From 86ddd8ac9ea0ee9674bdc2f12dd95f5be1db17b9 Mon Sep 17 00:00:00 2001 From: glass-ships Date: Tue, 5 Dec 2023 10:38:59 -0700 Subject: [PATCH 01/13] oaklib still requires prefixmaps < 0.2 --- backend/pyproject.toml | 23 ++++++++++++----------- 1 file changed, 12 insertions(+), 11 deletions(-) diff --git a/backend/pyproject.toml b/backend/pyproject.toml index 748077a20..a16076318 100644 --- a/backend/pyproject.toml +++ b/backend/pyproject.toml @@ -17,22 +17,23 @@ packages = [ [tool.poetry.dependencies] ### Core dependencies python = "^3.9" -pydantic = "^1.10.2" +pydantic = "^2" + +bioregistry = "^0.10.57" curies = "<1" -linkml = "^1.6.2" -prefixmaps = "^0.1.7" +linkml = "^1.6.3" +oaklib = ">=0.5.22" +prefixmaps = "^0.2" -requests = "^2.28.1" -typer = "^0.7.0" -typer-cli = "^0.0.13" -rich = "*" docker = "^6.0.1" -pystow = ">=0.5.0" -loguru = "*" fastapi = "^0.103.1" -oaklib = ">=0.5.19" gunicorn = "^21.2.0" -bioregistry = "^0.10.57" +loguru = "*" +pystow = ">=0.5.0" +requests = "^2.28.1" +rich = "*" +typer = "^0.7.0" +typer-cli = "^0.0.13" [tool.poetry.group.dev.dependencies] From a5ba69ffbe350b8a42cab4801ff7d28efd809bb8 Mon Sep 17 00:00:00 2001 From: glass-ships Date: Wed, 6 Dec 2023 11:28:52 -0700 Subject: [PATCH 02/13] update fixtures and scripts --- Makefile | 2 +- backend/poetry.lock | 1242 +++++++++-------- backend/pyproject.toml | 2 +- backend/src/monarch_py/datamodels/model.py | 228 ++- backend/src/monarch_py/datamodels/solr.py | 6 +- backend/src/monarch_py/utils/utils.py | 16 +- .../fixtures/association_counts_query.py | 2 +- .../fixtures/association_counts_response.py | 2 +- .../fixtures/association_query_direct.py | 2 +- .../fixtures/association_query_indirect.py | 2 +- backend/tests/fixtures/association_table.py | 27 +- .../fixtures/association_table_response.py | 2 +- backend/tests/fixtures/autocomplete_query.py | 2 +- backend/tests/fixtures/histopheno_query.py | 2 +- backend/tests/fixtures/histopheno_response.py | 2 +- backend/tests/fixtures/mapping_query.py | 2 +- backend/tests/fixtures/node.py | 8 +- .../fixtures/phenotype_explorer_compare.py | 2 +- backend/tests/fixtures/search_query.py | 2 +- backend/tests/fixtures/search_response.py | 2 +- frontend/fixtures/association-table.json | 34 +- frontend/fixtures/associations.json | 40 +- frontend/fixtures/autocomplete.json | 2 +- frontend/fixtures/node.json | 8 +- .../fixtures/phenotype-explorer-compare.json | 8 +- frontend/fixtures/search.json | 2 +- frontend/src/components/AppPredicateBadge.vue | 4 +- frontend/src/components/AppTable.vue | 4 +- 28 files changed, 827 insertions(+), 830 deletions(-) diff --git a/Makefile b/Makefile index 008a12bda..63f3bbf22 100644 --- a/Makefile +++ b/Makefile @@ -75,7 +75,7 @@ install-frontend: .PHONY: model model: install-backend - $(RUN) gen-pydantic $(SCHEMADIR)/model.yaml > $(SCHEMADIR)/model.py + $(RUN) gen-pydantic --pydantic-version 2 --extra-fields allow $(SCHEMADIR)/model.yaml > $(SCHEMADIR)/model.py $(RUN) gen-typescript $(SCHEMADIR)/model.yaml > frontend/src/api/model.ts make format diff --git a/backend/poetry.lock b/backend/poetry.lock index b9e59d3cc..28beed4f0 100644 --- a/backend/poetry.lock +++ b/backend/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. [[package]] name = "airium" @@ -26,6 +26,17 @@ files = [ {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"}, ] +[[package]] +name = "annotated-types" +version = "0.6.0" +description = "Reusable constraint types to use with typing.Annotated" +optional = false +python-versions = ">=3.8" +files = [ + {file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43"}, + {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"}, +] + [[package]] name = "antlr4-python3-runtime" version = "4.9.3" @@ -166,18 +177,18 @@ pyparsing = ">=2.0.3" [[package]] name = "bioregistry" -version = "0.10.68" +version = "0.10.96" 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"}, - 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"e05784289c82fa619f8e6a6355cbe78832b342368c35956ad884f7f3063e7f06" +content-hash = "e4b97baa712499ee10c0dae58ce7f940b1475bc3549e6eb49c923c0455903cee" diff --git a/backend/pyproject.toml b/backend/pyproject.toml index a16076318..2548fcba2 100644 --- a/backend/pyproject.toml +++ b/backend/pyproject.toml @@ -21,7 +21,7 @@ pydantic = "^2" bioregistry = "^0.10.57" curies = "<1" -linkml = "^1.6.3" +linkml = { git = "https://github.com/linkml/linkml.git", branch = "allow-extra-fields" } # "^1.6" oaklib = ">=0.5.22" prefixmaps = "^0.2" diff --git a/backend/src/monarch_py/datamodels/model.py b/backend/src/monarch_py/datamodels/model.py index 1c96d4a1b..6761a879c 100644 --- a/backend/src/monarch_py/datamodels/model.py +++ b/backend/src/monarch_py/datamodels/model.py @@ -15,20 +15,14 @@ version = "None" -class WeakRefShimBaseModel(BaseModel): - __slots__ = "__weakref__" - - -class ConfiguredBaseModel( - WeakRefShimBaseModel, - validate_assignment=True, - validate_all=True, - underscore_attrs_are_private=True, - extra="forbid", - arbitrary_types_allowed=True, - use_enum_values=True, -): - pass +class ConfiguredBaseModel(BaseModel): + model_config = ConfigDict( + validate_assignment=True, + validate_default=True, + extra="allow", + arbitrary_types_allowed=True, + use_enum_values=True, + ) class AssociationDirectionEnum(str, Enum): @@ -51,13 +45,11 @@ class Association(ConfiguredBaseModel): subject_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the subject entity""") subject_category: Optional[str] = Field(None, description="""The category of the subject entity""") subject_closure: Optional[List[str]] = Field( - default_factory=list, - description="""Field containing subject id and the ids of all of it's ancestors""", + default_factory=list, description="""Field containing subject id and the ids of all of it's ancestors""" ) subject_label: Optional[str] = Field(None, description="""The name of the subject entity""") subject_closure_label: Optional[List[str]] = Field( - default_factory=list, - description="""Field containing subject name and the names of all of it's ancestors""", + default_factory=list, description="""Field containing subject name and the names of all of it's ancestors""" ) subject_taxon: Optional[str] = Field(None) subject_taxon_label: Optional[str] = Field(None) @@ -67,13 +59,11 @@ class Association(ConfiguredBaseModel): object_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the object entity""") object_category: Optional[str] = Field(None, description="""The category of the object entity""") object_closure: Optional[List[str]] = Field( - default_factory=list, - description="""Field containing object id and the ids of all of it's ancestors""", + default_factory=list, description="""Field containing object id and the ids of all of it's ancestors""" ) object_label: Optional[str] = Field(None, description="""The name of the object entity""") object_closure_label: Optional[List[str]] = Field( - default_factory=list, - description="""Field containing object name and the names of all of it's ancestors""", + default_factory=list, description="""Field containing object name and the names of all of it's ancestors""" ) object_taxon: Optional[str] = Field(None) object_taxon_label: Optional[str] = Field(None) @@ -82,13 +72,11 @@ class Association(ConfiguredBaseModel): negated: Optional[bool] = Field(None) pathway: Optional[str] = Field(None) evidence_count: Optional[int] = Field( - None, - description="""count of supporting documents, evidence codes, and sources supplying evidence""", + None, description="""count of supporting documents, evidence codes, and sources supplying evidence""" ) has_evidence: Optional[List[str]] = Field(default_factory=list) has_evidence_links: Optional[List[ExpandedCurie]] = Field( - default_factory=list, - description="""List of ExpandedCuries with id and url for evidence""", + default_factory=list, description="""List of ExpandedCuries with id and url for evidence""" ) grouping_key: Optional[str] = Field( None, @@ -96,13 +84,11 @@ class Association(ConfiguredBaseModel): ) provided_by: Optional[str] = Field(None) provided_by_link: Optional[ExpandedCurie] = Field( - None, - description="""A link to the docs for the knowledge source that provided the node/edge.""", + None, description="""A link to the docs for the knowledge source that provided the node/edge.""" ) publications: Optional[List[str]] = Field(default_factory=list) publications_links: Optional[List[ExpandedCurie]] = Field( - default_factory=list, - description="""List of ExpandedCuries with id and url for publications""", + default_factory=list, description="""List of ExpandedCuries with id and url for publications""" ) qualifiers: Optional[List[str]] = Field(default_factory=list) frequency_qualifier: Optional[str] = Field(None) @@ -143,8 +129,7 @@ class Association(ConfiguredBaseModel): ) onset_qualifier_category: Optional[str] = Field(None, description="""The category of the onset_qualifier entity""") onset_qualifier_closure: Optional[List[str]] = Field( - default_factory=list, - description="""Field containing onset_qualifier id and the ids of all of it's ancestors""", + default_factory=list, description="""Field containing onset_qualifier id and the ids of all of it's ancestors""" ) onset_qualifier_closure_label: Optional[List[str]] = Field( default_factory=list, @@ -156,8 +141,7 @@ class Association(ConfiguredBaseModel): ) sex_qualifier_category: Optional[str] = Field(None, description="""The category of the sex_qualifier entity""") sex_qualifier_closure: Optional[List[str]] = Field( - default_factory=list, - description="""Field containing sex_qualifier id and the ids of all of it's ancestors""", + default_factory=list, description="""Field containing sex_qualifier id and the ids of all of it's ancestors""" ) sex_qualifier_closure_label: Optional[List[str]] = Field( default_factory=list, @@ -169,8 +153,7 @@ class Association(ConfiguredBaseModel): ) stage_qualifier_category: Optional[str] = Field(None, description="""The category of the stage_qualifier entity""") stage_qualifier_closure: Optional[List[str]] = Field( - default_factory=list, - description="""Field containing stage_qualifier id and the ids of all of it's ancestors""", + default_factory=list, description="""Field containing stage_qualifier id and the ids of all of it's ancestors""" ) stage_qualifier_closure_label: Optional[List[str]] = Field( default_factory=list, @@ -184,8 +167,7 @@ class AssociationCountList(ConfiguredBaseModel): """ items: List[AssociationCount] = Field( - default_factory=list, - description="""A collection of items, with the type to be overriden by slot_usage""", + default_factory=list, description="""A collection of items, with the type to be overriden by slot_usage""" ) @@ -195,21 +177,16 @@ class AssociationTypeMapping(ConfiguredBaseModel): """ subject_label: Optional[str] = Field( - None, - description="""A label to describe the subjects of the association type as a whole for use in the UI""", + None, description="""A label to describe the subjects of the association type as a whole for use in the UI""" ) object_label: Optional[str] = Field( - None, - description="""A label to describe the objects of the association type as a whole for use in the UI""", + None, description="""A label to describe the objects of the association type as a whole for use in the UI""" ) symmetric: bool = Field( False, description="""Whether the association type is symmetric, meaning that the subject and object labels should be interchangeable""", ) - category: str = Field( - ..., - description="""The biolink category to use in queries for this association type""", - ) + category: str = Field(..., description="""The biolink category to use in queries for this association type""") class DirectionalAssociation(Association): @@ -228,13 +205,11 @@ class DirectionalAssociation(Association): subject_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the subject entity""") subject_category: Optional[str] = Field(None, description="""The category of the subject entity""") subject_closure: Optional[List[str]] = Field( - default_factory=list, - description="""Field containing subject id and the ids of all of it's ancestors""", + default_factory=list, description="""Field containing subject id and the ids of all of it's ancestors""" ) subject_label: Optional[str] = Field(None, description="""The name of the subject entity""") subject_closure_label: Optional[List[str]] = Field( - default_factory=list, - description="""Field containing subject name and the names of all of it's ancestors""", + default_factory=list, description="""Field containing subject name and the names of all of it's ancestors""" ) subject_taxon: Optional[str] = Field(None) subject_taxon_label: Optional[str] = Field(None) @@ -244,13 +219,11 @@ class DirectionalAssociation(Association): object_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the object entity""") object_category: Optional[str] = Field(None, description="""The category of the object entity""") object_closure: Optional[List[str]] = Field( - default_factory=list, - description="""Field containing object id and the ids of all of it's ancestors""", + default_factory=list, description="""Field containing object id and the ids of all of it's ancestors""" ) object_label: Optional[str] = Field(None, description="""The name of the object entity""") object_closure_label: Optional[List[str]] = Field( - default_factory=list, - description="""Field containing object name and the names of all of it's ancestors""", + default_factory=list, description="""Field containing object name and the names of all of it's ancestors""" ) object_taxon: Optional[str] = Field(None) object_taxon_label: Optional[str] = Field(None) @@ -259,13 +232,11 @@ class DirectionalAssociation(Association): negated: Optional[bool] = Field(None) pathway: Optional[str] = Field(None) evidence_count: Optional[int] = Field( - None, - description="""count of supporting documents, evidence codes, and sources supplying evidence""", + None, description="""count of supporting documents, evidence codes, and sources supplying evidence""" ) has_evidence: Optional[List[str]] = Field(default_factory=list) has_evidence_links: Optional[List[ExpandedCurie]] = Field( - default_factory=list, - description="""List of ExpandedCuries with id and url for evidence""", + default_factory=list, description="""List of ExpandedCuries with id and url for evidence""" ) grouping_key: Optional[str] = Field( None, @@ -273,13 +244,11 @@ class DirectionalAssociation(Association): ) provided_by: Optional[str] = Field(None) provided_by_link: Optional[ExpandedCurie] = Field( - None, - description="""A link to the docs for the knowledge source that provided the node/edge.""", + None, description="""A link to the docs for the knowledge source that provided the node/edge.""" ) publications: Optional[List[str]] = Field(default_factory=list) publications_links: Optional[List[ExpandedCurie]] = Field( - default_factory=list, - description="""List of ExpandedCuries with id and url for publications""", + default_factory=list, description="""List of ExpandedCuries with id and url for publications""" ) qualifiers: Optional[List[str]] = Field(default_factory=list) frequency_qualifier: Optional[str] = Field(None) @@ -320,8 +289,7 @@ class DirectionalAssociation(Association): ) onset_qualifier_category: Optional[str] = Field(None, description="""The category of the onset_qualifier entity""") onset_qualifier_closure: Optional[List[str]] = Field( - default_factory=list, - description="""Field containing onset_qualifier id and the ids of all of it's ancestors""", + default_factory=list, description="""Field containing onset_qualifier id and the ids of all of it's ancestors""" ) onset_qualifier_closure_label: Optional[List[str]] = Field( default_factory=list, @@ -333,8 +301,7 @@ class DirectionalAssociation(Association): ) sex_qualifier_category: Optional[str] = Field(None, description="""The category of the sex_qualifier entity""") sex_qualifier_closure: Optional[List[str]] = Field( - default_factory=list, - description="""Field containing sex_qualifier id and the ids of all of it's ancestors""", + default_factory=list, description="""Field containing sex_qualifier id and the ids of all of it's ancestors""" ) sex_qualifier_closure_label: Optional[List[str]] = Field( default_factory=list, @@ -346,8 +313,7 @@ class DirectionalAssociation(Association): ) stage_qualifier_category: Optional[str] = Field(None, description="""The category of the stage_qualifier entity""") stage_qualifier_closure: Optional[List[str]] = Field( - default_factory=list, - description="""Field containing stage_qualifier id and the ids of all of it's ancestors""", + default_factory=list, description="""Field containing stage_qualifier id and the ids of all of it's ancestors""" ) stage_qualifier_closure_label: Optional[List[str]] = Field( default_factory=list, @@ -374,16 +340,14 @@ class Entity(ConfiguredBaseModel): 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.""", + 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) in_taxon: Optional[str] = Field(None, description="""The biolink taxon that the entity is in the closure of.""") in_taxon_label: Optional[str] = Field( - None, - description="""The label of the biolink taxon that the entity is in the closure of.""", + None, description="""The label of the biolink taxon that the entity is in the closure of.""" ) symbol: Optional[str] = Field(None) synonym: Optional[List[str]] = Field(default_factory=list) @@ -407,8 +371,7 @@ class FacetField(ConfiguredBaseModel): label: str = Field(...) facet_values: Optional[List[FacetValue]] = Field( - default_factory=list, - description="""Collection of FacetValue label/value instances belonging to a FacetField""", + default_factory=list, description="""Collection of FacetValue label/value instances belonging to a FacetField""" ) @@ -416,8 +379,7 @@ class HistoPheno(ConfiguredBaseModel): id: str = Field(...) items: List[HistoBin] = Field( - default_factory=list, - description="""A collection of items, with the type to be overriden by slot_usage""", + default_factory=list, description="""A collection of items, with the type to be overriden by slot_usage""" ) @@ -449,28 +411,23 @@ class Node(Entity): in_taxon: Optional[str] = Field(None, description="""The biolink taxon that the entity is in the closure of.""") in_taxon_label: Optional[str] = Field( - None, - description="""The label of the biolink taxon that the entity is in the closure of.""", + None, description="""The label of the biolink taxon that the entity is in the closure of.""" ) inheritance: Optional[Entity] = Field(None) causal_gene: Optional[List[Entity]] = Field( - default_factory=list, - description="""A list of genes that are known to be causally associated with a disease""", + default_factory=list, description="""A list of genes that are known to be causally associated with a disease""" ) causes_disease: Optional[List[Entity]] = Field( - default_factory=list, - description="""A list of diseases that are known to be causally associated with a gene""", + default_factory=list, description="""A list of diseases that are known to be causally associated with a gene""" ) mappings: Optional[List[ExpandedCurie]] = Field( - default_factory=list, - description="""List of ExpandedCuries with id and url for mapped entities""", + default_factory=list, description="""List of ExpandedCuries with id and url for mapped entities""" ) external_links: Optional[List[ExpandedCurie]] = Field( default_factory=list, description="""ExpandedCurie with id and url for xrefs""" ) provided_by_link: Optional[ExpandedCurie] = Field( - None, - description="""A link to the docs for the knowledge source that provided the node/edge.""", + None, description="""A link to the docs for the knowledge source that provided the node/edge.""" ) association_counts: List[AssociationCount] = Field(default_factory=list) node_hierarchy: Optional[NodeHierarchy] = Field(None) @@ -479,8 +436,7 @@ class Node(Entity): 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.""", + 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) @@ -506,8 +462,7 @@ class Results(ConfiguredBaseModel): class AssociationResults(Results): items: List[Association] = Field( - default_factory=list, - description="""A collection of items, with the type to be overriden by slot_usage""", + default_factory=list, description="""A collection of items, with the type to be overriden by slot_usage""" ) limit: int = Field(..., description="""number of items to return in a response""") offset: int = Field(..., description="""offset into the total number of items""") @@ -517,8 +472,7 @@ class AssociationResults(Results): class AssociationTableResults(Results): items: List[DirectionalAssociation] = Field( - default_factory=list, - description="""A collection of items, with the type to be overriden by slot_usage""", + default_factory=list, description="""A collection of items, with the type to be overriden by slot_usage""" ) limit: int = Field(..., description="""number of items to return in a response""") offset: int = Field(..., description="""offset into the total number of items""") @@ -532,8 +486,7 @@ class CategoryGroupedAssociationResults(Results): description="""The category of the counterpart entity in a given association, eg. the category of the entity that is not the subject""", ) items: List[Association] = Field( - default_factory=list, - description="""A collection of items, with the type to be overriden by slot_usage""", + default_factory=list, description="""A collection of items, with the type to be overriden by slot_usage""" ) limit: int = Field(..., description="""number of items to return in a response""") offset: int = Field(..., description="""offset into the total number of items""") @@ -543,8 +496,7 @@ class CategoryGroupedAssociationResults(Results): class EntityResults(Results): items: List[Entity] = Field( - default_factory=list, - description="""A collection of items, with the type to be overriden by slot_usage""", + default_factory=list, description="""A collection of items, with the type to be overriden by slot_usage""" ) limit: int = Field(..., description="""number of items to return in a response""") offset: int = Field(..., description="""offset into the total number of items""") @@ -557,8 +509,7 @@ class MappingResults(Results): """ items: List[Mapping] = Field( - default_factory=list, - description="""A collection of items, with the type to be overriden by slot_usage""", + default_factory=list, description="""A collection of items, with the type to be overriden by slot_usage""" ) limit: int = Field(..., description="""number of items to return in a response""") offset: int = Field(..., description="""offset into the total number of items""") @@ -584,16 +535,14 @@ class SearchResult(Entity): 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.""", + 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) in_taxon: Optional[str] = Field(None, description="""The biolink taxon that the entity is in the closure of.""") in_taxon_label: Optional[str] = Field( - None, - description="""The label of the biolink taxon that the entity is in the closure of.""", + None, description="""The label of the biolink taxon that the entity is in the closure of.""" ) symbol: Optional[str] = Field(None) synonym: Optional[List[str]] = Field(default_factory=list) @@ -603,12 +552,10 @@ class SearchResult(Entity): class SearchResults(Results): items: List[SearchResult] = Field( - default_factory=list, - description="""A collection of items, with the type to be overriden by slot_usage""", + default_factory=list, description="""A collection of items, with the type to be overriden by slot_usage""" ) facet_fields: Optional[List[FacetField]] = Field( - default_factory=list, - description="""Collection of facet field responses with the field values and counts""", + default_factory=list, description="""Collection of facet field responses with the field values and counts""" ) facet_queries: Optional[List[FacetValue]] = Field( default_factory=list, @@ -648,17 +595,14 @@ class TermPairwiseSimilarity(PairwiseSimilarity): subject_information_content: Optional[float] = Field(None, description="""The IC of the subject""") ancestor_information_content: Optional[float] = Field(None, description="""The IC of the object""") jaccard_similarity: Optional[float] = Field( - None, - description="""The number of concepts in the intersection divided by the number in the union""", + None, description="""The number of concepts in the intersection divided by the number in the union""" ) cosine_similarity: Optional[float] = Field( - None, - description="""the dot product of two node embeddings divided by the product of their lengths""", + None, description="""the dot product of two node embeddings divided by the product of their lengths""" ) dice_similarity: Optional[float] = Field(None) phenodigm_score: Optional[float] = Field( - None, - description="""the geometric mean of the jaccard similarity and the information content""", + None, description="""the geometric mean of the jaccard similarity and the information content""" ) @@ -694,33 +638,33 @@ class BestMatch(ConfiguredBaseModel): similarity: TermPairwiseSimilarity = Field(...) -# Update forward refs -# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/ -Association.update_forward_refs() -AssociationCountList.update_forward_refs() -AssociationTypeMapping.update_forward_refs() -DirectionalAssociation.update_forward_refs() -ExpandedCurie.update_forward_refs() -Entity.update_forward_refs() -FacetValue.update_forward_refs() -AssociationCount.update_forward_refs() -FacetField.update_forward_refs() -HistoPheno.update_forward_refs() -HistoBin.update_forward_refs() -Mapping.update_forward_refs() -Node.update_forward_refs() -NodeHierarchy.update_forward_refs() -Results.update_forward_refs() -AssociationResults.update_forward_refs() -AssociationTableResults.update_forward_refs() -CategoryGroupedAssociationResults.update_forward_refs() -EntityResults.update_forward_refs() -MappingResults.update_forward_refs() -MultiEntityAssociationResults.update_forward_refs() -SearchResult.update_forward_refs() -SearchResults.update_forward_refs() -PairwiseSimilarity.update_forward_refs() -TermPairwiseSimilarity.update_forward_refs() -TermSetPairwiseSimilarity.update_forward_refs() -TermInfo.update_forward_refs() -BestMatch.update_forward_refs() +# Model rebuild +# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model +Association.model_rebuild() +AssociationCountList.model_rebuild() +AssociationTypeMapping.model_rebuild() +DirectionalAssociation.model_rebuild() +ExpandedCurie.model_rebuild() +Entity.model_rebuild() +FacetValue.model_rebuild() +AssociationCount.model_rebuild() +FacetField.model_rebuild() +HistoPheno.model_rebuild() +HistoBin.model_rebuild() +Mapping.model_rebuild() +Node.model_rebuild() +NodeHierarchy.model_rebuild() +Results.model_rebuild() +AssociationResults.model_rebuild() +AssociationTableResults.model_rebuild() +CategoryGroupedAssociationResults.model_rebuild() +EntityResults.model_rebuild() +MappingResults.model_rebuild() +MultiEntityAssociationResults.model_rebuild() +SearchResult.model_rebuild() +SearchResults.model_rebuild() +PairwiseSimilarity.model_rebuild() +TermPairwiseSimilarity.model_rebuild() +TermSetPairwiseSimilarity.model_rebuild() +TermInfo.model_rebuild() +BestMatch.model_rebuild() diff --git a/backend/src/monarch_py/datamodels/solr.py b/backend/src/monarch_py/datamodels/solr.py index c89d923ea..9dd4972eb 100644 --- a/backend/src/monarch_py/datamodels/solr.py +++ b/backend/src/monarch_py/datamodels/solr.py @@ -40,7 +40,7 @@ class SolrQuery(BaseModel): rows: int = 20 start: int = 0 facet: bool = True - facet_min_count = 1 + facet_min_count: int = 1 facet_fields: Optional[List[str]] = Field(default_factory=list) facet_queries: Optional[List[str]] = Field(default_factory=list) filter_queries: Optional[List[str]] = Field(default_factory=list) @@ -48,8 +48,8 @@ class SolrQuery(BaseModel): def_type: str = "edismax" q_op: str = "AND" # See SOLR-8812, need this plus mm=100% to allow boolean operators in queries mm: str = "100%" # All tokens in the query must be found in the doc - boost: str = None - sort: str = None + boost: Optional[str] = None + sort: Optional[str] = None def add_field_filter_query(self, field, value): if field is not None and value is not None: diff --git a/backend/src/monarch_py/utils/utils.py b/backend/src/monarch_py/utils/utils.py index 422ff2f04..c4a8e9303 100644 --- a/backend/src/monarch_py/utils/utils.py +++ b/backend/src/monarch_py/utils/utils.py @@ -110,7 +110,7 @@ def get_headers_from_obj(obj: ConfiguredBaseModel) -> list: def to_json(obj: Union[ConfiguredBaseModel, Dict, List[ConfiguredBaseModel]], file: str): """Converts a pydantic model to a JSON string.""" if isinstance(obj, ConfiguredBaseModel): - json_value = obj.json(indent=4) + json_value = obj.model_dump_json(indent=4) elif isinstance(obj, dict): json_value = json.dumps(obj, indent=4) elif isinstance(obj, list): @@ -128,8 +128,8 @@ def to_tsv(obj: ConfiguredBaseModel, file: str) -> str: # Extract headers and rows from object if isinstance(obj, Entity): - headers = obj.dict().keys() - rows = [list(obj.dict().values())] + headers = obj.model_dump().keys() + rows = [list(obj.model_dump().values())] elif isinstance(obj, (AssociationCountList, HistoPheno, Results)): if not obj.items: headers = get_headers_from_obj(obj) @@ -159,15 +159,15 @@ def to_table(obj: ConfiguredBaseModel): console.print(f"\n[bold red]Table output not implemented for Node objects.