment",
- "musculature of lower limb",
- "lower limb segment",
- "autopod region",
- "Abnormality of the musculature of the limbs (HPO)",
- "abnormal muscle organ morphology",
- "Toe extensor amyotrophy (HPO)",
+ "vascular system",
+ "circulatory system",
+ "vasculature of trunk",
+ "vasculature of organ",
+ "ductus arteriosus",
+ "thoracic segment of trunk",
+ "trunk",
+ "thoracic segment organ",
+ "viscus",
+ "circulatory organ",
+ "All (HPO)",
+ "abnormal vasculature",
+ "abnormal phenotype by ontology source",
+ "continuant",
+ "abnormal artery morphology in the independent continuant",
+ "multicellular organism",
+ "outflow tract",
+ "coronary vessel",
+ "vasculature",
+ "subdivision of trunk",
+ "body proper",
+ "trunk region element",
+ "compound organ",
+ "vessel",
+ "Abnormality of cardiovascular system morphology (HPO)",
+ "abnormal great vessel of heart morphology",
+ "Phenotypic abnormality (HPO)",
+ "abnormal opening of the anatomical entity",
+ "abnormal anatomical entity morphology",
+ "abnormal systemic artery morphology",
"entity",
- "anatomical structure",
- "muscle structure",
+ "structure with developmental contribution from neural crest",
+ "thoracic cavity element",
+ "primary circulatory organ",
+ "abnormal coronary vessel morphology",
+ "Abnormality of the cardiovascular system (HPO)",
+ "Phenotypic abnormality",
+ "abnormal incomplete closing of the anatomical entity",
+ "Patent ductus arteriosus (HPO)",
+ "abnormal cardiovascular system morphology",
+ "abnormal anatomical entity morphology",
+ "quality",
+ "disconnected anatomical group",
+ "anatomical cluster",
"organism subdivision",
"organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "leg",
- "pelvic appendage musculature",
- "musculature of limb",
- "abnormal musculature of pes",
- "Abnormality of the musculature (HPO)",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "abnormal leg",
- "abnormal limb",
+ "anatomical conduit",
+ "systemic artery",
+ "heart blood vessel",
+ "heart plus pericardium",
+ "phenotype",
+ "abnormal incomplete closing of the ductus arteriosus",
+ "abnormal anatomical entity morphology in the independent continuant",
+ "Abnormal vascular morphology (HPO)",
+ "entity",
+ "independent continuant",
+ "subdivision of organism along main body axis",
+ "main body axis",
+ "abnormal anatomical entity morphology in the heart",
+ "abnormal multicellular organism morphology",
"material entity",
"anatomical entity",
- "limb",
- "pelvic appendage",
+ "blood vessel",
+ "arterial system",
+ "blood vasculature",
+ "cardiovascular system",
+ "anatomical structure",
+ "great vessel of heart",
+ "arterial blood vessel",
+ "trunk blood vessel",
+ "embryonic cardiovascular system",
+ "conceptus",
+ "systemic arterial system",
+ "Congenital malformation of the great arteries (HPO)",
+ "abnormal ductus arteriosus morphology",
+ "abnormal vascular system morphology",
+ "abnormal cardiovascular system",
+ "Abnormal heart morphology (HPO)",
+ "Abnormal morphology of the great vessels (HPO)",
+ "abnormal artery morphology",
+ "Abnormality of the vasculature (HPO)",
+ "abnormal heart morphology",
+ "Abnormal blood vessel morphology (HPO)",
"multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "posterior region of body",
- "multi-limb segment region",
- "limb segment",
- "pes",
+ "mesoderm-derived structure",
+ "artery",
+ "thoracic segment blood vessel",
+ "heart",
+ "heart vasculature",
],
+ "frequency_qualifier_label": "Occasional (HPO)",
+ "frequency_qualifier_category": "biolink:PhenotypicFeature",
+ "frequency_qualifier_namespace": "HP",
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Occasional (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0011916",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001643",
},
{
- "id": "uuid:c9c8bf2e-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:160500",
+ "id": "uuid:4e02df99-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["OMIM:160500"],
+ "publications": ["orphanet:589821"],
+ "frequency_qualifier": "HP:0040283",
"has_evidence": ["ECO:0000304"],
- "subject": "MONDO:0008050",
- "object": "HP:0002460",
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject": "MONDO:0035646",
+ "object": "HP:0001671",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Distal muscle weakness (HPO)",
+ "object_label": "Abnormal cardiac septum morphology (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "UPHENO:0082875",
- "UPHENO:0002320",
- "UPHENO:0001005",
+ "PR:000050567",
+ "UBERON:0000465",
+ "UPHENO:0019888",
+ "UPHENO:0080362",
+ "HP:0001627",
+ "UPHENO:0015280",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UBERON:0000468",
+ "UBERON:0011676",
+ "UBERON:0013701",
+ "HP:0001626",
+ "UPHENO:0001002",
"BFO:0000020",
+ "UPHENO:0015324",
+ "HP:0001671",
+ "BFO:0000002",
+ "UPHENO:0001001",
+ "UPHENO:0001003",
+ "BFO:0000001",
+ "UBERON:0015410",
+ "UPHENO:0076776",
+ "UPHENO:0081581",
+ "UPHENO:0076692",
+ "BFO:0000004",
+ "UBERON:0004535",
+ "UBERON:0000061",
+ "UBERON:0000475",
+ "UBERON:0000062",
+ "UPHENO:0075696",
+ "HP:0030680",
+ "BFO:0000002",
+ "UPHENO:0002536",
+ "UPHENO:0076810",
+ "UBERON:0002099",
+ "UBERON:0000948",
+ "UBERON:0009569",
+ "UBERON:0013702",
+ "UBERON:0005177",
+ "UBERON:0003103",
+ "UBERON:0000915",
+ "UBERON:0002100",
+ "UBERON:0005181",
+ "UBERON:0002075",
+ "UBERON:0015228",
+ "HP:0000118",
+ "UPHENO:0020584",
"PATO:0000001",
- "BFO:0000004",
- "UBERON:0000061",
+ "UBERON:0003037",
+ "UBERON:0010314",
"HP:0000001",
- "UPHENO:0001001",
- "HP:0000118",
- "BFO:0000001",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
- "UPHENO:0075696",
- "HP:0001324",
- "HP:0003011",
- "UPHENO:0002332",
- "UPHENO:0001003",
- "UPHENO:0002536",
- "HP:0002460",
- "HP:0011804",
- "BFO:0000002",
- "BFO:0000040",
- "UBERON:0005090",
- "UBERON:0001630",
- "UPHENO:0001002",
- "BFO:0000002",
- "UPHENO:0080555",
- "UPHENO:0002816",
- "UPHENO:0080556",
- "HP:0033127",
+ "UPHENO:0001005",
"BFO:0000001",
- "UBERON:0001062",
- "UBERON:0000465",
"UBERON:0010000",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
+ "UBERON:0000467",
+ "UBERON:0004120",
+ "UBERON:0001009",
+ "UBERON:0005178",
+ "UBERON:0007100",
],
"object_closure_label": [
+ "abnormal anatomical entity",
+ "quality",
+ "specifically dependent continuant",
+ "phenotype by ontology source",
+ "continuant",
+ "protein-containing material entity",
+ "material anatomical entity",
+ "circulatory system",
+ "thoracic segment of trunk",
+ "trunk",
+ "thoracic segment organ",
+ "viscus",
+ "circulatory organ",
"All (HPO)",
- "abnormality of muscle organ physiology",
+ "abnormal phenotype by ontology source",
+ "continuant",
+ "Abnormal cardiac septum morphology (HPO)",
+ "multicellular organism",
+ "subdivision of trunk",
+ "body proper",
+ "trunk region element",
+ "compound organ",
+ "Abnormality of cardiovascular system morphology (HPO)",
"Phenotypic abnormality (HPO)",
- "decreased anatomical entity strength",
- "abnormal musculature",
- "decreased muscle organ strength",
- "Abnormality of the musculoskeletal system (HPO)",
+ "abnormal anatomical entity morphology",
"entity",
- "independent continuant",
- "material anatomical entity",
- "anatomical structure",
- "multicellular anatomical structure",
- "abnormality of anatomical entity physiology",
- "phenotype",
+ "entity",
+ "septum",
+ "structure with developmental contribution from neural crest",
+ "thoracic cavity element",
+ "primary circulatory organ",
+ "Abnormality of the cardiovascular system (HPO)",
"Phenotypic abnormality",
- "continuant",
- "Distal muscle weakness (HPO)",
- "quality",
- "continuant",
+ "abnormal cardiovascular system morphology",
+ "abnormal anatomical entity morphology",
+ "organism subdivision",
+ "organ",
+ "heart plus pericardium",
+ "phenotype",
+ "abnormal anatomical entity morphology in the independent continuant",
+ "independent continuant",
+ "subdivision of organism along main body axis",
+ "main body axis",
+ "abnormal anatomical entity morphology in the heart",
+ "abnormal multicellular organism morphology",
"material entity",
- "abnormal phenotype by ontology source",
- "specifically dependent continuant",
- "Abnormal muscle physiology (HPO)",
- "entity",
"anatomical entity",
- "muscle structure",
- "organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "abnormal anatomical entity",
- "Muscle weakness (HPO)",
- "Abnormality of the musculature (HPO)",
- "abnormality of anatomical entity physiology",
- "phenotype by ontology source",
+ "cardiovascular system",
+ "anatomical structure",
"abnormal anatomical entity",
+ "abnormal cardiac septum morphology",
+ "abnormal cardiovascular system",
+ "Abnormal heart morphology (HPO)",
+ "abnormal heart morphology",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
+ "mesoderm-derived structure",
+ "cardiac septum",
+ "heart",
],
+ "frequency_qualifier_label": "Occasional (HPO)",
+ "frequency_qualifier_category": "biolink:PhenotypicFeature",
+ "frequency_qualifier_namespace": "HP",
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Occasional (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0002460",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001671",
},
{
- "id": "uuid:c9c8bf32-7529-11ee-b012-cbd37f5c3759",
- "original_subject": "OMIM:160500",
+ "id": "uuid:4e02df9a-842a-11ee-884f-6be035239f90",
+ "original_subject": "Orphanet:589821",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"primary_knowledge_source": "infores:hpo-annotations",
"provided_by": "hpoa_disease_to_phenotype_edges",
- "publications": ["OMIM:160500"],
- "has_evidence": ["ECO:0000501"],
- "subject": "MONDO:0008050",
- "object": "HP:0003805",
- "subject_label": "MYH7-related skeletal myopathy",
+ "publications": ["orphanet:589821"],
+ "frequency_qualifier": "HP:0040283",
+ "has_evidence": ["ECO:0000304"],
+ "subject": "MONDO:0035646",
+ "object": "HP:0002014",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
+ "disease",
+ "hypertrophic cardiomyopathy",
"disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
+ "myotonic syndrome",
],
- "object_label": "Rimmed vacuoles (HPO)",
+ "object_label": "Diarrhea (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "BFO:0000002",
- "BFO:0000020",
- "UPHENO:0076692",
+ "UPHENO:0002443",
+ "UPHENO:0002536",
+ "UBERON:0000465",
+ "UPHENO:0082875",
+ "HP:0002664",
"BFO:0000001",
- "BFO:0000004",
- "CL:0000255",
- "UBERON:0014892",
- "UBERON:0002036",
- "HP:0000001",
- "HP:0004303",
- "UPHENO:0001001",
+ "BFO:0000040",
+ "UBERON:0001062",
"UPHENO:0001002",
- "HP:0000118",
+ "BFO:0000020",
+ "HP:0011793",
+ "HP:0011458",
+ "BFO:0000002",
+ "UBERON:0001988",
+ "UPHENO:0001001",
+ "UPHENO:0002833",
"UPHENO:0001003",
- "UPHENO:0076710",
- "PATO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0000467",
- "CL:0000000",
+ "UBERON:0000463",
+ "UPHENO:0075696",
+ "HP:0002014",
+ "HP:0025031",
+ "BFO:0000004",
+ "UBERON:0000061",
+ "UBERON:0000174",
"UBERON:0000468",
- "UBERON:0011216",
- "CL:0000548",
- "UBERON:0001134",
- "HP:0003011",
- "UPHENO:0002536",
- "HP:0003805",
- "UBERON:0005090",
- "UBERON:0018254",
- "UBERON:0004120",
- "UBERON:0000479",
- "CL:0000003",
- "UBERON:0001630",
- "UBERON:0002385",
- "CL:0000188",
- "UPHENO:0001005",
- "HP:0011805",
- "HP:0025354",
- "UPHENO:0002816",
- "UPHENO:0081581",
- "HP:0033127",
"BFO:0000002",
- "UBERON:0001062",
- "UBERON:0000465",
- "RO:0002577",
- "UBERON:0000061",
+ "HP:0025032",
+ "PATO:0000001",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "HP:0000001",
+ "UPHENO:0001005",
+ "BFO:0000001",
"UBERON:0010000",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "CL:0002371",
+ "UBERON:0000467",
+ "UBERON:0001007",
],
"object_closure_label": [
+ "abnormality of anatomical entity physiology",
+ "abnormal digestive system",
+ "entity",
+ "abnormal anatomical entity",
+ "Diarrhea (HPO)",
+ "specifically dependent continuant",
+ "Abnormality of digestive system physiology (HPO)",
+ "phenotype by ontology source",
+ "continuant",
+ "material anatomical entity",
+ "digestive system",
"All (HPO)",
- "Abnormal muscle fiber morphology (HPO)",
- "Phenotypic abnormality",
+ "abnormal phenotype by ontology source",
+ "continuant",
+ "feces",
"Phenotypic abnormality (HPO)",
- "Abnormal cellular phenotype (HPO)",
- "abnormal musculature",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
+ "Phenotypic abnormality",
+ "Neoplasm by anatomical site (HPO)",
+ "Abdominal symptom (HPO)",
"quality",
- "independent continuant",
- "material anatomical entity",
- "system",
- "multicellular anatomical structure",
+ "organism substance",
+ "excreta",
+ "multicellular organism",
"phenotype",
- "abnormal phenotype by ontology source",
- "Abnormal skeletal muscle morphology (HPO)",
- "phenotype by ontology source",
- "tissue",
- "animal cell",
- "skeletal muscle tissue",
- "cell of skeletal muscle",
- "continuant",
- "specifically dependent continuant",
- "abnormal muscle organ morphology",
- "Rimmed vacuoles (HPO)",
+ "Neoplasm (HPO)",
"entity",
+ "independent continuant",
+ "abnormality of digestive system physiology",
+ "Abnormality of the digestive system (HPO)",
+ "material entity",
"anatomical entity",
"anatomical structure",
- "muscle structure",
- "skeletal musculature",
- "mesoderm-derived structure",
- "organ",
- "native cell",
- "muscle organ",
- "muscle tissue",
- "musculature of body",
- "musculature",
- "somatic cell",
- "Abnormality of the musculature (HPO)",
+ "abnormality of anatomical entity physiology",
"abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "entity",
- "continuant",
- "material entity",
+ "multicellular anatomical structure",
"anatomical system",
- "cell",
- "multicellular organism",
- "organ system subdivision",
- "eukaryotic cell",
- "skeletal muscle organ",
- "striated muscle tissue",
],
+ "frequency_qualifier_label": "Occasional (HPO)",
+ "frequency_qualifier_category": "biolink:PhenotypicFeature",
+ "frequency_qualifier_namespace": "HP",
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Occasional (HPO)"],
"evidence_count": 2,
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0003805",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0002014",
},
],
},
diff --git a/backend/tests/fixtures/association_table.py b/backend/tests/fixtures/association_table.py
index 327680630..6352d96ee 100644
--- a/backend/tests/fixtures/association_table.py
+++ b/backend/tests/fixtures/association_table.py
@@ -9,70 +9,70 @@ def association_table():
"total": 4027,
"items": [
{
- "id": "uuid:ca3946de-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4677e7a0-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"subject": "MONDO:0020793",
"original_subject": "OMIM:164310",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "BFO:0000020",
- "MONDO:0024458",
- "MONDO:0005336",
"MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0003382",
- "BFO:0000016",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0025193",
"MONDO:0020121",
"MONDO:0020793",
+ "MONDO:0003847",
+ "BFO:0000001",
+ "BFO:0000020",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
"BFO:0000017",
+ "MONDO:0003939",
+ "MONDO:0002022",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "BFO:0000002",
+ "MONDO:0005071",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000462",
- "MONDO:0020158",
- "MONDO:0000001",
"MONDO:0700223",
- "MONDO:0016106",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002022",
- "MONDO:0005328",
+ "MONDO:0024458",
+ "OGMS:0000031",
],
"subject_label": "oculopharyngodistal myopathy 1",
"subject_closure_label": [
- "oculopharyngodistal myopathy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
+ "disease",
+ "realizable entity",
"disease",
+ "specifically dependent continuant",
"muscle tissue disorder",
"disorder of orbital region",
"hereditary skeletal muscle disorder",
+ "continuant",
+ "eye adnexa disorder",
"eyelid disorder",
"disposition",
- "distal myopathy",
- "eyelids malposition disorder",
- "disease",
- "continuant",
- "specifically dependent continuant",
+ "human disease",
"disorder of visual system",
"myopathy",
- "hereditary disease",
- "eye adnexa disorder",
+ "distal myopathy",
"nervous system disorder",
+ "entity",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "oculopharyngodistal myopathy",
+ "muscular dystrophy",
"oculopharyngodistal myopathy 1",
- "realizable entity",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
- "eye disorder",
],
"subject_taxon": None,
"subject_taxon_label": None,
@@ -82,87 +82,87 @@ def association_table():
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
+ "UPHENO:0002816",
+ "BFO:0000001",
+ "UBERON:0000465",
"UPHENO:0082875",
- "UPHENO:0002320",
- "UPHENO:0001005",
+ "BFO:0000040",
+ "UBERON:0011216",
+ "HP:0001324",
+ "UPHENO:0080555",
+ "HP:0011804",
+ "BFO:0000002",
+ "UPHENO:0001001",
+ "UPHENO:0001002",
"BFO:0000020",
- "PATO:0000001",
+ "UPHENO:0001003",
+ "UPHENO:0002536",
+ "BFO:0000001",
+ "UBERON:0001062",
+ "UPHENO:0001005",
+ "HP:0033127",
"BFO:0000004",
"UBERON:0000061",
- "HP:0000001",
- "UPHENO:0001001",
- "HP:0000118",
- "BFO:0000001",
- "UBERON:0000467",
+ "UBERON:0000062",
"UBERON:0000468",
- "UBERON:0011216",
"UPHENO:0075696",
- "HP:0001324",
"HP:0003011",
+ "UPHENO:0002320",
+ "HP:0000118",
+ "BFO:0000002",
"UPHENO:0002332",
- "UPHENO:0001003",
- "UPHENO:0002536",
"HP:0002460",
- "HP:0011804",
- "BFO:0000002",
- "BFO:0000040",
+ "PATO:0000001",
+ "UBERON:0010000",
+ "HP:0000001",
+ "UPHENO:0080556",
+ "UBERON:0000467",
"UBERON:0005090",
"UBERON:0001630",
- "UPHENO:0001002",
- "BFO:0000002",
- "UPHENO:0080555",
- "UPHENO:0002816",
- "UPHENO:0080556",
- "HP:0033127",
- "BFO:0000001",
- "UBERON:0001062",
- "UBERON:0000465",
- "UBERON:0010000",
- "UBERON:0000062",
"UBERON:0000383",
"UBERON:0001015",
],
"object_label": "Distal muscle weakness (HPO)",
"object_closure_label": [
- "All (HPO)",
- "abnormality of muscle organ physiology",
- "Phenotypic abnormality (HPO)",
- "decreased anatomical entity strength",
- "abnormal musculature",
- "decreased muscle organ strength",
- "Abnormality of the musculoskeletal system (HPO)",
- "entity",
- "independent continuant",
- "material anatomical entity",
- "anatomical structure",
- "multicellular anatomical structure",
"abnormality of anatomical entity physiology",
- "phenotype",
"Phenotypic abnormality",
- "continuant",
- "Distal muscle weakness (HPO)",
+ "specifically dependent continuant",
"quality",
- "continuant",
- "material entity",
"abnormal phenotype by ontology source",
- "specifically dependent continuant",
+ "Abnormality of the musculature (HPO)",
+ "phenotype by ontology source",
+ "abnormal anatomical entity",
+ "continuant",
+ "material anatomical entity",
+ "muscle organ",
+ "All (HPO)",
+ "abnormal musculature",
"Abnormal muscle physiology (HPO)",
+ "organ system subdivision",
+ "abnormality of muscle organ physiology",
+ "Phenotypic abnormality (HPO)",
+ "continuant",
+ "decreased muscle organ strength",
+ "Distal muscle weakness (HPO)",
"entity",
+ "multicellular anatomical structure",
+ "Muscle weakness (HPO)",
"anatomical entity",
- "muscle structure",
"organ",
- "muscle organ",
+ "multicellular organism",
+ "phenotype",
+ "independent continuant",
+ "decreased anatomical entity strength",
+ "Abnormality of the musculoskeletal system (HPO)",
+ "entity",
+ "material entity",
+ "anatomical structure",
"musculature of body",
"musculature",
"abnormal anatomical entity",
- "Muscle weakness (HPO)",
- "Abnormality of the musculature (HPO)",
"abnormality of anatomical entity physiology",
- "phenotype by ontology source",
- "abnormal anatomical entity",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
+ "muscle structure",
],
"object_taxon": None,
"object_taxon_label": None,
@@ -198,8 +198,8 @@ def association_table():
"frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Frequent (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"],
"onset_qualifier_label": None,
"onset_qualifier_namespace": None,
"onset_qualifier_category": None,
@@ -218,70 +218,70 @@ def association_table():
"direction": "outgoing",
},
{
- "id": "uuid:ca3946ef-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4677e7b1-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"subject": "MONDO:0020793",
"original_subject": "OMIM:164310",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "BFO:0000020",
- "MONDO:0024458",
- "MONDO:0005336",
"MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0003382",
- "BFO:0000016",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0025193",
"MONDO:0020121",
"MONDO:0020793",
+ "MONDO:0003847",
+ "BFO:0000001",
+ "BFO:0000020",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
"BFO:0000017",
+ "MONDO:0003939",
+ "MONDO:0002022",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "BFO:0000002",
+ "MONDO:0005071",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000462",
- "MONDO:0020158",
- "MONDO:0000001",
"MONDO:0700223",
- "MONDO:0016106",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002022",
- "MONDO:0005328",
+ "MONDO:0024458",
+ "OGMS:0000031",
],
"subject_label": "oculopharyngodistal myopathy 1",
"subject_closure_label": [
- "oculopharyngodistal myopathy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
+ "realizable entity",
+ "disease",
+ "specifically dependent continuant",
"muscle tissue disorder",
"disorder of orbital region",
"hereditary skeletal muscle disorder",
+ "continuant",
+ "eye adnexa disorder",
"eyelid disorder",
"disposition",
- "distal myopathy",
- "eyelids malposition disorder",
- "disease",
- "continuant",
- "specifically dependent continuant",
+ "human disease",
"disorder of visual system",
"myopathy",
- "hereditary disease",
- "eye adnexa disorder",
+ "distal myopathy",
"nervous system disorder",
+ "entity",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "oculopharyngodistal myopathy",
+ "muscular dystrophy",
"oculopharyngodistal myopathy 1",
- "realizable entity",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
- "eye disorder",
],
"subject_taxon": None,
"subject_taxon_label": None,
@@ -291,141 +291,141 @@ def association_table():
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "UPHENO:0082875",
+ "UPHENO:0002443",
"UPHENO:0002471",
"HP:0025270",
- "UPHENO:0001005",
- "BFO:0000002",
- "BFO:0000020",
+ "UPHENO:0002536",
+ "UBERON:0000465",
+ "RO:0002577",
+ "UPHENO:0082875",
"HP:0002664",
+ "UPHENO:0004523",
+ "BFO:0000001",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UBERON:0011676",
+ "UBERON:0013701",
+ "BFO:0000020",
"HP:0011793",
- "PATO:0000001",
- "UPHENO:0002474",
- "HP:0012638",
- "BFO:0000004",
- "UBERON:0000061",
- "UBERON:0001007",
- "UBERON:0001016",
- "UBERON:0011676",
- "UBERON:0013701",
- "UBERON:0000915",
- "UBERON:0001043",
- "UBERON:0002100",
- "UBERON:0005181",
- "UBERON:0002075",
- "HP:0000001",
+ "BFO:0000002",
+ "UBERON:0005409",
"UPHENO:0001001",
- "HP:0000118",
- "UPHENO:0002433",
+ "UPHENO:0002833",
+ "HP:0002015",
+ "UPHENO:0001002",
"UPHENO:0001003",
- "BFO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0010000",
- "UBERON:0000467",
+ "UPHENO:0075696",
+ "UPHENO:0002433",
+ "HP:0025031",
+ "UPHENO:0002474",
+ "HP:0012638",
+ "BFO:0000004",
+ "UBERON:0000061",
+ "UBERON:0000475",
+ "UBERON:0000062",
"UBERON:0004111",
"UBERON:0000468",
- "UBERON:0000064",
- "UPHENO:0075696",
"HP:0011024",
- "UPHENO:0002443",
- "HP:0012719",
"UPHENO:0002725",
- "HP:0025032",
- "UPHENO:0002332",
- "UPHENO:0002536",
- "UPHENO:0004523",
"BFO:0000002",
- "UBERON:0000465",
- "UBERON:0005409",
+ "HP:0025032",
"UBERON:0009569",
"UBERON:0013702",
"UBERON:0013765",
"UBERON:0005177",
"UBERON:0000025",
+ "UBERON:0000915",
+ "UBERON:0001043",
+ "UBERON:0002100",
+ "UBERON:0005181",
+ "UBERON:0002075",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "PATO:0000001",
"UBERON:0001555",
"UBERON:0004921",
- "UPHENO:0002833",
- "HP:0002015",
- "UPHENO:0001002",
+ "HP:0000001",
+ "HP:0012719",
+ "UPHENO:0001005",
"HP:0000707",
- "HP:0025031",
- "UBERON:0001062",
- "RO:0002577",
- "UBERON:0000475",
- "UBERON:0000062",
+ "BFO:0000001",
+ "UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0000064",
+ "UBERON:0001007",
+ "UBERON:0001016",
"UBERON:0013522",
"UBERON:0005178",
"UBERON:0004908",
],
"object_label": "Dysphagia (HPO)",
"object_closure_label": [
- "All (HPO)",
- "abnormality of alimentary part of gastrointestinal system physiology",
- "Abnormal esophagus physiology (HPO)",
- "Functional abnormality of the gastrointestinal tract (HPO)",
- "Phenotypic abnormality (HPO)",
- "Abnormality of the nervous system (HPO)",
- "independent continuant",
- "system",
- "anatomical structure",
- "digestive system",
- "nervous system",
- "digestive tract",
- "subdivision of digestive tract",
"abnormality of anatomical entity physiology",
- "phenotype",
- "abnormality of digestive system physiology",
"abnormal digestive system",
"Dysphagia (HPO)",
"Phenotypic abnormality",
- "abnormality of nervous system physiology",
+ "quality",
+ "abnormal anatomical entity",
+ "specifically dependent continuant",
+ "Abnormality of digestive system physiology (HPO)",
"phenotype by ontology source",
"abnormal nervous system",
- "quality",
- "abnormality of esophagus physiology",
- "Abnormal nervous system physiology (HPO)",
"continuant",
"material anatomical entity",
+ "system",
+ "organ part",
+ "digestive system",
+ "nervous system",
+ "thoracic segment of trunk",
+ "esophagus",
+ "trunk",
+ "thoracic segment organ",
+ "viscus",
+ "All (HPO)",
+ "Functional abnormality of the gastrointestinal tract (HPO)",
+ "abnormal phenotype by ontology source",
+ "continuant",
+ "alimentary part of gastrointestinal system",
"subdivision of trunk",
"body proper",
"digestive system element",
"trunk region element",
"tube",
- "abnormal phenotype by ontology source",
- "continuant",
- "specifically dependent continuant",
- "Neoplasm (HPO)",
- "Neoplasm by anatomical site (HPO)",
+ "abnormal alimentary part of gastrointestinal system",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the nervous system (HPO)",
"entity",
- "anatomical entity",
+ "thoracic cavity element",
+ "upper digestive tract",
+ "abnormality of nervous system physiology",
+ "Neoplasm by anatomical site (HPO)",
"organism subdivision",
"organ",
- "alimentary part of gastrointestinal system",
+ "anatomical conduit",
+ "multicellular organism",
+ "phenotype",
+ "Neoplasm (HPO)",
+ "entity",
+ "independent continuant",
+ "subdivision of organism along main body axis",
+ "main body axis",
+ "abnormality of digestive system physiology",
+ "abnormality of alimentary part of gastrointestinal system physiology",
+ "Abnormal esophagus physiology (HPO)",
+ "Abnormality of the digestive system (HPO)",
+ "abnormality of esophagus physiology",
+ "Abnormal nervous system physiology (HPO)",
+ "material entity",
+ "anatomical entity",
+ "anatomical structure",
"subdivision of tube",
- "thoracic cavity element",
- "upper digestive tract",
- "abnormal anatomical entity",
"Abnormality of the gastrointestinal tract (HPO)",
- "abnormal alimentary part of gastrointestinal system",
- "Abnormality of digestive system physiology (HPO)",
"abnormality of anatomical entity physiology",
"abnormal anatomical entity",
- "entity",
- "Abnormality of the digestive system (HPO)",
- "material entity",
"multicellular anatomical structure",
"anatomical system",
- "anatomical conduit",
- "multicellular organism",
- "organ part",
- "subdivision of organism along main body axis",
- "main body axis",
- "thoracic segment of trunk",
- "esophagus",
- "trunk",
- "thoracic segment organ",
- "viscus",
+ "digestive tract",
+ "subdivision of digestive tract",
],
"object_taxon": None,
"object_taxon_label": None,
@@ -461,8 +461,8 @@ def association_table():
"frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Frequent (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"],
"onset_qualifier_label": None,
"onset_qualifier_namespace": None,
"onset_qualifier_category": None,
@@ -481,84 +481,84 @@ def association_table():
"direction": "outgoing",
},
{
- "id": "uuid:c6b3613a-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:42ef70e0-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"subject": "MONDO:0013049",
"original_subject": "OMIM:612937",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "BFO:0000020",
- "MONDO:0005336",
- "MONDO:0005021",
- "MONDO:0004994",
- "MONDO:0018276",
- "MONDO:0005071",
- "MONDO:0005267",
- "BFO:0000016",
"MONDO:0016333",
- "MONDO:0017749",
- "OGMS:0000031",
+ "MONDO:0002320",
+ "MONDO:0000001",
+ "MONDO:0013049",
+ "MONDO:0020121",
"MONDO:0003847",
"BFO:0000001",
- "MONDO:0020121",
- "MONDO:0004995",
+ "MONDO:0018276",
+ "BFO:0000020",
+ "MONDO:0005336",
+ "MONDO:0019052",
+ "MONDO:0005500",
+ "MONDO:0005066",
+ "MONDO:0024322",
"BFO:0000017",
+ "MONDO:0003939",
+ "MONDO:0002081",
+ "MONDO:0005021",
+ "MONDO:0019950",
+ "BFO:0000002",
"MONDO:0005217",
+ "MONDO:0015286",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0015286",
- "MONDO:0019052",
- "MONDO:0005500",
- "MONDO:0005066",
- "MONDO:0000001",
- "MONDO:0013049",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
- "MONDO:0024322",
+ "BFO:0000016",
"MONDO:0700096",
"MONDO:0000591",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
- "MONDO:0019950",
+ "MONDO:0017749",
+ "OGMS:0000031",
],
"subject_label": "DPM3-congenital disorder of glycosylation",
"subject_closure_label": [
- "cardiomyopathy",
- "muscular dystrophy",
- "cardiovascular disorder",
- "human disease",
- "intrinsic cardiomyopathy",
- "musculoskeletal system disorder",
+ "disease",
+ "disorder of glycosylation",
+ "realizable entity",
"disorder of multiple glycosylation",
"disease",
+ "specifically dependent continuant",
+ "familial cardiomyopathy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "disorder of glycosylation",
- "disposition",
- "congenital disorder of glycosylation",
- "disease",
- "DPM3-congenital disorder of glycosylation",
"continuant",
- "specifically dependent continuant",
- "myopathy",
- "familial dilated cardiomyopathy",
- "hereditary disease",
"inborn errors of metabolism",
"congenital disorder of glycosylation type I",
"metabolic disease",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
"muscular dystrophy-dystroglycanopathy",
+ "myopathy",
+ "dilated cardiomyopathy",
"nervous system disorder",
"heart disorder",
- "realizable entity",
- "familial cardiomyopathy",
- "skeletal muscle disorder",
- "neuromuscular disease",
- "dilated cardiomyopathy",
"entity",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "congenital nervous system disorder",
"congenital muscular dystrophy",
+ "DPM3-congenital disorder of glycosylation",
+ "muscular dystrophy",
+ "skeletal muscle disorder",
+ "neuromuscular disease",
+ "familial dilated cardiomyopathy",
+ "congenital disorder of glycosylation",
],
"subject_taxon": None,
"subject_taxon_label": None,
@@ -568,40 +568,70 @@ def association_table():
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "UPHENO:0082875",
- "UPHENO:0051763",
- "UPHENO:0001005",
- "BFO:0000020",
- "UPHENO:0077820",
- "BFO:0000001",
- "UPHENO:0051804",
- "BFO:0000015",
- "BFO:0000004",
- "GO:0032991",
- "CHEBI:23367",
- "UBERON:0000178",
+ "UPHENO:0046284",
+ "UPHENO:0077829",
+ "GO:0005575",
+ "CHEBI:24431",
+ "PR:000050567",
+ "UBERON:0000465",
+ "CHEBI:16541",
+ "CHEBI:35352",
+ "CHEBI:32988",
+ "CHEBI:36963",
+ "CHEBI:33285",
+ "HP:0004364",
+ "UPHENO:0082875",
+ "UPHENO:0004536",
+ "UPHENO:0051668",
+ "HP:0001871",
+ "UPHENO:0077821",
+ "BFO:0000001",
+ "GO:0008150",
+ "BFO:0000040",
+ "UBERON:0000468",
+ "UPHENO:0001002",
+ "BFO:0000020",
+ "UPHENO:0077820",
+ "HP:0002086",
+ "HP:0003236",
+ "BFO:0000003",
+ "BFO:0000002",
+ "GO:1902494",
+ "CHEBI:36357",
+ "CHEBI:33579",
"GO:1990234",
"CHEBI:33839",
"CHEBI:33675",
- "UBERON:0001004",
- "HP:0000001",
- "HP:0011021",
+ "UBERON:0002193",
+ "UBERON:0002390",
+ "UBERON:0000179",
"UPHENO:0001001",
- "UPHENO:0001002",
- "UPHENO:0077825",
- "HP:0000118",
- "HP:0001871",
+ "UPHENO:0051763",
"UPHENO:0051801",
"UPHENO:0001003",
- "HP:0001939",
- "HP:0032180",
- "PATO:0000001",
- "HP:0002795",
+ "UPHENO:0081547",
+ "UPHENO:0077826",
"BFO:0000001",
- "BFO:0000040",
- "GO:0008152",
- "UBERON:0000467",
- "UBERON:0000468",
+ "UBERON:0001062",
+ "UBERON:0000061",
+ "UBERON:0000463",
+ "CHEBI:50047",
+ "CHEBI:37622",
+ "CHEBI:33256",
+ "UPHENO:0075696",
+ "UPHENO:0076286",
+ "HP:0040081",
+ "HP:0002795",
+ "HP:0012415",
+ "UPHENO:0051612",
+ "UPHENO:0051804",
+ "BFO:0000015",
+ "BFO:0000004",
+ "GO:0032991",
+ "CHEBI:23367",
+ "UBERON:0000178",
+ "UBERON:0004120",
+ "UBERON:0006314",
"GO:0061695",
"CHEBI:16670",
"CHEBI:33302",
@@ -613,158 +643,128 @@ def association_table():
"CHEBI:25806",
"CHEBI:36962",
"CHEBI:50860",
- "UPHENO:0075696",
"UPHENO:0077817",
"UPHENO:0076289",
- "BFO:0000002",
- "UPHENO:0077821",
+ "UPHENO:0002448",
+ "UPHENO:0002536",
+ "HP:0032180",
+ "PATO:0000001",
+ "CHEBI:138675",
+ "UPHENO:0077825",
+ "HP:0000118",
"UPHENO:0004459",
"UPHENO:0002332",
- "UPHENO:0002536",
"HP:0500165",
- "HP:0002086",
- "HP:0003236",
- "BFO:0000003",
+ "HP:0000001",
+ "HP:0011021",
+ "UPHENO:0001005",
"BFO:0000002",
- "GO:0008150",
- "GO:0005575",
- "CHEBI:24431",
- "PR:000050567",
- "UBERON:0000465",
- "GO:1902494",
- "CHEBI:36357",
- "CHEBI:33579",
- "UBERON:0004120",
- "UBERON:0006314",
- "CHEBI:138675",
- "UBERON:0002193",
- "UBERON:0002390",
- "UBERON:0000179",
- "CHEBI:16541",
- "CHEBI:35352",
- "CHEBI:32988",
- "CHEBI:50047",
- "CHEBI:37622",
- "CHEBI:33256",
- "HP:0004364",
- "UPHENO:0002448",
- "UPHENO:0004536",
- "UPHENO:0051668",
- "UPHENO:0046284",
- "UPHENO:0077829",
"HP:0010876",
- "UPHENO:0076286",
- "HP:0040081",
- "UPHENO:0081547",
- "UPHENO:0077826",
- "HP:0012415",
- "UPHENO:0051612",
- "UBERON:0001062",
- "UBERON:0000061",
- "UBERON:0000463",
+ "HP:0001939",
+ "GO:0008152",
"UBERON:0010000",
- "CHEBI:36963",
- "CHEBI:33285",
+ "UBERON:0000467",
+ "UBERON:0001004",
],
"object_label": "Elevated circulating creatine kinase concentration (HPO)",
"object_closure_label": [
- "All (HPO)",
- "Abnormality of circulating enzyme level (HPO)",
- "abnormal multicellular organism chemical entity level",
- "Phenotypic abnormality",
- "abnormal blood gas molecular entity level",
- "Phenotypic abnormality (HPO)",
- "abnormal chemical entity level",
- "abnormal independent continuant oxygen molecular entity level",
- "Abnormal circulating protein concentration (HPO)",
- "abnormal role blood level",
- "Abnormal circulating creatine kinase concentration (HPO)",
- "Abnormality of metabolism/homeostasis (HPO)",
- "abnormal role bodily fluid level",
- "abnormal blood nitrogen molecular entity level",
- "quality",
- "Abnormal respiratory system physiology (HPO)",
- "process",
- "independent continuant",
- "protein-containing complex",
- "molecular entity",
- "blood",
- "multicellular anatomical structure",
- "respiratory system",
- "transferase complex, transferring phosphorus-containing groups",
- "peptide",
- "pnictogen molecular entity",
- "chalcogen molecular entity",
- "carbon group molecular entity",
- "protein polypeptide chain",
- "organonitrogen compound",
- "amide",
+ "Abnormal circulating nitrogen compound concentration (HPO)",
"abnormality of anatomical entity physiology",
- "phenotype",
- "Abnormality of blood and blood-forming tissues (HPO)",
"abnormal independent continuant protein polypeptide chain level",
+ "abnormal anatomical entity",
+ "Abnormality of metabolism/homeostasis (HPO)",
+ "metabolic process",
+ "abnormal anatomical entity",
+ "specifically dependent continuant",
"phenotype by ontology source",
- "Abnormal blood oxygen level (HPO)",
- "abnormal blood chemical entity level",
+ "abnormal role bodily fluid level",
+ "abnormal blood nitrogen molecular entity level",
"occurrent",
"continuant",
- "biological_process",
"cellular_component",
"chemical entity",
"protein-containing material entity",
"material anatomical entity",
- "gas molecular entity",
- "creatine kinase complex",
- "polypeptide",
- "nitrogen molecular entity",
- "oxygen molecular entity",
- "organochalcogen compound",
- "organic molecular entity",
- "carboxamide",
- "primary amide",
- "organic amino compound",
- "Abnormal circulating nitrogen compound concentration (HPO)",
- "abnormality of respiratory system physiology",
- "abnormal respiratory system",
- "abnormal independent continuant chemical entity level",
+ "transferase complex",
+ "macromolecule",
+ "p-block molecular entity",
+ "respiratory system",
+ "All (HPO)",
+ "Abnormality of circulating enzyme level (HPO)",
"abnormal phenotype by ontology source",
- "specifically dependent continuant",
- "abnormal independent continuant gas molecular entity level",
- "Abnormal circulating metabolite concentration (HPO)",
+ "abnormal chemical entity level",
+ "abnormal independent continuant oxygen molecular entity level",
"Abnormality of the respiratory system (HPO)",
"Elevated circulating creatine kinase concentration (HPO)",
+ "multicellular organism",
+ "hemolymphoid system",
+ "hematopoietic system",
+ "haemolymphatic fluid",
+ "protein polypeptide chain",
+ "organonitrogen compound",
+ "amide",
+ "organooxygen compound",
+ "heteroorganic entity",
+ "abnormal multicellular organism chemical entity level",
+ "abnormal blood gas molecular entity level",
+ "Phenotypic abnormality (HPO)",
+ "Abnormal circulating protein concentration (HPO)",
+ "Abnormal blood oxygen level (HPO)",
"entity",
+ "Phenotypic abnormality",
+ "abnormal independent continuant gas molecular entity level",
+ "quality",
"anatomical entity",
"anatomical structure",
"organism substance",
"mesoderm-derived structure",
"bodily fluid",
- "hemolymphoid system",
- "hematopoietic system",
- "haemolymphatic fluid",
- "organooxygen compound",
- "heteroorganic entity",
- "abnormal anatomical entity",
- "abnormal blood oxygen molecular entity level",
- "abnormal role independent continuant level",
+ "transferase complex, transferring phosphorus-containing groups",
+ "peptide",
+ "pnictogen molecular entity",
+ "chalcogen molecular entity",
+ "carbon group molecular entity",
+ "carboxamide",
+ "primary amide",
+ "organic amino compound",
+ "phenotype",
"continuant",
- "abnormal independent continuant nitrogen molecular entity level",
- "abnormal hematopoietic system",
- "abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
"entity",
+ "process",
+ "independent continuant",
+ "abnormal role blood level",
+ "Abnormal circulating creatine kinase concentration (HPO)",
+ "Abnormal respiratory system physiology (HPO)",
"Abnormal blood gas level (HPO)",
"abnormal blood protein polypeptide chain level",
+ "abnormal blood chemical entity level",
+ "biological_process",
"material entity",
- "metabolic process",
+ "protein-containing complex",
+ "molecular entity",
+ "blood",
"catalytic complex",
"polyatomic entity",
"main group molecular entity",
+ "abnormal blood oxygen molecular entity level",
+ "abnormal role independent continuant level",
+ "abnormality of respiratory system physiology",
+ "abnormal respiratory system",
+ "abnormal independent continuant chemical entity level",
+ "Abnormality of blood and blood-forming tissues (HPO)",
+ "abnormal independent continuant nitrogen molecular entity level",
+ "abnormal hematopoietic system",
+ "abnormality of anatomical entity physiology",
+ "Abnormal circulating metabolite concentration (HPO)",
+ "multicellular anatomical structure",
"anatomical system",
- "transferase complex",
- "macromolecule",
- "p-block molecular entity",
- "multicellular organism",
+ "gas molecular entity",
+ "creatine kinase complex",
+ "polypeptide",
+ "nitrogen molecular entity",
+ "oxygen molecular entity",
+ "organochalcogen compound",
+ "organic molecular entity",
],
"object_taxon": None,
"object_taxon_label": None,
@@ -799,8 +799,8 @@ def association_table():
"frequency_qualifier_label": "Obligate (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0000001", "HP:0040280"],
+ "frequency_qualifier_closure_label": ["Obligate (HPO)", "Frequency (HPO)", "All (HPO)"],
"onset_qualifier_label": None,
"onset_qualifier_namespace": None,
"onset_qualifier_category": None,
@@ -819,64 +819,64 @@ def association_table():
"direction": "outgoing",
},
{
- "id": "uuid:cb2a2f47-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:476a1081-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"subject": "MONDO:0009681",
"original_subject": "OMIM:254090",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000020",
- "MONDO:0005336",
- "MONDO:0005071",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0002320",
+ "MONDO:0000001",
"MONDO:0020121",
"MONDO:0019952",
+ "MONDO:0003847",
+ "MONDO:0005336",
+ "MONDO:0000355",
"BFO:0000017",
"MONDO:0100225",
+ "BFO:0000020",
+ "MONDO:0003939",
+ "MONDO:0002081",
+ "MONDO:0019950",
+ "MONDO:0005071",
+ "BFO:0000002",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0009681",
- "MONDO:0000355",
- "MONDO:0000001",
"MONDO:0700223",
- "BFO:0000002",
+ "BFO:0000016",
+ "MONDO:0016139",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
- "MONDO:0019950",
+ "MONDO:0009681",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_label": "Ullrich congenital muscular dystrophy 1",
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "disease",
+ "realizable entity",
+ "collagen 6-related myopathy",
+ "specifically dependent continuant",
+ "Ullrich congenital muscular dystrophy 1",
"disease",
"muscle tissue disorder",
- "congenital nervous system disorder",
"hereditary skeletal muscle disorder",
+ "Ullrich congenital muscular dystrophy",
"continuant",
"disposition",
"qualitative or quantitative protein defects in neuromuscular diseases",
- "Ullrich congenital muscular dystrophy 1",
- "disease",
- "specifically dependent continuant",
+ "human disease",
+ "entity",
"myopathy",
- "hereditary disease",
- "Ullrich congenital muscular dystrophy",
"nervous system disorder",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "congenital nervous system disorder",
+ "congenital muscular dystrophy",
+ "muscular dystrophy",
"congenital myopathy",
- "realizable entity",
- "collagen 6-related myopathy",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
- "congenital muscular dystrophy",
],
"subject_taxon": None,
"subject_taxon_label": None,
@@ -886,91 +886,91 @@ def association_table():
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "UPHENO:0082875",
- "HP:0001388",
- "UPHENO:0001005",
- "BFO:0000002",
- "BFO:0000020",
- "PATO:0000001",
- "HP:0011843",
- "BFO:0000004",
- "UBERON:0002204",
- "HP:0000001",
- "HP:0020152",
- "UPHENO:0001001",
- "UPHENO:0001002",
- "HP:0000118",
- "UPHENO:0002964",
- "BFO:0000001",
+ "HP:0011729",
+ "HP:0011843",
+ "UBERON:0000465",
+ "UPHENO:0082875",
+ "HP:0001388",
"BFO:0000001",
"BFO:0000040",
- "UBERON:0000467",
- "UBERON:0000468",
"UBERON:0011216",
"UBERON:0034921",
- "UPHENO:0075696",
- "HP:0011729",
- "HP:0034430",
- "HP:0000924",
- "UPHENO:0002332",
- "UPHENO:0001003",
- "UPHENO:0002536",
+ "UPHENO:0001002",
+ "BFO:0000020",
"BFO:0000002",
- "UBERON:0000465",
- "UBERON:0004770",
- "UBERON:0000982",
- "HP:0033127",
+ "UPHENO:0001001",
+ "UPHENO:0002964",
+ "UPHENO:0001003",
"UPHENO:0081440",
+ "BFO:0000001",
"UBERON:0001062",
"UBERON:0000061",
"UBERON:0034925",
+ "UPHENO:0075696",
+ "UPHENO:0001005",
+ "HP:0033127",
+ "BFO:0000004",
+ "UBERON:0004770",
+ "UBERON:0000468",
+ "HP:0034430",
+ "HP:0000924",
+ "BFO:0000002",
+ "UPHENO:0002536",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "PATO:0000001",
+ "UBERON:0000982",
+ "HP:0000001",
+ "HP:0020152",
"UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0002204",
"UBERON:0004905",
"UBERON:0001434",
],
"object_label": "Distal joint laxity (HPO)",
"object_closure_label": [
- "All (HPO)",
- "Distal joint laxity (HPO)",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "Abnormality of the musculoskeletal system (HPO)",
- "abnormality of musculoskeletal system physiology",
- "independent continuant",
- "multicellular anatomical structure",
- "musculoskeletal system",
- "skeletal joint",
"abnormality of anatomical entity physiology",
"Joint laxity (HPO)",
- "phenotype",
- "Abnormality of joint mobility (HPO)",
"abnormal skeletal system",
+ "abnormal anatomical entity",
"quality",
- "Abnormality of musculoskeletal physiology (HPO)",
+ "abnormal anatomical entity",
+ "abnormal phenotype by ontology source",
+ "specifically dependent continuant",
+ "phenotype by ontology source",
+ "abnormality of musculoskeletal system physiology",
"continuant",
"material anatomical entity",
- "abnormal phenotype by ontology source",
+ "musculoskeletal system",
+ "All (HPO)",
+ "Distal joint laxity (HPO)",
"continuant",
- "specifically dependent continuant",
+ "organ system subdivision",
+ "multi organ part structure",
+ "Abnormal joint physiology",
+ "Abnormality of the skeletal system (HPO)",
+ "Phenotypic abnormality (HPO)",
"entity",
+ "Phenotypic abnormality",
+ "Abnormality of musculoskeletal physiology (HPO)",
"anatomical entity",
"anatomical structure",
"anatomical collection",
"articular system",
+ "multicellular organism",
+ "phenotype",
+ "entity",
+ "independent continuant",
+ "Abnormality of joint mobility (HPO)",
+ "Abnormality of the musculoskeletal system (HPO)",
+ "material entity",
"articulation",
"skeletal system",
- "abnormal anatomical entity",
- "Abnormal joint physiology",
- "Abnormality of the skeletal system (HPO)",
"abnormality of anatomical entity physiology",
- "phenotype by ontology source",
- "abnormal anatomical entity",
- "entity",
- "material entity",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "multi organ part structure",
+ "skeletal joint",
],
"object_taxon": None,
"object_taxon_label": None,
@@ -1005,8 +1005,8 @@ def association_table():
"frequency_qualifier_label": "Obligate (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0000001", "HP:0040280"],
+ "frequency_qualifier_closure_label": ["Obligate (HPO)", "Frequency (HPO)", "All (HPO)"],
"onset_qualifier_label": None,
"onset_qualifier_namespace": None,
"onset_qualifier_category": None,
@@ -1025,66 +1025,66 @@ def association_table():
"direction": "outgoing",
},
{
- "id": "uuid:c9d8bdf9-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:46170673-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"subject": "MONDO:0009676",
"original_subject": "OMIM:253601",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "MONDO:0016971",
- "BFO:0000002",
+ "MONDO:0016145",
+ "MONDO:0000001",
+ "MONDO:0020121",
+ "MONDO:0003847",
+ "MONDO:0015152",
+ "MONDO:0000429",
"BFO:0000020",
+ "MONDO:0016106",
"MONDO:0005336",
+ "BFO:0000017",
+ "MONDO:0003939",
+ "MONDO:0006025",
+ "MONDO:0002081",
+ "BFO:0000002",
"MONDO:0009676",
- "MONDO:0015152",
- "MONDO:0000429",
+ "MONDO:0016971",
"MONDO:0005071",
- "MONDO:0006025",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
- "MONDO:0016145",
- "MONDO:0020121",
- "BFO:0000017",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
"MONDO:0700223",
- "MONDO:0016106",
+ "BFO:0000016",
+ "MONDO:0016139",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2B",
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
"disease",
+ "realizable entity",
+ "disease",
+ "specifically dependent continuant",
"muscle tissue disorder",
- "qualitative or quantitative defects of dysferlin",
"hereditary skeletal muscle disorder",
- "autosomal recessive disease",
+ "continuant",
+ "limb-girdle muscular dystrophy",
"disposition",
"qualitative or quantitative protein defects in neuromuscular diseases",
- "autosomal recessive limb-girdle muscular dystrophy type 2B",
- "disease",
- "continuant",
- "specifically dependent continuant",
- "myopathy",
- "hereditary disease",
+ "human disease",
+ "entity",
"autosomal genetic disease",
+ "autosomal recessive disease",
+ "myopathy",
"nervous system disorder",
- "realizable entity",
+ "autosomal recessive limb-girdle muscular dystrophy type 2B",
+ "autosomal recessive limb-girdle muscular dystrophy",
+ "qualitative or quantitative defects of dysferlin",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "muscular dystrophy",
"skeletal muscle disorder",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity",
],
"subject_taxon": None,
"subject_taxon_label": None,
@@ -1094,87 +1094,87 @@ def association_table():
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
+ "UPHENO:0002816",
+ "UPHENO:0002536",
+ "UBERON:0000465",
"UPHENO:0082875",
- "UPHENO:0002320",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UBERON:0011216",
+ "UPHENO:0001002",
+ "HP:0001324",
+ "UPHENO:0080555",
+ "HP:0011804",
"BFO:0000002",
- "BFO:0000004",
- "UBERON:0000061",
- "HP:0000001",
"UPHENO:0001001",
- "UPHENO:0001002",
- "HP:0000118",
- "BFO:0000020",
+ "HP:0003701",
"UPHENO:0001003",
"BFO:0000001",
- "PATO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0001062",
- "UBERON:0000467",
+ "BFO:0000020",
+ "HP:0033127",
+ "BFO:0000004",
+ "UBERON:0000061",
+ "UBERON:0000062",
"UBERON:0000468",
- "UBERON:0011216",
"UPHENO:0075696",
- "HP:0001324",
+ "BFO:0000002",
"HP:0003011",
+ "UPHENO:0002320",
+ "HP:0000118",
"UPHENO:0002332",
- "UPHENO:0002536",
- "HP:0011804",
- "BFO:0000002",
- "UBERON:0000465",
- "UBERON:0005090",
- "UBERON:0001630",
+ "PATO:0000001",
+ "HP:0000001",
"UPHENO:0001005",
- "HP:0003701",
- "UPHENO:0080555",
- "UPHENO:0002816",
"UPHENO:0080556",
- "HP:0033127",
+ "BFO:0000001",
"UBERON:0010000",
- "UBERON:0000062",
+ "UBERON:0000467",
+ "UBERON:0005090",
+ "UBERON:0001630",
"UBERON:0000383",
"UBERON:0001015",
],
"object_label": "Proximal muscle weakness (HPO)",
"object_closure_label": [
- "All (HPO)",
- "abnormality of muscle organ physiology",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "decreased anatomical entity strength",
- "abnormal musculature",
- "decreased muscle organ strength",
- "Abnormality of the musculoskeletal system (HPO)",
- "quality",
- "independent continuant",
- "anatomical structure",
- "multicellular anatomical structure",
"abnormality of anatomical entity physiology",
- "phenotype",
- "abnormal phenotype by ontology source",
"Proximal muscle weakness (HPO)",
- "specifically dependent continuant",
+ "quality",
+ "Abnormality of the musculature (HPO)",
"phenotype by ontology source",
"continuant",
"material anatomical entity",
+ "muscle organ",
+ "All (HPO)",
+ "abnormal phenotype by ontology source",
"continuant",
+ "abnormal musculature",
"Abnormal muscle physiology (HPO)",
+ "organ system subdivision",
+ "abnormality of muscle organ physiology",
+ "Phenotypic abnormality (HPO)",
+ "decreased muscle organ strength",
"entity",
- "muscle structure",
+ "entity",
+ "Phenotypic abnormality",
+ "Muscle weakness (HPO)",
+ "specifically dependent continuant",
"organ",
- "muscle organ",
+ "multicellular organism",
+ "phenotype",
+ "independent continuant",
+ "decreased anatomical entity strength",
+ "Abnormality of the musculoskeletal system (HPO)",
+ "material entity",
+ "anatomical entity",
+ "anatomical structure",
"musculature of body",
"musculature",
"abnormal anatomical entity",
- "Muscle weakness (HPO)",
- "Abnormality of the musculature (HPO)",
"abnormality of anatomical entity physiology",
"abnormal anatomical entity",
- "entity",
- "material entity",
- "anatomical entity",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
+ "muscle structure",
],
"object_taxon": None,
"object_taxon_label": None,
@@ -1209,8 +1209,8 @@ def association_table():
"frequency_qualifier_label": "Obligate (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0000001", "HP:0040280"],
+ "frequency_qualifier_closure_label": ["Obligate (HPO)", "Frequency (HPO)", "All (HPO)"],
"onset_qualifier_label": None,
"onset_qualifier_namespace": None,
"onset_qualifier_category": None,
diff --git a/backend/tests/fixtures/association_table_response.py b/backend/tests/fixtures/association_table_response.py
index 7e924a5ca..820b111af 100644
--- a/backend/tests/fixtures/association_table_response.py
+++ b/backend/tests/fixtures/association_table_response.py
@@ -5,7 +5,7 @@
def association_table_response():
return {
"responseHeader": {
- "QTime": 0,
+ "QTime": 1,
"params": {
"mm": "100%",
"q": "*:*",
@@ -27,7 +27,7 @@ def association_table_response():
"start": 0,
"docs": [
{
- "id": "uuid:ca3946de-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4677e7a0-842a-11ee-884f-6be035239f90",
"original_subject": "OMIM:164310",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
@@ -43,158 +43,158 @@ def association_table_response():
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "BFO:0000002",
- "BFO:0000020",
- "MONDO:0024458",
- "MONDO:0005336",
"MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0003382",
- "BFO:0000016",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0025193",
"MONDO:0020121",
"MONDO:0020793",
+ "MONDO:0003847",
+ "BFO:0000001",
+ "BFO:0000020",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
"BFO:0000017",
+ "MONDO:0003939",
+ "MONDO:0002022",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "BFO:0000002",
+ "MONDO:0005071",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000462",
- "MONDO:0020158",
- "MONDO:0000001",
"MONDO:0700223",
- "MONDO:0016106",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002022",
- "MONDO:0005328",
+ "MONDO:0024458",
+ "OGMS:0000031",
],
"subject_closure_label": [
- "oculopharyngodistal myopathy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
+ "disease",
+ "realizable entity",
"disease",
+ "specifically dependent continuant",
"muscle tissue disorder",
"disorder of orbital region",
"hereditary skeletal muscle disorder",
+ "continuant",
+ "eye adnexa disorder",
"eyelid disorder",
"disposition",
- "distal myopathy",
- "eyelids malposition disorder",
- "disease",
- "continuant",
- "specifically dependent continuant",
+ "human disease",
"disorder of visual system",
"myopathy",
- "hereditary disease",
- "eye adnexa disorder",
+ "distal myopathy",
"nervous system disorder",
+ "entity",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "oculopharyngodistal myopathy",
+ "muscular dystrophy",
"oculopharyngodistal myopathy 1",
- "realizable entity",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
- "eye disorder",
],
"object_label": "Distal muscle weakness (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
+ "UPHENO:0002816",
+ "BFO:0000001",
+ "UBERON:0000465",
"UPHENO:0082875",
- "UPHENO:0002320",
- "UPHENO:0001005",
+ "BFO:0000040",
+ "UBERON:0011216",
+ "HP:0001324",
+ "UPHENO:0080555",
+ "HP:0011804",
+ "BFO:0000002",
+ "UPHENO:0001001",
+ "UPHENO:0001002",
"BFO:0000020",
- "PATO:0000001",
+ "UPHENO:0001003",
+ "UPHENO:0002536",
+ "BFO:0000001",
+ "UBERON:0001062",
+ "UPHENO:0001005",
+ "HP:0033127",
"BFO:0000004",
"UBERON:0000061",
- "HP:0000001",
- "UPHENO:0001001",
- "HP:0000118",
- "BFO:0000001",
- "UBERON:0000467",
+ "UBERON:0000062",
"UBERON:0000468",
- "UBERON:0011216",
"UPHENO:0075696",
- "HP:0001324",
"HP:0003011",
+ "UPHENO:0002320",
+ "HP:0000118",
+ "BFO:0000002",
"UPHENO:0002332",
- "UPHENO:0001003",
- "UPHENO:0002536",
"HP:0002460",
- "HP:0011804",
- "BFO:0000002",
- "BFO:0000040",
+ "PATO:0000001",
+ "UBERON:0010000",
+ "HP:0000001",
+ "UPHENO:0080556",
+ "UBERON:0000467",
"UBERON:0005090",
"UBERON:0001630",
- "UPHENO:0001002",
- "BFO:0000002",
- "UPHENO:0080555",
- "UPHENO:0002816",
- "UPHENO:0080556",
- "HP:0033127",
- "BFO:0000001",
- "UBERON:0001062",
- "UBERON:0000465",
- "UBERON:0010000",
- "UBERON:0000062",
"UBERON:0000383",
"UBERON:0001015",
],
"object_closure_label": [
- "All (HPO)",
- "abnormality of muscle organ physiology",
- "Phenotypic abnormality (HPO)",
- "decreased anatomical entity strength",
- "abnormal musculature",
- "decreased muscle organ strength",
- "Abnormality of the musculoskeletal system (HPO)",
- "entity",
- "independent continuant",
- "material anatomical entity",
- "anatomical structure",
- "multicellular anatomical structure",
"abnormality of anatomical entity physiology",
- "phenotype",
"Phenotypic abnormality",
- "continuant",
- "Distal muscle weakness (HPO)",
+ "specifically dependent continuant",
"quality",
- "continuant",
- "material entity",
"abnormal phenotype by ontology source",
- "specifically dependent continuant",
+ "Abnormality of the musculature (HPO)",
+ "phenotype by ontology source",
+ "abnormal anatomical entity",
+ "continuant",
+ "material anatomical entity",
+ "muscle organ",
+ "All (HPO)",
+ "abnormal musculature",
"Abnormal muscle physiology (HPO)",
+ "organ system subdivision",
+ "abnormality of muscle organ physiology",
+ "Phenotypic abnormality (HPO)",
+ "continuant",
+ "decreased muscle organ strength",
+ "Distal muscle weakness (HPO)",
"entity",
+ "multicellular anatomical structure",
+ "Muscle weakness (HPO)",
"anatomical entity",
- "muscle structure",
"organ",
- "muscle organ",
+ "multicellular organism",
+ "phenotype",
+ "independent continuant",
+ "decreased anatomical entity strength",
+ "Abnormality of the musculoskeletal system (HPO)",
+ "entity",
+ "material entity",
+ "anatomical structure",
"musculature of body",
"musculature",
"abnormal anatomical entity",
- "Muscle weakness (HPO)",
- "Abnormality of the musculature (HPO)",
"abnormality of anatomical entity physiology",
- "phenotype by ontology source",
- "abnormal anatomical entity",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
+ "muscle structure",
],
"frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Frequent (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"],
"evidence_count": 4,
"grouping_key": "MONDO:0020793🍪🍪biolink:has_phenotype🍪HP:0002460",
},
{
- "id": "uuid:ca3946ef-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4677e7b1-842a-11ee-884f-6be035239f90",
"original_subject": "OMIM:164310",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
@@ -210,212 +210,212 @@ def association_table_response():
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "BFO:0000002",
- "BFO:0000020",
- "MONDO:0024458",
- "MONDO:0005336",
"MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0003382",
- "BFO:0000016",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0025193",
"MONDO:0020121",
"MONDO:0020793",
+ "MONDO:0003847",
+ "BFO:0000001",
+ "BFO:0000020",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
"BFO:0000017",
+ "MONDO:0003939",
+ "MONDO:0002022",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "BFO:0000002",
+ "MONDO:0005071",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000462",
- "MONDO:0020158",
- "MONDO:0000001",
"MONDO:0700223",
- "MONDO:0016106",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002022",
- "MONDO:0005328",
+ "MONDO:0024458",
+ "OGMS:0000031",
],
"subject_closure_label": [
- "oculopharyngodistal myopathy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
+ "realizable entity",
+ "disease",
+ "specifically dependent continuant",
"muscle tissue disorder",
"disorder of orbital region",
"hereditary skeletal muscle disorder",
+ "continuant",
+ "eye adnexa disorder",
"eyelid disorder",
"disposition",
- "distal myopathy",
- "eyelids malposition disorder",
- "disease",
- "continuant",
- "specifically dependent continuant",
+ "human disease",
"disorder of visual system",
"myopathy",
- "hereditary disease",
- "eye adnexa disorder",
+ "distal myopathy",
"nervous system disorder",
+ "entity",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "oculopharyngodistal myopathy",
+ "muscular dystrophy",
"oculopharyngodistal myopathy 1",
- "realizable entity",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
- "eye disorder",
],
"object_label": "Dysphagia (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "UPHENO:0082875",
+ "UPHENO:0002443",
"UPHENO:0002471",
"HP:0025270",
- "UPHENO:0001005",
- "BFO:0000002",
- "BFO:0000020",
+ "UPHENO:0002536",
+ "UBERON:0000465",
+ "RO:0002577",
+ "UPHENO:0082875",
"HP:0002664",
+ "UPHENO:0004523",
+ "BFO:0000001",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UBERON:0011676",
+ "UBERON:0013701",
+ "BFO:0000020",
"HP:0011793",
- "PATO:0000001",
- "UPHENO:0002474",
- "HP:0012638",
- "BFO:0000004",
- "UBERON:0000061",
- "UBERON:0001007",
- "UBERON:0001016",
- "UBERON:0011676",
- "UBERON:0013701",
- "UBERON:0000915",
- "UBERON:0001043",
- "UBERON:0002100",
- "UBERON:0005181",
- "UBERON:0002075",
- "HP:0000001",
+ "BFO:0000002",
+ "UBERON:0005409",
"UPHENO:0001001",
- "HP:0000118",
- "UPHENO:0002433",
+ "UPHENO:0002833",
+ "HP:0002015",
+ "UPHENO:0001002",
"UPHENO:0001003",
- "BFO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0010000",
- "UBERON:0000467",
+ "UPHENO:0075696",
+ "UPHENO:0002433",
+ "HP:0025031",
+ "UPHENO:0002474",
+ "HP:0012638",
+ "BFO:0000004",
+ "UBERON:0000061",
+ "UBERON:0000475",
+ "UBERON:0000062",
"UBERON:0004111",
"UBERON:0000468",
- "UBERON:0000064",
- "UPHENO:0075696",
"HP:0011024",
- "UPHENO:0002443",
- "HP:0012719",
"UPHENO:0002725",
- "HP:0025032",
- "UPHENO:0002332",
- "UPHENO:0002536",
- "UPHENO:0004523",
"BFO:0000002",
- "UBERON:0000465",
- "UBERON:0005409",
+ "HP:0025032",
"UBERON:0009569",
"UBERON:0013702",
"UBERON:0013765",
"UBERON:0005177",
"UBERON:0000025",
+ "UBERON:0000915",
+ "UBERON:0001043",
+ "UBERON:0002100",
+ "UBERON:0005181",
+ "UBERON:0002075",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "PATO:0000001",
"UBERON:0001555",
"UBERON:0004921",
- "UPHENO:0002833",
- "HP:0002015",
- "UPHENO:0001002",
+ "HP:0000001",
+ "HP:0012719",
+ "UPHENO:0001005",
"HP:0000707",
- "HP:0025031",
- "UBERON:0001062",
- "RO:0002577",
- "UBERON:0000475",
- "UBERON:0000062",
+ "BFO:0000001",
+ "UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0000064",
+ "UBERON:0001007",
+ "UBERON:0001016",
"UBERON:0013522",
"UBERON:0005178",
"UBERON:0004908",
],
"object_closure_label": [
- "All (HPO)",
- "abnormality of alimentary part of gastrointestinal system physiology",
- "Abnormal esophagus physiology (HPO)",
- "Functional abnormality of the gastrointestinal tract (HPO)",
- "Phenotypic abnormality (HPO)",
- "Abnormality of the nervous system (HPO)",
- "independent continuant",
- "system",
- "anatomical structure",
- "digestive system",
- "nervous system",
- "digestive tract",
- "subdivision of digestive tract",
"abnormality of anatomical entity physiology",
- "phenotype",
- "abnormality of digestive system physiology",
"abnormal digestive system",
"Dysphagia (HPO)",
"Phenotypic abnormality",
- "abnormality of nervous system physiology",
+ "quality",
+ "abnormal anatomical entity",
+ "specifically dependent continuant",
+ "Abnormality of digestive system physiology (HPO)",
"phenotype by ontology source",
"abnormal nervous system",
- "quality",
- "abnormality of esophagus physiology",
- "Abnormal nervous system physiology (HPO)",
"continuant",
"material anatomical entity",
+ "system",
+ "organ part",
+ "digestive system",
+ "nervous system",
+ "thoracic segment of trunk",
+ "esophagus",
+ "trunk",
+ "thoracic segment organ",
+ "viscus",
+ "All (HPO)",
+ "Functional abnormality of the gastrointestinal tract (HPO)",
+ "abnormal phenotype by ontology source",
+ "continuant",
+ "alimentary part of gastrointestinal system",
"subdivision of trunk",
"body proper",
"digestive system element",
"trunk region element",
"tube",
- "abnormal phenotype by ontology source",
- "continuant",
- "specifically dependent continuant",
- "Neoplasm (HPO)",
- "Neoplasm by anatomical site (HPO)",
+ "abnormal alimentary part of gastrointestinal system",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the nervous system (HPO)",
"entity",
- "anatomical entity",
+ "thoracic cavity element",
+ "upper digestive tract",
+ "abnormality of nervous system physiology",
+ "Neoplasm by anatomical site (HPO)",
"organism subdivision",
"organ",
- "alimentary part of gastrointestinal system",
+ "anatomical conduit",
+ "multicellular organism",
+ "phenotype",
+ "Neoplasm (HPO)",
+ "entity",
+ "independent continuant",
+ "subdivision of organism along main body axis",
+ "main body axis",
+ "abnormality of digestive system physiology",
+ "abnormality of alimentary part of gastrointestinal system physiology",
+ "Abnormal esophagus physiology (HPO)",
+ "Abnormality of the digestive system (HPO)",
+ "abnormality of esophagus physiology",
+ "Abnormal nervous system physiology (HPO)",
+ "material entity",
+ "anatomical entity",
+ "anatomical structure",
"subdivision of tube",
- "thoracic cavity element",
- "upper digestive tract",
- "abnormal anatomical entity",
"Abnormality of the gastrointestinal tract (HPO)",
- "abnormal alimentary part of gastrointestinal system",
- "Abnormality of digestive system physiology (HPO)",
"abnormality of anatomical entity physiology",
"abnormal anatomical entity",
- "entity",
- "Abnormality of the digestive system (HPO)",
- "material entity",
"multicellular anatomical structure",
"anatomical system",
- "anatomical conduit",
- "multicellular organism",
- "organ part",
- "subdivision of organism along main body axis",
- "main body axis",
- "thoracic segment of trunk",
- "esophagus",
- "trunk",
- "thoracic segment organ",
- "viscus",
+ "digestive tract",
+ "subdivision of digestive tract",
],
"frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Frequent (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"],
"evidence_count": 4,
"grouping_key": "MONDO:0020793🍪🍪biolink:has_phenotype🍪HP:0002015",
},
{
- "id": "uuid:c6b3613a-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:42ef70e0-842a-11ee-884f-6be035239f90",
"original_subject": "OMIM:612937",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
@@ -431,115 +431,145 @@ def association_table_response():
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "BFO:0000002",
- "BFO:0000020",
- "MONDO:0005336",
- "MONDO:0005021",
- "MONDO:0004994",
- "MONDO:0018276",
- "MONDO:0005071",
- "MONDO:0005267",
- "BFO:0000016",
"MONDO:0016333",
- "MONDO:0017749",
- "OGMS:0000031",
+ "MONDO:0002320",
+ "MONDO:0000001",
+ "MONDO:0013049",
+ "MONDO:0020121",
"MONDO:0003847",
"BFO:0000001",
- "MONDO:0020121",
- "MONDO:0004995",
+ "MONDO:0018276",
+ "BFO:0000020",
+ "MONDO:0005336",
+ "MONDO:0019052",
+ "MONDO:0005500",
+ "MONDO:0005066",
+ "MONDO:0024322",
"BFO:0000017",
+ "MONDO:0003939",
+ "MONDO:0002081",
+ "MONDO:0005021",
+ "MONDO:0019950",
+ "BFO:0000002",
"MONDO:0005217",
+ "MONDO:0015286",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0015286",
- "MONDO:0019052",
- "MONDO:0005500",
- "MONDO:0005066",
- "MONDO:0000001",
- "MONDO:0013049",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
- "MONDO:0024322",
+ "BFO:0000016",
"MONDO:0700096",
"MONDO:0000591",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
- "MONDO:0019950",
+ "MONDO:0017749",
+ "OGMS:0000031",
],
"subject_closure_label": [
- "cardiomyopathy",
- "muscular dystrophy",
- "cardiovascular disorder",
- "human disease",
- "intrinsic cardiomyopathy",
- "musculoskeletal system disorder",
+ "disease",
+ "disorder of glycosylation",
+ "realizable entity",
"disorder of multiple glycosylation",
"disease",
+ "specifically dependent continuant",
+ "familial cardiomyopathy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "disorder of glycosylation",