[/]\n") raise typer.Exit(1) elif isinstance(obj, Entity): - headers = obj.dict().keys() - rows = [list(obj.dict().values())] + headers = obj.model_dump().keys() + rows = [list(obj.model_dump().values())] elif isinstance(obj, (AssociationCountList, HistoPheno, Results)): if not obj.items: headers = get_headers_from_obj(obj) rows = [] else: - headers = obj.items[0].dict().keys() - rows = [list(item.dict().values()) for item in obj.items] + headers = obj.items[0].model_dump().keys() + rows = [list(item.model_dump().values()) for item in obj.items] else: console.print(f"\n[bold red]{FMT_INPUT_ERROR_MSG}[/]\n") raise typer.Exit(1) @@ -198,7 +198,7 @@ def to_yaml(obj: ConfiguredBaseModel, file: str): fh = open(file, "w") if file else sys.stdout if isinstance(obj, Entity): - yaml.dump(obj.dict(), fh, indent=4) + yaml.dump(obj.model_dump(), fh, indent=4) elif isinstance(obj, Results) or isinstance(obj, HistoPheno) or isinstance(obj, AssociationCountList): yaml.dump([item.dict() for item in obj.items], fh, indent=4) else: diff --git a/backend/tests/fixtures/association_counts_query.py b/backend/tests/fixtures/association_counts_query.py index be9f06dcc..95cf33cb8 100644 --- a/backend/tests/fixtures/association_counts_query.py +++ b/backend/tests/fixtures/association_counts_query.py @@ -8,6 +8,7 @@ def association_counts_query(): "rows": 20, "start": 0, "facet": True, + "facet_min_count": 1, "facet_fields": [], "facet_queries": [ '(category:"biolink:DiseaseToPhenotypicFeatureAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', @@ -44,5 +45,4 @@ def association_counts_query(): "mm": "100%", "boost": None, "sort": None, - "facet_min_count": 1, } diff --git a/backend/tests/fixtures/association_counts_response.py b/backend/tests/fixtures/association_counts_response.py index a36a793cb..b5dd2bad8 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": 3, + "QTime": 1, "params": { "facet.query": [ '(category:"biolink:DiseaseToPhenotypicFeatureAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', diff --git a/backend/tests/fixtures/association_query_direct.py b/backend/tests/fixtures/association_query_direct.py index c41d974d1..199833f85 100644 --- a/backend/tests/fixtures/association_query_direct.py +++ b/backend/tests/fixtures/association_query_direct.py @@ -8,6 +8,7 @@ def association_query_direct(): "rows": 100, "start": 100, "facet": True, + "facet_min_count": 1, "facet_fields": [], "facet_queries": [], "filter_queries": [ @@ -25,5 +26,4 @@ def association_query_direct(): "mm": "100%", "boost": None, "sort": None, - "facet_min_count": 1, } diff --git a/backend/tests/fixtures/association_query_indirect.py b/backend/tests/fixtures/association_query_indirect.py index bbeab8090..e9d3a78a2 100644 --- a/backend/tests/fixtures/association_query_indirect.py +++ b/backend/tests/fixtures/association_query_indirect.py @@ -8,6 +8,7 @@ def association_query_indirect(): "rows": 100, "start": 100, "facet": True, + "facet_min_count": 1, "facet_fields": [], "facet_queries": [], "filter_queries": [ @@ -25,5 +26,4 @@ def association_query_indirect(): "mm": "100%", "boost": None, "sort": None, - "facet_min_count": 1, } diff --git a/backend/tests/fixtures/association_table.py b/backend/tests/fixtures/association_table.py index 6352d96ee..25ea27090 100644 --- a/backend/tests/fixtures/association_table.py +++ b/backend/tests/fixtures/association_table.py @@ -181,9 +181,9 @@ def association_table(): }, "publications": ["PMID:21242490", "PMID:32493488", "PMID:31332380"], "publications_links": [ - {"id": "PMID:21242490", "url": "http://identifiers.org/pubmed/21242490"}, - {"id": "PMID:32493488", "url": "http://identifiers.org/pubmed/32493488"}, - {"id": "PMID:31332380", "url": "http://identifiers.org/pubmed/31332380"}, + {"id": "PMID:21242490", "url": None}, + {"id": "PMID:32493488", "url": None}, + {"id": "PMID:31332380", "url": None}, ], "qualifiers": [], "frequency_qualifier": "HP:0040282", @@ -444,9 +444,9 @@ def association_table(): }, "publications": ["PMID:21242490", "PMID:32493488", "PMID:31332380"], "publications_links": [ - {"id": "PMID:21242490", "url": "http://identifiers.org/pubmed/21242490"}, - {"id": "PMID:32493488", "url": "http://identifiers.org/pubmed/32493488"}, - {"id": "PMID:31332380", "url": "http://identifiers.org/pubmed/31332380"}, + {"id": "PMID:21242490", "url": None}, + {"id": "PMID:32493488", "url": None}, + {"id": "PMID:31332380", "url": None}, ], "qualifiers": [], "frequency_qualifier": "HP:0040282", @@ -782,10 +782,7 @@ def association_table(): "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, "publications": ["PMID:19576565", "PMID:28803818"], - "publications_links": [ - {"id": "PMID:19576565", "url": "http://identifiers.org/pubmed/19576565"}, - {"id": "PMID:28803818", "url": "http://identifiers.org/pubmed/28803818"}, - ], + "publications_links": [{"id": "PMID:19576565", "url": None}, {"id": "PMID:28803818", "url": None}], "qualifiers": [], "frequency_qualifier": "HP:0040280", "onset_qualifier": None, @@ -988,10 +985,7 @@ def association_table(): "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, "publications": ["PMID:16258657", "OMIM:254090"], - "publications_links": [ - {"id": "PMID:16258657", "url": "http://identifiers.org/pubmed/16258657"}, - {"id": "OMIM:254090", "url": "http://identifiers.org/mim/254090"}, - ], + "publications_links": [{"id": "PMID:16258657", "url": None}, {"id": "OMIM:254090", "url": None}], "qualifiers": [], "frequency_qualifier": "HP:0040280", "onset_qualifier": None, @@ -1192,10 +1186,7 @@ def association_table(): "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_links": [{"id": "PMID:9731527", "url": None}, {"id": "PMID:9009996", "url": None}], "qualifiers": [], "frequency_qualifier": "HP:0040280", "onset_qualifier": None, diff --git a/backend/tests/fixtures/association_table_response.py b/backend/tests/fixtures/association_table_response.py index 820b111af..5e7d23aa6 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": 1, + "QTime": 0, "params": { "mm": "100%", "q": "*:*", diff --git a/backend/tests/fixtures/autocomplete_query.py b/backend/tests/fixtures/autocomplete_query.py index 0eb1230e7..f327745af 100644 --- a/backend/tests/fixtures/autocomplete_query.py +++ b/backend/tests/fixtures/autocomplete_query.py @@ -8,6 +8,7 @@ def autocomplete_query(): "rows": 20, "start": 0, "facet": True, + "facet_min_count": 1, "facet_fields": [], "facet_queries": [], "filter_queries": [], @@ -17,5 +18,4 @@ def autocomplete_query(): "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),if(termfreq(deprecated,"true"),0.1,1))', "sort": None, - "facet_min_count": 1, } diff --git a/backend/tests/fixtures/histopheno_query.py b/backend/tests/fixtures/histopheno_query.py index 8ed9793aa..0bb065bde 100644 --- a/backend/tests/fixtures/histopheno_query.py +++ b/backend/tests/fixtures/histopheno_query.py @@ -8,6 +8,7 @@ def histopheno_query(): "rows": 0, "start": 0, "facet": True, + "facet_min_count": 1, "facet_fields": [], "facet_queries": [ 'object_closure:"HP:0000924"', @@ -38,5 +39,4 @@ def histopheno_query(): "mm": "100%", "boost": None, "sort": None, - "facet_min_count": 1, } diff --git a/backend/tests/fixtures/histopheno_response.py b/backend/tests/fixtures/histopheno_response.py index 6bc1cf57b..44789afcf 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": 4, + "QTime": 1, "params": { "facet.query": [ 'object_closure:"HP:0000924"', diff --git a/backend/tests/fixtures/mapping_query.py b/backend/tests/fixtures/mapping_query.py index 10c157459..101a1ad84 100644 --- a/backend/tests/fixtures/mapping_query.py +++ b/backend/tests/fixtures/mapping_query.py @@ -8,6 +8,7 @@ def mapping_query(): "rows": 20, "start": 0, "facet": True, + "facet_min_count": 1, "facet_fields": [], "facet_queries": [], "filter_queries": ['subject_id:"MONDO\\:0020121" OR object_id:"MONDO\\:0020121"'], @@ -17,5 +18,4 @@ def mapping_query(): "mm": "100%", "boost": None, "sort": None, - "facet_min_count": 1, } diff --git a/backend/tests/fixtures/node.py b/backend/tests/fixtures/node.py index 1732c8608..8a5306b96 100644 --- a/backend/tests/fixtures/node.py +++ b/backend/tests/fixtures/node.py @@ -21,12 +21,12 @@ def node(): "causal_gene": [], "causes_disease": [], "mappings": [ - {"id": "DOID:9884", "url": "http://purl.obolibrary.org/obo/DOID_9884"}, + {"id": "DOID:9884", "url": None}, {"id": "ICD10CM:G71.0", "url": "https://icd.codes/icd10cm/G71.0"}, - {"id": "MESH:D009136", "url": "http://identifiers.org/mesh/D009136"}, - {"id": "NCIT:C84910", "url": "http://purl.obolibrary.org/obo/NCIT_C84910"}, + {"id": "MESH:D009136", "url": None}, + {"id": "NCIT:C84910", "url": None}, {"id": "SCTID:73297009", "url": None}, - {"id": "UMLS:C0026850", "url": "http://identifiers.org/umls/C0026850"}, + {"id": "UMLS:C0026850", "url": None}, {"id": "Orphanet:98473", "url": None}, ], "external_links": [], diff --git a/backend/tests/fixtures/phenotype_explorer_compare.py b/backend/tests/fixtures/phenotype_explorer_compare.py index 660f9f571..0e0776f24 100644 --- a/backend/tests/fixtures/phenotype_explorer_compare.py +++ b/backend/tests/fixtures/phenotype_explorer_compare.py @@ -5,8 +5,8 @@ def phenotype_explorer_compare(): return { "subject_termset": { - "MP:0002169": {"id": "MP:0002169", "label": "no abnormal phenotype detected (MPO)"}, "MP:0010771": {"id": "MP:0010771", "label": "integument phenotype (MPO)"}, + "MP:0002169": {"id": "MP:0002169", "label": "no abnormal phenotype detected (MPO)"}, }, "object_termset": {"HP:0004325": {"id": "HP:0004325", "label": "Decreased body weight (HPO)"}}, "subject_best_matches": { diff --git a/backend/tests/fixtures/search_query.py b/backend/tests/fixtures/search_query.py index 9ce3b0eea..f9a8ba6f0 100644 --- a/backend/tests/fixtures/search_query.py +++ b/backend/tests/fixtures/search_query.py @@ -8,6 +8,7 @@ def search_query(): "rows": 20, "start": 0, "facet": True, + "facet_min_count": 1, "facet_fields": [], "facet_queries": [], "filter_queries": ["name:*"], @@ -17,5 +18,4 @@ def search_query(): "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),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 c096e99ff..07e1cdf67 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": 1, + "QTime": 0, "params": { "mm": "100%", "q": "fanconi", diff --git a/frontend/fixtures/association-table.json b/frontend/fixtures/association-table.json index d83957aba..557c1160a 100644 --- a/frontend/fixtures/association-table.json +++ b/frontend/fixtures/association-table.json @@ -173,7 +173,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], - "grouping_key": "MONDO:0020793\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0002460", + "grouping_key": "MONDO:0020793🍪🍪biolink:has_phenotype🍪HP:0002460", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -183,15 +183,15 @@ "publications_links": [ { "id": "PMID:21242490", - "url": "http://identifiers.org/pubmed/21242490" + "url": null }, { "id": "PMID:32493488", - "url": "http://identifiers.org/pubmed/32493488" + "url": null }, { "id": "PMID:31332380", - "url": "http://identifiers.org/pubmed/31332380" + "url": null } ], "qualifiers": [], @@ -454,7 +454,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], - "grouping_key": "MONDO:0020793\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0002015", + "grouping_key": "MONDO:0020793🍪🍪biolink:has_phenotype🍪HP:0002015", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -464,15 +464,15 @@ "publications_links": [ { "id": "PMID:21242490", - "url": "http://identifiers.org/pubmed/21242490" + "url": null }, { "id": "PMID:32493488", - "url": "http://identifiers.org/pubmed/32493488" + "url": null }, { "id": "PMID:31332380", - "url": "http://identifiers.org/pubmed/31332380" + "url": null } ], "qualifiers": [], @@ -811,7 +811,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], - "grouping_key": "MONDO:0013049\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0003236", + "grouping_key": "MONDO:0013049🍪🍪biolink:has_phenotype🍪HP:0003236", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -821,11 +821,11 @@ "publications_links": [ { "id": "PMID:19576565", - "url": "http://identifiers.org/pubmed/19576565" + "url": null }, { "id": "PMID:28803818", - "url": "http://identifiers.org/pubmed/28803818" + "url": null } ], "qualifiers": [], @@ -1032,7 +1032,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], - "grouping_key": "MONDO:0009681\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0020152", + "grouping_key": "MONDO:0009681🍪🍪biolink:has_phenotype🍪HP:0020152", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -1042,11 +1042,11 @@ "publications_links": [ { "id": "PMID:16258657", - "url": "http://identifiers.org/pubmed/16258657" + "url": null }, { "id": "OMIM:254090", - "url": "http://identifiers.org/mim/254090" + "url": null } ], "qualifiers": [], @@ -1251,7 +1251,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], - "grouping_key": "MONDO:0009676\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0003701", + "grouping_key": "MONDO:0009676🍪🍪biolink:has_phenotype🍪HP:0003701", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -1261,11 +1261,11 @@ "publications_links": [ { "id": "PMID:9731527", - "url": "http://identifiers.org/pubmed/9731527" + "url": null }, { "id": "PMID:9009996", - "url": "http://identifiers.org/pubmed/9009996" + "url": null } ], "qualifiers": [], diff --git a/frontend/fixtures/associations.json b/frontend/fixtures/associations.json index 053592aec..7d30eeee4 100644 --- a/frontend/fixtures/associations.json +++ b/frontend/fixtures/associations.json @@ -145,7 +145,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000304" } ], - "grouping_key": "MONDO:0035432\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0002465", + "grouping_key": "MONDO:0035432🍪🍪biolink:has_phenotype🍪HP:0002465", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -461,7 +461,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000304" } ], - "grouping_key": "MONDO:0035432\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0008981", + "grouping_key": "MONDO:0035432🍪🍪biolink:has_phenotype🍪HP:0008981", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -739,7 +739,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000304" } ], - "grouping_key": "MONDO:0035432\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0008994", + "grouping_key": "MONDO:0035432🍪🍪biolink:has_phenotype🍪HP:0008994", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -1037,7 +1037,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000304" } ], - "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0000256", + "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0000256", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -1343,7 +1343,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000304" } ], - "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0000297", + "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0000297", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -1665,7 +1665,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000304" } ], - "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0010804", + "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0010804", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -1901,7 +1901,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000304" } ], - "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0031843", + "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0031843", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -2151,7 +2151,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000304" } ], - "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0000736", + "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0000736", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -2387,7 +2387,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000304" } ], - "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0001622", + "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001622", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -2645,7 +2645,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000304" } ], - "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0001883", + "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001883", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -2869,7 +2869,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000304" } ], - "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0011098", + "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0011098", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -3097,7 +3097,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000304" } ], - "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0011710", + "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0011710", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -3325,7 +3325,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000304" } ], - "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0001513", + "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001513", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -3569,7 +3569,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000304" } ], - "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0000729", + "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0000729", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -3821,7 +3821,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000304" } ], - "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0000752", + "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0000752", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -4035,7 +4035,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000304" } ], - "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0001558", + "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001558", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -4251,7 +4251,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000304" } ], - "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0001561", + "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001561", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -4605,7 +4605,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000304" } ], - "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0001643", + "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001643", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -4881,7 +4881,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000304" } ], - "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0001671", + "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001671", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", @@ -5111,7 +5111,7 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000304" } ], - "grouping_key": "MONDO:0035646\ud83c\udf6a\ud83c\udf6abiolink:has_phenotype\ud83c\udf6aHP:0002014", + "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0002014", "provided_by": "hpoa_disease_to_phenotype_edges", "provided_by_link": { "id": "hpoa_disease_to_phenotype", diff --git a/frontend/fixtures/autocomplete.json b/frontend/fixtures/autocomplete.json index 4f598ad26..e8468e556 100644 --- a/frontend/fixtures/autocomplete.json +++ b/frontend/fixtures/autocomplete.json @@ -127,7 +127,7 @@ "in_taxon_label": null, "symbol": null, "synonym": [ - "DeToni-Debr\u00e9-Fanconi syndrome", + "DeToni-Debré-Fanconi syndrome", "FRTS1", "Fanconi renotubular syndrome", "Fanconi renotubular syndrome 1", diff --git a/frontend/fixtures/node.json b/frontend/fixtures/node.json index f6ced88f6..919607eea 100644 --- a/frontend/fixtures/node.json +++ b/frontend/fixtures/node.json @@ -18,7 +18,7 @@ "mappings": [ { "id": "DOID:9884", - "url": "http://purl.obolibrary.org/obo/DOID_9884" + "url": null }, { "id": "ICD10CM:G71.0", @@ -26,11 +26,11 @@ }, { "id": "MESH:D009136", - "url": "http://identifiers.org/mesh/D009136" + "url": null }, { "id": "NCIT:C84910", - "url": "http://purl.obolibrary.org/obo/NCIT_C84910" + "url": null }, { "id": "SCTID:73297009", @@ -38,7 +38,7 @@ }, { "id": "UMLS:C0026850", - "url": "http://identifiers.org/umls/C0026850" + "url": null }, { "id": "Orphanet:98473", diff --git a/frontend/fixtures/phenotype-explorer-compare.json b/frontend/fixtures/phenotype-explorer-compare.json index 47898790d..a623376e6 100644 --- a/frontend/fixtures/phenotype-explorer-compare.json +++ b/frontend/fixtures/phenotype-explorer-compare.json @@ -1,12 +1,12 @@ { "subject_termset": { - "MP:0002169": { - "id": "MP:0002169", - "label": "no abnormal phenotype detected (MPO)" - }, "MP:0010771": { "id": "MP:0010771", "label": "integument phenotype (MPO)" + }, + "MP:0002169": { + "id": "MP:0002169", + "label": "no abnormal phenotype detected (MPO)" } }, "object_termset": { diff --git a/frontend/fixtures/search.json b/frontend/fixtures/search.json index ef531a628..5eb7bb088 100644 --- a/frontend/fixtures/search.json +++ b/frontend/fixtures/search.json @@ -189,7 +189,7 @@ "in_taxon_label": null, "symbol": null, "synonym": [ - "DeToni-Debr\u00e9-Fanconi syndrome", + "DeToni-Debré-Fanconi syndrome", "FRTS1", "Fanconi renotubular syndrome", "Fanconi renotubular syndrome 1", diff --git a/frontend/src/components/AppPredicateBadge.vue b/frontend/src/components/AppPredicateBadge.vue index 52ca3caa4..82b0756b0 100644 --- a/frontend/src/components/AppPredicateBadge.vue +++ b/frontend/src/components/AppPredicateBadge.vue @@ -34,8 +34,8 @@ const arrowDirection = computed(() => ? "up" : "left" : props.vertical - ? "down" - : "right", + ? "down" + : "right", ); diff --git a/frontend/src/components/AppTable.vue b/frontend/src/components/AppTable.vue index 5645cccaf..51e61b4f3 100644 --- a/frontend/src/components/AppTable.vue +++ b/frontend/src/components/AppTable.vue @@ -383,8 +383,8 @@ const widths = computed((): string => col.slot === "divider" ? "20px" : expanded.value - ? `minmax(max-content, 99999px)` - : `${col.width || 1}fr`, + ? `minmax(max-content, 99999px)` + : `${col.width || 1}fr`, ) .join(" "), ); From 4fba0a551d27acdc06a49718d65b66d71fa7cac6 Mon Sep 17 00:00:00 2001 From: glass-ships Date: Wed, 6 Dec 2023 11:42:38 -0700 Subject: [PATCH 03/13] curie service and solr parser tests failing, not sure why --- backend/src/monarch_py/api/config.py | 18 +++++++++--------- backend/tests/unit/test_curie_service.py | 2 +- backend/tests/unit/test_solr_parsers.py | 16 ++++++++-------- 3 files changed, 18 insertions(+), 18 deletions(-) diff --git a/backend/src/monarch_py/api/config.py b/backend/src/monarch_py/api/config.py index 937791701..6593bb570 100644 --- a/backend/src/monarch_py/api/config.py +++ b/backend/src/monarch_py/api/config.py @@ -3,20 +3,20 @@ from functools import lru_cache -from pydantic import BaseSettings +from pydantic import BaseModel +# from pydantic_settings import BaseSettings from monarch_py.implementations.solr.solr_implementation import SolrImplementation from monarch_py.datamodels.model import TermSetPairwiseSimilarity -class Settings(BaseSettings): - solr_host = os.getenv("SOLR_HOST") if os.getenv("SOLR_HOST") else "127.0.0.1" - solr_port = os.getenv("SOLR_PORT") if os.getenv("SOLR_PORT") else 8983 - solr_url = os.getenv("SOLR_URL") if os.getenv("SOLR_URL") else f"http://{solr_host}:{solr_port}/solr" - phenio_db_path = os.getenv("PHENIO_DB_PATH") if os.getenv("PHENIO_DB_PATH") else "/data/phenio.db" - - oak_server_host = os.getenv("OAK_SERVER_HOST", "127.0.0.1") - oak_server_port = os.getenv("OAK_SERVER_PORT", 18811) +class Settings(BaseModel): + solr_host: str = os.getenv("SOLR_HOST") if os.getenv("SOLR_HOST") else "127.0.0.1" + solr_port: str = os.getenv("SOLR_PORT") if os.getenv("SOLR_PORT") else 8983 + solr_url: str = os.getenv("SOLR_URL") if os.getenv("SOLR_URL") else f"http://{solr_host}:{solr_port}/solr" + phenio_db_path: str = os.getenv("PHENIO_DB_PATH") if os.getenv("PHENIO_DB_PATH") else "/data/phenio.db" + oak_server_host: str = os.getenv("OAK_SERVER_HOST", "127.0.0.1") + oak_server_port: str = os.getenv("OAK_SERVER_PORT", 18811) settings = Settings() diff --git a/backend/tests/unit/test_curie_service.py b/backend/tests/unit/test_curie_service.py index 2b6cef03a..a7312b9bc 100644 --- a/backend/tests/unit/test_curie_service.py +++ b/backend/tests/unit/test_curie_service.py @@ -30,5 +30,5 @@ def test_curie_expansion(curie, expanded_curie_part): cs = CurieService() expanded_curie = cs.expand(curie) - # print(expanded_curie, expanded_curie_part) + print(f"expanded_curie: {expanded_curie}\nexpanded_curie_part: {expanded_curie_part}") assert expanded_curie_part in expanded_curie diff --git a/backend/tests/unit/test_solr_parsers.py b/backend/tests/unit/test_solr_parsers.py index 18aab675e..a8398d2b5 100644 --- a/backend/tests/unit/test_solr_parsers.py +++ b/backend/tests/unit/test_solr_parsers.py @@ -19,7 +19,7 @@ def test_parse_associations(association_response, associations): parsed = parse_associations(solr_response) assert ( parsed == associations - ), f"Parsed result is not as expected. Difference: {dict_diff(parsed.dict(), associations)}" + ), f"Parsed result is not as expected. Difference: {dict_diff(parsed.model_dump(), associations)}" def test_parse_association_counts(association_counts_response, association_counts, node): @@ -28,7 +28,7 @@ def test_parse_association_counts(association_counts_response, association_count parsed = parse_association_counts(solr_response, entity=Node(**node).id) assert ( parsed == association_counts - ), f"Parsed result is not as expected. Difference: {dict_diff(parsed.dict(), association_counts)}" + ), f"Parsed result is not as expected. Difference: {dict_diff(parsed.model_dump(), association_counts)}" def test_parse_association_table(association_table_response, association_table, node): @@ -37,26 +37,26 @@ def test_parse_association_table(association_table_response, association_table, parsed = parse_association_table(solr_response, entity=Node(**node).id, offset=0, limit=5) assert ( parsed == association_table - ), f"Parsed result is not as expected. Difference: {dict_diff(parsed.dict(), association_table)}" + ), f"Parsed result is not as expected. Difference: {dict_diff(parsed.model_dump(), association_table)}" def test_parse_entity(entity_response, node): parsed = parse_entity(entity_response) - assert all(parsed.dict()[k] == v for k, v in parsed.dict().items() if k in node) + assert all(parsed.model_dump()[k] == v for k, v in parsed.model_dump().items() if k in node) def test_parse_histopheno(histopheno_response, histopheno, node): histopheno_response["response"]["numFound"] = histopheno_response["response"].pop("num_found") solr_response = SolrQueryResult(**histopheno_response) parsed = parse_histopheno(solr_response, subject_closure=Node(**node).id) - assert parsed == histopheno, f"Parsed result is not as expected. Difference: {dict_diff(parsed.dict(), histopheno)}" + assert parsed == histopheno, f"Parsed result is not as expected. Difference: {dict_diff(parsed.model_dump(), histopheno)}" def test_parse_search(search_response, search): search_response["response"]["numFound"] = search_response["response"].pop("num_found") solr_response = SolrQueryResult(**search_response) parsed = parse_search(solr_response) - assert parsed == search, f"Parsed result is not as expected. Difference: {dict_diff(parsed.dict(), search)}" + assert parsed == search, f"Parsed result is not as expected. Difference: {dict_diff(parsed.model_dump(), search)}" def test_parse_autocomplete(autocomplete_response, autocomplete): @@ -65,11 +65,11 @@ def test_parse_autocomplete(autocomplete_response, autocomplete): parsed = parse_autocomplete(solr_response) assert ( parsed == autocomplete - ), f"Parsed result is not as expected. Difference: {dict_diff(parsed.dict(), autocomplete)}" + ), f"Parsed result is not as expected. Difference: {dict_diff(parsed.model_dump(), autocomplete)}" def test_parse_mappings(mapping_response, mappings): mapping_response["response"]["numFound"] = mapping_response["response"].pop("num_found") solr_response = SolrQueryResult(**mapping_response) parsed = parse_mappings(solr_response) - assert parsed == mappings, f"Parsed result is not as expected. Difference: {dict_diff(parsed.dict(), mappings)}" + assert parsed == mappings, f"Parsed result is not as expected. Difference: {dict_diff(parsed.model_dump(), mappings)}" From 88421a05588c38fa6151759580ccba1099d32497 Mon Sep 17 00:00:00 2001 From: glass-ships Date: Wed, 6 Dec 2023 12:22:23 -0700 Subject: [PATCH 04/13] curie service and solr parser tests failing, not sure why --- backend/tests/unit/test_solr_parsers.py | 1 + 1 file changed, 1 insertion(+) diff --git a/backend/tests/unit/test_solr_parsers.py b/backend/tests/unit/test_solr_parsers.py index a8398d2b5..49de1baa4 100644 --- a/backend/tests/unit/test_solr_parsers.py +++ b/backend/tests/unit/test_solr_parsers.py @@ -17,6 +17,7 @@ def test_parse_associations(association_response, associations): association_response["response"]["numFound"] = association_response["response"].pop("num_found") solr_response = SolrQueryResult(**association_response) parsed = parse_associations(solr_response) + print(f"parsed: {parsed.model_dump()}\nassociations: {associations.model_dump()}") assert ( parsed == associations ), f"Parsed result is not as expected. Difference: {dict_diff(parsed.model_dump(), associations)}" From b786b2ba7d192c371dd25387faaf442aa63d8b31 Mon Sep 17 00:00:00 2001 From: glass-ships Date: Wed, 6 Dec 2023 12:47:03 -0700 Subject: [PATCH 05/13] fixed solr parser tests --- Makefile | 2 +- backend/src/monarch_py/api/config.py | 1 + backend/src/monarch_py/datamodels/model.py | 2 +- .../fixtures/association_counts_response.py | 2 +- backend/tests/unit/test_solr_parsers.py | 39 +- dict1.py | 4883 +++++++++++++++++ dict2.py | 4883 +++++++++++++++++ scripts/generate_fixtures.py | 2 +- 8 files changed, 9791 insertions(+), 23 deletions(-) create mode 100644 dict1.py create mode 100644 dict2.py diff --git a/Makefile b/Makefile index 63f3bbf22..2ddce5a7d 100644 --- a/Makefile +++ b/Makefile @@ -75,7 +75,7 @@ install-frontend: .PHONY: model model: install-backend - $(RUN) gen-pydantic --pydantic-version 2 --extra-fields allow $(SCHEMADIR)/model.yaml > $(SCHEMADIR)/model.py + $(RUN) gen-pydantic --pydantic-version 2 --extra-fields ignore $(SCHEMADIR)/model.yaml > $(SCHEMADIR)/model.py $(RUN) gen-typescript $(SCHEMADIR)/model.yaml > frontend/src/api/model.ts make format diff --git a/backend/src/monarch_py/api/config.py b/backend/src/monarch_py/api/config.py index 6593bb570..6b4541480 100644 --- a/backend/src/monarch_py/api/config.py +++ b/backend/src/monarch_py/api/config.py @@ -4,6 +4,7 @@ from functools import lru_cache from pydantic import BaseModel + # from pydantic_settings import BaseSettings from monarch_py.implementations.solr.solr_implementation import SolrImplementation diff --git a/backend/src/monarch_py/datamodels/model.py b/backend/src/monarch_py/datamodels/model.py index 6761a879c..07c984dea 100644 --- a/backend/src/monarch_py/datamodels/model.py +++ b/backend/src/monarch_py/datamodels/model.py @@ -19,7 +19,7 @@ class ConfiguredBaseModel(BaseModel): model_config = ConfigDict( validate_assignment=True, validate_default=True, - extra="allow", + extra="ignore", arbitrary_types_allowed=True, use_enum_values=True, ) diff --git a/backend/tests/fixtures/association_counts_response.py b/backend/tests/fixtures/association_counts_response.py index b5dd2bad8..d8c1b48a6 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": 1, + "QTime": 0, "params": { "facet.query": [ '(category:"biolink:DiseaseToPhenotypicFeatureAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")', diff --git a/backend/tests/unit/test_solr_parsers.py b/backend/tests/unit/test_solr_parsers.py index 49de1baa4..db79a69c4 100644 --- a/backend/tests/unit/test_solr_parsers.py +++ b/backend/tests/unit/test_solr_parsers.py @@ -16,61 +16,62 @@ def test_parse_associations(association_response, associations): association_response["response"]["numFound"] = association_response["response"].pop("num_found") solr_response = SolrQueryResult(**association_response) - parsed = parse_associations(solr_response) - print(f"parsed: {parsed.model_dump()}\nassociations: {associations.model_dump()}") - assert ( - parsed == associations - ), f"Parsed result is not as expected. Difference: {dict_diff(parsed.model_dump(), associations)}" + parsed = parse_associations(solr_response).model_dump() + assert parsed == associations, f"Parsed result is not as expected. Difference: {dict_diff(parsed, associations)}" def test_parse_association_counts(association_counts_response, association_counts, node): association_counts_response["response"]["numFound"] = association_counts_response["response"].pop("num_found") solr_response = SolrQueryResult(**association_counts_response) - parsed = parse_association_counts(solr_response, entity=Node(**node).id) + parsed = parse_association_counts(solr_response, entity=Node(**node).id).model_dump() assert ( parsed == association_counts - ), f"Parsed result is not as expected. Difference: {dict_diff(parsed.model_dump(), association_counts)}" + ), f"Parsed result is not as expected. Difference: {dict_diff(parsed, association_counts)}" def test_parse_association_table(association_table_response, association_table, node): association_table_response["response"]["numFound"] = association_table_response["response"].pop("num_found") solr_response = SolrQueryResult(**association_table_response) - parsed = parse_association_table(solr_response, entity=Node(**node).id, offset=0, limit=5) + parsed = parse_association_table(solr_response, entity=Node(**node).id, offset=0, limit=5).model_dump() assert ( parsed == association_table - ), f"Parsed result is not as expected. Difference: {dict_diff(parsed.model_dump(), association_table)}" + ), f"Parsed result is not as expected. Difference: {dict_diff(parsed, association_table)}" def test_parse_entity(entity_response, node): - parsed = parse_entity(entity_response) - assert all(parsed.model_dump()[k] == v for k, v in parsed.model_dump().items() if k in node) + parsed = parse_entity(entity_response).model_dump() + assert all(parsed[k] == v for k, v in parsed.items() if k in node) def test_parse_histopheno(histopheno_response, histopheno, node): histopheno_response["response"]["numFound"] = histopheno_response["response"].pop("num_found") solr_response = SolrQueryResult(**histopheno_response) - parsed = parse_histopheno(solr_response, subject_closure=Node(**node).id) - assert parsed == histopheno, f"Parsed result is not as expected. Difference: {dict_diff(parsed.model_dump(), histopheno)}" + parsed = parse_histopheno(solr_response, subject_closure=Node(**node).id).model_dump() + assert ( + parsed == histopheno + ), f"Parsed result is not as expected. Difference: {dict_diff(parsed, histopheno)}" def test_parse_search(search_response, search): search_response["response"]["numFound"] = search_response["response"].pop("num_found") solr_response = SolrQueryResult(**search_response) - parsed = parse_search(solr_response) - assert parsed == search, f"Parsed result is not as expected. Difference: {dict_diff(parsed.model_dump(), search)}" + parsed = parse_search(solr_response).model_dump() + assert parsed == search, f"Parsed result is not as expected. Difference: {dict_diff(parsed, search)}" def test_parse_autocomplete(autocomplete_response, autocomplete): autocomplete_response["response"]["numFound"] = autocomplete_response["response"].pop("num_found") solr_response = SolrQueryResult(**autocomplete_response) - parsed = parse_autocomplete(solr_response) + parsed = parse_autocomplete(solr_response).model_dump() assert ( parsed == autocomplete - ), f"Parsed result is not as expected. Difference: {dict_diff(parsed.model_dump(), autocomplete)}" + ), f"Parsed result is not as expected. Difference: {dict_diff(parsed, autocomplete)}" def test_parse_mappings(mapping_response, mappings): mapping_response["response"]["numFound"] = mapping_response["response"].pop("num_found") solr_response = SolrQueryResult(**mapping_response) - parsed = parse_mappings(solr_response) - assert parsed == mappings, f"Parsed result is not as expected. Difference: {dict_diff(parsed.model_dump(), mappings)}" + parsed = parse_mappings(solr_response).model_dump() + assert ( + parsed == mappings + ), f"Parsed result is not as expected. Difference: {dict_diff(parsed, mappings)}" diff --git a/dict1.py b/dict1.py new file mode 100644 index 000000000..9bd8e25ce --- /dev/null +++ b/dict1.py @@ -0,0 +1,4883 @@ +dict = { + "limit": 20, + "offset": 0, + "total": 4838, + "items": [ + { + "id": "uuid:4e12a2a1-842a-11ee-884f-6be035239f90", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0035432", + "original_subject": "Orphanet:565899", + "subject_namespace": "MONDO", + "subject_category": "biolink:Disease", + "subject_closure": [ + "MONDO:0000001", + "MONDO:0020121", + "MONDO:0003847", + "BFO:0000001", + "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:0700223", + "BFO:0000016", + "MONDO:0700096", + "OGMS:0000031", + ], + "subject_label": "POMGNT2-related limb-girdle muscular dystrophy R24", + "subject_closure_label": [ + "disease", + "realizable entity", + "disease", + "POMGNT2-related limb-girdle muscular dystrophy R24", + "muscle tissue disorder", + "hereditary skeletal muscle disorder", + "limb-girdle muscular dystrophy", + "continuant", + "disposition", + "human disease", + "specifically dependent continuant", + "myopathy", + "nervous system disorder", + "entity", + "progressive muscular dystrophy", + "musculoskeletal system disorder", + "hereditary disease", + "muscular dystrophy", + "skeletal muscle disorder", + "neuromuscular disease", + ], + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0002465", + "original_object": None, + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "UPHENO:0002536", + "BFO:0000001", + "UBERON:0000465", + "UPHENO:0082875", + "BFO:0000002", + "UPHENO:0004523", + "BFO:0000040", + "UBERON:0001062", + "UPHENO:0001002", + "BFO:0000020", + "BFO:0000002", + "UPHENO:0001001", + "UPHENO:0001003", + "BFO:0000001", + "UPHENO:0075696", + "UPHENO:0002433", + "HP:0012638", + "BFO:0000004", + "UBERON:0000061", + "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": "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)", + "Poor speech (HPO)", + "abnormal phenotype by ontology source", + "Phenotypic abnormality (HPO)", + "Abnormality of the nervous system (HPO)", + "entity", + "Phenotypic abnormality", + "abnormality of nervous system physiology", + "quality", + "multicellular organism", + "phenotype", + "independent continuant", + "entity", + "Abnormal nervous system physiology (HPO)", + "material entity", + "anatomical entity", + "anatomical structure", + "continuant", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "multicellular anatomical structure", + "anatomical system", + ], + "object_taxon": None, + "object_taxon_label": None, + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "negated": None, + "pathway": None, + "evidence_count": 2, + "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": ["orphanet:565899"], + "publications_links": [{"id": "orphanet:565899", "url": None}], + "qualifiers": [], + "frequency_qualifier": "HP:0040282", + "onset_qualifier": None, + "sex_qualifier": None, + "stage_qualifier": None, + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_namespace": "HP", + "frequency_qualifier_category": "biolink:PhenotypicFeature", + "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, + "onset_qualifier_closure": [], + "onset_qualifier_closure_label": [], + "sex_qualifier_label": None, + "sex_qualifier_namespace": None, + "sex_qualifier_category": None, + "sex_qualifier_closure": [], + "sex_qualifier_closure_label": [], + "stage_qualifier_label": None, + "stage_qualifier_namespace": None, + "stage_qualifier_category": None, + "stage_qualifier_closure": [], + "stage_qualifier_closure_label": [], + }, + { + "id": "uuid:4e12a2a3-842a-11ee-884f-6be035239f90", + "category": "biolink:DiseaseToPhenotypicFeatureAssociation", + "subject": "MONDO:0035432", + "original_subject": "Orphanet:565899", + "subject_namespace": "MONDO", + "subject_category": "biolink:Disease", + "subject_closure": [ + "MONDO:0000001", + "MONDO:0020121", + "MONDO:0003847", + "BFO:0000001", + "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:0700223", + "BFO:0000016", + "MONDO:0700096", + "OGMS:0000031", + ], + "subject_label": "POMGNT2-related limb-girdle muscular dystrophy R24", + "subject_closure_label": [ + "disease", + "realizable entity", + "disease", + "POMGNT2-related limb-girdle muscular dystrophy R24", + "muscle tissue disorder", + "hereditary skeletal muscle disorder", + "limb-girdle muscular dystrophy", + "continuant", + "disposition", + "human disease", + "specifically dependent continuant", + "myopathy", + "nervous system disorder", + "entity", + "progressive muscular dystrophy", + "musculoskeletal system disorder", + "hereditary disease", + "muscular dystrophy", + "skeletal muscle disorder", + "neuromuscular disease", + ], + "subject_taxon": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0008981", + "original_object": None, + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "HP:0008981", + "UPHENO:0084535", + "UPHENO:0002816", + "HP:0030236", + "PR:000050567", + "UBERON:0000465", + "RO:0002577", + "UPHENO:0015280", + "HP:0001437", + "BFO:0000040", + "UBERON:0001062", + "UBERON:0011216", + "UBERON:0000154", + "UBERON:0006067", + "UPHENO:0001002", + "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:0033127", + "UPHENO:0001003", + "UPHENO:0076692", + "UPHENO:0003070", + "UPHENO:0002830", + "BFO:0000004", + "UBERON:0004708", + "UBERON:0000061", + "UBERON:0000475", + "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": "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)", + "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", + "Abnormality of the calf musculature (HPO)", + "specifically dependent continuant", + "abnormal anatomical entity morphology", + "abnormal leg", + "quality", + "organism subdivision", + "organ", + "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", + "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, + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "negated": None, + "pathway": None, + "evidence_count": 2, + "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": ["orphanet:565899"], + "publications_links": [{"id": "orphanet:565899", "url": None}], + "qualifiers": [], + "frequency_qualifier": "HP:0040282", + "onset_qualifier": None, + "sex_qualifier": None, + "stage_qualifier": None, + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "qualifiers_closure": [], + "qualifiers_closure_label": [], + "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_namespace": "HP", + 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"stage_qualifier_category": None, + "stage_qualifier_closure": [], + "stage_qualifier_closure_label": [], + }, + { + "id": "uuid:4e02df9a-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": None, + "subject_taxon_label": None, + "predicate": "biolink:has_phenotype", + "object": "HP:0002014", + "original_object": None, + "object_namespace": "HP", + "object_category": "biolink:PhenotypicFeature", + "object_closure": [ + "UPHENO:0002443", + "UPHENO:0002536", + "UBERON:0000465", + "UPHENO:0082875", + "HP:0002664", + "BFO:0000001", + "BFO:0000040", + "UBERON:0001062", + "UPHENO:0001002", + "BFO:0000020", + "HP:0011793", + "HP:0011458", + "BFO:0000002", + "UBERON:0001988", + "UPHENO:0001001", + "UPHENO:0002833", + "UPHENO:0001003", + "UBERON:0000463", + "UPHENO:0075696", + "HP:0002014", + "HP:0025031", + "BFO:0000004", + "UBERON:0000061", + "UBERON:0000174", + "UBERON:0000468", + "BFO:0000002", + "HP:0025032", + "PATO:0000001", + "HP:0000118", + "UPHENO:0002332", + "HP:0000001", + "UPHENO:0001005", + "BFO:0000001", + "UBERON:0010000", + "UBERON:0000467", + "UBERON:0001007", + ], + "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 phenotype by ontology source", + "continuant", + "feces", + "Phenotypic abnormality (HPO)", + "Phenotypic abnormality", + "Neoplasm by anatomical site (HPO)", + "Abdominal symptom (HPO)", + "quality", + "organism substance", + "excreta", + "multicellular organism", + "phenotype", + "Neoplasm (HPO)", + "entity", + "independent continuant", + "abnormality of digestive system physiology", + "Abnormality of the digestive system (HPO)", + "material entity", + "anatomical entity", + "anatomical structure", + "abnormality of anatomical entity physiology", + "abnormal anatomical entity", + "multicellular anatomical structure", + "anatomical system", + ], + "object_taxon": None, + "object_taxon_label": None, + "primary_knowledge_source": "infores:hpo-annotations", + "aggregator_knowledge_source": ["infores:monarchinitiative"], + "negated": None, + "pathway": None, + "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: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": ["orphanet:589821"], + "publications_links": [{"id": "orphanet:589821", "url": None}], + "qualifiers": [], + "frequency_qualifier": "HP:0040283", + "onset_qualifier": None, + "sex_qualifier": None, + "stage_qualifier": None, + "qualifiers_label": None, + "qualifiers_namespace": None, + "qualifiers_category": None, + "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": None, + "onset_qualifier_namespace": None, + "onset_qualifier_category": None, + "onset_qualifier_closure": [], + "onset_qualifier_closure_label": [], + "sex_qualifier_label": None, + "sex_qualifier_namespace": None, + "sex_qualifier_category": None, + "sex_qualifier_closure": [], + "sex_qualifier_closure_label": [], + "stage_qualifier_label": None, + "stage_qualifier_namespace": None, + "stage_qualifier_category": None, + "stage_qualifier_closure": [], + "stage_qualifier_closure_label": [], + }, + ], +} diff --git a/scripts/generate_fixtures.py b/scripts/generate_fixtures.py index 6939e22fc..4953ae619 100644 --- a/scripts/generate_fixtures.py +++ b/scripts/generate_fixtures.py @@ -49,7 +49,7 @@ def write_frontend_fixture(key, value): def write_backend_fixture(key, value): try: - contents = value.dict() + contents = value.model_dump() except AttributeError: contents = value filename = f"{backend_fixture_dir}/{key.replace('-', '_')}.py" From 477c19a39bdad3da028f05962f99cbeab883c4cf Mon Sep 17 00:00:00 2001 From: glass-ships Date: Wed, 6 Dec 2023 12:47:17 -0700 Subject: [PATCH 06/13] remove temp dict files --- dict1.py | 4883 ------------------------------------------------------ dict2.py | 4883 ------------------------------------------------------ 2 files changed, 9766 deletions(-) delete mode 100644 dict1.py delete mode 100644 dict2.py diff --git a/dict1.py b/dict1.py deleted file mode 100644 index 9bd8e25ce..000000000 --- a/dict1.py +++ /dev/null @@ -1,4883 +0,0 @@ -dict = { - "limit": 20, - "offset": 0, - "total": 4838, - "items": [ - { - "id": "uuid:4e12a2a1-842a-11ee-884f-6be035239f90", - "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035432", - "original_subject": "Orphanet:565899", - "subject_namespace": "MONDO", - "subject_category": "biolink:Disease", - "subject_closure": [ - "MONDO:0000001", - "MONDO:0020121", - "MONDO:0003847", - "BFO:0000001", - "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:0700223", - "BFO:0000016", - "MONDO:0700096", - "OGMS:0000031", - ], - "subject_label": "POMGNT2-related limb-girdle muscular dystrophy R24", - "subject_closure_label": [ - "disease", - "realizable entity", - "disease", - "POMGNT2-related limb-girdle muscular dystrophy 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"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": None, - "subject_taxon_label": None, - "predicate": "biolink:has_phenotype", - "object": "HP:0001671", - "original_object": None, - "object_namespace": "HP", - "object_category": "biolink:PhenotypicFeature", - "object_closure": [ - "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", - "UBERON:0003037", - "UBERON:0010314", - "HP:0000001", - "UPHENO:0001005", - "BFO:0000001", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0004120", - "UBERON:0001009", - "UBERON:0005178", - "UBERON:0007100", - ], - "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)", - "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)", - "abnormal anatomical entity morphology", - "entity", - "entity", - "septum", - "structure with developmental contribution from neural crest", - "thoracic cavity element", - "primary circulatory organ", - "Abnormality of the cardiovascular system (HPO)", - "Phenotypic abnormality", - "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", - "anatomical entity", - "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", - "mesoderm-derived structure", - "cardiac septum", - "heart", - ], - "object_taxon": None, - "object_taxon_label": None, - "primary_knowledge_source": "infores:hpo-annotations", - "aggregator_knowledge_source": ["infores:monarchinitiative"], - "negated": None, - "pathway": None, - "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: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": ["orphanet:589821"], - "publications_links": [{"id": "orphanet:589821", "url": None}], - "qualifiers": [], - "frequency_qualifier": "HP:0040283", - "onset_qualifier": None, - "sex_qualifier": None, - "stage_qualifier": None, - "qualifiers_label": None, - "qualifiers_namespace": None, - "qualifiers_category": None, - "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": None, - "onset_qualifier_namespace": None, - "onset_qualifier_category": None, - "onset_qualifier_closure": [], - "onset_qualifier_closure_label": [], - "sex_qualifier_label": None, - "sex_qualifier_namespace": None, - "sex_qualifier_category": None, - "sex_qualifier_closure": [], - "sex_qualifier_closure_label": [], - "stage_qualifier_label": None, - "stage_qualifier_namespace": None, - "stage_qualifier_category": None, - "stage_qualifier_closure": [], - "stage_qualifier_closure_label": [], - }, - { - "id": "uuid:4e02df9a-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": None, - "subject_taxon_label": None, - "predicate": "biolink:has_phenotype", - "object": "HP:0002014", - "original_object": None, - "object_namespace": "HP", - "object_category": "biolink:PhenotypicFeature", - "object_closure": [ - "UPHENO:0002443", - "UPHENO:0002536", - "UBERON:0000465", - "UPHENO:0082875", - "HP:0002664", - "BFO:0000001", - "BFO:0000040", - "UBERON:0001062", - "UPHENO:0001002", - "BFO:0000020", - "HP:0011793", - "HP:0011458", - "BFO:0000002", - "UBERON:0001988", - "UPHENO:0001001", - "UPHENO:0002833", - "UPHENO:0001003", - "UBERON:0000463", - "UPHENO:0075696", - "HP:0002014", - "HP:0025031", - "BFO:0000004", - "UBERON:0000061", - "UBERON:0000174", - "UBERON:0000468", - "BFO:0000002", - "HP:0025032", - "PATO:0000001", - "HP:0000118", - "UPHENO:0002332", - "HP:0000001", - "UPHENO:0001005", - "BFO:0000001", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0001007", - ], - "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 phenotype by ontology source", - "continuant", - "feces", - "Phenotypic abnormality (HPO)", - "Phenotypic abnormality", - "Neoplasm by anatomical site (HPO)", - "Abdominal symptom (HPO)", - "quality", - "organism substance", - "excreta", - "multicellular organism", - "phenotype", - "Neoplasm (HPO)", - "entity", - "independent continuant", - "abnormality of digestive system physiology", - "Abnormality of the digestive system (HPO)", - "material entity", - "anatomical entity", - "anatomical structure", - "abnormality of anatomical entity physiology", - "abnormal anatomical entity", - "multicellular anatomical structure", - "anatomical system", - ], - "object_taxon": None, - "object_taxon_label": None, - "primary_knowledge_source": "infores:hpo-annotations", - "aggregator_knowledge_source": ["infores:monarchinitiative"], - "negated": None, - "pathway": None, - "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: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": ["orphanet:589821"], - "publications_links": [{"id": "orphanet:589821", "url": None}], - "qualifiers": [], - "frequency_qualifier": "HP:0040283", - "onset_qualifier": None, - "sex_qualifier": None, - "stage_qualifier": None, - "qualifiers_label": None, - "qualifiers_namespace": None, - "qualifiers_category": None, - "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": None, - "onset_qualifier_namespace": None, - "onset_qualifier_category": None, - "onset_qualifier_closure": [], - "onset_qualifier_closure_label": [], - "sex_qualifier_label": None, - "sex_qualifier_namespace": None, - "sex_qualifier_category": None, - "sex_qualifier_closure": [], - "sex_qualifier_closure_label": [], - "stage_qualifier_label": None, - "stage_qualifier_namespace": None, - "stage_qualifier_category": None, - "stage_qualifier_closure": [], - "stage_qualifier_closure_label": [], - }, - ], -} From 3c8348ef3d97cfe746f39e10539dee061ca68439 Mon Sep 17 00:00:00 2001 From: glass-ships Date: Wed, 6 Dec 2023 13:17:04 -0700 Subject: [PATCH 07/13] couple tweaks --- Makefile | 2 +- backend/src/monarch_py/datamodels/model.py | 2 +- backend/src/monarch_py/datamodels/solr.py | 2 +- backend/src/monarch_py/utils/utils.py | 8 ++++---- .../fixtures/phenotype_explorer_compare.py | 12 ++++++------ backend/tests/unit/test_solr_parsers.py | 12 +++--------- backend/tests/unit/test_solr_queries.py | 12 ++++++------ .../fixtures/phenotype-explorer-compare.json | 18 +++++++++--------- 8 files changed, 31 insertions(+), 37 deletions(-) diff --git a/Makefile b/Makefile index 2ddce5a7d..63f3bbf22 100644 --- a/Makefile +++ b/Makefile @@ -75,7 +75,7 @@ install-frontend: .PHONY: model model: install-backend - $(RUN) gen-pydantic --pydantic-version 2 --extra-fields ignore $(SCHEMADIR)/model.yaml > $(SCHEMADIR)/model.py + $(RUN) gen-pydantic --pydantic-version 2 --extra-fields allow $(SCHEMADIR)/model.yaml > $(SCHEMADIR)/model.py $(RUN) gen-typescript $(SCHEMADIR)/model.yaml > frontend/src/api/model.ts make format diff --git a/backend/src/monarch_py/datamodels/model.py b/backend/src/monarch_py/datamodels/model.py index 07c984dea..6761a879c 100644 --- a/backend/src/monarch_py/datamodels/model.py +++ b/backend/src/monarch_py/datamodels/model.py @@ -19,7 +19,7 @@ class ConfiguredBaseModel(BaseModel): model_config = ConfigDict( validate_assignment=True, validate_default=True, - extra="ignore", + extra="allow", arbitrary_types_allowed=True, use_enum_values=True, ) diff --git a/backend/src/monarch_py/datamodels/solr.py b/backend/src/monarch_py/datamodels/solr.py index 9dd4972eb..6597af3e3 100644 --- a/backend/src/monarch_py/datamodels/solr.py +++ b/backend/src/monarch_py/datamodels/solr.py @@ -67,7 +67,7 @@ def add_filter_query(self, filter_query): def query_string(self): return urllib.parse.urlencode( - {self._solrize(k): self._solrize(v) for k, v in self.dict().items() if v is not None}, + {self._solrize(k): self._solrize(v) for k, v in self..model_dump().items() if v is not None}, doseq=True, ) diff --git a/backend/src/monarch_py/utils/utils.py b/backend/src/monarch_py/utils/utils.py index c4a8e9303..2b96b44f5 100644 --- a/backend/src/monarch_py/utils/utils.py +++ b/backend/src/monarch_py/utils/utils.py @@ -114,7 +114,7 @@ def to_json(obj: Union[ConfiguredBaseModel, Dict, List[ConfiguredBaseModel]], fi elif isinstance(obj, dict): json_value = json.dumps(obj, indent=4) elif isinstance(obj, list): - json_value = json.dumps({"items": [o.dict() for o in obj]}, indent=4) + json_value = json.dumps({"items": [o.model_dump() for o in obj]}, indent=4) if file: with open(file, "w") as f: f.write(json_value) @@ -135,8 +135,8 @@ def to_tsv(obj: ConfiguredBaseModel, file: str) -> str: headers = get_headers_from_obj(obj) rows = [] else: - headers = obj.items[0].dict().keys() - rows = [list(item.dict().values()) for item in obj.items] + headers = obj.items[0].model_dump().keys() + rows = [list(item.model_dump().values()) for item in obj.items] else: console.print(f"\n[bold red]{FMT_INPUT_ERROR_MSG}[/]\n") raise typer.Exit(1) @@ -200,7 +200,7 @@ def to_yaml(obj: ConfiguredBaseModel, file: str): if isinstance(obj, Entity): yaml.dump(obj.model_dump(), fh, indent=4) elif isinstance(obj, Results) or isinstance(obj, HistoPheno) or isinstance(obj, AssociationCountList): - yaml.dump([item.dict() for item in obj.items], fh, indent=4) + yaml.dump([item.model_dump() for item in obj.items], fh, indent=4) else: console.print(f"\n[bold red]{FMT_INPUT_ERROR_MSG}[/]\n") raise typer.Exit(1) diff --git a/backend/tests/fixtures/phenotype_explorer_compare.py b/backend/tests/fixtures/phenotype_explorer_compare.py index 0e0776f24..48dccccd0 100644 --- a/backend/tests/fixtures/phenotype_explorer_compare.py +++ b/backend/tests/fixtures/phenotype_explorer_compare.py @@ -5,8 +5,8 @@ def phenotype_explorer_compare(): return { "subject_termset": { - "MP:0010771": {"id": "MP:0010771", "label": "integument phenotype (MPO)"}, "MP:0002169": {"id": "MP:0002169", "label": "no abnormal phenotype detected (MPO)"}, + "MP:0010771": {"id": "MP:0010771", "label": "integument phenotype (MPO)"}, }, "object_termset": {"HP:0004325": {"id": "HP:0004325", "label": "Decreased body weight (HPO)"}}, "subject_best_matches": { @@ -69,8 +69,8 @@ def phenotype_explorer_compare(): "HP:0004325": { "match_source": "HP:0004325", "match_source_label": "Decreased body weight (HPO)", - "match_target": "MP:0010771", - "match_target_label": "integument phenotype (MPO)", + "match_target": "MP:0002169", + "match_target_label": "no abnormal phenotype detected (MPO)", "score": 1.4431977534690428, "match_subsumer": None, "match_subsumer_label": None, @@ -78,7 +78,7 @@ def phenotype_explorer_compare(): "subject_id": "HP:0004325", "subject_label": None, "subject_source": None, - "object_id": "MP:0010771", + "object_id": "MP:0002169", "object_label": None, "object_source": None, "ancestor_id": "UPHENO:0001003", @@ -87,10 +87,10 @@ def phenotype_explorer_compare(): "object_information_content": None, "subject_information_content": None, "ancestor_information_content": 1.4431977534690428, - "jaccard_similarity": 0.3333333333333333, + "jaccard_similarity": 0.16216216216216217, "cosine_similarity": None, "dice_similarity": None, - "phenodigm_score": 0.6935891563620457, + "phenodigm_score": 0.48376861011243283, }, } }, diff --git a/backend/tests/unit/test_solr_parsers.py b/backend/tests/unit/test_solr_parsers.py index db79a69c4..2875371c2 100644 --- a/backend/tests/unit/test_solr_parsers.py +++ b/backend/tests/unit/test_solr_parsers.py @@ -47,9 +47,7 @@ def test_parse_histopheno(histopheno_response, histopheno, node): histopheno_response["response"]["numFound"] = histopheno_response["response"].pop("num_found") solr_response = SolrQueryResult(**histopheno_response) parsed = parse_histopheno(solr_response, subject_closure=Node(**node).id).model_dump() - assert ( - parsed == histopheno - ), f"Parsed result is not as expected. Difference: {dict_diff(parsed, histopheno)}" + assert parsed == histopheno, f"Parsed result is not as expected. Difference: {dict_diff(parsed, histopheno)}" def test_parse_search(search_response, search): @@ -63,15 +61,11 @@ def test_parse_autocomplete(autocomplete_response, autocomplete): autocomplete_response["response"]["numFound"] = autocomplete_response["response"].pop("num_found") solr_response = SolrQueryResult(**autocomplete_response) parsed = parse_autocomplete(solr_response).model_dump() - assert ( - parsed == autocomplete - ), f"Parsed result is not as expected. Difference: {dict_diff(parsed, autocomplete)}" + assert parsed == autocomplete, f"Parsed result is not as expected. Difference: {dict_diff(parsed, autocomplete)}" def test_parse_mappings(mapping_response, mappings): mapping_response["response"]["numFound"] = mapping_response["response"].pop("num_found") solr_response = SolrQueryResult(**mapping_response) parsed = parse_mappings(solr_response).model_dump() - assert ( - parsed == mappings - ), f"Parsed result is not as expected. Difference: {dict_diff(parsed, mappings)}" + assert parsed == mappings, f"Parsed result is not as expected. Difference: {dict_diff(parsed, mappings)}" diff --git a/backend/tests/unit/test_solr_queries.py b/backend/tests/unit/test_solr_queries.py index 0e6c75a42..800923a37 100644 --- a/backend/tests/unit/test_solr_queries.py +++ b/backend/tests/unit/test_solr_queries.py @@ -33,7 +33,7 @@ def test_build_association_query( direct=direct, facet_fields=facet_fields, facet_queries=facet_queries, - ).dict() + ).model_dump() expected = association_query_direct if direct else association_query_indirect if facet_fields: expected["facet_fields"] = facet_fields @@ -91,30 +91,30 @@ def test_build_association_multiple_objects(): def test_build_association_counts_query(association_counts_query, node): - query = build_association_counts_query(entity=Node(**node).id).dict() + query = build_association_counts_query(entity=Node(**node).id).model_dump() expected = association_counts_query assert compare_dicts(query, expected), f"Query is not as expected. Difference: {dict_diff(query, expected)}" def test_build_histopheno_query(histopheno_query): - query = build_histopheno_query("MONDO:0020121").dict() + query = build_histopheno_query("MONDO:0020121").model_dump() expected = histopheno_query assert compare_dicts(query, expected), f"Query is not as expected. Difference: {dict_diff(query, expected)}" def test_build_search_query(search_query): - query = build_search_query(q="fanconi").dict() + query = build_search_query(q="fanconi").model_dump() expected = search_query assert compare_dicts(query, expected), f"Query is not as expected. Difference: {dict_diff(query, expected)}" def test_build_autocomplete_query(autocomplete_query): - query = build_autocomplete_query(q="fanc").dict() + query = build_autocomplete_query(q="fanc").model_dump() expected = autocomplete_query assert compare_dicts(query, expected), f"Query is not as expected. Difference: {dict_diff(query, expected)}" def test_build_mappings_query(mapping_query): - query = build_mapping_query(entity_id=["MONDO:0020121"]).dict() + query = build_mapping_query(entity_id=["MONDO:0020121"]).model_dump() expected = mapping_query assert compare_dicts(query, expected), f"Query is not as expected. Difference: {dict_diff(query, expected)}" diff --git a/frontend/fixtures/phenotype-explorer-compare.json b/frontend/fixtures/phenotype-explorer-compare.json index a623376e6..da14ac58e 100644 --- a/frontend/fixtures/phenotype-explorer-compare.json +++ b/frontend/fixtures/phenotype-explorer-compare.json @@ -1,12 +1,12 @@ { "subject_termset": { - "MP:0010771": { - "id": "MP:0010771", - "label": "integument phenotype (MPO)" - }, "MP:0002169": { "id": "MP:0002169", "label": "no abnormal phenotype detected (MPO)" + }, + "MP:0010771": { + "id": "MP:0010771", + "label": "integument phenotype (MPO)" } }, "object_termset": { @@ -75,8 +75,8 @@ "HP:0004325": { "match_source": "HP:0004325", "match_source_label": "Decreased body weight (HPO)", - "match_target": "MP:0010771", - "match_target_label": "integument phenotype (MPO)", + "match_target": "MP:0002169", + "match_target_label": "no abnormal phenotype detected (MPO)", "score": 1.4431977534690428, "match_subsumer": null, "match_subsumer_label": null, @@ -84,7 +84,7 @@ "subject_id": "HP:0004325", "subject_label": null, "subject_source": null, - "object_id": "MP:0010771", + "object_id": "MP:0002169", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0001003", @@ -93,10 +93,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 1.4431977534690428, - "jaccard_similarity": 0.3333333333333333, + "jaccard_similarity": 0.16216216216216217, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 0.6935891563620457 + "phenodigm_score": 0.48376861011243283 } } }, From f567ae0d4b94e819de59106c93ca79f6cd54eb4a Mon Sep 17 00:00:00 2001 From: glass-ships Date: Wed, 6 Dec 2023 13:20:56 -0700 Subject: [PATCH 08/13] oops, double dot in solr datamodel --- backend/src/monarch_py/datamodels/solr.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/backend/src/monarch_py/datamodels/solr.py b/backend/src/monarch_py/datamodels/solr.py index 6597af3e3..b8d484179 100644 --- a/backend/src/monarch_py/datamodels/solr.py +++ b/backend/src/monarch_py/datamodels/solr.py @@ -67,7 +67,7 @@ def add_filter_query(self, filter_query): def query_string(self): return urllib.parse.urlencode( - {self._solrize(k): self._solrize(v) for k, v in self..model_dump().items() if v is not None}, + {self._solrize(k): self._solrize(v) for k, v in self.model_dump().items() if v is not None}, doseq=True, ) From 95beb1b8d463d27d7094f04c77d275bd984843c5 Mon Sep 17 00:00:00 2001 From: glass-ships Date: Wed, 6 Dec 2023 18:42:03 -0700 Subject: [PATCH 09/13] add strict=True to converter.expand for debugging --- backend/src/monarch_py/api/config.py | 2 -- backend/src/monarch_py/service/curie_service.py | 2 +- backend/tests/unit/test_curie_service.py | 9 +++++---- 3 files changed, 6 insertions(+), 7 deletions(-) diff --git a/backend/src/monarch_py/api/config.py b/backend/src/monarch_py/api/config.py index 6b4541480..28fa439b5 100644 --- a/backend/src/monarch_py/api/config.py +++ b/backend/src/monarch_py/api/config.py @@ -1,10 +1,8 @@ import os import requests as rq - from functools import lru_cache from pydantic import BaseModel - # from pydantic_settings import BaseSettings from monarch_py.implementations.solr.solr_implementation import SolrImplementation diff --git a/backend/src/monarch_py/service/curie_service.py b/backend/src/monarch_py/service/curie_service.py index 888ac9eaa..18d9dfd7c 100644 --- a/backend/src/monarch_py/service/curie_service.py +++ b/backend/src/monarch_py/service/curie_service.py @@ -20,4 +20,4 @@ def initialize(self): self.converter = load_converter(["merged"]) def expand(self, curie: str) -> str: - return self.converter.expand(curie) + return self.converter.expand(curie, strict=True) diff --git a/backend/tests/unit/test_curie_service.py b/backend/tests/unit/test_curie_service.py index a7312b9bc..47f878396 100644 --- a/backend/tests/unit/test_curie_service.py +++ b/backend/tests/unit/test_curie_service.py @@ -11,20 +11,21 @@ ), # this is a little odd, fb vs. flybase, but both resolve ("FlyBase:FBgn0000008", "http://identifiers.org/fb/FBgn0000008"), ("MONDO:0005737", "http://purl.obolibrary.org/obo/MONDO_0005737"), - ("OMIM:613647", "http://identifiers.org/mim/613647"), ("NCBIGene:1017", "https://identifiers.org/ncbigene/1017"), ("ZFIN:ZDB-GENE-980526-166", "https://identifiers.org/zfin/ZDB-GENE-980526-166"), ("MGI:1918910", "https://identifiers.org/MGI/1918910"), - ("ENSEMBL:ENSG00000157764", "http://identifiers.org/ensembl/ENSG00000157764"), ("HP:0000001", "http://purl.obolibrary.org/obo/HP_0000001"), - ("UBERON:0000001", "http://purl.obolibrary.org/obo/UBERON_0000001"), ("GO:0000001", "http://purl.obolibrary.org/obo/GO_0000001"), ("CL:0000001", "http://purl.obolibrary.org/obo/CL_0000001"), - ("WormBase:WBGene00000001", "http://identifiers.org/wb/WBGene00000001"), ("WB:WBGene00000001", "https://identifiers.org/wb/WBGene00000001"), ("SGD:S000000001", "https://identifiers.org/sgd/S000000001"), ("RGD:1", "https://identifiers.org/rgd/1"), ("HGNC:5", "http://identifiers.org/hgnc/5"), + ### These prefixes are currently broken in the curie service + ("ENSEMBL:ENSG00000157764", "http://identifiers.org/ensembl/ENSG00000157764"), + ("OMIM:613647", "http://identifiers.org/mim/613647"), + ("UBERON:0000001", "http://purl.obolibrary.org/obo/UBERON_0000001"), + ("WormBase:WBGene00000001", "http://identifiers.org/wb/WBGene00000001"), ], ) def test_curie_expansion(curie, expanded_curie_part): From 996f21c883d31b6255fa7aac7352fdc2ac197bbe Mon Sep 17 00:00:00 2001 From: glass-ships Date: Sat, 16 Dec 2023 22:28:51 -0700 Subject: [PATCH 10/13] re-convert config to pydantic v2 style --- backend/src/monarch_py/api/config.py | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/backend/src/monarch_py/api/config.py b/backend/src/monarch_py/api/config.py index dd164e4e4..6615d4d99 100644 --- a/backend/src/monarch_py/api/config.py +++ b/backend/src/monarch_py/api/config.py @@ -3,6 +3,7 @@ from functools import lru_cache from typing import List +from pydantic import BaseModel # from pydantic_settings import BaseSettings from monarch_py.implementations.solr.solr_implementation import SolrImplementation @@ -10,14 +11,14 @@ from monarch_py.datamodels.model import TermSetPairwiseSimilarity, SemsimSearchResult -class Settings(BaseSettings): - solr_host = os.getenv("SOLR_HOST") if os.getenv("SOLR_HOST") else "127.0.0.1" - solr_port = os.getenv("SOLR_PORT") if os.getenv("SOLR_PORT") else 8983 - solr_url = os.getenv("SOLR_URL") if os.getenv("SOLR_URL") else f"http://{solr_host}:{solr_port}/solr" - phenio_db_path = os.getenv("PHENIO_DB_PATH") if os.getenv("PHENIO_DB_PATH") else "/data/phenio.db" +class Settings(BaseModel): + solr_host: str = os.getenv("SOLR_HOST") if os.getenv("SOLR_HOST") else "127.0.0.1" + solr_port: str = os.getenv("SOLR_PORT") if os.getenv("SOLR_PORT") else 8983 + solr_url: str = os.getenv("SOLR_URL") if os.getenv("SOLR_URL") else f"http://{solr_host}:{solr_port}/solr" + phenio_db_path: str = os.getenv("PHENIO_DB_PATH") if os.getenv("PHENIO_DB_PATH") else "/data/phenio.db" - semsim_server_host = os.getenv("SEMSIM_SERVER_HOST", "127.0.0.1") - semsim_server_port = os.getenv("SEMSIM_SERVER_PORT", 9999) + semsim_server_host: str = os.getenv("SEMSIM_SERVER_HOST", "127.0.0.1") + semsim_server_port: str = os.getenv("SEMSIM_SERVER_PORT", 9999) settings = Settings() From 8b75ee3ad1a5e266b6b608ec32662f868983461a Mon Sep 17 00:00:00 2001 From: glass-ships Date: Tue, 19 Dec 2023 16:56:28 -0700 Subject: [PATCH 11/13] try prefixmaps 0.2.1, no luck --- backend/poetry.lock | 394 ++++++++++++++++++++++---------------------- 1 file changed, 197 insertions(+), 197 deletions(-) diff --git a/backend/poetry.lock b/backend/poetry.lock index 63c3ab765..a4adbd52a 100644 --- a/backend/poetry.lock +++ b/backend/poetry.lock @@ -1637,110 +1637,110 @@ dev = ["Sphinx 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hash = "sha256:373b76eeb79e8c14f6d82cb1d4d5293f9e4059baec6c1b16dca7ad13b6131b39"}, ] [[package]] From 5b07041e8da28bf9c6ebb02588693df5f6c86579 Mon Sep 17 00:00:00 2001 From: glass-ships Date: Tue, 9 Jan 2024 20:22:28 -0700 Subject: [PATCH 12/13] try new converter --- backend/src/monarch_py/service/curie_service.