- "disposition",
- "congenital disorder of glycosylation",
- "disease",
- "DPM3-congenital disorder of glycosylation",
"continuant",
- "specifically dependent continuant",
- "myopathy",
- "familial dilated cardiomyopathy",
- "hereditary disease",
"inborn errors of metabolism",
"congenital disorder of glycosylation type I",
"metabolic disease",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
"muscular dystrophy-dystroglycanopathy",
+ "myopathy",
+ "dilated cardiomyopathy",
"nervous system disorder",
"heart disorder",
- "realizable entity",
- "familial cardiomyopathy",
- "skeletal muscle disorder",
- "neuromuscular disease",
- "dilated cardiomyopathy",
"entity",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "congenital nervous system disorder",
"congenital muscular dystrophy",
+ "DPM3-congenital disorder of glycosylation",
+ "muscular dystrophy",
+ "skeletal muscle disorder",
+ "neuromuscular disease",
+ "familial dilated cardiomyopathy",
+ "congenital disorder of glycosylation",
],
"object_label": "Elevated circulating creatine kinase concentration (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "UPHENO:0082875",
- "UPHENO:0051763",
- "UPHENO:0001005",
- "BFO:0000020",
- "UPHENO:0077820",
- "BFO:0000001",
- "UPHENO:0051804",
- "BFO:0000015",
- "BFO:0000004",
- "GO:0032991",
- "CHEBI:23367",
- "UBERON:0000178",
+ "UPHENO:0046284",
+ "UPHENO:0077829",
+ "GO:0005575",
+ "CHEBI:24431",
+ "PR:000050567",
+ "UBERON:0000465",
+ "CHEBI:16541",
+ "CHEBI:35352",
+ "CHEBI:32988",
+ "CHEBI:36963",
+ "CHEBI:33285",
+ "HP:0004364",
+ "UPHENO:0082875",
+ "UPHENO:0004536",
+ "UPHENO:0051668",
+ "HP:0001871",
+ "UPHENO:0077821",
+ "BFO:0000001",
+ "GO:0008150",
+ "BFO:0000040",
+ "UBERON:0000468",
+ "UPHENO:0001002",
+ "BFO:0000020",
+ "UPHENO:0077820",
+ "HP:0002086",
+ "HP:0003236",
+ "BFO:0000003",
+ "BFO:0000002",
+ "GO:1902494",
+ "CHEBI:36357",
+ "CHEBI:33579",
"GO:1990234",
"CHEBI:33839",
"CHEBI:33675",
- "UBERON:0001004",
- "HP:0000001",
- "HP:0011021",
+ "UBERON:0002193",
+ "UBERON:0002390",
+ "UBERON:0000179",
"UPHENO:0001001",
- "UPHENO:0001002",
- "UPHENO:0077825",
- "HP:0000118",
- "HP:0001871",
+ "UPHENO:0051763",
"UPHENO:0051801",
"UPHENO:0001003",
- "HP:0001939",
- "HP:0032180",
- "PATO:0000001",
- "HP:0002795",
+ "UPHENO:0081547",
+ "UPHENO:0077826",
"BFO:0000001",
- "BFO:0000040",
- "GO:0008152",
- "UBERON:0000467",
- "UBERON:0000468",
+ "UBERON:0001062",
+ "UBERON:0000061",
+ "UBERON:0000463",
+ "CHEBI:50047",
+ "CHEBI:37622",
+ "CHEBI:33256",
+ "UPHENO:0075696",
+ "UPHENO:0076286",
+ "HP:0040081",
+ "HP:0002795",
+ "HP:0012415",
+ "UPHENO:0051612",
+ "UPHENO:0051804",
+ "BFO:0000015",
+ "BFO:0000004",
+ "GO:0032991",
+ "CHEBI:23367",
+ "UBERON:0000178",
+ "UBERON:0004120",
+ "UBERON:0006314",
"GO:0061695",
"CHEBI:16670",
"CHEBI:33302",
@@ -551,168 +581,138 @@ def association_table_response():
"CHEBI:25806",
"CHEBI:36962",
"CHEBI:50860",
- "UPHENO:0075696",
"UPHENO:0077817",
"UPHENO:0076289",
- "BFO:0000002",
- "UPHENO:0077821",
+ "UPHENO:0002448",
+ "UPHENO:0002536",
+ "HP:0032180",
+ "PATO:0000001",
+ "CHEBI:138675",
+ "UPHENO:0077825",
+ "HP:0000118",
"UPHENO:0004459",
"UPHENO:0002332",
- "UPHENO:0002536",
"HP:0500165",
- "HP:0002086",
- "HP:0003236",
- "BFO:0000003",
+ "HP:0000001",
+ "HP:0011021",
+ "UPHENO:0001005",
"BFO:0000002",
- "GO:0008150",
- "GO:0005575",
- "CHEBI:24431",
- "PR:000050567",
- "UBERON:0000465",
- "GO:1902494",
- "CHEBI:36357",
- "CHEBI:33579",
- "UBERON:0004120",
- "UBERON:0006314",
- "CHEBI:138675",
- "UBERON:0002193",
- "UBERON:0002390",
- "UBERON:0000179",
- "CHEBI:16541",
- "CHEBI:35352",
- "CHEBI:32988",
- "CHEBI:50047",
- "CHEBI:37622",
- "CHEBI:33256",
- "HP:0004364",
- "UPHENO:0002448",
- "UPHENO:0004536",
- "UPHENO:0051668",
- "UPHENO:0046284",
- "UPHENO:0077829",
"HP:0010876",
- "UPHENO:0076286",
- "HP:0040081",
- "UPHENO:0081547",
- "UPHENO:0077826",
- "HP:0012415",
- "UPHENO:0051612",
- "UBERON:0001062",
- "UBERON:0000061",
- "UBERON:0000463",
+ "HP:0001939",
+ "GO:0008152",
"UBERON:0010000",
- "CHEBI:36963",
- "CHEBI:33285",
+ "UBERON:0000467",
+ "UBERON:0001004",
],
"object_closure_label": [
- "All (HPO)",
- "Abnormality of circulating enzyme level (HPO)",
- "abnormal multicellular organism chemical entity level",
- "Phenotypic abnormality",
- "abnormal blood gas molecular entity level",
- "Phenotypic abnormality (HPO)",
- "abnormal chemical entity level",
- "abnormal independent continuant oxygen molecular entity level",
- "Abnormal circulating protein concentration (HPO)",
- "abnormal role blood level",
- "Abnormal circulating creatine kinase concentration (HPO)",
- "Abnormality of metabolism/homeostasis (HPO)",
- "abnormal role bodily fluid level",
- "abnormal blood nitrogen molecular entity level",
- "quality",
- "Abnormal respiratory system physiology (HPO)",
- "process",
- "independent continuant",
- "protein-containing complex",
- "molecular entity",
- "blood",
- "multicellular anatomical structure",
- "respiratory system",
- "transferase complex, transferring phosphorus-containing groups",
- "peptide",
- "pnictogen molecular entity",
- "chalcogen molecular entity",
- "carbon group molecular entity",
- "protein polypeptide chain",
- "organonitrogen compound",
- "amide",
+ "Abnormal circulating nitrogen compound concentration (HPO)",
"abnormality of anatomical entity physiology",
- "phenotype",
- "Abnormality of blood and blood-forming tissues (HPO)",
"abnormal independent continuant protein polypeptide chain level",
+ "abnormal anatomical entity",
+ "Abnormality of metabolism/homeostasis (HPO)",
+ "metabolic process",
+ "abnormal anatomical entity",
+ "specifically dependent continuant",
"phenotype by ontology source",
- "Abnormal blood oxygen level (HPO)",
- "abnormal blood chemical entity level",
+ "abnormal role bodily fluid level",
+ "abnormal blood nitrogen molecular entity level",
"occurrent",
"continuant",
- "biological_process",
"cellular_component",
"chemical entity",
"protein-containing material entity",
"material anatomical entity",
- "gas molecular entity",
- "creatine kinase complex",
- "polypeptide",
- "nitrogen molecular entity",
- "oxygen molecular entity",
- "organochalcogen compound",
- "organic molecular entity",
- "carboxamide",
- "primary amide",
- "organic amino compound",
- "Abnormal circulating nitrogen compound concentration (HPO)",
- "abnormality of respiratory system physiology",
- "abnormal respiratory system",
- "abnormal independent continuant chemical entity level",
+ "transferase complex",
+ "macromolecule",
+ "p-block molecular entity",
+ "respiratory system",
+ "All (HPO)",
+ "Abnormality of circulating enzyme level (HPO)",
"abnormal phenotype by ontology source",
- "specifically dependent continuant",
- "abnormal independent continuant gas molecular entity level",
- "Abnormal circulating metabolite concentration (HPO)",
+ "abnormal chemical entity level",
+ "abnormal independent continuant oxygen molecular entity level",
"Abnormality of the respiratory system (HPO)",
"Elevated circulating creatine kinase concentration (HPO)",
+ "multicellular organism",
+ "hemolymphoid system",
+ "hematopoietic system",
+ "haemolymphatic fluid",
+ "protein polypeptide chain",
+ "organonitrogen compound",
+ "amide",
+ "organooxygen compound",
+ "heteroorganic entity",
+ "abnormal multicellular organism chemical entity level",
+ "abnormal blood gas molecular entity level",
+ "Phenotypic abnormality (HPO)",
+ "Abnormal circulating protein concentration (HPO)",
+ "Abnormal blood oxygen level (HPO)",
"entity",
+ "Phenotypic abnormality",
+ "abnormal independent continuant gas molecular entity level",
+ "quality",
"anatomical entity",
"anatomical structure",
"organism substance",
"mesoderm-derived structure",
"bodily fluid",
- "hemolymphoid system",
- "hematopoietic system",
- "haemolymphatic fluid",
- "organooxygen compound",
- "heteroorganic entity",
- "abnormal anatomical entity",
- "abnormal blood oxygen molecular entity level",
- "abnormal role independent continuant level",
+ "transferase complex, transferring phosphorus-containing groups",
+ "peptide",
+ "pnictogen molecular entity",
+ "chalcogen molecular entity",
+ "carbon group molecular entity",
+ "carboxamide",
+ "primary amide",
+ "organic amino compound",
+ "phenotype",
"continuant",
- "abnormal independent continuant nitrogen molecular entity level",
- "abnormal hematopoietic system",
- "abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
"entity",
+ "process",
+ "independent continuant",
+ "abnormal role blood level",
+ "Abnormal circulating creatine kinase concentration (HPO)",
+ "Abnormal respiratory system physiology (HPO)",
"Abnormal blood gas level (HPO)",
"abnormal blood protein polypeptide chain level",
+ "abnormal blood chemical entity level",
+ "biological_process",
"material entity",
- "metabolic process",
+ "protein-containing complex",
+ "molecular entity",
+ "blood",
"catalytic complex",
"polyatomic entity",
"main group molecular entity",
+ "abnormal blood oxygen molecular entity level",
+ "abnormal role independent continuant level",
+ "abnormality of respiratory system physiology",
+ "abnormal respiratory system",
+ "abnormal independent continuant chemical entity level",
+ "Abnormality of blood and blood-forming tissues (HPO)",
+ "abnormal independent continuant nitrogen molecular entity level",
+ "abnormal hematopoietic system",
+ "abnormality of anatomical entity physiology",
+ "Abnormal circulating metabolite concentration (HPO)",
+ "multicellular anatomical structure",
"anatomical system",
- "transferase complex",
- "macromolecule",
- "p-block molecular entity",
- "multicellular organism",
+ "gas molecular entity",
+ "creatine kinase complex",
+ "polypeptide",
+ "nitrogen molecular entity",
+ "oxygen molecular entity",
+ "organochalcogen compound",
+ "organic molecular entity",
],
"frequency_qualifier_label": "Obligate (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0000001", "HP:0040280"],
+ "frequency_qualifier_closure_label": ["Obligate (HPO)", "Frequency (HPO)", "All (HPO)"],
"evidence_count": 3,
"grouping_key": "MONDO:0013049🍪🍪biolink:has_phenotype🍪HP:0003236",
},
{
- "id": "uuid:cb2a2f47-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:476a1081-842a-11ee-884f-6be035239f90",
"original_subject": "OMIM:254090",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
@@ -728,156 +728,156 @@ def association_table_response():
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "BFO:0000020",
- "MONDO:0005336",
- "MONDO:0005071",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0002320",
+ "MONDO:0000001",
"MONDO:0020121",
"MONDO:0019952",
+ "MONDO:0003847",
+ "MONDO:0005336",
+ "MONDO:0000355",
"BFO:0000017",
"MONDO:0100225",
+ "BFO:0000020",
+ "MONDO:0003939",
+ "MONDO:0002081",
+ "MONDO:0019950",
+ "MONDO:0005071",
+ "BFO:0000002",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0009681",
- "MONDO:0000355",
- "MONDO:0000001",
"MONDO:0700223",
- "BFO:0000002",
+ "BFO:0000016",
+ "MONDO:0016139",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
- "MONDO:0019950",
+ "MONDO:0009681",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "disease",
+ "realizable entity",
+ "collagen 6-related myopathy",
+ "specifically dependent continuant",
+ "Ullrich congenital muscular dystrophy 1",
"disease",
"muscle tissue disorder",
- "congenital nervous system disorder",
"hereditary skeletal muscle disorder",
+ "Ullrich congenital muscular dystrophy",
"continuant",
"disposition",
"qualitative or quantitative protein defects in neuromuscular diseases",
- "Ullrich congenital muscular dystrophy 1",
- "disease",
- "specifically dependent continuant",
+ "human disease",
+ "entity",
"myopathy",
- "hereditary disease",
- "Ullrich congenital muscular dystrophy",
"nervous system disorder",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "congenital nervous system disorder",
+ "congenital muscular dystrophy",
+ "muscular dystrophy",
"congenital myopathy",
- "realizable entity",
- "collagen 6-related myopathy",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
- "congenital muscular dystrophy",
],
"object_label": "Distal joint laxity (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
- "UPHENO:0082875",
- "HP:0001388",
- "UPHENO:0001005",
- "BFO:0000002",
- "BFO:0000020",
- "PATO:0000001",
- "HP:0011843",
- "BFO:0000004",
- "UBERON:0002204",
- "HP:0000001",
- "HP:0020152",
- "UPHENO:0001001",
- "UPHENO:0001002",
- "HP:0000118",
- "UPHENO:0002964",
- "BFO:0000001",
+ "HP:0011729",
+ "HP:0011843",
+ "UBERON:0000465",
+ "UPHENO:0082875",
+ "HP:0001388",
"BFO:0000001",
"BFO:0000040",
- "UBERON:0000467",
- "UBERON:0000468",
"UBERON:0011216",
"UBERON:0034921",
- "UPHENO:0075696",
- "HP:0011729",
- "HP:0034430",
- "HP:0000924",
- "UPHENO:0002332",
- "UPHENO:0001003",
- "UPHENO:0002536",
+ "UPHENO:0001002",
+ "BFO:0000020",
"BFO:0000002",
- "UBERON:0000465",
- "UBERON:0004770",
- "UBERON:0000982",
- "HP:0033127",
+ "UPHENO:0001001",
+ "UPHENO:0002964",
+ "UPHENO:0001003",
"UPHENO:0081440",
+ "BFO:0000001",
"UBERON:0001062",
"UBERON:0000061",
"UBERON:0034925",
+ "UPHENO:0075696",
+ "UPHENO:0001005",
+ "HP:0033127",
+ "BFO:0000004",
+ "UBERON:0004770",
+ "UBERON:0000468",
+ "HP:0034430",
+ "HP:0000924",
+ "BFO:0000002",
+ "UPHENO:0002536",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "PATO:0000001",
+ "UBERON:0000982",
+ "HP:0000001",
+ "HP:0020152",
"UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0002204",
"UBERON:0004905",
"UBERON:0001434",
],
"object_closure_label": [
- "All (HPO)",
- "Distal joint laxity (HPO)",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "Abnormality of the musculoskeletal system (HPO)",
- "abnormality of musculoskeletal system physiology",
- "independent continuant",
- "multicellular anatomical structure",
- "musculoskeletal system",
- "skeletal joint",
"abnormality of anatomical entity physiology",
"Joint laxity (HPO)",
- "phenotype",
- "Abnormality of joint mobility (HPO)",
"abnormal skeletal system",
+ "abnormal anatomical entity",
"quality",
- "Abnormality of musculoskeletal physiology (HPO)",
+ "abnormal anatomical entity",
+ "abnormal phenotype by ontology source",
+ "specifically dependent continuant",
+ "phenotype by ontology source",
+ "abnormality of musculoskeletal system physiology",
"continuant",
"material anatomical entity",
- "abnormal phenotype by ontology source",
+ "musculoskeletal system",
+ "All (HPO)",
+ "Distal joint laxity (HPO)",
"continuant",
- "specifically dependent continuant",
+ "organ system subdivision",
+ "multi organ part structure",
+ "Abnormal joint physiology",
+ "Abnormality of the skeletal system (HPO)",
+ "Phenotypic abnormality (HPO)",
"entity",
+ "Phenotypic abnormality",
+ "Abnormality of musculoskeletal physiology (HPO)",
"anatomical entity",
"anatomical structure",
"anatomical collection",
"articular system",
+ "multicellular organism",
+ "phenotype",
+ "entity",
+ "independent continuant",
+ "Abnormality of joint mobility (HPO)",
+ "Abnormality of the musculoskeletal system (HPO)",
+ "material entity",
"articulation",
"skeletal system",
- "abnormal anatomical entity",
- "Abnormal joint physiology",
- "Abnormality of the skeletal system (HPO)",
"abnormality of anatomical entity physiology",
- "phenotype by ontology source",
- "abnormal anatomical entity",
- "entity",
- "material entity",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "multi organ part structure",
+ "skeletal joint",
],
"frequency_qualifier_label": "Obligate (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0000001", "HP:0040280"],
+ "frequency_qualifier_closure_label": ["Obligate (HPO)", "Frequency (HPO)", "All (HPO)"],
"evidence_count": 3,
"grouping_key": "MONDO:0009681🍪🍪biolink:has_phenotype🍪HP:0020152",
},
{
- "id": "uuid:c9d8bdf9-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:46170673-842a-11ee-884f-6be035239f90",
"original_subject": "OMIM:253601",
"predicate": "biolink:has_phenotype",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
@@ -893,149 +893,149 @@ def association_table_response():
"subject_category": "biolink:Disease",
"subject_namespace": "MONDO",
"subject_closure": [
- "MONDO:0016971",
- "BFO:0000002",
+ "MONDO:0016145",
+ "MONDO:0000001",
+ "MONDO:0020121",
+ "MONDO:0003847",
+ "MONDO:0015152",
+ "MONDO:0000429",
"BFO:0000020",
+ "MONDO:0016106",
"MONDO:0005336",
+ "BFO:0000017",
+ "MONDO:0003939",
+ "MONDO:0006025",
+ "MONDO:0002081",
+ "BFO:0000002",
"MONDO:0009676",
- "MONDO:0015152",
- "MONDO:0000429",
+ "MONDO:0016971",
"MONDO:0005071",
- "MONDO:0006025",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
- "MONDO:0016145",
- "MONDO:0020121",
- "BFO:0000017",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
"MONDO:0700223",
- "MONDO:0016106",
+ "BFO:0000016",
+ "MONDO:0016139",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
+ "OGMS:0000031",
+ "BFO:0000001",
],
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
"disease",
+ "realizable entity",
+ "disease",
+ "specifically dependent continuant",
"muscle tissue disorder",
- "qualitative or quantitative defects of dysferlin",
"hereditary skeletal muscle disorder",
- "autosomal recessive disease",
+ "continuant",
+ "limb-girdle muscular dystrophy",
"disposition",
"qualitative or quantitative protein defects in neuromuscular diseases",
- "autosomal recessive limb-girdle muscular dystrophy type 2B",
- "disease",
- "continuant",
- "specifically dependent continuant",
- "myopathy",
- "hereditary disease",
+ "human disease",
+ "entity",
"autosomal genetic disease",
+ "autosomal recessive disease",
+ "myopathy",
"nervous system disorder",
- "realizable entity",
+ "autosomal recessive limb-girdle muscular dystrophy type 2B",
+ "autosomal recessive limb-girdle muscular dystrophy",
+ "qualitative or quantitative defects of dysferlin",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "muscular dystrophy",
"skeletal muscle disorder",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity",
],
"object_label": "Proximal muscle weakness (HPO)",
"object_category": "biolink:PhenotypicFeature",
"object_namespace": "HP",
"object_closure": [
+ "UPHENO:0002816",
+ "UPHENO:0002536",
+ "UBERON:0000465",
"UPHENO:0082875",
- "UPHENO:0002320",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UBERON:0011216",
+ "UPHENO:0001002",
+ "HP:0001324",
+ "UPHENO:0080555",
+ "HP:0011804",
"BFO:0000002",
- "BFO:0000004",
- "UBERON:0000061",
- "HP:0000001",
"UPHENO:0001001",
- "UPHENO:0001002",
- "HP:0000118",
- "BFO:0000020",
+ "HP:0003701",
"UPHENO:0001003",
"BFO:0000001",
- "PATO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0001062",
- "UBERON:0000467",
+ "BFO:0000020",
+ "HP:0033127",
+ "BFO:0000004",
+ "UBERON:0000061",
+ "UBERON:0000062",
"UBERON:0000468",
- "UBERON:0011216",
"UPHENO:0075696",
- "HP:0001324",
+ "BFO:0000002",
"HP:0003011",
+ "UPHENO:0002320",
+ "HP:0000118",
"UPHENO:0002332",
- "UPHENO:0002536",
- "HP:0011804",
- "BFO:0000002",
- "UBERON:0000465",
- "UBERON:0005090",
- "UBERON:0001630",
+ "PATO:0000001",
+ "HP:0000001",
"UPHENO:0001005",
- "HP:0003701",
- "UPHENO:0080555",
- "UPHENO:0002816",
"UPHENO:0080556",
- "HP:0033127",
+ "BFO:0000001",
"UBERON:0010000",
- "UBERON:0000062",
+ "UBERON:0000467",
+ "UBERON:0005090",
+ "UBERON:0001630",
"UBERON:0000383",
"UBERON:0001015",
],
"object_closure_label": [
- "All (HPO)",
- "abnormality of muscle organ physiology",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "decreased anatomical entity strength",
- "abnormal musculature",
- "decreased muscle organ strength",
- "Abnormality of the musculoskeletal system (HPO)",
- "quality",
- "independent continuant",
- "anatomical structure",
- "multicellular anatomical structure",
"abnormality of anatomical entity physiology",
- "phenotype",
- "abnormal phenotype by ontology source",
"Proximal muscle weakness (HPO)",
- "specifically dependent continuant",
+ "quality",
+ "Abnormality of the musculature (HPO)",
"phenotype by ontology source",
"continuant",
"material anatomical entity",
+ "muscle organ",
+ "All (HPO)",
+ "abnormal phenotype by ontology source",
"continuant",
+ "abnormal musculature",
"Abnormal muscle physiology (HPO)",
+ "organ system subdivision",
+ "abnormality of muscle organ physiology",
+ "Phenotypic abnormality (HPO)",
+ "decreased muscle organ strength",
"entity",
- "muscle structure",
+ "entity",
+ "Phenotypic abnormality",
+ "Muscle weakness (HPO)",
+ "specifically dependent continuant",
"organ",
- "muscle organ",
+ "multicellular organism",
+ "phenotype",
+ "independent continuant",
+ "decreased anatomical entity strength",
+ "Abnormality of the musculoskeletal system (HPO)",
+ "material entity",
+ "anatomical entity",
+ "anatomical structure",
"musculature of body",
"musculature",
"abnormal anatomical entity",
- "Muscle weakness (HPO)",
- "Abnormality of the musculature (HPO)",
"abnormality of anatomical entity physiology",
"abnormal anatomical entity",
- "entity",
- "material entity",
- "anatomical entity",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
+ "muscle structure",
],
"frequency_qualifier_label": "Obligate (HPO)",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
"frequency_qualifier_namespace": "HP",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0000001", "HP:0040280"],
+ "frequency_qualifier_closure_label": ["Obligate (HPO)", "Frequency (HPO)", "All (HPO)"],
"evidence_count": 3,
"grouping_key": "MONDO:0009676🍪🍪biolink:has_phenotype🍪HP:0003701",
},
diff --git a/backend/tests/fixtures/associations.py b/backend/tests/fixtures/associations.py
index b85ec11ce..a321b8143 100644
--- a/backend/tests/fixtures/associations.py
+++ b/backend/tests/fixtures/associations.py
@@ -9,280 +9,132 @@ def associations():
"total": 4838,
"items": [
{
- "id": "uuid:c9c8bf2f-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e12a2a1-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0008050",
- "original_subject": "OMIM:160500",
+ "subject": "MONDO:0035432",
+ "original_subject": "Orphanet:565899",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
+ "MONDO:0000001",
+ "MONDO:0020121",
"MONDO:0003847",
"BFO:0000001",
- "MONDO:0020121",
- "MONDO:0019952",
+ "MONDO:0016106",
+ "MONDO:0005336",
"BFO:0000017",
+ "MONDO:0003939",
+ "MONDO:0035432",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0016971",
+ "MONDO:0005071",
+ "BFO:0000002",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
"MONDO:0700223",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "OGMS:0000031",
],
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject_label": "POMGNT2-related limb-girdle muscular dystrophy R24",
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
"disease",
+ "realizable entity",
+ "disease",
+ "POMGNT2-related limb-girdle muscular dystrophy R24",
"muscle tissue disorder",
- "congenital nervous system disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
+ "limb-girdle muscular dystrophy",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "disposition",
+ "human disease",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
"nervous system disorder",
- "congenital myopathy",
- "realizable entity",
- "specifically dependent continuant",
+ "entity",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "muscular dystrophy",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
],
"subject_taxon": None,
"subject_taxon_label": None,
"predicate": "biolink:has_phenotype",
- "object": "HP:0011399",
+ "object": "HP:0002465",
"original_object": None,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "UPHENO:0014121",
- "HP:0002814",
- "UPHENO:0068971",
- "UPHENO:0001005",
- "HP:0009127",
- "UPHENO:0014120",
- "UPHENO:0075195",
- "HP:0030236",
- "UPHENO:0020584",
- "UPHENO:0076692",
- "UPHENO:0003070",
- "PATO:0000001",
- "UPHENO:0012541",
- "BFO:0000004",
- "UBERON:0004708",
- "UBERON:0000154",
- "UBERON:0014892",
- "UBERON:0006058",
- "UBERON:0002529",
- "UBERON:0006067",
- "HP:0000001",
- "UPHENO:0002644",
- "UPHENO:0013936",
- "HP:0003202",
- "UPHENO:0075952",
- "UPHENO:0001002",
- "HP:0000118",
- "UPHENO:0015280",
- "UPHENO:0001003",
- "UPHENO:0076710",
- "BFO:0000001",
+ "UPHENO:0002536",
"BFO:0000001",
- "BFO:0000040",
- "UBERON:0010000",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
- "UBERON:0010709",
- "UBERON:0000366",
- "UBERON:0003661",
- "UBERON:0010890",
- "UBERON:0010538",
- "UBERON:0004466",
- "UBERON:0004256",
- "UBERON:0003823",
- "UPHENO:0075696",
- "HP:0002981",
- "HP:0003797",
- "UPHENO:0014111",
- "HP:0001430",
+ "UBERON:0000465",
+ "UPHENO:0082875",
"BFO:0000002",
- "HP:0008944",
+ "UPHENO:0004523",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UPHENO:0001002",
"BFO:0000020",
- "HP:0003011",
- "UPHENO:0002536",
- "HP:0001437",
- "UPHENO:0078056",
- "HP:0040064",
"BFO:0000002",
- "PR:000050567",
- "UBERON:0002101",
- "UBERON:0004709",
- "UBERON:0005090",
- "UBERON:0018254",
- "UBERON:0002103",
- "UBERON:0010707",
- "UBERON:0001630",
- "UBERON:0000026",
- "UBERON:0010758",
- "UBERON:0007271",
- "UBERON:0014792",
- "UBERON:0004482",
- "UBERON:0001383",
- "UBERON:0008784",
- "UBERON:0002471",
- "HP:0007210",
"UPHENO:0001001",
- "UPHENO:0075777",
- "HP:0011805",
- "HP:0003693",
- "UPHENO:0002816",
- "HP:0011399",
- "UPHENO:0081581",
- "HP:0033127",
- "UPHENO:0019778",
- "UPHENO:0002647",
- "UPHENO:0013920",
- "UPHENO:0002830",
- "UBERON:0001062",
- "UBERON:0000465",
- "RO:0002577",
+ "UPHENO:0001003",
+ "BFO:0000001",
+ "UPHENO:0075696",
+ "UPHENO:0002433",
+ "HP:0012638",
+ "BFO:0000004",
"UBERON:0000061",
- "UBERON:0015212",
- "UBERON:0000475",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "UBERON:0000978",
- "UBERON:0007270",
- "UBERON:0004480",
- "UBERON:0003663",
- "UBERON:0014795",
- "UBERON:0008230",
+ "UBERON:0000468",
+ "HP:0002167",
+ "PATO:0000001",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "HP:0000001",
+ "HP:0002465",
+ "UPHENO:0001005",
+ "HP:0000707",
+ "HP:0011446",
+ "UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0001016",
],
- "object_label": "Tibialis atrophy (HPO)",
+ "object_label": "Poor speech (HPO)",
"object_closure_label": [
+ "abnormality of anatomical entity physiology",
+ "Neurological speech impairment (HPO)",
+ "Abnormality of higher mental function (HPO)",
+ "abnormal anatomical entity",
+ "specifically dependent continuant",
+ "phenotype by ontology source",
+ "abnormal nervous system",
+ "continuant",
+ "material anatomical entity",
+ "nervous system",
"All (HPO)",
- "abnormal musculature of lower limb",
- "Abnormality of the lower limb (HPO)",
- "decreased size of the anatomical entity",
- "Phenotypic abnormality",
+ "Poor speech (HPO)",
+ "abnormal phenotype by ontology source",
"Phenotypic abnormality (HPO)",
- "Distal amyotrophy (HPO)",
- "abnormal musculature",
- "Tibialis atrophy (HPO)",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "abnormal musculature of limb",
- "independent continuant",
- "material anatomical entity",
- "system",
- "paired limb/fin",
- "lateral structure",
- "pelvic complex",
- "appendage musculature",
- "musculature of pelvic complex",
- "musculature of leg",
- "hindlimb zeugopod muscle",
- "hindlimb zeugopod",
- "musculature of limb atrophy",
- "Limb-girdle muscle atrophy (HPO)",
- "skeletal musculature atrophy",
- "abnormal hindlimb zeugopod muscle",
- "Abnormal skeletal muscle morphology (HPO)",
- "abnormal anatomical entity morphology in the independent continuant",
- "phenotype by ontology source",
- "Abnormality of muscle size (HPO)",
- "Abnormality of the musculature of the lower limbs (HPO)",
- "tibialis atrophy",
- "Abnormality of limbs (HPO)",
+ "Abnormality of the nervous system (HPO)",
+ "entity",
+ "Phenotypic abnormality",
+ "abnormality of nervous system physiology",
"quality",
- "decreased size of the anatomical entity in the independent continuant",
- "continuant",
- "protein-containing material entity",
- "hindlimb",
- "appendage girdle complex",
- "appendage",
- "subdivision of organism along appendicular axis",
- "flexor muscle",
- "limb muscle",
- "pelvic complex muscle",
- "paired limb/fin segment",
- "musculature of lower limb",
- "muscle of leg",
- "lower limb segment",
- "zeugopod",
- "Lower limb amyotrophy (HPO)",
+ "multicellular organism",
"phenotype",
- "abnormal phenotype by ontology source",
- "Abnormality of the musculature of the limbs (HPO)",
- "musculature of lower limb atrophy",
- "abnormal size of anatomical entity",
- "abnormal muscle organ morphology",
- "abnormal muscle organ morphology",
+ "independent continuant",
"entity",
+ "Abnormal nervous system physiology (HPO)",
+ "material entity",
"anatomical entity",
"anatomical structure",
- "muscle structure",
- "skeletal musculature",
- "organism subdivision",
- "organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "leg",
- "pelvic appendage musculature",
- "musculature of limb",
- "hindlimb muscle",
- "pelvic appendage muscle",
- "tibialis",
- "abnormal anatomical entity",
- "Abnormality of the calf (HPO)",
- "anatomical entity atrophy",
- "Skeletal muscle atrophy (HPO)",
- "abnormal hindlimb zeugopod",
- "Abnormality of the calf musculature (HPO)",
"continuant",
- "Distal lower limb amyotrophy (HPO)",
- "specifically dependent continuant",
- "Abnormality of the musculature (HPO)",
+ "abnormality of anatomical entity physiology",
"abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "abnormal anatomical entity morphology",
- "abnormal leg",
- "entity",
- "muscle organ atrophy",
- "abnormal limb",
- "material entity",
- "limb",
- "pelvic appendage",
"multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "posterior region of body",
- "skeletal muscle organ",
- "multi-limb segment region",
- "limb segment",
- "musculature of hindlimb zeugopod",
],
"object_taxon": None,
"object_taxon_label": None,
@@ -291,18 +143,18 @@ def associations():
"negated": None,
"pathway": None,
"evidence_count": 2,
- "has_evidence": ["ECO:0000269"],
- "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}],
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0011399",
+ "has_evidence": ["ECO:0000304"],
+ "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}],
+ "grouping_key": "MONDO:0035432🍪🍪biolink:has_phenotype🍪HP:0002465",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype",
},
- "publications": ["PMID:17548557"],
- "publications_links": [{"id": "PMID:17548557", "url": "http://identifiers.org/pubmed/17548557"}],
+ "publications": ["orphanet:565899"],
+ "publications_links": [{"id": "orphanet:565899", "url": None}],
"qualifiers": [],
- "frequency_qualifier": "HP:0040280",
+ "frequency_qualifier": "HP:0040282",
"onset_qualifier": None,
"sex_qualifier": None,
"stage_qualifier": None,
@@ -311,11 +163,11 @@ def associations():
"qualifiers_category": None,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"],
"onset_qualifier_label": None,
"onset_qualifier_namespace": None,
"onset_qualifier_category": None,
@@ -333,220 +185,258 @@ def associations():
"stage_qualifier_closure_label": [],
},
{
- "id": "uuid:c9c8bf30-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e12a2a3-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0008050",
- "original_subject": "OMIM:160500",
+ "subject": "MONDO:0035432",
+ "original_subject": "Orphanet:565899",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
+ "MONDO:0000001",
+ "MONDO:0020121",
"MONDO:0003847",
"BFO:0000001",
- "MONDO:0020121",
- "MONDO:0019952",
+ "MONDO:0016106",
+ "MONDO:0005336",
"BFO:0000017",
+ "MONDO:0003939",
+ "MONDO:0035432",
"BFO:0000020",
- "MONDO:0020120",
+ "MONDO:0002081",
+ "MONDO:0016971",
+ "MONDO:0005071",
+ "BFO:0000002",
+ "MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
"MONDO:0700223",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "OGMS:0000031",
],
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject_label": "POMGNT2-related limb-girdle muscular dystrophy R24",
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
"disease",
+ "realizable entity",
+ "disease",
+ "POMGNT2-related limb-girdle muscular dystrophy R24",
"muscle tissue disorder",
- "congenital nervous system disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
+ "limb-girdle muscular dystrophy",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "disposition",
+ "human disease",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
"nervous system disorder",
- "congenital myopathy",
- "realizable entity",
- "specifically dependent continuant",
+ "entity",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "muscular dystrophy",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
],
"subject_taxon": None,
"subject_taxon_label": None,
"predicate": "biolink:has_phenotype",
- "object": "HP:0031295",
+ "object": "HP:0008981",
"original_object": None,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "UPHENO:0001005",
- "BFO:0000002",
- "UPHENO:0075195",
- "UPHENO:0020584",
- "UPHENO:0076692",
- "BFO:0000004",
- "UBERON:0004535",
- "UBERON:0011676",
- "UBERON:0013701",
- "UBERON:0002081",
- "UBERON:0000915",
- "UBERON:0002100",
- "UBERON:0005181",
- "UBERON:0002075",
- "UBERON:0015228",
- "HP:0000001",
- "UPHENO:0019897",
- "HP:0030680",
- "HP:0000118",
- "HP:0001627",
- "BFO:0000020",
- "UPHENO:0019919",
- "UPHENO:0076776",
- "UPHENO:0015280",
- "UPHENO:0001020",
- "UPHENO:0001003",
- "BFO:0000001",
- "PATO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0000064",
- "UBERON:0002079",
- "UPHENO:0075696",
- "UPHENO:0015303",
- "HP:0001626",
- "UPHENO:0080362",
- "UPHENO:0065599",
- "HP:0031295",
- "UPHENO:0002536",
- "UPHENO:0076810",
+ "HP:0008981",
+ "UPHENO:0084535",
+ "UPHENO:0002816",
+ "HP:0030236",
"PR:000050567",
"UBERON:0000465",
- "UBERON:0004120",
- "UBERON:0035553",
- "UBERON:0000948",
- "UBERON:0001009",
- "UBERON:0004151",
- "UBERON:0009569",
- "UBERON:0013702",
- "UBERON:0005177",
- "UBERON:0003103",
- "UBERON:0015410",
- "UPHENO:0001001",
+ "RO:0002577",
+ "UPHENO:0015280",
+ "HP:0001437",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UBERON:0011216",
+ "UBERON:0000154",
+ "UBERON:0006067",
"UPHENO:0001002",
- "UPHENO:0015324",
- "HP:0025579",
+ "HP:0001430",
+ "UPHENO:0075195",
+ "UPHENO:0019778",
+ "UPHENO:0084489",
+ "BFO:0000002",
+ "UBERON:0002101",
+ "UBERON:0004709",
+ "UBERON:0015212",
+ "UBERON:0001630",
+ "UPHENO:0001001",
+ "UPHENO:0075777",
+ "HP:0011805",
+ "HP:0003712",
+ "UPHENO:0002647",
+ "BFO:0000001",
+ "UBERON:0004482",
+ "UBERON:0001383",
+ "UBERON:0008784",
+ "UBERON:0002471",
+ "UPHENO:0075696",
+ "UPHENO:0001005",
+ "HP:0009127",
+ "BFO:0000020",
"UPHENO:0001072",
"UPHENO:0081581",
- "HP:0005120",
- "UPHENO:0015329",
- "BFO:0000002",
- "UBERON:0001062",
- "RO:0002577",
+ "HP:0033127",
+ "UPHENO:0001003",
+ "UPHENO:0076692",
+ "UPHENO:0003070",
+ "UPHENO:0002830",
+ "BFO:0000004",
+ "UBERON:0004708",
"UBERON:0000061",
- "UBERON:0015212",
- "UBERON:0010314",
- "UBERON:0010000",
"UBERON:0000475",
"UBERON:0000062",
- "UBERON:0005178",
- "UBERON:0007100",
+ "UBERON:0000468",
+ "UBERON:0010709",
+ "HP:0002981",
+ "UPHENO:0065599",
+ "BFO:0000002",
+ "HP:0003011",
+ "UPHENO:0002536",
+ "UPHENO:0084715",
+ "UPHENO:0076710",
+ "HP:0040064",
+ "PATO:0000001",
+ "UBERON:0002103",
+ "UBERON:0010707",
+ "UBERON:0000026",
+ "UBERON:0010758",
+ "UBERON:0006058",
+ "UBERON:0004466",
+ "UBERON:0004256",
+ "UBERON:0003823",
+ "HP:0002814",
+ "UPHENO:0075952",
+ "HP:0000118",
+ "UPHENO:0020584",
+ "HP:0008968",
+ "UBERON:0007271",
+ "UBERON:0014792",
+ "UBERON:0003661",
+ "UBERON:0010890",
+ "UBERON:0010538",
+ "HP:0000001",
+ "UPHENO:0002644",
+ "BFO:0000001",
+ "UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0005090",
+ "UBERON:0018254",
+ "UBERON:0000383",
+ "UBERON:0001015",
+ "UBERON:0014892",
+ "UBERON:0000978",
+ "UBERON:0007270",
+ "UBERON:0004480",
+ "UBERON:0003663",
+ "UBERON:0014795",
+ "UBERON:0002529",
],
- "object_label": "Left atrial enlargement (HPO)",
+ "object_label": "Calf muscle hypertrophy (HPO)",
"object_closure_label": [
- "All (HPO)",
- "abnormal cardiac atrium morphology",
- "abnormal cardiovascular system",
"increased size of the anatomical entity in independent continuant",
- "Phenotypic abnormality (HPO)",
- "abnormal anatomical entity morphology in the heart",
- "Abnormal left atrium morphology (HPO)",
- "increased size of the anatomical entity",
- "abnormal multicellular organism morphology",
- "Abnormal cardiac atrium morphology (HPO)",
- "quality",
- "independent continuant",
- "system",
- "cardiovascular system",
- "lateral structure",
- "structure with developmental contribution from neural crest",
- "multicellular anatomical structure",
- "left cardiac atrium",
- "Abnormality of the cardiovascular system (HPO)",
- "Phenotypic abnormality",
- "Abnormal heart morphology (HPO)",
- "specifically dependent continuant",
- "abnormal left cardiac atrium morphology",
- "abnormal cardiovascular system morphology",
- "abnormal anatomical entity morphology in the independent continuant",
- "increased size of the left cardiac atrium",
- "phenotype by ontology source",
- "abnormal heart morphology",
+ "abnormal hindlimb zeugopod muscle",
+ "Abnormal skeletal muscle morphology (HPO)",
+ "Skeletal muscle hypertrophy (HPO)",
+ "abnormal anatomical entity",
+ "musculature of hindlimb zeugopod",
+ "abnormal anatomical entity",
+ "abnormal phenotype by ontology source",
+ "Abnormality of the musculature of the limbs (HPO)",
+ "Abnormality of the musculature (HPO)",
+ "Abnormality of the musculature of the lower limbs (HPO)",
+ "abnormal musculature of limb",
+ "continuant",
"protein-containing material entity",
"material anatomical entity",
- "left cardiac chamber",
- "heart",
- "subdivision of trunk",
- "body proper",
- "trunk region element",
- "compound organ",
- "heart plus pericardium",
- "phenotype",
- "abnormal phenotype by ontology source",
+ "system",
+ "multi-limb segment region",
+ "All (HPO)",
+ "abnormal musculature of lower limb",
"continuant",
- "abnormal size of anatomical entity",
+ "abnormal musculature",
+ "abnormal muscle organ morphology",
+ "hypertrophic multicellular anatomical structure",
+ "organ system subdivision",
+ "muscle organ",
+ "appendage",
+ "subdivision of organism along appendicular axis",
+ "Abnormality of the lower limb (HPO)",
+ "Phenotypic abnormality (HPO)",
+ "abnormal anatomical entity morphology",
+ "Muscle hypertrophy of the lower extremities (HPO)",
"entity",
- "anatomical entity",
- "anatomical structure",
- "mesoderm-derived structure",
+ "entity",
+ "leg",
+ "pelvic appendage musculature",
+ "musculature of limb",
+ "hindlimb muscle",
+ "pelvic appendage muscle",
+ "limb segment",
+ "Phenotypic abnormality",
+ "Abnormality of the calf musculature (HPO)",
+ "specifically dependent continuant",
+ "abnormal anatomical entity morphology",
+ "abnormal leg",
+ "quality",
"organism subdivision",
"organ",
- "circulatory system",
- "cardiac chamber",
- "thoracic cavity element",
- "primary circulatory organ",
- "abnormal anatomical entity",
- "abnormal cardiac atrium morphology in the heart",
- "Abnormality of cardiovascular system morphology (HPO)",
- "Left atrial enlargement (HPO)",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "abnormal anatomical entity morphology",
- "entity",
- "abnormal cardiac atrium morphology in the independent continuant",
- "continuant",
+ "multicellular organism",
+ "pelvic complex",
+ "musculature of lower limb",
+ "muscle of leg",
+ "lower limb segment",
+ "zeugopod",
+ "phenotype",
+ "abnormal hindlimb zeugopod",
+ "abnormal anatomical entity morphology in the independent continuant",
+ "abnormally increased volume of anatomical entity",
+ "independent continuant",
+ "posterior region of body",
+ "Calf muscle hypertrophy (HPO)",
+ "hypertrophic pelvic complex muscle",
+ "abnormal size of anatomical entity",
+ "increased size of the anatomical entity",
+ "abnormal multicellular organism morphology",
+ "Abnormality of the musculoskeletal system (HPO)",
+ "phenotype by ontology source",
+ "abnormal limb",
"material entity",
+ "anatomical entity",
+ "paired limb/fin",
+ "anatomical structure",
+ "limb",
+ "pelvic appendage",
+ "lateral structure",
+ "musculature of body",
+ "musculature",
+ "skeletal muscle organ",
+ "musculature of leg",
+ "hindlimb zeugopod muscle",
+ "hindlimb zeugopod",
+ "Abnormality of the calf (HPO)",
+ "Abnormality of muscle size (HPO)",
+ "abnormal muscle organ morphology",
+ "Abnormality of limbs (HPO)",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ part",
- "subdivision of organism along main body axis",
- "main body axis",
- "cardiac atrium",
- "thoracic segment of trunk",
- "trunk",
- "thoracic segment organ",
- "viscus",
- "circulatory organ",
+ "muscle structure",
+ "skeletal musculature",
+ "hindlimb",
+ "appendage girdle complex",
+ "appendage musculature",
+ "musculature of pelvic complex",
+ "limb muscle",
+ "pelvic complex muscle",
+ "paired limb/fin segment",
],
"object_taxon": None,
"object_taxon_label": None,
@@ -555,18 +445,18 @@ def associations():
"negated": None,
"pathway": None,
"evidence_count": 2,
- "has_evidence": ["ECO:0000269"],
- "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}],
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0031295",
+ "has_evidence": ["ECO:0000304"],
+ "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}],
+ "grouping_key": "MONDO:0035432🍪🍪biolink:has_phenotype🍪HP:0008981",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype",
},
- "publications": ["PMID:17548557"],
- "publications_links": [{"id": "PMID:17548557", "url": "http://identifiers.org/pubmed/17548557"}],
+ "publications": ["orphanet:565899"],
+ "publications_links": [{"id": "orphanet:565899", "url": None}],
"qualifiers": [],
- "frequency_qualifier": "HP:0040280",
+ "frequency_qualifier": "HP:0040282",
"onset_qualifier": None,
"sex_qualifier": None,
"stage_qualifier": None,
@@ -575,11 +465,11 @@ def associations():
"qualifiers_category": None,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"],
"onset_qualifier_label": None,
"onset_qualifier_namespace": None,
"onset_qualifier_category": None,
@@ -597,196 +487,220 @@ def associations():
"stage_qualifier_closure_label": [],
},
{
- "id": "uuid:c9c8bf31-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e12a2a4-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0008050",
- "original_subject": "OMIM:160500",
+ "subject": "MONDO:0035432",
+ "original_subject": "Orphanet:565899",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
+ "MONDO:0000001",
+ "MONDO:0020121",
"MONDO:0003847",
"BFO:0000001",
- "MONDO:0020121",
- "MONDO:0019952",
+ "MONDO:0016106",
+ "MONDO:0005336",
"BFO:0000017",
+ "MONDO:0003939",
+ "MONDO:0035432",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0016971",
+ "MONDO:0005071",
+ "BFO:0000002",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
"MONDO:0700223",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "OGMS:0000031",
],
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject_label": "POMGNT2-related limb-girdle muscular dystrophy R24",
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
"disease",
+ "realizable entity",
+ "disease",
+ "POMGNT2-related limb-girdle muscular dystrophy R24",
"muscle tissue disorder",
- "congenital nervous system disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
+ "limb-girdle muscular dystrophy",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "disposition",
+ "human disease",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
"nervous system disorder",
- "congenital myopathy",
- "realizable entity",
- "specifically dependent continuant",
+ "entity",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "muscular dystrophy",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
],
"subject_taxon": None,
"subject_taxon_label": None,
"predicate": "biolink:has_phenotype",
- "object": "HP:0002938",
+ "object": "HP:0008994",
"original_object": None,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "UPHENO:0001005",
- "HP:0009121",
- "UPHENO:0020584",
- "UPHENO:0076692",
- "BFO:0000001",
- "PATO:0000001",
- "BFO:0000004",
- "UBERON:0002204",
- "UBERON:0011676",
- "UBERON:0001137",
- "UBERON:0013701",
- "UBERON:0002100",
- "UBERON:0005462",
- "HP:0000001",
- "UPHENO:0076703",
- "HP:0000118",
- "BFO:0000020",
- "HP:0000925",
- "UPHENO:0015280",
- "UPHENO:0002964",
- "UPHENO:0001003",
- "HP:0003307",
- "UPHENO:0022529",
- "BFO:0000001",
+ "HP:0008994",
+ "UPHENO:0002816",
+ "UPHENO:0002536",
+ "PR:000050567",
+ "UBERON:0000465",
+ "RO:0002577",
+ "UPHENO:0082875",
+ "HP:0001437",
"BFO:0000040",
- "UBERON:0000467",
- "UBERON:0000468",
+ "UBERON:0001062",
"UBERON:0011216",
- "UPHENO:0075696",
- "HP:0000924",
- "UPHENO:0002536",
- "BFO:0000002",
- "UBERON:0004288",
- "UBERON:0009569",
- "UBERON:0013702",
- "UBERON:0000075",
- "UBERON:0002417",
- "UBERON:0011137",
- "UBERON:0006077",
- "UBERON:0011138",
- "UBERON:0002090",
- "UBERON:0005944",
- "UBERON:0001130",
- "UPHENO:0001001",
- "HP:0011842",
+ "UBERON:0000154",
+ "UBERON:0000026",
"UPHENO:0001002",
+ "HP:0001324",
+ "BFO:0000020",
+ "UPHENO:0080555",
+ "HP:0011804",
"BFO:0000002",
- "HP:0010674",
+ "UBERON:0002101",
+ "UBERON:0004709",
+ "UBERON:0015212",
+ "UPHENO:0001001",
+ "HP:0003701",
+ "HP:0011805",
+ "UPHENO:0001003",
+ "UPHENO:0002647",
+ "BFO:0000001",
+ "UBERON:0000061",
+ "UBERON:0004482",
+ "UBERON:0008784",
+ "UPHENO:0075696",
+ "UPHENO:0001005",
+ "HP:0009127",
"UPHENO:0081581",
"HP:0033127",
- "UPHENO:0002813",
- "HP:0002938",
- "UBERON:0001062",
- "UBERON:0000465",
- "UBERON:0000061",
- "UBERON:0034925",
+ "UPHENO:0076692",
+ "UPHENO:0003070",
+ "UPHENO:0002830",
+ "BFO:0000004",
+ "UBERON:0004708",
+ "UBERON:0000475",
+ "UBERON:0000062",
+ "UBERON:0000468",
+ "UBERON:0010709",
+ "HP:0003690",
+ "BFO:0000002",
+ "HP:0003011",
+ "UPHENO:0076710",
+ "HP:0040064",
+ "UBERON:0002103",
+ "UBERON:0010707",
+ "UBERON:0010758",
+ "UBERON:0006058",
+ "UPHENO:0002320",
+ "HP:0002814",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "PATO:0000001",
+ "UBERON:0007271",
+ "UBERON:0014792",
+ "UBERON:0010538",
+ "HP:0000001",
+ "UPHENO:0002644",
+ "UPHENO:0080556",
+ "BFO:0000001",
"UBERON:0010000",
- "UBERON:0000475",
- "UBERON:0010912",
- "UBERON:0001434",
- "UBERON:0006074",
+ "UBERON:0000467",
+ "UBERON:0005090",
+ "UBERON:0001630",
+ "UBERON:0000383",
+ "UBERON:0001015",
+ "UBERON:0000978",
+ "UBERON:0007270",
+ "UBERON:0004480",
+ "UBERON:0002529",
],
- "object_label": "Lumbar hyperlordosis (HPO)",
+ "object_label": "Proximal muscle weakness in lower limbs (HPO)",
"object_closure_label": [
- "All (HPO)",
- "Phenotypic abnormality (HPO)",
- "Abnormality of the curvature of the vertebral column (HPO)",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "Hyperlordosis (HPO)",
- "abnormal postcranial axial skeleton morphology",
- "independent continuant",
- "material anatomical entity",
- "multicellular anatomical structure",
- "musculoskeletal system",
- "abdominal segment of trunk",
- "axial skeletal system",
- "subdivision of vertebral column",
- "postcranial axial skeletal system",
- "postcranial axial skeleton",
- "axial skeleton plus cranial skeleton",
- "vertebral column",
- "Abnormal skeletal morphology (HPO)",
- "Phenotypic abnormality",
- "continuant",
+ "abnormality of anatomical entity physiology",
+ "Proximal muscle weakness (HPO)",
+ "Abnormal skeletal muscle morphology (HPO)",
+ "quality",
+ "abnormal anatomical entity",
+ "abnormal phenotype by ontology source",
+ "Abnormality of the musculature of the limbs (HPO)",
"specifically dependent continuant",
- "Abnormality of the vertebral column (HPO)",
- "abnormal anatomical entity morphology in the independent continuant",
- "abnormal skeletal system",
+ "Abnormality of the musculature (HPO)",
"phenotype by ontology source",
- "quality",
+ "Abnormality of the musculature of the lower limbs (HPO)",
+ "abnormal musculature of limb",
"continuant",
- "subdivision of trunk",
- "body proper",
- "subdivision of skeletal system",
- "phenotype",
- "abnormal phenotype by ontology source",
- "Abnormal axial skeleton morphology (HPO)",
- "abnormal vertebral column",
- "Lumbar hyperlordosis (HPO)",
+ "protein-containing material entity",
+ "material anatomical entity",
+ "system",
+ "muscle organ",
+ "multi-limb segment region",
+ "All (HPO)",
+ "abnormal musculature of lower limb",
+ "continuant",
+ "Proximal muscle weakness in lower limbs (HPO)",
+ "abnormal musculature",
+ "Abnormal muscle physiology (HPO)",
+ "organ system subdivision",
+ "subdivision of organism along appendicular axis",
+ "abnormality of muscle organ physiology",
+ "Abnormality of the lower limb (HPO)",
+ "Phenotypic abnormality (HPO)",
+ "Limb muscle weakness (HPO)",
+ "decreased muscle organ strength",
"entity",
- "anatomical entity",
+ "entity",
+ "leg",
+ "pelvic appendage musculature",
+ "musculature of limb",
+ "limb segment",
+ "Phenotypic abnormality",
+ "Muscle weakness (HPO)",
+ "abnormal anatomical entity morphology",
+ "abnormal leg",
"anatomical structure",
- "anatomical collection",
- "skeleton",
"organism subdivision",
- "subdivision of skeleton",
- "skeletal system",
- "lumbar region of vertebral column",
- "abnormal anatomical entity",
- "abnormal skeletal system morphology",
- "Abnormality of the skeletal system (HPO)",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "abnormal anatomical entity morphology",
- "entity",
+ "organ",
+ "multicellular organism",
+ "pelvic complex",
+ "musculature of lower limb",
+ "lower limb segment",
+ "phenotype",
+ "independent continuant",
+ "posterior region of body",
+ "appendage",
+ "decreased anatomical entity strength",
+ "abnormal multicellular organism morphology",
+ "Abnormality of the musculoskeletal system (HPO)",
+ "abnormal limb",
"material entity",
+ "anatomical entity",
+ "paired limb/fin",
+ "limb",
+ "pelvic appendage",
+ "lateral structure",
+ "musculature of body",
+ "musculature",
+ "abnormality of anatomical entity physiology",
+ "abnormal anatomical entity",
+ "abnormal muscle organ morphology",
+ "Abnormality of limbs (HPO)",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "subdivision of organism along main body axis",
- "dorsum",
- "main body axis",
- "trunk",
- "lower back",
+ "muscle structure",
+ "hindlimb",
+ "appendage girdle complex",
+ "appendage musculature",
+ "musculature of pelvic complex",
+ "paired limb/fin segment",
],
"object_taxon": None,
"object_taxon_label": None,
@@ -795,18 +709,18 @@ def associations():
"negated": None,
"pathway": None,
"evidence_count": 2,
- "has_evidence": ["ECO:0000269"],
- "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}],
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0002938",
+ "has_evidence": ["ECO:0000304"],
+ "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}],
+ "grouping_key": "MONDO:0035432🍪🍪biolink:has_phenotype🍪HP:0008994",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype",
},
- "publications": ["PMID:17548557"],
- "publications_links": [{"id": "PMID:17548557", "url": "http://identifiers.org/pubmed/17548557"}],
+ "publications": ["orphanet:565899"],
+ "publications_links": [{"id": "orphanet:565899", "url": None}],
"qualifiers": [],
- "frequency_qualifier": "HP:0040280",
+ "frequency_qualifier": "HP:0040282",
"onset_qualifier": None,
"sex_qualifier": None,
"stage_qualifier": None,
@@ -815,11 +729,11 @@ def associations():
"qualifiers_category": None,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"],
"onset_qualifier_label": None,
"onset_qualifier_namespace": None,
"onset_qualifier_category": None,
@@ -837,214 +751,240 @@ def associations():
"stage_qualifier_closure_label": [],
},
{
- "id": "uuid:c9c8bf38-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df81-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0008050",
- "original_subject": "OMIM:160500",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
+ "myotonic syndrome",
],
"subject_taxon": None,
"subject_taxon_label": None,
"predicate": "biolink:has_phenotype",
- "object": "HP:0001265",
+ "object": "HP:0000256",
"original_object": None,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "UPHENO:0082875",
- "UPHENO:0049622",
- "UPHENO:0001005",
- "BFO:0000020",
- "UPHENO:0050606",
- "HP:0012638",
- "BFO:0000015",
- "BFO:0000004",
- "GO:0050882",
- "NBO:0000338",
- "GO:0050905",
- "UBERON:0001016",
- "HP:0000001",
- "UPHENO:0001001",
- "UPHENO:0080585",
- "HP:0001265",
- "HP:0031826",
- "UPHENO:0001002",
- "HP:0000118",
- "UPHENO:0052178",
- "UPHENO:0002433",
- "HP:0001315",
- "UPHENO:0001003",
- "HP:0000708",
- "HP:0011446",
- "PATO:0000001",
+ "HP:0000256",
+ "UPHENO:0002536",
+ "UPHENO:0081566",
+ "HP:0000240",
+ "UBERON:0000465",
+ "UPHENO:0075220",
+ "UPHENO:0001208",
+ "UPHENO:0002844",
+ "UPHENO:0015280",
"BFO:0000001",
"BFO:0000040",
"UBERON:0001062",
- "GO:0050896",
- "GO:0032501",
- "GO:0060004",
- "GO:0050881",
- "NBO:0000313",
- "GO:0050877",
- "UBERON:0000467",
- "UBERON:0000468",
- "NBO:0000403",
- "NBO:0000001",
- "NBO:0000388",
- "UPHENO:0075696",
- "UPHENO:0078622",
- "UPHENO:0049586",
- "UPHENO:0080377",
- "HP:0100022",
- "UPHENO:0050613",
- "UPHENO:0005433",
- "UPHENO:0002332",
- "UPHENO:0002536",
- "UPHENO:0079826",
- "UPHENO:0004523",
- "UPHENO:0049587",
- "BFO:0000003",
- "BFO:0000002",
- "GO:0008150",
- "GO:0009605",
- "GO:0050879",
- "GO:0007610",
- "GO:0003008",
- "NBO:0000389",
- "UPHENO:0052915",
+ "UBERON:0011216",
+ "UBERON:0011676",
+ "UBERON:0013701",
+ "UPHENO:0075148",
+ "UPHENO:0001002",
+ "UPHENO:0075195",
+ "HP:0009121",
"BFO:0000002",
- "UPHENO:0005625",
- "UPHENO:0050079",
- "HP:0000707",
- "UPHENO:0079833",
+ "UPHENO:0001001",
+ "HP:0011842",
+ "BFO:0000020",
+ "UPHENO:0002964",
+ "UPHENO:0001003",
+ "UPHENO:0021447",
"BFO:0000001",
- "UBERON:0000465",
"UBERON:0000061",
+ "UBERON:0034925",
+ "HP:0040194",
+ "UPHENO:0075696",
+ "UPHENO:0001005",
+ "UPHENO:0002764",
+ "UPHENO:0001072",
+ "UPHENO:0081581",
+ "HP:0033127",
+ "UPHENO:0076692",
+ "UPHENO:0022529",
+ "BFO:0000004",
+ "UBERON:0004288",
+ "UBERON:0000475",
+ "UBERON:0000468",
+ "UBERON:0000153",
+ "UPHENO:0065599",
+ "HP:0000924",
+ "UBERON:0003129",
+ "UBERON:0007811",
+ "UBERON:0013702",
+ "UBERON:0000075",
+ "UBERON:0000033",
+ "UPHENO:0076703",
+ "HP:0000152",
+ "HP:0000118",
+ "BFO:0000002",
+ "UPHENO:0020584",
+ "PATO:0000001",
+ "UBERON:0010314",
+ "UBERON:0011137",
+ "UBERON:0010323",
+ "UBERON:0011138",
+ "UBERON:0002090",
+ "UBERON:0005944",
+ "HP:0000001",
+ "HP:0000929",
+ "HP:0000234",
"UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0002204",
+ "UBERON:0010912",
+ "UBERON:0001434",
],
- "object_label": "Hyporeflexia (HPO)",
+ "object_label": "Macrocephaly (HPO)",
"object_closure_label": [
- "All (HPO)",
- "abnormal behavior",
- "Abnormality of movement (HPO)",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "decreased reflex",
- "abnormal response to external stimulus",
- "Abnormality of the nervous system (HPO)",
- "Behavioral abnormality (HPO)",
- "Abnormality of higher mental function (HPO)",
- "abnormal voluntary movement behavior",
- "entity",
+ "abnormal size of skull",
+ "increased size of the anatomical entity in independent continuant",
+ "Abnormal skeletal morphology (HPO)",
+ "specifically dependent continuant",
+ "abnormal skeletal system",
"quality",
- "process",
- "independent continuant",
- "material anatomical entity",
- "multicellular anatomical structure",
- "nervous system",
- "voluntary movement behavior",
- "body part movement",
- "reflexive behavior",
- "abnormality of anatomical entity physiology",
- "phenotype",
- "continuant",
- "decreased qualitatively biological_process",
- "abnormality of nervous system physiology",
- "Reduced tendon reflexes (HPO)",
+ "Increased head circumference (HPO)",
+ "abnormal anatomical entity",
+ "abnormal phenotype by ontology source",
+ "abnormal craniocervical region",
"phenotype by ontology source",
- "abnormal behavior process",
- "abnormal nervous system",
- "abnormal biological_process",
- "Abnormal nervous system physiology (HPO)",
- "occurrent",
+ "abnormal head morphology",
"continuant",
- "biological_process",
- "response to external stimulus",
- "multicellular organismal movement",
- "behavior",
- "system process",
- "reflex",
- "musculoskeletal movement",
- "behavior process",
- "nervous system process",
- "involuntary movement behavior",
- "decreased qualitatively response to stimulus",
- "abnormal phenotype by ontology source",
- "specifically dependent continuant",
- "abnormal voluntary musculoskeletal movement",
+ "material anatomical entity",
+ "musculoskeletal system",
+ "head",
+ "All (HPO)",
+ "organ system subdivision",
+ "craniocervical region",
+ "body proper",
+ "subdivision of skeletal system",
+ "Abnormality of the skeletal system (HPO)",
+ "Phenotypic abnormality (HPO)",
+ "continuant",
+ "Abnormality of the head (HPO)",
+ "abnormal anatomical entity morphology",
"entity",
+ "structure with developmental contribution from neural crest",
+ "abnormal size of head",
+ "Phenotypic abnormality",
+ "abnormal anatomical entity morphology",
+ "Abnormality of skull size (HPO)",
"anatomical structure",
- "abnormal anatomical entity",
- "abnormal voluntary movement behavior",
- "changed biological_process rate",
- "abnormal response to stimulus",
- "abnormal behavior process",
- "Hyporeflexia (HPO)",
- "Abnormal reflex (HPO)",
- "abnormal musculoskeletal movement",
- "decreased biological_process",
- "abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
+ "anatomical collection",
+ "skeleton",
+ "organism subdivision",
+ "multicellular organism",
+ "anterior region of body",
+ "phenotype",
+ "abnormal skeletal system morphology",
+ "Abnormality of head or neck (HPO)",
+ "Abnormal skull morphology (HPO)",
+ "abnormal anatomical entity morphology in the independent continuant",
+ "entity",
+ "independent continuant",
+ "subdivision of organism along main body axis",
+ "main body axis",
+ "Macrocephaly (HPO)",
+ "abnormal size of anatomical entity",
+ "Abnormal axial skeleton morphology (HPO)",
+ "increased size of the anatomical entity",
+ "abnormal multicellular organism morphology",
+ "Abnormality of the musculoskeletal system (HPO)",
+ "abnormal postcranial axial skeleton morphology",
"material entity",
"anatomical entity",
- "response to stimulus",
- "multicellular organismal process",
+ "subdivision of skeleton",
+ "skeletal system",
+ "increased size of the head",
+ "abnormal head",
+ "abnormal anatomical entity",
+ "abnormal skull morphology",
+ "multicellular anatomical structure",
"anatomical system",
- "voluntary musculoskeletal movement",
- "kinesthetic behavior",
- "neuromuscular process",
- "multicellular organism",
+ "skull",
+ "axial skeletal system",
+ "cranial skeletal system",
+ "postcranial axial skeletal system",
+ "postcranial axial skeleton",
+ "axial skeleton plus cranial skeleton",
],
"object_taxon": None,
"object_taxon_label": None,
@@ -1053,18 +993,18 @@ def associations():
"negated": None,
"pathway": None,
"evidence_count": 2,
- "has_evidence": ["ECO:0000269"],
- "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}],
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0001265",
+ "has_evidence": ["ECO:0000304"],
+ "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}],
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0000256",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype",
},
- "publications": ["PMID:17548557"],
- "publications_links": [{"id": "PMID:17548557", "url": "http://identifiers.org/pubmed/17548557"}],
+ "publications": ["orphanet:589821"],
+ "publications_links": [{"id": "orphanet:589821", "url": None}],
"qualifiers": [],
- "frequency_qualifier": "HP:0040280",
+ "frequency_qualifier": "HP:0040281",
"onset_qualifier": None,
"sex_qualifier": None,
"stage_qualifier": None,
@@ -1073,11 +1013,11 @@ def associations():
"qualifiers_category": None,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Very frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040281", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Very frequent (HPO)"],
"onset_qualifier_label": None,
"onset_qualifier_namespace": None,
"onset_qualifier_category": None,
@@ -1095,228 +1035,248 @@ def associations():
"stage_qualifier_closure_label": [],
},
{
- "id": "uuid:c9c8bf3f-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df82-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0008050",
- "original_subject": "OMIM:160500",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
+ "myotonic syndrome",
],
"subject_taxon": None,
"subject_taxon_label": None,
"predicate": "biolink:has_phenotype",
- "object": "HP:0009053",
+ "object": "HP:0000297",
"original_object": None,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
+ "HP:0011799",
+ "UPHENO:0002816",
+ "UPHENO:0002536",
+ "UBERON:0000465",
+ "RO:0002577",
"UPHENO:0082875",
- "UPHENO:0002320",
- "HP:0002814",
- "UPHENO:0001005",
- "HP:0009127",
- "UPHENO:0076692",
- "UPHENO:0003070",
- "BFO:0000004",
- "UBERON:0004708",
- "UBERON:0000154",
- "UBERON:0000026",
- "UBERON:0014892",
- "UBERON:0006058",
- "UBERON:0002529",
- "HP:0000001",
- "HP:0000118",
- "BFO:0000002",
- "BFO:0000020",
- "UPHENO:0076710",
- "BFO:0000001",
- "PATO:0000001",
+ "UPHENO:0002910",
"BFO:0000001",
"BFO:0000040",
- "UBERON:0000467",
- "UBERON:0000468",
+ "UBERON:0001062",
"UBERON:0011216",
- "UBERON:0010709",
- "UBERON:0010890",
- "UBERON:0010538",
- "UPHENO:0075696",
- "UPHENO:0080575",
- "HP:0001324",
- "HP:0003690",
- "HP:0003011",
- "UPHENO:0002332",
- "UPHENO:0001003",
- "UPHENO:0002536",
- "HP:0002460",
- "HP:0040064",
- "HP:0009053",
+ "UBERON:0011676",
+ "UBERON:0013701",
+ "UPHENO:0001002",
"HP:0011804",
- "PR:000050567",
- "UBERON:0000465",
- "UBERON:0002101",
- "UBERON:0004709",
- "UBERON:0005090",
- "UBERON:0018254",
- "UBERON:0002103",
- "UBERON:0010707",
+ "BFO:0000002",
"UBERON:0001630",
- "UBERON:0010758",
- "UBERON:0007271",
- "UBERON:0014792",
- "UBERON:0008784",
- "HP:0007340",
+ "UBERON:0002376",
+ "UBERON:0015789",
"UPHENO:0001001",
"HP:0011805",
- "UPHENO:0001002",
- "UPHENO:0080555",
- "UPHENO:0002816",
- "UPHENO:0080556",
+ "BFO:0000020",
+ "UPHENO:0001003",
+ "BFO:0000001",
+ "UBERON:0000061",
+ "UPHENO:0075696",
+ "UPHENO:0001005",
+ "UPHENO:0002764",
"UPHENO:0081581",
"HP:0033127",
- "UPHENO:0002647",
- "UPHENO:0002830",
- "BFO:0000002",
- "UBERON:0001062",
- "RO:0002577",
- "UBERON:0000061",
- "UBERON:0015212",
- "UBERON:0010000",
+ "UPHENO:0076692",
+ "BFO:0000004",
"UBERON:0000475",
"UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "UBERON:0000978",
- "UBERON:0004480",
- ],
- "object_label": "Distal lower limb muscle weakness (HPO)",
- "object_closure_label": [
- "All (HPO)",
- "abnormality of muscle organ physiology",
- "Abnormality of the lower limb (HPO)",
- "Phenotypic abnormality (HPO)",
- "continuant",
- "decreased anatomical entity strength",
- "abnormal musculature",
- "decreased muscle organ strength",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "abnormal musculature of limb",
- "quality",
- "independent continuant",
- "system",
- "paired limb/fin",
- "lateral structure",
- "multicellular anatomical structure",
- "pelvic complex",
- "appendage musculature",
- "musculature of pelvic complex",
+ "UBERON:0000468",
+ "UBERON:0000153",
+ "UPHENO:0002844",
+ "BFO:0000002",
+ "HP:0003011",
+ "UPHENO:0076710",
+ "PATO:0000001",
+ "UPHENO:0002908",
+ "UBERON:0007811",
+ "UBERON:0001444",
+ "UBERON:0013702",
+ "UBERON:0000033",
+ "UPHENO:0002320",
+ "UPHENO:0082555",
+ "HP:0000152",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "HP:0001252",
+ "UPHENO:0082557",
+ "HP:0000297",
+ "HP:0000301",
+ "UBERON:0001456",
+ "UBERON:0008229",
+ "UBERON:0013700",
+ "UBERON:0010959",
+ "UBERON:0001577",
+ "HP:0000001",
+ "HP:0003808",
+ "HP:0000234",
+ "HP:0000271",
+ "UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0005090",
+ "UBERON:0018254",
+ "UBERON:0004120",
+ "UBERON:0000383",
+ "UBERON:0001015",
+ "UBERON:0014892",
+ "UBERON:0004461",
+ "UBERON:0004473",
+ ],
+ "object_label": "Facial hypotonia (HPO)",
+ "object_closure_label": [
"abnormality of anatomical entity physiology",
+ "abnormal head",
"Abnormal skeletal muscle morphology (HPO)",
- "Phenotypic abnormality",
"specifically dependent continuant",
- "Distal muscle weakness (HPO)",
- "Abnormality of limbs (HPO)",
- "Distal lower limb muscle weakness (HPO)",
- "protein-containing material entity",
- "material anatomical entity",
- "hindlimb",
- "appendage girdle complex",
- "subdivision of organism along appendicular axis",
- "pelvic complex muscle",
- "paired limb/fin segment",
- "lower limb segment",
- "Lower limb muscle weakness (HPO)",
- "phenotype",
+ "abnormal anatomical entity",
"abnormal phenotype by ontology source",
- "Abnormality of the musculature of the limbs (HPO)",
- "abnormal muscle organ morphology",
+ "abnormal craniocervical region",
+ "Abnormality of the musculature (HPO)",
+ "phenotype by ontology source",
+ "continuant",
+ "material anatomical entity",
+ "system",
+ "cranial or facial muscle",
+ "head",
+ "All (HPO)",
+ "Abnormal muscle tone (HPO)",
+ "continuant",
+ "abnormal musculature",
"Abnormal muscle physiology (HPO)",
+ "organ system subdivision",
+ "muscle organ",
+ "cranial muscle",
+ "craniocervical region",
+ "subdivision of head",
+ "body proper",
+ "abnormality of muscle organ physiology",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the head (HPO)",
+ "Abnormality of the face (HPO)",
+ "decreased muscle organ tone",
+ "Facial hypotonia (HPO)",
+ "Abnormality of facial musculature (HPO)",
"entity",
- "anatomical entity",
+ "skeletal musculature of head",
+ "musculature of face",
+ "Phenotypic abnormality",
+ "abnormal anatomical entity morphology",
+ "quality",
+ "abnormal facial muscle",
"anatomical structure",
- "muscle structure",
- "skeletal musculature",
"organism subdivision",
"organ",
- "muscle organ",
+ "multicellular organism",
+ "anterior region of body",
+ "phenotype",
+ "decreased anatomical entity tone",
+ "Abnormality of head or neck (HPO)",
+ "entity",
+ "independent continuant",
+ "subdivision of organism along main body axis",
+ "main body axis",
+ "Abnormality of facial soft tissue (HPO)",
+ "abnormal multicellular organism morphology",
+ "Abnormality of the musculoskeletal system (HPO)",
+ "material entity",
+ "anatomical entity",
"musculature of body",
"musculature",
- "leg",
- "musculature of limb",
- "abnormal anatomical entity",
- "decreased pelvic complex muscle strength",
- "Muscle weakness (HPO)",
- "Limb muscle weakness (HPO)",
- "Abnormality of the musculature (HPO)",
+ "skeletal muscle organ",
+ "abnormal face",
"abnormality of anatomical entity physiology",
- "phenotype by ontology source",
+ "Hypotonia (HPO)",
"abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "abnormal leg",
- "entity",
- "abnormal limb",
- "continuant",
- "material entity",
- "limb",
- "pelvic appendage",
+ "abnormal muscle organ morphology",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "posterior region of body",
- "appendage",
- "skeletal muscle organ",
- "multi-limb segment region",
- "limb segment",
+ "muscle structure",
+ "skeletal musculature",
+ "mesoderm-derived structure",
+ "face",
+ "craniocervical region musculature",
+ "axial musculature",
+ "craniocervical muscle",
+ "facial muscle",
],
"object_taxon": None,
"object_taxon_label": None,
@@ -1325,18 +1285,18 @@ def associations():
"negated": None,
"pathway": None,
"evidence_count": 2,
- "has_evidence": ["ECO:0000269"],
- "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}],
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0009053",
+ "has_evidence": ["ECO:0000304"],
+ "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}],
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0000297",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype",
},
- "publications": ["PMID:17548557"],
- "publications_links": [{"id": "PMID:17548557", "url": "http://identifiers.org/pubmed/17548557"}],
+ "publications": ["orphanet:589821"],
+ "publications_links": [{"id": "orphanet:589821", "url": None}],
"qualifiers": [],
- "frequency_qualifier": "HP:0040280",
+ "frequency_qualifier": "HP:0040281",
"onset_qualifier": None,
"sex_qualifier": None,
"stage_qualifier": None,
@@ -1345,11 +1305,11 @@ def associations():
"qualifiers_category": None,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Very frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040281", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Very frequent (HPO)"],
"onset_qualifier_label": None,
"onset_qualifier_namespace": None,
"onset_qualifier_category": None,
@@ -1367,222 +1327,264 @@ def associations():
"stage_qualifier_closure_label": [],
},
{
- "id": "uuid:c9c8bf41-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df83-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0008050",
- "original_subject": "OMIM:160500",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
+ "myotonic syndrome",
],
"subject_taxon": None,
"subject_taxon_label": None,
"predicate": "biolink:has_phenotype",
- "object": "HP:0009077",
+ "object": "HP:0010804",
"original_object": None,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "HP:0009127",
+ "HP:0000159",
+ "UPHENO:0076803",
+ "UBERON:0000465",
+ "UPHENO:0002910",
+ "UPHENO:0076800",
+ "UPHENO:0003064",
"BFO:0000002",
- "UPHENO:0002655",
- "UPHENO:0076692",
+ "HP:0002664",
+ "UPHENO:0015280",
+ "BFO:0000040",
+ "BFO:0000141",
+ "UBERON:0001062",
+ "UBERON:0011676",
+ "UBERON:0013701",
+ "UPHENO:0002828",
+ "UPHENO:0001002",
+ "BFO:0000020",
+ "HP:0011793",
+ "UPHENO:0076786",
+ "BFO:0000002",
+ "UBERON:0000167",
+ "UPHENO:0001001",
+ "HP:0000163",
+ "HP:0000177",
+ "UPHENO:0002833",
+ "HP:0000309",
+ "UPHENO:0001003",
+ "UPHENO:0002536",
"BFO:0000001",
- "PATO:0000001",
+ "UBERON:0000464",
+ "UPHENO:0075696",
+ "UPHENO:0002764",
+ "UPHENO:0081581",
+ "UPHENO:0076692",
+ "UPHENO:0020955",
+ "HP:0025031",
"BFO:0000004",
- "UBERON:0004708",
"UBERON:0000061",
+ "UBERON:0002553",
+ "UBERON:0000475",
+ "UBERON:0000062",
+ "UBERON:0004111",
+ "UBERON:0000468",
+ "UBERON:0001834",
"UBERON:0000153",
- "UBERON:0000026",
- "UBERON:0006058",
- "UBERON:0002529",
- "UBERON:0002398",
- "HP:0000001",
- "UPHENO:0002649",
- "UPHENO:0001001",
- "UPHENO:0001002",
+ "UPHENO:0002844",
+ "HP:0025033",
+ "UBERON:0000466",
+ "UBERON:0011595",
+ "UBERON:0001709",
+ "UBERON:0001833",
+ "UBERON:0007811",
+ "UBERON:0001444",
+ "UBERON:0013702",
+ "UBERON:0000025",
+ "UBERON:0000033",
+ "UBERON:0004089",
+ "HP:0000152",
+ "UPHENO:0075998",
"HP:0000118",
- "HP:0001446",
- "BFO:0000020",
- "UPHENO:0002708",
- "HP:0009077",
- "UPHENO:0076710",
+ "HP:0011339",
+ "HP:0010804",
+ "UPHENO:0020584",
+ "PATO:0000001",
+ "UBERON:0010314",
+ "UBERON:0003102",
+ "UBERON:0010000",
+ "UBERON:0001555",
+ "UBERON:0001456",
+ "UBERON:0004921",
+ "HP:0000001",
+ "UPHENO:0001005",
+ "HP:0031816",
+ "HP:0000153",
+ "HP:0000234",
+ "HP:0000271",
"BFO:0000001",
- "BFO:0000040",
"UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
- "UBERON:0010708",
- "UBERON:0010538",
- "UBERON:0004489",
- "HP:0001421",
- "HP:0030237",
- "HP:0002817",
- "HP:0003011",
- "UPHENO:0002536",
- "HP:0040064",
- "BFO:0000002",
- "PR:000050567",
- "UBERON:0000465",
- "UBERON:0002101",
- "UBERON:0004710",
- "UBERON:0005090",
- "UBERON:0002102",
- "UBERON:0010707",
- "UBERON:0001630",
- "UBERON:0010758",
- "UBERON:0007271",
- "UBERON:0014793",
- "UBERON:0004481",
- "UBERON:0002470",
- "UBERON:0008785",
- "UPHENO:0001005",
- "HP:0001155",
- "HP:0011805",
- "UPHENO:0002816",
- "UPHENO:0081581",
- "HP:0033127",
- "UPHENO:0001003",
- "UPHENO:0002647",
- "UPHENO:0002880",
- "UPHENO:0002830",
- "UBERON:0001062",
- "RO:0002577",
- "UBERON:0015212",
- "UBERON:0010000",
- "UBERON:0000475",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "UBERON:0001460",
- "UBERON:0004480",
- "UBERON:0007269",
- ],
- "object_label": "Weakness of long finger extensor muscles (HPO)",
- "object_closure_label": [
- "All (HPO)",
- "abnormal musculature of upper limb",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "abnormal musculature",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "phenotype by ontology source",
- "abnormal musculature of limb",
- "independent continuant",
- "system",
- "paired limb/fin",
- "anatomical structure",
- "lateral structure",
- "multicellular anatomical structure",
- "pectoral complex",
- "appendage musculature",
- "musculature of pectoral complex",
- "musculature of manus",
- "phenotype",
- "Abnormality of the musculature of the hand (HPO)",
- "abnormal phenotype by ontology source",
- "Abnormality of the hand (HPO)",
- "Abnormal skeletal muscle morphology (HPO)",
- "Abnormality of the musculature of the upper limbs (HPO)",
- "specifically dependent continuant",
- "abnormal manus",
- "Abnormality of limbs (HPO)",
+ "UBERON:0000064",
+ "UBERON:0001007",
+ "UBERON:0013522",
+ "UBERON:0000165",
+ ],
+ "object_label": "Tented upper lip vermilion (HPO)",
+ "object_closure_label": [
+ "abnormal head",
+ "abnormal digestive system",
+ "Abnormality of the midface (HPO)",
"quality",
+ "abnormal anatomical entity",
+ "abnormal craniocervical region",
+ "specifically dependent continuant",
+ "Abnormality of digestive system morphology (HPO)",
+ "phenotype by ontology source",
+ "abnormal anatomical entity",
"continuant",
- "protein-containing material entity",
"material anatomical entity",
- "forelimb",
- "appendage girdle complex",
- "subdivision of organism along appendicular axis",
- "paired limb/fin segment",
- "musculature of upper limb",
- "autopod region",
- "upper limb segment",
- "Abnormality of the musculature of the limbs (HPO)",
- "continuant",
- "abnormal musculature of manus",
- "Weakness of long finger extensor muscles (HPO)",
- "abnormal muscle organ morphology",
+ "organ part",
+ "digestive system",
+ "head",
+ "midface",
+ "All (HPO)",
+ "abnormal phenotype by ontology source",
+ "oral cavity",
+ "craniocervical region",
+ "subdivision of head",
+ "body proper",
+ "tube",
+ "Abnormal oral cavity morphology (HPO)",
+ "Abnormality of upper lip (HPO)",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the head (HPO)",
+ "Abnormality of the face (HPO)",
+ "abnormal anatomical entity morphology",
"entity",
- "anatomical entity",
- "muscle structure",
+ "entity",
+ "immaterial anatomical entity",
+ "structure with developmental contribution from neural crest",
+ "surface structure",
+ "multicellular anatomical structure",
+ "mouth",
+ "abnormal mouth",
+ "Phenotypic abnormality",
+ "Neoplasm by anatomical site (HPO)",
+ "abnormal oral cavity morphology",
+ "abnormal anatomical entity morphology",
+ "abnormal lip morphology",
+ "abnormal digestive system morphology",
+ "anatomical space",
+ "anatomical cavity",
"organism subdivision",
"organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "arm",
- "musculature of limb",
- "pectoral appendage musculature",
- "Hand muscle weakness (HPO)",
- "Abnormality of the upper limb (HPO)",
- "Abnormality of the musculature (HPO)",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "entity",
- "abnormal arm",
- "abnormal limb",
- "material entity",
- "limb",
- "pectoral appendage",
- "anatomical system",
+ "anatomical conduit",
"multicellular organism",
- "organ system subdivision",
+ "upper lip",
"anterior region of body",
- "appendage",
- "multi-limb segment region",
- "limb segment",
- "manus",
+ "phenotype",
+ "Abnormality of head or neck (HPO)",
+ "abnormal midface",
+ "Abnormal oral morphology (HPO)",
+ "Abnormality of the mouth (HPO)",
+ "Neoplasm (HPO)",
+ "abnormal anatomical entity morphology in the independent continuant",
+ "independent continuant",
+ "subdivision of organism along main body axis",
+ "main body axis",
+ "abnormal multicellular organism morphology",
+ "Abnormal lip morphology (HPO)",
+ "Abnormality of the digestive system (HPO)",
+ "material entity",
+ "immaterial entity",
+ "anatomical entity",
+ "anatomical structure",
+ "subdivision of tube",
+ "abnormal face",
+ "abnormal mouth morphology",
+ "abnormal upper lip",
+ "continuant",
+ "Abnormality of upper lip vermillion (HPO)",
+ "Tented upper lip vermilion (HPO)",
+ "anatomical system",
+ "jaw region",
+ "upper jaw region",
+ "lip",
+ "digestive tract",
+ "face",
+ "subdivision of digestive tract",
],
"object_taxon": None,
"object_taxon_label": None,
@@ -1591,18 +1593,18 @@ def associations():
"negated": None,
"pathway": None,
"evidence_count": 2,
- "has_evidence": ["ECO:0000269"],
- "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}],
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0009077",
+ "has_evidence": ["ECO:0000304"],
+ "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}],
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0010804",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype",
},
- "publications": ["PMID:17548557"],
- "publications_links": [{"id": "PMID:17548557", "url": "http://identifiers.org/pubmed/17548557"}],
+ "publications": ["orphanet:589821"],
+ "publications_links": [{"id": "orphanet:589821", "url": None}],
"qualifiers": [],
- "frequency_qualifier": "HP:0040280",
+ "frequency_qualifier": "HP:0040281",
"onset_qualifier": None,
"sex_qualifier": None,
"stage_qualifier": None,
@@ -1611,11 +1613,11 @@ def associations():
"qualifiers_category": None,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Very frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040281", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Very frequent (HPO)"],
"onset_qualifier_label": None,
"onset_qualifier_namespace": None,
"onset_qualifier_category": None,
@@ -1633,190 +1635,178 @@ def associations():
"stage_qualifier_closure_label": [],
},
{
- "id": "uuid:c9c8bf42-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df84-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0008050",
- "original_subject": "OMIM:160500",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
+ "myotonic syndrome",
],
"subject_taxon": None,
"subject_taxon_label": None,
"predicate": "biolink:has_phenotype",
- "object": "HP:0030051",
+ "object": "HP:0031843",
"original_object": None,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
+ "UBERON:0000465",
+ "GO:0050877",
"UPHENO:0082875",
- "UPHENO:0049622",
- "UPHENO:0001005",
+ "UPHENO:0004523",
+ "GO:0008150",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "GO:0003008",
+ "BFO:0000020",
+ "BFO:0000003",
"BFO:0000002",
- "UPHENO:0050606",
- "HP:0001288",
- "HP:0012638",
- "BFO:0000015",
- "BFO:0000004",
- "GO:0050882",
- "NBO:0000338",
- "GO:0050905",
- "UBERON:0001016",
- "HP:0000001",
"UPHENO:0001001",
- "UPHENO:0080585",
"UPHENO:0001002",
- "HP:0000118",
- "BFO:0000020",
- "UPHENO:0002433",
+ "HP:0031843",
"UPHENO:0001003",
- "HP:0000708",
- "HP:0011446",
"BFO:0000001",
+ "UBERON:0000061",
+ "GO:0050890",
+ "UPHENO:0001005",
+ "UPHENO:0002433",
+ "HP:0100543",
+ "HP:0012638",
+ "BFO:0000015",
+ "UBERON:0000468",
+ "UPHENO:0075696",
+ "BFO:0000002",
+ "UPHENO:0002536",
+ "BFO:0000004",
+ "HP:0000118",
+ "UPHENO:0002332",
"PATO:0000001",
+ "HP:0000001",
+ "HP:0000707",
+ "HP:0011446",
"BFO:0000001",
- "BFO:0000040",
"GO:0032501",
- "GO:0050881",
- "NBO:0000313",
- "GO:0050877",
"UBERON:0010000",
"UBERON:0000467",
- "UBERON:0000468",
- "NBO:0000403",
- "NBO:0000001",
- "UPHENO:0075696",
- "UPHENO:0078622",
- "UPHENO:0049586",
- "HP:0100022",
- "UPHENO:0050613",
- "UPHENO:0002332",
- "UPHENO:0002536",
- "UPHENO:0079826",
- "UPHENO:0004523",
- "UPHENO:0049587",
- "BFO:0000003",
- "GO:0008150",
- "GO:0050879",
- "GO:0007610",
- "GO:0003008",
- "HP:0030051",
- "HP:0000707",
- "UPHENO:0079833",
- "BFO:0000002",
- "UBERON:0001062",
- "UBERON:0000465",
- "UBERON:0000061",
+ "UBERON:0001016",
],
- "object_label": "Tip-toe gait (HPO)",
+ "object_label": "Bradyphrenia (HPO)",
"object_closure_label": [
- "All (HPO)",
- "abnormal behavior",
- "Abnormality of movement (HPO)",
+ "abnormality of anatomical entity physiology",
"Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "Tip-toe gait (HPO)",
- "Abnormality of the nervous system (HPO)",
- "Behavioral abnormality (HPO)",
+ "Bradyphrenia (HPO)",
+ "abnormal anatomical entity",
"Abnormality of higher mental function (HPO)",
- "abnormal voluntary movement behavior",
"quality",
- "process",
- "independent continuant",
- "material anatomical entity",
- "nervous system",
- "voluntary movement behavior",
- "body part movement",
- "abnormality of anatomical entity physiology",
- "phenotype",
+ "multicellular organismal process",
+ "abnormal phenotype by ontology source",
"specifically dependent continuant",
- "abnormality of nervous system physiology",
"phenotype by ontology source",
- "Gait disturbance (HPO)",
- "abnormal behavior process",
"abnormal nervous system",
- "abnormal biological_process",
- "Abnormal nervous system physiology (HPO)",
"occurrent",
- "biological_process",
- "multicellular organismal movement",
- "behavior",
- "system process",
- "musculoskeletal movement",
- "behavior process",
- "nervous system process",
- "abnormal phenotype by ontology source",
"continuant",
- "abnormal voluntary musculoskeletal movement",
+ "material anatomical entity",
+ "nervous system",
+ "All (HPO)",
+ "continuant",
+ "system process",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the nervous system (HPO)",
"entity",
- "anatomical entity",
+ "entity",
+ "cognition",
+ "abnormality of nervous system physiology",
"anatomical structure",
+ "multicellular organism",
+ "phenotype",
+ "process",
+ "nervous system process",
+ "Cognitive impairment (HPO)",
+ "Abnormal nervous system physiology (HPO)",
+ "biological_process",
+ "material entity",
+ "anatomical entity",
"abnormal anatomical entity",
- "abnormal voluntary movement behavior",
- "abnormal response to stimulus",
- "abnormal behavior process",
- "abnormal musculoskeletal movement",
"abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
- "entity",
- "continuant",
- "material entity",
- "multicellular organismal process",
+ "independent continuant",
"multicellular anatomical structure",
"anatomical system",
- "voluntary musculoskeletal movement",
- "kinesthetic behavior",
- "neuromuscular process",
- "multicellular organism",
],
"object_taxon": None,
"object_taxon_label": None,
@@ -1825,18 +1815,18 @@ def associations():
"negated": None,
"pathway": None,
"evidence_count": 2,
- "has_evidence": ["ECO:0000269"],
- "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}],
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0030051",
+ "has_evidence": ["ECO:0000304"],
+ "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}],
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0031843",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype",
},
- "publications": ["PMID:17548557"],
- "publications_links": [{"id": "PMID:17548557", "url": "http://identifiers.org/pubmed/17548557"}],
+ "publications": ["orphanet:589821"],
+ "publications_links": [{"id": "orphanet:589821", "url": None}],
"qualifiers": [],
- "frequency_qualifier": "HP:0040280",
+ "frequency_qualifier": "HP:0040281",
"onset_qualifier": None,
"sex_qualifier": None,
"stage_qualifier": None,
@@ -1845,11 +1835,11 @@ def associations():
"qualifiers_category": None,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Very frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040281", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Very frequent (HPO)"],
"onset_qualifier_label": None,
"onset_qualifier_namespace": None,
"onset_qualifier_category": None,
@@ -1867,206 +1857,192 @@ def associations():
"stage_qualifier_closure_label": [],
},
{
- "id": "uuid:c9c8bfed-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df85-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0009675",
- "original_subject": "OMIM:253600",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "MONDO:0016971",
- "MONDO:0005336",
- "MONDO:0015152",
- "MONDO:0000429",
- "MONDO:0005071",
- "MONDO:0006025",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
- "MONDO:0009675",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
- "MONDO:0016152",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
- "BFO:0000002",
- "MONDO:0016106",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003847",
- "MONDO:0003939",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
- "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
- "hereditary disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
"continuant",
- "autosomal recessive disease",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
"disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "disease",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "autosomal genetic disease",
+ "myotonic dystrophy",
"nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
- "autosomal recessive limb-girdle muscular dystrophy type 2A",
"skeletal muscle disorder",
- "qualitative or quantitative defects of calpain",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity",
+ "myotonic syndrome",
],
"subject_taxon": None,
"subject_taxon_label": None,
"predicate": "biolink:has_phenotype",
- "object": "HP:0001880",
+ "object": "HP:0000736",
"original_object": None,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "HP:0001879",
- "UPHENO:0001005",
+ "UBERON:0000465",
+ "NBO:0000313",
+ "NBO:0000308",
+ "UPHENO:0082875",
"BFO:0000002",
+ "UPHENO:0004523",
+ "UPHENO:0049587",
+ "GO:0008150",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "GO:0007610",
+ "UPHENO:0001002",
"BFO:0000020",
- "HP:0002715",
- "HP:0001911",
- "HP:0001880",
- "BFO:0000004",
- "UBERON:0000178",
- "CL:0000094",
- "CL:0002242",
- "CL:0000255",
- "CL:0000219",
- "HP:0000001",
- "HP:0032309",
- "HP:0010974",
- "HP:0000118",
- "HP:0001871",
- "HP:0020064",
+ "HP:0000736",
+ "BFO:0000003",
+ "BFO:0000002",
+ "UPHENO:0001001",
+ "UPHENO:0049622",
"UPHENO:0001003",
- "UPHENO:0002536",
"BFO:0000001",
+ "NBO:0000607",
+ "UPHENO:0075696",
+ "UPHENO:0002433",
+ "HP:0012638",
+ "BFO:0000015",
+ "BFO:0000004",
+ "UBERON:0000061",
+ "UBERON:0000468",
+ "NBO:0000455",
+ "UPHENO:0049586",
+ "UPHENO:0002536",
+ "HP:0000708",
+ "UPHENO:0080585",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "UPHENO:0079826",
"PATO:0000001",
+ "HP:0000001",
+ "UPHENO:0001005",
+ "HP:0000707",
+ "HP:0011446",
"BFO:0000001",
- "UBERON:0000467",
- "CL:0000000",
- "UBERON:0000468",
- "CL:0000738",
- "CL:0000548",
- "CL:0000763",
- "CL:0000081",
- "UPHENO:0002948",
- "UPHENO:0001002",
- "HP:0025461",
- "HP:0001881",
- "HP:0020047",
- "UPHENO:0004459",
- "HP:0032251",
- "BFO:0000002",
- "BFO:0000040",
- "PR:000050567",
- "UBERON:0000465",
- "CL:0000771",
- "UBERON:0004120",
- "UBERON:0006314",
- "UBERON:0015203",
- "CL:0000003",
- "UBERON:0002193",
- "UBERON:0002390",
- "UBERON:0000179",
- "UBERON:0002405",
- "CL:0000988",
- "HP:0011893",
- "UPHENO:0001001",
- "HP:0025354",
- "HP:0001974",
- "HP:0010987",
- "UBERON:0001062",
- "UBERON:0000061",
- "UBERON:0000463",
- "UBERON:0034923",
+ "GO:0032501",
"UBERON:0010000",
- "CL:0000766",
- "CL:0002371",
+ "UBERON:0000467",
+ "UBERON:0001016",
],
- "object_label": "Eosinophilia (HPO)",
+ "object_label": "Short attention span (HPO)",
"object_closure_label": [
- "All (HPO)",
- "Abnormal eosinophil morphology (HPO)",
- "Abnormal myeloid leukocyte morphology (HPO)",
- "Phenotypic abnormality (HPO)",
- "Abnormal cellular phenotype (HPO)",
- "Leukocytosis (HPO)",
- "Abnormal cellular immune system morphology (HPO)",
+ "abnormality of anatomical entity physiology",
+ "abnormal anatomical entity",
+ "Abnormality of higher mental function (HPO)",
"quality",
- "independent continuant",
- "blood",
- "granulocyte",
- "multicellular anatomical structure",
- "myeloid cell",
- "blood cell",
- "Abnormality of blood and blood-forming tissues (HPO)",
- "Abnormal eosinophil count (HPO)",
+ "multicellular organismal process",
+ "abnormal anatomical entity",
+ "specifically dependent continuant",
"phenotype by ontology source",
+ "abnormal nervous system",
+ "occurrent",
"continuant",
- "material entity",
- "protein-containing material entity",
"material anatomical entity",
- "leukocyte",
- "animal cell",
- "hematopoietic cell",
- "Abnormal leukocyte count (HPO)",
- "phenotype",
+ "nervous system",
+ "All (HPO)",
"abnormal phenotype by ontology source",
- "continuant",
- "specifically dependent continuant",
- "Abnormality of the immune system (HPO)",
- "Abnormal granulocyte morphology (HPO)",
- "Eosinophilia (HPO)",
- "abnormal anatomical entity",
- "Abnormal immune system morphology (HPO)",
+ "Short attention span (HPO)",
+ "behavior",
+ "abnormal behavior",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the nervous system (HPO)",
+ "abnormal behavior process",
"entity",
+ "entity",
+ "cognitive behavior",
+ "sensation behavior",
+ "Phenotypic abnormality",
+ "abnormality of nervous system physiology",
+ "multicellular organism",
+ "phenotype",
+ "abnormal behavior process",
+ "Behavioral abnormality (HPO)",
+ "abnormal biological_process",
+ "process",
+ "independent continuant",
+ "behavior process",
+ "Abnormal nervous system physiology (HPO)",
+ "biological_process",
+ "material entity",
"anatomical entity",
"anatomical structure",
- "organism substance",
- "disconnected anatomical group",
- "mesoderm-derived structure",
- "bodily fluid",
- "non-connected functional system",
- "native cell",
- "hemolymphoid system",
- "hematopoietic system",
- "haemolymphatic fluid",
- "immune system",
- "myeloid leukocyte",
- "somatic cell",
- "abnormal immune system",
- "Abnormal granulocyte count (HPO)",
- "Phenotypic abnormality",
- "Abnormal cell morphology (HPO)",
- "Abnormal leukocyte morphology (HPO)",
- "Abnormal myeloid cell morphology (HPO)",
- "abnormal hematopoietic system",
- "entity",
- "eosinophil",
+ "abnormal response to stimulus",
+ "continuant",
+ "abnormality of anatomical entity physiology",
+ "multicellular anatomical structure",
"anatomical system",
- "cell",
- "multicellular organism",
- "nucleate cell",
- "eukaryotic cell",
- "motile cell",
+ "attention behavior",
],
"object_taxon": None,
"object_taxon_label": None,
@@ -2075,16 +2051,16 @@ def associations():
"negated": None,
"pathway": None,
"evidence_count": 2,
- "has_evidence": ["ECO:0000269"],
- "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}],
- "grouping_key": "MONDO:0009675🍪🍪biolink:has_phenotype🍪HP:0001880",
+ "has_evidence": ["ECO:0000304"],
+ "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}],
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0000736",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype",
},
- "publications": ["PMID:16607617"],
- "publications_links": [{"id": "PMID:16607617", "url": "http://identifiers.org/pubmed/16607617"}],
+ "publications": ["orphanet:589821"],
+ "publications_links": [{"id": "orphanet:589821", "url": None}],
"qualifiers": [],
"frequency_qualifier": "HP:0040282",
"onset_qualifier": None,
@@ -2098,8 +2074,8 @@ def associations():
"frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Frequent (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"],
"onset_qualifier_label": None,
"onset_qualifier_namespace": None,
"onset_qualifier_category": None,
@@ -2117,144 +2093,178 @@ def associations():
"stage_qualifier_closure_label": [],
},
{
- "id": "uuid:c9c8bfee-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df87-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0009675",
- "original_subject": "OMIM:253600",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "MONDO:0016971",
- "MONDO:0005336",
- "MONDO:0015152",
- "MONDO:0000429",
- "MONDO:0005071",
- "MONDO:0006025",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
- "MONDO:0009675",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
- "MONDO:0016152",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
- "BFO:0000002",
- "MONDO:0016106",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003847",
- "MONDO:0003939",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
- "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
- "hereditary disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
"continuant",
- "autosomal recessive disease",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
"disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "disease",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "autosomal genetic disease",
+ "myotonic dystrophy",
"nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
- "autosomal recessive limb-girdle muscular dystrophy type 2A",
"skeletal muscle disorder",
- "qualitative or quantitative defects of calpain",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity",
+ "myotonic syndrome",
],
"subject_taxon": None,
"subject_taxon_label": None,
"predicate": "biolink:has_phenotype",
- "object": "HP:0002312",
+ "object": "HP:0001622",
"original_object": None,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "UPHENO:0082875",
- "UPHENO:0001005",
- "HP:0012638",
- "BFO:0000004",
- "UBERON:0000061",
- "UBERON:0001016",
- "HP:0000001",
- "HP:0000118",
- "BFO:0000020",
- "UPHENO:0002433",
- "UPHENO:0001003",
- "PATO:0000001",
+ "HP:0001197",
+ "UPHENO:0002536",
+ "GO:0008150",
+ "UBERON:0000465",
+ "GO:0007567",
+ "UPHENO:0049587",
"BFO:0000001",
"BFO:0000040",
- "UBERON:0000467",
- "UBERON:0000468",
- "UPHENO:0075696",
- "HP:0011442",
- "UPHENO:0001002",
- "UPHENO:0002332",
- "UPHENO:0002536",
- "UPHENO:0004523",
- "HP:0002312",
- "HP:0011443",
+ "UBERON:0001062",
+ "GO:0044706",
+ "GO:0000003",
+ "GO:0044703",
+ "BFO:0000003",
"BFO:0000002",
- "UBERON:0000465",
"UPHENO:0001001",
- "BFO:0000002",
- "HP:0000707",
- "HP:0002311",
+ "UPHENO:0001002",
+ "BFO:0000020",
+ "UPHENO:0001003",
"BFO:0000001",
- "UBERON:0001062",
+ "UPHENO:0001005",
+ "UPHENO:0049940",
+ "BFO:0000015",
+ "UBERON:0000061",
+ "UBERON:0000468",
+ "BFO:0000002",
+ "UPHENO:0049440",
+ "BFO:0000004",
+ "UBERON:0000922",
+ "HP:0001622",
+ "HP:0000118",
+ "UPHENO:0049449",
+ "HP:0001787",
+ "PATO:0000001",
+ "UBERON:0000323",
+ "HP:0000001",
+ "UPHENO:0075949",
+ "GO:0032501",
+ "GO:0022414",
"UBERON:0010000",
],
- "object_label": "Clumsiness (HPO)",
+ "object_label": "Premature birth (HPO)",
"object_closure_label": [
- "All (HPO)",
- "Abnormal central motor function (HPO)",
- "Phenotypic abnormality (HPO)",
- "Abnormality of the nervous system (HPO)",
- "entity",
- "quality",
- "independent continuant",
- "anatomical structure",
- "multicellular anatomical structure",
- "nervous system",
- "abnormality of anatomical entity physiology",
- "continuant",
+ "Phenotypic abnormality",
"specifically dependent continuant",
- "abnormality of nervous system physiology",
+ "quality",
+ "multicellular organismal process",
+ "reproductive process",
+ "abnormal phenotype by ontology source",
+ "premature biological_process",
"phenotype by ontology source",
- "abnormal nervous system",
- "Clumsiness (HPO)",
- "Abnormal nervous system physiology (HPO)",
+ "occurrent",
"continuant",
"material anatomical entity",
+ "All (HPO)",
+ "continuant",
+ "multi-multicellular organism process",
+ "reproduction",
+ "multi-organism reproductive process",
+ "embryo",
+ "Phenotypic abnormality (HPO)",
+ "abnormal late embryo",
+ "Abnormal delivery (HPO)",
+ "entity",
+ "biological_process",
+ "multicellular organism",
"phenotype",
- "abnormal phenotype by ontology source",
- "Incoordination (HPO)",
- "Abnormality of coordination (HPO)",
+ "Premature birth (HPO)",
+ "abnormal biological_process",
"entity",
+ "process",
+ "parturition",
+ "Abnormality of prenatal development or birth (HPO)",
+ "abnormal reproductive process",
+ "material entity",
"anatomical entity",
+ "anatomical structure",
+ "premature parturition",
"abnormal anatomical entity",
- "Phenotypic abnormality",
- "abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
- "material entity",
- "anatomical system",
- "multicellular organism",
+ "independent continuant",
+ "multicellular anatomical structure",
+ "late embryo",
],
"object_taxon": None,
"object_taxon_label": None,
@@ -2263,16 +2273,16 @@ def associations():
"negated": None,
"pathway": None,
"evidence_count": 2,
- "has_evidence": ["ECO:0000269"],
- "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}],
- "grouping_key": "MONDO:0009675🍪🍪biolink:has_phenotype🍪HP:0002312",
+ "has_evidence": ["ECO:0000304"],
+ "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}],
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001622",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype",
},
- "publications": ["PMID:16607617"],
- "publications_links": [{"id": "PMID:16607617", "url": "http://identifiers.org/pubmed/16607617"}],
+ "publications": ["orphanet:589821"],
+ "publications_links": [{"id": "orphanet:589821", "url": None}],
"qualifiers": [],
"frequency_qualifier": "HP:0040282",
"onset_qualifier": None,
@@ -2286,8 +2296,8 @@ def associations():
"frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Frequent (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"],
"onset_qualifier_label": None,
"onset_qualifier_namespace": None,
"onset_qualifier_category": None,
@@ -2305,148 +2315,200 @@ def associations():
"stage_qualifier_closure_label": [],
},
{
- "id": "uuid:c9c8bff4-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df88-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0009675",
- "original_subject": "OMIM:253600",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "MONDO:0016971",
- "MONDO:0005336",
- "MONDO:0015152",
- "MONDO:0000429",
- "MONDO:0005071",
- "MONDO:0006025",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
- "MONDO:0009675",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
- "MONDO:0016152",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
- "BFO:0000002",
- "MONDO:0016106",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003847",
- "MONDO:0003939",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
- "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
- "hereditary disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
"continuant",
- "autosomal recessive disease",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
"disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "disease",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "autosomal genetic disease",
+ "myotonic dystrophy",
"nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
- "autosomal recessive limb-girdle muscular dystrophy type 2A",
"skeletal muscle disorder",
- "qualitative or quantitative defects of calpain",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity",
+ "myotonic syndrome",
],
"subject_taxon": None,
"subject_taxon_label": None,
"predicate": "biolink:has_phenotype",
- "object": "HP:0032019",
+ "object": "HP:0001883",
"original_object": None,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "UPHENO:0001005",
- "BFO:0000002",
+ "PR:000050567",
+ "UBERON:0000465",
+ "RO:0002577",
+ "BFO:0000001",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UBERON:0000154",
+ "UPHENO:0001002",
"BFO:0000020",
- "UPHENO:0076692",
- "PATO:0000001",
- "BFO:0000004",
- "UBERON:0000061",
- "HP:0000001",
+ "UPHENO:0081575",
+ "BFO:0000002",
+ "UBERON:0002101",
+ "UBERON:0004709",
"UPHENO:0001001",
- "HP:0000118",
- "HP:0032019",
"UPHENO:0001003",
- "UPHENO:0076710",
- "BFO:0000001",
+ "UPHENO:0002536",
"BFO:0000001",
- "BFO:0000040",
- "UBERON:0000467",
+ "UBERON:0000061",
+ "UBERON:0008784",
+ "UBERON:0002470",
+ "UPHENO:0001005",
+ "UPHENO:0081581",
+ "UPHENO:0076692",
+ "UPHENO:0003070",
+ "UPHENO:0002830",
+ "BFO:0000004",
+ "UBERON:0004708",
+ "UBERON:0000475",
"UBERON:0000468",
- "UBERON:0011216",
- "HP:0003011",
- "UPHENO:0002536",
+ "UBERON:0010709",
+ "HP:0001883",
"BFO:0000002",
- "UBERON:0000465",
- "UBERON:0005090",
- "UBERON:0001630",
- "HP:0011805",
- "UPHENO:0001002",
- "UPHENO:0002816",
- "UPHENO:0081581",
- "HP:0033127",
- "UBERON:0001062",
+ "HP:0001760",
+ "HP:0040064",
+ "PATO:0000001",
+ "UBERON:0002103",
+ "UBERON:0010707",
+ "UBERON:0000026",
+ "UBERON:0010758",
+ "UBERON:0006058",
+ "UBERON:0002387",
+ "HP:0002814",
+ "HP:0005656",
+ "HP:0000118",
+ "UBERON:0015212",
+ "UBERON:0010538",
+ "HP:0000001",
"UBERON:0010000",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
+ "UBERON:0000978",
+ "UBERON:0002529",
],
- "object_label": "Muscle eosinophilia (HPO)",
+ "object_label": "Talipes (HPO)",
"object_closure_label": [
- "All (HPO)",
- "Phenotypic abnormality (HPO)",
- "abnormal musculature",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "independent continuant",
- "anatomical structure",
- "multicellular anatomical structure",
- "phenotype",
- "Abnormal skeletal muscle morphology (HPO)",
- "Phenotypic abnormality",
- "Muscle eosinophilia (HPO)",
+ "abnormal phenotype by ontology source",
+ "specifically dependent continuant",
"phenotype by ontology source",
- "quality",
+ "abnormal anatomical entity",
"continuant",
+ "protein-containing material entity",
"material anatomical entity",
- "abnormal phenotype by ontology source",
+ "system",
+ "multi-limb segment region",
+ "All (HPO)",
"continuant",
- "specifically dependent continuant",
- "abnormal muscle organ morphology",
+ "appendage",
+ "subdivision of organism along appendicular axis",
+ "Abnormality of the lower limb (HPO)",
+ "Phenotypic abnormality (HPO)",
"entity",
- "anatomical entity",
- "muscle structure",
- "organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "Abnormality of the musculature (HPO)",
- "abnormal anatomical entity",
+ "lateral structure",
+ "leg",
+ "limb segment",
+ "Phenotypic abnormality",
+ "abnormal pes morphology",
"abnormal anatomical entity morphology",
+ "abnormal leg",
+ "quality",
+ "anatomical structure",
+ "organism subdivision",
+ "multicellular organism",
+ "pelvic complex",
+ "lower limb segment",
+ "autopod region",
+ "phenotype",
+ "Positional foot deformity (HPO)",
+ "Abnormal foot morphology (HPO)",
"entity",
+ "independent continuant",
+ "posterior region of body",
+ "abnormal multicellular organism morphology",
+ "abnormal limb",
"material entity",
- "anatomical system",
- "multicellular organism",
- "organ system subdivision",
+ "anatomical entity",
+ "paired limb/fin",
+ "limb",
+ "pelvic appendage",
+ "pes",
+ "Talipes (HPO)",
+ "Abnormality of limbs (HPO)",
+ "multicellular anatomical structure",
+ "hindlimb",
+ "appendage girdle complex",
+ "paired limb/fin segment",
],
"object_taxon": None,
"object_taxon_label": None,
@@ -2455,18 +2517,18 @@ def associations():
"negated": None,
"pathway": None,
"evidence_count": 2,
- "has_evidence": ["ECO:0000269"],
- "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}],
- "grouping_key": "MONDO:0009675🍪🍪biolink:has_phenotype🍪HP:0032019",
+ "has_evidence": ["ECO:0000304"],
+ "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}],
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001883",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype",
},
- "publications": ["PMID:16607617"],
- "publications_links": [{"id": "PMID:16607617", "url": "http://identifiers.org/pubmed/16607617"}],
+ "publications": ["orphanet:589821"],
+ "publications_links": [{"id": "orphanet:589821", "url": None}],
"qualifiers": [],
- "frequency_qualifier": "HP:0040280",
+ "frequency_qualifier": "HP:0040282",
"onset_qualifier": None,
"sex_qualifier": None,
"stage_qualifier": None,
@@ -2475,11 +2537,11 @@ def associations():
"qualifiers_category": None,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"],
"onset_qualifier_label": None,
"onset_qualifier_namespace": None,
"onset_qualifier_category": None,
@@ -2497,206 +2559,166 @@ def associations():
"stage_qualifier_closure_label": [],
},
{
- "id": "uuid:c9c8bff5-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df8e-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0009675",
- "original_subject": "OMIM:253600",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "MONDO:0016971",
- "MONDO:0005336",
- "MONDO:0015152",
- "MONDO:0000429",
- "MONDO:0005071",
- "MONDO:0006025",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
- "MONDO:0009675",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
- "MONDO:0016152",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
- "BFO:0000002",
- "MONDO:0016106",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003847",
- "MONDO:0003939",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
- "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
- "hereditary disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
"continuant",
- "autosomal recessive disease",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
"disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "disease",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "autosomal genetic disease",
+ "myotonic dystrophy",
"nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
- "autosomal recessive limb-girdle muscular dystrophy type 2A",
"skeletal muscle disorder",
- "qualitative or quantitative defects of calpain",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity",
+ "myotonic syndrome",
],
"subject_taxon": None,
"subject_taxon_label": None,
"predicate": "biolink:has_phenotype",
- "object": "HP:0007340",
+ "object": "HP:0011098",
"original_object": None,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
+ "UBERON:0000465",
"UPHENO:0082875",
- "UPHENO:0002320",
- "UPHENO:0001005",
- "HP:0009127",
- "BFO:0000020",
- "UPHENO:0076692",
- "BFO:0000001",
- "BFO:0000004",
- "UBERON:0004708",
- "UBERON:0000061",
- "UBERON:0000026",
- "UBERON:0014892",
- "HP:0000001",
- "UPHENO:0001001",
- "UPHENO:0001002",
- "HP:0000118",
- "UPHENO:0076710",
- "PATO:0000001",
+ "HP:0011442",
+ "HP:0002186",
+ "UPHENO:0004523",
"BFO:0000001",
"BFO:0000040",
"UBERON:0001062",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
- "UBERON:0010709",
- "UBERON:0010890",
- "UPHENO:0075696",
- "UPHENO:0080575",
- "HP:0001324",
- "HP:0003690",
- "HP:0003011",
- "UPHENO:0002332",
+ "UPHENO:0001002",
+ "BFO:0000002",
+ "UPHENO:0001001",
+ "BFO:0000020",
"UPHENO:0001003",
"UPHENO:0002536",
- "HP:0040064",
- "HP:0011804",
- "BFO:0000002",
- "PR:000050567",
- "UBERON:0002101",
- "UBERON:0005090",
- "UBERON:0018254",
- "UBERON:0010707",
- "UBERON:0001630",
- "UBERON:0007271",
- "UBERON:0014792",
- "HP:0007340",
- "HP:0011805",
+ "BFO:0000001",
+ "UBERON:0000061",
+ "UPHENO:0075696",
+ "UPHENO:0001005",
+ "UPHENO:0002433",
+ "HP:0012638",
+ "BFO:0000004",
+ "UBERON:0000468",
"BFO:0000002",
- "UPHENO:0080555",
- "UPHENO:0002816",
- "UPHENO:0080556",
- "UPHENO:0081581",
- "HP:0033127",
- "UPHENO:0002647",
- "UPHENO:0002830",
- "UBERON:0000465",
- "RO:0002577",
- "UBERON:0015212",
+ "HP:0011098",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "PATO:0000001",
+ "HP:0000001",
+ "HP:0000707",
+ "HP:0011446",
"UBERON:0010000",
- "UBERON:0000475",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "UBERON:0004480",
+ "UBERON:0000467",
+ "UBERON:0001016",
],
- "object_label": "Lower limb muscle weakness (HPO)",
+ "object_label": "Speech apraxia (HPO)",
"object_closure_label": [
- "All (HPO)",
- "abnormality of muscle organ physiology",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "decreased anatomical entity strength",
- "abnormal musculature",
- "decreased muscle organ strength",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "abnormal musculature of limb",
- "quality",
- "independent continuant",
- "material anatomical entity",
- "system",
- "paired limb/fin",
- "anatomical structure",
- "lateral structure",
- "multicellular anatomical structure",
- "pelvic complex",
- "appendage musculature",
- "musculature of pelvic complex",
"abnormality of anatomical entity physiology",
- "phenotype",
- "Abnormal skeletal muscle morphology (HPO)",
- "continuant",
- "Abnormality of limbs (HPO)",
- "continuant",
- "protein-containing material entity",
- "appendage girdle complex",
- "pelvic complex muscle",
- "Lower limb muscle weakness (HPO)",
- "abnormal phenotype by ontology source",
- "Abnormality of the musculature of the limbs (HPO)",
"specifically dependent continuant",
- "abnormal muscle organ morphology",
- "Abnormal muscle physiology (HPO)",
- "entity",
- "muscle structure",
- "skeletal musculature",
- "organism subdivision",
- "organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "musculature of limb",
+ "Abnormality of higher mental function (HPO)",
+ "quality",
"abnormal anatomical entity",
- "decreased pelvic complex muscle strength",
- "Muscle weakness (HPO)",
- "Limb muscle weakness (HPO)",
- "Abnormality of the musculature (HPO)",
- "abnormality of anatomical entity physiology",
+ "abnormal phenotype by ontology source",
"phenotype by ontology source",
"abnormal anatomical entity",
- "abnormal anatomical entity morphology",
+ "abnormal nervous system",
+ "continuant",
+ "material anatomical entity",
+ "nervous system",
+ "All (HPO)",
+ "continuant",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the nervous system (HPO)",
"entity",
- "abnormal limb",
+ "Phenotypic abnormality",
+ "abnormality of nervous system physiology",
+ "anatomical structure",
+ "multicellular organism",
+ "phenotype",
+ "Speech apraxia (HPO)",
+ "entity",
+ "independent continuant",
+ "Abnormal nervous system physiology (HPO)",
"material entity",
"anatomical entity",
- "limb",
+ "Abnormal central motor function (HPO)",
+ "Apraxia (HPO)",
+ "abnormality of anatomical entity physiology",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "appendage",
- "skeletal muscle organ",
],
"object_taxon": None,
"object_taxon_label": None,
@@ -2705,16 +2727,16 @@ def associations():
"negated": None,
"pathway": None,
"evidence_count": 2,
- "has_evidence": ["ECO:0000269"],
- "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}],
- "grouping_key": "MONDO:0009675🍪🍪biolink:has_phenotype🍪HP:0007340",
+ "has_evidence": ["ECO:0000304"],
+ "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}],
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0011098",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype",
},
- "publications": ["PMID:16607617"],
- "publications_links": [{"id": "PMID:16607617", "url": "http://identifiers.org/pubmed/16607617"}],
+ "publications": ["orphanet:589821"],
+ "publications_links": [{"id": "orphanet:589821", "url": None}],
"qualifiers": [],
"frequency_qualifier": "HP:0040282",
"onset_qualifier": None,
@@ -2728,8 +2750,8 @@ def associations():
"frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Frequent (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"],
"onset_qualifier_label": None,
"onset_qualifier_namespace": None,
"onset_qualifier_category": None,
@@ -2747,156 +2769,170 @@ def associations():
"stage_qualifier_closure_label": [],
},
{
- "id": "uuid:c9d8bdf9-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df90-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0009676",
- "original_subject": "OMIM:253601",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "MONDO:0016971",
- "BFO:0000002",
- "BFO:0000020",
- "MONDO:0005336",
- "MONDO:0009676",
- "MONDO:0015152",
- "MONDO:0000429",
- "MONDO:0005071",
- "MONDO:0006025",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
- "MONDO:0016145",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
+ "BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
- "MONDO:0016106",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
- "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2B",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "qualitative or quantitative defects of dysferlin",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "autosomal recessive disease",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "autosomal recessive limb-girdle muscular dystrophy type 2B",
- "disease",
"continuant",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
"specifically dependent continuant",
"myopathy",
- "hereditary disease",
- "autosomal genetic disease",
+ "myotonic dystrophy",
"nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
"skeletal muscle disorder",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity",
+ "myotonic syndrome",
],
"subject_taxon": None,
"subject_taxon_label": None,
"predicate": "biolink:has_phenotype",
- "object": "HP:0003701",
+ "object": "HP:0011710",
"original_object": None,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
+ "UPHENO:0002536",
+ "PR:000050567",
+ "UBERON:0000465",
"UPHENO:0082875",
- "UPHENO:0002320",
+ "UPHENO:0080362",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "HP:0030956",
+ "HP:0001626",
+ "HP:0031546",
"BFO:0000002",
- "BFO:0000004",
- "UBERON:0000061",
- "HP:0000001",
"UPHENO:0001001",
"UPHENO:0001002",
- "HP:0000118",
- "BFO:0000020",
"UPHENO:0001003",
- "BFO:0000001",
- "PATO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0001062",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
"UPHENO:0075696",
- "HP:0001324",
- "HP:0003011",
- "UPHENO:0002332",
- "UPHENO:0002536",
- "HP:0011804",
- "BFO:0000002",
- "UBERON:0000465",
- "UBERON:0005090",
- "UBERON:0001630",
"UPHENO:0001005",
- "HP:0003701",
- "UPHENO:0080555",
- "UPHENO:0002816",
- "UPHENO:0080556",
- "HP:0033127",
+ "BFO:0000020",
+ "HP:0011710",
+ "UPHENO:0002406",
+ "BFO:0000004",
+ "UBERON:0004535",
+ "UBERON:0000061",
+ "UBERON:0000468",
+ "HP:0012722",
+ "HP:0000118",
+ "BFO:0000002",
+ "UPHENO:0002332",
+ "PATO:0000001",
+ "HP:0000001",
+ "HP:0011025",
+ "BFO:0000001",
+ "BFO:0000001",
"UBERON:0010000",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
+ "UBERON:0000467",
+ "UBERON:0001009",
],
- "object_label": "Proximal muscle weakness (HPO)",
+ "object_label": "Bundle branch block (HPO)",
"object_closure_label": [
- "All (HPO)",
- "abnormality of muscle organ physiology",
+ "abnormality of anatomical entity physiology",
"Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "decreased anatomical entity strength",
- "abnormal musculature",
- "decreased muscle organ strength",
- "Abnormality of the musculoskeletal system (HPO)",
+ "Abnormal cardiovascular system physiology (HPO)",
"quality",
- "independent continuant",
- "anatomical structure",
- "multicellular anatomical structure",
- "abnormality of anatomical entity physiology",
- "phenotype",
+ "entity",
+ "abnormal anatomical entity",
"abnormal phenotype by ontology source",
- "Proximal muscle weakness (HPO)",
- "specifically dependent continuant",
"phenotype by ontology source",
"continuant",
+ "protein-containing material entity",
"material anatomical entity",
+ "circulatory system",
+ "All (HPO)",
+ "Cardiac conduction abnormality (HPO)",
+ "Phenotypic abnormality (HPO)",
"continuant",
- "Abnormal muscle physiology (HPO)",
- "entity",
- "muscle structure",
- "organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "abnormal anatomical entity",
- "Muscle weakness (HPO)",
- "Abnormality of the musculature (HPO)",
- "abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
"entity",
+ "Abnormality of cardiovascular system electrophysiology (HPO)",
+ "Abnormality of the cardiovascular system (HPO)",
+ "specifically dependent continuant",
+ "multicellular organism",
+ "phenotype",
+ "independent continuant",
+ "Bundle branch block (HPO)",
+ "abnormality of cardiovascular system physiology",
"material entity",
"anatomical entity",
+ "cardiovascular system",
+ "anatomical structure",
+ "abnormal cardiovascular system",
+ "abnormality of anatomical entity physiology",
+ "abnormal anatomical entity",
+ "Heart block (HPO)",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
],
"object_taxon": None,
"object_taxon_label": None,
@@ -2904,22 +2940,19 @@ def associations():
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"negated": None,
"pathway": None,
- "evidence_count": 3,
- "has_evidence": ["ECO:0000269"],
- "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}],
- "grouping_key": "MONDO:0009676🍪🍪biolink:has_phenotype🍪HP:0003701",
+ "evidence_count": 2,
+ "has_evidence": ["ECO:0000304"],
+ "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}],
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0011710",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype",
},
- "publications": ["PMID:9731527", "PMID:9009996"],
- "publications_links": [
- {"id": "PMID:9731527", "url": "http://identifiers.org/pubmed/9731527"},
- {"id": "PMID:9009996", "url": "http://identifiers.org/pubmed/9009996"},
- ],
+ "publications": ["orphanet:589821"],
+ "publications_links": [{"id": "orphanet:589821", "url": None}],
"qualifiers": [],
- "frequency_qualifier": "HP:0040280",
+ "frequency_qualifier": "HP:0040282",
"onset_qualifier": None,
"sex_qualifier": None,
"stage_qualifier": None,
@@ -2928,11 +2961,11 @@ def associations():
"qualifiers_category": None,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Obligate (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"],
"onset_qualifier_label": None,
"onset_qualifier_namespace": None,
"onset_qualifier_category": None,
@@ -2950,152 +2983,170 @@ def associations():
"stage_qualifier_closure_label": [],
},
{
- "id": "uuid:c9c8bf35-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02dfa2-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0008050",
- "original_subject": "OMIM:160500",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
- ],
- "subject_label": "MYH7-related skeletal myopathy",
- "subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
+ ],
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
+ "subject_closure_label": [
+ "eyelids malposition disorder",
"disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
+ "myotonic syndrome",
],
"subject_taxon": None,
"subject_taxon_label": None,
"predicate": "biolink:has_phenotype",
- "object": "HP:0003701",
+ "object": "HP:0001513",
"original_object": None,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "UPHENO:0082875",
- "UPHENO:0002320",
+ "UPHENO:0049587",
+ "GO:0008150",
+ "UBERON:0000465",
+ "HP:0001513",
+ "BFO:0000001",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UBERON:0000468",
+ "UPHENO:0008273",
+ "UPHENO:0049874",
+ "BFO:0000003",
"BFO:0000002",
- "BFO:0000004",
- "UBERON:0000061",
- "HP:0000001",
"UPHENO:0001001",
"UPHENO:0001002",
- "HP:0000118",
- "BFO:0000020",
"UPHENO:0001003",
"BFO:0000001",
- "PATO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0001062",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
+ "UBERON:0000061",
"UPHENO:0075696",
- "HP:0001324",
- "HP:0003011",
- "UPHENO:0002332",
- "UPHENO:0002536",
- "HP:0011804",
- "BFO:0000002",
- "UBERON:0000465",
- "UBERON:0005090",
- "UBERON:0001630",
"UPHENO:0001005",
- "HP:0003701",
- "UPHENO:0080555",
- "UPHENO:0002816",
- "UPHENO:0080556",
- "HP:0033127",
+ "BFO:0000020",
+ "BFO:0000015",
+ "BFO:0000004",
+ "HP:0001507",
+ "BFO:0000002",
+ "UPHENO:0002536",
+ "HP:0000118",
+ "UPHENO:0010795",
+ "HP:0004323",
+ "UPHENO:0010763",
+ "PATO:0000001",
+ "HP:0000001",
+ "HP:0004324",
+ "UPHENO:0008312",
+ "GO:0040007",
"UBERON:0010000",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
],
- "object_label": "Proximal muscle weakness (HPO)",
+ "object_label": "Obesity (HPO)",
"object_closure_label": [
- "All (HPO)",
- "abnormality of muscle organ physiology",
"Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "decreased anatomical entity strength",
- "abnormal musculature",
- "decreased muscle organ strength",
- "Abnormality of the musculoskeletal system (HPO)",
+ "abnormal anatomical entity",
+ "increased multicellular organism mass",
"quality",
- "independent continuant",
- "anatomical structure",
- "multicellular anatomical structure",
- "abnormality of anatomical entity physiology",
- "phenotype",
+ "growth",
+ "abnormal anatomical entity",
"abnormal phenotype by ontology source",
- "Proximal muscle weakness (HPO)",
- "specifically dependent continuant",
"phenotype by ontology source",
+ "Obesity (HPO)",
+ "occurrent",
"continuant",
"material anatomical entity",
+ "All (HPO)",
"continuant",
- "Abnormal muscle physiology (HPO)",
+ "abnormal growth",
+ "multicellular organism",
+ "Phenotypic abnormality (HPO)",
+ "abnormality of anatomical entity mass",
"entity",
- "muscle structure",
- "organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "abnormal anatomical entity",
- "Muscle weakness (HPO)",
- "Abnormality of the musculature (HPO)",
- "abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
+ "biological_process",
+ "increased anatomical entity mass",
+ "specifically dependent continuant",
+ "anatomical structure",
+ "phenotype",
+ "Increased body weight (HPO)",
"entity",
+ "process",
+ "independent continuant",
+ "abnormal biological_process",
"material entity",
"anatomical entity",
- "anatomical system",
- "multicellular organism",
- "organ system subdivision",
+ "Growth abnormality (HPO)",
+ "abnormality of multicellular organism mass",
+ "Abnormality of body weight (HPO)",
+ "multicellular anatomical structure",
],
"object_taxon": None,
"object_taxon_label": None,
@@ -3106,16 +3157,16 @@ def associations():
"evidence_count": 2,
"has_evidence": ["ECO:0000304"],
"has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}],
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0003701",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001513",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype",
},
- "publications": ["OMIM:160500"],
- "publications_links": [{"id": "OMIM:160500", "url": "http://identifiers.org/mim/160500"}],
+ "publications": ["orphanet:589821"],
+ "publications_links": [{"id": "orphanet:589821", "url": None}],
"qualifiers": [],
- "frequency_qualifier": "HP:0040283",
+ "frequency_qualifier": "HP:0040284",
"onset_qualifier": None,
"sex_qualifier": None,
"stage_qualifier": None,
@@ -3124,11 +3175,11 @@ def associations():
"qualifiers_category": None,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": "Occasional (HPO)",
+ "frequency_qualifier_label": "Very rare (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040283", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Occasional (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0000001", "HP:0040284"],
+ "frequency_qualifier_closure_label": ["Very rare (HPO)", "Frequency (HPO)", "All (HPO)"],
"onset_qualifier_label": None,
"onset_qualifier_namespace": None,
"onset_qualifier_category": None,
@@ -3146,212 +3197,186 @@ def associations():
"stage_qualifier_closure_label": [],
},
{
- "id": "uuid:c9c8bf37-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df92-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0008050",
- "original_subject": "OMIM:160500",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
+ "myotonic syndrome",
],
"subject_taxon": None,
"subject_taxon_label": None,
"predicate": "biolink:has_phenotype",
- "object": "HP:0001644",
+ "object": "HP:0000729",
"original_object": None,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
+ "UPHENO:0002536",
+ "BFO:0000001",
+ "GO:0008150",
+ "UBERON:0000465",
+ "NBO:0000313",
"UPHENO:0082875",
- "HP:0001637",
- "UPHENO:0001005",
+ "UPHENO:0004523",
+ "UPHENO:0049587",
+ "BFO:0000040",
+ "GO:0007610",
+ "UBERON:0000468",
"BFO:0000020",
- "UPHENO:0077800",
- "UPHENO:0066927",
- "UPHENO:0076692",
- "PATO:0000001",
- "BFO:0000004",
- "UBERON:0004535",
- "UBERON:0011676",
- "UBERON:0013701",
- "UBERON:0002349",
- "UBERON:0000915",
- "UBERON:0002100",
- "UBERON:0005181",
- "UBERON:0002075",
- "UBERON:0015228",
- "HP:0000001",
+ "BFO:0000003",
+ "BFO:0000002",
"UPHENO:0001001",
- "HP:0001644",
- "HP:0030680",
+ "UPHENO:0049622",
"UPHENO:0001002",
- "HP:0000118",
- "HP:0001627",
- "UPHENO:0076776",
"UPHENO:0001003",
- "UPHENO:0024906",
"BFO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0010000",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
- "UBERON:0000064",
+ "UBERON:0001062",
+ "UBERON:0000061",
"UPHENO:0075696",
- "HP:0001626",
- "UPHENO:0080362",
- "HP:0001638",
+ "UPHENO:0001005",
+ "UPHENO:0002433",
+ "HP:0012638",
+ "BFO:0000015",
+ "UPHENO:0049586",
+ "HP:0000729",
"BFO:0000002",
+ "HP:0000708",
+ "BFO:0000004",
+ "UPHENO:0080585",
+ "HP:0000118",
"UPHENO:0002332",
- "UPHENO:0002536",
- "UPHENO:0076810",
- "BFO:0000002",
- "PR:000050567",
- "UBERON:0004120",
- "UBERON:0000948",
- "UBERON:0001009",
- "UBERON:0005983",
- "UBERON:0009569",
- "UBERON:0013702",
- "UBERON:0005177",
- "UBERON:0003103",
- "UBERON:0018260",
- "UBERON:0015410",
- "UPHENO:0076781",
- "UPHENO:0081581",
- "UBERON:0001062",
- "UBERON:0000465",
- "UBERON:0000061",
- "UBERON:0010314",
- "UBERON:0000475",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0000060",
- "UBERON:0004923",
- "UBERON:0005178",
- "UBERON:0007100",
+ "UPHENO:0079826",
+ "PATO:0000001",
+ "HP:0000001",
+ "HP:0000707",
+ "HP:0011446",
+ "GO:0032501",
+ "UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0001016",
],
- "object_label": "Dilated cardiomyopathy (HPO)",
+ "object_label": "Autistic behavior (HPO)",
"object_closure_label": [
- "All (HPO)",
- "abnormal cardiovascular system",
- "Cardiomyopathy (HPO)",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "abnormal myocardium morphology",
- "abnormal multicellular organism morphology",
- "independent continuant",
- "material anatomical entity",
- "cardiovascular system",
- "structure with developmental contribution from neural crest",
- "layer of muscle tissue",
"abnormality of anatomical entity physiology",
- "Abnormal myocardium morphology (HPO)",
- "phenotype",
- "Abnormality of the cardiovascular system (HPO)",
- "Abnormal heart morphology (HPO)",
- "abnormal cardiovascular system morphology",
- "phenotype by ontology source",
- "abnormally decreased functionality of the anatomical entity",
- "abnormal heart morphology",
+ "Phenotypic abnormality",
+ "Abnormality of higher mental function (HPO)",
"quality",
- "continuant",
- "protein-containing material entity",
- "heart",
- "subdivision of trunk",
- "body proper",
- "trunk region element",
- "compound organ",
- "heart plus pericardium",
+ "multicellular organismal process",
+ "abnormal anatomical entity",
"abnormal phenotype by ontology source",
"specifically dependent continuant",
- "abnormally decreased functionality of the myocardium",
- "anatomical entity dysfunction in independent continuant",
+ "phenotype by ontology source",
+ "abnormal nervous system",
+ "occurrent",
+ "continuant",
+ "material anatomical entity",
+ "nervous system",
+ "All (HPO)",
+ "continuant",
+ "behavior",
+ "multicellular organism",
+ "abnormal behavior",
+ "Autistic behavior (HPO)",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the nervous system (HPO)",
+ "abnormal behavior process",
"entity",
+ "biological_process",
+ "abnormality of nervous system physiology",
"anatomical entity",
"anatomical structure",
- "mesoderm-derived structure",
- "organism subdivision",
- "organ",
- "circulatory system",
- "heart layer",
- "musculature of body",
- "anatomical wall",
- "organ component layer",
- "thoracic cavity element",
- "primary circulatory organ",
- "abnormal anatomical entity",
- "Dilated cardiomyopathy (HPO)",
- "Abnormality of cardiovascular system morphology (HPO)",
- "continuant",
- "abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
+ "phenotype",
+ "abnormal behavior process",
+ "Behavioral abnormality (HPO)",
+ "abnormal biological_process",
+ "process",
+ "behavior process",
"entity",
+ "Abnormal nervous system physiology (HPO)",
"material entity",
+ "abnormal response to stimulus",
+ "abnormality of anatomical entity physiology",
+ "abnormal anatomical entity",
+ "independent continuant",
"multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "organ part",
- "subdivision of organism along main body axis",
- "main body axis",
- "myocardium",
- "thoracic segment of trunk",
- "trunk",
- "thoracic segment organ",
- "viscus",
- "circulatory organ",
],
"object_taxon": None,
"object_taxon_label": None,
@@ -3362,14 +3387,14 @@ def associations():
"evidence_count": 2,
"has_evidence": ["ECO:0000304"],
"has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}],
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0001644",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0000729",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype",
},
- "publications": ["OMIM:160500"],
- "publications_links": [{"id": "OMIM:160500", "url": "http://identifiers.org/mim/160500"}],
+ "publications": ["orphanet:589821"],
+ "publications_links": [{"id": "orphanet:589821", "url": None}],
"qualifiers": [],
"frequency_qualifier": "HP:0040283",
"onset_qualifier": None,
@@ -3383,8 +3408,8 @@ def associations():
"frequency_qualifier_label": "Occasional (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040283", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Occasional (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Occasional (HPO)"],
"onset_qualifier_label": None,
"onset_qualifier_namespace": None,
"onset_qualifier_category": None,
@@ -3402,292 +3427,194 @@ def associations():
"stage_qualifier_closure_label": [],
},
{
- "id": "uuid:c9c8bff0-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df94-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0009675",
- "original_subject": "OMIM:253600",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "MONDO:0016971",
- "MONDO:0005336",
- "MONDO:0015152",
- "MONDO:0000429",
- "MONDO:0005071",
- "MONDO:0006025",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
- "MONDO:0009675",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
- "MONDO:0016152",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
- "BFO:0000002",
- "MONDO:0016106",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003847",
- "MONDO:0003939",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
- "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
- "hereditary disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
"continuant",
- "autosomal recessive disease",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
"disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "disease",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "autosomal genetic disease",
+ "myotonic dystrophy",
"nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
- "autosomal recessive limb-girdle muscular dystrophy type 2A",
"skeletal muscle disorder",
- "qualitative or quantitative defects of calpain",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity",
+ "myotonic syndrome",
],
"subject_taxon": None,
"subject_taxon_label": None,
"predicate": "biolink:has_phenotype",
- "object": "HP:0010628",
+ "object": "HP:0000752",
"original_object": None,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
+ "UPHENO:0049587",
+ "NBO:0000030",
+ "GO:0008150",
+ "UBERON:0000465",
+ "NBO:0000313",
"UPHENO:0082875",
- "UPHENO:0076772",
- "UPHENO:0002320",
- "UPHENO:0005116",
- "HP:0031910",
- "HP:0011799",
- "HP:0410008",
- "UPHENO:0076692",
- "BFO:0000001",
- "PATO:0000001",
- "HP:0012638",
- "BFO:0000004",
- "UBERON:0001016",
- "UBERON:0001021",
- "UBERON:0000153",
- "UBERON:0011676",
- "UBERON:0013701",
- "UBERON:0014892",
- "UBERON:0015789",
- "UBERON:0011779",
- "UBERON:0000033",
- "HP:0000001",
- "HP:0000152",
- "UPHENO:0002764",
+ "UPHENO:0004523",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "GO:0007610",
+ "NBO:0000568",
+ "BFO:0000003",
+ "BFO:0000002",
+ "UPHENO:0001001",
+ "UPHENO:0049622",
"UPHENO:0001002",
- "HP:0000118",
- "BFO:0000020",
- "UPHENO:0002433",
- "HP:0000234",
- "HP:0000271",
- "HP:0010827",
"UPHENO:0001003",
- "HP:0012639",
- "UPHENO:0076710",
- "UPHENO:0002908",
"BFO:0000001",
- "BFO:0000040",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
- "UBERON:0001785",
- "UBERON:0010959",
- "UBERON:0001577",
+ "UBERON:0000061",
+ "HP:0000752",
"UPHENO:0075696",
- "HP:0045010",
- "UPHENO:0002844",
- "HP:0001291",
- "HP:0001324",
- "HP:0030319",
- "HP:0000759",
- "UPHENO:0081700",
- "HP:0003011",
- "UPHENO:0002332",
- "UPHENO:0078730",
- "UPHENO:0002536",
- "UPHENO:0081709",
- "HP:0000301",
- "UPHENO:0004523",
- "UPHENO:0004508",
- "HP:0011804",
- "BFO:0000002",
- "UBERON:0000465",
- "UBERON:0005090",
- "UBERON:0018254",
- "UBERON:0004120",
- "UBERON:0034713",
- "UBERON:0001647",
- "UBERON:0000122",
- "UBERON:0001630",
- "UBERON:0001033",
- "UBERON:0002376",
- "UBERON:0007811",
- "UBERON:0001444",
- "UBERON:0013702",
- "UBERON:0001456",
- "UBERON:0008229",
- "UBERON:0013700",
- "UPHENO:0001001",
- "UPHENO:0002910",
- "HP:0010628",
"UPHENO:0001005",
- "HP:0011805",
+ "BFO:0000020",
+ "UPHENO:0002433",
+ "HP:0012638",
+ "NBO:0000644",
+ "BFO:0000015",
+ "BFO:0000004",
+ "UBERON:0000468",
+ "UPHENO:0049586",
"BFO:0000002",
- "UPHENO:0076722",
- "UPHENO:0080555",
- "UPHENO:0003587",
- "UPHENO:0002816",
- "UPHENO:0080556",
+ "UPHENO:0002536",
+ "HP:0000708",
+ "NBO:0000243",
+ "UPHENO:0080585",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "UPHENO:0079826",
+ "PATO:0000001",
+ "HP:0000001",
"HP:0000707",
- "HP:0006824",
- "UPHENO:0081581",
- "HP:0033127",
- "UPHENO:0076702",
- "UBERON:0001062",
- "RO:0002577",
- "UBERON:0000061",
- "UBERON:0015212",
- "UBERON:0010314",
- "UBERON:0005162",
+ "HP:0011446",
+ "BFO:0000001",
+ "GO:0032501",
"UBERON:0010000",
- "UBERON:0000475",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "UBERON:0000010",
- "UBERON:0004461",
- "UBERON:0004473",
+ "UBERON:0000467",
+ "UBERON:0001016",
],
- "object_label": "Facial palsy (HPO)",
+ "object_label": "Hyperactivity (HPO)",
"object_closure_label": [
- "All (HPO)",
- "abnormality of muscle organ physiology",
- "abnormal peripheral nervous system",
- "Abnormal cranial nerve physiology (HPO)",
- "Abnormality of facial soft tissue (HPO)",
- "abnormal head",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "abnormal peripheral nervous system morphology",
- "decreased anatomical entity strength",
- "abnormal facial nerve",
- "abnormal musculature",
- "decreased muscle organ strength",
- "Abnormality of the nervous system (HPO)",
- "Cranial nerve paralysis (HPO)",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "Abnormal nervous system morphology (HPO)",
- "abnormal facial muscle",
- "independent continuant",
- "system",
- "lateral structure",
- "structure with developmental contribution from neural crest",
- "multi cell part structure",
- "multicellular anatomical structure",
- "nervous system",
- "cranial nerve",