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/backend/src/monarch_py/service/curie_service.py b/backend/src/monarch_py/service/curie_service.py index ebab07552..044f78b43 100644 --- a/backend/src/monarch_py/service/curie_service.py +++ b/backend/src/monarch_py/service/curie_service.py @@ -8,4 +8,4 @@ # 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) -converter = load_converter(["merged"]) +converter = load_converter("merged") From 299ef2cf94ef2ca31593e378155b5216b3ed93eb Mon Sep 17 00:00:00 2001 From: glass-ships Date: Tue, 9 Jan 2024 21:05:49 -0700 Subject: [PATCH 13/13] update fixtures --- backend/src/monarch_py/api/config.py | 1 + backend/tests/fixtures/association_counts.py | 4 +- .../fixtures/association_counts_response.py | 5950 +++++++--------- .../tests/fixtures/association_response.py | 5946 +++++++--------- backend/tests/fixtures/association_table.py | 1127 ++- .../fixtures/association_table_response.py | 1100 +-- backend/tests/fixtures/associations.py | 6032 ++++++++-------- backend/tests/fixtures/autocomplete.py | 95 +- .../tests/fixtures/autocomplete_response.py | 94 +- backend/tests/fixtures/entity_response.py | 2 +- backend/tests/fixtures/histopheno.py | 30 +- backend/tests/fixtures/histopheno_response.py | 32 +- backend/tests/fixtures/mapping_response.py | 23 +- backend/tests/fixtures/mappings.py | 24 +- backend/tests/fixtures/node.py | 84 +- .../fixtures/phenotype_explorer_search.py | 72 +- backend/tests/fixtures/search.py | 2 +- backend/tests/fixtures/search_response.py | 38 +- frontend/fixtures/association-counts.json | 4 +- frontend/fixtures/association-table.json | 1152 ++- frontend/fixtures/associations.json | 6222 ++++++++--------- frontend/fixtures/autocomplete.json | 95 +- frontend/fixtures/histopheno.json | 38 +- frontend/fixtures/mappings.json | 24 +- frontend/fixtures/node.json | 88 +- .../fixtures/phenotype-explorer-search.json | 108 +- frontend/fixtures/search.json | 2 +- frontend/src/pages/metadata.json | 14 +- 28 files changed, 12531 insertions(+), 15872 deletions(-) diff --git a/backend/src/monarch_py/api/config.py b/backend/src/monarch_py/api/config.py index f721c90f2..23b1fcf53 100644 --- a/backend/src/monarch_py/api/config.py +++ b/backend/src/monarch_py/api/config.py @@ -4,6 +4,7 @@ from typing import List from pydantic import BaseModel + # from pydantic_settings import BaseSettings from monarch_py.implementations.solr.solr_implementation import SolrImplementation diff --git a/backend/tests/fixtures/association_counts.py b/backend/tests/fixtures/association_counts.py index c9c7da8c6..9af52559e 100644 --- a/backend/tests/fixtures/association_counts.py +++ b/backend/tests/fixtures/association_counts.py @@ -5,8 +5,8 @@ def association_counts(): return { "items": [ - {"label": "Phenotypes", "count": 4027, "category": "biolink:DiseaseToPhenotypicFeatureAssociation"}, + {"label": "Phenotypes", "count": 3879, "category": "biolink:DiseaseToPhenotypicFeatureAssociation"}, {"label": "Causal Genes", "count": 124, "category": "biolink:CausalGeneToDiseaseAssociation"}, - {"label": "Correlated Genes", "count": 151, "category": "biolink:CorrelatedGeneToDiseaseAssociation"}, + {"label": "Correlated Genes", "count": 139, "category": "biolink:CorrelatedGeneToDiseaseAssociation"}, ] } diff --git a/backend/tests/fixtures/association_counts_response.py b/backend/tests/fixtures/association_counts_response.py index a19f9b0e4..948e64e07 100644 --- a/backend/tests/fixtures/association_counts_response.py +++ b/backend/tests/fixtures/association_counts_response.py @@ -45,4151 +45,3565 @@ def association_counts_response(): }, }, "response": { - "num_found": 4838, + "num_found": 4624, "start": 0, "docs": [ { - "id": "uuid:4e12a2a1-842a-11ee-884f-6be035239f90", - "original_subject": "Orphanet:565899", + "id": "uuid:89e15863-ae6f-11ee-9f7a-f78bc2e9ee32", + "original_subject": "OMIM:614830", "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:565899"], - "frequency_qualifier": "HP:0040282", - "has_evidence": ["ECO:0000304"], - "subject": "MONDO:0035432", - "object": "HP:0002465", - "subject_label": "POMGNT2-related limb-girdle muscular dystrophy R24", + "publications": ["PMID:22958903"], + "frequency_qualifier": "HP:0040280", + "has_evidence": ["ECO:0000269"], + "subject": "MONDO:0013904", + "object": "HP:0007260", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", "subject_category": "biolink:Disease", "subject_namespace": "MONDO", "subject_closure": [ + "MONDO:0005071", + "BFO:0000016", + "MONDO:0019052", "MONDO:0000001", - "MONDO:0020121", - "MONDO:0003847", - "BFO:0000001", - "MONDO:0016106", "MONDO:0005336", + "OGMS:0000031", + "MONDO:0700069", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0000171", + "MONDO:0020120", + "MONDO:0700096", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0700075", + "MONDO:0024322", "BFO:0000017", - "MONDO:0003939", - "MONDO:0035432", - "BFO:0000020", - "MONDO:0002081", - "MONDO:0016971", - "MONDO:0005071", + "MONDO:0013904", + "MONDO:0015286", + "MONDO:0017741", + "MONDO:0020121", "BFO:0000002", - "MONDO:0020120", - "MONDO:0019056", + "BFO:0000020", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", "MONDO:0700223", - "BFO:0000016", - "MONDO:0700096", - "OGMS:0000031", + "MONDO:0002081", + "MONDO:0002320", ], "subject_closure_label": [ + "nervous system disorder", + "continuant", + "musculoskeletal system disorder", + "muscular dystrophy-dystroglycanopathy, type A", + "myopathy caused by variation in POMGNT2", + "neuromuscular disease", + "skeletal muscle disorder", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", + "muscular dystrophy", + "myopathy", "disease", + "congenital muscular dystrophy", + "congenital muscular dystrophy caused by variation in POMGNT2", + "disorder of glycosylation", "realizable entity", - "disease", - "POMGNT2-related limb-girdle muscular dystrophy R24", - "muscle tissue disorder", + "human disease", + "congenital disorder of glycosylation", "hereditary skeletal muscle disorder", - "limb-girdle muscular dystrophy", - "continuant", "disposition", - "human disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", + "metabolic disease", + "disease", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", "specifically dependent continuant", - "myopathy", - "nervous system disorder", "entity", - "progressive muscular dystrophy", - "musculoskeletal system disorder", - "hereditary disease", - "muscular dystrophy", - "skeletal muscle disorder", - "neuromuscular disease", ], - "object_label": "Poor speech (HPO)", + "object_label": "Type II lissencephaly", "object_category": "biolink:PhenotypicFeature", "object_namespace": "HP", "object_closure": [ - "UPHENO:0002536", - "BFO:0000001", - "UBERON:0000465", - "UPHENO:0082875", - "BFO:0000002", - "UPHENO:0004523", - "BFO:0000040", - "UBERON:0001062", + "HP:0000001", + "HP:0002060", + "HP:0100547", + "UPHENO:0081603", + "HP:0012443", + "HP:0002538", "UPHENO:0001002", - "BFO:0000020", - "BFO:0000002", - 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"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", + "All", + "Abnormal cerebral morphology", "continuant", - "material anatomical entity", - "nervous system", - "All (HPO)", - "Poor speech (HPO)", + "abnormal cell motility", + "abnormal anatomical entity morphology", + "Lissencephaly", + "abnormal cerebral hemisphere morphology", + "Abnormality of brain morphology", + "quality", + "abnormal neuron migration", "abnormal phenotype by ontology source", - "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "entity", "Phenotypic abnormality", - "abnormality of nervous system physiology", - "quality", - "multicellular organism", + "Abnormal cortical gyration", + "abnormal nervous system", + "Abnormality of neuronal migration", + "abnormal telencephalon morphology", + "abnormal cell migration", + "abnormal nervous system morphology", + "abnormal anatomical entity", + "Abnormality of the nervous system", + "phenotype by ontology source", + "abnormal biological_process", "phenotype", - "independent continuant", - "entity", - "Abnormal nervous system physiology (HPO)", - "material entity", - "anatomical entity", - "anatomical structure", - "continuant", - "abnormality of anatomical entity physiology", + "Morphological central nervous system abnormality", + "Type II lissencephaly", + "abnormal brain morphology", + "abnormal cellular process", + "Abnormal forebrain morphology", + "abnormal cerebral cortex morphology", + "abnormal anatomical entity morphology in the brain", + "Abnormal nervous system morphology", + "abnormal forebrain morphology", + "Abnormal cerebral cortex morphology", + "abnormal locomotion", "abnormal anatomical entity", - "multicellular anatomical structure", - "anatomical system", + "Phenotypic abnormality", + "abnormal central nervous system morphology", + "abnormal forebrain morphology", + "specifically dependent continuant", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "entity", ], - "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_label": "Obligate", "frequency_qualifier_category": "biolink:PhenotypicFeature", "frequency_qualifier_namespace": "HP", - "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Obligate"], "evidence_count": 2, - "grouping_key": "MONDO:0035432🍪🍪biolink:has_phenotype🍪HP:0002465", + "grouping_key": "MONDO:0013904🍪🍪biolink:has_phenotype🍪HP:0007260", }, { - "id": "uuid:4e12a2a3-842a-11ee-884f-6be035239f90", - "original_subject": "Orphanet:565899", + "id": "uuid:89e15864-ae6f-11ee-9f7a-f78bc2e9ee32", + "original_subject": "OMIM:614830", "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:565899"], - "frequency_qualifier": "HP:0040282", - "has_evidence": ["ECO:0000304"], - "subject": "MONDO:0035432", - "object": "HP:0008981", - "subject_label": "POMGNT2-related limb-girdle muscular dystrophy R24", + "publications": ["PMID:22958903"], + "frequency_qualifier": "HP:0040280", + "has_evidence": ["ECO:0000269"], + "subject": "MONDO:0013904", + "object": "HP:0001321", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", "subject_category": "biolink:Disease", "subject_namespace": "MONDO", "subject_closure": [ + "MONDO:0005071", + "BFO:0000016", + "MONDO:0019052", "MONDO:0000001", - "MONDO:0020121", - "MONDO:0003847", - "BFO:0000001", - "MONDO:0016106", "MONDO:0005336", + "OGMS:0000031", + "MONDO:0700069", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0000171", + "MONDO:0020120", + "MONDO:0700096", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0700075", + "MONDO:0024322", "BFO:0000017", - "MONDO:0003939", - "MONDO:0035432", - "BFO:0000020", - "MONDO:0002081", - "MONDO:0016971", - "MONDO:0005071", + "MONDO:0013904", + "MONDO:0015286", + "MONDO:0017741", + "MONDO:0020121", "BFO:0000002", - "MONDO:0020120", - "MONDO:0019056", + "BFO:0000020", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", "MONDO:0700223", - "BFO:0000016", - "MONDO:0700096", - "OGMS:0000031", + "MONDO:0002081", + "MONDO:0002320", ], "subject_closure_label": [ + "nervous system disorder", + "continuant", + "musculoskeletal system disorder", + "muscular 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anatomical entity", + "Aplasia/Hypoplasia of the cerebellum", + "anatomical entity hypoplasia", + "aplasia or hypoplasia of cerebellum", "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", + "aplasia or hypoplasia of anatomical entity", + "abnormal cerebellum morphology", + "Cerebellar hypoplasia", + "Abnormality of brain morphology", + "Abnormal metencephalon morphology", + "Abnormal hindbrain morphology", "Phenotypic abnormality", - "Abnormality of the calf musculature (HPO)", - "specifically dependent continuant", - "abnormal anatomical entity morphology", - "abnormal leg", - "quality", - "organism subdivision", - "organ", - "multicellular organism", - "pelvic complex", - "musculature of lower limb", - "muscle of leg", - "lower limb segment", - "zeugopod", + "anatomical entity 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"abnormal orbital region", "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", + "abnormality of camera-type eye physiology", + "abnormal craniocervical region", "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", + "abnormality of anatomical entity physiology", + "Abnormal eye physiology", + "entity", "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 head", + "abnormal anatomical entity", + "Abnormality of the eye", + "Phenotypic abnormality", + "phenotype by ontology source", + "Abnormality of the head", + "quality", + "abnormality of anatomical entity physiology", + "Abnormality of head or neck", + "Glaucoma", "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", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity", + "specifically dependent continuant", + "Abnormality of the face", ], - "frequency_qualifier_label": "Very frequent (HPO)", + "frequency_qualifier_label": "Frequent", "frequency_qualifier_category": "biolink:PhenotypicFeature", "frequency_qualifier_namespace": "HP", - "frequency_qualifier_closure": ["HP:0040281", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Very frequent (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", 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"UBERON:0001016", + "UPHENO:0076804", + "UPHENO:0021038", + "UPHENO:0020584", ], "object_closure_label": [ - "abnormality of anatomical entity physiology", + "Abnormality of the orbital region", + "All", + "abnormal uvea morphology", + "Persistent pupillary membrane", + "abnormal pupil morphology", + "abnormal anatomical entity morphology", + "abnormal anterior uvea morphology", + "abnormal orbital region", + "abnormal craniocervical region", + "quality", + "Abnormal eye morphology", + "abnormal face morphology", "Phenotypic abnormality", - "Bradyphrenia (HPO)", + "Phenotypic abnormality", + "Abnormality iris morphology", + "abnormal camera-type eye morphology", + "abnormal head", + "continuant", + "abnormal iris morphology", + "abnormal pupil morphology", + "abnormal anterior segment of eyeball morphology", "abnormal anatomical entity", - "Abnormality of higher mental function (HPO)", - "quality", - "multicellular organismal process", - "abnormal phenotype by ontology source", - 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"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", + "Phenotypic abnormality", + "Abnormality of the musculature", + "abnormality of anatomical entity physiology", + "decreased length of anatomical entity in independent continuant", "entity", - "structure with developmental contribution from neural crest", - "thoracic cavity element", - "primary circulatory organ", - "abnormal coronary vessel morphology", - "Abnormality of the cardiovascular system (HPO)", + "decreased size of the anatomical entity", + "continuant", + "abnormality of musculoskeletal system physiology", + "abnormal muscle organ morphology", + "abnormal anatomical entity length", + "abnormal tendon morphology", + "Abnormal skeletal morphology", + "Abnormal skeletal muscle morphology", "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", - "anatomical conduit", - "systemic artery", - "heart blood vessel", - "heart plus pericardium", + "abnormal tendon morphology", + "phenotype by ontology source", + "abnormal connective tissue", + "Abnormal musculoskeletal physiology", "phenotype", - "abnormal incomplete closing of the ductus arteriosus", + "Abnormality of joint mobility", + "Abnormal tendon morphology", + "Joint contracture", + "decreased length of tendon", + "quality", + "abnormality of anatomical entity physiology", + "abnormal skeletal system morphology", + "Abnormal joint physiology", + "Abnormality of the skeletal system", + "abnormal musculature", + "abnormal anatomical entity", + "decreased size of the anatomical entity in the independent continuant", + "Abnormality of connective tissue", + "specifically dependent continuant", "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", - "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", - "mesoderm-derived structure", - "artery", - "thoracic segment blood vessel", - "heart", - "heart vasculature", + "abnormal skeletal system", + "abnormal anatomical entity morphology", ], - "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_label": "Frequent", "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)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "evidence_count": 2, - "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001643", + "grouping_key": "MONDO:0011925🍪🍪biolink:has_phenotype🍪HP:0001371", }, { - "id": "uuid:4e02df99-842a-11ee-884f-6be035239f90", - "original_subject": "Orphanet:589821", + "id": "uuid:89e15869-ae6f-11ee-9f7a-f78bc2e9ee32", + "original_subject": "OMIM:614830", "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"], + "publications": ["PMID:22958903"], "frequency_qualifier": "HP:0040283", - "has_evidence": ["ECO:0000304"], - "subject": "MONDO:0035646", - "object": "HP:0001671", - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "has_evidence": ["ECO:0000269"], + "subject": "MONDO:0013904", + "object": "HP:0000568", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", "subject_category": "biolink:Disease", "subject_namespace": "MONDO", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0019052", "MONDO:0000001", - "MONDO:0020121", + "MONDO:0005336", + "OGMS:0000031", + "MONDO:0700069", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0000171", + "MONDO:0020120", + "MONDO:0700096", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0700075", + "MONDO:0024322", "BFO:0000017", - "MONDO:0008056", - "MONDO:0035646", + "MONDO:0013904", + "MONDO:0015286", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000002", + "BFO:0000020", "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:0005066", "MONDO:0700223", - "MONDO:0003382", - "BFO:0000016", - "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", - "OGMS:0000031", - "BFO:0000001", + "MONDO:0002081", + "MONDO:0002320", ], "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", + "continuant", "musculoskeletal system disorder", - "hereditary disease", - "eye disorder", + "muscular dystrophy-dystroglycanopathy, type A", + "myopathy caused by variation in POMGNT2", + "neuromuscular disease", + "skeletal muscle disorder", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "myopathy", + "disease", + "congenital muscular dystrophy", + "congenital muscular dystrophy caused by variation in POMGNT2", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome", + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", + "metabolic disease", + "disease", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "entity", ], - "object_label": "Abnormal cardiac septum morphology (HPO)", + "object_label": "Microphthalmia", "object_category": "biolink:PhenotypicFeature", "object_namespace": "HP", "object_closure": [ - "PR:000050567", - "UBERON:0000465", - "UPHENO:0019888", - "UPHENO:0080362", - "HP:0001627", - "UPHENO:0015280", - "BFO:0000040", - "UBERON:0001062", - "UBERON:0000468", - "UBERON:0011676", - "UBERON:0013701", - "HP:0001626", + "HP:0000315", + "HP:0000001", + "UPHENO:0075219", + "HP:0000234", + "UPHENO:0075997", + "UPHENO:0080079", + "UPHENO:0001005", "UPHENO:0001002", - "BFO:0000020", - "UPHENO:0015324", - "HP:0001671", "BFO:0000002", - "UPHENO:0001001", + "UPHENO:0075696", + "HP:0000152", + "UPHENO:0087907", + "UPHENO:0002910", "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", + "HP:0000568", + "UPHENO:0015280", + "HP:0000271", + "UPHENO:0012541", + "UPHENO:0080209", + "UPHENO:0068971", + "UPHENO:0021474", + "UPHENO:0002844", + "BFO:0000020", + "HP:0008056", + "PATO:0000001", + "HP:0012372", + "UPHENO:0087472", + "HP:0000478", + "HP:0100887", + "UPHENO:0087924", + "UPHENO:0002764", + "UPHENO:0003020", "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", + "UPHENO:0069523", + "UPHENO:0001001", + "UPHENO:0086589", "HP:0000118", + "UPHENO:0075195", "UPHENO:0020584", - "PATO:0000001", - "UBERON:0003037", - "UBERON:0010314", - "HP:0000001", - "UPHENO:0001005", "BFO:0000001", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0004120", - "UBERON:0001009", - "UBERON:0005178", - "UBERON:0007100", ], "object_closure_label": [ - "abnormal anatomical entity", + "Abnormality of the orbital region", + "All", + "abnormal size of eyeball of camera-type eye", + "abnormal size of anatomical entity", + "abnormal anatomical entity morphology", + "abnormal orbital region", + "aplasia or hypoplasia of anatomical entity", + "abnormal craniocervical region", "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)", + "Abnormal eye morphology", + "abnormal face morphology", "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)", - "abnormal anatomical entity morphology", - "entity", - "entity", - "septum", - "structure with developmental contribution from neural crest", - "thoracic cavity element", - "primary circulatory organ", - "Abnormality of the cardiovascular system (HPO)", "Phenotypic abnormality", - "abnormal cardiovascular system morphology", - "abnormal anatomical entity morphology", - "organism subdivision", - "organ", - "heart plus pericardium", + "Phenotypic abnormality", + "Aplasia/Hypoplasia affecting the eye", + "entity", + "aplasia or hypoplasia of eyeball of camera-type eye", + "decreased size of the anatomical entity", + "abnormal camera-type eye morphology", + "abnormal head", + "continuant", + "abnormal anatomical entity", + "Abnormality of the eye", + "Abnormality of globe size", + "abnormal camera-type eye morphology", + "Microphthalmia", + "phenotype by ontology source", "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", - "anatomical entity", - "cardiovascular system", - "anatomical structure", + "abnormal craniocervical region morphology", + "Abnormality of the head", + "Abnormality of head or neck", + "abnormal head morphology", + "abnormal face", + "abnormal eyeball of camera-type eye", "abnormal anatomical entity", - "abnormal cardiac septum morphology", - "abnormal cardiovascular system", - "Abnormal heart morphology (HPO)", - "abnormal heart morphology", - "multicellular anatomical structure", - "anatomical system", - "mesoderm-derived structure", - "cardiac septum", - "heart", + "decreased size of the eyeball of camera-type eye", + "decreased size of the anatomical entity in the independent continuant", + "specifically dependent continuant", + "abnormal anatomical entity morphology in the independent continuant", + "Abnormality of the face", + "abnormal anatomical entity morphology", ], - "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_label": "Occasional", "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)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040283"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Occasional"], "evidence_count": 2, - "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001671", + "grouping_key": "MONDO:0013904🍪🍪biolink:has_phenotype🍪HP:0000568", }, { - "id": "uuid:4e02df9a-842a-11ee-884f-6be035239f90", - "original_subject": "Orphanet:589821", + "id": "uuid:89e159d4-ae6f-11ee-9f7a-f78bc2e9ee32", + "original_subject": "OMIM:613150", "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"], + "publications": ["OMIM:613150"], "frequency_qualifier": "HP:0040283", "has_evidence": ["ECO:0000304"], - "subject": "MONDO:0035646", - "object": "HP:0002014", - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject": "MONDO:0013154", + "object": "HP:0002084", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "subject_category": "biolink:Disease", "subject_namespace": "MONDO", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0018939", + "MONDO:0019052", + "MONDO:0018282", "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", + "MONDO:0013154", "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:0000171", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0015286", + "MONDO:0016155", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000020", + "MONDO:0700071", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", "BFO:0000001", + "MONDO:0002320", ], "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", + "disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "muscular dystrophy-dystroglycanopathy, type A", + "neuromuscular disease", + "muscle-eye-brain disease", + "skeletal muscle disorder", + "entity", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "continuant", + "myopathy", + "congenital muscular dystrophy", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome", + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "metabolic disease", + "qualitative or quantitative defects of alpha-dystroglycan", + "disease", + "myopathy caused by variation in POMT2", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", ], - "object_label": "Diarrhea (HPO)", + "object_label": "Encephalocele", "object_category": "biolink:PhenotypicFeature", "object_namespace": "HP", "object_closure": [ - "UPHENO:0002443", - "UPHENO:0002536", - "UBERON:0000465", - "UPHENO:0082875", - "HP:0002664", - "BFO:0000001", - "BFO:0000040", - "UBERON:0001062", + "HP:0000001", + "HP:0000924", + "UPHENO:0050108", + "UPHENO:0081436", + "HP:0000234", + "UPHENO:0020641", + "UPHENO:0087665", + "UPHENO:0076791", + "UPHENO:0087089", + "HP:0011815", + "UPHENO:0001005", "UPHENO:0001002", - "BFO:0000020", - "HP:0011793", - "HP:0011458", - "BFO:0000002", - "UBERON:0001988", - "UPHENO:0001001", - "UPHENO:0002833", - "UPHENO:0001003", - "UBERON:0000463", + "BFO:0000001", "UPHENO:0075696", - "HP:0002014", - "HP:0025031", - "BFO:0000004", - "UBERON:0000061", - "UBERON:0000174", - "UBERON:0000468", - "BFO:0000002", - "HP:0025032", + "UPHENO:0051077", + "UPHENO:0076703", + "HP:0000152", + "UPHENO:0087907", + "HP:0000929", + "HP:0000707", + "UPHENO:0001003", + "UPHENO:0076692", + "UPHENO:0022529", + "UPHENO:0076702", + "UPHENO:0087363", + "UPHENO:0051003", + "HP:0011842", + "UPHENO:0088123", + "HP:0045005", + "UPHENO:0015280", + "HP:0034237", + "UPHENO:0002964", + "HP:0012639", + "UPHENO:0049587", + "UPHENO:0002844", + "BFO:0000020", + "HP:0002084", + "HP:0410043", + "UPHENO:0004523", "PATO:0000001", + "UPHENO:0002764", + "HP:0002011", + "UPHENO:0002536", + "UPHENO:0081566", + "UPHENO:0001001", + "UPHENO:0086589", "HP:0000118", - "UPHENO:0002332", - "HP:0000001", - "UPHENO:0001005", - "BFO:0000001", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0001007", + "BFO:0000002", + "HP:0009121", + "HP:0033127", + "UPHENO:0020584", ], "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)", + "All", + "Abnormal axial skeleton morphology", + "Abnormality of the musculoskeletal system", + "abnormal anatomical entity morphology", + "abnormal craniocervical region", + "Abnormal skull morphology", + "abnormal neural tube morphology", + "quality", "abnormal phenotype by ontology source", - "continuant", - "feces", - "Phenotypic abnormality (HPO)", "Phenotypic abnormality", - "Neoplasm by anatomical site (HPO)", - "Abdominal symptom (HPO)", - "quality", - "organism substance", - "excreta", - "multicellular organism", + "Phenotypic abnormality", + "continuant", + "Encephalocele", + "Abnormal neural tube morphology", + "abnormal nervous system", + "abnormal head", + "abnormal axial skeleton plus cranial skeleton morphology", + "Cephalocele", + "abnormal postcranial axial skeleton morphology", + "abnormal nervous system morphology", + "abnormal neural tube morphology", + "abnormal anatomical entity", + "abnormal neural tube closure", + "abnormal tube formation", + "Abnormal skeletal morphology", + "abnormal embryonic tissue morphology", + "Neural tube defect", + "Abnormality of the nervous system", + "phenotype by ontology source", + "abnormal biological_process", "phenotype", - "Neoplasm (HPO)", - "entity", - "independent continuant", - "abnormality of digestive system physiology", - "Abnormality of the digestive system (HPO)", - "material entity", - "anatomical entity", - "anatomical structure", - "abnormality of anatomical entity physiology", + "abnormal craniocervical region morphology", + "Morphological central nervous system abnormality", + "abnormal developmental process", + "abnormal development of anatomical entity", + "Abnormality of the head", + "Abnormal nervous system morphology", + "abnormal embryo morphology", + "abnormal skeletal system morphology", + "Abnormality of head or neck", + "abnormal head morphology", + "Abnormality of the skeletal system", "abnormal anatomical entity", - "multicellular anatomical structure", - "anatomical system", + "abnormal skull morphology", + "abnormal central nervous system morphology", + "specifically dependent continuant", + "abnormal anatomical entity morphology in the independent continuant", + "Open neural tube defect", + "abnormal skeletal system", + "abnormal anatomical entity morphology", + "entity", ], - "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_label": "Occasional", "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)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040283"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Occasional"], "evidence_count": 2, - "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0002014", + "grouping_key": "MONDO:0013154🍪🍪biolink:has_phenotype🍪HP:0002084", }, ], }, "facet_counts": { "facet_fields": {}, "facet_queries": { - '(category:"biolink:DiseaseToPhenotypicFeatureAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")': 4027, + '(category:"biolink:DiseaseToPhenotypicFeatureAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")': 3879, '(category:"biolink:GeneToPhenotypicFeatureAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")': 0, '(category:"biolink:PairwiseGeneToGeneInteraction") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")': 0, '(category:"biolink:GeneToPathwayAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")': 0, @@ -4212,7 +3626,7 @@ def association_counts_response(): '(category:"biolink:MacromolecularMachineToCellularComponentAssociation") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121")': 0, '(category:"biolink:MacromolecularMachineToBiologicalProcessAssociation") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121")': 0, '(category:"biolink:CausalGeneToDiseaseAssociation") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121")': 124, - '(category:"biolink:CorrelatedGeneToDiseaseAssociation") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121")': 151, + '(category:"biolink:CorrelatedGeneToDiseaseAssociation") AND (object:"MONDO:0020121" OR object_closure:"MONDO:0020121")': 139, }, }, } diff --git a/backend/tests/fixtures/association_response.py b/backend/tests/fixtures/association_response.py index 04c1e96f6..69e07e3a3 100644 --- a/backend/tests/fixtures/association_response.py +++ b/backend/tests/fixtures/association_response.py @@ -19,4144 +19,3558 @@ def association_response(): }, }, "response": { - "num_found": 4838, + "num_found": 4624, "start": 0, "docs": [ { - "id": "uuid:4e12a2a1-842a-11ee-884f-6be035239f90", - "original_subject": "Orphanet:565899", + "id": "uuid:89e15863-ae6f-11ee-9f7a-f78bc2e9ee32", + "original_subject": "OMIM:614830", "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:565899"], - "frequency_qualifier": "HP:0040282", - "has_evidence": ["ECO:0000304"], - "subject": "MONDO:0035432", - "object": "HP:0002465", - "subject_label": "POMGNT2-related limb-girdle muscular dystrophy R24", + "publications": ["PMID:22958903"], + "frequency_qualifier": "HP:0040280", + "has_evidence": ["ECO:0000269"], + "subject": "MONDO:0013904", + "object": "HP:0007260", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", "subject_category": "biolink:Disease", "subject_namespace": "MONDO", "subject_closure": [ + "MONDO:0005071", + "BFO:0000016", + "MONDO:0019052", "MONDO:0000001", - "MONDO:0020121", - "MONDO:0003847", - "BFO:0000001", - "MONDO:0016106", "MONDO:0005336", + "OGMS:0000031", + "MONDO:0700069", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0000171", + "MONDO:0020120", + "MONDO:0700096", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0700075", + "MONDO:0024322", "BFO:0000017", - "MONDO:0003939", - "MONDO:0035432", - "BFO:0000020", - "MONDO:0002081", - "MONDO:0016971", - "MONDO:0005071", + "MONDO:0013904", + "MONDO:0015286", + "MONDO:0017741", + "MONDO:0020121", "BFO:0000002", - "MONDO:0020120", - "MONDO:0019056", + "BFO:0000020", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", "MONDO:0700223", - "BFO:0000016", - "MONDO:0700096", - "OGMS:0000031", + "MONDO:0002081", + "MONDO:0002320", ], "subject_closure_label": [ + "nervous system disorder", + "continuant", + "musculoskeletal system disorder", + "muscular dystrophy-dystroglycanopathy, type A", + "myopathy caused by variation in POMGNT2", + "neuromuscular disease", + "skeletal muscle disorder", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", + "muscular dystrophy", + "myopathy", "disease", + "congenital muscular dystrophy", + "congenital muscular dystrophy caused by variation in POMGNT2", + "disorder of glycosylation", "realizable entity", - "disease", - "POMGNT2-related limb-girdle muscular dystrophy R24", - "muscle tissue disorder", + "human disease", + "congenital disorder of glycosylation", "hereditary skeletal muscle disorder", - "limb-girdle muscular dystrophy", - "continuant", "disposition", - "human disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", + "metabolic disease", + "disease", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", "specifically dependent continuant", - "myopathy", - "nervous system disorder", "entity", - "progressive muscular dystrophy", - "musculoskeletal system disorder", - "hereditary disease", - "muscular dystrophy", - "skeletal muscle disorder", - "neuromuscular disease", ], - "object_label": "Poor speech (HPO)", + "object_label": "Type II lissencephaly", "object_category": "biolink:PhenotypicFeature", "object_namespace": "HP", "object_closure": [ - "UPHENO:0002536", - "BFO:0000001", - "UBERON:0000465", - "UPHENO:0082875", - "BFO:0000002", - "UPHENO:0004523", - "BFO:0000040", - "UBERON:0001062", + "HP:0000001", + "HP:0002060", + "HP:0100547", + "UPHENO:0081603", + "HP:0012443", + "HP:0002538", "UPHENO:0001002", - "BFO:0000020", - "BFO:0000002", - "UPHENO:0001001", - "UPHENO:0001003", + "UPHENO:0076791", + "UPHENO:0087518", + "UPHENO:0076799", + "HP:0001339", + "UPHENO:0001005", "BFO:0000001", "UPHENO:0075696", - "UPHENO:0002433", - "HP:0012638", - "BFO:0000004", - "UBERON:0000061", - "UBERON:0000468", - "HP:0002167", + "HP:0000707", + "UPHENO:0001003", + "UPHENO:0076692", + "UPHENO:0049643", + "UPHENO:0076702", + "UPHENO:0015280", + "UPHENO:0081435", + "HP:0012639", + "UPHENO:0020888", + "UPHENO:0049587", + "HP:0002269", + "BFO:0000002", + "BFO:0000020", + "HP:0002536", + "UPHENO:0004523", "PATO:0000001", + "UPHENO:0049852", + "UPHENO:0087531", + "HP:0002011", + "HP:0007260", + "UPHENO:0076805", + "UPHENO:0050121", + "UPHENO:0049855", + "UPHENO:0002536", + "UPHENO:0001001", "HP:0000118", - "UPHENO:0002332", - "HP:0000001", - "HP:0002465", - "UPHENO:0001005", - "HP:0000707", - "HP:0011446", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0001016", + "UPHENO:0049634", + "UPHENO:0020584", ], "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", + "All", + "Abnormal cerebral morphology", "continuant", - "material anatomical entity", - "nervous system", - "All (HPO)", - "Poor speech (HPO)", + "abnormal cell motility", + "abnormal anatomical entity morphology", + "Lissencephaly", + "abnormal cerebral hemisphere morphology", + "Abnormality of brain morphology", + "quality", + "abnormal neuron migration", "abnormal phenotype by ontology source", - "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "entity", "Phenotypic abnormality", - "abnormality of nervous system physiology", - "quality", - "multicellular organism", + "Abnormal cortical gyration", + "abnormal nervous system", + "Abnormality of neuronal migration", + "abnormal telencephalon morphology", + "abnormal cell migration", + "abnormal nervous system morphology", + "abnormal anatomical entity", + "Abnormality of the nervous system", + "phenotype by ontology source", + "abnormal biological_process", "phenotype", - "independent continuant", - "entity", - "Abnormal nervous system physiology (HPO)", - "material entity", - "anatomical entity", - "anatomical structure", - "continuant", - "abnormality of anatomical entity physiology", + "Morphological central nervous system abnormality", + "Type II lissencephaly", + "abnormal brain morphology", + "abnormal cellular process", + "Abnormal forebrain morphology", + "abnormal cerebral cortex morphology", + "abnormal anatomical entity morphology in the brain", + "Abnormal nervous system morphology", + "abnormal forebrain morphology", + "Abnormal cerebral cortex morphology", + "abnormal locomotion", "abnormal anatomical entity", - "multicellular anatomical structure", - "anatomical system", + "Phenotypic abnormality", + "abnormal central nervous system morphology", + "abnormal forebrain morphology", + "specifically dependent continuant", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "entity", ], - "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_label": "Obligate", "frequency_qualifier_category": "biolink:PhenotypicFeature", "frequency_qualifier_namespace": "HP", - "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Obligate"], "evidence_count": 2, - "grouping_key": "MONDO:0035432🍪🍪biolink:has_phenotype🍪HP:0002465", + "grouping_key": "MONDO:0013904🍪🍪biolink:has_phenotype🍪HP:0007260", }, { - "id": "uuid:4e12a2a3-842a-11ee-884f-6be035239f90", - "original_subject": "Orphanet:565899", + "id": "uuid:89e15864-ae6f-11ee-9f7a-f78bc2e9ee32", + "original_subject": "OMIM:614830", "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:565899"], - "frequency_qualifier": "HP:0040282", - "has_evidence": ["ECO:0000304"], - "subject": "MONDO:0035432", - "object": "HP:0008981", - "subject_label": "POMGNT2-related limb-girdle muscular dystrophy R24", + "publications": ["PMID:22958903"], + "frequency_qualifier": "HP:0040280", + "has_evidence": ["ECO:0000269"], + "subject": "MONDO:0013904", + "object": "HP:0001321", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", "subject_category": "biolink:Disease", "subject_namespace": "MONDO", "subject_closure": [ + "MONDO:0005071", + "BFO:0000016", + "MONDO:0019052", "MONDO:0000001", - "MONDO:0020121", - "MONDO:0003847", - "BFO:0000001", - "MONDO:0016106", "MONDO:0005336", + "OGMS:0000031", + "MONDO:0700069", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0000171", + "MONDO:0020120", + "MONDO:0700096", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0700075", + "MONDO:0024322", "BFO:0000017", - "MONDO:0003939", - "MONDO:0035432", - "BFO:0000020", - "MONDO:0002081", - "MONDO:0016971", - "MONDO:0005071", + "MONDO:0013904", + "MONDO:0015286", + "MONDO:0017741", + "MONDO:0020121", "BFO:0000002", - "MONDO:0020120", - "MONDO:0019056", + "BFO:0000020", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", "MONDO:0700223", - "BFO:0000016", - "MONDO:0700096", - "OGMS:0000031", + "MONDO:0002081", + "MONDO:0002320", ], "subject_closure_label": [ + "nervous system disorder", + "continuant", + "musculoskeletal system disorder", + "muscular dystrophy-dystroglycanopathy, type A", + "myopathy caused by variation in POMGNT2", + "neuromuscular disease", + "skeletal muscle disorder", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", + "muscular dystrophy", + "myopathy", "disease", + "congenital muscular