- "face",
- "craniocervical region musculature",
- "axial musculature",
"abnormality of anatomical entity physiology",
- "abnormal cranial nerve morphology",
- "Abnormality of peripheral nerves (HPO)",
- "Facial palsy (HPO)",
- "abnormal phenotype by ontology source",
- "Abnormal skeletal muscle morphology (HPO)",
- "continuant",
- "specifically dependent continuant",
- "abnormality of nervous system physiology",
- "Abnormality of the head (HPO)",
- "Abnormality of the face (HPO)",
- "Abnormality of the seventh cranial nerve (HPO)",
- "phenotype by ontology source",
- "Abnormality of the peripheral nervous system (HPO)",
- "paralysed cranial nerve",
- "Abnormality of facial musculature (HPO)",
- "abnormal nervous system",
- "abnormal nerve",
- "quality",
- "Abnormal nervous system physiology (HPO)",
- "continuant",
- "material anatomical entity",
- "cranial neuron projection bundle",
- "facial nerve",
- "neuron projection bundle",
- "craniocervical region",
- "subdivision of head",
- "body proper",
- "craniocervical muscle",
- "facial muscle",
- "phenotype",
- "abnormal face",
- "abnormal muscle organ morphology",
- "Abnormal muscle physiology (HPO)",
- "entity",
- "anatomical entity",
- "anatomical structure",
- "muscle structure",
- "skeletal musculature",
- "mesoderm-derived structure",
- "organism subdivision",
- "organ",
- "muscle organ",
- "gustatory system",
- "cranial muscle",
- "musculature of body",
- "musculature",
- "peripheral nervous system",
- "skeletal musculature of head",
- "musculature of face",
+ "Phenotypic abnormality",
"abnormal anatomical entity",
- "Abnormality of head or neck (HPO)",
- "abnormal craniocervical region",
- "Abnormal cranial nerve morphology (HPO)",
- "Muscle weakness (HPO)",
- "Weakness of facial musculature (HPO)",
- "Abnormal peripheral nervous system morphology (HPO)",
- "paralysed anatomical entity",
- "Abnormality of the musculature (HPO)",
- "abnormality of anatomical entity physiology",
- "abnormality of cranial nerve physiology",
+ "Abnormality of higher mental function (HPO)",
+ "quality",
+ "multicellular organismal process",
+ "Hyperactivity (HPO)",
"abnormal anatomical entity",
- "abnormal anatomical entity morphology",
+ "abnormal phenotype by ontology source",
+ "phenotype by ontology source",
+ "abnormal nervous system",
+ "kinesthetic behavior phenotype",
+ "occurrent",
+ "continuant",
+ "material anatomical entity",
+ "nervous system",
+ "All (HPO)",
+ "continuant",
+ "behavior",
+ "abnormal behavior",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the nervous system (HPO)",
+ "abnormal behavior process",
"entity",
- "abnormal nervous system morphology",
+ "entity",
+ "hyperactivity",
+ "biological_process",
+ "specifically dependent continuant",
+ "abnormality of nervous system physiology",
+ "anatomical structure",
+ "multicellular organism",
+ "phenotype",
+ "abnormal behavior process",
+ "Behavioral abnormality (HPO)",
+ "voluntary movement behavior phenotype",
+ "process",
+ "independent continuant",
+ "behavior process",
+ "abnormal biological_process",
+ "Abnormal nervous system physiology (HPO)",
"material entity",
+ "anatomical entity",
+ "abnormal response to stimulus",
+ "abnormality of anatomical entity physiology",
+ "behavioral phenotype",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "nerve",
- "anterior region of body",
- "subdivision of organism along main body axis",
- "main body axis",
- "skeletal muscle organ",
- "cranial or facial muscle",
- "nerve of head region",
- "head",
],
"object_taxon": None,
"object_taxon_label": None,
@@ -3698,14 +3625,14 @@ def associations():
"evidence_count": 2,
"has_evidence": ["ECO:0000304"],
"has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}],
- "grouping_key": "MONDO:0009675🍪🍪biolink:has_phenotype🍪HP:0010628",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0000752",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype",
},
- "publications": ["OMIM:253600"],
- "publications_links": [{"id": "OMIM:253600", "url": "http://identifiers.org/mim/253600"}],
+ "publications": ["orphanet:589821"],
+ "publications_links": [{"id": "orphanet:589821", "url": None}],
"qualifiers": [],
"frequency_qualifier": "HP:0040283",
"onset_qualifier": None,
@@ -3719,8 +3646,8 @@ def associations():
"frequency_qualifier_label": "Occasional (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040283", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Occasional (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Occasional (HPO)"],
"onset_qualifier_label": None,
"onset_qualifier_namespace": None,
"onset_qualifier_category": None,
@@ -3738,196 +3665,156 @@ def associations():
"stage_qualifier_closure_label": [],
},
{
- "id": "uuid:c9d8bdf7-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df96-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0009676",
- "original_subject": "OMIM:253601",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "MONDO:0016971",
- "BFO:0000002",
- "BFO:0000020",
- "MONDO:0005336",
- "MONDO:0009676",
- "MONDO:0015152",
- "MONDO:0000429",
- "MONDO:0005071",
- "MONDO:0006025",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
- "MONDO:0016145",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
+ "BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
- "MONDO:0016106",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
- "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2B",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "qualitative or quantitative defects of dysferlin",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "autosomal recessive disease",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "autosomal recessive limb-girdle muscular dystrophy type 2B",
- "disease",
"continuant",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
"specifically dependent continuant",
"myopathy",
- "hereditary disease",
- "autosomal genetic disease",
+ "myotonic dystrophy",
"nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
"skeletal muscle disorder",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity",
+ "myotonic syndrome",
],
"subject_taxon": None,
"subject_taxon_label": None,
"predicate": "biolink:has_phenotype",
- "object": "HP:0002505",
+ "object": "HP:0001558",
"original_object": None,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "UPHENO:0082875",
- "UPHENO:0049622",
- "UPHENO:0001005",
+ "HP:0001197",
+ "UBERON:0000465",
+ "HP:0034059",
+ "BFO:0000040",
+ "UBERON:0001062",
"BFO:0000002",
- "HP:0002540",
- "UPHENO:0050606",
- "HP:0001288",
- "HP:0012638",
- "BFO:0000015",
- "UBERON:0000061",
- "GO:0050882",
- "NBO:0000338",
- "GO:0050905",
- "UBERON:0001016",
- "HP:0000001",
"UPHENO:0001001",
- "UPHENO:0080585",
- "HP:0000118",
+ "UPHENO:0001002",
"BFO:0000020",
- "UPHENO:0002433",
"UPHENO:0001003",
- "HP:0000708",
- "HP:0011446",
- "BFO:0000001",
- "PATO:0000001",
"BFO:0000001",
+ "UPHENO:0001005",
+ "HP:0001558",
"BFO:0000004",
- "GO:0032501",
- "GO:0050881",
- "NBO:0000313",
- "GO:0050877",
- "UBERON:0000467",
+ "UBERON:0000061",
"UBERON:0000468",
- "NBO:0000403",
- "NBO:0000001",
- "UPHENO:0075696",
- "UPHENO:0078622",
- "HP:0002505",
- "UPHENO:0049586",
- "HP:0100022",
- "UPHENO:0001002",
- "UPHENO:0050613",
- "UPHENO:0002332",
- "UPHENO:0002536",
- "UPHENO:0079826",
- "UPHENO:0004523",
- "UPHENO:0049587",
- "BFO:0000003",
"BFO:0000002",
- "GO:0008150",
- "BFO:0000040",
- "GO:0050879",
- "GO:0007610",
- "GO:0003008",
- "HP:0000707",
- "UPHENO:0079833",
- "UBERON:0001062",
- "UBERON:0000465",
+ "UPHENO:0002536",
+ "HP:0001557",
+ "UBERON:0000922",
+ "HP:0000118",
+ "HP:0034057",
+ "PATO:0000001",
+ "UBERON:0000323",
+ "HP:0000001",
+ "UPHENO:0075949",
+ "BFO:0000001",
"UBERON:0010000",
],
- "object_label": "Loss of ambulation (HPO)",
+ "object_label": "Decreased fetal movement (HPO)",
"object_closure_label": [
- "All (HPO)",
- "abnormal behavior",
- "Abnormality of movement (HPO)",
- "Phenotypic abnormality (HPO)",
- "Abnormality of the nervous system (HPO)",
- "Behavioral abnormality (HPO)",
- "Abnormality of higher mental function (HPO)",
- "abnormal voluntary movement behavior",
- "quality",
- "process",
- "material anatomical entity",
- "anatomical structure",
- "multicellular anatomical structure",
- "nervous system",
- "voluntary movement behavior",
- "body part movement",
- "abnormality of anatomical entity physiology",
- "phenotype",
+ "Phenotypic abnormality",
"specifically dependent continuant",
- "abnormality of nervous system physiology",
+ "abnormal anatomical entity",
+ "quality",
+ "abnormal phenotype by ontology source",
"phenotype by ontology source",
- "Gait disturbance (HPO)",
- "abnormal behavior process",
- "abnormal nervous system",
- "abnormal biological_process",
- "Abnormal nervous system physiology (HPO)",
- "occurrent",
"continuant",
- "biological_process",
- "material entity",
- "multicellular organismal movement",
- "behavior",
- "system process",
- "musculoskeletal movement",
- "behavior process",
- "nervous system process",
- "abnormal phenotype by ontology source",
+ "material anatomical entity",
+ "All (HPO)",
"continuant",
- "Inability to walk (HPO)",
- "abnormal voluntary musculoskeletal movement",
+ "embryo",
+ "Phenotypic abnormality (HPO)",
+ "abnormal late embryo",
+ "Fetal anomaly (HPO)",
"entity",
- "independent continuant",
- "anatomical entity",
- "abnormal anatomical entity",
- "abnormal voluntary movement behavior",
- "Loss of ambulation (HPO)",
- "abnormal response to stimulus",
- "abnormal behavior process",
- "Phenotypic abnormality",
- "abnormal musculoskeletal movement",
- "abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
"entity",
- "multicellular organismal process",
- "anatomical system",
- "voluntary musculoskeletal movement",
- "kinesthetic behavior",
- "neuromuscular process",
+ "Decreased fetal movement (HPO)",
"multicellular organism",
+ "phenotype",
+ "Prenatal movement abnormality (HPO)",
+ "independent continuant",
+ "Abnormality of prenatal development or birth (HPO)",
+ "material entity",
+ "anatomical entity",
+ "anatomical structure",
+ "Abnormal fetal physiology (HPO)",
+ "multicellular anatomical structure",
+ "late embryo",
],
"object_taxon": None,
"object_taxon_label": None,
@@ -3936,16 +3823,16 @@ def associations():
"negated": None,
"pathway": None,
"evidence_count": 2,
- "has_evidence": ["ECO:0000269"],
- "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}],
- "grouping_key": "MONDO:0009676🍪🍪biolink:has_phenotype🍪HP:0002505",
+ "has_evidence": ["ECO:0000304"],
+ "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}],
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001558",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype",
},
- "publications": ["PMID:9731527"],
- "publications_links": [{"id": "PMID:9731527", "url": "http://identifiers.org/pubmed/9731527"}],
+ "publications": ["orphanet:589821"],
+ "publications_links": [{"id": "orphanet:589821", "url": None}],
"qualifiers": [],
"frequency_qualifier": "HP:0040283",
"onset_qualifier": None,
@@ -3959,8 +3846,8 @@ def associations():
"frequency_qualifier_label": "Occasional (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040283", "HP:0040279"],
- "frequency_qualifier_closure_label": ["All (HPO)", "Occasional (HPO)", "Frequency (HPO)"],
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Occasional (HPO)"],
"onset_qualifier_label": None,
"onset_qualifier_namespace": None,
"onset_qualifier_category": None,
@@ -3978,288 +3865,158 @@ def associations():
"stage_qualifier_closure_label": [],
},
{
- "id": "uuid:c9c8bf2b-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df97-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0008050",
- "original_subject": "OMIM:160500",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
- "myopathy",
- "hereditary disease",
- "nervous system disorder",
- "congenital myopathy",
- "realizable entity",
- "specifically dependent continuant",
- "skeletal muscle disorder",
- "neuromuscular disease",
- "entity",
- ],
- "subject_taxon": None,
- "subject_taxon_label": None,
- "predicate": "biolink:has_phenotype",
- "object": "HP:0010628",
- "original_object": None,
- "object_namespace": "HP",
- "object_category": "biolink:PhenotypicFeature",
- "object_closure": [
- "UPHENO:0082875",
- "UPHENO:0076772",
- "UPHENO:0002320",
- "UPHENO:0005116",
- "HP:0031910",
- "HP:0011799",
- "HP:0410008",
- "UPHENO:0076692",
- "BFO:0000001",
- "PATO:0000001",
- "HP:0012638",
- "BFO:0000004",
- "UBERON:0001016",
- "UBERON:0001021",
- "UBERON:0000153",
- "UBERON:0011676",
- "UBERON:0013701",
- "UBERON:0014892",
- "UBERON:0015789",
- "UBERON:0011779",
- "UBERON:0000033",
- "HP:0000001",
- "HP:0000152",
- "UPHENO:0002764",
- "UPHENO:0001002",
- "HP:0000118",
- "BFO:0000020",
- "UPHENO:0002433",
- "HP:0000234",
- "HP:0000271",
- "HP:0010827",
- "UPHENO:0001003",
- "HP:0012639",
- "UPHENO:0076710",
- "UPHENO:0002908",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
+ "myopathy",
+ "myotonic dystrophy",
+ "nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
+ "realizable entity",
+ "skeletal muscle disorder",
+ "neuromuscular disease",
+ "myotonic syndrome",
+ ],
+ "subject_taxon": None,
+ "subject_taxon_label": None,
+ "predicate": "biolink:has_phenotype",
+ "object": "HP:0001561",
+ "original_object": None,
+ "object_namespace": "HP",
+ "object_category": "biolink:PhenotypicFeature",
+ "object_closure": [
+ "HP:0001197",
+ "UPHENO:0075852",
+ "UPHENO:0002536",
+ "UBERON:0000465",
"BFO:0000001",
"BFO:0000040",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
- "UBERON:0001785",
- "UBERON:0010959",
- "UBERON:0001577",
- "UPHENO:0075696",
- "HP:0045010",
- "UPHENO:0002844",
- "HP:0001291",
- "HP:0001324",
- "HP:0030319",
- "HP:0000759",
- "UPHENO:0081700",
- "HP:0003011",
- "UPHENO:0002332",
- "UPHENO:0078730",
- "UPHENO:0002536",
- "UPHENO:0081709",
- "HP:0000301",
- "UPHENO:0004523",
- "UPHENO:0004508",
- "HP:0011804",
"BFO:0000002",
- "UBERON:0000465",
- "UBERON:0005090",
- "UBERON:0018254",
- "UBERON:0004120",
- "UBERON:0034713",
- "UBERON:0001647",
- "UBERON:0000122",
- "UBERON:0001630",
- "UBERON:0001033",
- "UBERON:0002376",
- "UBERON:0007811",
- "UBERON:0001444",
- "UBERON:0013702",
- "UBERON:0001456",
- "UBERON:0008229",
- "UBERON:0013700",
"UPHENO:0001001",
- "UPHENO:0002910",
- "HP:0010628",
- "UPHENO:0001005",
- "HP:0011805",
- "BFO:0000002",
- "UPHENO:0076722",
- "UPHENO:0080555",
- "UPHENO:0003587",
- "UPHENO:0002816",
- "UPHENO:0080556",
- "HP:0000707",
- "HP:0006824",
- "UPHENO:0081581",
- "HP:0033127",
- "UPHENO:0076702",
+ "UPHENO:0001002",
+ "UPHENO:0001003",
+ "BFO:0000001",
"UBERON:0001062",
- "RO:0002577",
"UBERON:0000061",
- "UBERON:0015212",
- "UBERON:0010314",
- "UBERON:0005162",
+ "UBERON:0000463",
+ "UPHENO:0001005",
+ "BFO:0000020",
+ "BFO:0000004",
+ "UBERON:0000173",
+ "UBERON:0000468",
+ "HP:0001561",
+ "UBERON:0000922",
+ "HP:0000118",
+ "PATO:0000001",
+ "UBERON:0000323",
+ "HP:0000001",
+ "BFO:0000002",
+ "UPHENO:0075949",
+ "HP:0001560",
"UBERON:0010000",
- "UBERON:0000475",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "UBERON:0000010",
- "UBERON:0004461",
- "UBERON:0004473",
],
- "object_label": "Facial palsy (HPO)",
+ "object_label": "Polyhydramnios (HPO)",
"object_closure_label": [
- "All (HPO)",
- "abnormality of muscle organ physiology",
- "abnormal peripheral nervous system",
- "Abnormal cranial nerve physiology (HPO)",
- "Abnormality of facial soft tissue (HPO)",
- "abnormal head",
"Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "abnormal peripheral nervous system morphology",
- "decreased anatomical entity strength",
- "abnormal facial nerve",
- "abnormal musculature",
- "decreased muscle organ strength",
- "Abnormality of the nervous system (HPO)",
- "Cranial nerve paralysis (HPO)",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "Abnormal nervous system morphology (HPO)",
- "abnormal facial muscle",
- "independent continuant",
- "system",
- "lateral structure",
- "structure with developmental contribution from neural crest",
- "multi cell part structure",
- "multicellular anatomical structure",
- "nervous system",
- "cranial nerve",
- "face",
- "craniocervical region musculature",
- "axial musculature",
- "abnormality of anatomical entity physiology",
- "abnormal cranial nerve morphology",
- "Abnormality of peripheral nerves (HPO)",
- "Facial palsy (HPO)",
+ "Abnormality of the amniotic fluid (HPO)",
+ "quality",
"abnormal phenotype by ontology source",
- "Abnormal skeletal muscle morphology (HPO)",
- "continuant",
- "specifically dependent continuant",
- "abnormality of nervous system physiology",
- "Abnormality of the head (HPO)",
- "Abnormality of the face (HPO)",
- "Abnormality of the seventh cranial nerve (HPO)",
"phenotype by ontology source",
- "Abnormality of the peripheral nervous system (HPO)",
- "paralysed cranial nerve",
- "Abnormality of facial musculature (HPO)",
- "abnormal nervous system",
- "abnormal nerve",
- "quality",
- "Abnormal nervous system physiology (HPO)",
"continuant",
"material anatomical entity",
- "cranial neuron projection bundle",
- "facial nerve",
- "neuron projection bundle",
- "craniocervical region",
- "subdivision of head",
- "body proper",
- "craniocervical muscle",
- "facial muscle",
- "phenotype",
- "abnormal face",
- "abnormal muscle organ morphology",
- "Abnormal muscle physiology (HPO)",
+ "All (HPO)",
+ "embryo",
+ "Phenotypic abnormality (HPO)",
+ "abnormal late embryo",
"entity",
+ "specifically dependent continuant",
"anatomical entity",
"anatomical structure",
- "muscle structure",
- "skeletal musculature",
- "mesoderm-derived structure",
- "organism subdivision",
- "organ",
- "muscle organ",
- "gustatory system",
- "cranial muscle",
- "musculature of body",
- "musculature",
- "peripheral nervous system",
- "skeletal musculature of head",
- "musculature of face",
- "abnormal anatomical entity",
- "Abnormality of head or neck (HPO)",
- "abnormal craniocervical region",
- "Abnormal cranial nerve morphology (HPO)",
- "Muscle weakness (HPO)",
- "Weakness of facial musculature (HPO)",
- "Abnormal peripheral nervous system morphology (HPO)",
- "paralysed anatomical entity",
- "Abnormality of the musculature (HPO)",
- "abnormality of anatomical entity physiology",
- "abnormality of cranial nerve physiology",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
+ "organism substance",
+ "amniotic fluid",
+ "multicellular organism",
+ "phenotype",
+ "continuant",
"entity",
- "abnormal nervous system morphology",
+ "independent continuant",
+ "Abnormality of prenatal development or birth (HPO)",
+ "abnormal amniotic fluid",
"material entity",
- "anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "nerve",
- "anterior region of body",
- "subdivision of organism along main body axis",
- "main body axis",
- "skeletal muscle organ",
- "cranial or facial muscle",
- "nerve of head region",
- "head",
+ "Polyhydramnios (HPO)",
+ "abnormal anatomical entity",
+ "multicellular anatomical structure",
+ "late embryo",
],
"object_taxon": None,
"object_taxon_label": None,
@@ -4270,16 +4027,16 @@ def associations():
"evidence_count": 2,
"has_evidence": ["ECO:0000304"],
"has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}],
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0010628",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001561",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype",
},
- "publications": ["OMIM:160500"],
- "publications_links": [{"id": "OMIM:160500", "url": "http://identifiers.org/mim/160500"}],
+ "publications": ["orphanet:589821"],
+ "publications_links": [{"id": "orphanet:589821", "url": None}],
"qualifiers": [],
- "frequency_qualifier": None,
+ "frequency_qualifier": "HP:0040283",
"onset_qualifier": None,
"sex_qualifier": None,
"stage_qualifier": None,
@@ -4288,11 +4045,11 @@ def associations():
"qualifiers_category": None,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": None,
- "frequency_qualifier_namespace": None,
- "frequency_qualifier_category": None,
- "frequency_qualifier_closure": [],
- "frequency_qualifier_closure_label": [],
+ "frequency_qualifier_label": "Occasional (HPO)",
+ "frequency_qualifier_namespace": "HP",
+ "frequency_qualifier_category": "biolink:PhenotypicFeature",
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Occasional (HPO)"],
"onset_qualifier_label": None,
"onset_qualifier_namespace": None,
"onset_qualifier_category": None,
@@ -4310,216 +4067,296 @@ def associations():
"stage_qualifier_closure_label": [],
},
{
- "id": "uuid:c9c8bf2d-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df98-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0008050",
- "original_subject": "OMIM:160500",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
+ "myotonic syndrome",
],
"subject_taxon": None,
- "subject_taxon_label": None,
- "predicate": "biolink:has_phenotype",
- "object": "HP:0011916",
- "original_object": None,
- "object_namespace": "HP",
- "object_category": "biolink:PhenotypicFeature",
- "object_closure": [
- "HP:0002814",
- "HP:0009127",
- "UPHENO:0076692",
- "UPHENO:0003070",
- "PATO:0000001",
- "BFO:0000004",
- "UBERON:0004708",
- "UBERON:0000154",
- "UBERON:0006058",
- "UBERON:0002529",
- "UBERON:0002387",
- "HP:0000001",
- "UPHENO:0002644",
- "UPHENO:0001001",
- "UPHENO:0001002",
- "HP:0000118",
- "BFO:0000020",
- "UPHENO:0001003",
- "UPHENO:0076710",
- "HP:0011916",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0001062",
- "UBERON:0010000",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
- "UBERON:0010709",
- "UBERON:0010538",
- "UBERON:0004488",
- "HP:0001436",
- "UPHENO:0002653",
- "HP:0003011",
- "UPHENO:0002536",
- "HP:0001437",
- "HP:0040064",
- "BFO:0000002",
- "PR:000050567",
- "UBERON:0000465",
- "UBERON:0002101",
- "UBERON:0004709",
- "UBERON:0005090",
- "UBERON:0002103",
- "UBERON:0010707",
- "UBERON:0001630",
- "UBERON:0000026",
- "UBERON:0010758",
- "UBERON:0007271",
- "UBERON:0014792",
- "UBERON:0004482",
- "UBERON:0008784",
- "UBERON:0002470",
- "UPHENO:0001005",
- "HP:0011805",
+ "subject_taxon_label": None,
+ "predicate": "biolink:has_phenotype",
+ "object": "HP:0001643",
+ "original_object": None,
+ "object_namespace": "HP",
+ "object_category": "biolink:PhenotypicFeature",
+ "object_closure": [
+ "HP:0030962",
+ "UPHENO:0019771",
+ "PR:000050567",
+ "UBERON:0000465",
+ "UPHENO:0020542",
+ "UPHENO:0076729",
+ "UPHENO:0080362",
+ "HP:0001627",
+ "UPHENO:0015280",
+ "BFO:0000001",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UBERON:0000468",
+ "UBERON:0011676",
+ "UBERON:0013701",
+ "UPHENO:0020119",
+ "HP:0001626",
+ "UPHENO:0001002",
+ "UPHENO:0033572",
+ "BFO:0000020",
+ "UPHENO:0015324",
+ "UPHENO:0015290",
"BFO:0000002",
- "UPHENO:0002816",
- "UPHENO:0081581",
- "HP:0033127",
- "UPHENO:0002647",
+ "UBERON:0013768",
+ "UBERON:0003509",
+ "UBERON:0003513",
+ "UBERON:0011695",
+ "UBERON:0004716",
+ "UBERON:0004145",
+ "UBERON:0005985",
+ "UBERON:0002049",
+ "UBERON:0002201",
+ "UBERON:0006876",
+ "UPHENO:0001001",
+ "UPHENO:0001003",
+ "UPHENO:0002536",
"BFO:0000001",
- "UPHENO:0002830",
- "RO:0002577",
+ "UBERON:0034923",
+ "UBERON:0015410",
+ "UPHENO:0075696",
+ "HP:0001643",
+ "UPHENO:0076776",
+ "UPHENO:0081581",
+ "UPHENO:0076692",
+ "BFO:0000004",
+ "UBERON:0001981",
+ "UBERON:0004537",
+ "UBERON:0004572",
+ "UBERON:0004535",
"UBERON:0000061",
- "UBERON:0015212",
+ "UBERON:0000477",
"UBERON:0000475",
"UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "UBERON:0000978",
- "UBERON:0007270",
- "UBERON:0004480",
+ "UBERON:0004111",
+ "UBERON:0004573",
+ "UBERON:0003498",
+ "HP:0011603",
+ "UPHENO:0020351",
+ "HP:0030680",
+ "UPHENO:0076765",
+ "BFO:0000002",
+ "HP:0025015",
+ "HP:0002597",
+ "UPHENO:0076810",
+ "HP:0033353",
+ "PATO:0000001",
+ "UBERON:0001637",
+ "UBERON:0003834",
+ "UBERON:0000948",
+ "UBERON:0009569",
+ "UBERON:0013702",
+ "UBERON:0005177",
+ "UBERON:0003103",
+ "UBERON:0000055",
+ "UBERON:0005440",
+ "UBERON:0000915",
+ "UBERON:0002100",
+ "UBERON:0005181",
+ "UBERON:0002075",
+ "UBERON:0015228",
+ "HP:0000118",
+ "UPHENO:0075655",
+ "UPHENO:0020584",
+ "UPHENO:0020587",
+ "UBERON:0010314",
+ "UBERON:0018674",
+ "HP:0000001",
+ "UPHENO:0002678",
+ "UPHENO:0001005",
+ "UPHENO:0033603",
+ "UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0004120",
+ "UBERON:0007798",
+ "UBERON:0001009",
+ "UBERON:0004571",
+ "UBERON:0005178",
+ "UBERON:0007100",
],
- "object_label": "Toe extensor amyotrophy (HPO)",
+ "object_label": "Patent ductus arteriosus (HPO)",
"object_closure_label": [
- "All (HPO)",
- "abnormal musculature of lower limb",
- "Abnormality of the lower limb (HPO)",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "abnormal musculature",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "abnormal musculature of limb",
- "entity",
- "independent continuant",
- "system",
- "paired limb/fin",
- "lateral structure",
- "pelvic complex",
- "appendage musculature",
- "musculature of pelvic complex",
- "musculature of pes",
- "phenotype",
- "Abnormality of the foot musculature (HPO)",
- "abnormal phenotype by ontology source",
- "Abnormal skeletal muscle morphology (HPO)",
- "continuant",
+ "abnormal blood vessel morphology",
+ "abnormal anatomical entity",
"specifically dependent continuant",
"phenotype by ontology source",
- "Abnormality of the musculature of the lower limbs (HPO)",
- "Abnormality of limbs (HPO)",
- "quality",
+ "abnormal anatomical entity",
"continuant",
"protein-containing material entity",
"material anatomical entity",
- "hindlimb",
- "appendage girdle complex",
- "appendage",
- "subdivision of organism along appendicular axis",
- "paired limb/fin segment",
- "musculature of lower limb",
- "lower limb segment",
- "autopod region",
- "Abnormality of the musculature of the limbs (HPO)",
- "abnormal muscle organ morphology",
- "Toe extensor amyotrophy (HPO)",
+ "vascular system",
+ "circulatory system",
+ "vasculature of trunk",
+ "vasculature of organ",
+ "ductus arteriosus",
+ "thoracic segment of trunk",
+ "trunk",
+ "thoracic segment organ",
+ "viscus",
+ "circulatory organ",
+ "All (HPO)",
+ "abnormal vasculature",
+ "abnormal phenotype by ontology source",
+ "continuant",
+ "abnormal artery morphology in the independent continuant",
+ "multicellular organism",
+ "outflow tract",
+ "coronary vessel",
+ "vasculature",
+ "subdivision of trunk",
+ "body proper",
+ "trunk region element",
+ "compound organ",
+ "vessel",
+ "Abnormality of cardiovascular system morphology (HPO)",
+ "abnormal great vessel of heart morphology",
+ "Phenotypic abnormality (HPO)",
+ "abnormal opening of the anatomical entity",
+ "abnormal anatomical entity morphology",
+ "abnormal systemic artery morphology",
"entity",
- "anatomical structure",
- "muscle structure",
+ "structure with developmental contribution from neural crest",
+ "thoracic cavity element",
+ "primary circulatory organ",
+ "abnormal coronary vessel morphology",
+ "Abnormality of the cardiovascular system (HPO)",
+ "Phenotypic abnormality",
+ "abnormal incomplete closing of the anatomical entity",
+ "Patent ductus arteriosus (HPO)",
+ "abnormal cardiovascular system morphology",
+ "abnormal anatomical entity morphology",
+ "quality",
+ "disconnected anatomical group",
+ "anatomical cluster",
"organism subdivision",
"organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "leg",
- "pelvic appendage musculature",
- "musculature of limb",
- "abnormal musculature of pes",
- "Abnormality of the musculature (HPO)",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "abnormal leg",
- "abnormal limb",
+ "anatomical conduit",
+ "systemic artery",
+ "heart blood vessel",
+ "heart plus pericardium",
+ "phenotype",
+ "abnormal incomplete closing of the ductus arteriosus",
+ "abnormal anatomical entity morphology in the independent continuant",
+ "Abnormal vascular morphology (HPO)",
+ "entity",
+ "independent continuant",
+ "subdivision of organism along main body axis",
+ "main body axis",
+ "abnormal anatomical entity morphology in the heart",
+ "abnormal multicellular organism morphology",
"material entity",
"anatomical entity",
- "limb",
- "pelvic appendage",
+ "blood vessel",
+ "arterial system",
+ "blood vasculature",
+ "cardiovascular system",
+ "anatomical structure",
+ "great vessel of heart",
+ "arterial blood vessel",
+ "trunk blood vessel",
+ "embryonic cardiovascular system",
+ "conceptus",
+ "systemic arterial system",
+ "Congenital malformation of the great arteries (HPO)",
+ "abnormal ductus arteriosus morphology",
+ "abnormal vascular system morphology",
+ "abnormal cardiovascular system",
+ "Abnormal heart morphology (HPO)",
+ "Abnormal morphology of the great vessels (HPO)",
+ "abnormal artery morphology",
+ "Abnormality of the vasculature (HPO)",
+ "abnormal heart morphology",
+ "Abnormal blood vessel morphology (HPO)",
"multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "posterior region of body",
- "multi-limb segment region",
- "limb segment",
- "pes",
+ "mesoderm-derived structure",
+ "artery",
+ "thoracic segment blood vessel",
+ "heart",
+ "heart vasculature",
],
"object_taxon": None,
"object_taxon_label": None,
@@ -4530,16 +4367,16 @@ def associations():
"evidence_count": 2,
"has_evidence": ["ECO:0000304"],
"has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}],
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0011916",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001643",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype",
},
- "publications": ["OMIM:160500"],
- "publications_links": [{"id": "OMIM:160500", "url": "http://identifiers.org/mim/160500"}],
+ "publications": ["orphanet:589821"],
+ "publications_links": [{"id": "orphanet:589821", "url": None}],
"qualifiers": [],
- "frequency_qualifier": None,
+ "frequency_qualifier": "HP:0040283",
"onset_qualifier": None,
"sex_qualifier": None,
"stage_qualifier": None,
@@ -4548,11 +4385,11 @@ def associations():
"qualifiers_category": None,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": None,
- "frequency_qualifier_namespace": None,
- "frequency_qualifier_category": None,
- "frequency_qualifier_closure": [],
- "frequency_qualifier_closure_label": [],
+ "frequency_qualifier_label": "Occasional (HPO)",
+ "frequency_qualifier_namespace": "HP",
+ "frequency_qualifier_category": "biolink:PhenotypicFeature",
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Occasional (HPO)"],
"onset_qualifier_label": None,
"onset_qualifier_namespace": None,
"onset_qualifier_category": None,
@@ -4570,152 +4407,218 @@ def associations():
"stage_qualifier_closure_label": [],
},
{
- "id": "uuid:c9c8bf2e-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df99-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0008050",
- "original_subject": "OMIM:160500",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
+ "myotonic syndrome",
],
"subject_taxon": None,
"subject_taxon_label": None,
"predicate": "biolink:has_phenotype",
- "object": "HP:0002460",
+ "object": "HP:0001671",
"original_object": None,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "UPHENO:0082875",
- "UPHENO:0002320",
- "UPHENO:0001005",
+ "PR:000050567",
+ "UBERON:0000465",
+ "UPHENO:0019888",
+ "UPHENO:0080362",
+ "HP:0001627",
+ "UPHENO:0015280",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UBERON:0000468",
+ "UBERON:0011676",
+ "UBERON:0013701",
+ "HP:0001626",
+ "UPHENO:0001002",
"BFO:0000020",
- "PATO:0000001",
- "BFO:0000004",
- "UBERON:0000061",
- "HP:0000001",
+ "UPHENO:0015324",
+ "HP:0001671",
+ "BFO:0000002",
"UPHENO:0001001",
- "HP:0000118",
- "BFO:0000001",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
- "UPHENO:0075696",
- "HP:0001324",
- "HP:0003011",
- "UPHENO:0002332",
"UPHENO:0001003",
- "UPHENO:0002536",
- "HP:0002460",
- "HP:0011804",
- "BFO:0000002",
- "BFO:0000040",
- "UBERON:0005090",
- "UBERON:0001630",
- "UPHENO:0001002",
+ "BFO:0000001",
+ "UBERON:0015410",
+ "UPHENO:0076776",
+ "UPHENO:0081581",
+ "UPHENO:0076692",
+ "BFO:0000004",
+ "UBERON:0004535",
+ "UBERON:0000061",
+ "UBERON:0000475",
+ "UBERON:0000062",
+ "UPHENO:0075696",
+ "HP:0030680",
"BFO:0000002",
- "UPHENO:0080555",
- "UPHENO:0002816",
- "UPHENO:0080556",
- "HP:0033127",
+ "UPHENO:0002536",
+ "UPHENO:0076810",
+ "UBERON:0002099",
+ "UBERON:0000948",
+ "UBERON:0009569",
+ "UBERON:0013702",
+ "UBERON:0005177",
+ "UBERON:0003103",
+ "UBERON:0000915",
+ "UBERON:0002100",
+ "UBERON:0005181",
+ "UBERON:0002075",
+ "UBERON:0015228",
+ "HP:0000118",
+ "UPHENO:0020584",
+ "PATO:0000001",
+ "UBERON:0003037",
+ "UBERON:0010314",
+ "HP:0000001",
+ "UPHENO:0001005",
"BFO:0000001",
- "UBERON:0001062",
- "UBERON:0000465",
"UBERON:0010000",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
+ "UBERON:0000467",
+ "UBERON:0004120",
+ "UBERON:0001009",
+ "UBERON:0005178",
+ "UBERON:0007100",
],
- "object_label": "Distal muscle weakness (HPO)",
+ "object_label": "Abnormal cardiac septum morphology (HPO)",
"object_closure_label": [
+ "abnormal anatomical entity",
+ "quality",
+ "specifically dependent continuant",
+ "phenotype by ontology source",
+ "continuant",
+ "protein-containing material entity",
+ "material anatomical entity",
+ "circulatory system",
+ "thoracic segment of trunk",
+ "trunk",
+ "thoracic segment organ",
+ "viscus",
+ "circulatory organ",
"All (HPO)",
- "abnormality of muscle organ physiology",
+ "abnormal phenotype by ontology source",
+ "continuant",
+ "Abnormal cardiac septum morphology (HPO)",
+ "multicellular organism",
+ "subdivision of trunk",
+ "body proper",
+ "trunk region element",
+ "compound organ",
+ "Abnormality of cardiovascular system morphology (HPO)",
"Phenotypic abnormality (HPO)",
- "decreased anatomical entity strength",
- "abnormal musculature",
- "decreased muscle organ strength",
- "Abnormality of the musculoskeletal system (HPO)",
+ "abnormal anatomical entity morphology",
"entity",
- "independent continuant",
- "material anatomical entity",
- "anatomical structure",
- "multicellular anatomical structure",
- "abnormality of anatomical entity physiology",
- "phenotype",
+ "entity",
+ "septum",
+ "structure with developmental contribution from neural crest",
+ "thoracic cavity element",
+ "primary circulatory organ",
+ "Abnormality of the cardiovascular system (HPO)",
"Phenotypic abnormality",
- "continuant",
- "Distal muscle weakness (HPO)",
- "quality",
- "continuant",
+ "abnormal cardiovascular system morphology",
+ "abnormal anatomical entity morphology",
+ "organism subdivision",
+ "organ",
+ "heart plus pericardium",
+ "phenotype",
+ "abnormal anatomical entity morphology in the independent continuant",
+ "independent continuant",
+ "subdivision of organism along main body axis",
+ "main body axis",
+ "abnormal anatomical entity morphology in the heart",
+ "abnormal multicellular organism morphology",
"material entity",
- "abnormal phenotype by ontology source",
- "specifically dependent continuant",
- "Abnormal muscle physiology (HPO)",
- "entity",
"anatomical entity",
- "muscle structure",
- "organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "abnormal anatomical entity",
- "Muscle weakness (HPO)",
- "Abnormality of the musculature (HPO)",
- "abnormality of anatomical entity physiology",
- "phenotype by ontology source",
+ "cardiovascular system",
+ "anatomical structure",
"abnormal anatomical entity",
+ "abnormal cardiac septum morphology",
+ "abnormal cardiovascular system",
+ "Abnormal heart morphology (HPO)",
+ "abnormal heart morphology",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
+ "mesoderm-derived structure",
+ "cardiac septum",
+ "heart",
],
"object_taxon": None,
"object_taxon_label": None,
@@ -4726,16 +4629,16 @@ def associations():
"evidence_count": 2,
"has_evidence": ["ECO:0000304"],
"has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}],
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0002460",
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001671",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype",
},
- "publications": ["OMIM:160500"],
- "publications_links": [{"id": "OMIM:160500", "url": "http://identifiers.org/mim/160500"}],
+ "publications": ["orphanet:589821"],
+ "publications_links": [{"id": "orphanet:589821", "url": None}],
"qualifiers": [],
- "frequency_qualifier": None,
+ "frequency_qualifier": "HP:0040283",
"onset_qualifier": None,
"sex_qualifier": None,
"stage_qualifier": None,
@@ -4744,11 +4647,11 @@ def associations():
"qualifiers_category": None,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": None,
- "frequency_qualifier_namespace": None,
- "frequency_qualifier_category": None,
- "frequency_qualifier_closure": [],
- "frequency_qualifier_closure_label": [],
+ "frequency_qualifier_label": "Occasional (HPO)",
+ "frequency_qualifier_namespace": "HP",
+ "frequency_qualifier_category": "biolink:PhenotypicFeature",
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Occasional (HPO)"],
"onset_qualifier_label": None,
"onset_qualifier_namespace": None,
"onset_qualifier_category": None,
@@ -4766,176 +4669,172 @@ def associations():
"stage_qualifier_closure_label": [],
},
{
- "id": "uuid:c9c8bf32-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df9a-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0008050",
- "original_subject": "OMIM:160500",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001",
],
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity",
+ "myotonic syndrome",
],
"subject_taxon": None,
"subject_taxon_label": None,
"predicate": "biolink:has_phenotype",
- "object": "HP:0003805",
+ "object": "HP:0002014",
"original_object": None,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "BFO:0000002",
- "BFO:0000020",
- "UPHENO:0076692",
+ "UPHENO:0002443",
+ "UPHENO:0002536",
+ "UBERON:0000465",
+ "UPHENO:0082875",
+ "HP:0002664",
"BFO:0000001",
- "BFO:0000004",
- "CL:0000255",
- "UBERON:0014892",
- "UBERON:0002036",
- "HP:0000001",
- "HP:0004303",
- "UPHENO:0001001",
+ "BFO:0000040",
+ "UBERON:0001062",
"UPHENO:0001002",
- "HP:0000118",
+ "BFO:0000020",
+ "HP:0011793",
+ "HP:0011458",
+ "BFO:0000002",
+ "UBERON:0001988",
+ "UPHENO:0001001",
+ "UPHENO:0002833",
"UPHENO:0001003",
- "UPHENO:0076710",
- "PATO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0000467",
- "CL:0000000",
+ "UBERON:0000463",
+ "UPHENO:0075696",
+ "HP:0002014",
+ "HP:0025031",
+ "BFO:0000004",
+ "UBERON:0000061",
+ "UBERON:0000174",
"UBERON:0000468",
- "UBERON:0011216",
- "CL:0000548",
- "UBERON:0001134",
- "HP:0003011",
- "UPHENO:0002536",
- "HP:0003805",
- "UBERON:0005090",
- "UBERON:0018254",
- "UBERON:0004120",
- "UBERON:0000479",
- "CL:0000003",
- "UBERON:0001630",
- "UBERON:0002385",
- "CL:0000188",
- "UPHENO:0001005",
- "HP:0011805",
- "HP:0025354",
- "UPHENO:0002816",
- "UPHENO:0081581",
- "HP:0033127",
"BFO:0000002",
- "UBERON:0001062",
- "UBERON:0000465",
- "RO:0002577",
- "UBERON:0000061",
+ "HP:0025032",
+ "PATO:0000001",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "HP:0000001",
+ "UPHENO:0001005",
+ "BFO:0000001",
"UBERON:0010000",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "CL:0002371",
+ "UBERON:0000467",
+ "UBERON:0001007",
],
- "object_label": "Rimmed vacuoles (HPO)",
+ "object_label": "Diarrhea (HPO)",
"object_closure_label": [
+ "abnormality of anatomical entity physiology",
+ "abnormal digestive system",
+ "entity",
+ "abnormal anatomical entity",
+ "Diarrhea (HPO)",
+ "specifically dependent continuant",
+ "Abnormality of digestive system physiology (HPO)",
+ "phenotype by ontology source",
+ "continuant",
+ "material anatomical entity",
+ "digestive system",
"All (HPO)",
- "Abnormal muscle fiber morphology (HPO)",
- "Phenotypic abnormality",
+ "abnormal phenotype by ontology source",
+ "continuant",
+ "feces",
"Phenotypic abnormality (HPO)",
- "Abnormal cellular phenotype (HPO)",
- "abnormal musculature",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
+ "Phenotypic abnormality",
+ "Neoplasm by anatomical site (HPO)",
+ "Abdominal symptom (HPO)",
"quality",
- "independent continuant",
- "material anatomical entity",
- "system",
- "multicellular anatomical structure",
+ "organism substance",
+ "excreta",
+ "multicellular organism",
"phenotype",
- "abnormal phenotype by ontology source",
- "Abnormal skeletal muscle morphology (HPO)",
- "phenotype by ontology source",
- "tissue",
- "animal cell",
- "skeletal muscle tissue",
- "cell of skeletal muscle",
- "continuant",
- "specifically dependent continuant",
- "abnormal muscle organ morphology",
- "Rimmed vacuoles (HPO)",
+ "Neoplasm (HPO)",
"entity",
+ "independent continuant",
+ "abnormality of digestive system physiology",
+ "Abnormality of the digestive system (HPO)",
+ "material entity",
"anatomical entity",
"anatomical structure",
- "muscle structure",
- "skeletal musculature",
- "mesoderm-derived structure",
- "organ",
- "native cell",
- "muscle organ",
- "muscle tissue",
- "musculature of body",
- "musculature",
- "somatic cell",
- "Abnormality of the musculature (HPO)",
+ "abnormality of anatomical entity physiology",
"abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "entity",
- "continuant",
- "material entity",
+ "multicellular anatomical structure",
"anatomical system",
- "cell",
- "multicellular organism",
- "organ system subdivision",
- "eukaryotic cell",
- "skeletal muscle organ",
- "striated muscle tissue",
],
"object_taxon": None,
"object_taxon_label": None,
@@ -4944,18 +4843,18 @@ def associations():
"negated": None,
"pathway": None,
"evidence_count": 2,
- "has_evidence": ["ECO:0000501"],
- "has_evidence_links": [{"id": "ECO:0000501", "url": "http://purl.obolibrary.org/obo/ECO_0000501"}],
- "grouping_key": "MONDO:0008050🍪🍪biolink:has_phenotype🍪HP:0003805",
+ "has_evidence": ["ECO:0000304"],
+ "has_evidence_links": [{"id": "ECO:0000304", "url": "http://purl.obolibrary.org/obo/ECO_0000304"}],
+ "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0002014",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype",
},
- "publications": ["OMIM:160500"],
- "publications_links": [{"id": "OMIM:160500", "url": "http://identifiers.org/mim/160500"}],
+ "publications": ["orphanet:589821"],
+ "publications_links": [{"id": "orphanet:589821", "url": None}],
"qualifiers": [],
- "frequency_qualifier": None,
+ "frequency_qualifier": "HP:0040283",
"onset_qualifier": None,
"sex_qualifier": None,
"stage_qualifier": None,
@@ -4964,11 +4863,11 @@ def associations():
"qualifiers_category": None,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": None,
- "frequency_qualifier_namespace": None,
- "frequency_qualifier_category": None,
- "frequency_qualifier_closure": [],
- "frequency_qualifier_closure_label": [],
+ "frequency_qualifier_label": "Occasional (HPO)",
+ "frequency_qualifier_namespace": "HP",
+ "frequency_qualifier_category": "biolink:PhenotypicFeature",
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
+ "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Occasional (HPO)"],
"onset_qualifier_label": None,
"onset_qualifier_namespace": None,
"onset_qualifier_category": None,
diff --git a/backend/tests/fixtures/autocomplete.py b/backend/tests/fixtures/autocomplete.py
index fc911209d..836d0c7eb 100644
--- a/backend/tests/fixtures/autocomplete.py
+++ b/backend/tests/fixtures/autocomplete.py
@@ -13,6 +13,7 @@ def autocomplete():
"category": "biolink:Disease",
"name": "Fanconi renotubular syndrome",
"full_name": None,
+ "deprecated": None,
"description": "A genetic or acquired disorder characterized by impairment of the function of the proximal tubules of the kidney. It results in decreased reabsorption of electrolytes, glucose, amino acids, and other nutrients.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -42,6 +43,7 @@ def autocomplete():
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group A",
"full_name": None,
+ "deprecated": None,
"description": "Fanconi anemia caused by mutations of the FANCA gene. FANCA gene mutations are the most common cause of Fanconi anemia. This gene provides instructions for making a protein that is involved in the Fanconi anemia (FA) pathway.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -70,6 +72,7 @@ def autocomplete():
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group L",
"full_name": None,
+ "deprecated": None,
"description": "Any Fanconi anemia in which the cause of the disease is a mutation in the FANCL gene.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -95,6 +98,7 @@ def autocomplete():
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group E",
"full_name": None,
+ "deprecated": None,
"description": "Fanconi anemia caused by mutations of the FANCE gene. This is a protein coding gene. It is required for the nuclear accumulation of FANCC and provides a critical bridge between the FA complex and FANCD2.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -120,6 +124,7 @@ def autocomplete():
"category": "biolink:Disease",
"name": "Fanconi renotubular syndrome 1",
"full_name": None,
+ "deprecated": None,
"description": None,
"xref": [],
"provided_by": "phenio_nodes",
@@ -147,6 +152,7 @@ def autocomplete():
"category": "biolink:Disease",
"name": "Fanconi anemia",
"full_name": None,
+ "deprecated": None,
"description": "Fanconi anemia (FA) is a hereditary DNA repair disorder characterized by progressive pancytopenia with bone marrow failure, variable congenital malformations and predisposition to develop hematological or solid tumors.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -171,6 +177,7 @@ def autocomplete():
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group O",
"full_name": None,
+ "deprecated": None,
"description": "Any Fanconi anemia in which the cause of the disease is a mutation in the RAD51C gene.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -196,6 +203,7 @@ def autocomplete():
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group P",
"full_name": None,
+ "deprecated": None,
"description": "Any Fanconi anemia in which the cause of the disease is a mutation in the SLX4 gene.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -221,6 +229,7 @@ def autocomplete():
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group V",
"full_name": None,
+ "deprecated": None,
"description": "Any Fanconi anemia in which the cause of the disease is a mutation in the MAD2L2 gene.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -246,6 +255,7 @@ def autocomplete():
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group B",
"full_name": None,
+ "deprecated": None,
"description": "Fanconi anemia caused by mutations of the FANCB gene. This gene encodes the protein for complementation group B.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -273,6 +283,7 @@ def autocomplete():
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group N",
"full_name": None,
+ "deprecated": None,
"description": "Any Fanconi anemia in which the cause of the disease is a mutation in the PALB2 gene.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -297,6 +308,7 @@ def autocomplete():
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group R",
"full_name": None,
+ "deprecated": None,
"description": "Any Fanconi anemia in which the cause of the disease is a mutation in the RAD51 gene.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -321,6 +333,7 @@ def autocomplete():
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group U",
"full_name": None,
+ "deprecated": None,
"description": "Any Fanconi anemia in which the cause of the disease is a mutation in the XRCC2 gene.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -340,27 +353,12 @@ def autocomplete():
"highlight": None,
"score": None,
},
- {
- "id": "MONDO:0100136",
- "category": "biolink:Disease",
- "name": "obsolete Fanconia anemia complementation group M",
- "full_name": None,
- "description": "OBSOLETE Any Fanconi anemia in which the cause of the disease is a mutation in the FANCM gene.",
- "xref": [],
- "provided_by": "phenio_nodes",
- "in_taxon": None,
- "in_taxon_label": None,
- "symbol": None,
- "synonym": ["FANCM Fanconi anemia", "Fanconi anemia caused by mutation in FANCM"],
- "uri": None,
- "highlight": None,
- "score": None,
- },
{
"id": "MONDO:0009213",
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group C",
"full_name": None,
+ "deprecated": None,
"description": "Fanconi anemia caused by mutations of the FANCC gene. This gene provides instructions for making a protein that delays the onset of apoptosis and promotes homologous recombination repair of damaged DNA.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -388,6 +386,7 @@ def autocomplete():
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group D2",
"full_name": None,
+ "deprecated": None,
"description": "Fanconi anemia caused by mutations of the FANCD2 gene. This gene is involved in the repair of DNA double-strand breaks, both by homologous recombination and single-strand annealing.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -414,6 +413,7 @@ def autocomplete():
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group I",
"full_name": None,
+ "deprecated": None,
"description": "Fanconi anemia caused by mutations in the FANCI gene, encoding Fanconi anemia group I protein.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -437,6 +437,7 @@ def autocomplete():
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group Q",
"full_name": None,
+ "deprecated": None,
"description": "Any Fanconi anemia in which the cause of the disease is a mutation in the ERCC4 gene.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -460,6 +461,7 @@ def autocomplete():
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group T",
"full_name": None,
+ "deprecated": None,
"description": "Any Fanconi anemia in which the cause of the disease is a mutation in the UBE2T gene.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -483,6 +485,7 @@ def autocomplete():
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group F",
"full_name": None,
+ "deprecated": None,
"description": "Fanconi anemia caused by mutations of the FANCF gene. This gene encodes a polypeptide with homology to the prokaryotic RNA-binding protein ROM.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -500,6 +503,29 @@ def autocomplete():
"highlight": None,
"score": None,
},
+ {
+ "id": "MONDO:0012187",
+ "category": "biolink:Disease",
+ "name": "Fanconi anemia complementation group J",
+ "full_name": None,
+ "deprecated": None,
+ "description": "Fanconi anemia caused by mutations in the BRIP1 gene, encoding Fanconi anemia group J protein.",
+ "xref": [],
+ "provided_by": "phenio_nodes",
+ "in_taxon": None,
+ "in_taxon_label": None,
+ "symbol": None,
+ "synonym": [
+ "FANCJ",
+ "Fanconi Anemia, complementation group type J",
+ "Fanconi anemia complementation group J",
+ "Fanconi anemia complementation group type J",
+ "Fanconi anemia, complementation group J",
+ ],
+ "uri": None,
+ "highlight": None,
+ "score": None,
+ },
],
"facet_fields": [],
"facet_queries": [],
diff --git a/backend/tests/fixtures/autocomplete_query.py b/backend/tests/fixtures/autocomplete_query.py
index cd5f4949d..0eb1230e7 100644
--- a/backend/tests/fixtures/autocomplete_query.py
+++ b/backend/tests/fixtures/autocomplete_query.py
@@ -15,7 +15,7 @@ def autocomplete_query():
"def_type": "edismax",
"q_op": "AND",
"mm": "100%",
- "boost": 'product(if(termfreq(category,"biolink:Disease"),10.0,1),if(and(termfreq(in_taxon,"NCBITaxon:9606"),termfreq(category,"biolink:Gene")),5.0,1))',
+ "boost": 'product(if(termfreq(category,"biolink:Disease"),10.0,1),if(and(termfreq(in_taxon,"NCBITaxon:9606"),termfreq(category,"biolink:Gene")),5.0,1),if(termfreq(deprecated,"true"),0.1,1))',
"sort": None,
"facet_min_count": 1,
}
diff --git a/backend/tests/fixtures/autocomplete_response.py b/backend/tests/fixtures/autocomplete_response.py
index 1779f34ce..fd24d788f 100644
--- a/backend/tests/fixtures/autocomplete_response.py
+++ b/backend/tests/fixtures/autocomplete_response.py
@@ -14,7 +14,7 @@ def autocomplete_response():
"qf": "id^100 name^10 name_t^5 name_ac symbol^10 symbol_t^5 symbol_ac synonym synonym_t synonym_ac",
"start": "0",
"q.op": "AND",
- "boost": 'product(if(termfreq(category,"biolink:Disease"),10.0,1),if(and(termfreq(in_taxon,"NCBITaxon:9606"),termfreq(category,"biolink:Gene")),5.0,1))',
+ "boost": 'product(if(termfreq(category,"biolink:Disease"),10.0,1),if(and(termfreq(in_taxon,"NCBITaxon:9606"),termfreq(category,"biolink:Gene")),5.0,1),if(termfreq(deprecated,"true"),0.1,1))',
"rows": "20",
"facet": "true",
},
@@ -250,14 +250,6 @@ def autocomplete_response():
],
"description": "Any Fanconi anemia in which the cause of the disease is a mutation in the XRCC2 gene.",
},
- {
- "id": "MONDO:0100136",
- "category": "biolink:Disease",
- "name": "obsolete Fanconia anemia complementation group M",
- "provided_by": "phenio_nodes",
- "synonym": ["FANCM Fanconi anemia", "Fanconi anemia caused by mutation in FANCM"],
- "description": "OBSOLETE Any Fanconi anemia in which the cause of the disease is a mutation in the FANCM gene.",
- },
{
"id": "MONDO:0009213",
"category": "biolink:Disease",
@@ -354,6 +346,20 @@ def autocomplete_response():
],
"description": "Fanconi anemia caused by mutations of the FANCF gene. This gene encodes a polypeptide with homology to the prokaryotic RNA-binding protein ROM.",
},
+ {
+ "id": "MONDO:0012187",
+ "category": "biolink:Disease",
+ "name": "Fanconi anemia complementation group J",
+ "provided_by": "phenio_nodes",
+ "synonym": [
+ "FANCJ",
+ "Fanconi Anemia, complementation group type J",
+ "Fanconi anemia complementation group J",
+ "Fanconi anemia complementation group type J",
+ "Fanconi anemia, complementation group J",
+ ],
+ "description": "Fanconi anemia caused by mutations in the BRIP1 gene, encoding Fanconi anemia group J protein.",
+ },
],
},
"facet_counts": {"facet_fields": {}, "facet_queries": {}},
diff --git a/backend/tests/fixtures/entity.py b/backend/tests/fixtures/entity.py
index c53c3edf6..a04599d72 100644
--- a/backend/tests/fixtures/entity.py
+++ b/backend/tests/fixtures/entity.py
@@ -8,6 +8,7 @@ def entity():
"category": "biolink:Disease",
"name": "muscular dystrophy",
"full_name": None,
+ "deprecated": None,
"description": "Muscular dystrophy (MD) refers to a group of more than 30 genetic diseases characterized by progressive weakness and degeneration of the skeletal muscles that control movement. Some forms of MD are seen in newborns, infants or children, while others have late-onset and may not appear until middle age or later. The disorders differ in terms of the distribution and extent of muscle weakness (some forms of MD also affect cardiac muscle), age of onset, rate of progression, and pattern of inheritance. The prognosis for people with MD varies according to the type and progression of the disorder. There is no specific treatment to stop or reverse any form of MD. Treatment is supportive and may include physical therapy, respiratory therapy, speech therapy, orthopedic appliances used for support, corrective orthopedic surgery, and medicationsincluding corticosteroids, anticonvulsants (seizure medications), immunosuppressants, and antibiotics. Some individuals may need assisted ventilation to treat respiratory muscle weaknessor a pacemaker for cardiac (heart)abnormalities.",
"xref": [],
"provided_by": "phenio_nodes",
diff --git a/backend/tests/fixtures/histopheno_response.py b/backend/tests/fixtures/histopheno_response.py
index 44789afcf..6bc1cf57b 100644
--- a/backend/tests/fixtures/histopheno_response.py
+++ b/backend/tests/fixtures/histopheno_response.py
@@ -5,7 +5,7 @@
def histopheno_response():
return {
"responseHeader": {
- "QTime": 1,
+ "QTime": 4,
"params": {
"facet.query": [
'object_closure:"HP:0000924"',
diff --git a/backend/tests/fixtures/mapping_response.py b/backend/tests/fixtures/mapping_response.py
index 7515868ce..92ee42cb3 100644
--- a/backend/tests/fixtures/mapping_response.py
+++ b/backend/tests/fixtures/mapping_response.py
@@ -29,7 +29,7 @@ def mapping_response():
"object_id": "DOID:9884",
"object_label": "muscular dystrophy",
"mapping_justification": "semapv:UnspecifiedMatching",
- "id": "cda26856-16a7-499c-956f-119cbaac5b96",
+ "id": "074f33ef-cab8-46e9-b535-5c637220dcd1",
},
{
"subject_id": "MONDO:0020121",
@@ -38,7 +38,7 @@ def mapping_response():
"object_id": "ICD10CM:G71.0",
"object_label": "Muscular dystrophy",
"mapping_justification": "semapv:UnspecifiedMatching",
- "id": "25777569-b997-4c8f-a1f3-5af352a16ee1",
+ "id": "575115b8-67a4-482d-88e7-1b1b60fdd99a",
},
{
"subject_id": "MONDO:0020121",
@@ -46,7 +46,7 @@ def mapping_response():
"predicate_id": "skos:exactMatch",
"object_id": "MESH:D009136",
"mapping_justification": "semapv:UnspecifiedMatching",
- "id": "819ab197-2ab1-4b73-8d0f-d7d4ec14d8a7",
+ "id": "a2f1233e-1951-4f40-9a79-60f591a24bb5",
},
{
"subject_id": "MONDO:0020121",
@@ -55,7 +55,7 @@ def mapping_response():
"object_id": "NCIT:C84910",
"object_label": "Muscular Dystrophy",
"mapping_justification": "semapv:UnspecifiedMatching",
- "id": "adb4b8ed-c4dc-4353-a08e-a4cb02b1826e",
+ "id": "73eaeaef-9868-4e50-a4ed-aee537a830ae",
},
{
"subject_id": "MONDO:0020121",
@@ -63,7 +63,7 @@ def mapping_response():
"predicate_id": "skos:exactMatch",
"object_id": "SCTID:73297009",
"mapping_justification": "semapv:UnspecifiedMatching",
- "id": "f6417283-c9d1-4289-aee6-16d30a4445b1",
+ "id": "3f7aa4af-411c-47fe-9b3a-d8248484ea2d",
},
{
"subject_id": "MONDO:0020121",
@@ -71,7 +71,7 @@ def mapping_response():
"predicate_id": "skos:exactMatch",
"object_id": "UMLS:C0026850",
"mapping_justification": "semapv:UnspecifiedMatching",
- "id": "93968631-eedb-448b-b58a-e31e3e411dde",
+ "id": "f8d6fe34-2d2a-4ace-a314-f4def3070e3a",
},
{
"subject_id": "MONDO:0020121",
@@ -79,7 +79,7 @@ def mapping_response():
"predicate_id": "skos:exactMatch",
"object_id": "Orphanet:98473",
"mapping_justification": "semapv:UnspecifiedMatching",
- "id": "e39e8ba9-8d7e-4b33-9f46-3867b652bdb5",
+ "id": "63588ca1-4204-4143-88b3-152b31ea0c41",
},
],
},
diff --git a/backend/tests/fixtures/mappings.py b/backend/tests/fixtures/mappings.py
index 7d3e92885..9badad32a 100644
--- a/backend/tests/fixtures/mappings.py
+++ b/backend/tests/fixtures/mappings.py
@@ -15,7 +15,7 @@ def mappings():
"object_id": "DOID:9884",
"object_label": "muscular dystrophy",
"mapping_justification": "semapv:UnspecifiedMatching",
- "id": "cda26856-16a7-499c-956f-119cbaac5b96",
+ "id": "074f33ef-cab8-46e9-b535-5c637220dcd1",
},
{
"subject_id": "MONDO:0020121",
@@ -24,7 +24,7 @@ def mappings():
"object_id": "ICD10CM:G71.0",
"object_label": "Muscular dystrophy",
"mapping_justification": "semapv:UnspecifiedMatching",
- "id": "25777569-b997-4c8f-a1f3-5af352a16ee1",
+ "id": "575115b8-67a4-482d-88e7-1b1b60fdd99a",
},
{
"subject_id": "MONDO:0020121",
@@ -33,7 +33,7 @@ def mappings():
"object_id": "MESH:D009136",
"object_label": None,
"mapping_justification": "semapv:UnspecifiedMatching",
- "id": "819ab197-2ab1-4b73-8d0f-d7d4ec14d8a7",
+ "id": "a2f1233e-1951-4f40-9a79-60f591a24bb5",
},
{
"subject_id": "MONDO:0020121",
@@ -42,7 +42,7 @@ def mappings():
"object_id": "NCIT:C84910",
"object_label": "Muscular Dystrophy",
"mapping_justification": "semapv:UnspecifiedMatching",
- "id": "adb4b8ed-c4dc-4353-a08e-a4cb02b1826e",
+ "id": "73eaeaef-9868-4e50-a4ed-aee537a830ae",
},
{
"subject_id": "MONDO:0020121",
@@ -51,7 +51,7 @@ def mappings():
"object_id": "SCTID:73297009",
"object_label": None,
"mapping_justification": "semapv:UnspecifiedMatching",
- "id": "f6417283-c9d1-4289-aee6-16d30a4445b1",
+ "id": "3f7aa4af-411c-47fe-9b3a-d8248484ea2d",
},
{
"subject_id": "MONDO:0020121",
@@ -60,7 +60,7 @@ def mappings():
"object_id": "UMLS:C0026850",
"object_label": None,
"mapping_justification": "semapv:UnspecifiedMatching",
- "id": "93968631-eedb-448b-b58a-e31e3e411dde",
+ "id": "f8d6fe34-2d2a-4ace-a314-f4def3070e3a",
},
{
"subject_id": "MONDO:0020121",
@@ -69,7 +69,7 @@ def mappings():
"object_id": "Orphanet:98473",
"object_label": None,
"mapping_justification": "semapv:UnspecifiedMatching",
- "id": "e39e8ba9-8d7e-4b33-9f46-3867b652bdb5",
+ "id": "63588ca1-4204-4143-88b3-152b31ea0c41",
},
],
}
diff --git a/backend/tests/fixtures/node.py b/backend/tests/fixtures/node.py
index b37dfc336..1732c8608 100644
--- a/backend/tests/fixtures/node.py
+++ b/backend/tests/fixtures/node.py
@@ -8,6 +8,7 @@ def node():
"category": "biolink:Disease",
"name": "muscular dystrophy",
"full_name": None,
+ "deprecated": None,
"description": "Muscular dystrophy (MD) refers to a group of more than 30 genetic diseases characterized by progressive weakness and degeneration of the skeletal muscles that control movement. Some forms of MD are seen in newborns, infants or children, while others have late-onset and may not appear until middle age or later. The disorders differ in terms of the distribution and extent of muscle weakness (some forms of MD also affect cardiac muscle), age of onset, rate of progression, and pattern of inheritance. The prognosis for people with MD varies according to the type and progression of the disorder. There is no specific treatment to stop or reverse any form of MD. Treatment is supportive and may include physical therapy, respiratory therapy, speech therapy, orthopedic appliances used for support, corrective orthopedic surgery, and medicationsincluding corticosteroids, anticonvulsants (seizure medications), immunosuppressants, and antibiotics. Some individuals may need assisted ventilation to treat respiratory muscle weaknessor a pacemaker for cardiac (heart)abnormalities.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -45,6 +46,7 @@ def node():
"category": "biolink:Disease",
"name": "neuromuscular disease",
"full_name": None,
+ "deprecated": None,
"description": None,
"xref": [],
"provided_by": None,
@@ -59,6 +61,7 @@ def node():
"category": "biolink:Disease",
"name": "hereditary skeletal muscle disorder",
"full_name": None,
+ "deprecated": None,
"description": None,
"xref": [],
"provided_by": None,
@@ -73,6 +76,7 @@ def node():
"category": "biolink:Disease",
"name": "myopathy",
"full_name": None,
+ "deprecated": None,
"description": None,
"xref": [],
"provided_by": None,
@@ -85,10 +89,11 @@ def node():
],
"sub_classes": [
{
- "id": "MONDO:0018949",
+ "id": "MONDO:0008028",
"category": "biolink:Disease",
- "name": "distal myopathy",
+ "name": "muscular dystrophy, Barnes type",
"full_name": None,
+ "deprecated": None,
"description": None,
"xref": [],
"provided_by": None,
@@ -99,10 +104,11 @@ def node():
"uri": None,
},
{
- "id": "MONDO:0019950",
+ "id": "MONDO:0010675",
"category": "biolink:Disease",
- "name": "congenital muscular dystrophy",
+ "name": "muscular dystrophy, cardiac type",
"full_name": None,
+ "deprecated": None,
"description": None,
"xref": [],
"provided_by": None,
@@ -113,10 +119,11 @@ def node():
"uri": None,
},
{
- "id": "MONDO:0023204",
+ "id": "MONDO:0010676",
"category": "biolink:Disease",
- "name": "Fukuda-Miyanomae-Nakata syndrome",
+ "name": "muscular dystrophy, Hemizygous lethal type",
"full_name": None,
+ "deprecated": None,
"description": None,
"xref": [],
"provided_by": None,
@@ -127,10 +134,11 @@ def node():
"uri": None,
},
{
- "id": "MONDO:0100228",
+ "id": "MONDO:0010677",
"category": "biolink:Disease",
- "name": "LAMA2-related muscular dystrophy",
+ "name": "muscular dystrophy, Mabry type",
"full_name": None,
+ "deprecated": None,
"description": None,
"xref": [],
"provided_by": None,
@@ -141,10 +149,11 @@ def node():
"uri": None,
},
{
- "id": "MONDO:0008028",
+ "id": "MONDO:0010678",
"category": "biolink:Disease",
- "name": "muscular dystrophy, Barnes type",
+ "name": "muscular dystrophy, progressive Pectorodorsal",
"full_name": None,
+ "deprecated": None,
"description": None,
"xref": [],
"provided_by": None,
@@ -155,10 +164,11 @@ def node():
"uri": None,
},
{
- "id": "MONDO:0010675",
+ "id": "MONDO:0019950",
"category": "biolink:Disease",
- "name": "muscular dystrophy, cardiac type",
+ "name": "congenital muscular dystrophy",
"full_name": None,
+ "deprecated": None,
"description": None,
"xref": [],
"provided_by": None,
@@ -169,10 +179,11 @@ def node():
"uri": None,
},
{
- "id": "MONDO:0010676",
+ "id": "MONDO:0023204",
"category": "biolink:Disease",
- "name": "muscular dystrophy, Hemizygous lethal type",
+ "name": "Fukuda-Miyanomae-Nakata syndrome",
"full_name": None,
+ "deprecated": None,
"description": None,
"xref": [],
"provided_by": None,
@@ -183,10 +194,11 @@ def node():
"uri": None,
},
{
- "id": "MONDO:0010677",
+ "id": "MONDO:0100228",
"category": "biolink:Disease",
- "name": "muscular dystrophy, Mabry type",
+ "name": "LAMA2-related muscular dystrophy",
"full_name": None,
+ "deprecated": None,
"description": None,
"xref": [],
"provided_by": None,
@@ -197,10 +209,11 @@ def node():
"uri": None,
},
{
- "id": "MONDO:0010678",
+ "id": "MONDO:0018949",
"category": "biolink:Disease",
- "name": "muscular dystrophy, progressive Pectorodorsal",
+ "name": "distal myopathy",
"full_name": None,
+ "deprecated": None,
"description": None,
"xref": [],
"provided_by": None,
@@ -215,6 +228,7 @@ def node():
"category": "biolink:Disease",
"name": "progressive muscular dystrophy",
"full_name": None,
+ "deprecated": None,
"description": None,
"xref": [],
"provided_by": None,
diff --git a/backend/tests/fixtures/search.py b/backend/tests/fixtures/search.py
index ada436fc0..26c2b7beb 100644
--- a/backend/tests/fixtures/search.py
+++ b/backend/tests/fixtures/search.py
@@ -13,6 +13,7 @@ def search():
"category": "biolink:Disease",
"name": "Fanconi anemia",
"full_name": None,
+ "deprecated": None,
"description": "Fanconi anemia (FA) is a hereditary DNA repair disorder characterized by progressive pancytopenia with bone marrow failure, variable congenital malformations and predisposition to develop hematological or solid tumors.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -37,6 +38,7 @@ def search():
"category": "biolink:Disease",
"name": "Fanconi renotubular syndrome",
"full_name": None,
+ "deprecated": None,
"description": "A genetic or acquired disorder characterized by impairment of the function of the proximal tubules of the kidney. It results in decreased reabsorption of electrolytes, glucose, amino acids, and other nutrients.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -66,6 +68,7 @@ def search():
"category": "biolink:Disease",
"name": "primary Fanconi syndrome",
"full_name": None,
+ "deprecated": None,
"description": "A condition in which the kidneys do not absorb certain substances into the body. These substances, such as cysteine, fructose, galactose, or glycogen, are lost in the urine. Fanconi syndrome is thought to be caused by genetic and environmental factors, and it may be diagnosed at any age. Symptoms of Fanconi syndrome include increased urine production (which may cause dehydration), weakness, and abnormalities of the bones.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -82,6 +85,7 @@ def search():
"category": "biolink:Disease",
"name": "Fanconi-like syndrome",
"full_name": None,
+ "deprecated": None,
"description": "A syndrome characterized by pancytopenia, immune deficiency and cutaneous malignancies.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -98,6 +102,7 @@ def search():
"category": "biolink:Disease",
"name": "adult Fanconi syndrome",
"full_name": None,
+ "deprecated": None,
"description": "Probably related to a recessive gene, this is Fanconi Syndrome, characterised by adult onset.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -114,6 +119,7 @@ def search():
"category": "biolink:Disease",
"name": "acquired Fanconi syndrome",
"full_name": None,
+ "deprecated": None,
"description": "Fanconi Syndrome caused by exposure to noxious agents.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -125,27 +131,12 @@ def search():
"highlight": None,
"score": None,
},
- {
- "id": "MONDO:0000026",
- "category": "biolink:Disease",
- "name": "obsolete Fanconi renotubular syndrome",
- "full_name": None,
- "description": None,
- "xref": [],
- "provided_by": "phenio_nodes",
- "in_taxon": None,
- "in_taxon_label": None,
- "symbol": None,
- "synonym": [],
- "uri": None,
- "highlight": None,
- "score": None,
- },
{
"id": "MONDO:0013247",
"category": "biolink:Disease",
"name": "Fanconi renotubular syndrome 2",
"full_name": None,
+ "deprecated": None,
"description": "Any Fanconi syndrome in which the cause of the disease is a mutation in the SLC34A1 gene.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -168,6 +159,7 @@ def search():
"category": "biolink:Disease",
"name": "Fanconi renotubular syndrome 3",
"full_name": None,
+ "deprecated": None,
"description": "Any Fanconi syndrome in which the cause of the disease is a mutation in the EHHADH gene.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -190,6 +182,7 @@ def search():
"category": "biolink:Disease",
"name": "Fanconi renotubular syndrome 1",
"full_name": None,
+ "deprecated": None,
"description": None,
"xref": [],
"provided_by": "phenio_nodes",
@@ -217,6 +210,7 @@ def search():
"category": "biolink:Disease",
"name": "Fanconi renotubular syndrome 5",
"full_name": None,
+ "deprecated": None,
"description": None,
"xref": [],
"provided_by": "phenio_nodes",
@@ -238,6 +232,7 @@ def search():
"category": "biolink:Disease",
"name": "inherited Fanconi renotubular syndrome",
"full_name": None,
+ "deprecated": None,
"description": "An instance of Fanconi renotubular syndrome that is inherited.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -254,6 +249,7 @@ def search():
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group C",
"full_name": None,
+ "deprecated": None,
"description": "Fanconi anemia caused by mutations of the FANCC gene. This gene provides instructions for making a protein that delays the onset of apoptosis and promotes homologous recombination repair of damaged DNA.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -281,6 +277,7 @@ def search():
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group D2",
"full_name": None,
+ "deprecated": None,
"description": "Fanconi anemia caused by mutations of the FANCD2 gene. This gene is involved in the repair of DNA double-strand breaks, both by homologous recombination and single-strand annealing.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -307,6 +304,7 @@ def search():
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group A",
"full_name": None,
+ "deprecated": None,
"description": "Fanconi anemia caused by mutations of the FANCA gene. FANCA gene mutations are the most common cause of Fanconi anemia. This gene provides instructions for making a protein that is involved in the Fanconi anemia (FA) pathway.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -335,6 +333,7 @@ def search():
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group B",
"full_name": None,
+ "deprecated": None,
"description": "Fanconi anemia caused by mutations of the FANCB gene. This gene encodes the protein for complementation group B.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -362,6 +361,7 @@ def search():
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group E",
"full_name": None,
+ "deprecated": None,
"description": "Fanconi anemia caused by mutations of the FANCE gene. This is a protein coding gene. It is required for the nuclear accumulation of FANCC and provides a critical bridge between the FA complex and FANCD2.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -387,6 +387,7 @@ def search():
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group F",
"full_name": None,
+ "deprecated": None,
"description": "Fanconi anemia caused by mutations of the FANCF gene. This gene encodes a polypeptide with homology to the prokaryotic RNA-binding protein ROM.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -409,6 +410,7 @@ def search():
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group D1",
"full_name": None,
+ "deprecated": None,
"description": "Inherited cancer-predisposing syndrome due to biallelic BRCA2 mutations is a rare cancer-predisposing syndrome, associated with the D1 subgroup of Fanconi anemia (FA), characterized by progressive bone marrow failure, cardiac, brain, intestinal or skeletal abnormalities and predisposition to various malignancies. Bone marrow suppression and the incidence of developmental abnormalities are less frequent than in other FA, but cancer risk is very high with the spectrum of childhood cancers including Wilms tumor, brain tumor (often medulloblastoma) and ALL/AML.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -432,6 +434,7 @@ def search():
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group I",
"full_name": None,
+ "deprecated": None,
"description": "Fanconi anemia caused by mutations in the FANCI gene, encoding Fanconi anemia group I protein.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -450,6 +453,29 @@ def search():
"highlight": None,
"score": None,
},
+ {
+ "id": "MONDO:0012187",
+ "category": "biolink:Disease",
+ "name": "Fanconi anemia complementation group J",
+ "full_name": None,
+ "deprecated": None,
+ "description": "Fanconi anemia caused by mutations in the BRIP1 gene, encoding Fanconi anemia group J protein.",
+ "xref": [],
+ "provided_by": "phenio_nodes",
+ "in_taxon": None,
+ "in_taxon_label": None,
+ "symbol": None,
+ "synonym": [
+ "FANCJ",
+ "Fanconi Anemia, complementation group type J",
+ "Fanconi anemia complementation group J",
+ "Fanconi anemia complementation group type J",
+ "Fanconi anemia, complementation group J",
+ ],
+ "uri": None,
+ "highlight": None,
+ "score": None,
+ },
],
"facet_fields": [],
"facet_queries": [],
diff --git a/backend/tests/fixtures/search_query.py b/backend/tests/fixtures/search_query.py
index 64dbc1f84..9ce3b0eea 100644
--- a/backend/tests/fixtures/search_query.py
+++ b/backend/tests/fixtures/search_query.py
@@ -15,7 +15,7 @@ def search_query():
"def_type": "edismax",
"q_op": "AND",
"mm": "100%",
- "boost": 'product(if(termfreq(category,"biolink:Disease"),10.0,1),if(and(termfreq(in_taxon,"NCBITaxon:9606"),termfreq(category,"biolink:Gene")),5.0,1))',
+ "boost": 'product(if(termfreq(category,"biolink:Disease"),10.0,1),if(and(termfreq(in_taxon,"NCBITaxon:9606"),termfreq(category,"biolink:Gene")),5.0,1),if(termfreq(deprecated,"true"),0.1,1))',
"sort": None,
"facet_min_count": 1,
}
diff --git a/backend/tests/fixtures/search_response.py b/backend/tests/fixtures/search_response.py
index c2791ef80..c096e99ff 100644
--- a/backend/tests/fixtures/search_response.py
+++ b/backend/tests/fixtures/search_response.py
@@ -5,7 +5,7 @@
def search_response():
return {
"responseHeader": {
- "QTime": 0,
+ "QTime": 1,
"params": {
"mm": "100%",
"q": "fanconi",
@@ -14,7 +14,7 @@ def search_response():
"qf": "id^100 name^10 name_t^5 name_ac symbol^10 symbol_t^5 symbol_ac synonym synonym_t synonym_ac",
"start": "0",
"q.op": "AND",
- "boost": 'product(if(termfreq(category,"biolink:Disease"),10.0,1),if(and(termfreq(in_taxon,"NCBITaxon:9606"),termfreq(category,"biolink:Gene")),5.0,1))',
+ "boost": 'product(if(termfreq(category,"biolink:Disease"),10.0,1),if(and(termfreq(in_taxon,"NCBITaxon:9606"),termfreq(category,"biolink:Gene")),5.0,1),if(termfreq(deprecated,"true"),0.1,1))',
"fq": "name:*",
"rows": "20",
"facet": "true",
@@ -93,12 +93,6 @@ def search_response():
"synonym": ["acquired Fanconi syndrome"],
"description": "Fanconi Syndrome caused by exposure to noxious agents.",
},
- {
- "id": "MONDO:0000026",
- "category": "biolink:Disease",
- "name": "obsolete Fanconi renotubular syndrome",
- "provided_by": "phenio_nodes",
- },
{
"id": "MONDO:0013247",
"category": "biolink:Disease",
@@ -302,6 +296,20 @@ def search_response():
],
"description": "Fanconi anemia caused by mutations in the FANCI gene, encoding Fanconi anemia group I protein.",
},
+ {
+ "id": "MONDO:0012187",
+ "category": "biolink:Disease",
+ "name": "Fanconi anemia complementation group J",
+ "provided_by": "phenio_nodes",
+ "synonym": [
+ "FANCJ",
+ "Fanconi Anemia, complementation group type J",
+ "Fanconi anemia complementation group J",
+ "Fanconi anemia complementation group type J",
+ "Fanconi anemia, complementation group J",
+ ],
+ "description": "Fanconi anemia caused by mutations in the BRIP1 gene, encoding Fanconi anemia group J protein.",
+ },
],
},
"facet_counts": {"facet_fields": {}, "facet_queries": {}},
diff --git a/frontend/fixtures/association-counts.json b/frontend/fixtures/association-counts.json
new file mode 100644
index 000000000..207c58a9c
--- /dev/null
+++ b/frontend/fixtures/association-counts.json
@@ -0,0 +1,19 @@
+{
+ "items": [
+ {
+ "label": "Phenotypes",
+ "count": 4027,
+ "category": "biolink:DiseaseToPhenotypicFeatureAssociation"
+ },
+ {
+ "label": "Causal Genes",
+ "count": 124,
+ "category": "biolink:CausalGeneToDiseaseAssociation"
+ },
+ {
+ "label": "Correlated Genes",
+ "count": 151,
+ "category": "biolink:CorrelatedGeneToDiseaseAssociation"
+ }
+ ]
+}
diff --git a/frontend/fixtures/association-table.json b/frontend/fixtures/association-table.json
index b312b5bd0..d83957aba 100644
--- a/frontend/fixtures/association-table.json
+++ b/frontend/fixtures/association-table.json
@@ -4,70 +4,70 @@
"total": 4027,
"items": [
{
- "id": "uuid:ca3946de-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4677e7a0-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"subject": "MONDO:0020793",
"original_subject": "OMIM:164310",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "BFO:0000020",
- "MONDO:0024458",
- "MONDO:0005336",
"MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0003382",
- "BFO:0000016",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0025193",
"MONDO:0020121",
"MONDO:0020793",
+ "MONDO:0003847",
+ "BFO:0000001",
+ "BFO:0000020",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
"BFO:0000017",
+ "MONDO:0003939",
+ "MONDO:0002022",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "BFO:0000002",
+ "MONDO:0005071",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000462",
- "MONDO:0020158",
- "MONDO:0000001",
"MONDO:0700223",
- "MONDO:0016106",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002022",
- "MONDO:0005328"
+ "MONDO:0024458",
+ "OGMS:0000031"
],
"subject_label": "oculopharyngodistal myopathy 1",
"subject_closure_label": [
- "oculopharyngodistal myopathy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
+ "disease",
+ "realizable entity",
"disease",
+ "specifically dependent continuant",
"muscle tissue disorder",
"disorder of orbital region",
"hereditary skeletal muscle disorder",
+ "continuant",
+ "eye adnexa disorder",
"eyelid disorder",
"disposition",
- "distal myopathy",
- "eyelids malposition disorder",
- "disease",
- "continuant",
- "specifically dependent continuant",
+ "human disease",
"disorder of visual system",
"myopathy",
- "hereditary disease",
- "eye adnexa disorder",
+ "distal myopathy",
"nervous system disorder",
+ "entity",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "oculopharyngodistal myopathy",
+ "muscular dystrophy",
"oculopharyngodistal myopathy 1",
- "realizable entity",
"skeletal muscle disorder",
- "neuromuscular disease",
- "entity",
- "eye disorder"
+ "neuromuscular disease"
],
"subject_taxon": null,
"subject_taxon_label": null,
@@ -77,87 +77,87 @@
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
+ "UPHENO:0002816",
+ "BFO:0000001",
+ "UBERON:0000465",
"UPHENO:0082875",
- "UPHENO:0002320",
- "UPHENO:0001005",
+ "BFO:0000040",
+ "UBERON:0011216",
+ "HP:0001324",
+ "UPHENO:0080555",
+ "HP:0011804",
+ "BFO:0000002",
+ "UPHENO:0001001",
+ "UPHENO:0001002",
"BFO:0000020",
- "PATO:0000001",
+ "UPHENO:0001003",
+ "UPHENO:0002536",
+ "BFO:0000001",
+ "UBERON:0001062",
+ "UPHENO:0001005",
+ "HP:0033127",
"BFO:0000004",
"UBERON:0000061",
- "HP:0000001",
- "UPHENO:0001001",
- "HP:0000118",
- "BFO:0000001",
- "UBERON:0000467",
+ "UBERON:0000062",
"UBERON:0000468",
- "UBERON:0011216",
"UPHENO:0075696",
- "HP:0001324",
"HP:0003011",
+ "UPHENO:0002320",
+ "HP:0000118",
+ "BFO:0000002",
"UPHENO:0002332",
- "UPHENO:0001003",
- "UPHENO:0002536",
"HP:0002460",
- "HP:0011804",
- "BFO:0000002",
- "BFO:0000040",
+ "PATO:0000001",
+ "UBERON:0010000",
+ "HP:0000001",
+ "UPHENO:0080556",
+ "UBERON:0000467",
"UBERON:0005090",
"UBERON:0001630",
- "UPHENO:0001002",
- "BFO:0000002",
- "UPHENO:0080555",
- "UPHENO:0002816",
- "UPHENO:0080556",
- "HP:0033127",
- "BFO:0000001",
- "UBERON:0001062",
- "UBERON:0000465",
- "UBERON:0010000",
- "UBERON:0000062",
"UBERON:0000383",
"UBERON:0001015"
],
"object_label": "Distal muscle weakness (HPO)",
"object_closure_label": [
- "All (HPO)",
- "abnormality of muscle organ physiology",
- "Phenotypic abnormality (HPO)",
- "decreased anatomical entity strength",
- "abnormal musculature",
- "decreased muscle organ strength",
- "Abnormality of the musculoskeletal system (HPO)",
- "entity",
- "independent continuant",
- "material anatomical entity",
- "anatomical structure",
- "multicellular anatomical structure",
"abnormality of anatomical entity physiology",
- "phenotype",
"Phenotypic abnormality",
- "continuant",
- "Distal muscle weakness (HPO)",
+ "specifically dependent continuant",
"quality",
- "continuant",
- "material entity",
"abnormal phenotype by ontology source",
- "specifically dependent continuant",
+ "Abnormality of the musculature (HPO)",
+ "phenotype by ontology source",
+ "abnormal anatomical entity",
+ "continuant",
+ "material anatomical entity",
+ "muscle organ",
+ "All (HPO)",
+ "abnormal musculature",
"Abnormal muscle physiology (HPO)",
+ "organ system subdivision",
+ "abnormality of muscle organ physiology",
+ "Phenotypic abnormality (HPO)",
+ "continuant",
+ "decreased muscle organ strength",
+ "Distal muscle weakness (HPO)",
"entity",
+ "multicellular anatomical structure",
+ "Muscle weakness (HPO)",
"anatomical entity",
- "muscle structure",
"organ",
- "muscle organ",
+ "multicellular organism",
+ "phenotype",
+ "independent continuant",
+ "decreased anatomical entity strength",
+ "Abnormality of the musculoskeletal system (HPO)",
+ "entity",
+ "material entity",
+ "anatomical structure",
"musculature of body",
"musculature",
"abnormal anatomical entity",
- "Muscle weakness (HPO)",
- "Abnormality of the musculature (HPO)",
"abnormality of anatomical entity physiology",
- "phenotype by ontology source",
- "abnormal anatomical entity",
"anatomical system",
- "multicellular organism",
- "organ system subdivision"
+ "muscle structure"
],
"object_taxon": null,
"object_taxon_label": null,
@@ -207,11 +207,11 @@
"frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
"frequency_qualifier_closure_label": [
- "All (HPO)",
+ "Frequency (HPO)",
"Frequent (HPO)",
- "Frequency (HPO)"
+ "All (HPO)"
],
"onset_qualifier_label": null,
"onset_qualifier_namespace": null,
@@ -231,70 +231,70 @@
"direction": "outgoing"
},
{
- "id": "uuid:ca3946ef-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4677e7b1-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"subject": "MONDO:0020793",
"original_subject": "OMIM:164310",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "BFO:0000020",
- "MONDO:0024458",
- "MONDO:0005336",
"MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0003382",
- "BFO:0000016",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0025193",
"MONDO:0020121",
"MONDO:0020793",
+ "MONDO:0003847",
+ "BFO:0000001",
+ "BFO:0000020",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
"BFO:0000017",
+ "MONDO:0003939",
+ "MONDO:0002022",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "BFO:0000002",
+ "MONDO:0005071",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000462",
- "MONDO:0020158",
- "MONDO:0000001",
"MONDO:0700223",
- "MONDO:0016106",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002022",
- "MONDO:0005328"
+ "MONDO:0024458",
+ "OGMS:0000031"
],
"subject_label": "oculopharyngodistal myopathy 1",
"subject_closure_label": [
- "oculopharyngodistal myopathy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
+ "disease",
+ "realizable entity",
"disease",
+ "specifically dependent continuant",
"muscle tissue disorder",
"disorder of orbital region",
"hereditary skeletal muscle disorder",
+ "continuant",
+ "eye adnexa disorder",
"eyelid disorder",
"disposition",
- "distal myopathy",
- "eyelids malposition disorder",
- "disease",
- "continuant",
- "specifically dependent continuant",
+ "human disease",
"disorder of visual system",
"myopathy",
- "hereditary disease",
- "eye adnexa disorder",
+ "distal myopathy",
"nervous system disorder",
+ "entity",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "oculopharyngodistal myopathy",
+ "muscular dystrophy",
"oculopharyngodistal myopathy 1",
- "realizable entity",
"skeletal muscle disorder",
- "neuromuscular disease",
- "entity",
- "eye disorder"
+ "neuromuscular disease"
],
"subject_taxon": null,
"subject_taxon_label": null,
@@ -304,141 +304,141 @@
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "UPHENO:0082875",
+ "UPHENO:0002443",
"UPHENO:0002471",
"HP:0025270",
- "UPHENO:0001005",
- "BFO:0000002",
- "BFO:0000020",
+ "UPHENO:0002536",
+ "UBERON:0000465",
+ "RO:0002577",
+ "UPHENO:0082875",
"HP:0002664",
+ "UPHENO:0004523",
+ "BFO:0000001",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UBERON:0011676",
+ "UBERON:0013701",
+ "BFO:0000020",
"HP:0011793",
- "PATO:0000001",
+ "BFO:0000002",
+ "UBERON:0005409",
+ "UPHENO:0001001",
+ "UPHENO:0002833",
+ "HP:0002015",
+ "UPHENO:0001002",
+ "UPHENO:0001003",
+ "UPHENO:0075696",
+ "UPHENO:0002433",
+ "HP:0025031",
"UPHENO:0002474",
"HP:0012638",
"BFO:0000004",
"UBERON:0000061",
- "UBERON:0001007",
- "UBERON:0001016",
- "UBERON:0011676",
- "UBERON:0013701",
- "UBERON:0000915",
- "UBERON:0001043",
- "UBERON:0002100",
- "UBERON:0005181",
- "UBERON:0002075",
- "HP:0000001",
- "UPHENO:0001001",
- "HP:0000118",
- "UPHENO:0002433",
- "UPHENO:0001003",
- "BFO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0010000",
- "UBERON:0000467",
+ "UBERON:0000475",
+ "UBERON:0000062",
"UBERON:0004111",
"UBERON:0000468",
- "UBERON:0000064",
- "UPHENO:0075696",
"HP:0011024",
- "UPHENO:0002443",
- "HP:0012719",
"UPHENO:0002725",
- "HP:0025032",
- "UPHENO:0002332",
- "UPHENO:0002536",
- "UPHENO:0004523",
"BFO:0000002",
- "UBERON:0000465",
- "UBERON:0005409",
+ "HP:0025032",
"UBERON:0009569",
"UBERON:0013702",
"UBERON:0013765",
"UBERON:0005177",
"UBERON:0000025",
+ "UBERON:0000915",
+ "UBERON:0001043",
+ "UBERON:0002100",
+ "UBERON:0005181",
+ "UBERON:0002075",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "PATO:0000001",
"UBERON:0001555",
"UBERON:0004921",
- "UPHENO:0002833",
- "HP:0002015",
- "UPHENO:0001002",
+ "HP:0000001",
+ "HP:0012719",
+ "UPHENO:0001005",
"HP:0000707",
- "HP:0025031",
- "UBERON:0001062",
- "RO:0002577",
- "UBERON:0000475",
- "UBERON:0000062",
+ "BFO:0000001",
+ "UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0000064",
+ "UBERON:0001007",
+ "UBERON:0001016",
"UBERON:0013522",
"UBERON:0005178",
"UBERON:0004908"
],
"object_label": "Dysphagia (HPO)",
"object_closure_label": [
- "All (HPO)",
- "abnormality of alimentary part of gastrointestinal system physiology",
- "Abnormal esophagus physiology (HPO)",
- "Functional abnormality of the gastrointestinal tract (HPO)",
- "Phenotypic abnormality (HPO)",
- "Abnormality of the nervous system (HPO)",
- "independent continuant",
- "system",
- "anatomical structure",
- "digestive system",
- "nervous system",
- "digestive tract",
- "subdivision of digestive tract",
"abnormality of anatomical entity physiology",
- "phenotype",
- "abnormality of digestive system physiology",
"abnormal digestive system",
"Dysphagia (HPO)",
"Phenotypic abnormality",
- "abnormality of nervous system physiology",
+ "quality",
+ "abnormal anatomical entity",
+ "specifically dependent continuant",
+ "Abnormality of digestive system physiology (HPO)",
"phenotype by ontology source",
"abnormal nervous system",
- "quality",
- "abnormality of esophagus physiology",
- "Abnormal nervous system physiology (HPO)",
"continuant",
"material anatomical entity",
+ "system",
+ "organ part",
+ "digestive system",
+ "nervous system",
+ "thoracic segment of trunk",
+ "esophagus",
+ "trunk",
+ "thoracic segment organ",
+ "viscus",
+ "All (HPO)",
+ "Functional abnormality of the gastrointestinal tract (HPO)",
+ "abnormal phenotype by ontology source",
+ "continuant",
+ "alimentary part of gastrointestinal system",
"subdivision of trunk",
"body proper",
"digestive system element",
"trunk region element",
"tube",
- "abnormal phenotype by ontology source",
- "continuant",
- "specifically dependent continuant",
- "Neoplasm (HPO)",
- "Neoplasm by anatomical site (HPO)",
+ "abnormal alimentary part of gastrointestinal system",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the nervous system (HPO)",
"entity",
- "anatomical entity",
+ "thoracic cavity element",
+ "upper digestive tract",
+ "abnormality of nervous system physiology",
+ "Neoplasm by anatomical site (HPO)",
"organism subdivision",
"organ",
- "alimentary part of gastrointestinal system",
+ "anatomical conduit",
+ "multicellular organism",
+ "phenotype",
+ "Neoplasm (HPO)",
+ "entity",
+ "independent continuant",
+ "subdivision of organism along main body axis",
+ "main body axis",
+ "abnormality of digestive system physiology",
+ "abnormality of alimentary part of gastrointestinal system physiology",
+ "Abnormal esophagus physiology (HPO)",
+ "Abnormality of the digestive system (HPO)",
+ "abnormality of esophagus physiology",
+ "Abnormal nervous system physiology (HPO)",
+ "material entity",
+ "anatomical entity",
+ "anatomical structure",
"subdivision of tube",
- "thoracic cavity element",
- "upper digestive tract",
- "abnormal anatomical entity",
"Abnormality of the gastrointestinal tract (HPO)",
- "abnormal alimentary part of gastrointestinal system",
- "Abnormality of digestive system physiology (HPO)",
"abnormality of anatomical entity physiology",
"abnormal anatomical entity",
- "entity",
- "Abnormality of the digestive system (HPO)",
- "material entity",
"multicellular anatomical structure",
"anatomical system",
- "anatomical conduit",
- "multicellular organism",
- "organ part",
- "subdivision of organism along main body axis",
- "main body axis",
- "thoracic segment of trunk",
- "esophagus",
- "trunk",
- "thoracic segment organ",
- "viscus"
+ "digestive tract",
+ "subdivision of digestive tract"
],
"object_taxon": null,
"object_taxon_label": null,
@@ -488,11 +488,11 @@
"frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
"frequency_qualifier_closure_label": [
- "All (HPO)",
+ "Frequency (HPO)",
"Frequent (HPO)",
- "Frequency (HPO)"
+ "All (HPO)"
],
"onset_qualifier_label": null,
"onset_qualifier_namespace": null,
@@ -512,84 +512,84 @@
"direction": "outgoing"
},
{
- "id": "uuid:c6b3613a-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:42ef70e0-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"subject": "MONDO:0013049",
"original_subject": "OMIM:612937",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "BFO:0000020",
- "MONDO:0005336",
- "MONDO:0005021",
- "MONDO:0004994",
- "MONDO:0018276",
- "MONDO:0005071",
- "MONDO:0005267",
- "BFO:0000016",
"MONDO:0016333",
- "MONDO:0017749",
- "OGMS:0000031",
+ "MONDO:0002320",
+ "MONDO:0000001",
+ "MONDO:0013049",
+ "MONDO:0020121",
"MONDO:0003847",
"BFO:0000001",
- "MONDO:0020121",
- "MONDO:0004995",
+ "MONDO:0018276",
+ "BFO:0000020",
+ "MONDO:0005336",
+ "MONDO:0019052",
+ "MONDO:0005500",
+ "MONDO:0005066",
+ "MONDO:0024322",
"BFO:0000017",
+ "MONDO:0003939",
+ "MONDO:0002081",
+ "MONDO:0005021",
+ "MONDO:0019950",
+ "BFO:0000002",
"MONDO:0005217",
+ "MONDO:0015286",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0015286",
- "MONDO:0019052",
- "MONDO:0005500",
- "MONDO:0005066",
- "MONDO:0000001",
- "MONDO:0013049",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
- "MONDO:0024322",
+ "BFO:0000016",
"MONDO:0700096",
"MONDO:0000591",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
- "MONDO:0019950"
+ "MONDO:0017749",
+ "OGMS:0000031"
],
"subject_label": "DPM3-congenital disorder of glycosylation",
"subject_closure_label": [
- "cardiomyopathy",
- "muscular dystrophy",
- "cardiovascular disorder",
- "human disease",
- "intrinsic cardiomyopathy",
- "musculoskeletal system disorder",
+ "disease",
+ "disorder of glycosylation",
+ "realizable entity",
"disorder of multiple glycosylation",
"disease",
+ "specifically dependent continuant",
+ "familial cardiomyopathy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "disorder of glycosylation",
- "disposition",
- "congenital disorder of glycosylation",
- "disease",
- "DPM3-congenital disorder of glycosylation",
"continuant",
- "specifically dependent continuant",
- "myopathy",
- "familial dilated cardiomyopathy",
- "hereditary disease",
"inborn errors of metabolism",
"congenital disorder of glycosylation type I",
"metabolic disease",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
"muscular dystrophy-dystroglycanopathy",
+ "myopathy",
+ "dilated cardiomyopathy",
"nervous system disorder",
"heart disorder",
- "realizable entity",
- "familial cardiomyopathy",
+ "entity",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "congenital nervous system disorder",
+ "congenital muscular dystrophy",
+ "DPM3-congenital disorder of glycosylation",
+ "muscular dystrophy",
"skeletal muscle disorder",
"neuromuscular disease",
- "dilated cardiomyopathy",
- "entity",
- "congenital muscular dystrophy"
+ "familial dilated cardiomyopathy",
+ "congenital disorder of glycosylation"
],
"subject_taxon": null,
"subject_taxon_label": null,
@@ -599,40 +599,70 @@
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
+ "UPHENO:0046284",
+ "UPHENO:0077829",
+ "GO:0005575",
+ "CHEBI:24431",
+ "PR:000050567",
+ "UBERON:0000465",
+ "CHEBI:16541",
+ "CHEBI:35352",
+ "CHEBI:32988",
+ "CHEBI:36963",
+ "CHEBI:33285",
+ "HP:0004364",
"UPHENO:0082875",
- "UPHENO:0051763",
- "UPHENO:0001005",
- "BFO:0000020",
- "UPHENO:0077820",
+ "UPHENO:0004536",
+ "UPHENO:0051668",
+ "HP:0001871",
+ "UPHENO:0077821",
"BFO:0000001",
- "UPHENO:0051804",
- "BFO:0000015",
- "BFO:0000004",
- "GO:0032991",
- "CHEBI:23367",
- "UBERON:0000178",
- "GO:1990234",
- "CHEBI:33839",
- "CHEBI:33675",
- "UBERON:0001004",
- "HP:0000001",
- "HP:0011021",
- "UPHENO:0001001",
+ "GO:0008150",
+ "BFO:0000040",
+ "UBERON:0000468",
"UPHENO:0001002",
- "UPHENO:0077825",
- "HP:0000118",
- "HP:0001871",
+ "BFO:0000020",
+ "UPHENO:0077820",
+ "HP:0002086",
+ "HP:0003236",
+ "BFO:0000003",
+ "BFO:0000002",
+ "GO:1902494",
+ "CHEBI:36357",
+ "CHEBI:33579",
+ "GO:1990234",
+ "CHEBI:33839",
+ "CHEBI:33675",
+ "UBERON:0002193",
+ "UBERON:0002390",
+ "UBERON:0000179",
+ "UPHENO:0001001",
+ "UPHENO:0051763",
"UPHENO:0051801",
"UPHENO:0001003",
- "HP:0001939",
- "HP:0032180",
- "PATO:0000001",
- "HP:0002795",
+ "UPHENO:0081547",
+ "UPHENO:0077826",
"BFO:0000001",
- "BFO:0000040",
- "GO:0008152",
- "UBERON:0000467",
- "UBERON:0000468",
+ "UBERON:0001062",
+ "UBERON:0000061",
+ "UBERON:0000463",
+ "CHEBI:50047",
+ "CHEBI:37622",
+ "CHEBI:33256",
+ "UPHENO:0075696",
+ "UPHENO:0076286",
+ "HP:0040081",
+ "HP:0002795",
+ "HP:0012415",
+ "UPHENO:0051612",
+ "UPHENO:0051804",
+ "BFO:0000015",
+ "BFO:0000004",
+ "GO:0032991",
+ "CHEBI:23367",
+ "UBERON:0000178",
+ "UBERON:0004120",
+ "UBERON:0006314",
"GO:0061695",
"CHEBI:16670",
"CHEBI:33302",
@@ -644,158 +674,128 @@
"CHEBI:25806",
"CHEBI:36962",
"CHEBI:50860",
- "UPHENO:0075696",
"UPHENO:0077817",
"UPHENO:0076289",
- "BFO:0000002",
- "UPHENO:0077821",
+ "UPHENO:0002448",
+ "UPHENO:0002536",
+ "HP:0032180",
+ "PATO:0000001",
+ "CHEBI:138675",
+ "UPHENO:0077825",
+ "HP:0000118",
"UPHENO:0004459",
"UPHENO:0002332",
- "UPHENO:0002536",
"HP:0500165",
- "HP:0002086",
- "HP:0003236",
- "BFO:0000003",
+ "HP:0000001",
+ "HP:0011021",
+ "UPHENO:0001005",
"BFO:0000002",
- "GO:0008150",
- "GO:0005575",
- "CHEBI:24431",
- "PR:000050567",
- "UBERON:0000465",
- "GO:1902494",
- "CHEBI:36357",
- "CHEBI:33579",
- "UBERON:0004120",
- "UBERON:0006314",
- "CHEBI:138675",
- "UBERON:0002193",
- "UBERON:0002390",
- "UBERON:0000179",
- "CHEBI:16541",
- "CHEBI:35352",
- "CHEBI:32988",
- "CHEBI:50047",
- "CHEBI:37622",
- "CHEBI:33256",
- "HP:0004364",
- "UPHENO:0002448",
- "UPHENO:0004536",
- "UPHENO:0051668",
- "UPHENO:0046284",
- "UPHENO:0077829",
"HP:0010876",
- "UPHENO:0076286",
- "HP:0040081",
- "UPHENO:0081547",
- "UPHENO:0077826",
- "HP:0012415",
- "UPHENO:0051612",
- "UBERON:0001062",
- "UBERON:0000061",
- "UBERON:0000463",
+ "HP:0001939",
+ "GO:0008152",
"UBERON:0010000",
- "CHEBI:36963",
- "CHEBI:33285"
+ "UBERON:0000467",
+ "UBERON:0001004"
],
"object_label": "Elevated circulating creatine kinase concentration (HPO)",
"object_closure_label": [
- "All (HPO)",
- "Abnormality of circulating enzyme level (HPO)",
- "abnormal multicellular organism chemical entity level",
- "Phenotypic abnormality",
- "abnormal blood gas molecular entity level",
- "Phenotypic abnormality (HPO)",
- "abnormal chemical entity level",
- "abnormal independent continuant oxygen molecular entity level",
- "Abnormal circulating protein concentration (HPO)",
- "abnormal role blood level",
- "Abnormal circulating creatine kinase concentration (HPO)",
- "Abnormality of metabolism/homeostasis (HPO)",
- "abnormal role bodily fluid level",
- "abnormal blood nitrogen molecular entity level",
- "quality",
- "Abnormal respiratory system physiology (HPO)",
- "process",
- "independent continuant",
- "protein-containing complex",
- "molecular entity",
- "blood",
- "multicellular anatomical structure",
- "respiratory system",
- "transferase complex, transferring phosphorus-containing groups",
- "peptide",
- "pnictogen molecular entity",
- "chalcogen molecular entity",
- "carbon group molecular entity",
- "protein polypeptide chain",
- "organonitrogen compound",
- "amide",
+ "Abnormal circulating nitrogen compound concentration (HPO)",
"abnormality of anatomical entity physiology",
- "phenotype",
- "Abnormality of blood and blood-forming tissues (HPO)",
"abnormal independent continuant protein polypeptide chain level",
+ "abnormal anatomical entity",
+ "Abnormality of metabolism/homeostasis (HPO)",
+ "metabolic process",
+ "abnormal anatomical entity",
+ "specifically dependent continuant",
"phenotype by ontology source",
- "Abnormal blood oxygen level (HPO)",
- "abnormal blood chemical entity level",
+ "abnormal role bodily fluid level",
+ "abnormal blood nitrogen molecular entity level",
"occurrent",
"continuant",
- "biological_process",
"cellular_component",
"chemical entity",
"protein-containing material entity",
"material anatomical entity",
- "gas molecular entity",
- "creatine kinase complex",
- "polypeptide",
- "nitrogen molecular entity",
- "oxygen molecular entity",
- "organochalcogen compound",
- "organic molecular entity",
- "carboxamide",
- "primary amide",
- "organic amino compound",
- "Abnormal circulating nitrogen compound concentration (HPO)",
- "abnormality of respiratory system physiology",
- "abnormal respiratory system",
- "abnormal independent continuant chemical entity level",
+ "transferase complex",
+ "macromolecule",
+ "p-block molecular entity",
+ "respiratory system",
+ "All (HPO)",
+ "Abnormality of circulating enzyme level (HPO)",
"abnormal phenotype by ontology source",
- "specifically dependent continuant",
- "abnormal independent continuant gas molecular entity level",
- "Abnormal circulating metabolite concentration (HPO)",
+ "abnormal chemical entity level",
+ "abnormal independent continuant oxygen molecular entity level",
"Abnormality of the respiratory system (HPO)",
"Elevated circulating creatine kinase concentration (HPO)",
+ "multicellular organism",
+ "hemolymphoid system",
+ "hematopoietic system",
+ "haemolymphatic fluid",
+ "protein polypeptide chain",
+ "organonitrogen compound",
+ "amide",
+ "organooxygen compound",
+ "heteroorganic entity",
+ "abnormal multicellular organism chemical entity level",
+ "abnormal blood gas molecular entity level",
+ "Phenotypic abnormality (HPO)",
+ "Abnormal circulating protein concentration (HPO)",
+ "Abnormal blood oxygen level (HPO)",
"entity",
+ "Phenotypic abnormality",
+ "abnormal independent continuant gas molecular entity level",
+ "quality",
"anatomical entity",
"anatomical structure",
"organism substance",
"mesoderm-derived structure",
"bodily fluid",
- "hemolymphoid system",
- "hematopoietic system",
- "haemolymphatic fluid",
- "organooxygen compound",
- "heteroorganic entity",
- "abnormal anatomical entity",
- "abnormal blood oxygen molecular entity level",
- "abnormal role independent continuant level",
+ "transferase complex, transferring phosphorus-containing groups",
+ "peptide",
+ "pnictogen molecular entity",
+ "chalcogen molecular entity",
+ "carbon group molecular entity",
+ "carboxamide",
+ "primary amide",
+ "organic amino compound",
+ "phenotype",
"continuant",
- "abnormal independent continuant nitrogen molecular entity level",
- "abnormal hematopoietic system",
- "abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
"entity",
+ "process",
+ "independent continuant",
+ "abnormal role blood level",
+ "Abnormal circulating creatine kinase concentration (HPO)",
+ "Abnormal respiratory system physiology (HPO)",
"Abnormal blood gas level (HPO)",
"abnormal blood protein polypeptide chain level",
+ "abnormal blood chemical entity level",
+ "biological_process",
"material entity",
- "metabolic process",
+ "protein-containing complex",
+ "molecular entity",
+ "blood",
"catalytic complex",
"polyatomic entity",
"main group molecular entity",
+ "abnormal blood oxygen molecular entity level",
+ "abnormal role independent continuant level",
+ "abnormality of respiratory system physiology",
+ "abnormal respiratory system",
+ "abnormal independent continuant chemical entity level",
+ "Abnormality of blood and blood-forming tissues (HPO)",
+ "abnormal independent continuant nitrogen molecular entity level",
+ "abnormal hematopoietic system",
+ "abnormality of anatomical entity physiology",
+ "Abnormal circulating metabolite concentration (HPO)",
+ "multicellular anatomical structure",
"anatomical system",
- "transferase complex",
- "macromolecule",
- "p-block molecular entity",
- "multicellular organism"
+ "gas molecular entity",
+ "creatine kinase complex",
+ "polypeptide",
+ "nitrogen molecular entity",
+ "oxygen molecular entity",
+ "organochalcogen compound",
+ "organic molecular entity"
],
"object_taxon": null,
"object_taxon_label": null,
@@ -841,11 +841,11 @@
"frequency_qualifier_label": "Obligate (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0000001", "HP:0040280"],
"frequency_qualifier_closure_label": [
- "All (HPO)",
"Obligate (HPO)",
- "Frequency (HPO)"
+ "Frequency (HPO)",
+ "All (HPO)"
],
"onset_qualifier_label": null,
"onset_qualifier_namespace": null,
@@ -865,64 +865,64 @@
"direction": "outgoing"
},
{
- "id": "uuid:cb2a2f47-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:476a1081-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"subject": "MONDO:0009681",
"original_subject": "OMIM:254090",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000020",
- "MONDO:0005336",
- "MONDO:0005071",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0002320",
+ "MONDO:0000001",
"MONDO:0020121",
"MONDO:0019952",
+ "MONDO:0003847",
+ "MONDO:0005336",
+ "MONDO:0000355",
"BFO:0000017",
"MONDO:0100225",
+ "BFO:0000020",
+ "MONDO:0003939",
+ "MONDO:0002081",
+ "MONDO:0019950",
+ "MONDO:0005071",
+ "BFO:0000002",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0009681",
- "MONDO:0000355",
- "MONDO:0000001",
"MONDO:0700223",
- "BFO:0000002",
+ "BFO:0000016",
+ "MONDO:0016139",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320",
- "MONDO:0019950"
+ "MONDO:0009681",
+ "OGMS:0000031",
+ "BFO:0000001"
],
"subject_label": "Ullrich congenital muscular dystrophy 1",
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "disease",
+ "realizable entity",
+ "collagen 6-related myopathy",
+ "specifically dependent continuant",
+ "Ullrich congenital muscular dystrophy 1",
"disease",
"muscle tissue disorder",
- "congenital nervous system disorder",
"hereditary skeletal muscle disorder",
+ "Ullrich congenital muscular dystrophy",
"continuant",
"disposition",
"qualitative or quantitative protein defects in neuromuscular diseases",
- "Ullrich congenital muscular dystrophy 1",
- "disease",
- "specifically dependent continuant",
+ "human disease",
+ "entity",
"myopathy",
- "hereditary disease",
- "Ullrich congenital muscular dystrophy",
"nervous system disorder",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "congenital nervous system disorder",
+ "congenital muscular dystrophy",
+ "muscular dystrophy",
"congenital myopathy",
- "realizable entity",
- "collagen 6-related myopathy",
"skeletal muscle disorder",
- "neuromuscular disease",
- "entity",
- "congenital muscular dystrophy"
+ "neuromuscular disease"
],
"subject_taxon": null,
"subject_taxon_label": null,
@@ -932,91 +932,91 @@
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "UPHENO:0082875",
- "HP:0001388",
- "UPHENO:0001005",
- "BFO:0000002",
- "BFO:0000020",
- "PATO:0000001",
+ "HP:0011729",
"HP:0011843",
- "BFO:0000004",
- "UBERON:0002204",
- "HP:0000001",
- "HP:0020152",
- "UPHENO:0001001",
- "UPHENO:0001002",
- "HP:0000118",
- "UPHENO:0002964",
- "BFO:0000001",
+ "UBERON:0000465",
+ "UPHENO:0082875",
+ "HP:0001388",
"BFO:0000001",
"BFO:0000040",
- "UBERON:0000467",
- "UBERON:0000468",
"UBERON:0011216",
"UBERON:0034921",
- "UPHENO:0075696",
- "HP:0011729",
- "HP:0034430",
- "HP:0000924",
- "UPHENO:0002332",
- "UPHENO:0001003",
- "UPHENO:0002536",
+ "UPHENO:0001002",
+ "BFO:0000020",
"BFO:0000002",
- "UBERON:0000465",
- "UBERON:0004770",
- "UBERON:0000982",
- "HP:0033127",
+ "UPHENO:0001001",
+ "UPHENO:0002964",
+ "UPHENO:0001003",
"UPHENO:0081440",
+ "BFO:0000001",
"UBERON:0001062",
"UBERON:0000061",
"UBERON:0034925",
+ "UPHENO:0075696",
+ "UPHENO:0001005",
+ "HP:0033127",
+ "BFO:0000004",
+ "UBERON:0004770",
+ "UBERON:0000468",
+ "HP:0034430",
+ "HP:0000924",
+ "BFO:0000002",
+ "UPHENO:0002536",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "PATO:0000001",
+ "UBERON:0000982",
+ "HP:0000001",
+ "HP:0020152",
"UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0002204",
"UBERON:0004905",
"UBERON:0001434"
],
"object_label": "Distal joint laxity (HPO)",
"object_closure_label": [
- "All (HPO)",
- "Distal joint laxity (HPO)",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "Abnormality of the musculoskeletal system (HPO)",
- "abnormality of musculoskeletal system physiology",
- "independent continuant",
- "multicellular anatomical structure",
- "musculoskeletal system",
- "skeletal joint",
"abnormality of anatomical entity physiology",
"Joint laxity (HPO)",
- "phenotype",
- "Abnormality of joint mobility (HPO)",
"abnormal skeletal system",
+ "abnormal anatomical entity",
"quality",
- "Abnormality of musculoskeletal physiology (HPO)",
+ "abnormal anatomical entity",
+ "abnormal phenotype by ontology source",
+ "specifically dependent continuant",
+ "phenotype by ontology source",
+ "abnormality of musculoskeletal system physiology",
"continuant",
"material anatomical entity",
- "abnormal phenotype by ontology source",
+ "musculoskeletal system",
+ "All (HPO)",
+ "Distal joint laxity (HPO)",
"continuant",
- "specifically dependent continuant",
+ "organ system subdivision",
+ "multi organ part structure",
+ "Abnormal joint physiology",
+ "Abnormality of the skeletal system (HPO)",
+ "Phenotypic abnormality (HPO)",
"entity",
+ "Phenotypic abnormality",
+ "Abnormality of musculoskeletal physiology (HPO)",
"anatomical entity",
"anatomical structure",
"anatomical collection",
"articular system",
+ "multicellular organism",
+ "phenotype",
+ "entity",
+ "independent continuant",
+ "Abnormality of joint mobility (HPO)",
+ "Abnormality of the musculoskeletal system (HPO)",
+ "material entity",
"articulation",
"skeletal system",
- "abnormal anatomical entity",
- "Abnormal joint physiology",
- "Abnormality of the skeletal system (HPO)",
"abnormality of anatomical entity physiology",
- "phenotype by ontology source",
- "abnormal anatomical entity",
- "entity",
- "material entity",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "multi organ part structure"
+ "skeletal joint"
],
"object_taxon": null,
"object_taxon_label": null,
@@ -1062,11 +1062,11 @@
"frequency_qualifier_label": "Obligate (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0000001", "HP:0040280"],
"frequency_qualifier_closure_label": [
- "All (HPO)",
"Obligate (HPO)",
- "Frequency (HPO)"
+ "Frequency (HPO)",
+ "All (HPO)"
],
"onset_qualifier_label": null,
"onset_qualifier_namespace": null,
@@ -1086,66 +1086,66 @@
"direction": "outgoing"
},
{
- "id": "uuid:c9d8bdf9-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:46170673-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
"subject": "MONDO:0009676",
"original_subject": "OMIM:253601",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "MONDO:0016971",
- "BFO:0000002",
+ "MONDO:0016145",
+ "MONDO:0000001",
+ "MONDO:0020121",
+ "MONDO:0003847",
+ "MONDO:0015152",
+ "MONDO:0000429",
"BFO:0000020",
+ "MONDO:0016106",
"MONDO:0005336",
+ "BFO:0000017",
+ "MONDO:0003939",
+ "MONDO:0006025",
+ "MONDO:0002081",
+ "BFO:0000002",
"MONDO:0009676",
- "MONDO:0015152",
- "MONDO:0000429",
+ "MONDO:0016971",
"MONDO:0005071",
- "MONDO:0006025",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
- "MONDO:0016145",
- "MONDO:0020121",
- "BFO:0000017",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
"MONDO:0700223",
- "MONDO:0016106",
+ "BFO:0000016",
+ "MONDO:0016139",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939"
+ "OGMS:0000031",
+ "BFO:0000001"
],
"subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2B",
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
"disease",
+ "realizable entity",
+ "disease",
+ "specifically dependent continuant",
"muscle tissue disorder",
- "qualitative or quantitative defects of dysferlin",
"hereditary skeletal muscle disorder",
- "autosomal recessive disease",
+ "continuant",
+ "limb-girdle muscular dystrophy",
"disposition",
"qualitative or quantitative protein defects in neuromuscular diseases",
- "autosomal recessive limb-girdle muscular dystrophy type 2B",
- "disease",
- "continuant",
- "specifically dependent continuant",
- "myopathy",
- "hereditary disease",
+ "human disease",
+ "entity",
"autosomal genetic disease",
+ "autosomal recessive disease",
+ "myopathy",
"nervous system disorder",
- "realizable entity",
- "skeletal muscle disorder",
- "neuromuscular disease",
+ "autosomal recessive limb-girdle muscular dystrophy type 2B",
"autosomal recessive limb-girdle muscular dystrophy",
- "entity"
+ "qualitative or quantitative defects of dysferlin",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "muscular dystrophy",
+ "skeletal muscle disorder",
+ "neuromuscular disease"
],
"subject_taxon": null,
"subject_taxon_label": null,
@@ -1155,87 +1155,87 @@
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
+ "UPHENO:0002816",
+ "UPHENO:0002536",
+ "UBERON:0000465",
"UPHENO:0082875",
- "UPHENO:0002320",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UBERON:0011216",
+ "UPHENO:0001002",
+ "HP:0001324",
+ "UPHENO:0080555",
+ "HP:0011804",
"BFO:0000002",
- "BFO:0000004",
- "UBERON:0000061",
- "HP:0000001",
"UPHENO:0001001",
- "UPHENO:0001002",
- "HP:0000118",
- "BFO:0000020",
+ "HP:0003701",
"UPHENO:0001003",
"BFO:0000001",
- "PATO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0001062",
- "UBERON:0000467",
+ "BFO:0000020",
+ "HP:0033127",
+ "BFO:0000004",
+ "UBERON:0000061",
+ "UBERON:0000062",
"UBERON:0000468",
- "UBERON:0011216",
"UPHENO:0075696",
- "HP:0001324",
+ "BFO:0000002",
"HP:0003011",
+ "UPHENO:0002320",
+ "HP:0000118",
"UPHENO:0002332",
- "UPHENO:0002536",
- "HP:0011804",
- "BFO:0000002",
- "UBERON:0000465",
- "UBERON:0005090",
- "UBERON:0001630",
+ "PATO:0000001",
+ "HP:0000001",
"UPHENO:0001005",
- "HP:0003701",
- "UPHENO:0080555",
- "UPHENO:0002816",
"UPHENO:0080556",
- "HP:0033127",
+ "BFO:0000001",
"UBERON:0010000",
- "UBERON:0000062",
+ "UBERON:0000467",
+ "UBERON:0005090",
+ "UBERON:0001630",
"UBERON:0000383",
"UBERON:0001015"
],
"object_label": "Proximal muscle weakness (HPO)",
"object_closure_label": [
- "All (HPO)",
- "abnormality of muscle organ physiology",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "decreased anatomical entity strength",
- "abnormal musculature",
- "decreased muscle organ strength",
- "Abnormality of the musculoskeletal system (HPO)",
- "quality",
- "independent continuant",
- "anatomical structure",
- "multicellular anatomical structure",
"abnormality of anatomical entity physiology",
- "phenotype",
- "abnormal phenotype by ontology source",
"Proximal muscle weakness (HPO)",
- "specifically dependent continuant",
+ "quality",
+ "Abnormality of the musculature (HPO)",
"phenotype by ontology source",
"continuant",
"material anatomical entity",
+ "muscle organ",
+ "All (HPO)",
+ "abnormal phenotype by ontology source",
"continuant",
+ "abnormal musculature",
"Abnormal muscle physiology (HPO)",
+ "organ system subdivision",
+ "abnormality of muscle organ physiology",
+ "Phenotypic abnormality (HPO)",
+ "decreased muscle organ strength",
+ "entity",
"entity",
- "muscle structure",
+ "Phenotypic abnormality",
+ "Muscle weakness (HPO)",
+ "specifically dependent continuant",
"organ",
- "muscle organ",
+ "multicellular organism",
+ "phenotype",
+ "independent continuant",
+ "decreased anatomical entity strength",
+ "Abnormality of the musculoskeletal system (HPO)",
+ "material entity",
+ "anatomical entity",
+ "anatomical structure",
"musculature of body",
"musculature",
"abnormal anatomical entity",
- "Muscle weakness (HPO)",
- "Abnormality of the musculature (HPO)",
"abnormality of anatomical entity physiology",
"abnormal anatomical entity",
- "entity",
- "material entity",
- "anatomical entity",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision"
+ "muscle structure"
],
"object_taxon": null,
"object_taxon_label": null,
@@ -1281,11 +1281,11 @@
"frequency_qualifier_label": "Obligate (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0000001", "HP:0040280"],
"frequency_qualifier_closure_label": [
- "All (HPO)",
"Obligate (HPO)",
- "Frequency (HPO)"
+ "Frequency (HPO)",
+ "All (HPO)"
],
"onset_qualifier_label": null,
"onset_qualifier_namespace": null,
diff --git a/frontend/fixtures/associations.json b/frontend/fixtures/associations.json
index 13258976e..053592aec 100644
--- a/frontend/fixtures/associations.json
+++ b/frontend/fixtures/associations.json
@@ -4,280 +4,132 @@
"total": 4838,
"items": [
{
- "id": "uuid:c9c8bf2f-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e12a2a1-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0008050",
- "original_subject": "OMIM:160500",
+ "subject": "MONDO:0035432",
+ "original_subject": "Orphanet:565899",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
+ "MONDO:0000001",
+ "MONDO:0020121",
"MONDO:0003847",
"BFO:0000001",
- "MONDO:0020121",
- "MONDO:0019952",
+ "MONDO:0016106",
+ "MONDO:0005336",
"BFO:0000017",
+ "MONDO:0003939",
+ "MONDO:0035432",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0016971",
+ "MONDO:0005071",
+ "BFO:0000002",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
"MONDO:0700223",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320"
+ "OGMS:0000031"
],
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject_label": "POMGNT2-related limb-girdle muscular dystrophy R24",
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
"disease",
+ "realizable entity",
+ "disease",
+ "POMGNT2-related limb-girdle muscular dystrophy R24",
"muscle tissue disorder",
- "congenital nervous system disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
+ "limb-girdle muscular dystrophy",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "disposition",
+ "human disease",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
"nervous system disorder",
- "congenital myopathy",
- "realizable entity",
- "specifically dependent continuant",
+ "entity",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "muscular dystrophy",
"skeletal muscle disorder",
- "neuromuscular disease",
- "entity"
+ "neuromuscular disease"
],
"subject_taxon": null,
"subject_taxon_label": null,
"predicate": "biolink:has_phenotype",
- "object": "HP:0011399",
+ "object": "HP:0002465",
"original_object": null,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "UPHENO:0014121",
- "HP:0002814",
- "UPHENO:0068971",
- "UPHENO:0001005",
- "HP:0009127",
- "UPHENO:0014120",
- "UPHENO:0075195",
- "HP:0030236",
- "UPHENO:0020584",
- "UPHENO:0076692",
- "UPHENO:0003070",
- "PATO:0000001",
- "UPHENO:0012541",
- "BFO:0000004",
- "UBERON:0004708",
- "UBERON:0000154",
- "UBERON:0014892",
- "UBERON:0006058",
- "UBERON:0002529",
- "UBERON:0006067",
- "HP:0000001",
- "UPHENO:0002644",
- "UPHENO:0013936",
- "HP:0003202",
- "UPHENO:0075952",
- "UPHENO:0001002",
- "HP:0000118",
- "UPHENO:0015280",
- "UPHENO:0001003",
- "UPHENO:0076710",
- "BFO:0000001",
+ "UPHENO:0002536",
"BFO:0000001",
- "BFO:0000040",
- "UBERON:0010000",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
- "UBERON:0010709",
- "UBERON:0000366",
- "UBERON:0003661",
- "UBERON:0010890",
- "UBERON:0010538",
- "UBERON:0004466",
- "UBERON:0004256",
- "UBERON:0003823",
- "UPHENO:0075696",
- "HP:0002981",
- "HP:0003797",
- "UPHENO:0014111",
- "HP:0001430",
+ "UBERON:0000465",
+ "UPHENO:0082875",
"BFO:0000002",
- "HP:0008944",
+ "UPHENO:0004523",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UPHENO:0001002",
"BFO:0000020",
- "HP:0003011",
- "UPHENO:0002536",
- "HP:0001437",
- "UPHENO:0078056",
- "HP:0040064",
"BFO:0000002",
- "PR:000050567",
- "UBERON:0002101",
- "UBERON:0004709",
- "UBERON:0005090",
- "UBERON:0018254",
- "UBERON:0002103",
- "UBERON:0010707",
- "UBERON:0001630",
- "UBERON:0000026",
- "UBERON:0010758",
- "UBERON:0007271",
- "UBERON:0014792",
- "UBERON:0004482",
- "UBERON:0001383",
- "UBERON:0008784",
- "UBERON:0002471",
- "HP:0007210",
"UPHENO:0001001",
- "UPHENO:0075777",
- "HP:0011805",
- "HP:0003693",
- "UPHENO:0002816",
- "HP:0011399",
- "UPHENO:0081581",
- "HP:0033127",
- "UPHENO:0019778",
- "UPHENO:0002647",
- "UPHENO:0013920",
- "UPHENO:0002830",
- "UBERON:0001062",
- "UBERON:0000465",
- "RO:0002577",
+ "UPHENO:0001003",
+ "BFO:0000001",
+ "UPHENO:0075696",
+ "UPHENO:0002433",
+ "HP:0012638",
+ "BFO:0000004",
"UBERON:0000061",
- "UBERON:0015212",
- "UBERON:0000475",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "UBERON:0000978",
- "UBERON:0007270",
- "UBERON:0004480",
- "UBERON:0003663",
- "UBERON:0014795",
- "UBERON:0008230"
+ "UBERON:0000468",
+ "HP:0002167",
+ "PATO:0000001",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "HP:0000001",
+ "HP:0002465",
+ "UPHENO:0001005",
+ "HP:0000707",
+ "HP:0011446",
+ "UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0001016"
],
- "object_label": "Tibialis atrophy (HPO)",
+ "object_label": "Poor speech (HPO)",
"object_closure_label": [
+ "abnormality of anatomical entity physiology",
+ "Neurological speech impairment (HPO)",
+ "Abnormality of higher mental function (HPO)",
+ "abnormal anatomical entity",
+ "specifically dependent continuant",
+ "phenotype by ontology source",
+ "abnormal nervous system",
+ "continuant",
+ "material anatomical entity",
+ "nervous system",
"All (HPO)",
- "abnormal musculature of lower limb",
- "Abnormality of the lower limb (HPO)",
- "decreased size of the anatomical entity",
- "Phenotypic abnormality",
+ "Poor speech (HPO)",
+ "abnormal phenotype by ontology source",
"Phenotypic abnormality (HPO)",
- "Distal amyotrophy (HPO)",
- "abnormal musculature",
- "Tibialis atrophy (HPO)",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "abnormal musculature of limb",
- "independent continuant",
- "material anatomical entity",
- "system",
- "paired limb/fin",
- "lateral structure",
- "pelvic complex",
- "appendage musculature",
- "musculature of pelvic complex",
- "musculature of leg",
- "hindlimb zeugopod muscle",
- "hindlimb zeugopod",
- "musculature of limb atrophy",
- "Limb-girdle muscle atrophy (HPO)",
- "skeletal musculature atrophy",
- "abnormal hindlimb zeugopod muscle",
- "Abnormal skeletal muscle morphology (HPO)",
- "abnormal anatomical entity morphology in the independent continuant",
- "phenotype by ontology source",
- "Abnormality of muscle size (HPO)",
- "Abnormality of the musculature of the lower limbs (HPO)",
- "tibialis atrophy",
- "Abnormality of limbs (HPO)",
+ "Abnormality of the nervous system (HPO)",
+ "entity",
+ "Phenotypic abnormality",
+ "abnormality of nervous system physiology",
"quality",
- "decreased size of the anatomical entity in the independent continuant",
- "continuant",
- "protein-containing material entity",
- "hindlimb",
- "appendage girdle complex",
- "appendage",
- "subdivision of organism along appendicular axis",
- "flexor muscle",
- "limb muscle",
- "pelvic complex muscle",
- "paired limb/fin segment",
- "musculature of lower limb",
- "muscle of leg",
- "lower limb segment",
- "zeugopod",
- "Lower limb amyotrophy (HPO)",
+ "multicellular organism",
"phenotype",
- "abnormal phenotype by ontology source",
- "Abnormality of the musculature of the limbs (HPO)",
- "musculature of lower limb atrophy",
- "abnormal size of anatomical entity",
- "abnormal muscle organ morphology",
- "abnormal muscle organ morphology",
+ "independent continuant",
"entity",
+ "Abnormal nervous system physiology (HPO)",
+ "material entity",
"anatomical entity",
"anatomical structure",
- "muscle structure",
- "skeletal musculature",
- "organism subdivision",
- "organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "leg",
- "pelvic appendage musculature",
- "musculature of limb",
- "hindlimb muscle",
- "pelvic appendage muscle",
- "tibialis",
- "abnormal anatomical entity",
- "Abnormality of the calf (HPO)",
- "anatomical entity atrophy",
- "Skeletal muscle atrophy (HPO)",
- "abnormal hindlimb zeugopod",
- "Abnormality of the calf musculature (HPO)",
"continuant",
- "Distal lower limb amyotrophy (HPO)",
- "specifically dependent continuant",
- "Abnormality of the musculature (HPO)",
+ "abnormality of anatomical entity physiology",
"abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "abnormal anatomical entity morphology",
- "abnormal leg",
- "entity",
- "muscle organ atrophy",
- "abnormal limb",
- "material entity",
- "limb",
- "pelvic appendage",
"multicellular anatomical structure",
- "anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "posterior region of body",
- "skeletal muscle organ",
- "multi-limb segment region",
- "limb segment",
- "musculature of hindlimb zeugopod"
+ "anatomical system"
],
"object_taxon": null,
"object_taxon_label": null,
@@ -286,28 +138,28 @@
"negated": null,
"pathway": null,
"evidence_count": 2,
- "has_evidence": ["ECO:0000269"],
+ "has_evidence": ["ECO:0000304"],
"has_evidence_links": [
{
- "id": "ECO:0000269",
- "url": "http://purl.obolibrary.org/obo/ECO_0000269"
+ "id": "ECO:0000304",
+ "url": "http://purl.obolibrary.org/obo/ECO_0000304"
}
],
- "grouping_key": "MONDO:0008050\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0011399",
+ "grouping_key": "MONDO:0035432\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0002465",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype"
},
- "publications": ["PMID:17548557"],
+ "publications": ["orphanet:565899"],
"publications_links": [
{
- "id": "PMID:17548557",
- "url": "http://identifiers.org/pubmed/17548557"
+ "id": "orphanet:565899",
+ "url": null
}
],
"qualifiers": [],
- "frequency_qualifier": "HP:0040280",
+ "frequency_qualifier": "HP:0040282",
"onset_qualifier": null,
"sex_qualifier": null,
"stage_qualifier": null,
@@ -316,14 +168,14 @@
"qualifiers_category": null,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
"frequency_qualifier_closure_label": [
- "All (HPO)",
- "Obligate (HPO)",
- "Frequency (HPO)"
+ "Frequency (HPO)",
+ "Frequent (HPO)",
+ "All (HPO)"
],
"onset_qualifier_label": null,
"onset_qualifier_namespace": null,
@@ -342,474 +194,258 @@
"stage_qualifier_closure_label": []
},
{
- "id": "uuid:c9c8bf30-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e12a2a3-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0008050",
- "original_subject": "OMIM:160500",
+ "subject": "MONDO:0035432",
+ "original_subject": "Orphanet:565899",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
+ "MONDO:0000001",
+ "MONDO:0020121",
"MONDO:0003847",
"BFO:0000001",
- "MONDO:0020121",
- "MONDO:0019952",
+ "MONDO:0016106",
+ "MONDO:0005336",
"BFO:0000017",
+ "MONDO:0003939",
+ "MONDO:0035432",
"BFO:0000020",
- "MONDO:0020120",
- "MONDO:0019056",
- "MONDO:0000001",
- "MONDO:0700223",
- "MONDO:0700096",
"MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320"
- ],
- "subject_label": "MYH7-related skeletal myopathy",
- "subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
- "disease",
- "muscle tissue disorder",
- "congenital nervous system disorder",
- "hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
- "continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
- "myopathy",
- "hereditary disease",
- "nervous system disorder",
- "congenital myopathy",
- "realizable entity",
- "specifically dependent continuant",
- "skeletal muscle disorder",
- "neuromuscular disease",
- "entity"
- ],
- "subject_taxon": null,
- "subject_taxon_label": null,
- "predicate": "biolink:has_phenotype",
- "object": "HP:0031295",
- "original_object": null,
- "object_namespace": "HP",
- "object_category": "biolink:PhenotypicFeature",
- "object_closure": [
- "UPHENO:0001005",
- "BFO:0000002",
- "UPHENO:0075195",
- "UPHENO:0020584",
- "UPHENO:0076692",
- "BFO:0000004",
- "UBERON:0004535",
- "UBERON:0011676",
- "UBERON:0013701",
- "UBERON:0002081",
- "UBERON:0000915",
- "UBERON:0002100",
- "UBERON:0005181",
- "UBERON:0002075",
- "UBERON:0015228",
- "HP:0000001",
- "UPHENO:0019897",
- "HP:0030680",
- "HP:0000118",
- "HP:0001627",
- "BFO:0000020",
- "UPHENO:0019919",
- "UPHENO:0076776",
- "UPHENO:0015280",
- "UPHENO:0001020",
- "UPHENO:0001003",
- "BFO:0000001",
- "PATO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0000064",
- "UBERON:0002079",
- "UPHENO:0075696",
- "UPHENO:0015303",
- "HP:0001626",
- "UPHENO:0080362",
- "UPHENO:0065599",
- "HP:0031295",
- "UPHENO:0002536",
- "UPHENO:0076810",
- "PR:000050567",
- "UBERON:0000465",
- "UBERON:0004120",
- "UBERON:0035553",
- "UBERON:0000948",
- "UBERON:0001009",
- "UBERON:0004151",
- "UBERON:0009569",
- "UBERON:0013702",
- "UBERON:0005177",
- "UBERON:0003103",
- "UBERON:0015410",
- "UPHENO:0001001",
- "UPHENO:0001002",
- "UPHENO:0015324",
- "HP:0025579",
- "UPHENO:0001072",
- "UPHENO:0081581",
- "HP:0005120",
- "UPHENO:0015329",
- "BFO:0000002",
- "UBERON:0001062",
- "RO:0002577",
- "UBERON:0000061",
- "UBERON:0015212",
- "UBERON:0010314",
- "UBERON:0010000",
- "UBERON:0000475",
- "UBERON:0000062",
- "UBERON:0005178",
- "UBERON:0007100"
- ],
- "object_label": "Left atrial enlargement (HPO)",
- "object_closure_label": [
- "All (HPO)",
- "abnormal cardiac atrium morphology",
- "abnormal cardiovascular system",
- "increased size of the anatomical entity in independent continuant",
- "Phenotypic abnormality (HPO)",
- "abnormal anatomical entity morphology in the heart",
- "Abnormal left atrium morphology (HPO)",
- "increased size of the anatomical entity",
- "abnormal multicellular organism morphology",
- "Abnormal cardiac atrium morphology (HPO)",
- "quality",
- "independent continuant",
- "system",
- "cardiovascular system",
- "lateral structure",
- "structure with developmental contribution from neural crest",
- "multicellular anatomical structure",
- "left cardiac atrium",
- "Abnormality of the cardiovascular system (HPO)",
- "Phenotypic abnormality",
- "Abnormal heart morphology (HPO)",
- "specifically dependent continuant",
- "abnormal left cardiac atrium morphology",
- "abnormal cardiovascular system morphology",
- "abnormal anatomical entity morphology in the independent continuant",
- "increased size of the left cardiac atrium",
- "phenotype by ontology source",
- "abnormal heart morphology",
- "protein-containing material entity",
- "material anatomical entity",
- "left cardiac chamber",
- "heart",
- "subdivision of trunk",
- "body proper",
- "trunk region element",
- "compound organ",
- "heart plus pericardium",
- "phenotype",
- "abnormal phenotype by ontology source",
- "continuant",
- "abnormal size of anatomical entity",
- "entity",
- "anatomical entity",
- "anatomical structure",
- "mesoderm-derived structure",
- "organism subdivision",
- "organ",
- "circulatory system",
- "cardiac chamber",
- "thoracic cavity element",
- "primary circulatory organ",
- "abnormal anatomical entity",
- "abnormal cardiac atrium morphology in the heart",
- "Abnormality of cardiovascular system morphology (HPO)",
- "Left atrial enlargement (HPO)",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "abnormal anatomical entity morphology",
- "entity",
- "abnormal cardiac atrium morphology in the independent continuant",
- "continuant",
- "material entity",
- "anatomical system",
- "multicellular organism",
- "organ part",
- "subdivision of organism along main body axis",
- "main body axis",
- "cardiac atrium",
- "thoracic segment of trunk",
- "trunk",
- "thoracic segment organ",
- "viscus",
- "circulatory organ"
- ],
- "object_taxon": null,
- "object_taxon_label": null,
- "primary_knowledge_source": "infores:hpo-annotations",
- "aggregator_knowledge_source": ["infores:monarchinitiative"],
- "negated": null,
- "pathway": null,
- "evidence_count": 2,
- "has_evidence": ["ECO:0000269"],
- "has_evidence_links": [
- {
- "id": "ECO:0000269",
- "url": "http://purl.obolibrary.org/obo/ECO_0000269"
- }
- ],
- "grouping_key": "MONDO:0008050\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0031295",
- "provided_by": "hpoa_disease_to_phenotype_edges",
- "provided_by_link": {
- "id": "hpoa_disease_to_phenotype",
- "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype"
- },
- "publications": ["PMID:17548557"],
- "publications_links": [
- {
- "id": "PMID:17548557",
- "url": "http://identifiers.org/pubmed/17548557"
- }
- ],
- "qualifiers": [],
- "frequency_qualifier": "HP:0040280",
- "onset_qualifier": null,
- "sex_qualifier": null,
- "stage_qualifier": null,
- "qualifiers_label": null,
- "qualifiers_namespace": null,
- "qualifiers_category": null,
- "qualifiers_closure": [],
- "qualifiers_closure_label": [],
- "frequency_qualifier_label": "Obligate (HPO)",
- "frequency_qualifier_namespace": "HP",
- "frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
- "frequency_qualifier_closure_label": [
- "All (HPO)",
- "Obligate (HPO)",
- "Frequency (HPO)"
- ],
- "onset_qualifier_label": null,
- "onset_qualifier_namespace": null,
- "onset_qualifier_category": null,
- "onset_qualifier_closure": [],
- "onset_qualifier_closure_label": [],
- "sex_qualifier_label": null,
- "sex_qualifier_namespace": null,
- "sex_qualifier_category": null,
- "sex_qualifier_closure": [],
- "sex_qualifier_closure_label": [],
- "stage_qualifier_label": null,
- "stage_qualifier_namespace": null,
- "stage_qualifier_category": null,
- "stage_qualifier_closure": [],
- "stage_qualifier_closure_label": []
- },
- {
- "id": "uuid:c9c8bf31-7529-11ee-b012-cbd37f5c3759",
- "category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0008050",
- "original_subject": "OMIM:160500",
- "subject_namespace": "MONDO",
- "subject_category": "biolink:Disease",
- "subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
+ "MONDO:0016971",
"MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
- "MONDO:0020121",
- "MONDO:0019952",
- "BFO:0000017",
- "BFO:0000020",
+ "BFO:0000002",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
"MONDO:0700223",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320"
+ "OGMS:0000031"
],
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject_label": "POMGNT2-related limb-girdle muscular dystrophy R24",
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
"disease",
+ "realizable entity",
+ "disease",
+ "POMGNT2-related limb-girdle muscular dystrophy R24",
"muscle tissue disorder",
- "congenital nervous system disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
+ "limb-girdle muscular dystrophy",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "disposition",
+ "human disease",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
"nervous system disorder",
- "congenital myopathy",
- "realizable entity",
- "specifically dependent continuant",
+ "entity",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "muscular dystrophy",
"skeletal muscle disorder",
- "neuromuscular disease",
- "entity"
+ "neuromuscular disease"
],
"subject_taxon": null,
"subject_taxon_label": null,
"predicate": "biolink:has_phenotype",
- "object": "HP:0002938",
+ "object": "HP:0008981",
"original_object": null,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "UPHENO:0001005",
- "HP:0009121",
- "UPHENO:0020584",
- "UPHENO:0076692",
- "BFO:0000001",
- "PATO:0000001",
- "BFO:0000004",
- "UBERON:0002204",
- "UBERON:0011676",
- "UBERON:0001137",
- "UBERON:0013701",
- "UBERON:0002100",
- "UBERON:0005462",
- "HP:0000001",
- "UPHENO:0076703",
- "HP:0000118",
- "BFO:0000020",
- "HP:0000925",
+ "HP:0008981",
+ "UPHENO:0084535",
+ "UPHENO:0002816",
+ "HP:0030236",
+ "PR:000050567",
+ "UBERON:0000465",
+ "RO:0002577",
"UPHENO:0015280",
- "UPHENO:0002964",
- "UPHENO:0001003",
- "HP:0003307",
- "UPHENO:0022529",
- "BFO:0000001",
+ "HP:0001437",
"BFO:0000040",
- "UBERON:0000467",
- "UBERON:0000468",
+ "UBERON:0001062",
"UBERON:0011216",
- "UPHENO:0075696",
- "HP:0000924",
- "UPHENO:0002536",
- "BFO:0000002",
- "UBERON:0004288",
- "UBERON:0009569",
- "UBERON:0013702",
- "UBERON:0000075",
- "UBERON:0002417",
- "UBERON:0011137",
- "UBERON:0006077",
- "UBERON:0011138",
- "UBERON:0002090",
- "UBERON:0005944",
- "UBERON:0001130",
- "UPHENO:0001001",
- "HP:0011842",
+ "UBERON:0000154",
+ "UBERON:0006067",
"UPHENO:0001002",
+ "HP:0001430",
+ "UPHENO:0075195",
+ "UPHENO:0019778",
+ "UPHENO:0084489",
"BFO:0000002",
- "HP:0010674",
+ "UBERON:0002101",
+ "UBERON:0004709",