dystrophy", + "congenital muscular dystrophy caused by variation in POMGNT2", + "disorder of glycosylation", "realizable entity", - "disease", - "POMGNT2-related limb-girdle muscular dystrophy R24", - "muscle tissue disorder", + "human disease", + "congenital disorder of glycosylation", "hereditary skeletal muscle disorder", - "limb-girdle muscular dystrophy", - "continuant", "disposition", - "human disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", + "metabolic disease", + "disease", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", "specifically dependent continuant", - "myopathy", - "nervous system disorder", "entity", - "progressive muscular dystrophy", - "musculoskeletal system disorder", - "hereditary disease", - "muscular dystrophy", - "skeletal muscle disorder", - "neuromuscular disease", ], - "object_label": "Calf muscle hypertrophy (HPO)", + "object_label": "Cerebellar hypoplasia", "object_category": "biolink:PhenotypicFeature", "object_namespace": "HP", "object_closure": [ - "HP:0008981", - "UPHENO:0084535", - "UPHENO:0002816", - "HP:0030236", - "PR:000050567", - "UBERON:0000465", - "RO:0002577", - "UPHENO:0015280", - "HP:0001437", - "BFO:0000040", - "UBERON:0001062", - "UBERON:0011216", - "UBERON:0000154", - "UBERON:0006067", + "HP:0000001", + "HP:0012443", + "HP:0011283", "UPHENO:0001002", - "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", + "UPHENO:0081099", + "UPHENO:0076791", + "UPHENO:0081601", + "HP:0001317", + "UPHENO:0080079", + "UPHENO:0076720", + "HP:0001321", + "UPHENO:0081091", + "UPHENO:0080089", "BFO:0000001", - "UBERON:0004482", - "UBERON:0001383", - "UBERON:0008784", - "UBERON:0002471", "UPHENO:0075696", - "UPHENO:0001005", - "HP:0009127", - "BFO:0000020", - "UPHENO:0001072", - "UPHENO:0081581", - "HP:0033127", + "HP:0002977", + "HP:0000707", "UPHENO:0001003", "UPHENO:0076692", - "UPHENO:0003070", - "UPHENO:0002830", - "BFO:0000004", - "UBERON:0004708", - "UBERON:0000061", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0000468", - "UBERON:0010709", - "HP:0002981", - "UPHENO:0065599", + "UPHENO:0076702", + "UPHENO:0086932", + "UPHENO:0015280", + "UPHENO:0020013", + "UPHENO:0081435", + "HP:0012639", + "UPHENO:0012541", + "UPHENO:0068971", "BFO:0000002", - "HP:0003011", + "BFO:0000020", + "UPHENO:0081790", + "UPHENO:0004523", + "HP:0011282", + "HP:0002011", + "UPHENO:0076805", + "UPHENO:0068984", "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", + "UPHENO:0001001", + "UPHENO:0001005", "HP:0000118", + "UPHENO:0075195", + "HP:0007360", "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_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", + "All", "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)", + "abnormal size of anatomical entity", + "Aplasia/Hypoplasia of the cerebellum", + "anatomical entity hypoplasia", + "aplasia or hypoplasia of cerebellum", "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", + "aplasia or hypoplasia of anatomical entity", + "abnormal cerebellum morphology", + "Cerebellar hypoplasia", + "Abnormality of brain morphology", + "Abnormal metencephalon morphology", + "Abnormal hindbrain morphology", "Phenotypic abnormality", - "Abnormality of the calf musculature (HPO)", - "specifically dependent continuant", - "abnormal anatomical entity morphology", - "abnormal leg", - "quality", - "organism subdivision", - "organ", - "multicellular organism", - "pelvic complex", - "musculature of lower limb", - "muscle of leg", - "lower limb segment", - "zeugopod", + "anatomical entity hypoplasia in independent continuant", + "abnormal nervous system", + "decreased size of the anatomical entity", + "Abnormal cerebellum morphology", + "abnormal nervous system morphology", + "abnormal hindbrain morphology", + "abnormal anatomical entity", + "Aplasia/Hypoplasia involving the central nervous system", + "Abnormality of the nervous system", + "phenotype by ontology source", "phenotype", - "abnormal hindlimb zeugopod", + "abnormal phenotype by ontology source", + "Morphological central nervous system abnormality", + "abnormal brain morphology", + "abnormal anatomical entity morphology in the brain", + "Abnormal nervous system morphology", + "quality", + "decreased size of the cerebellum", + "abnormal anatomical entity", + "decreased size of the anatomical entity in the independent continuant", + "Phenotypic abnormality", + "cerebellum hypoplasia", + "abnormal central nervous system morphology", + "abnormal metencephalon morphology", + "specifically dependent continuant", "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", - "muscle structure", - "skeletal musculature", - "hindlimb", - "appendage girdle complex", - "appendage musculature", - "musculature of pelvic complex", - "limb muscle", - "pelvic complex muscle", - "paired limb/fin segment", + "abnormal hindbrain morphology", + "abnormal anatomical entity morphology", + "entity", ], - "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_label": "Obligate", "frequency_qualifier_category": "biolink:PhenotypicFeature", "frequency_qualifier_namespace": "HP", - "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Obligate"], "evidence_count": 2, - "grouping_key": "MONDO:0035432🍪🍪biolink:has_phenotype🍪HP:0008981", + "grouping_key": "MONDO:0013904🍪🍪biolink:has_phenotype🍪HP:0001321", }, { - "id": "uuid:4e12a2a4-842a-11ee-884f-6be035239f90", - "original_subject": "Orphanet:565899", + "id": "uuid:89e15866-ae6f-11ee-9f7a-f78bc2e9ee32", + "original_subject": "OMIM:614830", "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:565899"], + "publications": ["PMID:22958903"], "frequency_qualifier": "HP:0040282", - "has_evidence": ["ECO:0000304"], - "subject": "MONDO:0035432", - "object": "HP:0008994", - "subject_label": "POMGNT2-related limb-girdle muscular 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"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", - "UBERON:0010314", - "UBERON:0003102", - "UBERON:0010000", - "UBERON:0001555", - "UBERON:0001456", - "UBERON:0004921", - "HP:0000001", + "BFO:0000002", + "BFO:0000020", + "HP:0012373", + "HP:0000478", "UPHENO:0001005", - "HP:0031816", - "HP:0000153", - "HP:0000234", - "HP:0000271", + "UPHENO:0002219", + "UPHENO:0002764", + "UPHENO:0003020", + "UPHENO:0002536", + "PATO:0000001", + "HP:0000118", "BFO:0000001", - "UBERON:0000467", - "UBERON:0000064", - "UBERON:0001007", - "UBERON:0013522", - "UBERON:0000165", ], "object_closure_label": [ - "abnormal head", - "abnormal digestive system", - "Abnormality of the midface (HPO)", - "quality", - "abnormal anatomical entity", - "abnormal 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"BFO:0000016", + "MONDO:0000171", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0015286", + "MONDO:0016155", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000020", + "MONDO:0700071", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", "BFO:0000001", + "MONDO:0002320", ], "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", - 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"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", + "disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "muscular dystrophy-dystroglycanopathy, type A", + "neuromuscular disease", + "muscle-eye-brain disease", + "skeletal muscle disorder", + "entity", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "continuant", + "myopathy", + "congenital muscular dystrophy", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome", + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "metabolic disease", + "qualitative or quantitative defects of alpha-dystroglycan", + "disease", + "myopathy caused by variation in POMT2", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", ], - "object_label": "Polyhydramnios (HPO)", + "object_label": "Increased variability in muscle fiber diameter", "object_category": "biolink:PhenotypicFeature", "object_namespace": "HP", "object_closure": [ - "HP:0001197", - "UPHENO:0075852", - "UPHENO:0002536", - "UBERON:0000465", - "BFO:0000001", - "BFO:0000040", - "BFO:0000002", - "UPHENO:0001001", + "HP:0000001", + "HP:0004303", + "HP:0025461", + "UPHENO:0088180", + "UPHENO:0086172", "UPHENO:0001002", - "UPHENO:0001003", - "BFO:0000001", - "UBERON:0001062", - "UBERON:0000061", - "UBERON:0000463", + "HP:0003557", + "UPHENO:0076710", + "UPHENO:0084928", + "UPHENO:0085097", "UPHENO:0001005", + "BFO:0000002", + "HP:0003011", + "UPHENO:0006889", + "UPHENO:0075696", + "UPHENO:0080626", + "UPHENO:0001003", + "UPHENO:0076692", + "UPHENO:0077801", + "UPHENO:0085135", + "HP:0011805", "BFO:0000020", - "BFO:0000004", - "UBERON:0000173", - "UBERON:0000468", - "HP:0001561", - "UBERON:0000922", - "HP:0000118", + "UPHENO:0015280", + "HP:0012084", + "UPHENO:0086462", + "UPHENO:0087047", + "HP:0025354", + "UPHENO:0085099", + "UPHENO:0002816", + "UPHENO:0002536", "PATO:0000001", - "UBERON:0000323", - "HP:0000001", - "BFO:0000002", - "UPHENO:0075949", - "HP:0001560", - "UBERON:0010000", + "UPHENO:0001001", + "UPHENO:0067691", + "HP:0000118", + "UPHENO:0075195", + "HP:0033127", + "UPHENO:0086457", + "UPHENO:0020584", + "BFO:0000001", ], "object_closure_label": [ - "Phenotypic abnormality", - "Abnormality of the amniotic fluid (HPO)", - "quality", + "All", + "Abnormal muscle fiber morphology", + "abnormal size of anatomical entity", + "Abnormality of the musculoskeletal system", + "abnormal anatomical entity morphology", + "abnormal size of cell", + "abnormal cell morphology", + "abnormal muscle cell morphology", + "abnormal skeletal muscle tissue morphology", + "abnormal cellular_component", + "abnormal cell of skeletal muscle morphology", "abnormal phenotype by ontology source", - "phenotype by ontology source", - "continuant", - "material anatomical entity", - "All (HPO)", - "embryo", - "Phenotypic abnormality (HPO)", - "abnormal late embryo", + "Phenotypic abnormality", + "Abnormality of the musculature", + "Abnormality of skeletal muscle fiber size", + "abnormal size of skeletal muscle fiber", "entity", + "continuant", + "Increased variability in muscle fiber diameter", + "abnormal muscle organ morphology", + "abnormal anatomical entity", + "Abnormal skeletal muscle morphology", "specifically dependent continuant", - "anatomical entity", - "anatomical structure", - "organism substance", - "amniotic fluid", - "multicellular organism", + "phenotype by ontology source", "phenotype", - "continuant", - "entity", - "independent continuant", - "Abnormality of prenatal development or birth (HPO)", - "abnormal amniotic fluid", - "material entity", - "Polyhydramnios (HPO)", + "abnormal morphology of cellular_component", + "Abnormal cellular phenotype", + "quality", + "abnormal cell", + "abnormal size of cellular_component", + "Abnormal cell morphology", + "abnormal cell of skeletal muscle morphology", + "abnormal musculature", "abnormal anatomical entity", - "multicellular anatomical structure", - "late embryo", + "abnormal myotube morphology", + "Phenotypic abnormality", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal size of cell of skeletal muscle", + "abnormal anatomical entity morphology", ], - "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_label": "Obligate", "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)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Obligate"], "evidence_count": 2, - "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001561", + "grouping_key": "MONDO:0013154🍪🍪biolink:has_phenotype🍪HP:0003557", }, { - "id": "uuid:4e02df98-842a-11ee-884f-6be035239f90", - "original_subject": "Orphanet:589821", + "id": "uuid:89ed09a8-ae6f-11ee-9f7a-f78bc2e9ee32", + "original_subject": "OMIM:607855", "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", + "publications": ["PMID:12552556"], + "frequency_qualifier": "HP:0040282", + "has_evidence": ["ECO:0000269"], + "subject": "MONDO:0011925", + "object": "HP:0001371", + "subject_label": "congenital merosin-deficient muscular dystrophy 1A", "subject_category": "biolink:Disease", "subject_namespace": "MONDO", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", "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:0100228", "MONDO:0019056", - "MONDO:0004994", - "MONDO:0004995", - "MONDO:0700223", - "MONDO:0003382", - "BFO:0000016", + "BFO:0000001", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", - "BFO:0000001", + "MONDO:0019950", + "BFO:0000017", + "MONDO:0020121", + "BFO:0000002", + "BFO:0000020", + "MONDO:0011925", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0700223", + "MONDO:0002081", + "MONDO:0002320", ], "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", + "continuant", "musculoskeletal system disorder", - "hereditary disease", - "eye disorder", + "disease", + "LAMA2-related muscular dystrophy", + "congenital merosin-deficient muscular dystrophy 1A", + "neuromuscular disease", + "skeletal muscle disorder", + "congenital nervous system disorder", "muscular dystrophy", + "myopathy", + "congenital muscular dystrophy", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome", + "human disease", + "hereditary skeletal muscle disorder", + "disposition", + "disease", + "hereditary disease", + "muscle tissue disorder", + "specifically dependent continuant", + "entity", ], - "object_label": "Patent ductus arteriosus (HPO)", + "object_label": "Flexion contracture", "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", + "HP:0000001", + "HP:0034430", + "HP:0000924", + "HP:0011843", + "UPHENO:0082875", + "UPHENO:0081440", + "UPHENO:0076710", + "UPHENO:0088186", + "HP:0001371", + "UPHENO:0001005", "BFO:0000002", - "UBERON:0013768", - "UBERON:0003509", - "UBERON:0003513", - "UBERON:0011695", - "UBERON:0004716", - "UBERON:0004145", - "UBERON:0005985", - "UBERON:0002049", - "UBERON:0002201", - "UBERON:0006876", - "UPHENO:0001001", + "HP:0003011", + "UPHENO:0076703", + "UPHENO:0002332", "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "UBERON:0034923", - "UBERON:0015410", + "UPHENO:0076692", + "HP:0003549", + "HP:0011842", + "HP:0011805", + "UPHENO:0001002", + "UPHENO:0021425", + "UPHENO:0015280", + "UPHENO:0002964", + "UPHENO:0046759", + "UPHENO:0002712", + "UPHENO:0012541", + "UPHENO:0068971", + "BFO:0000020", + "UPHENO:0031839", + "UPHENO:0046505", "UPHENO:0075696", - "HP:0001643", - "UPHENO:0076776", - "UPHENO:0081581", - "UPHENO:0076692", - "BFO:0000004", - "UBERON:0001981", - "UBERON:0004537", - "UBERON:0004572", - "UBERON:0004535", - "UBERON:0000061", - "UBERON:0000477", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0004111", - "UBERON:0004573", - "UBERON:0003498", - "HP:0011603", - "UPHENO:0020351", - "HP:0030680", - "UPHENO:0076765", - "BFO:0000002", - "HP:0025015", - "HP:0002597", - "UPHENO:0076810", - "HP:0033353", + "UPHENO:0087888", + "HP:0034392", + "UPHENO:0002816", + "UPHENO:0002536", "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", + "UPHENO:0001001", + "HP:0011729", + "HP:0100261", "HP:0000118", - "UPHENO:0075655", + "UPHENO:0075195", + "HP:0033127", "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", + "BFO:0000001", ], "object_closure_label": [ - "abnormal blood vessel morphology", - "abnormal anatomical entity", - "specifically dependent continuant", - "phenotype by ontology source", + "All", + "abnormal size of anatomical entity", + "Abnormality of the musculoskeletal system", + "abnormal anatomical entity morphology", + "Flexion contracture", + "decreased length of anatomical entity", "abnormal anatomical entity", - "continuant", - "protein-containing material entity", - "material anatomical entity", - "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", + "Phenotypic abnormality", + "Abnormality of the musculature", + "abnormality of anatomical entity physiology", + "decreased length of anatomical entity in independent continuant", "entity", - "structure with developmental contribution from neural crest", - "thoracic cavity element", - "primary circulatory organ", - "abnormal coronary vessel morphology", - "Abnormality of the cardiovascular system (HPO)", + "decreased size of the anatomical entity", + "continuant", + "abnormality of musculoskeletal system physiology", + "abnormal muscle organ morphology", + "abnormal anatomical entity length", + "abnormal tendon morphology", + "Abnormal skeletal morphology", + "Abnormal skeletal muscle morphology", "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", - "anatomical conduit", - "systemic artery", - "heart blood vessel", - "heart plus pericardium", + "abnormal tendon morphology", + "phenotype by ontology source", + "abnormal connective tissue", + "Abnormal musculoskeletal physiology", "phenotype", - "abnormal incomplete closing of the ductus arteriosus", + "Abnormality of joint mobility", + "Abnormal tendon morphology", + "Joint contracture", + "decreased length of tendon", + "quality", + "abnormality of anatomical entity physiology", + "abnormal skeletal system morphology", + "Abnormal joint physiology", + "Abnormality of the skeletal system", + "abnormal musculature", + "abnormal anatomical entity", + "decreased size of the anatomical entity in the independent continuant", + "Abnormality of connective tissue", + "specifically dependent continuant", "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", - "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", - "mesoderm-derived structure", - "artery", - "thoracic segment blood vessel", - "heart", - "heart vasculature", + "abnormal skeletal system", + "abnormal anatomical entity morphology", ], - "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_label": "Frequent", "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)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "evidence_count": 2, - "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001643", + "grouping_key": "MONDO:0011925🍪🍪biolink:has_phenotype🍪HP:0001371", }, { - "id": "uuid:4e02df99-842a-11ee-884f-6be035239f90", - "original_subject": "Orphanet:589821", + "id": "uuid:89e15869-ae6f-11ee-9f7a-f78bc2e9ee32", + "original_subject": "OMIM:614830", "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"], + "publications": ["PMID:22958903"], "frequency_qualifier": "HP:0040283", - "has_evidence": ["ECO:0000304"], - "subject": "MONDO:0035646", - "object": "HP:0001671", - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "has_evidence": ["ECO:0000269"], + "subject": "MONDO:0013904", + "object": "HP:0000568", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", "subject_category": "biolink:Disease", "subject_namespace": "MONDO", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0019052", "MONDO:0000001", - "MONDO:0020121", + "MONDO:0005336", + "OGMS:0000031", + "MONDO:0700069", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0000171", + "MONDO:0020120", + "MONDO:0700096", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0700075", + "MONDO:0024322", "BFO:0000017", - "MONDO:0008056", - "MONDO:0035646", + "MONDO:0013904", + "MONDO:0015286", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000002", + "BFO:0000020", "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:0005066", "MONDO:0700223", - "MONDO:0003382", - "BFO:0000016", - "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", - "OGMS:0000031", - "BFO:0000001", + "MONDO:0002081", + "MONDO:0002320", ], "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", + "continuant", "musculoskeletal system disorder", - "hereditary disease", - "eye disorder", + "muscular dystrophy-dystroglycanopathy, type A", + "myopathy caused by variation in POMGNT2", + "neuromuscular disease", + "skeletal muscle disorder", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "myopathy", + "disease", + "congenital muscular dystrophy", + "congenital muscular dystrophy caused by variation in POMGNT2", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome", + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", + "metabolic disease", + "disease", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "entity", ], - "object_label": "Abnormal cardiac septum morphology (HPO)", + "object_label": "Microphthalmia", "object_category": "biolink:PhenotypicFeature", "object_namespace": "HP", "object_closure": [ - "PR:000050567", - "UBERON:0000465", - "UPHENO:0019888", - "UPHENO:0080362", - "HP:0001627", - "UPHENO:0015280", - "BFO:0000040", - "UBERON:0001062", - "UBERON:0000468", - "UBERON:0011676", - "UBERON:0013701", - "HP:0001626", + "HP:0000315", + "HP:0000001", + "UPHENO:0075219", + "HP:0000234", + "UPHENO:0075997", + "UPHENO:0080079", + "UPHENO:0001005", "UPHENO:0001002", - "BFO:0000020", - "UPHENO:0015324", - "HP:0001671", "BFO:0000002", - "UPHENO:0001001", + "UPHENO:0075696", + "HP:0000152", + "UPHENO:0087907", + "UPHENO:0002910", "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", + "HP:0000568", + "UPHENO:0015280", + "HP:0000271", + "UPHENO:0012541", + "UPHENO:0080209", + "UPHENO:0068971", + "UPHENO:0021474", + "UPHENO:0002844", + "BFO:0000020", + "HP:0008056", + "PATO:0000001", + "HP:0012372", + "UPHENO:0087472", + "HP:0000478", + "HP:0100887", + "UPHENO:0087924", + "UPHENO:0002764", + "UPHENO:0003020", "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", + "UPHENO:0069523", + "UPHENO:0001001", + "UPHENO:0086589", "HP:0000118", + "UPHENO:0075195", "UPHENO:0020584", - "PATO:0000001", - "UBERON:0003037", - "UBERON:0010314", - "HP:0000001", - "UPHENO:0001005", "BFO:0000001", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0004120", - "UBERON:0001009", - "UBERON:0005178", - "UBERON:0007100", ], "object_closure_label": [ - "abnormal anatomical entity", + "Abnormality of the orbital region", + "All", + "abnormal size of eyeball of camera-type eye", + "abnormal size of anatomical entity", + "abnormal anatomical entity morphology", + "abnormal orbital region", + "aplasia or hypoplasia of anatomical entity", + "abnormal craniocervical region", "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)", + "Abnormal eye morphology", + "abnormal face morphology", "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)", - "abnormal anatomical entity morphology", - "entity", - "entity", - "septum", - "structure with developmental contribution from neural crest", - "thoracic cavity element", - "primary circulatory organ", - "Abnormality of the cardiovascular system (HPO)", "Phenotypic abnormality", - "abnormal cardiovascular system morphology", - "abnormal anatomical entity morphology", - "organism subdivision", - "organ", - "heart plus pericardium", + "Phenotypic abnormality", + "Aplasia/Hypoplasia affecting the eye", + "entity", + "aplasia or hypoplasia of eyeball of camera-type eye", + "decreased size of the anatomical entity", + "abnormal camera-type eye morphology", + "abnormal head", + "continuant", + "abnormal anatomical entity", + "Abnormality of the eye", + "Abnormality of globe size", + "abnormal camera-type eye morphology", + "Microphthalmia", + "phenotype by ontology source", "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", - "anatomical entity", - "cardiovascular system", - "anatomical structure", + "abnormal craniocervical region morphology", + "Abnormality of the head", + "Abnormality of head or neck", + "abnormal head morphology", + "abnormal face", + "abnormal eyeball of camera-type eye", "abnormal anatomical entity", - "abnormal cardiac septum morphology", - "abnormal cardiovascular system", - "Abnormal heart morphology (HPO)", - "abnormal heart morphology", - "multicellular anatomical structure", - "anatomical system", - "mesoderm-derived structure", - "cardiac septum", - "heart", + "decreased size of the eyeball of camera-type eye", + "decreased size of the anatomical entity in the independent continuant", + "specifically dependent continuant", + "abnormal anatomical entity morphology in the independent continuant", + "Abnormality of the face", + "abnormal anatomical entity morphology", ], - "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_label": "Occasional", "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)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040283"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Occasional"], "evidence_count": 2, - "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001671", + "grouping_key": "MONDO:0013904🍪🍪biolink:has_phenotype🍪HP:0000568", }, { - "id": "uuid:4e02df9a-842a-11ee-884f-6be035239f90", - "original_subject": "Orphanet:589821", + "id": "uuid:89e159d4-ae6f-11ee-9f7a-f78bc2e9ee32", + "original_subject": "OMIM:613150", "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"], + "publications": ["OMIM:613150"], "frequency_qualifier": "HP:0040283", "has_evidence": ["ECO:0000304"], - "subject": "MONDO:0035646", - "object": "HP:0002014", - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject": "MONDO:0013154", + "object": "HP:0002084", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "subject_category": "biolink:Disease", "subject_namespace": "MONDO", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0018939", + "MONDO:0019052", + "MONDO:0018282", "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", + "MONDO:0013154", "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:0000171", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0015286", + "MONDO:0016155", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000020", + "MONDO:0700071", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", "BFO:0000001", + "MONDO:0002320", ], "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", + "disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "muscular dystrophy-dystroglycanopathy, type A", + "neuromuscular disease", + "muscle-eye-brain disease", + "skeletal muscle disorder", + "entity", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "continuant", + "myopathy", + "congenital muscular dystrophy", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome", + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "metabolic disease", + "qualitative or quantitative defects of alpha-dystroglycan", + "disease", + "myopathy caused by variation in POMT2", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", ], - "object_label": "Diarrhea (HPO)", + "object_label": "Encephalocele", "object_category": "biolink:PhenotypicFeature", "object_namespace": "HP", "object_closure": [ - "UPHENO:0002443", - "UPHENO:0002536", - "UBERON:0000465", - "UPHENO:0082875", - "HP:0002664", - "BFO:0000001", - "BFO:0000040", - "UBERON:0001062", + "HP:0000001", + "HP:0000924", + "UPHENO:0050108", + "UPHENO:0081436", + "HP:0000234", + "UPHENO:0020641", + "UPHENO:0087665", + "UPHENO:0076791", + "UPHENO:0087089", + "HP:0011815", + "UPHENO:0001005", "UPHENO:0001002", - "BFO:0000020", - "HP:0011793", - "HP:0011458", - "BFO:0000002", - "UBERON:0001988", - "UPHENO:0001001", - "UPHENO:0002833", - "UPHENO:0001003", - "UBERON:0000463", + "BFO:0000001", "UPHENO:0075696", - "HP:0002014", - "HP:0025031", - "BFO:0000004", - "UBERON:0000061", - "UBERON:0000174", - "UBERON:0000468", - "BFO:0000002", - "HP:0025032", + "UPHENO:0051077", + "UPHENO:0076703", + "HP:0000152", + "UPHENO:0087907", + "HP:0000929", + "HP:0000707", + "UPHENO:0001003", + "UPHENO:0076692", + "UPHENO:0022529", + "UPHENO:0076702", + "UPHENO:0087363", + "UPHENO:0051003", + "HP:0011842", + "UPHENO:0088123", + "HP:0045005", + "UPHENO:0015280", + "HP:0034237", + "UPHENO:0002964", + "HP:0012639", + "UPHENO:0049587", + "UPHENO:0002844", + "BFO:0000020", + "HP:0002084", + "HP:0410043", + "UPHENO:0004523", "PATO:0000001", + "UPHENO:0002764", + "HP:0002011", + "UPHENO:0002536", + "UPHENO:0081566", + "UPHENO:0001001", + "UPHENO:0086589", "HP:0000118", - "UPHENO:0002332", - "HP:0000001", - "UPHENO:0001005", - "BFO:0000001", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0001007", + "BFO:0000002", + "HP:0009121", + "HP:0033127", + "UPHENO:0020584", ], "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)", + "All", + "Abnormal axial skeleton morphology", + "Abnormality of the musculoskeletal system", + "abnormal anatomical entity morphology", + "abnormal craniocervical region", + "Abnormal skull morphology", + "abnormal neural tube morphology", + "quality", "abnormal phenotype by ontology source", - "continuant", - "feces", - "Phenotypic abnormality (HPO)", "Phenotypic abnormality", - "Neoplasm by anatomical site (HPO)", - "Abdominal symptom (HPO)", - "quality", - "organism substance", - "excreta", - "multicellular organism", + "Phenotypic abnormality", + "continuant", + "Encephalocele", + "Abnormal neural tube morphology", + "abnormal nervous system", + "abnormal head", + "abnormal axial skeleton plus cranial skeleton morphology", + "Cephalocele", + "abnormal postcranial axial skeleton morphology", + "abnormal nervous system morphology", + "abnormal neural tube morphology", + "abnormal anatomical entity", + "abnormal neural tube closure", + "abnormal tube formation", + "Abnormal skeletal morphology", + "abnormal embryonic tissue morphology", + "Neural tube defect", + "Abnormality of the nervous system", + "phenotype by ontology source", + "abnormal biological_process", "phenotype", - "Neoplasm (HPO)", - "entity", - "independent continuant", - "abnormality of digestive system physiology", - "Abnormality of the digestive system (HPO)", - "material entity", - "anatomical entity", - "anatomical structure", - "abnormality of anatomical entity physiology", + "abnormal craniocervical region morphology", + "Morphological central nervous system abnormality", + "abnormal developmental process", + "abnormal development of anatomical entity", + "Abnormality of the head", + "Abnormal nervous system morphology", + "abnormal embryo morphology", + "abnormal skeletal system morphology", + "Abnormality of head or neck", + "abnormal head morphology", + "Abnormality of the skeletal system", "abnormal anatomical entity", - "multicellular anatomical structure", - "anatomical system", + "abnormal skull morphology", + "abnormal central nervous system morphology", + "specifically dependent continuant", + "abnormal anatomical entity morphology in the independent continuant", + "Open neural tube defect", + "abnormal skeletal system", + "abnormal anatomical entity morphology", + "entity", ], - "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_label": "Occasional", "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)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040283"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Occasional"], "evidence_count": 2, - "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0002014", + "grouping_key": "MONDO:0013154🍪🍪biolink:has_phenotype🍪HP:0002084", }, ], }, diff --git a/backend/tests/fixtures/association_table.py b/backend/tests/fixtures/association_table.py index 25ea27090..5565737f1 100644 --- a/backend/tests/fixtures/association_table.py +++ b/backend/tests/fixtures/association_table.py @@ -6,73 +6,61 @@ def association_table(): return { "limit": 5, "offset": 0, - "total": 4027, + "total": 3879, "items": [ { - "id": "uuid:4677e7a0-842a-11ee-884f-6be035239f90", + "id": "uuid:8b925f4a-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0020793", "original_subject": "OMIM:164310", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018949", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", "MONDO:0000001", + "MONDO:0016106", + "MONDO:0005336", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0020120", + "MONDO:0700096", + "OGMS:0000031", + "BFO:0000017", + "MONDO:0018949", "MONDO:0025193", "MONDO:0020121", + "BFO:0000002", "MONDO:0020793", - "MONDO:0003847", - "BFO:0000001", "BFO:0000020", - "MONDO:0016106", - "MONDO:0005336", - "MONDO:0000462", - "BFO:0000017", + "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0002081", - "MONDO:0005328", - "BFO:0000002", - "MONDO:0005071", - "MONDO:0020120", - "MONDO:0019056", "MONDO:0700223", - "MONDO:0003382", - "BFO:0000016", - "MONDO:0700096", - "MONDO:0024458", - "OGMS:0000031", + "MONDO:0002081", ], "subject_label": "oculopharyngodistal myopathy 1", "subject_closure_label": [ - "eyelids malposition disorder", + "nervous system disorder", + "continuant", + "oculopharyngodistal myopathy 1", + "musculoskeletal system disorder", "disease", + "neuromuscular disease", + "skeletal muscle disorder", + "oculopharyngodistal myopathy", + "muscular dystrophy", + "progressive muscular dystrophy", + "myopathy", "realizable entity", - "disease", - "specifically dependent continuant", - "muscle tissue disorder", - "disorder of orbital region", + "human disease", "hereditary skeletal muscle disorder", - "continuant", - "eye adnexa disorder", - "eyelid disorder", "disposition", - "human disease", - "disorder of visual system", - "myopathy", + "disease", + "hereditary disease", + "muscle tissue disorder", "distal myopathy", - "nervous system disorder", + "specifically dependent continuant", "entity", - "progressive muscular dystrophy", - "musculoskeletal system disorder", - "hereditary disease", - "eye disorder", - "oculopharyngodistal myopathy", - "muscular dystrophy", - "oculopharyngodistal myopathy 1", - "skeletal muscle disorder", - "neuromuscular disease", ], "subject_taxon": None, "subject_taxon_label": None, @@ -82,87 +70,55 @@ def association_table(): "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "UPHENO:0002816", - "BFO:0000001", - "UBERON:0000465", + "HP:0000001", "UPHENO:0082875", - "BFO:0000040", - "UBERON:0011216", "HP:0001324", "UPHENO:0080555", - "HP:0011804", - "BFO:0000002", - "UPHENO:0001001", - "UPHENO:0001002", - "BFO:0000020", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "UBERON:0001062", "UPHENO:0001005", - "HP:0033127", - "BFO:0000004", - "UBERON:0000061", - "UBERON:0000062", - "UBERON:0000468", - "UPHENO:0075696", + "UPHENO:0001002", "HP:0003011", - "UPHENO:0002320", - "HP:0000118", - "BFO:0000002", + "UPHENO:0075696", "UPHENO:0002332", + "UPHENO:0001003", + "UPHENO:0080556", + "UPHENO:0002320", + "BFO:0000020", "HP:0002460", + "UPHENO:0002816", + "UPHENO:0002536", + "HP:0011804", "PATO:0000001", - "UBERON:0010000", - "HP:0000001", - "UPHENO:0080556", - "UBERON:0000467", - "UBERON:0005090", - "UBERON:0001630", - "UBERON:0000383", - "UBERON:0001015", + "UPHENO:0001001", + "HP:0000118", + "BFO:0000002", + "HP:0033127", + "BFO:0000001", ], - "object_label": "Distal muscle weakness (HPO)", + "object_label": "Distal muscle weakness", "object_closure_label": [ - "abnormality of anatomical entity physiology", - "Phenotypic abnormality", - "specifically dependent continuant", - "quality", + "All", + "Abnormality of the musculoskeletal system", "abnormal phenotype by ontology source", - "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)", + "Phenotypic abnormality", + "Phenotypic abnormality", "continuant", - "decreased muscle organ strength", - "Distal muscle weakness (HPO)", + "Abnormality of the musculature", + "abnormality of anatomical entity physiology", + "Distal muscle weakness", "entity", - "multicellular anatomical structure", - "Muscle weakness (HPO)", - "anatomical entity", - "organ", - "multicellular organism", - "phenotype", - "independent continuant", + "abnormality of muscle organ physiology", "decreased anatomical entity strength", - "Abnormality of the musculoskeletal system (HPO)", - "entity", - "material entity", - "anatomical structure", - "musculature of body", - "musculature", "abnormal anatomical entity", + "phenotype by ontology source", + "phenotype", + "Abnormal muscle physiology", + "quality", "abnormality of anatomical entity physiology", - "anatomical system", - "muscle structure", + "abnormal musculature", + "abnormal anatomical entity", + "Muscle weakness", + "specifically dependent continuant", + "decreased muscle organ strength", ], "object_taxon": None, "object_taxon_label": None, @@ -181,9 +137,9 @@ def association_table(): }, "publications": ["PMID:21242490", "PMID:32493488", "PMID:31332380"], "publications_links": [ - {"id": "PMID:21242490", "url": None}, - {"id": "PMID:32493488", "url": None}, - {"id": "PMID:31332380", "url": None}, + {"id": "PMID:21242490", "url": "http://identifiers.org/pubmed/21242490"}, + {"id": "PMID:32493488", "url": "http://identifiers.org/pubmed/32493488"}, + {"id": "PMID:31332380", "url": "http://identifiers.org/pubmed/31332380"}, ], "qualifiers": [], "frequency_qualifier": "HP:0040282", @@ -195,11 +151,11 @@ def association_table(): "qualifiers_category": None, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_label": "Frequent", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -218,70 +174,58 @@ def association_table(): "direction": "outgoing", }, { - "id": "uuid:4677e7b1-842a-11ee-884f-6be035239f90", + "id": "uuid:8b925f5b-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0020793", "original_subject": "OMIM:164310", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018949", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", "MONDO:0000001", + "MONDO:0016106", + "MONDO:0005336", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0020120", + "MONDO:0700096", + "OGMS:0000031", + "BFO:0000017", + "MONDO:0018949", "MONDO:0025193", "MONDO:0020121", + "BFO:0000002", "MONDO:0020793", - "MONDO:0003847", - "BFO:0000001", "BFO:0000020", - "MONDO:0016106", - "MONDO:0005336", - "MONDO:0000462", - "BFO:0000017", + "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0002081", - "MONDO:0005328", - "BFO:0000002", - "MONDO:0005071", - "MONDO:0020120", - "MONDO:0019056", "MONDO:0700223", - "MONDO:0003382", - "BFO:0000016", - "MONDO:0700096", - "MONDO:0024458", - "OGMS:0000031", + "MONDO:0002081", ], "subject_label": "oculopharyngodistal myopathy 1", "subject_closure_label": [ - "eyelids malposition disorder", + "nervous system disorder", + "continuant", + "oculopharyngodistal myopathy 1", + "musculoskeletal system disorder", "disease", + "neuromuscular disease", + "skeletal muscle disorder", + "oculopharyngodistal myopathy", + "muscular dystrophy", + "progressive muscular dystrophy", + "myopathy", "realizable entity", - "disease", - "specifically dependent continuant", - "muscle tissue disorder", - "disorder of orbital region", + "human disease", "hereditary skeletal muscle disorder", - "continuant", - "eye adnexa disorder", - "eyelid disorder", "disposition", - "human disease", - "disorder of visual system", - "myopathy", + "disease", + "hereditary disease", + "muscle tissue disorder", "distal myopathy", - "nervous system disorder", + "specifically dependent continuant", "entity", - "progressive muscular dystrophy", - "musculoskeletal system disorder", - "hereditary disease", - "eye disorder", - "oculopharyngodistal myopathy", - "muscular dystrophy", - "oculopharyngodistal myopathy 1", - "skeletal muscle disorder", - "neuromuscular disease", ], "subject_taxon": None, "subject_taxon_label": None, @@ -291,141 +235,71 @@ def association_table(): "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "UPHENO:0002443", + "HP:0000001", "UPHENO:0002471", "HP:0025270", - "UPHENO:0002536", - "UBERON:0000465", - "RO:0002577", + "UPHENO:0002725", + "UPHENO:0002433", "UPHENO:0082875", "HP:0002664", - "UPHENO:0004523", "BFO:0000001", - "BFO:0000040", - "UBERON:0001062", - "UBERON:0011676", - "UBERON:0013701", - "BFO:0000020", - "HP:0011793", - "BFO:0000002", - "UBERON:0005409", - "UPHENO:0001001", + "UPHENO:0075696", + "UPHENO:0002332", + "HP:0000707", + "UPHENO:0001003", + "HP:0011024", + "UPHENO:0002443", "UPHENO:0002833", "HP:0002015", "UPHENO:0001002", - "UPHENO:0001003", - "UPHENO:0075696", - "UPHENO:0002433", "HP:0025031", "UPHENO:0002474", "HP:0012638", - "BFO:0000004", - "UBERON:0000061", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0004111", - "UBERON:0000468", - "HP:0011024", - "UPHENO:0002725", + "UPHENO:0001001", + "HP:0012719", "BFO:0000002", + "BFO:0000020", + "HP:0011793", + "UPHENO:0004523", "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", + "UPHENO:0002536", "PATO:0000001", - "UBERON:0001555", - "UBERON:0004921", - "HP:0000001", - "HP:0012719", "UPHENO:0001005", - "HP:0000707", - "BFO:0000001", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000064", - "UBERON:0001007", - "UBERON:0001016", - "UBERON:0013522", - "UBERON:0005178", - "UBERON:0004908", + "HP:0000118", ], - "object_label": "Dysphagia (HPO)", + "object_label": "Dysphagia", "object_closure_label": [ + "All", + "abnormality of alimentary part of gastrointestinal system physiology", + "Abnormal esophagus physiology", + "continuant", + "Neoplasm", + "Phenotypic abnormality", "abnormality of anatomical entity physiology", + "Neoplasm by anatomical site", + "abnormal nervous system", + "phenotype", + "Functional abnormality of the gastrointestinal tract", + "abnormal anatomical entity", "abnormal digestive system", - "Dysphagia (HPO)", + "Dysphagia", "Phenotypic abnormality", - "quality", - "abnormal anatomical entity", - "specifically dependent continuant", - "Abnormality of digestive system physiology (HPO)", + "Abnormality of the nervous system", "phenotype by ontology source", - "abnormal nervous system", - "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", + "quality", + "abnormality of anatomical entity physiology", "abnormal alimentary part of gastrointestinal system", - "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "entity", - "thoracic cavity element", - "upper digestive tract", "abnormality of nervous system physiology", - "Neoplasm by anatomical site (HPO)", - "organism subdivision", - "organ", - "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", - "Abnormality of the gastrointestinal tract (HPO)", - "abnormality of anatomical entity physiology", + "Abnormality of digestive system physiology", "abnormal anatomical entity", - "multicellular anatomical structure", - "anatomical system", - "digestive tract", - "subdivision of digestive tract", + "Abnormality of the digestive system", + "abnormality of esophagus physiology", + "Abnormal nervous system physiology", + "Abnormality of the gastrointestinal tract", + "abnormality of digestive system physiology", + "specifically dependent continuant", + "entity", ], "object_taxon": None, "object_taxon_label": None, @@ -444,9 +318,9 @@ def association_table(): }, "publications": ["PMID:21242490", "PMID:32493488", "PMID:31332380"], "publications_links": [ - {"id": "PMID:21242490", "url": None}, - {"id": "PMID:32493488", "url": None}, - {"id": "PMID:31332380", "url": None}, + {"id": "PMID:21242490", "url": "http://identifiers.org/pubmed/21242490"}, + {"id": "PMID:32493488", "url": "http://identifiers.org/pubmed/32493488"}, + {"id": "PMID:31332380", "url": "http://identifiers.org/pubmed/31332380"}, ], "qualifiers": [], "frequency_qualifier": "HP:0040282", @@ -458,11 +332,11 @@ def association_table(): "qualifiers_category": None, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_label": "Frequent", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -481,84 +355,84 @@ def association_table(): "direction": "outgoing", }, { - "id": "uuid:42ef70e0-842a-11ee-884f-6be035239f90", + "id": "uuid:8904bb34-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0013049", "original_subject": "OMIM:612937", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0016333", - "MONDO:0002320", + "MONDO:0004994", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0019052", "MONDO:0000001", - "MONDO:0013049", - "MONDO:0020121", - "MONDO:0003847", - "BFO:0000001", - "MONDO:0018276", - "BFO:0000020", "MONDO:0005336", - "MONDO:0019052", - "MONDO:0005500", - "MONDO:0005066", - "MONDO:0024322", - "BFO:0000017", - "MONDO:0003939", - "MONDO:0002081", - "MONDO:0005021", - "MONDO:0019950", + "OGMS:0000031", "BFO:0000002", "MONDO:0005217", - "MONDO:0015286", - "MONDO:0005071", + "MONDO:0019056", + "BFO:0000001", "MONDO:0005267", "MONDO:0020120", - "MONDO:0019056", - "MONDO:0004994", - "MONDO:0004995", - "MONDO:0700223", - "BFO:0000016", "MONDO:0700096", - "MONDO:0000591", + "MONDO:0005021", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0024322", + "BFO:0000017", "MONDO:0017749", - "OGMS:0000031", + "MONDO:0015286", + "MONDO:0020121", + "MONDO:0004995", + "BFO:0000020", + "MONDO:0000591", + "MONDO:0013049", + "MONDO:0016333", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005500", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", + "MONDO:0002320", ], "subject_label": "DPM3-congenital disorder of glycosylation", "subject_closure_label": [ + "cardiomyopathy", + "nervous system disorder", + "musculoskeletal system disorder", + "dilated cardiomyopathy", + "neuromuscular disease", + "familial cardiomyopathy", + "skeletal muscle disorder", + "intrinsic cardiomyopathy", + "congenital nervous system disorder", + "muscular dystrophy", + "cardiovascular disorder", + "continuant", + "myopathy", "disease", + "congenital muscular dystrophy", + "DPM3-congenital disorder of glycosylation", "disorder of glycosylation", "realizable entity", + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", "disorder of multiple glycosylation", + "congenital disorder of glycosylation type I", + "metabolic disease", "disease", - "specifically dependent continuant", - "familial cardiomyopathy", + "heart disorder", + "familial dilated cardiomyopathy", + "hereditary disease", "muscle tissue disorder", - "cardiomyopathy", - "cardiovascular disorder", - "hereditary skeletal muscle disorder", - "continuant", "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", + "specifically dependent continuant", "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, @@ -568,203 +442,71 @@ def association_table(): "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:0004536", - "UPHENO:0051668", - "HP:0001871", - "UPHENO:0077821", + "HP:0000001", + "HP:0011021", + "UPHENO:0051763", + "UPHENO:0004459", "BFO:0000001", - "GO:0008150", - "BFO:0000040", - "UBERON:0000468", + "HP:0004364", "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:0002193", - "UBERON:0002390", - "UBERON:0000179", - "UPHENO:0001001", - "UPHENO:0051763", - "UPHENO:0051801", - "UPHENO:0001003", "UPHENO:0081547", "UPHENO:0077826", - "BFO:0000001", - "UBERON:0001062", - "UBERON:0000061", - "UBERON:0000463", - "CHEBI:50047", - "CHEBI:37622", - "CHEBI:33256", - "UPHENO:0075696", - "UPHENO:0076286", - "HP:0040081", - "HP:0002795", - "HP:0012415", + "HP:0032180", + "UPHENO:0076289", + "HP:0001871", + "UPHENO:0001003", + "UPHENO:0051801", + "HP:0001939", "UPHENO:0051612", "UPHENO:0051804", - "BFO:0000015", - "BFO:0000004", - "GO:0032991", - "CHEBI:23367", - "UBERON:0000178", - "UBERON:0004120", - "UBERON:0006314", - "GO:0061695", - "CHEBI:16670", - "CHEBI:33302", - "CHEBI:33304", - "CHEBI:33582", - "GO:0002185", - "CHEBI:15841", - "CHEBI:51143", - "CHEBI:25806", - "CHEBI:36962", - "CHEBI:50860", - "UPHENO:0077817", - "UPHENO:0076289", - "UPHENO:0002448", - "UPHENO:0002536", - "HP:0032180", + "UPHENO:0077821", + "BFO:0000020", + "HP:0010876", "PATO:0000001", - "CHEBI:138675", - "UPHENO:0077825", - "HP:0000118", - "UPHENO:0004459", - "UPHENO:0002332", - "HP:0500165", - "HP:0000001", - "HP:0011021", - "UPHENO:0001005", + "UPHENO:0051668", "BFO:0000002", - "HP:0010876", - "HP:0001939", - "GO:0008152", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0001004", + "UPHENO:0046284", + "UPHENO:0002536", + "HP:0003236", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0000118", + "UPHENO:0076286", + "HP:0040081", ], - "object_label": "Elevated circulating creatine kinase concentration (HPO)", + "object_label": "Elevated circulating creatine kinase concentration", "object_closure_label": [ - "Abnormal circulating nitrogen compound concentration (HPO)", - "abnormality of anatomical entity physiology", - "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 role bodily fluid level", - "abnormal blood nitrogen molecular entity level", - "occurrent", - "continuant", - "cellular_component", - "chemical entity", - "protein-containing material entity", - "material anatomical entity", - "transferase complex", - "macromolecule", - "p-block molecular entity", - "respiratory system", - "All (HPO)", - "Abnormality of circulating enzyme level (HPO)", - "abnormal phenotype by ontology source", - "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", + "All", + "Abnormality of circulating enzyme level", "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)", + "abnormal independent continuant nitrogen molecular entity level", + "abnormal role blood level", + "Abnormal circulating creatine kinase concentration", + "Abnormality of blood and blood-forming tissues", "entity", - "Phenotypic abnormality", - "abnormal independent continuant gas molecular entity level", "quality", - "anatomical entity", - "anatomical structure", - "organism substance", - "mesoderm-derived structure", - "bodily fluid", - "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", - "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", - "protein-containing complex", - "molecular entity", - "blood", - "catalytic complex", - "polyatomic entity", - "main group molecular entity", - "abnormal blood oxygen molecular entity level", + "Phenotypic abnormality", + "Abnormal circulating protein concentration", + "abnormal role bodily fluid level", + "abnormal blood nitrogen molecular entity level", + "Abnormal circulating metabolite concentration", "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", + "phenotype by ontology source", + "phenotype", + "abnormal phenotype by ontology source", + "continuant", "abnormal hematopoietic system", - "abnormality of anatomical entity physiology", - "Abnormal circulating metabolite concentration (HPO)", - "multicellular anatomical structure", - "anatomical system", - "gas molecular entity", - "creatine kinase complex", - "polypeptide", - "nitrogen molecular entity", - "oxygen molecular entity", - "organochalcogen compound", - "organic molecular entity", + "Abnormality of metabolism/homeostasis", + "Elevated circulating creatine kinase concentration", + "Abnormal circulating nitrogen compound concentration", + "abnormal chemical entity level", + "abnormal anatomical entity", + "abnormal blood protein polypeptide chain level", + "abnormal blood chemical entity level", + "Phenotypic abnormality", + "specifically dependent continuant", + "abnormal independent continuant protein polypeptide chain level", ], "object_taxon": None, "object_taxon_label": None, @@ -782,7 +524,10 @@ def association_table(): "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, "publications": ["PMID:19576565", "PMID:28803818"], - "publications_links": [{"id": "PMID:19576565", "url": None}, {"id": "PMID:28803818", "url": None}], + "publications_links": [ + {"id": "PMID:19576565", "url": "http://identifiers.org/pubmed/19576565"}, + {"id": "PMID:28803818", "url": "http://identifiers.org/pubmed/28803818"}, + ], "qualifiers": [], "frequency_qualifier": "HP:0040280", "onset_qualifier": None, @@ -793,11 +538,11 @@ def association_table(): "qualifiers_category": None, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_label": "Obligate", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040279", "HP:0000001", "HP:0040280"], - "frequency_qualifier_closure_label": ["Obligate (HPO)", "Frequency (HPO)", "All (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Obligate"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -816,64 +561,64 @@ def association_table(): "direction": "outgoing", }, { - "id": "uuid:476a1081-842a-11ee-884f-6be035239f90", + "id": "uuid:8c422f2b-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0009681", "original_subject": "OMIM:254090", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0002320", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0000355", "MONDO:0000001", - "MONDO:0020121", - "MONDO:0019952", - "MONDO:0003847", "MONDO:0005336", - "MONDO:0000355", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0020120", + "MONDO:0700096", + "OGMS:0000031", + "MONDO:0019950", "BFO:0000017", - "MONDO:0100225", + "MONDO:0016139", + "MONDO:0020121", + "MONDO:0019952", "BFO:0000020", + "MONDO:0100225", + "MONDO:0009681", + "MONDO:0003847", "MONDO:0003939", - "MONDO:0002081", - "MONDO:0019950", - "MONDO:0005071", - "BFO:0000002", - "MONDO:0020120", - "MONDO:0019056", "MONDO:0700223", - "BFO:0000016", - "MONDO:0016139", - "MONDO:0700096", - "MONDO:0009681", - "OGMS:0000031", - "BFO:0000001", + "BFO:0000002", + "MONDO:0002081", + "MONDO:0002320", ], "subject_label": "Ullrich congenital muscular dystrophy 1", "subject_closure_label": [ + "nervous system disorder", + "congenital myopathy", + "musculoskeletal system disorder", "disease", - "realizable entity", - "collagen 6-related myopathy", - "specifically dependent continuant", + "neuromuscular disease", + "continuant", + "skeletal muscle disorder", "Ullrich congenital muscular dystrophy 1", + "congenital nervous system disorder", + "muscular dystrophy", + "myopathy", + "congenital muscular dystrophy", + "realizable entity", + "human disease", + "hereditary skeletal muscle disorder", + "disposition", "disease", + "hereditary disease", "muscle tissue disorder", - "hereditary skeletal muscle disorder", "Ullrich congenital muscular dystrophy", - "continuant", - "disposition", + "specifically dependent continuant", + "collagen 6-related myopathy", "qualitative or quantitative protein defects in neuromuscular diseases", - "human disease", "entity", - "myopathy", - "nervous system disorder", - "musculoskeletal system disorder", - "hereditary disease", - "congenital nervous system disorder", - "congenital muscular dystrophy", - "muscular dystrophy", - "congenital myopathy", - "skeletal muscle disorder", - "neuromuscular disease", ], "subject_taxon": None, "subject_taxon_label": None, @@ -883,91 +628,55 @@ def association_table(): "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0011729", + "HP:0000001", + "HP:0020152", + "HP:0034430", + "HP:0000924", "HP:0011843", - "UBERON:0000465", "UPHENO:0082875", - "HP:0001388", - "BFO:0000001", - "BFO:0000040", - "UBERON:0011216", - "UBERON:0034921", "UPHENO:0001002", - "BFO:0000020", - "BFO:0000002", - "UPHENO:0001001", - "UPHENO:0002964", - "UPHENO:0001003", "UPHENO:0081440", + "HP:0001388", "BFO:0000001", - "UBERON:0001062", - "UBERON:0000061", - "UBERON:0034925", "UPHENO:0075696", - "UPHENO:0001005", - "HP:0033127", - "BFO:0000004", - "UBERON:0004770", - "UBERON:0000468", - "HP:0034430", - "HP:0000924", + "UPHENO:0002332", + "UPHENO:0001003", + "UPHENO:0002964", + "BFO:0000020", + "PATO:0000001", "BFO:0000002", "UPHENO:0002536", + "UPHENO:0001001", + "HP:0011729", + "UPHENO:0001005", "HP:0000118", - "UPHENO:0002332", - "PATO:0000001", - "UBERON:0000982", - "HP:0000001", - "HP:0020152", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0002204", - "UBERON:0004905", - "UBERON:0001434", + "HP:0033127", ], - "object_label": "Distal joint laxity (HPO)", + "object_label": "Distal joint laxity", "object_closure_label": [ - "abnormality of anatomical entity physiology", - "Joint laxity (HPO)", - "abnormal skeletal system", - "abnormal anatomical entity", + "All", + "Distal joint laxity", + "Abnormality of the musculoskeletal system", + "Joint laxity", "quality", + "Phenotypic abnormality", + "abnormality of anatomical entity physiology", + "abnormality of musculoskeletal system physiology", "abnormal anatomical entity", - "abnormal phenotype by ontology source", - "specifically dependent continuant", "phenotype by ontology source", - "abnormality of musculoskeletal system physiology", - "continuant", - "material anatomical entity", - "musculoskeletal system", - "All (HPO)", - "Distal joint laxity (HPO)", + "Abnormal musculoskeletal physiology", + "phenotype", + "Abnormality of joint mobility", + "abnormal phenotype by ontology source", "continuant", - "organ system subdivision", - "multi organ part structure", + "abnormality of anatomical entity physiology", "Abnormal joint physiology", - "Abnormality of the skeletal system (HPO)", - "Phenotypic abnormality (HPO)", - "entity", + "Abnormality of the skeletal system", + "abnormal anatomical entity", "Phenotypic abnormality", - "Abnormality of musculoskeletal physiology (HPO)", - "anatomical entity", - "anatomical structure", - "anatomical collection", - "articular system", - "multicellular organism", - "phenotype", + "specifically dependent continuant", + "abnormal skeletal system", "entity", - "independent continuant", - "Abnormality of joint mobility (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "material entity", - "articulation", - "skeletal system", - "abnormality of anatomical entity physiology", - "multicellular anatomical structure", - "anatomical system", - "skeletal joint", ], "object_taxon": None, "object_taxon_label": None, @@ -985,7 +694,10 @@ def association_table(): "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, "publications": ["PMID:16258657", "OMIM:254090"], - "publications_links": [{"id": "PMID:16258657", "url": None}, {"id": "OMIM:254090", "url": None}], + "publications_links": [ + {"id": "PMID:16258657", "url": "http://identifiers.org/pubmed/16258657"}, + {"id": "OMIM:254090", "url": "http://identifiers.org/mim/254090"}, + ], "qualifiers": [], "frequency_qualifier": "HP:0040280", "onset_qualifier": None, @@ -996,11 +708,11 @@ def association_table(): "qualifiers_category": None, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_label": "Obligate", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040279", "HP:0000001", "HP:0040280"], - "frequency_qualifier_closure_label": ["Obligate (HPO)", "Frequency (HPO)", "All (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Obligate"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -1019,66 +731,66 @@ def association_table(): "direction": "outgoing", }, { - "id": "uuid:46170673-842a-11ee-884f-6be035239f90", + "id": "uuid:8b4c43bf-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0009676", "original_subject": "OMIM:253601", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0016145", + "MONDO:0005071", + "MONDO:0006025", + "BFO:0000016", + "MONDO:0009676", "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:0016971", - "MONDO:0005071", - "MONDO:0020120", + "MONDO:0000429", "MONDO:0019056", - "MONDO:0700223", - "BFO:0000016", - "MONDO:0016139", + "BFO:0000001", + "MONDO:0020120", "MONDO:0700096", "OGMS:0000031", - "BFO:0000001", + "MONDO:0016145", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0016971", + "MONDO:0020121", + "BFO:0000002", + "BFO:0000020", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0700223", + "MONDO:0002081", + "MONDO:0015152", ], "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2B", "subject_closure_label": [ - "disease", - "realizable entity", - "disease", - "specifically dependent continuant", - "muscle tissue disorder", - "hereditary skeletal muscle disorder", + "nervous system disorder", "continuant", - "limb-girdle muscular dystrophy", - "disposition", - "qualitative or quantitative protein defects in neuromuscular diseases", - "human disease", - "entity", + "musculoskeletal system disorder", + "disease", "autosomal genetic disease", - "autosomal recessive disease", - "myopathy", - "nervous system disorder", + "neuromuscular disease", "autosomal recessive limb-girdle muscular dystrophy type 2B", + "skeletal muscle disorder", "autosomal recessive limb-girdle muscular dystrophy", - "qualitative or quantitative defects of dysferlin", + "limb-girdle muscular dystrophy", + "muscular dystrophy", "progressive muscular dystrophy", - "musculoskeletal system disorder", + "myopathy", + "realizable entity", + "human disease", + "hereditary skeletal muscle disorder", + "disposition", + "disease", + "autosomal recessive disease", "hereditary disease", - "muscular dystrophy", - "skeletal muscle disorder", - "neuromuscular disease", + "muscle tissue disorder", + "qualitative or quantitative defects of dysferlin", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", + "entity", ], "subject_taxon": None, "subject_taxon_label": None, @@ -1088,87 +800,55 @@ def association_table(): "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "UPHENO:0002816", - "UPHENO:0002536", - "UBERON:0000465", + "HP:0000001", "UPHENO:0082875", - "BFO:0000040", - "UBERON:0001062", - "UBERON:0011216", "UPHENO:0001002", "HP:0001324", "UPHENO:0080555", - "HP:0011804", - "BFO:0000002", - "UPHENO:0001001", - "HP:0003701", - "UPHENO:0001003", + "HP:0003011", "BFO:0000001", - "BFO:0000020", - "HP:0033127", - "BFO:0000004", - "UBERON:0000061", - "UBERON:0000062", - "UBERON:0000468", "UPHENO:0075696", - "BFO:0000002", - "HP:0003011", - "UPHENO:0002320", - "HP:0000118", "UPHENO:0002332", + "UPHENO:0001003", + "HP:0003701", + "UPHENO:0080556", + "UPHENO:0002320", + "UPHENO:0001001", + "BFO:0000002", + "BFO:0000020", "PATO:0000001", - "HP:0000001", + "UPHENO:0002816", + "UPHENO:0002536", + "HP:0011804", "UPHENO:0001005", - "UPHENO:0080556", - "BFO:0000001", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0005090", - "UBERON:0001630", - "UBERON:0000383", - "UBERON:0001015", + "HP:0000118", + "HP:0033127", ], - "object_label": "Proximal muscle weakness (HPO)", + "object_label": "Proximal muscle weakness", "object_closure_label": [ - "abnormality of anatomical entity physiology", - "Proximal muscle weakness (HPO)", - "quality", - "Abnormality of the musculature (HPO)", - "phenotype by ontology source", + "All", "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", + "Abnormality of the musculoskeletal system", + "quality", "Phenotypic abnormality", - "Muscle weakness (HPO)", - "specifically dependent continuant", - "organ", - "multicellular organism", + "Abnormality of the musculature", + "abnormality of anatomical entity physiology", + "abnormality of muscle organ physiology", "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", + "Proximal muscle weakness", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "Abnormal muscle physiology", "abnormality of anatomical entity physiology", + "abnormal musculature", "abnormal anatomical entity", - "multicellular anatomical structure", - "anatomical system", - "muscle structure", + "Phenotypic abnormality", + "Muscle weakness", + "specifically dependent continuant", + "decreased muscle organ strength", + "entity", ], "object_taxon": None, "object_taxon_label": None, @@ -1186,7 +866,10 @@ def association_table(): "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/hpoa/#disease_to_phenotype", }, "publications": ["PMID:9731527", "PMID:9009996"], - "publications_links": [{"id": "PMID:9731527", "url": None}, {"id": "PMID:9009996", "url": None}], + "publications_links": [ + {"id": "PMID:9731527", "url": "http://identifiers.org/pubmed/9731527"}, + {"id": "PMID:9009996", "url": "http://identifiers.org/pubmed/9009996"}, + ], "qualifiers": [], "frequency_qualifier": "HP:0040280", "onset_qualifier": None, @@ -1197,11 +880,11 @@ def association_table(): "qualifiers_category": None, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_label": "Obligate", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040279", "HP:0000001", "HP:0040280"], - "frequency_qualifier_closure_label": ["Obligate (HPO)", "Frequency (HPO)", "All (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Obligate"], "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 820b111af..de150b2b9 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": 1, + "QTime": 0, "params": { "mm": "100%", "q": "*:*", @@ -23,11 +23,11 @@ def association_table_response(): }, }, "response": { - "num_found": 4027, + "num_found": 3879, "start": 0, "docs": [ { - "id": "uuid:4677e7a0-842a-11ee-884f-6be035239f90", + "id": "uuid:8b925f4a-ae6f-11ee-9f7a-f78bc2e9ee32", "original_subject": "OMIM:164310", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", @@ -43,158 +43,114 @@ def association_table_response(): "subject_category": "biolink:Disease", "subject_namespace": "MONDO", "subject_closure": [ - "MONDO:0018949", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", "MONDO:0000001", + "MONDO:0016106", + "MONDO:0005336", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0020120", + "MONDO:0700096", + "OGMS:0000031", + "BFO:0000017", + "MONDO:0018949", "MONDO:0025193", "MONDO:0020121", + "BFO:0000002", "MONDO:0020793", - "MONDO:0003847", - "BFO:0000001", "BFO:0000020", - "MONDO:0016106", - "MONDO:0005336", - "MONDO:0000462", - "BFO:0000017", + "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0002081", - "MONDO:0005328", - "BFO:0000002", - "MONDO:0005071", - "MONDO:0020120", - "MONDO:0019056", "MONDO:0700223", - "MONDO:0003382", - "BFO:0000016", - "MONDO:0700096", - "MONDO:0024458", - "OGMS:0000031", + "MONDO:0002081", ], "subject_closure_label": [ - "eyelids malposition disorder", + "nervous system disorder", + "continuant", + "oculopharyngodistal myopathy 1", + "musculoskeletal system disorder", "disease", + "neuromuscular disease", + "skeletal muscle disorder", + "oculopharyngodistal myopathy", + "muscular dystrophy", + "progressive muscular dystrophy", + "myopathy", "realizable entity", - "disease", - "specifically dependent continuant", - "muscle tissue disorder", - "disorder of orbital region", + "human disease", "hereditary skeletal muscle disorder", - "continuant", - "eye adnexa disorder", - "eyelid disorder", "disposition", - "human disease", - "disorder of visual system", - "myopathy", + "disease", + "hereditary disease", + "muscle tissue disorder", "distal myopathy", - "nervous system disorder", + "specifically dependent continuant", "entity", - "progressive muscular dystrophy", - "musculoskeletal system disorder", - "hereditary disease", - "eye disorder", - "oculopharyngodistal myopathy", - "muscular dystrophy", - "oculopharyngodistal myopathy 1", - "skeletal muscle disorder", - "neuromuscular disease", ], - "object_label": "Distal muscle weakness (HPO)", + "object_label": "Distal muscle weakness", "object_category": "biolink:PhenotypicFeature", "object_namespace": "HP", "object_closure": [ - "UPHENO:0002816", - "BFO:0000001", - "UBERON:0000465", + "HP:0000001", "UPHENO:0082875", - "BFO:0000040", - "UBERON:0011216", "HP:0001324", "UPHENO:0080555", - "HP:0011804", - "BFO:0000002", - "UPHENO:0001001", - "UPHENO:0001002", - "BFO:0000020", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "UBERON:0001062", "UPHENO:0001005", - "HP:0033127", - "BFO:0000004", - "UBERON:0000061", - "UBERON:0000062", - "UBERON:0000468", - "UPHENO:0075696", + "UPHENO:0001002", "HP:0003011", - "UPHENO:0002320", - "HP:0000118", - "BFO:0000002", + "UPHENO:0075696", "UPHENO:0002332", + "UPHENO:0001003", + "UPHENO:0080556", + "UPHENO:0002320", + "BFO:0000020", "HP:0002460", + "UPHENO:0002816", + "UPHENO:0002536", + "HP:0011804", "PATO:0000001", - "UBERON:0010000", - "HP:0000001", - "UPHENO:0080556", - "UBERON:0000467", - "UBERON:0005090", - "UBERON:0001630", - "UBERON:0000383", - "UBERON:0001015", + "UPHENO:0001001", + "HP:0000118", + "BFO:0000002", + "HP:0033127", + "BFO:0000001", ], "object_closure_label": [ - "abnormality of anatomical entity physiology", - "Phenotypic abnormality", - "specifically dependent continuant", - "quality", + "All", + "Abnormality of the musculoskeletal system", "abnormal phenotype by ontology source", - "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)", + "Phenotypic abnormality", + "Phenotypic abnormality", "continuant", - "decreased muscle organ strength", - "Distal muscle weakness (HPO)", + "Abnormality of the musculature", + "abnormality of anatomical entity physiology", + "Distal muscle weakness", "entity", - "multicellular anatomical structure", - "Muscle weakness (HPO)", - "anatomical entity", - "organ", - "multicellular organism", - "phenotype", - "independent continuant", + "abnormality of muscle organ physiology", "decreased anatomical entity strength", - "Abnormality of the musculoskeletal system (HPO)", - "entity", - "material entity", - "anatomical structure", - "musculature of body", - "musculature", "abnormal anatomical entity", + "phenotype by ontology source", + "phenotype", + "Abnormal muscle physiology", + "quality", "abnormality of anatomical entity physiology", - "anatomical system", - "muscle structure", + "abnormal musculature", + "abnormal anatomical entity", + "Muscle weakness", + "specifically dependent continuant", + "decreased muscle organ strength", ], - "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_label": "Frequent", "frequency_qualifier_category": "biolink:PhenotypicFeature", "frequency_qualifier_namespace": "HP", - "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "evidence_count": 4, "grouping_key": "MONDO:0020793🍪🍪biolink:has_phenotype🍪HP:0002460", }, { - "id": "uuid:4677e7b1-842a-11ee-884f-6be035239f90", + "id": "uuid:8b925f5b-ae6f-11ee-9f7a-f78bc2e9ee32", "original_subject": "OMIM:164310", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", @@ -210,212 +166,130 @@ def association_table_response(): "subject_category": "biolink:Disease", "subject_namespace": "MONDO", "subject_closure": [ - "MONDO:0018949", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", "MONDO:0000001", + "MONDO:0016106", + "MONDO:0005336", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0020120", + "MONDO:0700096", + "OGMS:0000031", + "BFO:0000017", + "MONDO:0018949", "MONDO:0025193", "MONDO:0020121", + "BFO:0000002", "MONDO:0020793", - "MONDO:0003847", - "BFO:0000001", "BFO:0000020", - "MONDO:0016106", - "MONDO:0005336", - "MONDO:0000462", - "BFO:0000017", + "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0002081", - "MONDO:0005328", - "BFO:0000002", - "MONDO:0005071", - "MONDO:0020120", - "MONDO:0019056", "MONDO:0700223", - "MONDO:0003382", - "BFO:0000016", - "MONDO:0700096", - "MONDO:0024458", - "OGMS:0000031", + "MONDO:0002081", ], "subject_closure_label": [ - "eyelids malposition disorder", + "nervous system disorder", + "continuant", + "oculopharyngodistal myopathy 1", + "musculoskeletal system disorder", "disease", + "neuromuscular disease", + "skeletal muscle