+ "UBERON:0015212",
+ "UBERON:0001630",
+ "UPHENO:0001001",
+ "UPHENO:0075777",
+ "HP:0011805",
+ "HP:0003712",
+ "UPHENO:0002647",
+ "BFO:0000001",
+ "UBERON:0004482",
+ "UBERON:0001383",
+ "UBERON:0008784",
+ "UBERON:0002471",
+ "UPHENO:0075696",
+ "UPHENO:0001005",
+ "HP:0009127",
+ "BFO:0000020",
+ "UPHENO:0001072",
"UPHENO:0081581",
"HP:0033127",
- "UPHENO:0002813",
- "HP:0002938",
- "UBERON:0001062",
- "UBERON:0000465",
+ "UPHENO:0001003",
+ "UPHENO:0076692",
+ "UPHENO:0003070",
+ "UPHENO:0002830",
+ "BFO:0000004",
+ "UBERON:0004708",
"UBERON:0000061",
- "UBERON:0034925",
- "UBERON:0010000",
"UBERON:0000475",
- "UBERON:0010912",
- "UBERON:0001434",
- "UBERON:0006074"
+ "UBERON:0000062",
+ "UBERON:0000468",
+ "UBERON:0010709",
+ "HP:0002981",
+ "UPHENO:0065599",
+ "BFO:0000002",
+ "HP:0003011",
+ "UPHENO:0002536",
+ "UPHENO:0084715",
+ "UPHENO:0076710",
+ "HP:0040064",
+ "PATO:0000001",
+ "UBERON:0002103",
+ "UBERON:0010707",
+ "UBERON:0000026",
+ "UBERON:0010758",
+ "UBERON:0006058",
+ "UBERON:0004466",
+ "UBERON:0004256",
+ "UBERON:0003823",
+ "HP:0002814",
+ "UPHENO:0075952",
+ "HP:0000118",
+ "UPHENO:0020584",
+ "HP:0008968",
+ "UBERON:0007271",
+ "UBERON:0014792",
+ "UBERON:0003661",
+ "UBERON:0010890",
+ "UBERON:0010538",
+ "HP:0000001",
+ "UPHENO:0002644",
+ "BFO:0000001",
+ "UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0005090",
+ "UBERON:0018254",
+ "UBERON:0000383",
+ "UBERON:0001015",
+ "UBERON:0014892",
+ "UBERON:0000978",
+ "UBERON:0007270",
+ "UBERON:0004480",
+ "UBERON:0003663",
+ "UBERON:0014795",
+ "UBERON:0002529"
],
- "object_label": "Lumbar hyperlordosis (HPO)",
+ "object_label": "Calf muscle hypertrophy (HPO)",
"object_closure_label": [
+ "increased size of the anatomical entity in independent continuant",
+ "abnormal hindlimb zeugopod muscle",
+ "Abnormal skeletal muscle morphology (HPO)",
+ "Skeletal muscle hypertrophy (HPO)",
+ "abnormal anatomical entity",
+ "musculature of hindlimb zeugopod",
+ "abnormal anatomical entity",
+ "abnormal phenotype by ontology source",
+ "Abnormality of the musculature of the limbs (HPO)",
+ "Abnormality of the musculature (HPO)",
+ "Abnormality of the musculature of the lower limbs (HPO)",
+ "abnormal musculature of limb",
+ "continuant",
+ "protein-containing material entity",
+ "material anatomical entity",
+ "system",
+ "multi-limb segment region",
"All (HPO)",
+ "abnormal musculature of lower limb",
+ "continuant",
+ "abnormal musculature",
+ "abnormal muscle organ morphology",
+ "hypertrophic multicellular anatomical structure",
+ "organ system subdivision",
+ "muscle organ",
+ "appendage",
+ "subdivision of organism along appendicular axis",
+ "Abnormality of the lower limb (HPO)",
"Phenotypic abnormality (HPO)",
- "Abnormality of the curvature of the vertebral column (HPO)",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "Hyperlordosis (HPO)",
- "abnormal postcranial axial skeleton morphology",
- "independent continuant",
- "material anatomical entity",
- "multicellular anatomical structure",
- "musculoskeletal system",
- "abdominal segment of trunk",
- "axial skeletal system",
- "subdivision of vertebral column",
- "postcranial axial skeletal system",
- "postcranial axial skeleton",
- "axial skeleton plus cranial skeleton",
- "vertebral column",
- "Abnormal skeletal morphology (HPO)",
+ "abnormal anatomical entity morphology",
+ "Muscle hypertrophy of the lower extremities (HPO)",
+ "entity",
+ "entity",
+ "leg",
+ "pelvic appendage musculature",
+ "musculature of limb",
+ "hindlimb muscle",
+ "pelvic appendage muscle",
+ "limb segment",
"Phenotypic abnormality",
- "continuant",
+ "Abnormality of the calf musculature (HPO)",
"specifically dependent continuant",
- "Abnormality of the vertebral column (HPO)",
- "abnormal anatomical entity morphology in the independent continuant",
- "abnormal skeletal system",
- "phenotype by ontology source",
+ "abnormal anatomical entity morphology",
+ "abnormal leg",
"quality",
- "continuant",
- "subdivision of trunk",
- "body proper",
- "subdivision of skeletal system",
+ "organism subdivision",
+ "organ",
+ "multicellular organism",
+ "pelvic complex",
+ "musculature of lower limb",
+ "muscle of leg",
+ "lower limb segment",
+ "zeugopod",
"phenotype",
- "abnormal phenotype by ontology source",
- "Abnormal axial skeleton morphology (HPO)",
- "abnormal vertebral column",
- "Lumbar hyperlordosis (HPO)",
- "entity",
+ "abnormal hindlimb zeugopod",
+ "abnormal anatomical entity morphology in the independent continuant",
+ "abnormally increased volume of anatomical entity",
+ "independent continuant",
+ "posterior region of body",
+ "Calf muscle hypertrophy (HPO)",
+ "hypertrophic pelvic complex muscle",
+ "abnormal size of anatomical entity",
+ "increased size of the anatomical entity",
+ "abnormal multicellular organism morphology",
+ "Abnormality of the musculoskeletal system (HPO)",
+ "phenotype by ontology source",
+ "abnormal limb",
+ "material entity",
"anatomical entity",
+ "paired limb/fin",
"anatomical structure",
- "anatomical collection",
- "skeleton",
- "organism subdivision",
- "subdivision of skeleton",
- "skeletal system",
- "lumbar region of vertebral column",
- "abnormal anatomical entity",
- "abnormal skeletal system morphology",
- "Abnormality of the skeletal system (HPO)",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "abnormal anatomical entity morphology",
- "entity",
- "material entity",
+ "limb",
+ "pelvic appendage",
+ "lateral structure",
+ "musculature of body",
+ "musculature",
+ "skeletal muscle organ",
+ "musculature of leg",
+ "hindlimb zeugopod muscle",
+ "hindlimb zeugopod",
+ "Abnormality of the calf (HPO)",
+ "Abnormality of muscle size (HPO)",
+ "abnormal muscle organ morphology",
+ "Abnormality of limbs (HPO)",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "subdivision of organism along main body axis",
- "dorsum",
- "main body axis",
- "trunk",
- "lower back"
+ "muscle structure",
+ "skeletal musculature",
+ "hindlimb",
+ "appendage girdle complex",
+ "appendage musculature",
+ "musculature of pelvic complex",
+ "limb muscle",
+ "pelvic complex muscle",
+ "paired limb/fin segment"
],
"object_taxon": null,
"object_taxon_label": null,
@@ -818,28 +454,28 @@
"negated": null,
"pathway": null,
"evidence_count": 2,
- "has_evidence": ["ECO:0000269"],
+ "has_evidence": ["ECO:0000304"],
"has_evidence_links": [
{
- "id": "ECO:0000269",
- "url": "http://purl.obolibrary.org/obo/ECO_0000269"
+ "id": "ECO:0000304",
+ "url": "http://purl.obolibrary.org/obo/ECO_0000304"
}
],
- "grouping_key": "MONDO:0008050\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0002938",
+ "grouping_key": "MONDO:0035432\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0008981",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype"
},
- "publications": ["PMID:17548557"],
+ "publications": ["orphanet:565899"],
"publications_links": [
{
- "id": "PMID:17548557",
- "url": "http://identifiers.org/pubmed/17548557"
+ "id": "orphanet:565899",
+ "url": null
}
],
"qualifiers": [],
- "frequency_qualifier": "HP:0040280",
+ "frequency_qualifier": "HP:0040282",
"onset_qualifier": null,
"sex_qualifier": null,
"stage_qualifier": null,
@@ -848,14 +484,14 @@
"qualifiers_category": null,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
"frequency_qualifier_closure_label": [
- "All (HPO)",
- "Obligate (HPO)",
- "Frequency (HPO)"
+ "Frequency (HPO)",
+ "Frequent (HPO)",
+ "All (HPO)"
],
"onset_qualifier_label": null,
"onset_qualifier_namespace": null,
@@ -874,214 +510,220 @@
"stage_qualifier_closure_label": []
},
{
- "id": "uuid:c9c8bf38-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e12a2a4-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0008050",
- "original_subject": "OMIM:160500",
+ "subject": "MONDO:0035432",
+ "original_subject": "Orphanet:565899",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
+ "MONDO:0000001",
+ "MONDO:0020121",
"MONDO:0003847",
"BFO:0000001",
- "MONDO:0020121",
- "MONDO:0019952",
+ "MONDO:0016106",
+ "MONDO:0005336",
"BFO:0000017",
+ "MONDO:0003939",
+ "MONDO:0035432",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0016971",
+ "MONDO:0005071",
+ "BFO:0000002",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
"MONDO:0700223",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320"
+ "OGMS:0000031"
],
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject_label": "POMGNT2-related limb-girdle muscular dystrophy R24",
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
"disease",
+ "realizable entity",
+ "disease",
+ "POMGNT2-related limb-girdle muscular dystrophy R24",
"muscle tissue disorder",
- "congenital nervous system disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
+ "limb-girdle muscular dystrophy",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "disposition",
+ "human disease",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
"nervous system disorder",
- "congenital myopathy",
- "realizable entity",
- "specifically dependent continuant",
+ "entity",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "muscular dystrophy",
"skeletal muscle disorder",
- "neuromuscular disease",
- "entity"
+ "neuromuscular disease"
],
"subject_taxon": null,
"subject_taxon_label": null,
"predicate": "biolink:has_phenotype",
- "object": "HP:0001265",
+ "object": "HP:0008994",
"original_object": null,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
+ "HP:0008994",
+ "UPHENO:0002816",
+ "UPHENO:0002536",
+ "PR:000050567",
+ "UBERON:0000465",
+ "RO:0002577",
"UPHENO:0082875",
- "UPHENO:0049622",
- "UPHENO:0001005",
+ "HP:0001437",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UBERON:0011216",
+ "UBERON:0000154",
+ "UBERON:0000026",
+ "UPHENO:0001002",
+ "HP:0001324",
"BFO:0000020",
- "UPHENO:0050606",
- "HP:0012638",
- "BFO:0000015",
- "BFO:0000004",
- "GO:0050882",
- "NBO:0000338",
- "GO:0050905",
- "UBERON:0001016",
- "HP:0000001",
+ "UPHENO:0080555",
+ "HP:0011804",
+ "BFO:0000002",
+ "UBERON:0002101",
+ "UBERON:0004709",
+ "UBERON:0015212",
"UPHENO:0001001",
- "UPHENO:0080585",
- "HP:0001265",
- "HP:0031826",
- "UPHENO:0001002",
- "HP:0000118",
- "UPHENO:0052178",
- "UPHENO:0002433",
- "HP:0001315",
+ "HP:0003701",
+ "HP:0011805",
"UPHENO:0001003",
- "HP:0000708",
- "HP:0011446",
- "PATO:0000001",
+ "UPHENO:0002647",
"BFO:0000001",
- "BFO:0000040",
- "UBERON:0001062",
- "GO:0050896",
- "GO:0032501",
- "GO:0060004",
- "GO:0050881",
- "NBO:0000313",
- "GO:0050877",
- "UBERON:0000467",
- "UBERON:0000468",
- "NBO:0000403",
- "NBO:0000001",
- "NBO:0000388",
+ "UBERON:0000061",
+ "UBERON:0004482",
+ "UBERON:0008784",
"UPHENO:0075696",
- "UPHENO:0078622",
- "UPHENO:0049586",
- "UPHENO:0080377",
- "HP:0100022",
- "UPHENO:0050613",
- "UPHENO:0005433",
- "UPHENO:0002332",
- "UPHENO:0002536",
- "UPHENO:0079826",
- "UPHENO:0004523",
- "UPHENO:0049587",
- "BFO:0000003",
- "BFO:0000002",
- "GO:0008150",
- "GO:0009605",
- "GO:0050879",
- "GO:0007610",
- "GO:0003008",
- "NBO:0000389",
- "UPHENO:0052915",
+ "UPHENO:0001005",
+ "HP:0009127",
+ "UPHENO:0081581",
+ "HP:0033127",
+ "UPHENO:0076692",
+ "UPHENO:0003070",
+ "UPHENO:0002830",
+ "BFO:0000004",
+ "UBERON:0004708",
+ "UBERON:0000475",
+ "UBERON:0000062",
+ "UBERON:0000468",
+ "UBERON:0010709",
+ "HP:0003690",
"BFO:0000002",
- "UPHENO:0005625",
- "UPHENO:0050079",
- "HP:0000707",
- "UPHENO:0079833",
+ "HP:0003011",
+ "UPHENO:0076710",
+ "HP:0040064",
+ "UBERON:0002103",
+ "UBERON:0010707",
+ "UBERON:0010758",
+ "UBERON:0006058",
+ "UPHENO:0002320",
+ "HP:0002814",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "PATO:0000001",
+ "UBERON:0007271",
+ "UBERON:0014792",
+ "UBERON:0010538",
+ "HP:0000001",
+ "UPHENO:0002644",
+ "UPHENO:0080556",
"BFO:0000001",
- "UBERON:0000465",
- "UBERON:0000061",
- "UBERON:0010000"
+ "UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0005090",
+ "UBERON:0001630",
+ "UBERON:0000383",
+ "UBERON:0001015",
+ "UBERON:0000978",
+ "UBERON:0007270",
+ "UBERON:0004480",
+ "UBERON:0002529"
],
- "object_label": "Hyporeflexia (HPO)",
+ "object_label": "Proximal muscle weakness in lower limbs (HPO)",
"object_closure_label": [
- "All (HPO)",
- "abnormal behavior",
- "Abnormality of movement (HPO)",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "decreased reflex",
- "abnormal response to external stimulus",
- "Abnormality of the nervous system (HPO)",
- "Behavioral abnormality (HPO)",
- "Abnormality of higher mental function (HPO)",
- "abnormal voluntary movement behavior",
- "entity",
- "quality",
- "process",
- "independent continuant",
- "material anatomical entity",
- "multicellular anatomical structure",
- "nervous system",
- "voluntary movement behavior",
- "body part movement",
- "reflexive behavior",
"abnormality of anatomical entity physiology",
- "phenotype",
- "continuant",
- "decreased qualitatively biological_process",
- "abnormality of nervous system physiology",
- "Reduced tendon reflexes (HPO)",
- "phenotype by ontology source",
- "abnormal behavior process",
- "abnormal nervous system",
- "abnormal biological_process",
- "Abnormal nervous system physiology (HPO)",
- "occurrent",
- "continuant",
- "biological_process",
- "response to external stimulus",
- "multicellular organismal movement",
- "behavior",
- "system process",
- "reflex",
- "musculoskeletal movement",
- "behavior process",
- "nervous system process",
- "involuntary movement behavior",
- "decreased qualitatively response to stimulus",
+ "Proximal muscle weakness (HPO)",
+ "Abnormal skeletal muscle morphology (HPO)",
+ "quality",
+ "abnormal anatomical entity",
"abnormal phenotype by ontology source",
+ "Abnormality of the musculature of the limbs (HPO)",
"specifically dependent continuant",
- "abnormal voluntary musculoskeletal movement",
+ "Abnormality of the musculature (HPO)",
+ "phenotype by ontology source",
+ "Abnormality of the musculature of the lower limbs (HPO)",
+ "abnormal musculature of limb",
+ "continuant",
+ "protein-containing material entity",
+ "material anatomical entity",
+ "system",
+ "muscle organ",
+ "multi-limb segment region",
+ "All (HPO)",
+ "abnormal musculature of lower limb",
+ "continuant",
+ "Proximal muscle weakness in lower limbs (HPO)",
+ "abnormal musculature",
+ "Abnormal muscle physiology (HPO)",
+ "organ system subdivision",
+ "subdivision of organism along appendicular axis",
+ "abnormality of muscle organ physiology",
+ "Abnormality of the lower limb (HPO)",
+ "Phenotypic abnormality (HPO)",
+ "Limb muscle weakness (HPO)",
+ "decreased muscle organ strength",
"entity",
+ "entity",
+ "leg",
+ "pelvic appendage musculature",
+ "musculature of limb",
+ "limb segment",
+ "Phenotypic abnormality",
+ "Muscle weakness (HPO)",
+ "abnormal anatomical entity morphology",
+ "abnormal leg",
"anatomical structure",
- "abnormal anatomical entity",
- "abnormal voluntary movement behavior",
- "changed biological_process rate",
- "abnormal response to stimulus",
- "abnormal behavior process",
- "Hyporeflexia (HPO)",
- "Abnormal reflex (HPO)",
- "abnormal musculoskeletal movement",
- "decreased biological_process",
- "abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
+ "organism subdivision",
+ "organ",
+ "multicellular organism",
+ "pelvic complex",
+ "musculature of lower limb",
+ "lower limb segment",
+ "phenotype",
+ "independent continuant",
+ "posterior region of body",
+ "appendage",
+ "decreased anatomical entity strength",
+ "abnormal multicellular organism morphology",
+ "Abnormality of the musculoskeletal system (HPO)",
+ "abnormal limb",
"material entity",
"anatomical entity",
- "response to stimulus",
- "multicellular organismal process",
+ "paired limb/fin",
+ "limb",
+ "pelvic appendage",
+ "lateral structure",
+ "musculature of body",
+ "musculature",
+ "abnormality of anatomical entity physiology",
+ "abnormal anatomical entity",
+ "abnormal muscle organ morphology",
+ "Abnormality of limbs (HPO)",
+ "multicellular anatomical structure",
"anatomical system",
- "voluntary musculoskeletal movement",
- "kinesthetic behavior",
- "neuromuscular process",
- "multicellular organism"
+ "muscle structure",
+ "hindlimb",
+ "appendage girdle complex",
+ "appendage musculature",
+ "musculature of pelvic complex",
+ "paired limb/fin segment"
],
"object_taxon": null,
"object_taxon_label": null,
@@ -1090,28 +732,28 @@
"negated": null,
"pathway": null,
"evidence_count": 2,
- "has_evidence": ["ECO:0000269"],
+ "has_evidence": ["ECO:0000304"],
"has_evidence_links": [
{
- "id": "ECO:0000269",
- "url": "http://purl.obolibrary.org/obo/ECO_0000269"
+ "id": "ECO:0000304",
+ "url": "http://purl.obolibrary.org/obo/ECO_0000304"
}
],
- "grouping_key": "MONDO:0008050\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0001265",
+ "grouping_key": "MONDO:0035432\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0008994",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype"
},
- "publications": ["PMID:17548557"],
+ "publications": ["orphanet:565899"],
"publications_links": [
{
- "id": "PMID:17548557",
- "url": "http://identifiers.org/pubmed/17548557"
+ "id": "orphanet:565899",
+ "url": null
}
],
"qualifiers": [],
- "frequency_qualifier": "HP:0040280",
+ "frequency_qualifier": "HP:0040282",
"onset_qualifier": null,
"sex_qualifier": null,
"stage_qualifier": null,
@@ -1120,14 +762,14 @@
"qualifiers_category": null,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
"frequency_qualifier_closure_label": [
- "All (HPO)",
- "Obligate (HPO)",
- "Frequency (HPO)"
+ "Frequency (HPO)",
+ "Frequent (HPO)",
+ "All (HPO)"
],
"onset_qualifier_label": null,
"onset_qualifier_namespace": null,
@@ -1146,228 +788,240 @@
"stage_qualifier_closure_label": []
},
{
- "id": "uuid:c9c8bf3f-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df81-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0008050",
- "original_subject": "OMIM:160500",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320"
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001"
],
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
+ "disease",
+ "hypertrophic cardiomyopathy",
"disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity"
+ "myotonic syndrome"
],
"subject_taxon": null,
"subject_taxon_label": null,
"predicate": "biolink:has_phenotype",
- "object": "HP:0009053",
+ "object": "HP:0000256",
"original_object": null,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "UPHENO:0082875",
- "UPHENO:0002320",
- "HP:0002814",
- "UPHENO:0001005",
- "HP:0009127",
- "UPHENO:0076692",
- "UPHENO:0003070",
- "BFO:0000004",
- "UBERON:0004708",
- "UBERON:0000154",
- "UBERON:0000026",
- "UBERON:0014892",
- "UBERON:0006058",
- "UBERON:0002529",
- "HP:0000001",
- "HP:0000118",
- "BFO:0000002",
- "BFO:0000020",
- "UPHENO:0076710",
- "BFO:0000001",
- "PATO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
- "UBERON:0010709",
- "UBERON:0010890",
- "UBERON:0010538",
- "UPHENO:0075696",
- "UPHENO:0080575",
- "HP:0001324",
- "HP:0003690",
- "HP:0003011",
- "UPHENO:0002332",
- "UPHENO:0001003",
+ "HP:0000256",
"UPHENO:0002536",
- "HP:0002460",
- "HP:0040064",
- "HP:0009053",
- "HP:0011804",
- "PR:000050567",
+ "UPHENO:0081566",
+ "HP:0000240",
"UBERON:0000465",
- "UBERON:0002101",
- "UBERON:0004709",
- "UBERON:0005090",
- "UBERON:0018254",
- "UBERON:0002103",
- "UBERON:0010707",
- "UBERON:0001630",
- "UBERON:0010758",
- "UBERON:0007271",
- "UBERON:0014792",
- "UBERON:0008784",
- "HP:0007340",
- "UPHENO:0001001",
- "HP:0011805",
+ "UPHENO:0075220",
+ "UPHENO:0001208",
+ "UPHENO:0002844",
+ "UPHENO:0015280",
+ "BFO:0000001",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UBERON:0011216",
+ "UBERON:0011676",
+ "UBERON:0013701",
+ "UPHENO:0075148",
"UPHENO:0001002",
- "UPHENO:0080555",
- "UPHENO:0002816",
- "UPHENO:0080556",
+ "UPHENO:0075195",
+ "HP:0009121",
+ "BFO:0000002",
+ "UPHENO:0001001",
+ "HP:0011842",
+ "BFO:0000020",
+ "UPHENO:0002964",
+ "UPHENO:0001003",
+ "UPHENO:0021447",
+ "BFO:0000001",
+ "UBERON:0000061",
+ "UBERON:0034925",
+ "HP:0040194",
+ "UPHENO:0075696",
+ "UPHENO:0001005",
+ "UPHENO:0002764",
+ "UPHENO:0001072",
"UPHENO:0081581",
"HP:0033127",
- "UPHENO:0002647",
- "UPHENO:0002830",
+ "UPHENO:0076692",
+ "UPHENO:0022529",
+ "BFO:0000004",
+ "UBERON:0004288",
+ "UBERON:0000475",
+ "UBERON:0000468",
+ "UBERON:0000153",
+ "UPHENO:0065599",
+ "HP:0000924",
+ "UBERON:0003129",
+ "UBERON:0007811",
+ "UBERON:0013702",
+ "UBERON:0000075",
+ "UBERON:0000033",
+ "UPHENO:0076703",
+ "HP:0000152",
+ "HP:0000118",
"BFO:0000002",
- "UBERON:0001062",
- "RO:0002577",
- "UBERON:0000061",
- "UBERON:0015212",
+ "UPHENO:0020584",
+ "PATO:0000001",
+ "UBERON:0010314",
+ "UBERON:0011137",
+ "UBERON:0010323",
+ "UBERON:0011138",
+ "UBERON:0002090",
+ "UBERON:0005944",
+ "HP:0000001",
+ "HP:0000929",
+ "HP:0000234",
"UBERON:0010000",
- "UBERON:0000475",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "UBERON:0000978",
- "UBERON:0004480"
+ "UBERON:0000467",
+ "UBERON:0002204",
+ "UBERON:0010912",
+ "UBERON:0001434"
],
- "object_label": "Distal lower limb muscle weakness (HPO)",
+ "object_label": "Macrocephaly (HPO)",
"object_closure_label": [
+ "abnormal size of skull",
+ "increased size of the anatomical entity in independent continuant",
+ "Abnormal skeletal morphology (HPO)",
+ "specifically dependent continuant",
+ "abnormal skeletal system",
+ "quality",
+ "Increased head circumference (HPO)",
+ "abnormal anatomical entity",
+ "abnormal phenotype by ontology source",
+ "abnormal craniocervical region",
+ "phenotype by ontology source",
+ "abnormal head morphology",
+ "continuant",
+ "material anatomical entity",
+ "musculoskeletal system",
+ "head",
"All (HPO)",
- "abnormality of muscle organ physiology",
- "Abnormality of the lower limb (HPO)",
+ "organ system subdivision",
+ "craniocervical region",
+ "body proper",
+ "subdivision of skeletal system",
+ "Abnormality of the skeletal system (HPO)",
"Phenotypic abnormality (HPO)",
"continuant",
- "decreased anatomical entity strength",
- "abnormal musculature",
- "decreased muscle organ strength",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "abnormal musculature of limb",
- "quality",
- "independent continuant",
- "system",
- "paired limb/fin",
- "lateral structure",
- "multicellular anatomical structure",
- "pelvic complex",
- "appendage musculature",
- "musculature of pelvic complex",
- "abnormality of anatomical entity physiology",
- "Abnormal skeletal muscle morphology (HPO)",
- "Phenotypic abnormality",
- "specifically dependent continuant",
- "Distal muscle weakness (HPO)",
- "Abnormality of limbs (HPO)",
- "Distal lower limb muscle weakness (HPO)",
- "protein-containing material entity",
- "material anatomical entity",
- "hindlimb",
- "appendage girdle complex",
- "subdivision of organism along appendicular axis",
- "pelvic complex muscle",
- "paired limb/fin segment",
- "lower limb segment",
- "Lower limb muscle weakness (HPO)",
- "phenotype",
- "abnormal phenotype by ontology source",
- "Abnormality of the musculature of the limbs (HPO)",
- "abnormal muscle organ morphology",
- "Abnormal muscle physiology (HPO)",
+ "Abnormality of the head (HPO)",
+ "abnormal anatomical entity morphology",
"entity",
- "anatomical entity",
+ "structure with developmental contribution from neural crest",
+ "abnormal size of head",
+ "Phenotypic abnormality",
+ "abnormal anatomical entity morphology",
+ "Abnormality of skull size (HPO)",
"anatomical structure",
- "muscle structure",
- "skeletal musculature",
+ "anatomical collection",
+ "skeleton",
"organism subdivision",
- "organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "leg",
- "musculature of limb",
- "abnormal anatomical entity",
- "decreased pelvic complex muscle strength",
- "Muscle weakness (HPO)",
- "Limb muscle weakness (HPO)",
- "Abnormality of the musculature (HPO)",
- "abnormality of anatomical entity physiology",
- "phenotype by ontology source",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "abnormal leg",
+ "multicellular organism",
+ "anterior region of body",
+ "phenotype",
+ "abnormal skeletal system morphology",
+ "Abnormality of head or neck (HPO)",
+ "Abnormal skull morphology (HPO)",
+ "abnormal anatomical entity morphology in the independent continuant",
"entity",
- "abnormal limb",
- "continuant",
+ "independent continuant",
+ "subdivision of organism along main body axis",
+ "main body axis",
+ "Macrocephaly (HPO)",
+ "abnormal size of anatomical entity",
+ "Abnormal axial skeleton morphology (HPO)",
+ "increased size of the anatomical entity",
+ "abnormal multicellular organism morphology",
+ "Abnormality of the musculoskeletal system (HPO)",
+ "abnormal postcranial axial skeleton morphology",
"material entity",
- "limb",
- "pelvic appendage",
+ "anatomical entity",
+ "subdivision of skeleton",
+ "skeletal system",
+ "increased size of the head",
+ "abnormal head",
+ "abnormal anatomical entity",
+ "abnormal skull morphology",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "posterior region of body",
- "appendage",
- "skeletal muscle organ",
- "multi-limb segment region",
- "limb segment"
+ "skull",
+ "axial skeletal system",
+ "cranial skeletal system",
+ "postcranial axial skeletal system",
+ "postcranial axial skeleton",
+ "axial skeleton plus cranial skeleton"
],
"object_taxon": null,
"object_taxon_label": null,
@@ -1376,28 +1030,28 @@
"negated": null,
"pathway": null,
"evidence_count": 2,
- "has_evidence": ["ECO:0000269"],
+ "has_evidence": ["ECO:0000304"],
"has_evidence_links": [
{
- "id": "ECO:0000269",
- "url": "http://purl.obolibrary.org/obo/ECO_0000269"
+ "id": "ECO:0000304",
+ "url": "http://purl.obolibrary.org/obo/ECO_0000304"
}
],
- "grouping_key": "MONDO:0008050\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0009053",
+ "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0000256",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype"
},
- "publications": ["PMID:17548557"],
+ "publications": ["orphanet:589821"],
"publications_links": [
{
- "id": "PMID:17548557",
- "url": "http://identifiers.org/pubmed/17548557"
+ "id": "orphanet:589821",
+ "url": null
}
],
"qualifiers": [],
- "frequency_qualifier": "HP:0040280",
+ "frequency_qualifier": "HP:0040281",
"onset_qualifier": null,
"sex_qualifier": null,
"stage_qualifier": null,
@@ -1406,14 +1060,14 @@
"qualifiers_category": null,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Very frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
+ "frequency_qualifier_closure": ["HP:0040281", "HP:0040279", "HP:0000001"],
"frequency_qualifier_closure_label": [
+ "Frequency (HPO)",
"All (HPO)",
- "Obligate (HPO)",
- "Frequency (HPO)"
+ "Very frequent (HPO)"
],
"onset_qualifier_label": null,
"onset_qualifier_namespace": null,
@@ -1432,222 +1086,248 @@
"stage_qualifier_closure_label": []
},
{
- "id": "uuid:c9c8bf41-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df82-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0008050",
- "original_subject": "OMIM:160500",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320"
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001"
],
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
+ "disease",
+ "hypertrophic cardiomyopathy",
"disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
- "neuromuscular disease",
- "entity"
- ],
- "subject_taxon": null,
- "subject_taxon_label": null,
- "predicate": "biolink:has_phenotype",
- "object": "HP:0009077",
- "original_object": null,
- "object_namespace": "HP",
- "object_category": "biolink:PhenotypicFeature",
- "object_closure": [
- "HP:0009127",
- "BFO:0000002",
- "UPHENO:0002655",
- "UPHENO:0076692",
- "BFO:0000001",
- "PATO:0000001",
- "BFO:0000004",
- "UBERON:0004708",
- "UBERON:0000061",
- "UBERON:0000153",
- "UBERON:0000026",
- "UBERON:0006058",
- "UBERON:0002529",
- "UBERON:0002398",
- "HP:0000001",
- "UPHENO:0002649",
- "UPHENO:0001001",
- "UPHENO:0001002",
- "HP:0000118",
- "HP:0001446",
- "BFO:0000020",
- "UPHENO:0002708",
- "HP:0009077",
- "UPHENO:0076710",
+ "neuromuscular disease",
+ "myotonic syndrome"
+ ],
+ "subject_taxon": null,
+ "subject_taxon_label": null,
+ "predicate": "biolink:has_phenotype",
+ "object": "HP:0000297",
+ "original_object": null,
+ "object_namespace": "HP",
+ "object_category": "biolink:PhenotypicFeature",
+ "object_closure": [
+ "HP:0011799",
+ "UPHENO:0002816",
+ "UPHENO:0002536",
+ "UBERON:0000465",
+ "RO:0002577",
+ "UPHENO:0082875",
+ "UPHENO:0002910",
"BFO:0000001",
"BFO:0000040",
- "UBERON:0000467",
- "UBERON:0000468",
+ "UBERON:0001062",
"UBERON:0011216",
- "UBERON:0010708",
- "UBERON:0010538",
- "UBERON:0004489",
- "HP:0001421",
- "HP:0030237",
- "HP:0002817",
- "HP:0003011",
- "UPHENO:0002536",
- "HP:0040064",
+ "UBERON:0011676",
+ "UBERON:0013701",
+ "UPHENO:0001002",
+ "HP:0011804",
"BFO:0000002",
- "PR:000050567",
- "UBERON:0000465",
- "UBERON:0002101",
- "UBERON:0004710",
- "UBERON:0005090",
- "UBERON:0002102",
- "UBERON:0010707",
"UBERON:0001630",
- "UBERON:0010758",
- "UBERON:0007271",
- "UBERON:0014793",
- "UBERON:0004481",
- "UBERON:0002470",
- "UBERON:0008785",
- "UPHENO:0001005",
- "HP:0001155",
+ "UBERON:0002376",
+ "UBERON:0015789",
+ "UPHENO:0001001",
"HP:0011805",
- "UPHENO:0002816",
+ "BFO:0000020",
+ "UPHENO:0001003",
+ "BFO:0000001",
+ "UBERON:0000061",
+ "UPHENO:0075696",
+ "UPHENO:0001005",
+ "UPHENO:0002764",
"UPHENO:0081581",
"HP:0033127",
- "UPHENO:0001003",
- "UPHENO:0002647",
- "UPHENO:0002880",
- "UPHENO:0002830",
- "UBERON:0001062",
- "RO:0002577",
- "UBERON:0015212",
- "UBERON:0010000",
+ "UPHENO:0076692",
+ "BFO:0000004",
"UBERON:0000475",
"UBERON:0000062",
+ "UBERON:0000468",
+ "UBERON:0000153",
+ "UPHENO:0002844",
+ "BFO:0000002",
+ "HP:0003011",
+ "UPHENO:0076710",
+ "PATO:0000001",
+ "UPHENO:0002908",
+ "UBERON:0007811",
+ "UBERON:0001444",
+ "UBERON:0013702",
+ "UBERON:0000033",
+ "UPHENO:0002320",
+ "UPHENO:0082555",
+ "HP:0000152",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "HP:0001252",
+ "UPHENO:0082557",
+ "HP:0000297",
+ "HP:0000301",
+ "UBERON:0001456",
+ "UBERON:0008229",
+ "UBERON:0013700",
+ "UBERON:0010959",
+ "UBERON:0001577",
+ "HP:0000001",
+ "HP:0003808",
+ "HP:0000234",
+ "HP:0000271",
+ "UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0005090",
+ "UBERON:0018254",
+ "UBERON:0004120",
"UBERON:0000383",
"UBERON:0001015",
- "UBERON:0001460",
- "UBERON:0004480",
- "UBERON:0007269"
+ "UBERON:0014892",
+ "UBERON:0004461",
+ "UBERON:0004473"
],
- "object_label": "Weakness of long finger extensor muscles (HPO)",
+ "object_label": "Facial hypotonia (HPO)",
"object_closure_label": [
- "All (HPO)",
- "abnormal musculature of upper limb",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "abnormal musculature",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "phenotype by ontology source",
- "abnormal musculature of limb",
- "independent continuant",
- "system",
- "paired limb/fin",
- "anatomical structure",
- "lateral structure",
- "multicellular anatomical structure",
- "pectoral complex",
- "appendage musculature",
- "musculature of pectoral complex",
- "musculature of manus",
- "phenotype",
- "Abnormality of the musculature of the hand (HPO)",
- "abnormal phenotype by ontology source",
- "Abnormality of the hand (HPO)",
+ "abnormality of anatomical entity physiology",
+ "abnormal head",
"Abnormal skeletal muscle morphology (HPO)",
- "Abnormality of the musculature of the upper limbs (HPO)",
"specifically dependent continuant",
- "abnormal manus",
- "Abnormality of limbs (HPO)",
- "quality",
+ "abnormal anatomical entity",
+ "abnormal phenotype by ontology source",
+ "abnormal craniocervical region",
+ "Abnormality of the musculature (HPO)",
+ "phenotype by ontology source",
"continuant",
- "protein-containing material entity",
"material anatomical entity",
- "forelimb",
- "appendage girdle complex",
- "subdivision of organism along appendicular axis",
- "paired limb/fin segment",
- "musculature of upper limb",
- "autopod region",
- "upper limb segment",
- "Abnormality of the musculature of the limbs (HPO)",
+ "system",
+ "cranial or facial muscle",
+ "head",
+ "All (HPO)",
+ "Abnormal muscle tone (HPO)",
"continuant",
- "abnormal musculature of manus",
- "Weakness of long finger extensor muscles (HPO)",
- "abnormal muscle organ morphology",
+ "abnormal musculature",
+ "Abnormal muscle physiology (HPO)",
+ "organ system subdivision",
+ "muscle organ",
+ "cranial muscle",
+ "craniocervical region",
+ "subdivision of head",
+ "body proper",
+ "abnormality of muscle organ physiology",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the head (HPO)",
+ "Abnormality of the face (HPO)",
+ "decreased muscle organ tone",
+ "Facial hypotonia (HPO)",
+ "Abnormality of facial musculature (HPO)",
"entity",
- "anatomical entity",
- "muscle structure",
+ "skeletal musculature of head",
+ "musculature of face",
+ "Phenotypic abnormality",
+ "abnormal anatomical entity morphology",
+ "quality",
+ "abnormal facial muscle",
+ "anatomical structure",
"organism subdivision",
"organ",
- "muscle organ",
+ "multicellular organism",
+ "anterior region of body",
+ "phenotype",
+ "decreased anatomical entity tone",
+ "Abnormality of head or neck (HPO)",
+ "entity",
+ "independent continuant",
+ "subdivision of organism along main body axis",
+ "main body axis",
+ "Abnormality of facial soft tissue (HPO)",
+ "abnormal multicellular organism morphology",
+ "Abnormality of the musculoskeletal system (HPO)",
+ "material entity",
+ "anatomical entity",
"musculature of body",
"musculature",
- "arm",
- "musculature of limb",
- "pectoral appendage musculature",
- "Hand muscle weakness (HPO)",
- "Abnormality of the upper limb (HPO)",
- "Abnormality of the musculature (HPO)",
+ "skeletal muscle organ",
+ "abnormal face",
+ "abnormality of anatomical entity physiology",
+ "Hypotonia (HPO)",
"abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "entity",
- "abnormal arm",
- "abnormal limb",
- "material entity",
- "limb",
- "pectoral appendage",
+ "abnormal muscle organ morphology",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "anterior region of body",
- "appendage",
- "multi-limb segment region",
- "limb segment",
- "manus"
+ "muscle structure",
+ "skeletal musculature",
+ "mesoderm-derived structure",
+ "face",
+ "craniocervical region musculature",
+ "axial musculature",
+ "craniocervical muscle",
+ "facial muscle"
],
"object_taxon": null,
"object_taxon_label": null,
@@ -1656,28 +1336,28 @@
"negated": null,
"pathway": null,
"evidence_count": 2,
- "has_evidence": ["ECO:0000269"],
+ "has_evidence": ["ECO:0000304"],
"has_evidence_links": [
{
- "id": "ECO:0000269",
- "url": "http://purl.obolibrary.org/obo/ECO_0000269"
+ "id": "ECO:0000304",
+ "url": "http://purl.obolibrary.org/obo/ECO_0000304"
}
],
- "grouping_key": "MONDO:0008050\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0009077",
+ "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0000297",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype"
},
- "publications": ["PMID:17548557"],
+ "publications": ["orphanet:589821"],
"publications_links": [
{
- "id": "PMID:17548557",
- "url": "http://identifiers.org/pubmed/17548557"
+ "id": "orphanet:589821",
+ "url": null
}
],
"qualifiers": [],
- "frequency_qualifier": "HP:0040280",
+ "frequency_qualifier": "HP:0040281",
"onset_qualifier": null,
"sex_qualifier": null,
"stage_qualifier": null,
@@ -1686,14 +1366,14 @@
"qualifiers_category": null,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Very frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
+ "frequency_qualifier_closure": ["HP:0040281", "HP:0040279", "HP:0000001"],
"frequency_qualifier_closure_label": [
+ "Frequency (HPO)",
"All (HPO)",
- "Obligate (HPO)",
- "Frequency (HPO)"
+ "Very frequent (HPO)"
],
"onset_qualifier_label": null,
"onset_qualifier_namespace": null,
@@ -1712,190 +1392,264 @@
"stage_qualifier_closure_label": []
},
{
- "id": "uuid:c9c8bf42-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df83-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0008050",
- "original_subject": "OMIM:160500",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320"
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001"
],
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity"
+ "myotonic syndrome"
],
"subject_taxon": null,
"subject_taxon_label": null,
"predicate": "biolink:has_phenotype",
- "object": "HP:0030051",
+ "object": "HP:0010804",
"original_object": null,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "UPHENO:0082875",
- "UPHENO:0049622",
- "UPHENO:0001005",
+ "HP:0000159",
+ "UPHENO:0076803",
+ "UBERON:0000465",
+ "UPHENO:0002910",
+ "UPHENO:0076800",
+ "UPHENO:0003064",
"BFO:0000002",
- "UPHENO:0050606",
- "HP:0001288",
- "HP:0012638",
- "BFO:0000015",
- "BFO:0000004",
- "GO:0050882",
- "NBO:0000338",
- "GO:0050905",
- "UBERON:0001016",
- "HP:0000001",
- "UPHENO:0001001",
- "UPHENO:0080585",
+ "HP:0002664",
+ "UPHENO:0015280",
+ "BFO:0000040",
+ "BFO:0000141",
+ "UBERON:0001062",
+ "UBERON:0011676",
+ "UBERON:0013701",
+ "UPHENO:0002828",
"UPHENO:0001002",
+ "BFO:0000020",
+ "HP:0011793",
+ "UPHENO:0076786",
+ "BFO:0000002",
+ "UBERON:0000167",
+ "UPHENO:0001001",
+ "HP:0000163",
+ "HP:0000177",
+ "UPHENO:0002833",
+ "HP:0000309",
+ "UPHENO:0001003",
+ "UPHENO:0002536",
+ "BFO:0000001",
+ "UBERON:0000464",
+ "UPHENO:0075696",
+ "UPHENO:0002764",
+ "UPHENO:0081581",
+ "UPHENO:0076692",
+ "UPHENO:0020955",
+ "HP:0025031",
+ "BFO:0000004",
+ "UBERON:0000061",
+ "UBERON:0002553",
+ "UBERON:0000475",
+ "UBERON:0000062",
+ "UBERON:0004111",
+ "UBERON:0000468",
+ "UBERON:0001834",
+ "UBERON:0000153",
+ "UPHENO:0002844",
+ "HP:0025033",
+ "UBERON:0000466",
+ "UBERON:0011595",
+ "UBERON:0001709",
+ "UBERON:0001833",
+ "UBERON:0007811",
+ "UBERON:0001444",
+ "UBERON:0013702",
+ "UBERON:0000025",
+ "UBERON:0000033",
+ "UBERON:0004089",
+ "HP:0000152",
+ "UPHENO:0075998",
"HP:0000118",
- "BFO:0000020",
- "UPHENO:0002433",
- "UPHENO:0001003",
- "HP:0000708",
- "HP:0011446",
- "BFO:0000001",
+ "HP:0011339",
+ "HP:0010804",
+ "UPHENO:0020584",
"PATO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "GO:0032501",
- "GO:0050881",
- "NBO:0000313",
- "GO:0050877",
+ "UBERON:0010314",
+ "UBERON:0003102",
"UBERON:0010000",
+ "UBERON:0001555",
+ "UBERON:0001456",
+ "UBERON:0004921",
+ "HP:0000001",
+ "UPHENO:0001005",
+ "HP:0031816",
+ "HP:0000153",
+ "HP:0000234",
+ "HP:0000271",
+ "BFO:0000001",
"UBERON:0000467",
- "UBERON:0000468",
- "NBO:0000403",
- "NBO:0000001",
- "UPHENO:0075696",
- "UPHENO:0078622",
- "UPHENO:0049586",
- "HP:0100022",
- "UPHENO:0050613",
- "UPHENO:0002332",
- "UPHENO:0002536",
- "UPHENO:0079826",
- "UPHENO:0004523",
- "UPHENO:0049587",
- "BFO:0000003",
- "GO:0008150",
- "GO:0050879",
- "GO:0007610",
- "GO:0003008",
- "HP:0030051",
- "HP:0000707",
- "UPHENO:0079833",
- "BFO:0000002",
- "UBERON:0001062",
- "UBERON:0000465",
- "UBERON:0000061"
+ "UBERON:0000064",
+ "UBERON:0001007",
+ "UBERON:0013522",
+ "UBERON:0000165"
],
- "object_label": "Tip-toe gait (HPO)",
+ "object_label": "Tented upper lip vermilion (HPO)",
"object_closure_label": [
- "All (HPO)",
- "abnormal behavior",
- "Abnormality of movement (HPO)",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "Tip-toe gait (HPO)",
- "Abnormality of the nervous system (HPO)",
- "Behavioral abnormality (HPO)",
- "Abnormality of higher mental function (HPO)",
- "abnormal voluntary movement behavior",
+ "abnormal head",
+ "abnormal digestive system",
+ "Abnormality of the midface (HPO)",
"quality",
- "process",
- "independent continuant",
- "material anatomical entity",
- "nervous system",
- "voluntary movement behavior",
- "body part movement",
- "abnormality of anatomical entity physiology",
- "phenotype",
+ "abnormal anatomical entity",
+ "abnormal craniocervical region",
"specifically dependent continuant",
- "abnormality of nervous system physiology",
+ "Abnormality of digestive system morphology (HPO)",
"phenotype by ontology source",
- "Gait disturbance (HPO)",
- "abnormal behavior process",
- "abnormal nervous system",
- "abnormal biological_process",
- "Abnormal nervous system physiology (HPO)",
- "occurrent",
- "biological_process",
- "multicellular organismal movement",
- "behavior",
- "system process",
- "musculoskeletal movement",
- "behavior process",
- "nervous system process",
- "abnormal phenotype by ontology source",
+ "abnormal anatomical entity",
"continuant",
- "abnormal voluntary musculoskeletal movement",
+ "material anatomical entity",
+ "organ part",
+ "digestive system",
+ "head",
+ "midface",
+ "All (HPO)",
+ "abnormal phenotype by ontology source",
+ "oral cavity",
+ "craniocervical region",
+ "subdivision of head",
+ "body proper",
+ "tube",
+ "Abnormal oral cavity morphology (HPO)",
+ "Abnormality of upper lip (HPO)",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the head (HPO)",
+ "Abnormality of the face (HPO)",
+ "abnormal anatomical entity morphology",
+ "entity",
"entity",
+ "immaterial anatomical entity",
+ "structure with developmental contribution from neural crest",
+ "surface structure",
+ "multicellular anatomical structure",
+ "mouth",
+ "abnormal mouth",
+ "Phenotypic abnormality",
+ "Neoplasm by anatomical site (HPO)",
+ "abnormal oral cavity morphology",
+ "abnormal anatomical entity morphology",
+ "abnormal lip morphology",
+ "abnormal digestive system morphology",
+ "anatomical space",
+ "anatomical cavity",
+ "organism subdivision",
+ "organ",
+ "anatomical conduit",
+ "multicellular organism",
+ "upper lip",
+ "anterior region of body",
+ "phenotype",
+ "Abnormality of head or neck (HPO)",
+ "abnormal midface",
+ "Abnormal oral morphology (HPO)",
+ "Abnormality of the mouth (HPO)",
+ "Neoplasm (HPO)",
+ "abnormal anatomical entity morphology in the independent continuant",
+ "independent continuant",
+ "subdivision of organism along main body axis",
+ "main body axis",
+ "abnormal multicellular organism morphology",
+ "Abnormal lip morphology (HPO)",
+ "Abnormality of the digestive system (HPO)",
+ "material entity",
+ "immaterial entity",
"anatomical entity",
"anatomical structure",
- "abnormal anatomical entity",
- "abnormal voluntary movement behavior",
- "abnormal response to stimulus",
- "abnormal behavior process",
- "abnormal musculoskeletal movement",
- "abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
- "entity",
+ "subdivision of tube",
+ "abnormal face",
+ "abnormal mouth morphology",
+ "abnormal upper lip",
"continuant",
- "material entity",
- "multicellular organismal process",
- "multicellular anatomical structure",
+ "Abnormality of upper lip vermillion (HPO)",
+ "Tented upper lip vermilion (HPO)",
"anatomical system",
- "voluntary musculoskeletal movement",
- "kinesthetic behavior",
- "neuromuscular process",
- "multicellular organism"
+ "jaw region",
+ "upper jaw region",
+ "lip",
+ "digestive tract",
+ "face",
+ "subdivision of digestive tract"
],
"object_taxon": null,
"object_taxon_label": null,
@@ -1904,28 +1658,28 @@
"negated": null,
"pathway": null,
"evidence_count": 2,
- "has_evidence": ["ECO:0000269"],
+ "has_evidence": ["ECO:0000304"],
"has_evidence_links": [
{
- "id": "ECO:0000269",
- "url": "http://purl.obolibrary.org/obo/ECO_0000269"
+ "id": "ECO:0000304",
+ "url": "http://purl.obolibrary.org/obo/ECO_0000304"
}
],
- "grouping_key": "MONDO:0008050\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0030051",
+ "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0010804",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype"
},
- "publications": ["PMID:17548557"],
+ "publications": ["orphanet:589821"],
"publications_links": [
{
- "id": "PMID:17548557",
- "url": "http://identifiers.org/pubmed/17548557"
+ "id": "orphanet:589821",
+ "url": null
}
],
"qualifiers": [],
- "frequency_qualifier": "HP:0040280",
+ "frequency_qualifier": "HP:0040281",
"onset_qualifier": null,
"sex_qualifier": null,
"stage_qualifier": null,
@@ -1934,14 +1688,14 @@
"qualifiers_category": null,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Very frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
+ "frequency_qualifier_closure": ["HP:0040281", "HP:0040279", "HP:0000001"],
"frequency_qualifier_closure_label": [
+ "Frequency (HPO)",
"All (HPO)",
- "Obligate (HPO)",
- "Frequency (HPO)"
+ "Very frequent (HPO)"
],
"onset_qualifier_label": null,
"onset_qualifier_namespace": null,
@@ -1960,206 +1714,178 @@
"stage_qualifier_closure_label": []
},
{
- "id": "uuid:c9c8bfed-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df84-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0009675",
- "original_subject": "OMIM:253600",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "MONDO:0016971",
- "MONDO:0005336",
- "MONDO:0015152",
- "MONDO:0000429",
- "MONDO:0005071",
- "MONDO:0006025",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
- "MONDO:0009675",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
- "MONDO:0016152",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
- "BFO:0000002",
- "MONDO:0016106",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003847",
- "MONDO:0003939"
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001"
],
- "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
- "hereditary disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
"continuant",
- "autosomal recessive disease",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
"disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "disease",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "autosomal genetic disease",
+ "myotonic dystrophy",
"nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
- "autosomal recessive limb-girdle muscular dystrophy type 2A",
"skeletal muscle disorder",
- "qualitative or quantitative defects of calpain",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity"
+ "myotonic syndrome"
],
"subject_taxon": null,
"subject_taxon_label": null,
"predicate": "biolink:has_phenotype",
- "object": "HP:0001880",
+ "object": "HP:0031843",
"original_object": null,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "HP:0001879",
+ "UBERON:0000465",
+ "GO:0050877",
+ "UPHENO:0082875",
+ "UPHENO:0004523",
+ "GO:0008150",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "GO:0003008",
+ "BFO:0000020",
+ "BFO:0000003",
+ "BFO:0000002",
+ "UPHENO:0001001",
+ "UPHENO:0001002",
+ "HP:0031843",
+ "UPHENO:0001003",
+ "BFO:0000001",
+ "UBERON:0000061",
+ "GO:0050890",
"UPHENO:0001005",
+ "UPHENO:0002433",
+ "HP:0100543",
+ "HP:0012638",
+ "BFO:0000015",
+ "UBERON:0000468",
+ "UPHENO:0075696",
"BFO:0000002",
- "BFO:0000020",
- "HP:0002715",
- "HP:0001911",
- "HP:0001880",
+ "UPHENO:0002536",
"BFO:0000004",
- "UBERON:0000178",
- "CL:0000094",
- "CL:0002242",
- "CL:0000255",
- "CL:0000219",
- "HP:0000001",
- "HP:0032309",
- "HP:0010974",
"HP:0000118",
- "HP:0001871",
- "HP:0020064",
- "UPHENO:0001003",
- "UPHENO:0002536",
- "BFO:0000001",
+ "UPHENO:0002332",
"PATO:0000001",
+ "HP:0000001",
+ "HP:0000707",
+ "HP:0011446",
"BFO:0000001",
- "UBERON:0000467",
- "CL:0000000",
- "UBERON:0000468",
- "CL:0000738",
- "CL:0000548",
- "CL:0000763",
- "CL:0000081",
- "UPHENO:0002948",
- "UPHENO:0001002",
- "HP:0025461",
- "HP:0001881",
- "HP:0020047",
- "UPHENO:0004459",
- "HP:0032251",
- "BFO:0000002",
- "BFO:0000040",
- "PR:000050567",
- "UBERON:0000465",
- "CL:0000771",
- "UBERON:0004120",
- "UBERON:0006314",
- "UBERON:0015203",
- "CL:0000003",
- "UBERON:0002193",
- "UBERON:0002390",
- "UBERON:0000179",
- "UBERON:0002405",
- "CL:0000988",
- "HP:0011893",
- "UPHENO:0001001",
- "HP:0025354",
- "HP:0001974",
- "HP:0010987",
- "UBERON:0001062",
- "UBERON:0000061",
- "UBERON:0000463",
- "UBERON:0034923",
+ "GO:0032501",
"UBERON:0010000",
- "CL:0000766",
- "CL:0002371"
+ "UBERON:0000467",
+ "UBERON:0001016"
],
- "object_label": "Eosinophilia (HPO)",
+ "object_label": "Bradyphrenia (HPO)",
"object_closure_label": [
- "All (HPO)",
- "Abnormal eosinophil morphology (HPO)",
- "Abnormal myeloid leukocyte morphology (HPO)",
- "Phenotypic abnormality (HPO)",
- "Abnormal cellular phenotype (HPO)",
- "Leukocytosis (HPO)",
- "Abnormal cellular immune system morphology (HPO)",
+ "abnormality of anatomical entity physiology",
+ "Phenotypic abnormality",
+ "Bradyphrenia (HPO)",
+ "abnormal anatomical entity",
+ "Abnormality of higher mental function (HPO)",
"quality",
- "independent continuant",
- "blood",
- "granulocyte",
- "multicellular anatomical structure",
- "myeloid cell",
- "blood cell",
- "Abnormality of blood and blood-forming tissues (HPO)",
- "Abnormal eosinophil count (HPO)",
+ "multicellular organismal process",
+ "abnormal phenotype by ontology source",
+ "specifically dependent continuant",
"phenotype by ontology source",
+ "abnormal nervous system",
+ "occurrent",
"continuant",
- "material entity",
- "protein-containing material entity",
"material anatomical entity",
- "leukocyte",
- "animal cell",
- "hematopoietic cell",
- "Abnormal leukocyte count (HPO)",
- "phenotype",
- "abnormal phenotype by ontology source",
+ "nervous system",
+ "All (HPO)",
"continuant",
- "specifically dependent continuant",
- "Abnormality of the immune system (HPO)",
- "Abnormal granulocyte morphology (HPO)",
- "Eosinophilia (HPO)",
- "abnormal anatomical entity",
- "Abnormal immune system morphology (HPO)",
+ "system process",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the nervous system (HPO)",
"entity",
- "anatomical entity",
- "anatomical structure",
- "organism substance",
- "disconnected anatomical group",
- "mesoderm-derived structure",
- "bodily fluid",
- "non-connected functional system",
- "native cell",
- "hemolymphoid system",
- "hematopoietic system",
- "haemolymphatic fluid",
- "immune system",
- "myeloid leukocyte",
- "somatic cell",
- "abnormal immune system",
- "Abnormal granulocyte count (HPO)",
- "Phenotypic abnormality",
- "Abnormal cell morphology (HPO)",
- "Abnormal leukocyte morphology (HPO)",
- "Abnormal myeloid cell morphology (HPO)",
- "abnormal hematopoietic system",
"entity",
- "eosinophil",
- "anatomical system",
- "cell",
+ "cognition",
+ "abnormality of nervous system physiology",
+ "anatomical structure",
"multicellular organism",
- "nucleate cell",
- "eukaryotic cell",
- "motile cell"
+ "phenotype",
+ "process",
+ "nervous system process",
+ "Cognitive impairment (HPO)",
+ "Abnormal nervous system physiology (HPO)",
+ "biological_process",
+ "material entity",
+ "anatomical entity",
+ "abnormal anatomical entity",
+ "abnormality of anatomical entity physiology",
+ "independent continuant",
+ "multicellular anatomical structure",
+ "anatomical system"
],
"object_taxon": null,
"object_taxon_label": null,
@@ -2168,28 +1894,28 @@
"negated": null,
"pathway": null,
"evidence_count": 2,
- "has_evidence": ["ECO:0000269"],
+ "has_evidence": ["ECO:0000304"],
"has_evidence_links": [
{
- "id": "ECO:0000269",
- "url": "http://purl.obolibrary.org/obo/ECO_0000269"
+ "id": "ECO:0000304",
+ "url": "http://purl.obolibrary.org/obo/ECO_0000304"
}
],
- "grouping_key": "MONDO:0009675\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0001880",
+ "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0031843",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype"
},
- "publications": ["PMID:16607617"],
+ "publications": ["orphanet:589821"],
"publications_links": [
{
- "id": "PMID:16607617",
- "url": "http://identifiers.org/pubmed/16607617"
+ "id": "orphanet:589821",
+ "url": null
}
],
"qualifiers": [],
- "frequency_qualifier": "HP:0040282",
+ "frequency_qualifier": "HP:0040281",
"onset_qualifier": null,
"sex_qualifier": null,
"stage_qualifier": null,
@@ -2198,14 +1924,14 @@
"qualifiers_category": null,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": "Frequent (HPO)",
+ "frequency_qualifier_label": "Very frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"],
+ "frequency_qualifier_closure": ["HP:0040281", "HP:0040279", "HP:0000001"],
"frequency_qualifier_closure_label": [
+ "Frequency (HPO)",
"All (HPO)",
- "Frequent (HPO)",
- "Frequency (HPO)"
+ "Very frequent (HPO)"
],
"onset_qualifier_label": null,
"onset_qualifier_namespace": null,
@@ -2224,144 +1950,192 @@
"stage_qualifier_closure_label": []
},
{
- "id": "uuid:c9c8bfee-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df85-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0009675",
- "original_subject": "OMIM:253600",
- "subject_namespace": "MONDO",
- "subject_category": "biolink:Disease",
- "subject_closure": [
- "MONDO:0016971",
- "MONDO:0005336",
- "MONDO:0015152",
- "MONDO:0000429",
- "MONDO:0005071",
- "MONDO:0006025",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "BFO:0000001",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
+ "subject_namespace": "MONDO",
+ "subject_category": "biolink:Disease",
+ "subject_closure": [
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
- "MONDO:0009675",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
- "MONDO:0016152",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
- "BFO:0000002",
- "MONDO:0016106",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003847",
- "MONDO:0003939"
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001"
],
- "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
- "hereditary disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
"continuant",
- "autosomal recessive disease",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
"disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "disease",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "autosomal genetic disease",
+ "myotonic dystrophy",
"nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
- "autosomal recessive limb-girdle muscular dystrophy type 2A",
"skeletal muscle disorder",
- "qualitative or quantitative defects of calpain",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity"
+ "myotonic syndrome"
],
"subject_taxon": null,
"subject_taxon_label": null,
"predicate": "biolink:has_phenotype",
- "object": "HP:0002312",
+ "object": "HP:0000736",
"original_object": null,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
+ "UBERON:0000465",
+ "NBO:0000313",
+ "NBO:0000308",
"UPHENO:0082875",
- "UPHENO:0001005",
- "HP:0012638",
- "BFO:0000004",
- "UBERON:0000061",
- "UBERON:0001016",
- "HP:0000001",
- "HP:0000118",
+ "BFO:0000002",
+ "UPHENO:0004523",
+ "UPHENO:0049587",
+ "GO:0008150",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "GO:0007610",
+ "UPHENO:0001002",
"BFO:0000020",
- "UPHENO:0002433",
+ "HP:0000736",
+ "BFO:0000003",
+ "BFO:0000002",
+ "UPHENO:0001001",
+ "UPHENO:0049622",
"UPHENO:0001003",
- "PATO:0000001",
"BFO:0000001",
- "BFO:0000040",
- "UBERON:0000467",
- "UBERON:0000468",
+ "NBO:0000607",
"UPHENO:0075696",
- "HP:0011442",
- "UPHENO:0001002",
- "UPHENO:0002332",
+ "UPHENO:0002433",
+ "HP:0012638",
+ "BFO:0000015",
+ "BFO:0000004",
+ "UBERON:0000061",
+ "UBERON:0000468",
+ "NBO:0000455",
+ "UPHENO:0049586",
"UPHENO:0002536",
- "UPHENO:0004523",
- "HP:0002312",
- "HP:0011443",
- "BFO:0000002",
- "UBERON:0000465",
- "UPHENO:0001001",
- "BFO:0000002",
+ "HP:0000708",
+ "UPHENO:0080585",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "UPHENO:0079826",
+ "PATO:0000001",
+ "HP:0000001",
+ "UPHENO:0001005",
"HP:0000707",
- "HP:0002311",
+ "HP:0011446",
"BFO:0000001",
- "UBERON:0001062",
- "UBERON:0010000"
+ "GO:0032501",
+ "UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0001016"
],
- "object_label": "Clumsiness (HPO)",
+ "object_label": "Short attention span (HPO)",
"object_closure_label": [
- "All (HPO)",
- "Abnormal central motor function (HPO)",
- "Phenotypic abnormality (HPO)",
- "Abnormality of the nervous system (HPO)",
- "entity",
- "quality",
- "independent continuant",
- "anatomical structure",
- "multicellular anatomical structure",
- "nervous system",
"abnormality of anatomical entity physiology",
- "continuant",
+ "abnormal anatomical entity",
+ "Abnormality of higher mental function (HPO)",
+ "quality",
+ "multicellular organismal process",
+ "abnormal anatomical entity",
"specifically dependent continuant",
- "abnormality of nervous system physiology",
"phenotype by ontology source",
"abnormal nervous system",
- "Clumsiness (HPO)",
- "Abnormal nervous system physiology (HPO)",
+ "occurrent",
"continuant",
"material anatomical entity",
- "phenotype",
+ "nervous system",
+ "All (HPO)",
"abnormal phenotype by ontology source",
- "Incoordination (HPO)",
- "Abnormality of coordination (HPO)",
+ "Short attention span (HPO)",
+ "behavior",
+ "abnormal behavior",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the nervous system (HPO)",
+ "abnormal behavior process",
"entity",
- "anatomical entity",
- "abnormal anatomical entity",
+ "entity",
+ "cognitive behavior",
+ "sensation behavior",
"Phenotypic abnormality",
- "abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
+ "abnormality of nervous system physiology",
+ "multicellular organism",
+ "phenotype",
+ "abnormal behavior process",
+ "Behavioral abnormality (HPO)",
+ "abnormal biological_process",
+ "process",
+ "independent continuant",
+ "behavior process",
+ "Abnormal nervous system physiology (HPO)",
+ "biological_process",
"material entity",
+ "anatomical entity",
+ "anatomical structure",
+ "abnormal response to stimulus",
+ "continuant",
+ "abnormality of anatomical entity physiology",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism"
+ "attention behavior"
],
"object_taxon": null,
"object_taxon_label": null,
@@ -2370,24 +2144,24 @@
"negated": null,
"pathway": null,
"evidence_count": 2,
- "has_evidence": ["ECO:0000269"],
+ "has_evidence": ["ECO:0000304"],
"has_evidence_links": [
{
- "id": "ECO:0000269",
- "url": "http://purl.obolibrary.org/obo/ECO_0000269"
+ "id": "ECO:0000304",
+ "url": "http://purl.obolibrary.org/obo/ECO_0000304"
}
],
- "grouping_key": "MONDO:0009675\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0002312",
+ "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0000736",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype"
},
- "publications": ["PMID:16607617"],
+ "publications": ["orphanet:589821"],
"publications_links": [
{
- "id": "PMID:16607617",
- "url": "http://identifiers.org/pubmed/16607617"
+ "id": "orphanet:589821",
+ "url": null
}
],
"qualifiers": [],
@@ -2403,11 +2177,11 @@
"frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
"frequency_qualifier_closure_label": [
- "All (HPO)",
+ "Frequency (HPO)",
"Frequent (HPO)",
- "Frequency (HPO)"
+ "All (HPO)"
],
"onset_qualifier_label": null,
"onset_qualifier_namespace": null,
@@ -2426,148 +2200,178 @@
"stage_qualifier_closure_label": []
},
{
- "id": "uuid:c9c8bff4-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df87-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0009675",
- "original_subject": "OMIM:253600",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "MONDO:0016971",
- "MONDO:0005336",
- "MONDO:0015152",
- "MONDO:0000429",
- "MONDO:0005071",
- "MONDO:0006025",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
- "MONDO:0009675",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
- "MONDO:0016152",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
- "BFO:0000002",
- "MONDO:0016106",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003847",
- "MONDO:0003939"
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001"
],
- "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
- "hereditary disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
"continuant",
- "autosomal recessive disease",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
"disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "disease",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "autosomal genetic disease",
+ "myotonic dystrophy",
"nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
- "autosomal recessive limb-girdle muscular dystrophy type 2A",
"skeletal muscle disorder",
- "qualitative or quantitative defects of calpain",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity"
+ "myotonic syndrome"
],
"subject_taxon": null,
"subject_taxon_label": null,
"predicate": "biolink:has_phenotype",
- "object": "HP:0032019",
+ "object": "HP:0001622",
"original_object": null,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "UPHENO:0001005",
+ "HP:0001197",
+ "UPHENO:0002536",
+ "GO:0008150",
+ "UBERON:0000465",
+ "GO:0007567",
+ "UPHENO:0049587",
+ "BFO:0000001",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "GO:0044706",
+ "GO:0000003",
+ "GO:0044703",
+ "BFO:0000003",
"BFO:0000002",
- "BFO:0000020",
- "UPHENO:0076692",
- "PATO:0000001",
- "BFO:0000004",
- "UBERON:0000061",
- "HP:0000001",
"UPHENO:0001001",
- "HP:0000118",
- "HP:0032019",
+ "UPHENO:0001002",
+ "BFO:0000020",
"UPHENO:0001003",
- "UPHENO:0076710",
- "BFO:0000001",
"BFO:0000001",
- "BFO:0000040",
- "UBERON:0000467",
+ "UPHENO:0001005",
+ "UPHENO:0049940",
+ "BFO:0000015",
+ "UBERON:0000061",
"UBERON:0000468",
- "UBERON:0011216",
- "HP:0003011",
- "UPHENO:0002536",
"BFO:0000002",
- "UBERON:0000465",
- "UBERON:0005090",
- "UBERON:0001630",
- "HP:0011805",
- "UPHENO:0001002",
- "UPHENO:0002816",
- "UPHENO:0081581",
- "HP:0033127",
- "UBERON:0001062",
- "UBERON:0010000",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015"
+ "UPHENO:0049440",
+ "BFO:0000004",
+ "UBERON:0000922",
+ "HP:0001622",
+ "HP:0000118",
+ "UPHENO:0049449",
+ "HP:0001787",
+ "PATO:0000001",
+ "UBERON:0000323",
+ "HP:0000001",
+ "UPHENO:0075949",
+ "GO:0032501",
+ "GO:0022414",
+ "UBERON:0010000"
],
- "object_label": "Muscle eosinophilia (HPO)",
+ "object_label": "Premature birth (HPO)",
"object_closure_label": [
- "All (HPO)",
- "Phenotypic abnormality (HPO)",
- "abnormal musculature",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "independent continuant",
- "anatomical structure",
- "multicellular anatomical structure",
- "phenotype",
- "Abnormal skeletal muscle morphology (HPO)",
"Phenotypic abnormality",
- "Muscle eosinophilia (HPO)",
- "phenotype by ontology source",
+ "specifically dependent continuant",
"quality",
+ "multicellular organismal process",
+ "reproductive process",
+ "abnormal phenotype by ontology source",
+ "premature biological_process",
+ "phenotype by ontology source",
+ "occurrent",
"continuant",
"material anatomical entity",
- "abnormal phenotype by ontology source",
+ "All (HPO)",
"continuant",
- "specifically dependent continuant",
- "abnormal muscle organ morphology",
+ "multi-multicellular organism process",
+ "reproduction",
+ "multi-organism reproductive process",
+ "embryo",
+ "Phenotypic abnormality (HPO)",
+ "abnormal late embryo",
+ "Abnormal delivery (HPO)",
"entity",
- "anatomical entity",
- "muscle structure",
- "organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "Abnormality of the musculature (HPO)",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
+ "biological_process",
+ "multicellular organism",
+ "phenotype",
+ "Premature birth (HPO)",
+ "abnormal biological_process",
"entity",
+ "process",
+ "parturition",
+ "Abnormality of prenatal development or birth (HPO)",
+ "abnormal reproductive process",
"material entity",
- "anatomical system",
- "multicellular organism",
- "organ system subdivision"
+ "anatomical entity",
+ "anatomical structure",
+ "premature parturition",
+ "abnormal anatomical entity",
+ "independent continuant",
+ "multicellular anatomical structure",
+ "late embryo"
],
"object_taxon": null,
"object_taxon_label": null,
@@ -2576,28 +2380,28 @@
"negated": null,
"pathway": null,
"evidence_count": 2,
- "has_evidence": ["ECO:0000269"],
+ "has_evidence": ["ECO:0000304"],
"has_evidence_links": [
{
- "id": "ECO:0000269",
- "url": "http://purl.obolibrary.org/obo/ECO_0000269"
+ "id": "ECO:0000304",
+ "url": "http://purl.obolibrary.org/obo/ECO_0000304"
}
],
- "grouping_key": "MONDO:0009675\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0032019",
+ "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0001622",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype"
},
- "publications": ["PMID:16607617"],
+ "publications": ["orphanet:589821"],
"publications_links": [
{
- "id": "PMID:16607617",
- "url": "http://identifiers.org/pubmed/16607617"
+ "id": "orphanet:589821",
+ "url": null
}
],
"qualifiers": [],
- "frequency_qualifier": "HP:0040280",
+ "frequency_qualifier": "HP:0040282",
"onset_qualifier": null,
"sex_qualifier": null,
"stage_qualifier": null,
@@ -2606,14 +2410,14 @@
"qualifiers_category": null,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
"frequency_qualifier_closure_label": [
- "All (HPO)",
- "Obligate (HPO)",
- "Frequency (HPO)"
+ "Frequency (HPO)",
+ "Frequent (HPO)",
+ "All (HPO)"
],
"onset_qualifier_label": null,
"onset_qualifier_namespace": null,
@@ -2632,206 +2436,200 @@
"stage_qualifier_closure_label": []
},
{
- "id": "uuid:c9c8bff5-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df88-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0009675",
- "original_subject": "OMIM:253600",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "MONDO:0016971",
- "MONDO:0005336",
- "MONDO:0015152",
- "MONDO:0000429",
- "MONDO:0005071",
- "MONDO:0006025",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
- "MONDO:0009675",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
- "MONDO:0016152",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
- "BFO:0000002",
- "MONDO:0016106",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003847",
- "MONDO:0003939"
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001"
],
- "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
- "hereditary disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
"continuant",
- "autosomal recessive disease",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
"disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "disease",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "autosomal genetic disease",
+ "myotonic dystrophy",
"nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
- "autosomal recessive limb-girdle muscular dystrophy type 2A",
"skeletal muscle disorder",
- "qualitative or quantitative defects of calpain",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity"
+ "myotonic syndrome"
],
"subject_taxon": null,
"subject_taxon_label": null,
"predicate": "biolink:has_phenotype",
- "object": "HP:0007340",
+ "object": "HP:0001883",
"original_object": null,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "UPHENO:0082875",
- "UPHENO:0002320",
- "UPHENO:0001005",
- "HP:0009127",
+ "PR:000050567",
+ "UBERON:0000465",
+ "RO:0002577",
+ "BFO:0000001",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UBERON:0000154",
+ "UPHENO:0001002",
"BFO:0000020",
- "UPHENO:0076692",
+ "UPHENO:0081575",
+ "BFO:0000002",
+ "UBERON:0002101",
+ "UBERON:0004709",
+ "UPHENO:0001001",
+ "UPHENO:0001003",
+ "UPHENO:0002536",
"BFO:0000001",
+ "UBERON:0000061",
+ "UBERON:0008784",
+ "UBERON:0002470",
+ "UPHENO:0001005",
+ "UPHENO:0081581",
+ "UPHENO:0076692",
+ "UPHENO:0003070",
+ "UPHENO:0002830",
"BFO:0000004",
"UBERON:0004708",
- "UBERON:0000061",
- "UBERON:0000026",
- "UBERON:0014892",
- "HP:0000001",
- "UPHENO:0001001",
- "UPHENO:0001002",
- "HP:0000118",
- "UPHENO:0076710",
- "PATO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0001062",
- "UBERON:0000467",