disorder", + "oculopharyngodistal myopathy", + "muscular dystrophy", + "progressive muscular dystrophy", + "myopathy", "realizable entity", - "disease", - "specifically dependent continuant", - "muscle tissue disorder", - "disorder of orbital region", + "human disease", "hereditary skeletal muscle disorder", - "continuant", - "eye adnexa disorder", - "eyelid disorder", "disposition", - "human disease", - "disorder of visual system", - "myopathy", + "disease", + "hereditary disease", + "muscle tissue disorder", "distal myopathy", - "nervous system disorder", + "specifically dependent continuant", "entity", - "progressive muscular dystrophy", - "musculoskeletal system disorder", - "hereditary disease", - "eye disorder", - "oculopharyngodistal myopathy", - "muscular dystrophy", - "oculopharyngodistal myopathy 1", - "skeletal muscle disorder", - "neuromuscular disease", ], - "object_label": "Dysphagia (HPO)", + "object_label": "Dysphagia", "object_category": "biolink:PhenotypicFeature", "object_namespace": "HP", "object_closure": [ - "UPHENO:0002443", + "HP:0000001", "UPHENO:0002471", "HP:0025270", - "UPHENO:0002536", - "UBERON:0000465", - "RO:0002577", + "UPHENO:0002725", + "UPHENO:0002433", "UPHENO:0082875", "HP:0002664", - "UPHENO:0004523", "BFO:0000001", - "BFO:0000040", - "UBERON:0001062", - "UBERON:0011676", - "UBERON:0013701", - "BFO:0000020", - "HP:0011793", - "BFO:0000002", - "UBERON:0005409", - "UPHENO:0001001", + "UPHENO:0075696", + "UPHENO:0002332", + "HP:0000707", + "UPHENO:0001003", + "HP:0011024", + "UPHENO:0002443", "UPHENO:0002833", "HP:0002015", "UPHENO:0001002", - "UPHENO:0001003", - "UPHENO:0075696", - "UPHENO:0002433", "HP:0025031", "UPHENO:0002474", "HP:0012638", - "BFO:0000004", - "UBERON:0000061", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0004111", - "UBERON:0000468", - "HP:0011024", - "UPHENO:0002725", + "UPHENO:0001001", + "HP:0012719", "BFO:0000002", + "BFO:0000020", + "HP:0011793", + "UPHENO:0004523", "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", + "UPHENO:0002536", "PATO:0000001", - "UBERON:0001555", - "UBERON:0004921", - "HP:0000001", - "HP:0012719", "UPHENO:0001005", - "HP:0000707", - "BFO:0000001", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000064", - "UBERON:0001007", - "UBERON:0001016", - "UBERON:0013522", - "UBERON:0005178", - "UBERON:0004908", + "HP:0000118", ], "object_closure_label": [ + "All", + "abnormality of alimentary part of gastrointestinal system physiology", + "Abnormal esophagus physiology", + "continuant", + "Neoplasm", + "Phenotypic abnormality", "abnormality of anatomical entity physiology", + "Neoplasm by anatomical site", + "abnormal nervous system", + "phenotype", + "Functional abnormality of the gastrointestinal tract", + "abnormal anatomical entity", "abnormal digestive system", - "Dysphagia (HPO)", + "Dysphagia", "Phenotypic abnormality", - "quality", - "abnormal anatomical entity", - "specifically dependent continuant", - "Abnormality of digestive system physiology (HPO)", + "Abnormality of the nervous system", "phenotype by ontology source", - "abnormal nervous system", - "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", + "quality", + "abnormality of anatomical entity physiology", "abnormal alimentary part of gastrointestinal system", - "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "entity", - "thoracic cavity element", - "upper digestive tract", "abnormality of nervous system physiology", - "Neoplasm by anatomical site (HPO)", - "organism subdivision", - "organ", - "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", - "Abnormality of the gastrointestinal tract (HPO)", - "abnormality of anatomical entity physiology", + "Abnormality of digestive system physiology", "abnormal anatomical entity", - "multicellular anatomical structure", - "anatomical system", - "digestive tract", - "subdivision of digestive tract", + "Abnormality of the digestive system", + "abnormality of esophagus physiology", + "Abnormal nervous system physiology", + "Abnormality of the gastrointestinal tract", + "abnormality of digestive system physiology", + "specifically dependent continuant", + "entity", ], - "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_label": "Frequent", "frequency_qualifier_category": "biolink:PhenotypicFeature", "frequency_qualifier_namespace": "HP", - "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "evidence_count": 4, "grouping_key": "MONDO:0020793🍪🍪biolink:has_phenotype🍪HP:0002015", }, { - "id": "uuid:42ef70e0-842a-11ee-884f-6be035239f90", + "id": "uuid:8904bb34-ae6f-11ee-9f7a-f78bc2e9ee32", "original_subject": "OMIM:612937", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", @@ -431,288 +305,156 @@ def association_table_response(): "subject_category": "biolink:Disease", "subject_namespace": "MONDO", "subject_closure": [ - "MONDO:0016333", - "MONDO:0002320", + "MONDO:0004994", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0019052", "MONDO:0000001", - "MONDO:0013049", - "MONDO:0020121", - "MONDO:0003847", - "BFO:0000001", - "MONDO:0018276", - "BFO:0000020", "MONDO:0005336", - "MONDO:0019052", - "MONDO:0005500", - "MONDO:0005066", - "MONDO:0024322", - "BFO:0000017", - "MONDO:0003939", - "MONDO:0002081", - "MONDO:0005021", - "MONDO:0019950", + "OGMS:0000031", "BFO:0000002", "MONDO:0005217", - "MONDO:0015286", - "MONDO:0005071", + "MONDO:0019056", + "BFO:0000001", "MONDO:0005267", "MONDO:0020120", - "MONDO:0019056", - "MONDO:0004994", - "MONDO:0004995", - "MONDO:0700223", - "BFO:0000016", "MONDO:0700096", - "MONDO:0000591", + "MONDO:0005021", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0024322", + "BFO:0000017", "MONDO:0017749", - "OGMS:0000031", + "MONDO:0015286", + "MONDO:0020121", + "MONDO:0004995", + "BFO:0000020", + "MONDO:0000591", + "MONDO:0013049", + "MONDO:0016333", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005500", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", + "MONDO:0002320", ], "subject_closure_label": [ + "cardiomyopathy", + "nervous system disorder", + "musculoskeletal system disorder", + "dilated cardiomyopathy", + "neuromuscular disease", + "familial cardiomyopathy", + "skeletal muscle disorder", + "intrinsic cardiomyopathy", + "congenital nervous system disorder", + "muscular dystrophy", + "cardiovascular disorder", + "continuant", + "myopathy", "disease", + "congenital muscular dystrophy", + "DPM3-congenital disorder of glycosylation", "disorder of glycosylation", "realizable entity", + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", "disorder of multiple glycosylation", + "congenital disorder of glycosylation type I", + "metabolic disease", "disease", - "specifically dependent continuant", - "familial cardiomyopathy", + "heart disorder", + "familial dilated cardiomyopathy", + "hereditary disease", "muscle tissue disorder", - "cardiomyopathy", - "cardiovascular disorder", - "hereditary skeletal muscle disorder", - "continuant", "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", + "specifically dependent continuant", "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_label": "Elevated circulating creatine kinase concentration", "object_category": "biolink:PhenotypicFeature", "object_namespace": "HP", "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:0004536", - "UPHENO:0051668", - "HP:0001871", - "UPHENO:0077821", + "HP:0000001", + "HP:0011021", + "UPHENO:0051763", + "UPHENO:0004459", "BFO:0000001", - "GO:0008150", - "BFO:0000040", - "UBERON:0000468", + "HP:0004364", "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:0002193", - "UBERON:0002390", - "UBERON:0000179", - "UPHENO:0001001", - "UPHENO:0051763", - "UPHENO:0051801", - "UPHENO:0001003", "UPHENO:0081547", "UPHENO:0077826", - "BFO:0000001", - "UBERON:0001062", - "UBERON:0000061", - "UBERON:0000463", - "CHEBI:50047", - "CHEBI:37622", - "CHEBI:33256", - "UPHENO:0075696", - "UPHENO:0076286", - "HP:0040081", - "HP:0002795", - "HP:0012415", + "HP:0032180", + "UPHENO:0076289", + "HP:0001871", + "UPHENO:0001003", + "UPHENO:0051801", + "HP:0001939", "UPHENO:0051612", "UPHENO:0051804", - "BFO:0000015", - "BFO:0000004", - "GO:0032991", - "CHEBI:23367", - "UBERON:0000178", - "UBERON:0004120", - "UBERON:0006314", - "GO:0061695", - "CHEBI:16670", - "CHEBI:33302", - "CHEBI:33304", - "CHEBI:33582", - "GO:0002185", - "CHEBI:15841", - "CHEBI:51143", - "CHEBI:25806", - "CHEBI:36962", - "CHEBI:50860", - "UPHENO:0077817", - "UPHENO:0076289", - "UPHENO:0002448", - "UPHENO:0002536", - "HP:0032180", + "UPHENO:0077821", + "BFO:0000020", + "HP:0010876", "PATO:0000001", - "CHEBI:138675", - "UPHENO:0077825", - "HP:0000118", - "UPHENO:0004459", - "UPHENO:0002332", - "HP:0500165", - "HP:0000001", - "HP:0011021", - "UPHENO:0001005", + "UPHENO:0051668", "BFO:0000002", - "HP:0010876", - "HP:0001939", - "GO:0008152", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0001004", + "UPHENO:0046284", + "UPHENO:0002536", + "HP:0003236", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0000118", + "UPHENO:0076286", + "HP:0040081", ], "object_closure_label": [ - "Abnormal circulating nitrogen compound concentration (HPO)", - "abnormality of anatomical entity physiology", - "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 role bodily fluid level", - "abnormal blood nitrogen molecular entity level", - "occurrent", - "continuant", - "cellular_component", - "chemical entity", - "protein-containing material entity", - "material anatomical entity", - "transferase complex", - "macromolecule", - "p-block molecular entity", - "respiratory system", - "All (HPO)", - "Abnormality of circulating enzyme level (HPO)", - "abnormal phenotype by ontology source", - "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", + "All", + "Abnormality of circulating enzyme level", "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)", + "abnormal independent continuant nitrogen molecular entity level", + "abnormal role blood level", + "Abnormal circulating creatine kinase concentration", + "Abnormality of blood and blood-forming tissues", "entity", - "Phenotypic abnormality", - "abnormal independent continuant gas molecular entity level", "quality", - "anatomical entity", - "anatomical structure", - "organism substance", - "mesoderm-derived structure", - "bodily fluid", - "transferase complex, transferring phosphorus-containing groups", - "peptide", - "pnictogen molecular entity", - "chalcogen molecular entity", - "carbon group molecular entity", - "carboxamide", - "primary amide", - "organic amino compound", + "Phenotypic abnormality", + "Abnormal circulating protein concentration", + "abnormal role bodily fluid level", + "abnormal blood nitrogen molecular entity level", + "Abnormal circulating metabolite concentration", + "abnormal role independent continuant level", + "abnormal independent continuant chemical entity level", + "phenotype by ontology source", "phenotype", + "abnormal phenotype by ontology source", "continuant", - "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 hematopoietic system", + "Abnormality of metabolism/homeostasis", + "Elevated circulating creatine kinase concentration", + "Abnormal circulating nitrogen compound concentration", + "abnormal chemical entity level", + "abnormal anatomical entity", "abnormal blood protein polypeptide chain level", "abnormal blood chemical entity level", - "biological_process", - "material entity", - "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", - "gas molecular entity", - "creatine kinase complex", - "polypeptide", - "nitrogen molecular entity", - "oxygen molecular entity", - "organochalcogen compound", - "organic molecular entity", + "Phenotypic abnormality", + "specifically dependent continuant", + "abnormal independent continuant protein polypeptide chain level", ], - "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_label": "Obligate", "frequency_qualifier_category": "biolink:PhenotypicFeature", "frequency_qualifier_namespace": "HP", - "frequency_qualifier_closure": ["HP:0040279", "HP:0000001", "HP:0040280"], - "frequency_qualifier_closure_label": ["Obligate (HPO)", "Frequency (HPO)", "All (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Obligate"], "evidence_count": 3, "grouping_key": "MONDO:0013049🍪🍪biolink:has_phenotype🍪HP:0003236", }, { - "id": "uuid:476a1081-842a-11ee-884f-6be035239f90", + "id": "uuid:8c422f2b-ae6f-11ee-9f7a-f78bc2e9ee32", "original_subject": "OMIM:254090", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", @@ -728,156 +470,120 @@ def association_table_response(): "subject_category": "biolink:Disease", "subject_namespace": "MONDO", "subject_closure": [ - "MONDO:0002320", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0000355", "MONDO:0000001", - "MONDO:0020121", - "MONDO:0019952", - "MONDO:0003847", "MONDO:0005336", - "MONDO:0000355", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0020120", + "MONDO:0700096", + "OGMS:0000031", + "MONDO:0019950", "BFO:0000017", - "MONDO:0100225", + "MONDO:0016139", + "MONDO:0020121", + "MONDO:0019952", "BFO:0000020", + "MONDO:0100225", + "MONDO:0009681", + "MONDO:0003847", "MONDO:0003939", - "MONDO:0002081", - "MONDO:0019950", - "MONDO:0005071", - "BFO:0000002", - "MONDO:0020120", - "MONDO:0019056", "MONDO:0700223", - "BFO:0000016", - "MONDO:0016139", - "MONDO:0700096", - "MONDO:0009681", - "OGMS:0000031", - "BFO:0000001", + "BFO:0000002", + "MONDO:0002081", + "MONDO:0002320", ], "subject_closure_label": [ + "nervous system disorder", + "congenital myopathy", + "musculoskeletal system disorder", "disease", - "realizable entity", - "collagen 6-related myopathy", - "specifically dependent continuant", + "neuromuscular disease", + "continuant", + "skeletal muscle disorder", "Ullrich congenital muscular dystrophy 1", + "congenital nervous system disorder", + "muscular dystrophy", + "myopathy", + "congenital muscular dystrophy", + "realizable entity", + "human disease", + "hereditary skeletal muscle disorder", + "disposition", "disease", + "hereditary disease", "muscle tissue disorder", - "hereditary skeletal muscle disorder", "Ullrich congenital muscular dystrophy", - "continuant", - "disposition", + "specifically dependent continuant", + "collagen 6-related myopathy", "qualitative or quantitative protein defects in neuromuscular diseases", - "human disease", "entity", - "myopathy", - "nervous system disorder", - "musculoskeletal system disorder", - "hereditary disease", - "congenital nervous system disorder", - "congenital muscular dystrophy", - "muscular dystrophy", - "congenital myopathy", - "skeletal muscle disorder", - "neuromuscular disease", ], - "object_label": "Distal joint laxity (HPO)", + "object_label": "Distal joint laxity", "object_category": "biolink:PhenotypicFeature", "object_namespace": "HP", "object_closure": [ - "HP:0011729", + "HP:0000001", + "HP:0020152", + "HP:0034430", + "HP:0000924", "HP:0011843", - "UBERON:0000465", "UPHENO:0082875", - "HP:0001388", - "BFO:0000001", - "BFO:0000040", - "UBERON:0011216", - "UBERON:0034921", "UPHENO:0001002", - "BFO:0000020", - "BFO:0000002", - "UPHENO:0001001", - "UPHENO:0002964", - "UPHENO:0001003", "UPHENO:0081440", + "HP:0001388", "BFO:0000001", - "UBERON:0001062", - "UBERON:0000061", - "UBERON:0034925", "UPHENO:0075696", - "UPHENO:0001005", - "HP:0033127", - "BFO:0000004", - "UBERON:0004770", - "UBERON:0000468", - "HP:0034430", - "HP:0000924", + "UPHENO:0002332", + "UPHENO:0001003", + "UPHENO:0002964", + "BFO:0000020", + "PATO:0000001", "BFO:0000002", "UPHENO:0002536", + "UPHENO:0001001", + "HP:0011729", + "UPHENO:0001005", "HP:0000118", - "UPHENO:0002332", - "PATO:0000001", - "UBERON:0000982", - "HP:0000001", - "HP:0020152", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0002204", - "UBERON:0004905", - "UBERON:0001434", + "HP:0033127", ], "object_closure_label": [ - "abnormality of anatomical entity physiology", - "Joint laxity (HPO)", - "abnormal skeletal system", - "abnormal anatomical entity", + "All", + "Distal joint laxity", + "Abnormality of the musculoskeletal system", + "Joint laxity", "quality", + "Phenotypic abnormality", + "abnormality of anatomical entity physiology", + "abnormality of musculoskeletal system physiology", "abnormal anatomical entity", - "abnormal phenotype by ontology source", - "specifically dependent continuant", "phenotype by ontology source", - "abnormality of musculoskeletal system physiology", - "continuant", - "material anatomical entity", - "musculoskeletal system", - "All (HPO)", - "Distal joint laxity (HPO)", + "Abnormal musculoskeletal physiology", + "phenotype", + "Abnormality of joint mobility", + "abnormal phenotype by ontology source", "continuant", - "organ system subdivision", - "multi organ part structure", + "abnormality of anatomical entity physiology", "Abnormal joint physiology", - "Abnormality of the skeletal system (HPO)", - "Phenotypic abnormality (HPO)", - "entity", + "Abnormality of the skeletal system", + "abnormal anatomical entity", "Phenotypic abnormality", - "Abnormality of musculoskeletal physiology (HPO)", - "anatomical entity", - "anatomical structure", - "anatomical collection", - "articular system", - "multicellular organism", - "phenotype", + "specifically dependent continuant", + "abnormal skeletal system", "entity", - "independent continuant", - "Abnormality of joint mobility (HPO)", - "Abnormality of the musculoskeletal system (HPO)", - "material entity", - "articulation", - "skeletal system", - "abnormality of anatomical entity physiology", - "multicellular anatomical structure", - "anatomical system", - "skeletal joint", ], - "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_label": "Obligate", "frequency_qualifier_category": "biolink:PhenotypicFeature", "frequency_qualifier_namespace": "HP", - "frequency_qualifier_closure": ["HP:0040279", "HP:0000001", "HP:0040280"], - "frequency_qualifier_closure_label": ["Obligate (HPO)", "Frequency (HPO)", "All (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Obligate"], "evidence_count": 3, "grouping_key": "MONDO:0009681🍪🍪biolink:has_phenotype🍪HP:0020152", }, { - "id": "uuid:46170673-842a-11ee-884f-6be035239f90", + "id": "uuid:8b4c43bf-ae6f-11ee-9f7a-f78bc2e9ee32", "original_subject": "OMIM:253601", "predicate": "biolink:has_phenotype", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", @@ -893,149 +599,117 @@ def association_table_response(): "subject_category": "biolink:Disease", "subject_namespace": "MONDO", "subject_closure": [ - "MONDO:0016145", + "MONDO:0005071", + "MONDO:0006025", + "BFO:0000016", + "MONDO:0009676", "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:0016971", - "MONDO:0005071", - "MONDO:0020120", + "MONDO:0000429", "MONDO:0019056", - "MONDO:0700223", - "BFO:0000016", - "MONDO:0016139", + "BFO:0000001", + "MONDO:0020120", "MONDO:0700096", "OGMS:0000031", - "BFO:0000001", + "MONDO:0016145", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0016971", + "MONDO:0020121", + "BFO:0000002", + "BFO:0000020", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0700223", + "MONDO:0002081", + "MONDO:0015152", ], "subject_closure_label": [ - "disease", - "realizable entity", - "disease", - "specifically dependent continuant", - "muscle tissue disorder", - "hereditary skeletal muscle disorder", + "nervous system disorder", "continuant", - "limb-girdle muscular dystrophy", - "disposition", - "qualitative or quantitative protein defects in neuromuscular diseases", - "human disease", - "entity", + "musculoskeletal system disorder", + "disease", "autosomal genetic disease", - "autosomal recessive disease", - "myopathy", - "nervous system disorder", + "neuromuscular disease", "autosomal recessive limb-girdle muscular dystrophy type 2B", + "skeletal muscle disorder", "autosomal recessive limb-girdle muscular dystrophy", - "qualitative or quantitative defects of dysferlin", + "limb-girdle muscular dystrophy", + "muscular dystrophy", "progressive muscular dystrophy", - "musculoskeletal system disorder", + "myopathy", + "realizable entity", + "human disease", + "hereditary skeletal muscle disorder", + "disposition", + "disease", + "autosomal recessive disease", "hereditary disease", - "muscular dystrophy", - "skeletal muscle disorder", - "neuromuscular disease", + "muscle tissue disorder", + "qualitative or quantitative defects of dysferlin", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", + "entity", ], - "object_label": "Proximal muscle weakness (HPO)", + "object_label": "Proximal muscle weakness", "object_category": "biolink:PhenotypicFeature", "object_namespace": "HP", "object_closure": [ - "UPHENO:0002816", - "UPHENO:0002536", - "UBERON:0000465", + "HP:0000001", "UPHENO:0082875", - "BFO:0000040", - "UBERON:0001062", - "UBERON:0011216", "UPHENO:0001002", "HP:0001324", "UPHENO:0080555", - "HP:0011804", - "BFO:0000002", - "UPHENO:0001001", - "HP:0003701", - "UPHENO:0001003", + "HP:0003011", "BFO:0000001", - "BFO:0000020", - "HP:0033127", - "BFO:0000004", - "UBERON:0000061", - "UBERON:0000062", - "UBERON:0000468", "UPHENO:0075696", - "BFO:0000002", - "HP:0003011", - "UPHENO:0002320", - "HP:0000118", "UPHENO:0002332", + "UPHENO:0001003", + "HP:0003701", + "UPHENO:0080556", + "UPHENO:0002320", + "UPHENO:0001001", + "BFO:0000002", + "BFO:0000020", "PATO:0000001", - "HP:0000001", + "UPHENO:0002816", + "UPHENO:0002536", + "HP:0011804", "UPHENO:0001005", - "UPHENO:0080556", - "BFO:0000001", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0005090", - "UBERON:0001630", - "UBERON:0000383", - "UBERON:0001015", + "HP:0000118", + "HP:0033127", ], "object_closure_label": [ - "abnormality of anatomical entity physiology", - "Proximal muscle weakness (HPO)", - "quality", - "Abnormality of the musculature (HPO)", - "phenotype by ontology source", + "All", "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", + "Abnormality of the musculoskeletal system", + "quality", "Phenotypic abnormality", - "Muscle weakness (HPO)", - "specifically dependent continuant", - "organ", - "multicellular organism", + "Abnormality of the musculature", + "abnormality of anatomical entity physiology", + "abnormality of muscle organ physiology", "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", + "Proximal muscle weakness", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "Abnormal muscle physiology", "abnormality of anatomical entity physiology", + "abnormal musculature", "abnormal anatomical entity", - "multicellular anatomical structure", - "anatomical system", - "muscle structure", + "Phenotypic abnormality", + "Muscle weakness", + "specifically dependent continuant", + "decreased muscle organ strength", + "entity", ], - "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_label": "Obligate", "frequency_qualifier_category": "biolink:PhenotypicFeature", "frequency_qualifier_namespace": "HP", - "frequency_qualifier_closure": ["HP:0040279", "HP:0000001", "HP:0040280"], - "frequency_qualifier_closure_label": ["Obligate (HPO)", "Frequency (HPO)", "All (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Obligate"], "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 a321b8143..390969cef 100644 --- a/backend/tests/fixtures/associations.py +++ b/backend/tests/fixtures/associations.py @@ -6,135 +6,175 @@ def associations(): return { "limit": 20, "offset": 0, - "total": 4838, + "total": 4624, "items": [ { - "id": "uuid:4e12a2a1-842a-11ee-884f-6be035239f90", + "id": "uuid:89e15863-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035432", - "original_subject": "Orphanet:565899", + "subject": "MONDO:0013904", + "original_subject": "OMIM:614830", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0005071", + "BFO:0000016", + "MONDO:0019052", "MONDO:0000001", - "MONDO:0020121", - "MONDO:0003847", - "BFO:0000001", - "MONDO:0016106", "MONDO:0005336", + "OGMS:0000031", + "MONDO:0700069", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0000171", + "MONDO:0020120", + "MONDO:0700096", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0700075", + "MONDO:0024322", "BFO:0000017", - "MONDO:0003939", - "MONDO:0035432", - "BFO:0000020", - "MONDO:0002081", - "MONDO:0016971", - "MONDO:0005071", + "MONDO:0013904", + "MONDO:0015286", + "MONDO:0017741", + "MONDO:0020121", "BFO:0000002", - "MONDO:0020120", - "MONDO:0019056", + "BFO:0000020", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", "MONDO:0700223", - "BFO:0000016", - "MONDO:0700096", - "OGMS:0000031", + "MONDO:0002081", + "MONDO:0002320", ], - "subject_label": "POMGNT2-related limb-girdle muscular dystrophy R24", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", "subject_closure_label": [ + "nervous system disorder", + "continuant", + "musculoskeletal system disorder", + "muscular dystrophy-dystroglycanopathy, type A", + "myopathy caused by variation in POMGNT2", + "neuromuscular disease", + "skeletal muscle disorder", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", + "muscular dystrophy", + "myopathy", "disease", + "congenital muscular dystrophy", + "congenital muscular dystrophy caused by variation in POMGNT2", + "disorder of glycosylation", "realizable entity", - "disease", - "POMGNT2-related limb-girdle muscular dystrophy R24", - "muscle tissue disorder", + "human disease", + "congenital disorder of glycosylation", "hereditary skeletal muscle disorder", - "limb-girdle muscular dystrophy", - "continuant", "disposition", - "human disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", + "metabolic disease", + "disease", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", "specifically dependent continuant", - "myopathy", - "nervous system disorder", "entity", - "progressive muscular dystrophy", - "musculoskeletal system disorder", - "hereditary disease", - "muscular dystrophy", - "skeletal muscle disorder", - "neuromuscular disease", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0002465", + "object": "HP:0007260", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "UPHENO:0002536", - "BFO:0000001", - "UBERON:0000465", - "UPHENO:0082875", - "BFO:0000002", - "UPHENO:0004523", - "BFO:0000040", - "UBERON:0001062", + "HP:0000001", + "HP:0002060", + "HP:0100547", + "UPHENO:0081603", + "HP:0012443", + "HP:0002538", "UPHENO:0001002", - "BFO:0000020", - "BFO:0000002", - "UPHENO:0001001", - "UPHENO:0001003", + "UPHENO:0076791", + "UPHENO:0087518", + "UPHENO:0076799", + "HP:0001339", + "UPHENO:0001005", "BFO:0000001", "UPHENO:0075696", - "UPHENO:0002433", - "HP:0012638", - "BFO:0000004", - "UBERON:0000061", - "UBERON:0000468", - "HP:0002167", + "HP:0000707", + "UPHENO:0001003", + "UPHENO:0076692", + "UPHENO:0049643", + "UPHENO:0076702", + "UPHENO:0015280", + "UPHENO:0081435", + "HP:0012639", + "UPHENO:0020888", + "UPHENO:0049587", + "HP:0002269", + "BFO:0000002", + "BFO:0000020", + "HP:0002536", + "UPHENO:0004523", "PATO:0000001", + "UPHENO:0049852", + "UPHENO:0087531", + "HP:0002011", + "HP:0007260", + "UPHENO:0076805", + "UPHENO:0050121", + "UPHENO:0049855", + "UPHENO:0002536", + "UPHENO:0001001", "HP:0000118", - "UPHENO:0002332", - "HP:0000001", - "HP:0002465", - "UPHENO:0001005", - "HP:0000707", - "HP:0011446", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0001016", + "UPHENO:0049634", + "UPHENO:0020584", ], - "object_label": "Poor speech (HPO)", + "object_label": "Type II lissencephaly", "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", + "All", + "Abnormal cerebral morphology", "continuant", - "material anatomical entity", - "nervous system", - "All (HPO)", - "Poor speech (HPO)", + "abnormal cell motility", + "abnormal anatomical entity morphology", + "Lissencephaly", + "abnormal cerebral hemisphere morphology", + "Abnormality of brain morphology", + "quality", + "abnormal neuron migration", "abnormal phenotype by ontology source", - "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "entity", "Phenotypic abnormality", - "abnormality of nervous system physiology", - "quality", - "multicellular organism", + "Abnormal cortical gyration", + "abnormal nervous system", + "Abnormality of neuronal migration", + "abnormal telencephalon morphology", + "abnormal cell migration", + "abnormal nervous system morphology", + "abnormal anatomical entity", + "Abnormality of the nervous system", + "phenotype by ontology source", + "abnormal biological_process", "phenotype", - "independent continuant", - "entity", - "Abnormal nervous system physiology (HPO)", - "material entity", - "anatomical entity", - "anatomical structure", - "continuant", - "abnormality of anatomical entity physiology", + "Morphological central nervous system abnormality", + "Type II lissencephaly", + "abnormal brain morphology", + "abnormal cellular process", + "Abnormal forebrain morphology", + "abnormal cerebral cortex morphology", + "abnormal anatomical entity morphology in the brain", + "Abnormal nervous system morphology", + "abnormal forebrain morphology", + "Abnormal cerebral cortex morphology", + "abnormal locomotion", "abnormal anatomical entity", - "multicellular anatomical structure", - "anatomical system", + "Phenotypic abnormality", + "abnormal central nervous system morphology", + "abnormal forebrain morphology", + "specifically dependent continuant", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "entity", ], "object_taxon": None, "object_taxon_label": None, @@ -143,18 +183,18 @@ def associations(): "negated": None, "pathway": None, "evidence_count": 2, - "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", + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0013904🍪🍪biolink:has_phenotype🍪HP:0007260", "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:565899"], - "publications_links": [{"id": "orphanet:565899", "url": None}], + "publications": ["PMID:22958903"], + "publications_links": [{"id": "PMID:22958903", "url": "http://identifiers.org/pubmed/22958903"}], "qualifiers": [], - "frequency_qualifier": "HP:0040282", + "frequency_qualifier": "HP:0040280", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, @@ -163,11 +203,11 @@ def associations(): "qualifiers_category": None, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_label": "Obligate", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Obligate"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -185,258 +225,174 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:4e12a2a3-842a-11ee-884f-6be035239f90", + "id": "uuid:89e15864-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035432", - "original_subject": "Orphanet:565899", + "subject": "MONDO:0013904", + "original_subject": "OMIM:614830", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0005071", + "BFO:0000016", + "MONDO:0019052", "MONDO:0000001", - "MONDO:0020121", - "MONDO:0003847", - "BFO:0000001", - "MONDO:0016106", "MONDO:0005336", + "OGMS:0000031", + "MONDO:0700069", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0000171", + "MONDO:0020120", + "MONDO:0700096", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0700075", + "MONDO:0024322", "BFO:0000017", - "MONDO:0003939", - "MONDO:0035432", - "BFO:0000020", - "MONDO:0002081", - "MONDO:0016971", - "MONDO:0005071", + "MONDO:0013904", + "MONDO:0015286", + "MONDO:0017741", + "MONDO:0020121", "BFO:0000002", - "MONDO:0020120", - "MONDO:0019056", + "BFO:0000020", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", "MONDO:0700223", - "BFO:0000016", - "MONDO:0700096", - "OGMS:0000031", + "MONDO:0002081", + "MONDO:0002320", ], - "subject_label": "POMGNT2-related limb-girdle muscular dystrophy R24", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", "subject_closure_label": [ + "nervous system disorder", + "continuant", + "musculoskeletal system disorder", + "muscular dystrophy-dystroglycanopathy, type A", + "myopathy caused by variation in POMGNT2", + "neuromuscular disease", + "skeletal muscle disorder", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", + "muscular dystrophy", + "myopathy", "disease", + "congenital muscular dystrophy", + "congenital muscular dystrophy caused by variation in POMGNT2", + "disorder of glycosylation", "realizable entity", - "disease", - "POMGNT2-related limb-girdle muscular dystrophy R24", - "muscle tissue disorder", + "human disease", + "congenital disorder of glycosylation", "hereditary skeletal muscle disorder", - "limb-girdle muscular dystrophy", - "continuant", "disposition", - "human disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", + "metabolic disease", + "disease", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", "specifically dependent continuant", - "myopathy", - "nervous system disorder", "entity", - "progressive muscular dystrophy", - "musculoskeletal system disorder", - "hereditary disease", - "muscular dystrophy", - "skeletal muscle disorder", - "neuromuscular disease", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0008981", + "object": "HP:0001321", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0008981", - "UPHENO:0084535", - "UPHENO:0002816", - "HP:0030236", - "PR:000050567", - "UBERON:0000465", - "RO:0002577", - "UPHENO:0015280", - "HP:0001437", - "BFO:0000040", - "UBERON:0001062", - "UBERON:0011216", - "UBERON:0000154", - "UBERON:0006067", + "HP:0000001", + "HP:0012443", + "HP:0011283", "UPHENO:0001002", - "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", + "UPHENO:0081099", + "UPHENO:0076791", + "UPHENO:0081601", + "HP:0001317", + "UPHENO:0080079", + "UPHENO:0076720", + "HP:0001321", + "UPHENO:0081091", + "UPHENO:0080089", "BFO:0000001", - "UBERON:0004482", - "UBERON:0001383", - "UBERON:0008784", - "UBERON:0002471", "UPHENO:0075696", - "UPHENO:0001005", - "HP:0009127", - "BFO:0000020", - "UPHENO:0001072", - "UPHENO:0081581", - "HP:0033127", + "HP:0002977", + "HP:0000707", "UPHENO:0001003", "UPHENO:0076692", - "UPHENO:0003070", - "UPHENO:0002830", - "BFO:0000004", - "UBERON:0004708", - "UBERON:0000061", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0000468", - "UBERON:0010709", - "HP:0002981", - "UPHENO:0065599", + "UPHENO:0076702", + "UPHENO:0086932", + "UPHENO:0015280", + "UPHENO:0020013", + "UPHENO:0081435", + "HP:0012639", + "UPHENO:0012541", + "UPHENO:0068971", "BFO:0000002", - "HP:0003011", + "BFO:0000020", + "UPHENO:0081790", + "UPHENO:0004523", + "HP:0011282", + "HP:0002011", + "UPHENO:0076805", + "UPHENO:0068984", "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", + "UPHENO:0001001", + "UPHENO:0001005", "HP:0000118", + "UPHENO:0075195", + "HP:0007360", "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": "Calf muscle hypertrophy (HPO)", + "object_label": "Cerebellar hypoplasia", "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", + "All", "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)", + "abnormal size of anatomical entity", + "Aplasia/Hypoplasia of the cerebellum", + "anatomical entity hypoplasia", + "aplasia or hypoplasia of cerebellum", "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", + "aplasia or hypoplasia of anatomical entity", + "abnormal cerebellum morphology", + "Cerebellar hypoplasia", + "Abnormality