+ "UBERON:0000475",
"UBERON:0000468",
- "UBERON:0011216",
"UBERON:0010709",
- "UBERON:0010890",
- "UPHENO:0075696",
- "UPHENO:0080575",
- "HP:0001324",
- "HP:0003690",
- "HP:0003011",
- "UPHENO:0002332",
- "UPHENO:0001003",
- "UPHENO:0002536",
- "HP:0040064",
- "HP:0011804",
+ "HP:0001883",
"BFO:0000002",
- "PR:000050567",
- "UBERON:0002101",
- "UBERON:0005090",
- "UBERON:0018254",
+ "HP:0001760",
+ "HP:0040064",
+ "PATO:0000001",
+ "UBERON:0002103",
"UBERON:0010707",
- "UBERON:0001630",
- "UBERON:0007271",
- "UBERON:0014792",
- "HP:0007340",
- "HP:0011805",
- "BFO:0000002",
- "UPHENO:0080555",
- "UPHENO:0002816",
- "UPHENO:0080556",
- "UPHENO:0081581",
- "HP:0033127",
- "UPHENO:0002647",
- "UPHENO:0002830",
- "UBERON:0000465",
- "RO:0002577",
+ "UBERON:0000026",
+ "UBERON:0010758",
+ "UBERON:0006058",
+ "UBERON:0002387",
+ "HP:0002814",
+ "HP:0005656",
+ "HP:0000118",
"UBERON:0015212",
+ "UBERON:0010538",
+ "HP:0000001",
"UBERON:0010000",
- "UBERON:0000475",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "UBERON:0004480"
+ "UBERON:0000978",
+ "UBERON:0002529"
],
- "object_label": "Lower limb muscle weakness (HPO)",
+ "object_label": "Talipes (HPO)",
"object_closure_label": [
+ "abnormal phenotype by ontology source",
+ "specifically dependent continuant",
+ "phenotype by ontology source",
+ "abnormal anatomical entity",
+ "continuant",
+ "protein-containing material entity",
+ "material anatomical entity",
+ "system",
+ "multi-limb segment region",
"All (HPO)",
- "abnormality of muscle organ physiology",
- "Phenotypic abnormality",
+ "continuant",
+ "appendage",
+ "subdivision of organism along appendicular axis",
+ "Abnormality of the lower limb (HPO)",
"Phenotypic abnormality (HPO)",
- "decreased anatomical entity strength",
- "abnormal musculature",
- "decreased muscle organ strength",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "abnormal musculature of limb",
+ "entity",
+ "lateral structure",
+ "leg",
+ "limb segment",
+ "Phenotypic abnormality",
+ "abnormal pes morphology",
+ "abnormal anatomical entity morphology",
+ "abnormal leg",
"quality",
- "independent continuant",
- "material anatomical entity",
- "system",
- "paired limb/fin",
"anatomical structure",
- "lateral structure",
- "multicellular anatomical structure",
+ "organism subdivision",
+ "multicellular organism",
"pelvic complex",
- "appendage musculature",
- "musculature of pelvic complex",
- "abnormality of anatomical entity physiology",
+ "lower limb segment",
+ "autopod region",
"phenotype",
- "Abnormal skeletal muscle morphology (HPO)",
- "continuant",
- "Abnormality of limbs (HPO)",
- "continuant",
- "protein-containing material entity",
- "appendage girdle complex",
- "pelvic complex muscle",
- "Lower limb muscle weakness (HPO)",
- "abnormal phenotype by ontology source",
- "Abnormality of the musculature of the limbs (HPO)",
- "specifically dependent continuant",
- "abnormal muscle organ morphology",
- "Abnormal muscle physiology (HPO)",
- "entity",
- "muscle structure",
- "skeletal musculature",
- "organism subdivision",
- "organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "musculature of limb",
- "abnormal anatomical entity",
- "decreased pelvic complex muscle strength",
- "Muscle weakness (HPO)",
- "Limb muscle weakness (HPO)",
- "Abnormality of the musculature (HPO)",
- "abnormality of anatomical entity physiology",
- "phenotype by ontology source",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
+ "Positional foot deformity (HPO)",
+ "Abnormal foot morphology (HPO)",
"entity",
+ "independent continuant",
+ "posterior region of body",
+ "abnormal multicellular organism morphology",
"abnormal limb",
"material entity",
"anatomical entity",
+ "paired limb/fin",
"limb",
- "anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "appendage",
- "skeletal muscle organ"
+ "pelvic appendage",
+ "pes",
+ "Talipes (HPO)",
+ "Abnormality of limbs (HPO)",
+ "multicellular anatomical structure",
+ "hindlimb",
+ "appendage girdle complex",
+ "paired limb/fin segment"
],
"object_taxon": null,
"object_taxon_label": null,
@@ -2840,24 +2638,24 @@
"negated": null,
"pathway": null,
"evidence_count": 2,
- "has_evidence": ["ECO:0000269"],
+ "has_evidence": ["ECO:0000304"],
"has_evidence_links": [
{
- "id": "ECO:0000269",
- "url": "http://purl.obolibrary.org/obo/ECO_0000269"
+ "id": "ECO:0000304",
+ "url": "http://purl.obolibrary.org/obo/ECO_0000304"
}
],
- "grouping_key": "MONDO:0009675\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0007340",
+ "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0001883",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype"
},
- "publications": ["PMID:16607617"],
+ "publications": ["orphanet:589821"],
"publications_links": [
{
- "id": "PMID:16607617",
- "url": "http://identifiers.org/pubmed/16607617"
+ "id": "orphanet:589821",
+ "url": null
}
],
"qualifiers": [],
@@ -2873,11 +2671,11 @@
"frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0040282", "HP:0000001", "HP:0040279"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
"frequency_qualifier_closure_label": [
- "All (HPO)",
+ "Frequency (HPO)",
"Frequent (HPO)",
- "Frequency (HPO)"
+ "All (HPO)"
],
"onset_qualifier_label": null,
"onset_qualifier_namespace": null,
@@ -2896,156 +2694,166 @@
"stage_qualifier_closure_label": []
},
{
- "id": "uuid:c9d8bdf9-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df8e-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0009676",
- "original_subject": "OMIM:253601",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "MONDO:0016971",
- "BFO:0000002",
- "BFO:0000020",
- "MONDO:0005336",
- "MONDO:0009676",
- "MONDO:0015152",
- "MONDO:0000429",
- "MONDO:0005071",
- "MONDO:0006025",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
- "MONDO:0016145",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
+ "BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
- "MONDO:0016106",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939"
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001"
],
- "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2B",
- "subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
+ "subject_closure_label": [
+ "eyelids malposition disorder",
+ "disease",
+ "hypertrophic cardiomyopathy",
"disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "qualitative or quantitative defects of dysferlin",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "autosomal recessive disease",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "autosomal recessive limb-girdle muscular dystrophy type 2B",
- "disease",
"continuant",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
"specifically dependent continuant",
"myopathy",
- "hereditary disease",
- "autosomal genetic disease",
+ "myotonic dystrophy",
"nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
"skeletal muscle disorder",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity"
+ "myotonic syndrome"
],
"subject_taxon": null,
"subject_taxon_label": null,
"predicate": "biolink:has_phenotype",
- "object": "HP:0003701",
+ "object": "HP:0011098",
"original_object": null,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
+ "UBERON:0000465",
"UPHENO:0082875",
- "UPHENO:0002320",
+ "HP:0011442",
+ "HP:0002186",
+ "UPHENO:0004523",
+ "BFO:0000001",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UPHENO:0001002",
"BFO:0000002",
- "BFO:0000004",
- "UBERON:0000061",
- "HP:0000001",
"UPHENO:0001001",
- "UPHENO:0001002",
- "HP:0000118",
"BFO:0000020",
"UPHENO:0001003",
+ "UPHENO:0002536",
"BFO:0000001",
- "PATO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0001062",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
+ "UBERON:0000061",
"UPHENO:0075696",
- "HP:0001324",
- "HP:0003011",
- "UPHENO:0002332",
- "UPHENO:0002536",
- "HP:0011804",
- "BFO:0000002",
- "UBERON:0000465",
- "UBERON:0005090",
- "UBERON:0001630",
"UPHENO:0001005",
- "HP:0003701",
- "UPHENO:0080555",
- "UPHENO:0002816",
- "UPHENO:0080556",
- "HP:0033127",
+ "UPHENO:0002433",
+ "HP:0012638",
+ "BFO:0000004",
+ "UBERON:0000468",
+ "BFO:0000002",
+ "HP:0011098",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "PATO:0000001",
+ "HP:0000001",
+ "HP:0000707",
+ "HP:0011446",
"UBERON:0010000",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015"
+ "UBERON:0000467",
+ "UBERON:0001016"
],
- "object_label": "Proximal muscle weakness (HPO)",
+ "object_label": "Speech apraxia (HPO)",
"object_closure_label": [
- "All (HPO)",
- "abnormality of muscle organ physiology",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "decreased anatomical entity strength",
- "abnormal musculature",
- "decreased muscle organ strength",
- "Abnormality of the musculoskeletal system (HPO)",
- "quality",
- "independent continuant",
- "anatomical structure",
- "multicellular anatomical structure",
"abnormality of anatomical entity physiology",
- "phenotype",
- "abnormal phenotype by ontology source",
- "Proximal muscle weakness (HPO)",
"specifically dependent continuant",
+ "Abnormality of higher mental function (HPO)",
+ "quality",
+ "abnormal anatomical entity",
+ "abnormal phenotype by ontology source",
"phenotype by ontology source",
+ "abnormal anatomical entity",
+ "abnormal nervous system",
"continuant",
"material anatomical entity",
+ "nervous system",
+ "All (HPO)",
"continuant",
- "Abnormal muscle physiology (HPO)",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the nervous system (HPO)",
"entity",
- "muscle structure",
- "organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "abnormal anatomical entity",
- "Muscle weakness (HPO)",
- "Abnormality of the musculature (HPO)",
- "abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
+ "Phenotypic abnormality",
+ "abnormality of nervous system physiology",
+ "anatomical structure",
+ "multicellular organism",
+ "phenotype",
+ "Speech apraxia (HPO)",
"entity",
+ "independent continuant",
+ "Abnormal nervous system physiology (HPO)",
"material entity",
"anatomical entity",
- "anatomical system",
- "multicellular organism",
- "organ system subdivision"
+ "Abnormal central motor function (HPO)",
+ "Apraxia (HPO)",
+ "abnormality of anatomical entity physiology",
+ "multicellular anatomical structure",
+ "anatomical system"
],
"object_taxon": null,
"object_taxon_label": null,
@@ -3053,33 +2861,29 @@
"aggregator_knowledge_source": ["infores:monarchinitiative"],
"negated": null,
"pathway": null,
- "evidence_count": 3,
- "has_evidence": ["ECO:0000269"],
+ "evidence_count": 2,
+ "has_evidence": ["ECO:0000304"],
"has_evidence_links": [
{
- "id": "ECO:0000269",
- "url": "http://purl.obolibrary.org/obo/ECO_0000269"
+ "id": "ECO:0000304",
+ "url": "http://purl.obolibrary.org/obo/ECO_0000304"
}
],
- "grouping_key": "MONDO:0009676\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0003701",
+ "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0011098",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype"
},
- "publications": ["PMID:9731527", "PMID:9009996"],
+ "publications": ["orphanet:589821"],
"publications_links": [
{
- "id": "PMID:9731527",
- "url": "http://identifiers.org/pubmed/9731527"
- },
- {
- "id": "PMID:9009996",
- "url": "http://identifiers.org/pubmed/9009996"
+ "id": "orphanet:589821",
+ "url": null
}
],
"qualifiers": [],
- "frequency_qualifier": "HP:0040280",
+ "frequency_qualifier": "HP:0040282",
"onset_qualifier": null,
"sex_qualifier": null,
"stage_qualifier": null,
@@ -3088,14 +2892,14 @@
"qualifiers_category": null,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": "Obligate (HPO)",
+ "frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
"frequency_qualifier_closure_label": [
- "All (HPO)",
- "Obligate (HPO)",
- "Frequency (HPO)"
+ "Frequency (HPO)",
+ "Frequent (HPO)",
+ "All (HPO)"
],
"onset_qualifier_label": null,
"onset_qualifier_namespace": null,
@@ -3114,152 +2918,170 @@
"stage_qualifier_closure_label": []
},
{
- "id": "uuid:c9c8bf35-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df90-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0008050",
- "original_subject": "OMIM:160500",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320"
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001"
],
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity"
+ "myotonic syndrome"
],
"subject_taxon": null,
"subject_taxon_label": null,
"predicate": "biolink:has_phenotype",
- "object": "HP:0003701",
+ "object": "HP:0011710",
"original_object": null,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
+ "UPHENO:0002536",
+ "PR:000050567",
+ "UBERON:0000465",
"UPHENO:0082875",
- "UPHENO:0002320",
+ "UPHENO:0080362",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "HP:0030956",
+ "HP:0001626",
+ "HP:0031546",
"BFO:0000002",
- "BFO:0000004",
- "UBERON:0000061",
- "HP:0000001",
"UPHENO:0001001",
"UPHENO:0001002",
- "HP:0000118",
- "BFO:0000020",
"UPHENO:0001003",
- "BFO:0000001",
- "PATO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0001062",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
"UPHENO:0075696",
- "HP:0001324",
- "HP:0003011",
- "UPHENO:0002332",
- "UPHENO:0002536",
- "HP:0011804",
- "BFO:0000002",
- "UBERON:0000465",
- "UBERON:0005090",
- "UBERON:0001630",
"UPHENO:0001005",
- "HP:0003701",
- "UPHENO:0080555",
- "UPHENO:0002816",
- "UPHENO:0080556",
- "HP:0033127",
+ "BFO:0000020",
+ "HP:0011710",
+ "UPHENO:0002406",
+ "BFO:0000004",
+ "UBERON:0004535",
+ "UBERON:0000061",
+ "UBERON:0000468",
+ "HP:0012722",
+ "HP:0000118",
+ "BFO:0000002",
+ "UPHENO:0002332",
+ "PATO:0000001",
+ "HP:0000001",
+ "HP:0011025",
+ "BFO:0000001",
+ "BFO:0000001",
"UBERON:0010000",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015"
+ "UBERON:0000467",
+ "UBERON:0001009"
],
- "object_label": "Proximal muscle weakness (HPO)",
+ "object_label": "Bundle branch block (HPO)",
"object_closure_label": [
- "All (HPO)",
- "abnormality of muscle organ physiology",
+ "abnormality of anatomical entity physiology",
"Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "decreased anatomical entity strength",
- "abnormal musculature",
- "decreased muscle organ strength",
- "Abnormality of the musculoskeletal system (HPO)",
+ "Abnormal cardiovascular system physiology (HPO)",
"quality",
- "independent continuant",
- "anatomical structure",
- "multicellular anatomical structure",
- "abnormality of anatomical entity physiology",
- "phenotype",
+ "entity",
+ "abnormal anatomical entity",
"abnormal phenotype by ontology source",
- "Proximal muscle weakness (HPO)",
- "specifically dependent continuant",
"phenotype by ontology source",
"continuant",
+ "protein-containing material entity",
"material anatomical entity",
+ "circulatory system",
+ "All (HPO)",
+ "Cardiac conduction abnormality (HPO)",
+ "Phenotypic abnormality (HPO)",
"continuant",
- "Abnormal muscle physiology (HPO)",
- "entity",
- "muscle structure",
- "organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "abnormal anatomical entity",
- "Muscle weakness (HPO)",
- "Abnormality of the musculature (HPO)",
- "abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
"entity",
+ "Abnormality of cardiovascular system electrophysiology (HPO)",
+ "Abnormality of the cardiovascular system (HPO)",
+ "specifically dependent continuant",
+ "multicellular organism",
+ "phenotype",
+ "independent continuant",
+ "Bundle branch block (HPO)",
+ "abnormality of cardiovascular system physiology",
"material entity",
"anatomical entity",
- "anatomical system",
- "multicellular organism",
- "organ system subdivision"
+ "cardiovascular system",
+ "anatomical structure",
+ "abnormal cardiovascular system",
+ "abnormality of anatomical entity physiology",
+ "abnormal anatomical entity",
+ "Heart block (HPO)",
+ "multicellular anatomical structure",
+ "anatomical system"
],
"object_taxon": null,
"object_taxon_label": null,
@@ -3275,21 +3097,21 @@
"url": "http://purl.obolibrary.org/obo/ECO_0000304"
}
],
- "grouping_key": "MONDO:0008050\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0003701",
+ "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0011710",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype"
},
- "publications": ["OMIM:160500"],
+ "publications": ["orphanet:589821"],
"publications_links": [
{
- "id": "OMIM:160500",
- "url": "http://identifiers.org/mim/160500"
+ "id": "orphanet:589821",
+ "url": null
}
],
"qualifiers": [],
- "frequency_qualifier": "HP:0040283",
+ "frequency_qualifier": "HP:0040282",
"onset_qualifier": null,
"sex_qualifier": null,
"stage_qualifier": null,
@@ -3298,14 +3120,14 @@
"qualifiers_category": null,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": "Occasional (HPO)",
+ "frequency_qualifier_label": "Frequent (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040283", "HP:0040279"],
+ "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"],
"frequency_qualifier_closure_label": [
- "All (HPO)",
- "Occasional (HPO)",
- "Frequency (HPO)"
+ "Frequency (HPO)",
+ "Frequent (HPO)",
+ "All (HPO)"
],
"onset_qualifier_label": null,
"onset_qualifier_namespace": null,
@@ -3324,212 +3146,170 @@
"stage_qualifier_closure_label": []
},
{
- "id": "uuid:c9c8bf37-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02dfa2-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0008050",
- "original_subject": "OMIM:160500",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320"
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001"
],
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity"
+ "myotonic syndrome"
],
"subject_taxon": null,
"subject_taxon_label": null,
"predicate": "biolink:has_phenotype",
- "object": "HP:0001644",
+ "object": "HP:0001513",
"original_object": null,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "UPHENO:0082875",
- "HP:0001637",
- "UPHENO:0001005",
- "BFO:0000020",
- "UPHENO:0077800",
- "UPHENO:0066927",
- "UPHENO:0076692",
- "PATO:0000001",
- "BFO:0000004",
- "UBERON:0004535",
- "UBERON:0011676",
- "UBERON:0013701",
- "UBERON:0002349",
- "UBERON:0000915",
- "UBERON:0002100",
- "UBERON:0005181",
- "UBERON:0002075",
- "UBERON:0015228",
- "HP:0000001",
+ "UPHENO:0049587",
+ "GO:0008150",
+ "UBERON:0000465",
+ "HP:0001513",
+ "BFO:0000001",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UBERON:0000468",
+ "UPHENO:0008273",
+ "UPHENO:0049874",
+ "BFO:0000003",
+ "BFO:0000002",
"UPHENO:0001001",
- "HP:0001644",
- "HP:0030680",
"UPHENO:0001002",
- "HP:0000118",
- "HP:0001627",
- "UPHENO:0076776",
"UPHENO:0001003",
- "UPHENO:0024906",
- "BFO:0000001",
"BFO:0000001",
- "BFO:0000040",
- "UBERON:0010000",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
- "UBERON:0000064",
+ "UBERON:0000061",
"UPHENO:0075696",
- "HP:0001626",
- "UPHENO:0080362",
- "HP:0001638",
+ "UPHENO:0001005",
+ "BFO:0000020",
+ "BFO:0000015",
+ "BFO:0000004",
+ "HP:0001507",
"BFO:0000002",
- "UPHENO:0002332",
"UPHENO:0002536",
- "UPHENO:0076810",
- "BFO:0000002",
- "PR:000050567",
- "UBERON:0004120",
- "UBERON:0000948",
- "UBERON:0001009",
- "UBERON:0005983",
- "UBERON:0009569",
- "UBERON:0013702",
- "UBERON:0005177",
- "UBERON:0003103",
- "UBERON:0018260",
- "UBERON:0015410",
- "UPHENO:0076781",
- "UPHENO:0081581",
- "UBERON:0001062",
- "UBERON:0000465",
- "UBERON:0000061",
- "UBERON:0010314",
- "UBERON:0000475",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0000060",
- "UBERON:0004923",
- "UBERON:0005178",
- "UBERON:0007100"
+ "HP:0000118",
+ "UPHENO:0010795",
+ "HP:0004323",
+ "UPHENO:0010763",
+ "PATO:0000001",
+ "HP:0000001",
+ "HP:0004324",
+ "UPHENO:0008312",
+ "GO:0040007",
+ "UBERON:0010000"
],
- "object_label": "Dilated cardiomyopathy (HPO)",
+ "object_label": "Obesity (HPO)",
"object_closure_label": [
- "All (HPO)",
- "abnormal cardiovascular system",
- "Cardiomyopathy (HPO)",
"Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "abnormal myocardium morphology",
- "abnormal multicellular organism morphology",
- "independent continuant",
- "material anatomical entity",
- "cardiovascular system",
- "structure with developmental contribution from neural crest",
- "layer of muscle tissue",
- "abnormality of anatomical entity physiology",
- "Abnormal myocardium morphology (HPO)",
- "phenotype",
- "Abnormality of the cardiovascular system (HPO)",
- "Abnormal heart morphology (HPO)",
- "abnormal cardiovascular system morphology",
- "phenotype by ontology source",
- "abnormally decreased functionality of the anatomical entity",
- "abnormal heart morphology",
+ "abnormal anatomical entity",
+ "increased multicellular organism mass",
"quality",
- "continuant",
- "protein-containing material entity",
- "heart",
- "subdivision of trunk",
- "body proper",
- "trunk region element",
- "compound organ",
- "heart plus pericardium",
+ "growth",
+ "abnormal anatomical entity",
"abnormal phenotype by ontology source",
- "specifically dependent continuant",
- "abnormally decreased functionality of the myocardium",
- "anatomical entity dysfunction in independent continuant",
+ "phenotype by ontology source",
+ "Obesity (HPO)",
+ "occurrent",
+ "continuant",
+ "material anatomical entity",
+ "All (HPO)",
+ "continuant",
+ "abnormal growth",
+ "multicellular organism",
+ "Phenotypic abnormality (HPO)",
+ "abnormality of anatomical entity mass",
"entity",
- "anatomical entity",
+ "biological_process",
+ "increased anatomical entity mass",
+ "specifically dependent continuant",
"anatomical structure",
- "mesoderm-derived structure",
- "organism subdivision",
- "organ",
- "circulatory system",
- "heart layer",
- "musculature of body",
- "anatomical wall",
- "organ component layer",
- "thoracic cavity element",
- "primary circulatory organ",
- "abnormal anatomical entity",
- "Dilated cardiomyopathy (HPO)",
- "Abnormality of cardiovascular system morphology (HPO)",
- "continuant",
- "abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
+ "phenotype",
+ "Increased body weight (HPO)",
"entity",
+ "process",
+ "independent continuant",
+ "abnormal biological_process",
"material entity",
- "multicellular anatomical structure",
- "anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "organ part",
- "subdivision of organism along main body axis",
- "main body axis",
- "myocardium",
- "thoracic segment of trunk",
- "trunk",
- "thoracic segment organ",
- "viscus",
- "circulatory organ"
+ "anatomical entity",
+ "Growth abnormality (HPO)",
+ "abnormality of multicellular organism mass",
+ "Abnormality of body weight (HPO)",
+ "multicellular anatomical structure"
],
"object_taxon": null,
"object_taxon_label": null,
@@ -3545,21 +3325,21 @@
"url": "http://purl.obolibrary.org/obo/ECO_0000304"
}
],
- "grouping_key": "MONDO:0008050\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0001644",
+ "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0001513",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype"
},
- "publications": ["OMIM:160500"],
+ "publications": ["orphanet:589821"],
"publications_links": [
{
- "id": "OMIM:160500",
- "url": "http://identifiers.org/mim/160500"
+ "id": "orphanet:589821",
+ "url": null
}
],
"qualifiers": [],
- "frequency_qualifier": "HP:0040283",
+ "frequency_qualifier": "HP:0040284",
"onset_qualifier": null,
"sex_qualifier": null,
"stage_qualifier": null,
@@ -3568,14 +3348,14 @@
"qualifiers_category": null,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": "Occasional (HPO)",
+ "frequency_qualifier_label": "Very rare (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040283", "HP:0040279"],
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0000001", "HP:0040284"],
"frequency_qualifier_closure_label": [
- "All (HPO)",
- "Occasional (HPO)",
- "Frequency (HPO)"
+ "Very rare (HPO)",
+ "Frequency (HPO)",
+ "All (HPO)"
],
"onset_qualifier_label": null,
"onset_qualifier_namespace": null,
@@ -3594,292 +3374,186 @@
"stage_qualifier_closure_label": []
},
{
- "id": "uuid:c9c8bff0-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df92-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0009675",
- "original_subject": "OMIM:253600",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "MONDO:0016971",
- "MONDO:0005336",
- "MONDO:0015152",
- "MONDO:0000429",
- "MONDO:0005071",
- "MONDO:0006025",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
- "MONDO:0009675",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
- "MONDO:0016152",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
- "BFO:0000002",
- "MONDO:0016106",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003847",
- "MONDO:0003939"
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001"
],
- "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2A",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
- "hereditary disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
"continuant",
- "autosomal recessive disease",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
"disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "disease",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "autosomal genetic disease",
+ "myotonic dystrophy",
"nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
- "autosomal recessive limb-girdle muscular dystrophy type 2A",
"skeletal muscle disorder",
- "qualitative or quantitative defects of calpain",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity"
+ "myotonic syndrome"
],
- "subject_taxon": null,
- "subject_taxon_label": null,
- "predicate": "biolink:has_phenotype",
- "object": "HP:0010628",
- "original_object": null,
- "object_namespace": "HP",
- "object_category": "biolink:PhenotypicFeature",
- "object_closure": [
- "UPHENO:0082875",
- "UPHENO:0076772",
- "UPHENO:0002320",
- "UPHENO:0005116",
- "HP:0031910",
- "HP:0011799",
- "HP:0410008",
- "UPHENO:0076692",
- "BFO:0000001",
- "PATO:0000001",
- "HP:0012638",
- "BFO:0000004",
- "UBERON:0001016",
- "UBERON:0001021",
- "UBERON:0000153",
- "UBERON:0011676",
- "UBERON:0013701",
- "UBERON:0014892",
- "UBERON:0015789",
- "UBERON:0011779",
- "UBERON:0000033",
- "HP:0000001",
- "HP:0000152",
- "UPHENO:0002764",
- "UPHENO:0001002",
- "HP:0000118",
- "BFO:0000020",
- "UPHENO:0002433",
- "HP:0000234",
- "HP:0000271",
- "HP:0010827",
- "UPHENO:0001003",
- "HP:0012639",
- "UPHENO:0076710",
- "UPHENO:0002908",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
- "UBERON:0001785",
- "UBERON:0010959",
- "UBERON:0001577",
- "UPHENO:0075696",
- "HP:0045010",
- "UPHENO:0002844",
- "HP:0001291",
- "HP:0001324",
- "HP:0030319",
- "HP:0000759",
- "UPHENO:0081700",
- "HP:0003011",
- "UPHENO:0002332",
- "UPHENO:0078730",
+ "subject_taxon": null,
+ "subject_taxon_label": null,
+ "predicate": "biolink:has_phenotype",
+ "object": "HP:0000729",
+ "original_object": null,
+ "object_namespace": "HP",
+ "object_category": "biolink:PhenotypicFeature",
+ "object_closure": [
"UPHENO:0002536",
- "UPHENO:0081709",
- "HP:0000301",
+ "BFO:0000001",
+ "GO:0008150",
+ "UBERON:0000465",
+ "NBO:0000313",
+ "UPHENO:0082875",
"UPHENO:0004523",
- "UPHENO:0004508",
- "HP:0011804",
+ "UPHENO:0049587",
+ "BFO:0000040",
+ "GO:0007610",
+ "UBERON:0000468",
+ "BFO:0000020",
+ "BFO:0000003",
"BFO:0000002",
- "UBERON:0000465",
- "UBERON:0005090",
- "UBERON:0018254",
- "UBERON:0004120",
- "UBERON:0034713",
- "UBERON:0001647",
- "UBERON:0000122",
- "UBERON:0001630",
- "UBERON:0001033",
- "UBERON:0002376",
- "UBERON:0007811",
- "UBERON:0001444",
- "UBERON:0013702",
- "UBERON:0001456",
- "UBERON:0008229",
- "UBERON:0013700",
"UPHENO:0001001",
- "UPHENO:0002910",
- "HP:0010628",
+ "UPHENO:0049622",
+ "UPHENO:0001002",
+ "UPHENO:0001003",
+ "BFO:0000001",
+ "UBERON:0001062",
+ "UBERON:0000061",
+ "UPHENO:0075696",
"UPHENO:0001005",
- "HP:0011805",
+ "UPHENO:0002433",
+ "HP:0012638",
+ "BFO:0000015",
+ "UPHENO:0049586",
+ "HP:0000729",
"BFO:0000002",
- "UPHENO:0076722",
- "UPHENO:0080555",
- "UPHENO:0003587",
- "UPHENO:0002816",
- "UPHENO:0080556",
+ "HP:0000708",
+ "BFO:0000004",
+ "UPHENO:0080585",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "UPHENO:0079826",
+ "PATO:0000001",
+ "HP:0000001",
"HP:0000707",
- "HP:0006824",
- "UPHENO:0081581",
- "HP:0033127",
- "UPHENO:0076702",
- "UBERON:0001062",
- "RO:0002577",
- "UBERON:0000061",
- "UBERON:0015212",
- "UBERON:0010314",
- "UBERON:0005162",
+ "HP:0011446",
+ "GO:0032501",
"UBERON:0010000",
- "UBERON:0000475",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "UBERON:0000010",
- "UBERON:0004461",
- "UBERON:0004473"
+ "UBERON:0000467",
+ "UBERON:0001016"
],
- "object_label": "Facial palsy (HPO)",
+ "object_label": "Autistic behavior (HPO)",
"object_closure_label": [
- "All (HPO)",
- "abnormality of muscle organ physiology",
- "abnormal peripheral nervous system",
- "Abnormal cranial nerve physiology (HPO)",
- "Abnormality of facial soft tissue (HPO)",
- "abnormal head",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "abnormal peripheral nervous system morphology",
- "decreased anatomical entity strength",
- "abnormal facial nerve",
- "abnormal musculature",
- "decreased muscle organ strength",
- "Abnormality of the nervous system (HPO)",
- "Cranial nerve paralysis (HPO)",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "Abnormal nervous system morphology (HPO)",
- "abnormal facial muscle",
- "independent continuant",
- "system",
- "lateral structure",
- "structure with developmental contribution from neural crest",
- "multi cell part structure",
- "multicellular anatomical structure",
- "nervous system",
- "cranial nerve",
- "face",
- "craniocervical region musculature",
- "axial musculature",
"abnormality of anatomical entity physiology",
- "abnormal cranial nerve morphology",
- "Abnormality of peripheral nerves (HPO)",
- "Facial palsy (HPO)",
+ "Phenotypic abnormality",
+ "Abnormality of higher mental function (HPO)",
+ "quality",
+ "multicellular organismal process",
+ "abnormal anatomical entity",
"abnormal phenotype by ontology source",
- "Abnormal skeletal muscle morphology (HPO)",
- "continuant",
"specifically dependent continuant",
- "abnormality of nervous system physiology",
- "Abnormality of the head (HPO)",
- "Abnormality of the face (HPO)",
- "Abnormality of the seventh cranial nerve (HPO)",
"phenotype by ontology source",
- "Abnormality of the peripheral nervous system (HPO)",
- "paralysed cranial nerve",
- "Abnormality of facial musculature (HPO)",
"abnormal nervous system",
- "abnormal nerve",
- "quality",
- "Abnormal nervous system physiology (HPO)",
+ "occurrent",
"continuant",
"material anatomical entity",
- "cranial neuron projection bundle",
- "facial nerve",
- "neuron projection bundle",
- "craniocervical region",
- "subdivision of head",
- "body proper",
- "craniocervical muscle",
- "facial muscle",
- "phenotype",
- "abnormal face",
- "abnormal muscle organ morphology",
- "Abnormal muscle physiology (HPO)",
+ "nervous system",
+ "All (HPO)",
+ "continuant",
+ "behavior",
+ "multicellular organism",
+ "abnormal behavior",
+ "Autistic behavior (HPO)",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the nervous system (HPO)",
+ "abnormal behavior process",
"entity",
+ "biological_process",
+ "abnormality of nervous system physiology",
"anatomical entity",
"anatomical structure",
- "muscle structure",
- "skeletal musculature",
- "mesoderm-derived structure",
- "organism subdivision",
- "organ",
- "muscle organ",
- "gustatory system",
- "cranial muscle",
- "musculature of body",
- "musculature",
- "peripheral nervous system",
- "skeletal musculature of head",
- "musculature of face",
- "abnormal anatomical entity",
- "Abnormality of head or neck (HPO)",
- "abnormal craniocervical region",
- "Abnormal cranial nerve morphology (HPO)",
- "Muscle weakness (HPO)",
- "Weakness of facial musculature (HPO)",
- "Abnormal peripheral nervous system morphology (HPO)",
- "paralysed anatomical entity",
- "Abnormality of the musculature (HPO)",
- "abnormality of anatomical entity physiology",
- "abnormality of cranial nerve physiology",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
+ "phenotype",
+ "abnormal behavior process",
+ "Behavioral abnormality (HPO)",
+ "abnormal biological_process",
+ "process",
+ "behavior process",
"entity",
- "abnormal nervous system morphology",
+ "Abnormal nervous system physiology (HPO)",
"material entity",
- "anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "nerve",
- "anterior region of body",
- "subdivision of organism along main body axis",
- "main body axis",
- "skeletal muscle organ",
- "cranial or facial muscle",
- "nerve of head region",
- "head"
+ "abnormal response to stimulus",
+ "abnormality of anatomical entity physiology",
+ "abnormal anatomical entity",
+ "independent continuant",
+ "multicellular anatomical structure",
+ "anatomical system"
],
"object_taxon": null,
"object_taxon_label": null,
@@ -3895,17 +3569,17 @@
"url": "http://purl.obolibrary.org/obo/ECO_0000304"
}
],
- "grouping_key": "MONDO:0009675\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0010628",
+ "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0000729",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype"
},
- "publications": ["OMIM:253600"],
+ "publications": ["orphanet:589821"],
"publications_links": [
{
- "id": "OMIM:253600",
- "url": "http://identifiers.org/mim/253600"
+ "id": "orphanet:589821",
+ "url": null
}
],
"qualifiers": [],
@@ -3921,11 +3595,11 @@
"frequency_qualifier_label": "Occasional (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040283", "HP:0040279"],
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
"frequency_qualifier_closure_label": [
+ "Frequency (HPO)",
"All (HPO)",
- "Occasional (HPO)",
- "Frequency (HPO)"
+ "Occasional (HPO)"
],
"onset_qualifier_label": null,
"onset_qualifier_namespace": null,
@@ -3944,196 +3618,194 @@
"stage_qualifier_closure_label": []
},
{
- "id": "uuid:c9d8bdf7-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df94-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0009676",
- "original_subject": "OMIM:253601",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "MONDO:0016971",
- "BFO:0000002",
- "BFO:0000020",
- "MONDO:0005336",
- "MONDO:0009676",
- "MONDO:0015152",
- "MONDO:0000429",
- "MONDO:0005071",
- "MONDO:0006025",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
- "MONDO:0016145",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
+ "BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
- "MONDO:0016106",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939"
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001"
],
- "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2B",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "limb-girdle muscular dystrophy",
- "muscular dystrophy",
- "progressive muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "qualitative or quantitative defects of dysferlin",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "autosomal recessive disease",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "autosomal recessive limb-girdle muscular dystrophy type 2B",
- "disease",
"continuant",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
"specifically dependent continuant",
"myopathy",
- "hereditary disease",
- "autosomal genetic disease",
+ "myotonic dystrophy",
"nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
"skeletal muscle disorder",
"neuromuscular disease",
- "autosomal recessive limb-girdle muscular dystrophy",
- "entity"
+ "myotonic syndrome"
],
"subject_taxon": null,
"subject_taxon_label": null,
"predicate": "biolink:has_phenotype",
- "object": "HP:0002505",
+ "object": "HP:0000752",
"original_object": null,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
+ "UPHENO:0049587",
+ "NBO:0000030",
+ "GO:0008150",
+ "UBERON:0000465",
+ "NBO:0000313",
"UPHENO:0082875",
- "UPHENO:0049622",
- "UPHENO:0001005",
+ "UPHENO:0004523",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "GO:0007610",
+ "NBO:0000568",
+ "BFO:0000003",
"BFO:0000002",
- "HP:0002540",
- "UPHENO:0050606",
- "HP:0001288",
- "HP:0012638",
- "BFO:0000015",
- "UBERON:0000061",
- "GO:0050882",
- "NBO:0000338",
- "GO:0050905",
- "UBERON:0001016",
- "HP:0000001",
"UPHENO:0001001",
- "UPHENO:0080585",
- "HP:0000118",
- "BFO:0000020",
- "UPHENO:0002433",
+ "UPHENO:0049622",
+ "UPHENO:0001002",
"UPHENO:0001003",
- "HP:0000708",
- "HP:0011446",
- "BFO:0000001",
- "PATO:0000001",
"BFO:0000001",
+ "UBERON:0000061",
+ "HP:0000752",
+ "UPHENO:0075696",
+ "UPHENO:0001005",
+ "BFO:0000020",
+ "UPHENO:0002433",
+ "HP:0012638",
+ "NBO:0000644",
+ "BFO:0000015",
"BFO:0000004",
- "GO:0032501",
- "GO:0050881",
- "NBO:0000313",
- "GO:0050877",
- "UBERON:0000467",
"UBERON:0000468",
- "NBO:0000403",
- "NBO:0000001",
- "UPHENO:0075696",
- "UPHENO:0078622",
- "HP:0002505",
"UPHENO:0049586",
- "HP:0100022",
- "UPHENO:0001002",
- "UPHENO:0050613",
- "UPHENO:0002332",
- "UPHENO:0002536",
- "UPHENO:0079826",
- "UPHENO:0004523",
- "UPHENO:0049587",
- "BFO:0000003",
"BFO:0000002",
- "GO:0008150",
- "BFO:0000040",
- "GO:0050879",
- "GO:0007610",
- "GO:0003008",
+ "UPHENO:0002536",
+ "HP:0000708",
+ "NBO:0000243",
+ "UPHENO:0080585",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "UPHENO:0079826",
+ "PATO:0000001",
+ "HP:0000001",
"HP:0000707",
- "UPHENO:0079833",
- "UBERON:0001062",
- "UBERON:0000465",
- "UBERON:0010000"
+ "HP:0011446",
+ "BFO:0000001",
+ "GO:0032501",
+ "UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0001016"
],
- "object_label": "Loss of ambulation (HPO)",
+ "object_label": "Hyperactivity (HPO)",
"object_closure_label": [
- "All (HPO)",
- "abnormal behavior",
- "Abnormality of movement (HPO)",
- "Phenotypic abnormality (HPO)",
- "Abnormality of the nervous system (HPO)",
- "Behavioral abnormality (HPO)",
+ "abnormality of anatomical entity physiology",
+ "Phenotypic abnormality",
+ "abnormal anatomical entity",
"Abnormality of higher mental function (HPO)",
- "abnormal voluntary movement behavior",
"quality",
- "process",
+ "multicellular organismal process",
+ "Hyperactivity (HPO)",
+ "abnormal anatomical entity",
+ "abnormal phenotype by ontology source",
+ "phenotype by ontology source",
+ "abnormal nervous system",
+ "kinesthetic behavior phenotype",
+ "occurrent",
+ "continuant",
"material anatomical entity",
- "anatomical structure",
- "multicellular anatomical structure",
"nervous system",
- "voluntary movement behavior",
- "body part movement",
- "abnormality of anatomical entity physiology",
- "phenotype",
+ "All (HPO)",
+ "continuant",
+ "behavior",
+ "abnormal behavior",
+ "Phenotypic abnormality (HPO)",
+ "Abnormality of the nervous system (HPO)",
+ "abnormal behavior process",
+ "entity",
+ "entity",
+ "hyperactivity",
+ "biological_process",
"specifically dependent continuant",
"abnormality of nervous system physiology",
- "phenotype by ontology source",
- "Gait disturbance (HPO)",
+ "anatomical structure",
+ "multicellular organism",
+ "phenotype",
"abnormal behavior process",
- "abnormal nervous system",
+ "Behavioral abnormality (HPO)",
+ "voluntary movement behavior phenotype",
+ "process",
+ "independent continuant",
+ "behavior process",
"abnormal biological_process",
"Abnormal nervous system physiology (HPO)",
- "occurrent",
- "continuant",
- "biological_process",
"material entity",
- "multicellular organismal movement",
- "behavior",
- "system process",
- "musculoskeletal movement",
- "behavior process",
- "nervous system process",
- "abnormal phenotype by ontology source",
- "continuant",
- "Inability to walk (HPO)",
- "abnormal voluntary musculoskeletal movement",
- "entity",
- "independent continuant",
"anatomical entity",
- "abnormal anatomical entity",
- "abnormal voluntary movement behavior",
- "Loss of ambulation (HPO)",
"abnormal response to stimulus",
- "abnormal behavior process",
- "Phenotypic abnormality",
- "abnormal musculoskeletal movement",
"abnormality of anatomical entity physiology",
- "abnormal anatomical entity",
- "entity",
- "multicellular organismal process",
- "anatomical system",
- "voluntary musculoskeletal movement",
- "kinesthetic behavior",
- "neuromuscular process",
- "multicellular organism"
+ "behavioral phenotype",
+ "multicellular anatomical structure",
+ "anatomical system"
],
"object_taxon": null,
"object_taxon_label": null,
@@ -4142,24 +3814,24 @@
"negated": null,
"pathway": null,
"evidence_count": 2,
- "has_evidence": ["ECO:0000269"],
+ "has_evidence": ["ECO:0000304"],
"has_evidence_links": [
{
- "id": "ECO:0000269",
- "url": "http://purl.obolibrary.org/obo/ECO_0000269"
+ "id": "ECO:0000304",
+ "url": "http://purl.obolibrary.org/obo/ECO_0000304"
}
],
- "grouping_key": "MONDO:0009676\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0002505",
+ "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0000752",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype"
},
- "publications": ["PMID:9731527"],
+ "publications": ["orphanet:589821"],
"publications_links": [
{
- "id": "PMID:9731527",
- "url": "http://identifiers.org/pubmed/9731527"
+ "id": "orphanet:589821",
+ "url": null
}
],
"qualifiers": [],
@@ -4175,11 +3847,11 @@
"frequency_qualifier_label": "Occasional (HPO)",
"frequency_qualifier_namespace": "HP",
"frequency_qualifier_category": "biolink:PhenotypicFeature",
- "frequency_qualifier_closure": ["HP:0000001", "HP:0040283", "HP:0040279"],
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
"frequency_qualifier_closure_label": [
+ "Frequency (HPO)",
"All (HPO)",
- "Occasional (HPO)",
- "Frequency (HPO)"
+ "Occasional (HPO)"
],
"onset_qualifier_label": null,
"onset_qualifier_namespace": null,
@@ -4198,288 +3870,156 @@
"stage_qualifier_closure_label": []
},
{
- "id": "uuid:c9c8bf2b-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df96-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0008050",
- "original_subject": "OMIM:160500",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320"
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001"
],
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
+ "disease",
+ "hypertrophic cardiomyopathy",
"disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity"
+ "myotonic syndrome"
],
"subject_taxon": null,
"subject_taxon_label": null,
"predicate": "biolink:has_phenotype",
- "object": "HP:0010628",
+ "object": "HP:0001558",
"original_object": null,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "UPHENO:0082875",
- "UPHENO:0076772",
- "UPHENO:0002320",
- "UPHENO:0005116",
- "HP:0031910",
- "HP:0011799",
- "HP:0410008",
- "UPHENO:0076692",
- "BFO:0000001",
- "PATO:0000001",
- "HP:0012638",
- "BFO:0000004",
- "UBERON:0001016",
- "UBERON:0001021",
- "UBERON:0000153",
- "UBERON:0011676",
- "UBERON:0013701",
- "UBERON:0014892",
- "UBERON:0015789",
- "UBERON:0011779",
- "UBERON:0000033",
- "HP:0000001",
- "HP:0000152",
- "UPHENO:0002764",
+ "HP:0001197",
+ "UBERON:0000465",
+ "HP:0034059",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "BFO:0000002",
+ "UPHENO:0001001",
"UPHENO:0001002",
- "HP:0000118",
"BFO:0000020",
- "UPHENO:0002433",
- "HP:0000234",
- "HP:0000271",
- "HP:0010827",
"UPHENO:0001003",
- "HP:0012639",
- "UPHENO:0076710",
- "UPHENO:0002908",
"BFO:0000001",
- "BFO:0000040",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
- "UBERON:0001785",
- "UBERON:0010959",
- "UBERON:0001577",
- "UPHENO:0075696",
- "HP:0045010",
- "UPHENO:0002844",
- "HP:0001291",
- "HP:0001324",
- "HP:0030319",
- "HP:0000759",
- "UPHENO:0081700",
- "HP:0003011",
- "UPHENO:0002332",
- "UPHENO:0078730",
- "UPHENO:0002536",
- "UPHENO:0081709",
- "HP:0000301",
- "UPHENO:0004523",
- "UPHENO:0004508",
- "HP:0011804",
- "BFO:0000002",
- "UBERON:0000465",
- "UBERON:0005090",
- "UBERON:0018254",
- "UBERON:0004120",
- "UBERON:0034713",
- "UBERON:0001647",
- "UBERON:0000122",
- "UBERON:0001630",
- "UBERON:0001033",
- "UBERON:0002376",
- "UBERON:0007811",
- "UBERON:0001444",
- "UBERON:0013702",
- "UBERON:0001456",
- "UBERON:0008229",
- "UBERON:0013700",
- "UPHENO:0001001",
- "UPHENO:0002910",
- "HP:0010628",
"UPHENO:0001005",
- "HP:0011805",
- "BFO:0000002",
- "UPHENO:0076722",
- "UPHENO:0080555",
- "UPHENO:0003587",
- "UPHENO:0002816",
- "UPHENO:0080556",
- "HP:0000707",
- "HP:0006824",
- "UPHENO:0081581",
- "HP:0033127",
- "UPHENO:0076702",
- "UBERON:0001062",
- "RO:0002577",
- "UBERON:0000061",
- "UBERON:0015212",
- "UBERON:0010314",
- "UBERON:0005162",
- "UBERON:0010000",
- "UBERON:0000475",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "UBERON:0000010",
- "UBERON:0004461",
- "UBERON:0004473"
- ],
- "object_label": "Facial palsy (HPO)",
- "object_closure_label": [
- "All (HPO)",
- "abnormality of muscle organ physiology",
- "abnormal peripheral nervous system",
- "Abnormal cranial nerve physiology (HPO)",
- "Abnormality of facial soft tissue (HPO)",
- "abnormal head",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "abnormal peripheral nervous system morphology",
- "decreased anatomical entity strength",
- "abnormal facial nerve",
- "abnormal musculature",
- "decreased muscle organ strength",
- "Abnormality of the nervous system (HPO)",
- "Cranial nerve paralysis (HPO)",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "Abnormal nervous system morphology (HPO)",
- "abnormal facial muscle",
- "independent continuant",
- "system",
- "lateral structure",
- "structure with developmental contribution from neural crest",
- "multi cell part structure",
- "multicellular anatomical structure",
- "nervous system",
- "cranial nerve",
- "face",
- "craniocervical region musculature",
- "axial musculature",
- "abnormality of anatomical entity physiology",
- "abnormal cranial nerve morphology",
- "Abnormality of peripheral nerves (HPO)",
- "Facial palsy (HPO)",
- "abnormal phenotype by ontology source",
- "Abnormal skeletal muscle morphology (HPO)",
- "continuant",
- "specifically dependent continuant",
- "abnormality of nervous system physiology",
- "Abnormality of the head (HPO)",
- "Abnormality of the face (HPO)",
- "Abnormality of the seventh cranial nerve (HPO)",
- "phenotype by ontology source",
- "Abnormality of the peripheral nervous system (HPO)",
- "paralysed cranial nerve",
- "Abnormality of facial musculature (HPO)",
- "abnormal nervous system",
- "abnormal nerve",
- "quality",
- "Abnormal nervous system physiology (HPO)",
- "continuant",
- "material anatomical entity",
- "cranial neuron projection bundle",
- "facial nerve",
- "neuron projection bundle",
- "craniocervical region",
- "subdivision of head",
- "body proper",
- "craniocervical muscle",
- "facial muscle",
- "phenotype",
- "abnormal face",
- "abnormal muscle organ morphology",
- "Abnormal muscle physiology (HPO)",
- "entity",
- "anatomical entity",
- "anatomical structure",
- "muscle structure",
- "skeletal musculature",
- "mesoderm-derived structure",
- "organism subdivision",
- "organ",
- "muscle organ",
- "gustatory system",
- "cranial muscle",
- "musculature of body",
- "musculature",
- "peripheral nervous system",
- "skeletal musculature of head",
- "musculature of face",
- "abnormal anatomical entity",
- "Abnormality of head or neck (HPO)",
- "abnormal craniocervical region",
- "Abnormal cranial nerve morphology (HPO)",
- "Muscle weakness (HPO)",
- "Weakness of facial musculature (HPO)",
- "Abnormal peripheral nervous system morphology (HPO)",
- "paralysed anatomical entity",
- "Abnormality of the musculature (HPO)",
- "abnormality of anatomical entity physiology",
- "abnormality of cranial nerve physiology",
+ "HP:0001558",
+ "BFO:0000004",
+ "UBERON:0000061",
+ "UBERON:0000468",
+ "BFO:0000002",
+ "UPHENO:0002536",
+ "HP:0001557",
+ "UBERON:0000922",
+ "HP:0000118",
+ "HP:0034057",
+ "PATO:0000001",
+ "UBERON:0000323",
+ "HP:0000001",
+ "UPHENO:0075949",
+ "BFO:0000001",
+ "UBERON:0010000"
+ ],
+ "object_label": "Decreased fetal movement (HPO)",
+ "object_closure_label": [
+ "Phenotypic abnormality",
+ "specifically dependent continuant",
"abnormal anatomical entity",
- "abnormal anatomical entity morphology",
+ "quality",
+ "abnormal phenotype by ontology source",
+ "phenotype by ontology source",
+ "continuant",
+ "material anatomical entity",
+ "All (HPO)",
+ "continuant",
+ "embryo",
+ "Phenotypic abnormality (HPO)",
+ "abnormal late embryo",
+ "Fetal anomaly (HPO)",
"entity",
- "abnormal nervous system morphology",
- "material entity",
- "anatomical system",
+ "entity",
+ "Decreased fetal movement (HPO)",
"multicellular organism",
- "organ system subdivision",
- "nerve",
- "anterior region of body",
- "subdivision of organism along main body axis",
- "main body axis",
- "skeletal muscle organ",
- "cranial or facial muscle",
- "nerve of head region",
- "head"
+ "phenotype",
+ "Prenatal movement abnormality (HPO)",
+ "independent continuant",
+ "Abnormality of prenatal development or birth (HPO)",
+ "material entity",
+ "anatomical entity",
+ "anatomical structure",
+ "Abnormal fetal physiology (HPO)",
+ "multicellular anatomical structure",
+ "late embryo"
],
"object_taxon": null,
"object_taxon_label": null,
@@ -4495,21 +4035,21 @@
"url": "http://purl.obolibrary.org/obo/ECO_0000304"
}
],
- "grouping_key": "MONDO:0008050\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0010628",
+ "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0001558",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype"
},
- "publications": ["OMIM:160500"],
+ "publications": ["orphanet:589821"],
"publications_links": [
{
- "id": "OMIM:160500",
- "url": "http://identifiers.org/mim/160500"
+ "id": "orphanet:589821",
+ "url": null
}
],
"qualifiers": [],
- "frequency_qualifier": null,
+ "frequency_qualifier": "HP:0040283",
"onset_qualifier": null,
"sex_qualifier": null,
"stage_qualifier": null,
@@ -4518,11 +4058,15 @@
"qualifiers_category": null,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": null,
- "frequency_qualifier_namespace": null,
- "frequency_qualifier_category": null,
- "frequency_qualifier_closure": [],
- "frequency_qualifier_closure_label": [],
+ "frequency_qualifier_label": "Occasional (HPO)",
+ "frequency_qualifier_namespace": "HP",
+ "frequency_qualifier_category": "biolink:PhenotypicFeature",
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
+ "frequency_qualifier_closure_label": [
+ "Frequency (HPO)",
+ "All (HPO)",
+ "Occasional (HPO)"
+ ],
"onset_qualifier_label": null,
"onset_qualifier_namespace": null,
"onset_qualifier_category": null,
@@ -4540,216 +4084,512 @@
"stage_qualifier_closure_label": []
},
{
- "id": "uuid:c9c8bf2d-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df97-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0008050",
- "original_subject": "OMIM:160500",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320"
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001"
],
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
+ "disease",
+ "hypertrophic cardiomyopathy",
"disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity"
+ "myotonic syndrome"
],
"subject_taxon": null,
"subject_taxon_label": null,
"predicate": "biolink:has_phenotype",
- "object": "HP:0011916",
+ "object": "HP:0001561",
"original_object": null,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "HP:0002814",
- "HP:0009127",
- "UPHENO:0076692",
- "UPHENO:0003070",
- "PATO:0000001",
- "BFO:0000004",
- "UBERON:0004708",
- "UBERON:0000154",
- "UBERON:0006058",
- "UBERON:0002529",
- "UBERON:0002387",
- "HP:0000001",
- "UPHENO:0002644",
+ "HP:0001197",
+ "UPHENO:0075852",
+ "UPHENO:0002536",
+ "UBERON:0000465",
+ "BFO:0000001",
+ "BFO:0000040",
+ "BFO:0000002",
"UPHENO:0001001",
"UPHENO:0001002",
- "HP:0000118",
- "BFO:0000020",
"UPHENO:0001003",
- "UPHENO:0076710",
- "HP:0011916",
"BFO:0000001",
- "BFO:0000040",
"UBERON:0001062",
- "UBERON:0010000",
- "UBERON:0000467",
+ "UBERON:0000061",
+ "UBERON:0000463",
+ "UPHENO:0001005",
+ "BFO:0000020",
+ "BFO:0000004",
+ "UBERON:0000173",
"UBERON:0000468",
- "UBERON:0011216",
- "UBERON:0010709",
- "UBERON:0010538",
- "UBERON:0004488",
- "HP:0001436",
- "UPHENO:0002653",
- "HP:0003011",
- "UPHENO:0002536",
- "HP:0001437",
- "HP:0040064",
+ "HP:0001561",
+ "UBERON:0000922",
+ "HP:0000118",
+ "PATO:0000001",
+ "UBERON:0000323",
+ "HP:0000001",
"BFO:0000002",
- "PR:000050567",
- "UBERON:0000465",
- "UBERON:0002101",
- "UBERON:0004709",
- "UBERON:0005090",
- "UBERON:0002103",
- "UBERON:0010707",
- "UBERON:0001630",
- "UBERON:0000026",
- "UBERON:0010758",
- "UBERON:0007271",
- "UBERON:0014792",
- "UBERON:0004482",
- "UBERON:0008784",
- "UBERON:0002470",
- "UPHENO:0001005",
- "HP:0011805",
+ "UPHENO:0075949",
+ "HP:0001560",
+ "UBERON:0010000"
+ ],
+ "object_label": "Polyhydramnios (HPO)",
+ "object_closure_label": [
+ "Phenotypic abnormality",
+ "Abnormality of the amniotic fluid (HPO)",
+ "quality",
+ "abnormal phenotype by ontology source",
+ "phenotype by ontology source",
+ "continuant",
+ "material anatomical entity",
+ "All (HPO)",
+ "embryo",
+ "Phenotypic abnormality (HPO)",
+ "abnormal late embryo",
+ "entity",
+ "specifically dependent continuant",
+ "anatomical entity",
+ "anatomical structure",
+ "organism substance",
+ "amniotic fluid",
+ "multicellular organism",
+ "phenotype",
+ "continuant",
+ "entity",
+ "independent continuant",
+ "Abnormality of prenatal development or birth (HPO)",
+ "abnormal amniotic fluid",
+ "material entity",
+ "Polyhydramnios (HPO)",
+ "abnormal anatomical entity",
+ "multicellular anatomical structure",
+ "late embryo"
+ ],
+ "object_taxon": null,
+ "object_taxon_label": null,
+ "primary_knowledge_source": "infores:hpo-annotations",
+ "aggregator_knowledge_source": ["infores:monarchinitiative"],
+ "negated": null,
+ "pathway": null,
+ "evidence_count": 2,
+ "has_evidence": ["ECO:0000304"],
+ "has_evidence_links": [
+ {
+ "id": "ECO:0000304",
+ "url": "http://purl.obolibrary.org/obo/ECO_0000304"
+ }
+ ],
+ "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0001561",
+ "provided_by": "hpoa_disease_to_phenotype_edges",
+ "provided_by_link": {
+ "id": "hpoa_disease_to_phenotype",
+ "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype"
+ },
+ "publications": ["orphanet:589821"],
+ "publications_links": [
+ {
+ "id": "orphanet:589821",
+ "url": null
+ }
+ ],
+ "qualifiers": [],
+ "frequency_qualifier": "HP:0040283",
+ "onset_qualifier": null,
+ "sex_qualifier": null,
+ "stage_qualifier": null,
+ "qualifiers_label": null,
+ "qualifiers_namespace": null,
+ "qualifiers_category": null,
+ "qualifiers_closure": [],
+ "qualifiers_closure_label": [],
+ "frequency_qualifier_label": "Occasional (HPO)",
+ "frequency_qualifier_namespace": "HP",
+ "frequency_qualifier_category": "biolink:PhenotypicFeature",
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
+ "frequency_qualifier_closure_label": [
+ "Frequency (HPO)",
+ "All (HPO)",
+ "Occasional (HPO)"
+ ],
+ "onset_qualifier_label": null,
+ "onset_qualifier_namespace": null,
+ "onset_qualifier_category": null,
+ "onset_qualifier_closure": [],
+ "onset_qualifier_closure_label": [],
+ "sex_qualifier_label": null,
+ "sex_qualifier_namespace": null,
+ "sex_qualifier_category": null,
+ "sex_qualifier_closure": [],
+ "sex_qualifier_closure_label": [],
+ "stage_qualifier_label": null,
+ "stage_qualifier_namespace": null,
+ "stage_qualifier_category": null,
+ "stage_qualifier_closure": [],
+ "stage_qualifier_closure_label": []
+ },
+ {
+ "id": "uuid:4e02df98-842a-11ee-884f-6be035239f90",
+ "category": "biolink:DiseaseToPhenotypicFeatureAssociation",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
+ "subject_namespace": "MONDO",
+ "subject_category": "biolink:Disease",
+ "subject_closure": [
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
+ "MONDO:0020121",
+ "BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
+ "BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
+ "MONDO:0020120",
+ "MONDO:0019056",
+ "MONDO:0004994",
+ "MONDO:0004995",
+ "MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
+ "MONDO:0700096",
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001"
+ ],
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
+ "subject_closure_label": [
+ "eyelids malposition disorder",
+ "disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
+ "muscle tissue disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
+ "hereditary skeletal muscle disorder",
+ "continuant",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
+ "myopathy",
+ "myotonic dystrophy",
+ "nervous system disorder",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
+ "realizable entity",
+ "skeletal muscle disorder",
+ "neuromuscular disease",
+ "myotonic syndrome"
+ ],
+ "subject_taxon": null,
+ "subject_taxon_label": null,
+ "predicate": "biolink:has_phenotype",
+ "object": "HP:0001643",
+ "original_object": null,
+ "object_namespace": "HP",
+ "object_category": "biolink:PhenotypicFeature",
+ "object_closure": [
+ "HP:0030962",
+ "UPHENO:0019771",
+ "PR:000050567",
+ "UBERON:0000465",
+ "UPHENO:0020542",
+ "UPHENO:0076729",
+ "UPHENO:0080362",
+ "HP:0001627",
+ "UPHENO:0015280",
+ "BFO:0000001",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UBERON:0000468",
+ "UBERON:0011676",
+ "UBERON:0013701",
+ "UPHENO:0020119",
+ "HP:0001626",
+ "UPHENO:0001002",
+ "UPHENO:0033572",
+ "BFO:0000020",
+ "UPHENO:0015324",
+ "UPHENO:0015290",
"BFO:0000002",
- "UPHENO:0002816",
- "UPHENO:0081581",
- "HP:0033127",
- "UPHENO:0002647",
+ "UBERON:0013768",
+ "UBERON:0003509",
+ "UBERON:0003513",
+ "UBERON:0011695",
+ "UBERON:0004716",
+ "UBERON:0004145",
+ "UBERON:0005985",
+ "UBERON:0002049",
+ "UBERON:0002201",
+ "UBERON:0006876",
+ "UPHENO:0001001",
+ "UPHENO:0001003",
+ "UPHENO:0002536",
"BFO:0000001",
- "UPHENO:0002830",
- "RO:0002577",
+ "UBERON:0034923",
+ "UBERON:0015410",
+ "UPHENO:0075696",
+ "HP:0001643",
+ "UPHENO:0076776",
+ "UPHENO:0081581",
+ "UPHENO:0076692",
+ "BFO:0000004",
+ "UBERON:0001981",
+ "UBERON:0004537",
+ "UBERON:0004572",
+ "UBERON:0004535",
"UBERON:0000061",
- "UBERON:0015212",
+ "UBERON:0000477",
"UBERON:0000475",
"UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "UBERON:0000978",
- "UBERON:0007270",
- "UBERON:0004480"
+ "UBERON:0004111",
+ "UBERON:0004573",
+ "UBERON:0003498",
+ "HP:0011603",
+ "UPHENO:0020351",
+ "HP:0030680",
+ "UPHENO:0076765",
+ "BFO:0000002",
+ "HP:0025015",
+ "HP:0002597",
+ "UPHENO:0076810",
+ "HP:0033353",
+ "PATO:0000001",
+ "UBERON:0001637",
+ "UBERON:0003834",
+ "UBERON:0000948",
+ "UBERON:0009569",
+ "UBERON:0013702",
+ "UBERON:0005177",
+ "UBERON:0003103",
+ "UBERON:0000055",
+ "UBERON:0005440",
+ "UBERON:0000915",
+ "UBERON:0002100",
+ "UBERON:0005181",
+ "UBERON:0002075",
+ "UBERON:0015228",
+ "HP:0000118",
+ "UPHENO:0075655",
+ "UPHENO:0020584",
+ "UPHENO:0020587",
+ "UBERON:0010314",
+ "UBERON:0018674",
+ "HP:0000001",
+ "UPHENO:0002678",
+ "UPHENO:0001005",
+ "UPHENO:0033603",
+ "UBERON:0010000",
+ "UBERON:0000467",
+ "UBERON:0004120",
+ "UBERON:0007798",
+ "UBERON:0001009",
+ "UBERON:0004571",
+ "UBERON:0005178",
+ "UBERON:0007100"
],
- "object_label": "Toe extensor amyotrophy (HPO)",
+ "object_label": "Patent ductus arteriosus (HPO)",
"object_closure_label": [
- "All (HPO)",
- "abnormal musculature of lower limb",
- "Abnormality of the lower limb (HPO)",
- "Phenotypic abnormality",
- "Phenotypic abnormality (HPO)",
- "abnormal musculature",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
- "abnormal musculature of limb",
- "entity",
- "independent continuant",
- "system",
- "paired limb/fin",
- "lateral structure",
- "pelvic complex",
- "appendage musculature",
- "musculature of pelvic complex",
- "musculature of pes",
- "phenotype",
- "Abnormality of the foot musculature (HPO)",
- "abnormal phenotype by ontology source",
- "Abnormal skeletal muscle morphology (HPO)",
- "continuant",
+ "abnormal blood vessel morphology",
+ "abnormal anatomical entity",
"specifically dependent continuant",
"phenotype by ontology source",
- "Abnormality of the musculature of the lower limbs (HPO)",
- "Abnormality of limbs (HPO)",
- "quality",
+ "abnormal anatomical entity",
"continuant",
"protein-containing material entity",
"material anatomical entity",
- "hindlimb",
- "appendage girdle complex",
- "appendage",
- "subdivision of organism along appendicular axis",
- "paired limb/fin segment",
- "musculature of lower limb",
- "lower limb segment",
- "autopod region",
- "Abnormality of the musculature of the limbs (HPO)",
- "abnormal muscle organ morphology",
- "Toe extensor amyotrophy (HPO)",
+ "vascular system",
+ "circulatory system",
+ "vasculature of trunk",
+ "vasculature of organ",
+ "ductus arteriosus",
+ "thoracic segment of trunk",
+ "trunk",
+ "thoracic segment organ",
+ "viscus",
+ "circulatory organ",
+ "All (HPO)",
+ "abnormal vasculature",
+ "abnormal phenotype by ontology source",
+ "continuant",
+ "abnormal artery morphology in the independent continuant",
+ "multicellular organism",
+ "outflow tract",
+ "coronary vessel",
+ "vasculature",
+ "subdivision of trunk",
+ "body proper",
+ "trunk region element",
+ "compound organ",
+ "vessel",
+ "Abnormality of cardiovascular system morphology (HPO)",
+ "abnormal great vessel of heart morphology",
+ "Phenotypic abnormality (HPO)",
+ "abnormal opening of the anatomical entity",
+ "abnormal anatomical entity morphology",
+ "abnormal systemic artery morphology",
"entity",
- "anatomical structure",
- "muscle structure",
+ "structure with developmental contribution from neural crest",
+ "thoracic cavity element",
+ "primary circulatory organ",
+ "abnormal coronary vessel morphology",
+ "Abnormality of the cardiovascular system (HPO)",
+ "Phenotypic abnormality",
+ "abnormal incomplete closing of the anatomical entity",
+ "Patent ductus arteriosus (HPO)",
+ "abnormal cardiovascular system morphology",
+ "abnormal anatomical entity morphology",
+ "quality",
+ "disconnected anatomical group",
+ "anatomical cluster",
"organism subdivision",
"organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "leg",
- "pelvic appendage musculature",
- "musculature of limb",
- "abnormal musculature of pes",
- "Abnormality of the musculature (HPO)",
- "abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "abnormal leg",
- "abnormal limb",
+ "anatomical conduit",
+ "systemic artery",
+ "heart blood vessel",
+ "heart plus pericardium",
+ "phenotype",
+ "abnormal incomplete closing of the ductus arteriosus",
+ "abnormal anatomical entity morphology in the independent continuant",
+ "Abnormal vascular morphology (HPO)",
+ "entity",
+ "independent continuant",
+ "subdivision of organism along main body axis",
+ "main body axis",
+ "abnormal anatomical entity morphology in the heart",
+ "abnormal multicellular organism morphology",
"material entity",
"anatomical entity",
- "limb",
- "pelvic appendage",
+ "blood vessel",
+ "arterial system",
+ "blood vasculature",
+ "cardiovascular system",
+ "anatomical structure",
+ "great vessel of heart",
+ "arterial blood vessel",
+ "trunk blood vessel",
+ "embryonic cardiovascular system",
+ "conceptus",
+ "systemic arterial system",
+ "Congenital malformation of the great arteries (HPO)",
+ "abnormal ductus arteriosus morphology",
+ "abnormal vascular system morphology",
+ "abnormal cardiovascular system",
+ "Abnormal heart morphology (HPO)",
+ "Abnormal morphology of the great vessels (HPO)",
+ "abnormal artery morphology",
+ "Abnormality of the vasculature (HPO)",
+ "abnormal heart morphology",
+ "Abnormal blood vessel morphology (HPO)",
"multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision",
- "posterior region of body",
- "multi-limb segment region",
- "limb segment",
- "pes"
+ "mesoderm-derived structure",
+ "artery",
+ "thoracic segment blood vessel",
+ "heart",
+ "heart vasculature"
],
"object_taxon": null,
"object_taxon_label": null,
@@ -4765,21 +4605,21 @@
"url": "http://purl.obolibrary.org/obo/ECO_0000304"
}
],
- "grouping_key": "MONDO:0008050\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0011916",
+ "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0001643",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype"
},
- "publications": ["OMIM:160500"],
+ "publications": ["orphanet:589821"],
"publications_links": [
{
- "id": "OMIM:160500",
- "url": "http://identifiers.org/mim/160500"
+ "id": "orphanet:589821",
+ "url": null
}
],
"qualifiers": [],
- "frequency_qualifier": null,
+ "frequency_qualifier": "HP:0040283",
"onset_qualifier": null,
"sex_qualifier": null,
"stage_qualifier": null,
@@ -4788,11 +4628,15 @@
"qualifiers_category": null,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": null,
- "frequency_qualifier_namespace": null,
- "frequency_qualifier_category": null,
- "frequency_qualifier_closure": [],
- "frequency_qualifier_closure_label": [],
+ "frequency_qualifier_label": "Occasional (HPO)",
+ "frequency_qualifier_namespace": "HP",
+ "frequency_qualifier_category": "biolink:PhenotypicFeature",
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
+ "frequency_qualifier_closure_label": [
+ "Frequency (HPO)",
+ "All (HPO)",
+ "Occasional (HPO)"
+ ],
"onset_qualifier_label": null,
"onset_qualifier_namespace": null,
"onset_qualifier_category": null,
@@ -4810,152 +4654,218 @@
"stage_qualifier_closure_label": []
},
{
- "id": "uuid:c9c8bf2e-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df99-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0008050",
- "original_subject": "OMIM:160500",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320"
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001"
],
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
+ "disease",
+ "hypertrophic cardiomyopathy",
"disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity"
+ "myotonic syndrome"
],
"subject_taxon": null,
"subject_taxon_label": null,
"predicate": "biolink:has_phenotype",
- "object": "HP:0002460",
+ "object": "HP:0001671",
"original_object": null,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "UPHENO:0082875",
- "UPHENO:0002320",
- "UPHENO:0001005",
+ "PR:000050567",
+ "UBERON:0000465",
+ "UPHENO:0019888",
+ "UPHENO:0080362",
+ "HP:0001627",
+ "UPHENO:0015280",
+ "BFO:0000040",
+ "UBERON:0001062",
+ "UBERON:0000468",
+ "UBERON:0011676",
+ "UBERON:0013701",
+ "HP:0001626",
+ "UPHENO:0001002",
"BFO:0000020",
- "PATO:0000001",
- "BFO:0000004",
- "UBERON:0000061",
- "HP:0000001",
+ "UPHENO:0015324",
+ "HP:0001671",
+ "BFO:0000002",
"UPHENO:0001001",
- "HP:0000118",
+ "UPHENO:0001003",
"BFO:0000001",
- "UBERON:0000467",
- "UBERON:0000468",
- "UBERON:0011216",
+ "UBERON:0015410",
+ "UPHENO:0076776",
+ "UPHENO:0081581",
+ "UPHENO:0076692",
+ "BFO:0000004",
+ "UBERON:0004535",
+ "UBERON:0000061",
+ "UBERON:0000475",
+ "UBERON:0000062",
"UPHENO:0075696",
- "HP:0001324",
- "HP:0003011",
- "UPHENO:0002332",
- "UPHENO:0001003",
- "UPHENO:0002536",
- "HP:0002460",
- "HP:0011804",
- "BFO:0000002",
- "BFO:0000040",
- "UBERON:0005090",
- "UBERON:0001630",
- "UPHENO:0001002",
+ "HP:0030680",
"BFO:0000002",
- "UPHENO:0080555",
- "UPHENO:0002816",
- "UPHENO:0080556",
- "HP:0033127",
+ "UPHENO:0002536",
+ "UPHENO:0076810",
+ "UBERON:0002099",
+ "UBERON:0000948",
+ "UBERON:0009569",
+ "UBERON:0013702",
+ "UBERON:0005177",
+ "UBERON:0003103",
+ "UBERON:0000915",
+ "UBERON:0002100",
+ "UBERON:0005181",
+ "UBERON:0002075",
+ "UBERON:0015228",
+ "HP:0000118",
+ "UPHENO:0020584",
+ "PATO:0000001",
+ "UBERON:0003037",
+ "UBERON:0010314",
+ "HP:0000001",
+ "UPHENO:0001005",
"BFO:0000001",
- "UBERON:0001062",
- "UBERON:0000465",
"UBERON:0010000",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015"
+ "UBERON:0000467",
+ "UBERON:0004120",
+ "UBERON:0001009",
+ "UBERON:0005178",
+ "UBERON:0007100"
],
- "object_label": "Distal muscle weakness (HPO)",
+ "object_label": "Abnormal cardiac septum morphology (HPO)",
"object_closure_label": [
+ "abnormal anatomical entity",
+ "quality",
+ "specifically dependent continuant",
+ "phenotype by ontology source",
+ "continuant",
+ "protein-containing material entity",
+ "material anatomical entity",
+ "circulatory system",
+ "thoracic segment of trunk",
+ "trunk",
+ "thoracic segment organ",
+ "viscus",
+ "circulatory organ",
"All (HPO)",
- "abnormality of muscle organ physiology",
+ "abnormal phenotype by ontology source",
+ "continuant",
+ "Abnormal cardiac septum morphology (HPO)",
+ "multicellular organism",
+ "subdivision of trunk",
+ "body proper",
+ "trunk region element",
+ "compound organ",
+ "Abnormality of cardiovascular system morphology (HPO)",
"Phenotypic abnormality (HPO)",
- "decreased anatomical entity strength",
- "abnormal musculature",
- "decreased muscle organ strength",
- "Abnormality of the musculoskeletal system (HPO)",
+ "abnormal anatomical entity morphology",
"entity",
- "independent continuant",
- "material anatomical entity",
- "anatomical structure",
- "multicellular anatomical structure",
- "abnormality of anatomical entity physiology",
- "phenotype",
+ "entity",
+ "septum",
+ "structure with developmental contribution from neural crest",
+ "thoracic cavity element",
+ "primary circulatory organ",
+ "Abnormality of the cardiovascular system (HPO)",
"Phenotypic abnormality",
- "continuant",
- "Distal muscle weakness (HPO)",
- "quality",
- "continuant",
+ "abnormal cardiovascular system morphology",
+ "abnormal anatomical entity morphology",
+ "organism subdivision",
+ "organ",
+ "heart plus pericardium",
+ "phenotype",
+ "abnormal anatomical entity morphology in the independent continuant",
+ "independent continuant",
+ "subdivision of organism along main body axis",
+ "main body axis",
+ "abnormal anatomical entity morphology in the heart",
+ "abnormal multicellular organism morphology",
"material entity",
- "abnormal phenotype by ontology source",
- "specifically dependent continuant",
- "Abnormal muscle physiology (HPO)",
- "entity",
"anatomical entity",
- "muscle structure",
- "organ",
- "muscle organ",
- "musculature of body",
- "musculature",
- "abnormal anatomical entity",
- "Muscle weakness (HPO)",
- "Abnormality of the musculature (HPO)",
- "abnormality of anatomical entity physiology",
- "phenotype by ontology source",
+ "cardiovascular system",
+ "anatomical structure",
"abnormal anatomical entity",
+ "abnormal cardiac septum morphology",
+ "abnormal cardiovascular system",
+ "Abnormal heart morphology (HPO)",
+ "abnormal heart morphology",
+ "multicellular anatomical structure",
"anatomical system",
- "multicellular organism",
- "organ system subdivision"
+ "mesoderm-derived structure",
+ "cardiac septum",
+ "heart"
],
"object_taxon": null,
"object_taxon_label": null,
@@ -4971,21 +4881,21 @@
"url": "http://purl.obolibrary.org/obo/ECO_0000304"
}
],
- "grouping_key": "MONDO:0008050\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0002460",
+ "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0001671",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype"
},
- "publications": ["OMIM:160500"],
+ "publications": ["orphanet:589821"],
"publications_links": [
{
- "id": "OMIM:160500",
- "url": "http://identifiers.org/mim/160500"
+ "id": "orphanet:589821",
+ "url": null
}
],
"qualifiers": [],
- "frequency_qualifier": null,
+ "frequency_qualifier": "HP:0040283",
"onset_qualifier": null,
"sex_qualifier": null,
"stage_qualifier": null,
@@ -4994,11 +4904,15 @@
"qualifiers_category": null,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": null,
- "frequency_qualifier_namespace": null,
- "frequency_qualifier_category": null,
- "frequency_qualifier_closure": [],
- "frequency_qualifier_closure_label": [],
+ "frequency_qualifier_label": "Occasional (HPO)",
+ "frequency_qualifier_namespace": "HP",
+ "frequency_qualifier_category": "biolink:PhenotypicFeature",
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
+ "frequency_qualifier_closure_label": [
+ "Frequency (HPO)",
+ "All (HPO)",
+ "Occasional (HPO)"
+ ],
"onset_qualifier_label": null,
"onset_qualifier_namespace": null,
"onset_qualifier_category": null,
@@ -5016,176 +4930,172 @@
"stage_qualifier_closure_label": []
},
{
- "id": "uuid:c9c8bf32-7529-11ee-b012-cbd37f5c3759",
+ "id": "uuid:4e02df9a-842a-11ee-884f-6be035239f90",
"category": "biolink:DiseaseToPhenotypicFeatureAssociation",
- "subject": "MONDO:0008050",
- "original_subject": "OMIM:160500",
+ "subject": "MONDO:0035646",
+ "original_subject": "Orphanet:589821",
"subject_namespace": "MONDO",
"subject_category": "biolink:Disease",
"subject_closure": [
- "BFO:0000002",
- "MONDO:0016195",
- "MONDO:0005336",
- "MONDO:0018949",
- "MONDO:0005071",
- "MONDO:0008050",
- "BFO:0000016",
- "MONDO:0016139",
- "OGMS:0000031",
- "MONDO:0003847",
- "BFO:0000001",
+ "MONDO:0024573",
+ "MONDO:0020158",
+ "MONDO:0000001",
"MONDO:0020121",
- "MONDO:0019952",
"BFO:0000017",
+ "MONDO:0008056",
+ "MONDO:0035646",
+ "MONDO:0003847",
+ "MONDO:0016106",
+ "MONDO:0005336",
+ "MONDO:0000462",
+ "MONDO:0002254",
+ "MONDO:0003939",
+ "MONDO:0002022",
"BFO:0000020",
+ "MONDO:0002081",
+ "MONDO:0005328",
+ "MONDO:0005045",
+ "BFO:0000002",
+ "MONDO:0005217",
+ "MONDO:0016120",
+ "MONDO:0016107",
+ "MONDO:0005071",
+ "MONDO:0005267",
"MONDO:0020120",
"MONDO:0019056",
- "MONDO:0000001",
+ "MONDO:0004994",
+ "MONDO:0004995",
"MONDO:0700223",
+ "MONDO:0003382",
+ "BFO:0000016",
"MONDO:0700096",
- "MONDO:0002081",
- "MONDO:0003939",
- "MONDO:0002320"
+ "MONDO:0000591",
+ "MONDO:0024458",
+ "OGMS:0000031",
+ "BFO:0000001"
],
- "subject_label": "MYH7-related skeletal myopathy",
+ "subject_label": "congenital-onset Steinert myotonic dystrophy",
"subject_closure_label": [
- "muscular dystrophy",
- "human disease",
- "musculoskeletal system disorder",
+ "eyelids malposition disorder",
"disease",
+ "hypertrophic cardiomyopathy",
+ "disease",
+ "familial cardiomyopathy",
+ "syndromic disease",
+ "congenital-onset Steinert myotonic dystrophy",
"muscle tissue disorder",
- "congenital nervous system disorder",
+ "disorder of orbital region",
+ "cardiomyopathy",
+ "cardiovascular disorder",
"hereditary skeletal muscle disorder",
- "MYH7-related skeletal myopathy",
- "disposition",
- "qualitative or quantitative protein defects in neuromuscular diseases",
- "distal myopathy",
- "disease",
"continuant",
- "qualitative or quantitative defects of beta-myosin heavy chain (MYH7)",
+ "familial hypertrophic cardiomyopathy",
+ "eye adnexa disorder",
+ "eyelid disorder",
+ "disposition",
+ "human disease",
+ "intrinsic cardiomyopathy",
+ "disorder of visual system",
+ "entity",
+ "specifically dependent continuant",
"myopathy",
- "hereditary disease",
+ "myotonic dystrophy",
"nervous system disorder",
- "congenital myopathy",
+ "heart disorder",
+ "myotonic dystrophy type 1",
+ "progressive muscular dystrophy",
+ "musculoskeletal system disorder",
+ "hereditary disease",
+ "eye disorder",
+ "muscular dystrophy",
"realizable entity",
- "specifically dependent continuant",
"skeletal muscle disorder",
"neuromuscular disease",
- "entity"
+ "myotonic syndrome"
],
"subject_taxon": null,
"subject_taxon_label": null,
"predicate": "biolink:has_phenotype",
- "object": "HP:0003805",
+ "object": "HP:0002014",
"original_object": null,
"object_namespace": "HP",
"object_category": "biolink:PhenotypicFeature",
"object_closure": [
- "BFO:0000002",
- "BFO:0000020",
- "UPHENO:0076692",
+ "UPHENO:0002443",
+ "UPHENO:0002536",
+ "UBERON:0000465",
+ "UPHENO:0082875",
+ "HP:0002664",
"BFO:0000001",
- "BFO:0000004",
- "CL:0000255",
- "UBERON:0014892",
- "UBERON:0002036",
- "HP:0000001",
- "HP:0004303",
- "UPHENO:0001001",
+ "BFO:0000040",
+ "UBERON:0001062",
"UPHENO:0001002",
- "HP:0000118",
+ "BFO:0000020",
+ "HP:0011793",
+ "HP:0011458",
+ "BFO:0000002",
+ "UBERON:0001988",
+ "UPHENO:0001001",
+ "UPHENO:0002833",
"UPHENO:0001003",
- "UPHENO:0076710",
- "PATO:0000001",
- "BFO:0000001",
- "BFO:0000040",
- "UBERON:0000467",
- "CL:0000000",
+ "UBERON:0000463",
+ "UPHENO:0075696",
+ "HP:0002014",
+ "HP:0025031",
+ "BFO:0000004",
+ "UBERON:0000061",
+ "UBERON:0000174",
"UBERON:0000468",
- "UBERON:0011216",
- "CL:0000548",
- "UBERON:0001134",
- "HP:0003011",
- "UPHENO:0002536",
- "HP:0003805",
- "UBERON:0005090",
- "UBERON:0018254",
- "UBERON:0004120",
- "UBERON:0000479",
- "CL:0000003",
- "UBERON:0001630",
- "UBERON:0002385",
- "CL:0000188",
- "UPHENO:0001005",
- "HP:0011805",
- "HP:0025354",
- "UPHENO:0002816",
- "UPHENO:0081581",
- "HP:0033127",
"BFO:0000002",
- "UBERON:0001062",
- "UBERON:0000465",
- "RO:0002577",
- "UBERON:0000061",
+ "HP:0025032",
+ "PATO:0000001",
+ "HP:0000118",
+ "UPHENO:0002332",
+ "HP:0000001",
+ "UPHENO:0001005",
+ "BFO:0000001",
"UBERON:0010000",
- "UBERON:0000062",
- "UBERON:0000383",
- "UBERON:0001015",
- "CL:0002371"
+ "UBERON:0000467",
+ "UBERON:0001007"
],
- "object_label": "Rimmed vacuoles (HPO)",
+ "object_label": "Diarrhea (HPO)",
"object_closure_label": [
+ "abnormality of anatomical entity physiology",
+ "abnormal digestive system",
+ "entity",
+ "abnormal anatomical entity",
+ "Diarrhea (HPO)",
+ "specifically dependent continuant",
+ "Abnormality of digestive system physiology (HPO)",
+ "phenotype by ontology source",
+ "continuant",
+ "material anatomical entity",
+ "digestive system",
"All (HPO)",
- "Abnormal muscle fiber morphology (HPO)",
- "Phenotypic abnormality",
+ "abnormal phenotype by ontology source",
+ "continuant",
+ "feces",
"Phenotypic abnormality (HPO)",
- "Abnormal cellular phenotype (HPO)",
- "abnormal musculature",
- "abnormal multicellular organism morphology",
- "Abnormality of the musculoskeletal system (HPO)",
+ "Phenotypic abnormality",
+ "Neoplasm by anatomical site (HPO)",
+ "Abdominal symptom (HPO)",
"quality",
- "independent continuant",
- "material anatomical entity",
- "system",
- "multicellular anatomical structure",
+ "organism substance",
+ "excreta",
+ "multicellular organism",
"phenotype",
- "abnormal phenotype by ontology source",
- "Abnormal skeletal muscle morphology (HPO)",
- "phenotype by ontology source",
- "tissue",
- "animal cell",
- "skeletal muscle tissue",
- "cell of skeletal muscle",
- "continuant",
- "specifically dependent continuant",
- "abnormal muscle organ morphology",
- "Rimmed vacuoles (HPO)",
+ "Neoplasm (HPO)",
"entity",
+ "independent continuant",
+ "abnormality of digestive system physiology",
+ "Abnormality of the digestive system (HPO)",
+ "material entity",
"anatomical entity",
"anatomical structure",
- "muscle structure",
- "skeletal musculature",
- "mesoderm-derived structure",
- "organ",
- "native cell",
- "muscle organ",
- "muscle tissue",
- "musculature of body",
- "musculature",
- "somatic cell",
- "Abnormality of the musculature (HPO)",
+ "abnormality of anatomical entity physiology",
"abnormal anatomical entity",
- "abnormal anatomical entity morphology",
- "entity",
- "continuant",
- "material entity",
- "anatomical system",
- "cell",
- "multicellular organism",
- "organ system subdivision",
- "eukaryotic cell",
- "skeletal muscle organ",
- "striated muscle tissue"
+ "multicellular anatomical structure",
+ "anatomical system"
],
"object_taxon": null,
"object_taxon_label": null,
@@ -5194,28 +5104,28 @@
"negated": null,
"pathway": null,
"evidence_count": 2,
- "has_evidence": ["ECO:0000501"],
+ "has_evidence": ["ECO:0000304"],
"has_evidence_links": [
{
- "id": "ECO:0000501",
- "url": "http://purl.obolibrary.org/obo/ECO_0000501"
+ "id": "ECO:0000304",
+ "url": "http://purl.obolibrary.org/obo/ECO_0000304"
}
],
- "grouping_key": "MONDO:0008050\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0003805",
+ "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0002014",
"provided_by": "hpoa_disease_to_phenotype_edges",
"provided_by_link": {
"id": "hpoa_disease_to_phenotype",
"url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype"
},
- "publications": ["OMIM:160500"],
+ "publications": ["orphanet:589821"],
"publications_links": [
{
- "id": "OMIM:160500",
- "url": "http://identifiers.org/mim/160500"
+ "id": "orphanet:589821",
+ "url": null
}
],
"qualifiers": [],
- "frequency_qualifier": null,
+ "frequency_qualifier": "HP:0040283",
"onset_qualifier": null,
"sex_qualifier": null,
"stage_qualifier": null,
@@ -5224,11 +5134,15 @@
"qualifiers_category": null,
"qualifiers_closure": [],
"qualifiers_closure_label": [],
- "frequency_qualifier_label": null,
- "frequency_qualifier_namespace": null,
- "frequency_qualifier_category": null,
- "frequency_qualifier_closure": [],
- "frequency_qualifier_closure_label": [],
+ "frequency_qualifier_label": "Occasional (HPO)",
+ "frequency_qualifier_namespace": "HP",
+ "frequency_qualifier_category": "biolink:PhenotypicFeature",
+ "frequency_qualifier_closure": ["HP:0040279", "HP:0040283", "HP:0000001"],
+ "frequency_qualifier_closure_label": [
+ "Frequency (HPO)",
+ "All (HPO)",
+ "Occasional (HPO)"
+ ],
"onset_qualifier_label": null,
"onset_qualifier_namespace": null,
"onset_qualifier_category": null,
diff --git a/frontend/fixtures/autocomplete.json b/frontend/fixtures/autocomplete.json
index bf9100203..4f598ad26 100644
--- a/frontend/fixtures/autocomplete.json
+++ b/frontend/fixtures/autocomplete.json
@@ -8,6 +8,7 @@
"category": "biolink:Disease",
"name": "Fanconi renotubular syndrome",
"full_name": null,
+ "deprecated": null,
"description": "A genetic or acquired disorder characterized by impairment of the function of the proximal tubules of the kidney. It results in decreased reabsorption of electrolytes, glucose, amino acids, and other nutrients.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -37,6 +38,7 @@
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group A",
"full_name": null,
+ "deprecated": null,
"description": "Fanconi anemia caused by mutations of the FANCA gene. FANCA gene mutations are the most common cause of Fanconi anemia. This gene provides instructions for making a protein that is involved in the Fanconi anemia (FA) pathway.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -65,6 +67,7 @@
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group L",
"full_name": null,
+ "deprecated": null,
"description": "Any Fanconi anemia in which the cause of the disease is a mutation in the FANCL gene.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -90,6 +93,7 @@
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group E",
"full_name": null,
+ "deprecated": null,
"description": "Fanconi anemia caused by mutations of the FANCE gene. This is a protein coding gene. It is required for the nuclear accumulation of FANCC and provides a critical bridge between the FA complex and FANCD2.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -115,6 +119,7 @@
"category": "biolink:Disease",
"name": "Fanconi renotubular syndrome 1",
"full_name": null,
+ "deprecated": null,
"description": null,
"xref": [],
"provided_by": "phenio_nodes",
@@ -142,6 +147,7 @@
"category": "biolink:Disease",
"name": "Fanconi anemia",
"full_name": null,
+ "deprecated": null,
"description": "Fanconi anemia (FA) is a hereditary DNA repair disorder characterized by progressive pancytopenia with bone marrow failure, variable congenital malformations and predisposition to develop hematological or solid tumors.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -166,6 +172,7 @@
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group O",
"full_name": null,
+ "deprecated": null,
"description": "Any Fanconi anemia in which the cause of the disease is a mutation in the RAD51C gene.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -191,6 +198,7 @@
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group P",
"full_name": null,
+ "deprecated": null,
"description": "Any Fanconi anemia in which the cause of the disease is a mutation in the SLX4 gene.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -216,6 +224,7 @@
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group V",
"full_name": null,
+ "deprecated": null,
"description": "Any Fanconi anemia in which the cause of the disease is a mutation in the MAD2L2 gene.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -241,6 +250,7 @@
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group B",
"full_name": null,
+ "deprecated": null,
"description": "Fanconi anemia caused by mutations of the FANCB gene. This gene encodes the protein for complementation group B.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -268,6 +278,7 @@
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group N",
"full_name": null,
+ "deprecated": null,
"description": "Any Fanconi anemia in which the cause of the disease is a mutation in the PALB2 gene.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -292,6 +303,7 @@
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group R",
"full_name": null,
+ "deprecated": null,
"description": "Any Fanconi anemia in which the cause of the disease is a mutation in the RAD51 gene.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -316,6 +328,7 @@
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group U",
"full_name": null,
+ "deprecated": null,
"description": "Any Fanconi anemia in which the cause of the disease is a mutation in the XRCC2 gene.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -335,30 +348,12 @@
"highlight": null,
"score": null
},
- {
- "id": "MONDO:0100136",
- "category": "biolink:Disease",
- "name": "obsolete Fanconia anemia complementation group M",
- "full_name": null,
- "description": "OBSOLETE Any Fanconi anemia in which the cause of the disease is a mutation in the FANCM gene.",
- "xref": [],
- "provided_by": "phenio_nodes",
- "in_taxon": null,
- "in_taxon_label": null,
- "symbol": null,
- "synonym": [
- "FANCM Fanconi anemia",
- "Fanconi anemia caused by mutation in FANCM"
- ],
- "uri": null,
- "highlight": null,
- "score": null
- },
{
"id": "MONDO:0009213",
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group C",
"full_name": null,
+ "deprecated": null,
"description": "Fanconi anemia caused by mutations of the FANCC gene. This gene provides instructions for making a protein that delays the onset of apoptosis and promotes homologous recombination repair of damaged DNA.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -386,6 +381,7 @@
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group D2",
"full_name": null,
+ "deprecated": null,
"description": "Fanconi anemia caused by mutations of the FANCD2 gene. This gene is involved in the repair of DNA double-strand breaks, both by homologous recombination and single-strand annealing.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -412,6 +408,7 @@
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group I",
"full_name": null,
+ "deprecated": null,
"description": "Fanconi anemia caused by mutations in the FANCI gene, encoding Fanconi anemia group I protein.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -435,6 +432,7 @@
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group Q",
"full_name": null,
+ "deprecated": null,
"description": "Any Fanconi anemia in which the cause of the disease is a mutation in the ERCC4 gene.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -458,6 +456,7 @@
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group T",
"full_name": null,
+ "deprecated": null,
"description": "Any Fanconi anemia in which the cause of the disease is a mutation in the UBE2T gene.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -481,6 +480,7 @@
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group F",
"full_name": null,
+ "deprecated": null,
"description": "Fanconi anemia caused by mutations of the FANCF gene. This gene encodes a polypeptide with homology to the prokaryotic RNA-binding protein ROM.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -497,6 +497,29 @@
"uri": null,
"highlight": null,
"score": null
+ },
+ {
+ "id": "MONDO:0012187",
+ "category": "biolink:Disease",
+ "name": "Fanconi anemia complementation group J",
+ "full_name": null,
+ "deprecated": null,
+ "description": "Fanconi anemia caused by mutations in the BRIP1 gene, encoding Fanconi anemia group J protein.",
+ "xref": [],
+ "provided_by": "phenio_nodes",
+ "in_taxon": null,
+ "in_taxon_label": null,
+ "symbol": null,
+ "synonym": [
+ "FANCJ",
+ "Fanconi Anemia, complementation group type J",
+ "Fanconi anemia complementation group J",
+ "Fanconi anemia complementation group type J",
+ "Fanconi anemia, complementation group J"
+ ],
+ "uri": null,
+ "highlight": null,
+ "score": null
}
],
"facet_fields": [],
diff --git a/frontend/fixtures/entity.json b/frontend/fixtures/entity.json
new file mode 100644
index 000000000..342d85492
--- /dev/null
+++ b/frontend/fixtures/entity.json
@@ -0,0 +1,15 @@
+{
+ "id": "MONDO:0020121",
+ "category": "biolink:Disease",
+ "name": "muscular dystrophy",
+ "full_name": null,
+ "deprecated": null,
+ "description": "Muscular dystrophy (MD) refers to a group of more than 30 genetic diseases characterized by progressive weakness and degeneration of the skeletal muscles that control movement. Some forms of MD are seen in newborns, infants or children, while others have late-onset and may not appear until middle age or later. The disorders differ in terms of the distribution and extent of muscle weakness (some forms of MD also affect cardiac muscle), age of onset, rate of progression, and pattern of inheritance. The prognosis for people with MD varies according to the type and progression of the disorder. There is no specific treatment to stop or reverse any form of MD. Treatment is supportive and may include physical therapy, respiratory therapy, speech therapy, orthopedic appliances used for support, corrective orthopedic surgery, and medicationsincluding corticosteroids, anticonvulsants (seizure medications), immunosuppressants, and antibiotics. Some individuals may need assisted ventilation to treat respiratory muscle weaknessor a pacemaker for cardiac (heart)abnormalities.",
+ "xref": [],
+ "provided_by": "phenio_nodes",
+ "in_taxon": null,
+ "in_taxon_label": null,
+ "symbol": null,
+ "synonym": [],
+ "uri": "http://purl.obolibrary.org/obo/MONDO_0020121"
+}
diff --git a/frontend/fixtures/mappings.json b/frontend/fixtures/mappings.json
index 016753b75..aa55cfae2 100644
--- a/frontend/fixtures/mappings.json
+++ b/frontend/fixtures/mappings.json
@@ -10,7 +10,7 @@
"object_id": "DOID:9884",
"object_label": "muscular dystrophy",
"mapping_justification": "semapv:UnspecifiedMatching",
- "id": "cda26856-16a7-499c-956f-119cbaac5b96"
+ "id": "074f33ef-cab8-46e9-b535-5c637220dcd1"
},
{
"subject_id": "MONDO:0020121",
@@ -19,7 +19,7 @@
"object_id": "ICD10CM:G71.0",
"object_label": "Muscular dystrophy",
"mapping_justification": "semapv:UnspecifiedMatching",
- "id": "25777569-b997-4c8f-a1f3-5af352a16ee1"
+ "id": "575115b8-67a4-482d-88e7-1b1b60fdd99a"
},
{
"subject_id": "MONDO:0020121",
@@ -28,7 +28,7 @@
"object_id": "MESH:D009136",
"object_label": null,
"mapping_justification": "semapv:UnspecifiedMatching",
- "id": "819ab197-2ab1-4b73-8d0f-d7d4ec14d8a7"
+ "id": "a2f1233e-1951-4f40-9a79-60f591a24bb5"
},
{
"subject_id": "MONDO:0020121",
@@ -37,7 +37,7 @@
"object_id": "NCIT:C84910",
"object_label": "Muscular Dystrophy",
"mapping_justification": "semapv:UnspecifiedMatching",
- "id": "adb4b8ed-c4dc-4353-a08e-a4cb02b1826e"
+ "id": "73eaeaef-9868-4e50-a4ed-aee537a830ae"
},
{
"subject_id": "MONDO:0020121",
@@ -46,7 +46,7 @@
"object_id": "SCTID:73297009",
"object_label": null,
"mapping_justification": "semapv:UnspecifiedMatching",
- "id": "f6417283-c9d1-4289-aee6-16d30a4445b1"
+ "id": "3f7aa4af-411c-47fe-9b3a-d8248484ea2d"
},
{
"subject_id": "MONDO:0020121",
@@ -55,7 +55,7 @@
"object_id": "UMLS:C0026850",
"object_label": null,
"mapping_justification": "semapv:UnspecifiedMatching",
- "id": "93968631-eedb-448b-b58a-e31e3e411dde"
+ "id": "f8d6fe34-2d2a-4ace-a314-f4def3070e3a"
},
{
"subject_id": "MONDO:0020121",
@@ -64,7 +64,7 @@
"object_id": "Orphanet:98473",
"object_label": null,
"mapping_justification": "semapv:UnspecifiedMatching",
- "id": "e39e8ba9-8d7e-4b33-9f46-3867b652bdb5"
+ "id": "63588ca1-4204-4143-88b3-152b31ea0c41"
}
]
}
diff --git a/frontend/fixtures/node.json b/frontend/fixtures/node.json
index 59c31e723..f6ced88f6 100644
--- a/frontend/fixtures/node.json
+++ b/frontend/fixtures/node.json
@@ -3,6 +3,7 @@
"category": "biolink:Disease",
"name": "muscular dystrophy",
"full_name": null,
+ "deprecated": null,
"description": "Muscular dystrophy (MD) refers to a group of more than 30 genetic diseases characterized by progressive weakness and degeneration of the skeletal muscles that control movement. Some forms of MD are seen in newborns, infants or children, while others have late-onset and may not appear until middle age or later. The disorders differ in terms of the distribution and extent of muscle weakness (some forms of MD also affect cardiac muscle), age of onset, rate of progression, and pattern of inheritance. The prognosis for people with MD varies according to the type and progression of the disorder. There is no specific treatment to stop or reverse any form of MD. Treatment is supportive and may include physical therapy, respiratory therapy, speech therapy, orthopedic appliances used for support, corrective orthopedic surgery, and medicationsincluding corticosteroids, anticonvulsants (seizure medications), immunosuppressants, and antibiotics. Some individuals may need assisted ventilation to treat respiratory muscle weaknessor a pacemaker for cardiac (heart)abnormalities.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -10,6 +11,7 @@
"in_taxon_label": null,
"symbol": null,
"synonym": [],
+ "uri": null,
"inheritance": null,
"causal_gene": [],
"causes_disease": [],
@@ -68,43 +70,49 @@
"node_hierarchy": {
"super_classes": [
{
- "id": "MONDO:0005336",
+ "id": "MONDO:0019056",
"category": "biolink:Disease",
- "name": "myopathy",
+ "name": "neuromuscular disease",
"full_name": null,
+ "deprecated": null,
"description": null,
"xref": [],
"provided_by": null,
"in_taxon": null,
"in_taxon_label": null,
"symbol": null,
- "synonym": []
+ "synonym": [],
+ "uri": null
},
{
"id": "MONDO:0700223",
"category": "biolink:Disease",
"name": "hereditary skeletal muscle disorder",
"full_name": null,
+ "deprecated": null,
"description": null,
"xref": [],
"provided_by": null,
"in_taxon": null,
"in_taxon_label": null,
"symbol": null,
- "synonym": []
+ "synonym": [],
+ "uri": null
},
{
- "id": "MONDO:0019056",
+ "id": "MONDO:0005336",
"category": "biolink:Disease",
- "name": "neuromuscular disease",
+ "name": "myopathy",
"full_name": null,
+ "deprecated": null,
"description": null,
"xref": [],
"provided_by": null,
"in_taxon": null,
"in_taxon_label": null,
"symbol": null,
- "synonym": []
+ "synonym": [],
+ "uri": null
}
],
"sub_classes": [
@@ -113,130 +121,150 @@
"category": "biolink:Disease",
"name": "muscular dystrophy, Barnes type",
"full_name": null,
+ "deprecated": null,
"description": null,
"xref": [],
"provided_by": null,
"in_taxon": null,
"in_taxon_label": null,
"symbol": null,
- "synonym": []
+ "synonym": [],
+ "uri": null
},
{
"id": "MONDO:0010675",
"category": "biolink:Disease",
"name": "muscular dystrophy, cardiac type",
"full_name": null,
+ "deprecated": null,
"description": null,
"xref": [],
"provided_by": null,
"in_taxon": null,
"in_taxon_label": null,
"symbol": null,
- "synonym": []
+ "synonym": [],
+ "uri": null
},
{
"id": "MONDO:0010676",
"category": "biolink:Disease",
"name": "muscular dystrophy, Hemizygous lethal type",
"full_name": null,
+ "deprecated": null,
"description": null,
"xref": [],
"provided_by": null,
"in_taxon": null,
"in_taxon_label": null,
"symbol": null,
- "synonym": []
+ "synonym": [],
+ "uri": null
},
{
"id": "MONDO:0010677",
"category": "biolink:Disease",
"name": "muscular dystrophy, Mabry type",
"full_name": null,
+ "deprecated": null,
"description": null,
"xref": [],
"provided_by": null,
"in_taxon": null,
"in_taxon_label": null,
"symbol": null,
- "synonym": []
+ "synonym": [],
+ "uri": null
},
{
"id": "MONDO:0010678",
"category": "biolink:Disease",
"name": "muscular dystrophy, progressive Pectorodorsal",
"full_name": null,
+ "deprecated": null,
"description": null,
"xref": [],
"provided_by": null,
"in_taxon": null,
"in_taxon_label": null,
"symbol": null,
- "synonym": []
+ "synonym": [],
+ "uri": null
},
{
- "id": "MONDO:0016106",
+ "id": "MONDO:0019950",
"category": "biolink:Disease",
- "name": "progressive muscular dystrophy",
+ "name": "congenital muscular dystrophy",
"full_name": null,
+ "deprecated": null,
"description": null,
"xref": [],
"provided_by": null,
"in_taxon": null,
"in_taxon_label": null,
"symbol": null,
- "synonym": []
+ "synonym": [],
+ "uri": null
},
{
- "id": "MONDO:0018949",
+ "id": "MONDO:0023204",
"category": "biolink:Disease",
- "name": "distal myopathy",
+ "name": "Fukuda-Miyanomae-Nakata syndrome",
"full_name": null,
+ "deprecated": null,
"description": null,
"xref": [],
"provided_by": null,
"in_taxon": null,
"in_taxon_label": null,
"symbol": null,
- "synonym": []
+ "synonym": [],
+ "uri": null
},
{
- "id": "MONDO:0019950",
+ "id": "MONDO:0100228",
"category": "biolink:Disease",
- "name": "congenital muscular dystrophy",
+ "name": "LAMA2-related muscular dystrophy",
"full_name": null,
+ "deprecated": null,
"description": null,
"xref": [],
"provided_by": null,
"in_taxon": null,
"in_taxon_label": null,
"symbol": null,
- "synonym": []
+ "synonym": [],
+ "uri": null
},
{
- "id": "MONDO:0023204",
+ "id": "MONDO:0018949",
"category": "biolink:Disease",
- "name": "Fukuda-Miyanomae-Nakata syndrome",
+ "name": "distal myopathy",
"full_name": null,
+ "deprecated": null,
"description": null,
"xref": [],
"provided_by": null,
"in_taxon": null,
"in_taxon_label": null,
"symbol": null,
- "synonym": []
+ "synonym": [],
+ "uri": null
},
{
- "id": "MONDO:0100228",
+ "id": "MONDO:0016106",
"category": "biolink:Disease",
- "name": "LAMA2-related muscular dystrophy",
+ "name": "progressive muscular dystrophy",
"full_name": null,
+ "deprecated": null,
"description": null,
"xref": [],
"provided_by": null,
"in_taxon": null,
"in_taxon_label": null,
"symbol": null,
- "synonym": []
+ "synonym": [],
+ "uri": null
}
]
}
diff --git a/frontend/fixtures/phenotype-explorer-compare.json b/frontend/fixtures/phenotype-explorer-compare.json
index 0002ff6b2..47898790d 100644
--- a/frontend/fixtures/phenotype-explorer-compare.json
+++ b/frontend/fixtures/phenotype-explorer-compare.json
@@ -1,4291 +1,106 @@
{
"subject_termset": {
- "HP:0000869": {
- "id": "HP:0000869",
- "label": "Secondary amenorrhea (HPO)"
+ "MP:0002169": {
+ "id": "MP:0002169",
+ "label": "no abnormal phenotype detected (MPO)"
},
- "HP:0000135": {
- "id": "HP:0000135",
- "label": "Hypogonadism (HPO)"
- },
- "HP:0007495": {
- "id": "HP:0007495",
- "label": "Prematurely aged appearance (HPO)"
- },
- "HP:0000822": {
- "id": "HP:0000822",
- "label": "Hypertension (HPO)"
- },
- "HP:0010721": {
- "id": "HP:0010721",
- "label": "Abnormal hair whorl (HPO)"
- },
- "HP:0100659": {
- "id": "HP:0100659",
- "label": "Abnormal cerebral vascular morphology (HPO)"
- },
- "HP:0000939": {
- "id": "HP:0000939",
- "label": "Osteoporosis (HPO)"
- },
- "HP:0040217": {
- "id": "HP:0040217",
- "label": "Elevated hemoglobin A1c (HPO)"
- },
- "HP:0100585": {
- "id": "HP:0100585",
- "label": "Telangiectasia of the skin (HPO)"
- },
- "HP:0005328": {
- "id": "HP:0005328",
- "label": "Progeroid facial appearance (HPO)"
- },
- "HP:0002209": {
- "id": "HP:0002209",
- "label": "Sparse scalp hair (HPO)"
- },
- "HP:0004415": {
- "id": "HP:0004415",
- "label": "Pulmonary artery stenosis (HPO)"
- },
- "HP:0000855": {
- "id": "HP:0000855",
- "label": "Insulin resistance (HPO)"
- },
- "HP:0002621": {
- "id": "HP:0002621",
- "label": "Atherosclerosis (HPO)"
- },
- "HP:0002216": {
- "id": "HP:0002216",
- "label": "Premature graying of hair (HPO)"
- },
- "HP:0012056": {
- "id": "HP:0012056",
- "label": "Cutaneous melanoma (HPO)"
- },
- "HP:0002664": {
- "id": "HP:0002664",
- "label": "Neoplasm (HPO)"
- },
- "HP:0000320": {
- "id": "HP:0000320",
- "label": "Bird-like facies (HPO)"
- },
- "HP:0002293": {
- "id": "HP:0002293",
- "label": "Alopecia of scalp (HPO)"
- },
- "HP:0002861": {
- "id": "HP:0002861",
- "label": "Melanoma (HPO)"
- },
- "HP:0009125": {
- "id": "HP:0009125",
- "label": "Lipodystrophy (HPO)"
- },
- "HP:0003002": {
- "id": "HP:0003002",
- "label": "Breast carcinoma (HPO)"
- },
- "HP:0200042": {
- "id": "HP:0200042",
- "label": "Skin ulcer (HPO)"
- },
- "HP:0004349": {
- "id": "HP:0004349",
- "label": "Reduced bone mineral density (HPO)"
- },
- "HP:0001620": {
- "id": "HP:0001620",
- "label": "High pitched voice (HPO)"
- },
- "HP:0002211": {
- "id": "HP:0002211",
- "label": "White forelock (HPO)"
- },
- "HP:0000765": {
- "id": "HP:0000765",
- "label": "Abnormal thorax morphology (HPO)"
- },
- "HP:0000035": {
- "id": "HP:0000035",
- "label": "Abnormal testis morphology (HPO)"
- },
- "HP:0002890": {
- "id": "HP:0002890",
- "label": "Thyroid carcinoma (HPO)"
- },
- "HP:0000934": {
- "id": "HP:0000934",
- "label": "Chondrocalcinosis (HPO)"
- },
- "HP:0002672": {
- "id": "HP:0002672",
- "label": "Gastrointestinal carcinoma (HPO)"
- },
- "HP:0002860": {
- "id": "HP:0002860",
- "label": "Squamous cell carcinoma (HPO)"
- },
- "HP:0003777": {
- "id": "HP:0003777",
- "label": "Pili torti (HPO)"
- },
- "HP:0011001": {
- "id": "HP:0011001",
- "label": "Increased bone mineral density (HPO)"
- },
- "HP:0005177": {
- "id": "HP:0005177",
- "label": "Premature arteriosclerosis (HPO)"
- },
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- "id": "HP:0010468",
- "label": "Aplasia/Hypoplasia of the testes (HPO)"
- },
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- "id": "HP:0001608",
- "label": "Abnormality of the voice (HPO)"
- },
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- "id": "HP:0012060",
- "label": "Acral lentiginous melanoma (HPO)"
- },
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- "id": "HP:0000144",
- "label": "Decreased fertility (HPO)"
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- "id": "HP:0001601",
- "label": "Laryngomalacia (HPO)"
- },
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- "id": "HP:0001387",
- "label": "Joint stiffness (HPO)"
- },
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- "id": "HP:0002669",
- "label": "Osteosarcoma (HPO)"
- },
- "HP:0000819": {
- "id": "HP:0000819",
- "label": "Diabetes mellitus (HPO)"
- },
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- "id": "HP:0002155",
- "label": "Hypertriglyceridemia (HPO)"
- },
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- "id": "HP:0007703",
- "label": "Abnormality of retinal pigmentation (HPO)"
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- "id": "HP:0000518",
- "label": "Cataract (HPO)"
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- "id": "HP:0000444",
- "label": "Convex nasal ridge (HPO)"
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- "id": "HP:0200055",
- "label": "Small hand (HPO)"
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- "id": "HP:0004322",
- "label": "Short stature (HPO)"
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- "id": "HP:0100679",
- "label": "Lack of skin elasticity (HPO)"
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- "id": "HP:0100578",
- "label": "Lipoatrophy (HPO)"
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- "id": "HP:0100324",
- "label": "Scleroderma (HPO)"
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- "id": "HP:0031964",
- "label": "Elevated circulating alanine aminotransferase concentration (HPO)"
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- "id": "HP:0003419",
- "label": "Low back pain (HPO)"
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- "id": "HP:0100833",
- "label": "Neoplasm of the small intestine (HPO)"
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- "id": "HP:0005978",
- "label": "Type II diabetes mellitus (HPO)"
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- "id": "HP:0001838",
- "label": "Rocker bottom foot (HPO)"
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- "label": "Skeletal muscle atrophy (HPO)"
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- "label": "Subcutaneous calcification (HPO)"
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- "id": "HP:0000962",
- "label": "Hyperkeratosis (HPO)"
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- "id": "HP:0000546",
- "label": "Retinal degeneration (HPO)"
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- "id": "HP:0100615",
- "label": "Ovarian neoplasm (HPO)"
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- "id": "HP:0100649",
- "label": "Neoplasm of the oral cavity (HPO)"
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- "id": "HP:0002858",
- "label": "Meningioma (HPO)"
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- "id": "HP:0100526",
- "label": "Neoplasm of the lung (HPO)"
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- "id": "HP:0001635",
- "label": "Congestive heart failure (HPO)"
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- "id": "HP:0009726",
- "label": "Renal neoplasm (HPO)"
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- "id": "HP:0001533",
- "label": "Slender build (HPO)"
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- "id": "HP:0100242",
- "label": "Sarcoma (HPO)"
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- "id": "HP:0031956",
- "label": "Elevated circulating aspartate aminotransferase concentration (HPO)"
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}
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- "id": "HP:0002020",
- "label": "Gastroesophageal reflux (HPO)"
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- "id": "HP:0007495",
- "label": "Prematurely aged appearance (HPO)"
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- "label": "Epicanthus (HPO)"
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- "label": "Abnormal heart valve physiology (HPO)"
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- "match_target_label": "Pulmonary artery stenosis (HPO)",
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- "ancestor_id": "HP:0011004",
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- "HP:0006243": {
- "match_source": "HP:0006243",
- "match_source_label": "Phalangeal dislocation (HPO)",
- "match_target": "HP:0000934",
- "match_target_label": "Chondrocalcinosis (HPO)",
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- "HP:0007495": {
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- "match_source_label": "Prematurely aged appearance (HPO)",
- "match_target": "HP:0007495",
- "match_target_label": "Prematurely aged appearance (HPO)",
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- "ancestor_id": "HP:0007495",
- "ancestor_label": "Prematurely aged appearance (HPO)",
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- "HP:0009763": {
- "match_source": "HP:0009763",
- "match_source_label": "Limb pain (HPO)",
- "match_target": "HP:0003419",
- "match_target_label": "Low back pain (HPO)",
- "score": 12.074278328576016,
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- "match_subsumer_label": null,
- "similarity": {
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- "object_id": "HP:0003419",
- "object_label": null,
- "object_source": null,
- "ancestor_id": "HP:0012531",
- "ancestor_label": "",
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- "object_information_content": null,
- "subject_information_content": null,
- "ancestor_information_content": 12.074278328576016,
- "jaccard_similarity": 0.5185185185185185,
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- "phenodigm_score": 2.5021464607639357
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- "HP:0010749": {
- "match_source": "HP:0010749",
- "match_source_label": "Blepharochalasis (HPO)",
- "match_target": "HP:0000320",
- "match_target_label": "Bird-like facies (HPO)",
- "score": 12.311317525876866,
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- "match_subsumer_label": null,
- "similarity": {
- "subject_id": "HP:0010749",
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- "subject_source": null,
- "object_id": "HP:0000320",
- "object_label": null,
- "object_source": null,
- "ancestor_id": "HP:0001999",
- "ancestor_label": "",
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- "subject_information_content": null,
- "ancestor_information_content": 12.311317525876866,
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- "phenodigm_score": 2.2531826311761236
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- },
- "HP:0010750": {
- "match_source": "HP:0010750",
- "match_source_label": "Dermatochalasis (HPO)",
- "match_target": "HP:0007703",
- "match_target_label": "Abnormality of retinal pigmentation (HPO)",
- "score": 7.709281511796768,
- "match_subsumer": null,
- "match_subsumer_label": null,
- "similarity": {
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- "object_id": "HP:0007703",
- "object_label": null,
- "object_source": null,
- "ancestor_id": "HP:0000315",
- "ancestor_label": "",
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- "ancestor_information_content": 7.709281511796768,
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- "phenodigm_score": 2.0555484159025257
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- "HP:0010754": {
- "match_source": "HP:0010754",
- "match_source_label": "Abnormality of the temporomandibular joint (HPO)",
- "match_target": "HP:0100649",
- "match_target_label": "Neoplasm of the oral cavity (HPO)",
- "score": 9.152888163272383,
- "match_subsumer": null,
- "match_subsumer_label": null,
- "similarity": {
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- "subject_source": null,
- "object_id": "HP:0100649",
- "object_label": null,
- "object_source": null,
- "ancestor_id": "HP:0031816",
- "ancestor_label": "",
- "ancestor_source": null,
- "object_information_content": null,
- "subject_information_content": null,
- "ancestor_information_content": 9.152888163272383,
- "jaccard_similarity": 0.41353383458646614,
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- "phenodigm_score": 1.9455150833902846
- }
- },
- "HP:0012378": {
- "match_source": "HP:0012378",
- "match_source_label": "Fatigue (HPO)",
- "match_target": "HP:0003419",
- "match_target_label": "Low back pain (HPO)",
- "score": 11.324256581584363,
- "match_subsumer": null,
- "match_subsumer_label": null,
- "similarity": {
- "subject_id": "HP:0012378",
- "subject_label": null,
- "subject_source": null,
- "object_id": "HP:0003419",
- "object_label": null,
- "object_source": null,
- "ancestor_id": "HP:0025142",
- "ancestor_label": "",
- "ancestor_source": null,
- "object_information_content": null,
- "subject_information_content": null,
- "ancestor_information_content": 11.324256581584363,
- "jaccard_similarity": 0.36,
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- "phenodigm_score": 2.0190919665459446
- }
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- "HP:0012450": {
- "match_source": "HP:0012450",
- "match_source_label": "Chronic constipation (HPO)",
- "match_target": "HP:0100833",
- "match_target_label": "Neoplasm of the small intestine (HPO)",
- "score": 7.826350815132431,
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- "match_subsumer_label": null,
- "similarity": {
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- "subject_label": null,
- "subject_source": null,
- "object_id": "HP:0100833",
- "object_label": null,
- "object_source": null,
- "ancestor_id": "HP:0025031",
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- "ancestor_information_content": 7.826350815132431,
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- "HP:0025014": {
- "match_source": "HP:0025014",
- "match_source_label": "Subcutaneous spheroids (HPO)",
- "match_target": "HP:0008065",
- "match_target_label": "Aplasia/Hypoplasia of the skin (HPO)",
- "score": 10.72635502515571,
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- "match_subsumer_label": null,
- "similarity": {
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- "subject_source": null,
- "object_id": "HP:0008065",
- "object_label": null,
- "object_source": null,
- "ancestor_id": "HP:0011355",
- "ancestor_label": "",
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- "object_information_content": null,
- "subject_information_content": null,
- "ancestor_information_content": 10.72635502515571,
- "jaccard_similarity": 0.8333333333333334,
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- "phenodigm_score": 2.9897540346372575
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- "HP:0025019": {
- "match_source": "HP:0025019",
- "match_source_label": "Arterial rupture (HPO)",
- "match_target": "HP:0000822",
- "match_target_label": "Hypertension (HPO)",
- "score": 9.47121402147955,
- "match_subsumer": null,
- "match_subsumer_label": null,
- "similarity": {
- "subject_id": "HP:0025019",
- "subject_label": null,
- "subject_source": null,
- "object_id": "HP:0000822",
- "object_label": null,
- "object_source": null,
- "ancestor_id": "HP:0011025",
- "ancestor_label": "",
- "ancestor_source": null,
- "object_information_content": null,
- "subject_information_content": null,
- "ancestor_information_content": 9.47121402147955,
- "jaccard_similarity": 0.6557377049180327,
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- "dice_similarity": null,
- "phenodigm_score": 2.4921139912196013
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- },
- "HP:0025509": {
- "match_source": "HP:0025509",
- "match_source_label": "Piezogenic pedal papules (HPO)",
- "match_target": "HP:0200042",
- "match_target_label": "Skin ulcer (HPO)",
- "score": 10.72635502515571,
- "match_subsumer": null,
- "match_subsumer_label": null,
- "similarity": {
- "subject_id": "HP:0025509",
- "subject_label": null,
- "subject_source": null,
- "object_id": "HP:0200042",
- "object_label": null,
- "object_source": null,
- "ancestor_id": "HP:0011355",
- "ancestor_label": "",
- "ancestor_source": null,
- "object_information_content": null,
- "subject_information_content": null,
- "ancestor_information_content": 10.72635502515571,
- "jaccard_similarity": 0.9210526315789473,
- "cosine_similarity": null,
- "dice_similarity": null,
- "phenodigm_score": 3.143173161499336
- }
- },
- "HP:0030009": {
- "match_source": "HP:0030009",
- "match_source_label": "Cervical insufficiency (HPO)",
- "match_target": "HP:0100615",
- "match_target_label": "Ovarian neoplasm (HPO)",
- "score": 11.350488123157543,
- "match_subsumer": null,
- "match_subsumer_label": null,
- "similarity": {
- "subject_id": "HP:0030009",
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- "subject_source": null,
- "object_id": "HP:0100615",
- "object_label": null,
- "object_source": null,
- "ancestor_id": "HP:0000008",
- "ancestor_label": "",
- "ancestor_source": null,
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- "subject_information_content": null,
- "ancestor_information_content": 11.350488123157543,
- "jaccard_similarity": 0.6301369863013698,
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- "phenodigm_score": 2.674390094764783
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- },
- "HP:0031364": {
- "match_source": "HP:0031364",
- "match_source_label": "Ecchymosis (HPO)",
- "match_target": "HP:0007618",
- "match_target_label": "Subcutaneous calcification (HPO)",
- "score": 14.533709947213314,
- "match_subsumer": null,
- "match_subsumer_label": null,
- "similarity": {
- "subject_id": "HP:0031364",
- "subject_label": null,
- "subject_source": null,
- "object_id": "HP:0007618",
- "object_label": null,
- "object_source": null,
- "ancestor_id": "UBERON:0011818",
- "ancestor_label": "",
- "ancestor_source": null,
- "object_information_content": null,
- "subject_information_content": null,
- "ancestor_information_content": 14.533709947213314,
- "jaccard_similarity": 0.4222222222222222,
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- "phenodigm_score": 2.47718697539076
- }
- },
- "HP:0031653": {
- "match_source": "HP:0031653",
- "match_source_label": "Abnormal heart valve physiology (HPO)",
- "match_target": "HP:0001635",
- "match_target_label": "Congestive heart failure (HPO)",
- "score": 9.47121402147955,
+ }
+ },
+ "object_best_matches": {
+ "HP:0004325": {
+ "match_source": "HP:0004325",
+ "match_source_label": "Decreased body weight (HPO)",
+ "match_target": "MP:0010771",
+ "match_target_label": "integument phenotype (MPO)",
+ "score": 1.4431977534690428,
"match_subsumer": null,
"match_subsumer_label": null,
"similarity": {
- "subject_id": "HP:0031653",
+ "subject_id": "HP:0004325",
"subject_label": null,
"subject_source": null,
- "object_id": "HP:0001635",
+ "object_id": "MP:0010771",
"object_label": null,
"object_source": null,
- "ancestor_id": "HP:0011025",
+ "ancestor_id": "UPHENO:0001003",
"ancestor_label": "",
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"subject_information_content": null,
- "ancestor_information_content": 9.47121402147955,
- "jaccard_similarity": 0.3972602739726027,
+ "ancestor_information_content": 1.4431977534690428,
+ "jaccard_similarity": 0.3333333333333333,
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- "phenodigm_score": 1.9397260314348834
+ "phenodigm_score": 0.6935891563620457
}
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},
- "average_score": 9.923734289544303,
- "best_score": 17.11867244793447,
+ "average_score": 1.4431977534690428,
+ "best_score": 1.4431977534690428,
"metric": "ancestor_information_content"
}
diff --git a/frontend/fixtures/search.json b/frontend/fixtures/search.json
index 92510b879..ef531a628 100644
--- a/frontend/fixtures/search.json
+++ b/frontend/fixtures/search.json
@@ -8,6 +8,7 @@
"category": "biolink:Disease",
"name": "Fanconi anemia",
"full_name": null,
+ "deprecated": null,
"description": "Fanconi anemia (FA) is a hereditary DNA repair disorder characterized by progressive pancytopenia with bone marrow failure, variable congenital malformations and predisposition to develop hematological or solid tumors.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -32,6 +33,7 @@
"category": "biolink:Disease",
"name": "Fanconi renotubular syndrome",
"full_name": null,
+ "deprecated": null,
"description": "A genetic or acquired disorder characterized by impairment of the function of the proximal tubules of the kidney. It results in decreased reabsorption of electrolytes, glucose, amino acids, and other nutrients.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -61,6 +63,7 @@
"category": "biolink:Disease",
"name": "primary Fanconi syndrome",
"full_name": null,
+ "deprecated": null,
"description": "A condition in which the kidneys do not absorb certain substances into the body. These substances, such as cysteine, fructose, galactose, or glycogen, are lost in the urine. Fanconi syndrome is thought to be caused by genetic and environmental factors, and it may be diagnosed at any age. Symptoms of Fanconi syndrome include increased urine production (which may cause dehydration), weakness, and abnormalities of the bones.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -81,6 +84,7 @@
"category": "biolink:Disease",
"name": "Fanconi-like syndrome",
"full_name": null,
+ "deprecated": null,
"description": "A syndrome characterized by pancytopenia, immune deficiency and cutaneous malignancies.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -97,6 +101,7 @@
"category": "biolink:Disease",
"name": "adult Fanconi syndrome",
"full_name": null,
+ "deprecated": null,
"description": "Probably related to a recessive gene, this is Fanconi Syndrome, characterised by adult onset.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -113,6 +118,7 @@
"category": "biolink:Disease",
"name": "acquired Fanconi syndrome",
"full_name": null,
+ "deprecated": null,
"description": "Fanconi Syndrome caused by exposure to noxious agents.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -124,27 +130,12 @@
"highlight": null,
"score": null
},
- {
- "id": "MONDO:0000026",
- "category": "biolink:Disease",
- "name": "obsolete Fanconi renotubular syndrome",
- "full_name": null,
- "description": null,
- "xref": [],
- "provided_by": "phenio_nodes",
- "in_taxon": null,
- "in_taxon_label": null,
- "symbol": null,
- "synonym": [],
- "uri": null,
- "highlight": null,
- "score": null
- },
{
"id": "MONDO:0013247",
"category": "biolink:Disease",
"name": "Fanconi renotubular syndrome 2",
"full_name": null,
+ "deprecated": null,
"description": "Any Fanconi syndrome in which the cause of the disease is a mutation in the SLC34A1 gene.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -167,6 +158,7 @@
"category": "biolink:Disease",
"name": "Fanconi renotubular syndrome 3",
"full_name": null,
+ "deprecated": null,
"description": "Any Fanconi syndrome in which the cause of the disease is a mutation in the EHHADH gene.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -189,6 +181,7 @@
"category": "biolink:Disease",
"name": "Fanconi renotubular syndrome 1",
"full_name": null,
+ "deprecated": null,
"description": null,
"xref": [],
"provided_by": "phenio_nodes",
@@ -216,6 +209,7 @@
"category": "biolink:Disease",
"name": "Fanconi renotubular syndrome 5",
"full_name": null,
+ "deprecated": null,
"description": null,
"xref": [],
"provided_by": "phenio_nodes",
@@ -237,6 +231,7 @@
"category": "biolink:Disease",
"name": "inherited Fanconi renotubular syndrome",
"full_name": null,
+ "deprecated": null,
"description": "An instance of Fanconi renotubular syndrome that is inherited.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -253,6 +248,7 @@
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group C",
"full_name": null,
+ "deprecated": null,
"description": "Fanconi anemia caused by mutations of the FANCC gene. This gene provides instructions for making a protein that delays the onset of apoptosis and promotes homologous recombination repair of damaged DNA.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -280,6 +276,7 @@
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group D2",
"full_name": null,
+ "deprecated": null,
"description": "Fanconi anemia caused by mutations of the FANCD2 gene. This gene is involved in the repair of DNA double-strand breaks, both by homologous recombination and single-strand annealing.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -306,6 +303,7 @@
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group A",
"full_name": null,
+ "deprecated": null,
"description": "Fanconi anemia caused by mutations of the FANCA gene. FANCA gene mutations are the most common cause of Fanconi anemia. This gene provides instructions for making a protein that is involved in the Fanconi anemia (FA) pathway.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -334,6 +332,7 @@
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group B",
"full_name": null,
+ "deprecated": null,
"description": "Fanconi anemia caused by mutations of the FANCB gene. This gene encodes the protein for complementation group B.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -361,6 +360,7 @@
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group E",
"full_name": null,
+ "deprecated": null,
"description": "Fanconi anemia caused by mutations of the FANCE gene. This is a protein coding gene. It is required for the nuclear accumulation of FANCC and provides a critical bridge between the FA complex and FANCD2.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -386,6 +386,7 @@
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group F",
"full_name": null,
+ "deprecated": null,
"description": "Fanconi anemia caused by mutations of the FANCF gene. This gene encodes a polypeptide with homology to the prokaryotic RNA-binding protein ROM.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -408,6 +409,7 @@
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group D1",
"full_name": null,
+ "deprecated": null,
"description": "Inherited cancer-predisposing syndrome due to biallelic BRCA2 mutations is a rare cancer-predisposing syndrome, associated with the D1 subgroup of Fanconi anemia (FA), characterized by progressive bone marrow failure, cardiac, brain, intestinal or skeletal abnormalities and predisposition to various malignancies. Bone marrow suppression and the incidence of developmental abnormalities are less frequent than in other FA, but cancer risk is very high with the spectrum of childhood cancers including Wilms tumor, brain tumor (often medulloblastoma) and ALL/AML.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -431,6 +433,7 @@
"category": "biolink:Disease",
"name": "Fanconi anemia complementation group I",
"full_name": null,
+ "deprecated": null,
"description": "Fanconi anemia caused by mutations in the FANCI gene, encoding Fanconi anemia group I protein.",
"xref": [],
"provided_by": "phenio_nodes",
@@ -448,6 +451,29 @@
"uri": null,
"highlight": null,
"score": null
+ },
+ {
+ "id": "MONDO:0012187",
+ "category": "biolink:Disease",
+ "name": "Fanconi anemia complementation group J",
+ "full_name": null,
+ "deprecated": null,
+ "description": "Fanconi anemia caused by mutations in the BRIP1 gene, encoding Fanconi anemia group J protein.",
+ "xref": [],
+ "provided_by": "phenio_nodes",
+ "in_taxon": null,
+ "in_taxon_label": null,
+ "symbol": null,
+ "synonym": [
+ "FANCJ",
+ "Fanconi Anemia, complementation group type J",
+ "Fanconi anemia complementation group J",
+ "Fanconi anemia complementation group type J",
+ "Fanconi anemia, complementation group J"
+ ],
+ "uri": null,
+ "highlight": null,
+ "score": null
}
],
"facet_fields": [],
diff --git a/frontend/src/App.vue b/frontend/src/App.vue
index 8ee4306e3..932b21bc6 100644
--- a/frontend/src/App.vue
+++ b/frontend/src/App.vue
@@ -15,8 +15,8 @@
>DEV VERSION successor to the
old web app here. Not all features are implemented yet. Please use the feedback form to
- tell us what you think!
+ >. Not all features are implemented yet. Please use the feedback form
+ on any page to tell us what you think!
diff --git a/frontend/src/api/model.ts b/frontend/src/api/model.ts
index 50ce66b3b..cc7263ce7 100644
--- a/frontend/src/api/model.ts
+++ b/frontend/src/api/model.ts
@@ -64,6 +64,8 @@ export interface Association {
has_evidence?: string[],
/** List of ExpandedCuries with id and url for evidence */
has_evidence_links?: ExpandedCurie[],
+ /** A concatenation of fields used to group associations with the same essential/defining properties */
+ grouping_key?: string,
provided_by?: string,
/** A link to the docs for the knowledge source that provided the node/edge. */
provided_by_link?: ExpandedCurie,
@@ -234,6 +236,8 @@ export interface DirectionalAssociation extends Association {
has_evidence?: string[],
/** List of ExpandedCuries with id and url for evidence */
has_evidence_links?: ExpandedCurie[],
+ /** A concatenation of fields used to group associations with the same essential/defining properties */
+ grouping_key?: string,
provided_by?: string,
/** A link to the docs for the knowledge source that provided the node/edge. */
provided_by_link?: ExpandedCurie,
@@ -312,6 +316,8 @@ export interface Entity {
name?: string,
/** The long form name of an entity */
full_name?: string,
+ /** A boolean flag indicating that an entity is no longer considered current or valid. */
+ deprecated?: boolean,
description?: string,
xref?: string[],
provided_by?: string,
@@ -321,6 +327,8 @@ export interface Entity {
in_taxon_label?: string,
symbol?: string,
synonym?: string[],
+ /** The URI of the entity */
+ uri?: string,
};
export interface EntityResults extends Results {
@@ -358,7 +366,6 @@ export interface HistoBin extends FacetValue {
/** count of documents */
count?: number,
};
-
/**
* A minimal class to hold a SSSOM mapping
*/
@@ -424,11 +431,15 @@ export interface Node extends Entity {
name?: string,
/** The long form name of an entity */
full_name?: string,
+ /** A boolean flag indicating that an entity is no longer considered current or valid. */
+ deprecated?: boolean,
description?: string,
xref?: string[],
provided_by?: string,
symbol?: string,
synonym?: string[],
+ /** The URI of the entity */
+ uri?: string,
};
export interface NodeHierarchy {
@@ -454,6 +465,8 @@ export interface SearchResult extends Entity {
name: string,
/** The long form name of an entity */
full_name?: string,
+ /** A boolean flag indicating that an entity is no longer considered current or valid. */
+ deprecated?: boolean,
description?: string,
xref?: string[],
provided_by?: string,
@@ -463,6 +476,8 @@ export interface SearchResult extends Entity {
in_taxon_label?: string,
symbol?: string,
synonym?: string[],
+ /** The URI of the entity */
+ uri?: string,
};
export interface SearchResults extends Results {
@@ -488,14 +503,12 @@ export interface PairwiseSimilarity {
* A simple pairwise similarity between two atomic concepts/terms
*/
export interface TermPairwiseSimilarity extends PairwiseSimilarity {
- /** The first of the two entities being compared */
subject_id: string,
/** The name of the subject entity */
subject_label?: string,
/** the source for the first entity */
subject_source?: string,
- /** The second of the two entities being compared */
- object_id?: string,
+ object_id: string,
/** The name of the object entity */
object_label?: string,
/** the source for the second entity */
@@ -506,11 +519,11 @@ export interface TermPairwiseSimilarity extends PairwiseSimilarity {
ancestor_label?: string,
ancestor_source?: string,
/** The IC of the object */
- object_information_content?: string,
+ object_information_content?: number,
/** The IC of the subject */
- subject_information_content?: string,
+ subject_information_content?: number,
/** The IC of the object */
- ancestor_information_content?: string,
+ ancestor_information_content?: number,
/** The number of concepts in the intersection divided by the number in the union */
jaccard_similarity?: number,
/** the dot product of two node embeddings divided by the product of their lengths */
diff --git a/frontend/src/api/phenotype-explorer.ts b/frontend/src/api/phenotype-explorer.ts
index efb4f647e..678cebef5 100644
--- a/frontend/src/api/phenotype-explorer.ts
+++ b/frontend/src/api/phenotype-explorer.ts
@@ -64,7 +64,7 @@ const getPhenotypeAssociations = async (id = ""): Promise => {
"biolink:GeneToPhenotypicFeatureAssociation",
"biolink:DiseaseToPhenotypicFeatureAssociation",
],
- limit: 500,
+ limit: 1000,
direct: true,
};
diff --git a/frontend/src/assets/architecture.png b/frontend/src/assets/architecture.png
index 4163f950f..47c9fe396 100644
Binary files a/frontend/src/assets/architecture.png and b/frontend/src/assets/architecture.png differ
diff --git a/frontend/src/assets/icons/resource-exomiser.svg b/frontend/src/assets/icons/resource-exomiser.svg
new file mode 100644
index 000000000..d4368f4fa
--- /dev/null
+++ b/frontend/src/assets/icons/resource-exomiser.svg
@@ -0,0 +1,22 @@
+
diff --git a/frontend/src/assets/icons/resource-hpo.svg b/frontend/src/assets/icons/resource-hpo.svg
new file mode 100644
index 000000000..8d23ce137
--- /dev/null
+++ b/frontend/src/assets/icons/resource-hpo.svg
@@ -0,0 +1,44 @@
+
+
+
diff --git a/frontend/src/assets/icons/resource-linkml.svg b/frontend/src/assets/icons/resource-linkml.svg
new file mode 100644
index 000000000..92028b021
--- /dev/null
+++ b/frontend/src/assets/icons/resource-linkml.svg
@@ -0,0 +1,38 @@
+
diff --git a/frontend/src/assets/icons/resource-monarch.svg b/frontend/src/assets/icons/resource-monarch.svg
new file mode 100644
index 000000000..1914a5c3a
--- /dev/null
+++ b/frontend/src/assets/icons/resource-monarch.svg
@@ -0,0 +1,50 @@
+
+
+
diff --git a/frontend/src/assets/icons/resource-mondo.svg b/frontend/src/assets/icons/resource-mondo.svg
new file mode 100644
index 000000000..50cfa61c2
--- /dev/null
+++ b/frontend/src/assets/icons/resource-mondo.svg
@@ -0,0 +1,35 @@
+
+
diff --git a/frontend/src/assets/icons/resource-oak.svg b/frontend/src/assets/icons/resource-oak.svg
new file mode 100644
index 000000000..05c1782f8
--- /dev/null
+++ b/frontend/src/assets/icons/resource-oak.svg
@@ -0,0 +1,227 @@
+
diff --git a/frontend/src/assets/icons/resource-phenopackets.svg b/frontend/src/assets/icons/resource-phenopackets.svg
new file mode 100644
index 000000000..5aa5bd170
--- /dev/null
+++ b/frontend/src/assets/icons/resource-phenopackets.svg
@@ -0,0 +1,55 @@
+
diff --git a/frontend/src/assets/icons/resource-sssom.svg b/frontend/src/assets/icons/resource-sssom.svg
new file mode 100644
index 000000000..6e84f328c
--- /dev/null
+++ b/frontend/src/assets/icons/resource-sssom.svg
@@ -0,0 +1,37 @@
+
diff --git a/frontend/src/assets/icons/resource-upheno.svg b/frontend/src/assets/icons/resource-upheno.svg
new file mode 100644
index 000000000..ca4637bd9
--- /dev/null
+++ b/frontend/src/assets/icons/resource-upheno.svg
@@ -0,0 +1,29 @@
+
diff --git a/frontend/src/components/AppButton.vue b/frontend/src/components/AppButton.vue
index 78739eea1..3df70500b 100644
--- a/frontend/src/components/AppButton.vue
+++ b/frontend/src/components/AppButton.vue
@@ -132,7 +132,6 @@ defineExpose({ button });
}
&.small {
- flex-direction: row-reverse;
padding: 3px;
border-radius: $rounded;
diff --git a/frontend/src/components/AppIcon.vue b/frontend/src/components/AppIcon.vue
index d0a1bb4d1..3bb965758 100644
--- a/frontend/src/components/AppIcon.vue
+++ b/frontend/src/components/AppIcon.vue
@@ -105,6 +105,11 @@ const thickness = computed(() => {
.custom {
height: 1em;
+ /** resource icon styles */
+ &[data-icon^="resource-"] {
+ filter: brightness(0.2);
+ }
+
/** category icon styles */
&[data-icon^="category-"],
&[data-icon^="association-"] {
diff --git a/frontend/src/components/AppSelectTags.vue b/frontend/src/components/AppSelectTags.vue
index ccc33e3fd..8aa1d1444 100644
--- a/frontend/src/components/AppSelectTags.vue
+++ b/frontend/src/components/AppSelectTags.vue
@@ -314,12 +314,17 @@ const {
isError,
} = useQuery(
/** get list of results */
- async function () {
+ async function (passedSearch?: string, forceAutoAccept = false) {
/** reset highlighted */
highlighted.value = 0;
/** get results */
- return await props.options(search.value);
+ const result = await props.options(search.value);
+
+ /** force auto-accept */
+ if (forceAutoAccept) result.autoAccept = true;
+
+ return result;
},
/** default value */
@@ -390,6 +395,14 @@ watch(highlighted, () => {
.querySelector(`#option-${id}-${highlighted.value} > *`)
?.scrollIntoView({ block: "nearest" });
});
+
+/** programmatically set search, query results, and auto-accept */
+function runSearch(value: string) {
+ search.value = value;
+ runGetResults("", true);
+}
+
+defineExpose({ runSearch });