of brain morphology", + "Abnormal metencephalon morphology", + "Abnormal hindbrain morphology", "Phenotypic abnormality", - "Abnormality of the calf musculature (HPO)", - "specifically dependent continuant", - "abnormal anatomical entity morphology", - "abnormal leg", - "quality", - "organism subdivision", - "organ", - "multicellular organism", - "pelvic complex", - "musculature of lower limb", - "muscle of leg", - "lower limb segment", - "zeugopod", + "anatomical entity hypoplasia in independent continuant", + "abnormal nervous system", + "decreased size of the anatomical entity", + "Abnormal cerebellum morphology", + "abnormal nervous system morphology", + "abnormal hindbrain morphology", + "abnormal anatomical entity", + "Aplasia/Hypoplasia involving the central nervous system", + "Abnormality of the nervous system", + "phenotype by ontology source", "phenotype", - "abnormal hindlimb zeugopod", + "abnormal phenotype by ontology source", + "Morphological central nervous system abnormality", + "abnormal brain morphology", + "abnormal anatomical entity morphology in the brain", + "Abnormal nervous system morphology", + "quality", + "decreased size of the cerebellum", + "abnormal anatomical entity", + "decreased size of the anatomical entity in the independent continuant", + "Phenotypic abnormality", + "cerebellum hypoplasia", + "abnormal central nervous system morphology", + "abnormal metencephalon morphology", + "specifically dependent continuant", "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", - "muscle structure", - "skeletal musculature", - "hindlimb", - "appendage girdle complex", - "appendage musculature", - "musculature of pelvic complex", - "limb muscle", - "pelvic complex muscle", - "paired limb/fin segment", + "abnormal hindbrain morphology", + "abnormal anatomical entity morphology", + "entity", ], "object_taxon": None, "object_taxon_label": None, @@ -445,18 +401,18 @@ def associations(): "negated": None, "pathway": None, "evidence_count": 2, - "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", + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0013904🍪🍪biolink:has_phenotype🍪HP:0001321", "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:565899"], - "publications_links": [{"id": "orphanet:565899", "url": None}], + "publications": ["PMID:22958903"], + "publications_links": [{"id": "PMID:22958903", "url": "http://identifiers.org/pubmed/22958903"}], "qualifiers": [], - "frequency_qualifier": "HP:0040282", + "frequency_qualifier": "HP:0040280", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, @@ -465,11 +421,11 @@ def associations(): "qualifiers_category": None, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_label": "Obligate", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Obligate"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -487,220 +443,134 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:4e12a2a4-842a-11ee-884f-6be035239f90", + "id": "uuid:89e15866-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035432", - "original_subject": "Orphanet:565899", + "subject": "MONDO:0013904", + "original_subject": "OMIM:614830", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0005071", + "BFO:0000016", + "MONDO:0019052", "MONDO:0000001", - "MONDO:0020121", - "MONDO:0003847", - "BFO:0000001", - "MONDO:0016106", "MONDO:0005336", + "OGMS:0000031", + "MONDO:0700069", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0000171", + "MONDO:0020120", + "MONDO:0700096", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0700075", + "MONDO:0024322", "BFO:0000017", - "MONDO:0003939", - "MONDO:0035432", - "BFO:0000020", - "MONDO:0002081", - "MONDO:0016971", - "MONDO:0005071", + "MONDO:0013904", + "MONDO:0015286", + "MONDO:0017741", + "MONDO:0020121", "BFO:0000002", - "MONDO:0020120", - "MONDO:0019056", + "BFO:0000020", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", "MONDO:0700223", - "BFO:0000016", - "MONDO:0700096", - "OGMS:0000031", + "MONDO:0002081", + "MONDO:0002320", ], - "subject_label": "POMGNT2-related limb-girdle muscular dystrophy R24", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", "subject_closure_label": [ + "nervous system disorder", + "continuant", + "musculoskeletal system disorder", + "muscular dystrophy-dystroglycanopathy, type A", + "myopathy caused by variation in POMGNT2", + "neuromuscular disease", + "skeletal muscle disorder", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", + "muscular dystrophy", + "myopathy", "disease", + "congenital muscular dystrophy", + "congenital muscular dystrophy caused by variation in POMGNT2", + "disorder of glycosylation", "realizable entity", - "disease", - "POMGNT2-related limb-girdle muscular dystrophy R24", - "muscle tissue disorder", + "human disease", + "congenital disorder of glycosylation", "hereditary skeletal muscle disorder", - "limb-girdle muscular dystrophy", - "continuant", "disposition", - "human disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", + "metabolic disease", + "disease", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", "specifically dependent continuant", - "myopathy", - "nervous system disorder", "entity", - "progressive muscular dystrophy", - "musculoskeletal system disorder", - "hereditary disease", - "muscular dystrophy", - "skeletal muscle disorder", - "neuromuscular disease", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0008994", + "object": "HP:0001252", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0008994", - "UPHENO:0002816", - "UPHENO:0002536", - "PR:000050567", - "UBERON:0000465", - "RO:0002577", + "HP:0000001", + "UPHENO:0082555", "UPHENO:0082875", - "HP:0001437", - "BFO:0000040", - "UBERON:0001062", - "UBERON:0011216", - "UBERON:0000154", - "UBERON:0000026", + "UPHENO:0001005", "UPHENO:0001002", - "HP:0001324", - "BFO:0000020", - "UPHENO:0080555", - "HP:0011804", "BFO:0000002", - "UBERON:0002101", - "UBERON:0004709", - "UBERON:0015212", - "UPHENO:0001001", - "HP:0003701", - "HP:0011805", - "UPHENO:0001003", - "UPHENO:0002647", + "HP:0003011", + "HP:0001252", "BFO:0000001", - "UBERON:0000061", - "UBERON:0004482", - "UBERON:0008784", "UPHENO:0075696", - "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", - "HP:0003011", - "UPHENO:0076710", - "HP:0040064", - "UBERON:0002103", - "UBERON:0010707", - "UBERON:0010758", - "UBERON:0006058", - "UPHENO:0002320", - "HP:0002814", - "HP:0000118", "UPHENO:0002332", + "UPHENO:0001003", + "UPHENO:0002320", + "BFO:0000020", "PATO:0000001", - "UBERON:0007271", - "UBERON:0014792", - "UBERON:0010538", - "HP:0000001", - "UPHENO:0002644", - "UPHENO:0080556", - "BFO:0000001", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0005090", - "UBERON:0001630", - "UBERON:0000383", - "UBERON:0001015", - "UBERON:0000978", - "UBERON:0007270", - "UBERON:0004480", - "UBERON:0002529", + "UPHENO:0002816", + "UPHENO:0002536", + "HP:0011804", + "UPHENO:0001001", + "HP:0003808", + "HP:0000118", + "HP:0033127", + "UPHENO:0082557", ], - "object_label": "Proximal muscle weakness in lower limbs (HPO)", + "object_label": "Hypotonia", "object_closure_label": [ - "abnormality of anatomical entity physiology", - "Proximal muscle weakness (HPO)", - "Abnormal skeletal muscle morphology (HPO)", + "All", + "decreased anatomical entity tone", + "Abnormality of the musculoskeletal system", + "Hypotonia", "quality", - "abnormal anatomical entity", "abnormal phenotype by ontology source", - "Abnormality of the musculature of the limbs (HPO)", - "specifically dependent continuant", - "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", - "organism subdivision", - "organ", - "multicellular organism", - "pelvic complex", - "musculature of lower limb", - "lower limb segment", + "Phenotypic abnormality", + "Abnormality of the musculature", + "abnormality of anatomical entity physiology", + "abnormality of muscle organ physiology", + "continuant", + "abnormal anatomical entity", + "phenotype by ontology source", "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", + "Abnormal muscle tone", + "Abnormal muscle physiology", "abnormality of anatomical entity physiology", + "abnormal musculature", "abnormal anatomical entity", - "abnormal muscle organ morphology", - "Abnormality of limbs (HPO)", - "multicellular anatomical structure", - "anatomical system", - "muscle structure", - "hindlimb", - "appendage girdle complex", - "appendage musculature", - "musculature of pelvic complex", - "paired limb/fin segment", + "specifically dependent continuant", + "decreased muscle organ tone", + "entity", ], "object_taxon": None, "object_taxon_label": None, @@ -709,16 +579,16 @@ def associations(): "negated": None, "pathway": None, "evidence_count": 2, - "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", + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0013904🍪🍪biolink:has_phenotype🍪HP:0001252", "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:565899"], - "publications_links": [{"id": "orphanet:565899", "url": None}], + "publications": ["PMID:22958903"], + "publications_links": [{"id": "PMID:22958903", "url": "http://identifiers.org/pubmed/22958903"}], "qualifiers": [], "frequency_qualifier": "HP:0040282", "onset_qualifier": None, @@ -729,11 +599,11 @@ def associations(): "qualifiers_category": None, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_label": "Frequent", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -751,240 +621,124 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:4e02df81-842a-11ee-884f-6be035239f90", + "id": "uuid:89e15867-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013904", + "original_subject": "OMIM:614830", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0019052", "MONDO:0000001", - "MONDO:0020121", + "MONDO:0005336", + "OGMS:0000031", + "MONDO:0700069", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0000171", + "MONDO:0020120", + "MONDO:0700096", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0700075", + "MONDO:0024322", "BFO:0000017", - "MONDO:0008056", - "MONDO:0035646", + "MONDO:0013904", + "MONDO:0015286", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000002", + "BFO:0000020", "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:0005066", "MONDO:0700223", - "MONDO:0003382", - "BFO:0000016", - "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", - "OGMS:0000031", - "BFO:0000001", + "MONDO:0002081", + "MONDO:0002320", ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", "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", + "continuant", "musculoskeletal system disorder", - "hereditary disease", - "eye disorder", + "muscular dystrophy-dystroglycanopathy, type A", + "myopathy caused by variation in POMGNT2", + "neuromuscular disease", + "skeletal muscle disorder", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "myopathy", + "disease", + "congenital muscular dystrophy", + "congenital muscular dystrophy caused by variation in POMGNT2", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome", + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", + "metabolic disease", + "disease", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "entity", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0000256", + "object": "HP:0003560", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000256", - "UPHENO:0002536", - "UPHENO:0081566", - "HP:0000240", - "UBERON:0000465", - "UPHENO:0075220", - "UPHENO:0001208", - "UPHENO:0002844", - "UPHENO:0015280", - "BFO:0000001", - "BFO:0000040", - "UBERON:0001062", - "UBERON:0011216", - "UBERON:0011676", - "UBERON:0013701", - "UPHENO:0075148", + "HP:0000001", "UPHENO:0001002", - "UPHENO:0075195", - "HP:0009121", - "BFO:0000002", - "UPHENO:0001001", - "HP:0011842", - "BFO:0000020", - "UPHENO:0002964", - "UPHENO:0001003", - "UPHENO:0021447", + "UPHENO:0076710", + "HP:0003011", "BFO:0000001", - "UBERON:0000061", - "UBERON:0034925", - "HP:0040194", - "UPHENO:0075696", - "UPHENO:0001005", - "UPHENO:0002764", - "UPHENO:0001072", - "UPHENO:0081581", - "HP:0033127", + "UPHENO:0001003", "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", + "HP:0011805", + "HP:0003560", "BFO:0000002", - "UPHENO:0020584", + "BFO:0000020", "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", + "UPHENO:0002816", + "UPHENO:0002536", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0000118", + "HP:0033127", ], - "object_label": "Macrocephaly (HPO)", + "object_label": "Muscular dystrophy", "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", + "All", "continuant", - "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)", + "Abnormality of the musculoskeletal system", "abnormal anatomical entity morphology", - "entity", - "structure with developmental contribution from neural crest", - "abnormal size of head", + "quality", "Phenotypic abnormality", - "abnormal anatomical entity morphology", - "Abnormality of skull size (HPO)", - "anatomical structure", - "anatomical collection", - "skeleton", - "organism subdivision", - "multicellular organism", - "anterior region of body", + "Abnormality of the musculature", + "abnormal muscle organ morphology", + "Abnormal skeletal muscle morphology", + "Muscular dystrophy", + "phenotype by ontology source", "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", - "subdivision of skeleton", - "skeletal system", - "increased size of the head", - "abnormal head", + "abnormal phenotype by ontology source", + "abnormal musculature", "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", + "Phenotypic abnormality", + "specifically dependent continuant", + "entity", ], "object_taxon": None, "object_taxon_label": None, @@ -993,18 +747,18 @@ def associations(): "negated": None, "pathway": None, "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:0000256", + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0013904🍪🍪biolink:has_phenotype🍪HP:0003560", "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": None}], + "publications": ["PMID:22958903"], + "publications_links": [{"id": "PMID:22958903", "url": "http://identifiers.org/pubmed/22958903"}], "qualifiers": [], - "frequency_qualifier": "HP:0040281", + "frequency_qualifier": "HP:0040280", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, @@ -1013,11 +767,11 @@ def associations(): "qualifiers_category": None, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Very frequent (HPO)", + "frequency_qualifier_label": "Obligate", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040281", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Very frequent (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Obligate"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -1035,248 +789,176 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:4e02df82-842a-11ee-884f-6be035239f90", + "id": "uuid:89e1586b-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013904", + "original_subject": "OMIM:614830", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0019052", "MONDO:0000001", - "MONDO:0020121", + "MONDO:0005336", + "OGMS:0000031", + "MONDO:0700069", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0000171", + "MONDO:0020120", + "MONDO:0700096", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0700075", + "MONDO:0024322", "BFO:0000017", - "MONDO:0008056", - "MONDO:0035646", + "MONDO:0013904", + "MONDO:0015286", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000002", + "BFO:0000020", "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:0005066", "MONDO:0700223", - "MONDO:0003382", - "BFO:0000016", - "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", - "OGMS:0000031", - "BFO:0000001", + "MONDO:0002081", + "MONDO:0002320", ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", "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", + "continuant", "musculoskeletal system disorder", - "hereditary disease", - "eye disorder", + "muscular dystrophy-dystroglycanopathy, type A", + "myopathy caused by variation in POMGNT2", + "neuromuscular disease", + "skeletal muscle disorder", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "myopathy", + "disease", + "congenital muscular dystrophy", + "congenital muscular dystrophy caused by variation in POMGNT2", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome", + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", + "metabolic disease", + "disease", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "entity", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0000297", + "object": "HP:0007973", "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:0002910", - "BFO:0000001", - "BFO:0000040", - "UBERON:0001062", - "UBERON:0011216", - "UBERON:0011676", - "UBERON:0013701", - "UPHENO:0001002", - "HP:0011804", + "HP:0000315", + "HP:0000001", + "HP:0000234", + "UPHENO:0076782", + "UPHENO:0088038", + "UPHENO:0075997", "BFO:0000002", - "UBERON:0001630", - "UBERON:0002376", - "UBERON:0015789", - "UPHENO:0001001", - "HP:0011805", - "BFO:0000020", - "UPHENO:0001003", "BFO:0000001", - "UBERON:0000061", "UPHENO:0075696", - "UPHENO:0001005", - "UPHENO:0002764", - "UPHENO:0081581", - "HP:0033127", + "HP:0000152", + "UPHENO:0087907", + "UPHENO:0002910", + "UPHENO:0087596", + "HP:0000707", + "UPHENO:0001003", "UPHENO:0076692", - "BFO:0000004", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0000468", - "UBERON:0000153", + "HP:0007973", + "UPHENO:0076702", + "UPHENO:0001002", + "UPHENO:0021656", + "UPHENO:0015280", + "HP:0000271", + "HP:0012639", + "UPHENO:0021037", + "UPHENO:0021474", "UPHENO:0002844", - "BFO:0000002", - "HP:0003011", - "UPHENO:0076710", + "BFO:0000020", + "UPHENO:0004523", + "HP:0000479", + "HP:0012372", + "UPHENO:0087472", + "HP:0000478", + "UPHENO:0087924", + "UPHENO:0001005", + "HP:0001098", + "UPHENO:0002764", + "HP:0004329", + "UPHENO:0003020", + "UPHENO:0002536", "PATO:0000001", - "UPHENO:0002908", - "UBERON:0007811", - "UBERON:0001444", - "UBERON:0013702", - "UBERON:0000033", - "UPHENO:0002320", - "UPHENO:0082555", - "HP:0000152", + "UPHENO:0001001", + "UPHENO:0086589", "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", + "UPHENO:0020584", ], - "object_label": "Facial hypotonia (HPO)", + "object_label": "Retinal dysplasia", "object_closure_label": [ - "abnormality of anatomical entity physiology", - "abnormal head", - "Abnormal skeletal muscle morphology (HPO)", - "specifically dependent continuant", - "abnormal anatomical entity", + "Abnormality of the orbital region", + "All", + "abnormal anatomical entity morphology", + "abnormal orbital region", "abnormal phenotype by ontology source", + "Abnormal fundus 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)", + "Abnormal posterior eye segment morphology", + "abnormal posterior segment of eyeball morphology", + "abnormal retina morphology", + "Abnormal retinal morphology", + "Abnormal eye morphology", + "abnormal face morphology", + "Phenotypic abnormality", + "abnormal nervous system", + "abnormal posterior segment of eyeball morphology", + "abnormal camera-type eye morphology", + "abnormal head", "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", - "skeletal musculature of head", - "musculature of face", + "abnormal ocular fundus morphology", + "Retinal dysplasia", + "abnormal nervous system morphology", + "abnormal anatomical entity", + "Abnormality of the eye", + "abnormal camera-type eye morphology", "Phenotypic abnormality", - "abnormal anatomical entity morphology", - "quality", - "abnormal facial muscle", - "anatomical structure", - "organism subdivision", - "organ", - "multicellular organism", - "anterior region of body", + "abnormal ocular fundus morphology", + "Abnormality of the nervous system", + "phenotype by ontology source", "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", - "skeletal muscle organ", + "abnormal craniocervical region morphology", + "Abnormality of the head", + "Abnormal nervous system morphology", + "quality", + "Abnormality of head or neck", + "abnormal head morphology", "abnormal face", - "abnormality of anatomical entity physiology", - "Hypotonia (HPO)", + "abnormal eyeball of camera-type eye", "abnormal anatomical entity", - "abnormal muscle organ morphology", - "multicellular anatomical structure", - "anatomical system", - "muscle structure", - "skeletal musculature", - "mesoderm-derived structure", - "face", - "craniocervical region musculature", - "axial musculature", - "craniocervical muscle", - "facial muscle", + "specifically dependent continuant", + "abnormal anatomical entity morphology in the independent continuant", + "Abnormality of the face", + "abnormal anatomical entity morphology", + "entity", ], "object_taxon": None, "object_taxon_label": None, @@ -1285,18 +967,18 @@ def associations(): "negated": None, "pathway": None, "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:0000297", + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0013904🍪🍪biolink:has_phenotype🍪HP:0007973", "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": None}], + "publications": ["PMID:22958903"], + "publications_links": [{"id": "PMID:22958903", "url": "http://identifiers.org/pubmed/22958903"}], "qualifiers": [], - "frequency_qualifier": "HP:0040281", + "frequency_qualifier": "HP:0040282", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, @@ -1305,11 +987,11 @@ def associations(): "qualifiers_category": None, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Very frequent (HPO)", + "frequency_qualifier_label": "Frequent", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040281", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Very frequent (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -1327,264 +1009,142 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:4e02df83-842a-11ee-884f-6be035239f90", + "id": "uuid:89e1586c-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013904", + "original_subject": "OMIM:614830", "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", + "MONDO:0019052", + "MONDO:0000001", + "MONDO:0005336", "OGMS:0000031", + "MONDO:0700069", + "MONDO:0019056", "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", + "MONDO:0000171", + "MONDO:0020120", + "MONDO:0700096", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0700075", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0013904", + "MONDO:0015286", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000002", + "BFO:0000020", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", + "MONDO:0002320", + ], + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", + "subject_closure_label": [ "nervous system disorder", - "heart disorder", - "myotonic dystrophy type 1", - "progressive muscular dystrophy", + "continuant", "musculoskeletal system disorder", - "hereditary disease", - "eye disorder", + "muscular dystrophy-dystroglycanopathy, type A", + "myopathy caused by variation in POMGNT2", + "neuromuscular disease", + "skeletal muscle disorder", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "myopathy", + "disease", + "congenital muscular dystrophy", + "congenital muscular dystrophy caused by variation in POMGNT2", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome", + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", + "metabolic disease", + "disease", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "entity", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0010804", + "object": "HP:0000501", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000159", - "UPHENO:0076803", - "UBERON:0000465", + "HP:0000315", + "HP:0000001", + "HP:0000234", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "HP:0000152", + "HP:0000501", "UPHENO:0002910", - "UPHENO:0076800", - "UPHENO:0003064", - "BFO:0000002", - "HP:0002664", - "UPHENO:0015280", - "BFO:0000040", - "BFO:0000141", - "UBERON:0001062", - "UBERON:0011676", - "UBERON:0013701", - "UPHENO:0002828", + "UPHENO:0002332", + "UPHENO:0001003", "UPHENO:0001002", - "BFO:0000020", - "HP:0011793", - "UPHENO:0076786", - "BFO:0000002", - "UBERON:0000167", + "HP:0000271", "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", - "HP:0011339", - "HP:0010804", - "UPHENO:0020584", - "PATO:0000001", - "UBERON:0010314", - "UBERON:0003102", - "UBERON:0010000", - "UBERON:0001555", - "UBERON:0001456", - "UBERON:0004921", - "HP:0000001", + "BFO:0000002", + "BFO:0000020", + "HP:0012373", + "HP:0000478", "UPHENO:0001005", - "HP:0031816", - "HP:0000153", - "HP:0000234", - "HP:0000271", + "UPHENO:0002219", + "UPHENO:0002764", + "UPHENO:0003020", + "UPHENO:0002536", + "PATO:0000001", + "HP:0000118", "BFO:0000001", - "UBERON:0000467", - "UBERON:0000064", - "UBERON:0001007", - "UBERON:0013522", - "UBERON:0000165", ], - "object_label": "Tented upper lip vermilion (HPO)", + "object_label": "Glaucoma", "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", + "Abnormality of the orbital region", + "All", "continuant", - "material anatomical entity", - "organ part", - "digestive system", - "head", - "midface", - "All (HPO)", + "abnormal orbital region", "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", + "abnormality of camera-type eye physiology", + "abnormal craniocervical region", "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", + "abnormality of anatomical entity physiology", + "Abnormal eye physiology", + "entity", "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 head", + "abnormal anatomical entity", + "Abnormality of the eye", + "Phenotypic abnormality", + "phenotype by ontology source", + "Abnormality of the head", + "quality", + "abnormality of anatomical entity physiology", + "Abnormality of head or neck", + "Glaucoma", "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", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity", + "specifically dependent continuant", + "Abnormality of the face", ], "object_taxon": None, "object_taxon_label": None, @@ -1593,18 +1153,18 @@ def associations(): "negated": None, "pathway": None, "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:0010804", + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0013904🍪🍪biolink:has_phenotype🍪HP:0000501", "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": None}], + "publications": ["PMID:22958903"], + "publications_links": [{"id": "PMID:22958903", "url": "http://identifiers.org/pubmed/22958903"}], "qualifiers": [], - "frequency_qualifier": "HP:0040281", + "frequency_qualifier": "HP:0040282", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, @@ -1613,11 +1173,11 @@ def associations(): "qualifiers_category": None, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Very frequent (HPO)", + "frequency_qualifier_label": "Frequent", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040281", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Very frequent (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -1635,178 +1195,182 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:4e02df84-842a-11ee-884f-6be035239f90", + "id": "uuid:89e159cd-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013154", + "original_subject": "OMIM:613150", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0018939", + "MONDO:0019052", + "MONDO:0018282", "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", + "MONDO:0013154", "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:0000171", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0015286", + "MONDO:0016155", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000020", + "MONDO:0700071", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", "BFO:0000001", + "MONDO:0002320", ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "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", + "disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "muscular dystrophy-dystroglycanopathy, type A", + "neuromuscular disease", + "muscle-eye-brain disease", + "skeletal muscle disorder", + "entity", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "continuant", + "myopathy", + "congenital muscular dystrophy", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome", + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "metabolic disease", + "qualitative or quantitative defects of alpha-dystroglycan", + "disease", + "myopathy caused by variation in POMT2", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0031843", + "object": "HP:0009917", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "UBERON:0000465", - "GO:0050877", - "UPHENO:0082875", - "UPHENO:0004523", - "GO:0008150", - "BFO:0000040", - "UBERON:0001062", - "GO:0003008", - "BFO:0000020", - "BFO:0000003", - "BFO:0000002", - "UPHENO:0001001", + "HP:0000315", + "HP:0000001", + "HP:0000234", + "HP:0000615", + "UPHENO:0021672", + "UPHENO:0021663", + "UPHENO:0087597", + "UPHENO:0075997", "UPHENO:0001002", - "HP:0031843", - "UPHENO:0001003", + "BFO:0000002", "BFO:0000001", - "UBERON:0000061", - "GO:0050890", - "UPHENO:0001005", - "UPHENO:0002433", - "HP:0100543", - "HP:0012638", - "BFO:0000015", - "UBERON:0000468", "UPHENO:0075696", - "BFO:0000002", + "HP:0000152", + "UPHENO:0087907", + "UPHENO:0002910", + "UPHENO:0001003", + "HP:0009917", + "UPHENO:0088042", + "UPHENO:0076692", + "UPHENO:0086817", + "HP:0004328", + "HP:0000553", + "UPHENO:0015280", + "HP:0000271", + "UPHENO:0088050", + "UPHENO:0021474", + "UPHENO:0002844", + "BFO:0000020", + "HP:0000525", + "PATO:0000001", + "HP:0012372", + "UPHENO:0087472", + "HP:0000478", + "UPHENO:0087924", + "UPHENO:0002764", + "UPHENO:0003020", "UPHENO:0002536", - "BFO:0000004", + "UPHENO:0001001", + "UPHENO:0086589", + "UPHENO:0001005", "HP:0000118", - "UPHENO:0002332", - "PATO:0000001", - "HP:0000001", - "HP:0000707", - "HP:0011446", - "BFO:0000001", - "GO:0032501", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0001016", + "UPHENO:0076804", + "UPHENO:0021038", + "UPHENO:0020584", ], - "object_label": "Bradyphrenia (HPO)", + "object_label": "Persistent pupillary membrane", "object_closure_label": [ - "abnormality of anatomical entity physiology", + "Abnormality of the orbital region", + "All", + "abnormal uvea morphology", + "Persistent pupillary membrane", + "abnormal pupil morphology", + "abnormal anatomical entity morphology", + "abnormal anterior uvea morphology", + "abnormal orbital region", + "abnormal craniocervical region", + "quality", + "Abnormal eye morphology", + "abnormal face morphology", + "Phenotypic abnormality", "Phenotypic abnormality", - "Bradyphrenia (HPO)", + "Abnormality iris morphology", + "abnormal camera-type eye morphology", + "abnormal head", + "continuant", + "abnormal iris morphology", + "abnormal pupil morphology", + "abnormal anterior segment of eyeball morphology", "abnormal anatomical entity", - "Abnormality of higher mental function (HPO)", - "quality", - "multicellular organismal process", - "abnormal phenotype by ontology source", - "specifically dependent continuant", + "Abnormality of the eye", + "abnormal camera-type eye morphology", "phenotype by ontology source", - "abnormal nervous system", - "occurrent", - "continuant", - "material anatomical entity", - "nervous system", - "All (HPO)", - "continuant", - "system process", - "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "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 craniocervical region morphology", + "abnormal phenotype by ontology source", + "Abnormality of the head", + "Abnormal pupil morphology", + "abnormal anterior segment of eyeball morphology", + "Abnormality of head or neck", + "abnormal head morphology", + "abnormal face", + "abnormal eyeball of camera-type eye", "abnormal anatomical entity", - "abnormality of anatomical entity physiology", - "independent continuant", - "multicellular anatomical structure", - "anatomical system", + "abnormal iris morphology", + "Abnormal anterior eye segment morphology", + "Abnormal uvea morphology", + "specifically dependent continuant", + "abnormal anatomical entity morphology in the independent continuant", + "Abnormality of the face", + "abnormal anatomical entity morphology", + "entity", ], "object_taxon": None, "object_taxon_label": None, @@ -1815,18 +1379,18 @@ def associations(): "negated": None, "pathway": None, "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:0031843", + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0013154🍪🍪biolink:has_phenotype🍪HP:0009917", "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": None}], + "publications": ["PMID:15894594"], + "publications_links": [{"id": "PMID:15894594", "url": "http://identifiers.org/pubmed/15894594"}], "qualifiers": [], - "frequency_qualifier": "HP:0040281", + "frequency_qualifier": "HP:0040282", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, @@ -1835,11 +1399,11 @@ def associations(): "qualifiers_category": None, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Very frequent (HPO)", + "frequency_qualifier_label": "Frequent", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040281", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": ["Frequency (HPO)", "All (HPO)", "Very frequent (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -1857,192 +1421,212 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:4e02df85-842a-11ee-884f-6be035239f90", + "id": "uuid:89e159d3-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013154", + "original_subject": "OMIM:613150", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0018939", + "MONDO:0019052", + "MONDO:0018282", "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", + "MONDO:0013154", "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:0000171", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0015286", + "MONDO:0016155", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000020", + "MONDO:0700071", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", "BFO:0000001", + "MONDO:0002320", ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "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", + "disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "muscular dystrophy-dystroglycanopathy, type A", + "neuromuscular disease", + "muscle-eye-brain disease", + "skeletal muscle disorder", + "entity", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "continuant", + "myopathy", + "congenital muscular dystrophy", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome", + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "metabolic disease", + "qualitative or quantitative defects of alpha-dystroglycan", + "disease", + "myopathy caused by variation in POMT2", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0000736", + "object": "HP:0001274", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", - "object_closure": [ - "UBERON:0000465", - "NBO:0000313", - "NBO:0000308", - "UPHENO:0082875", - "BFO:0000002", - "UPHENO:0004523", - "UPHENO:0049587", - "GO:0008150", - "BFO:0000040", - "UBERON:0001062", - "GO:0007610", + "object_closure": [ + "HP:0000001", + "HP:0002060", + "HP:0010993", + "HP:0100547", + "HP:0007364", + "HP:0012443", + "UPHENO:0026506", + "UPHENO:0021803", + "HP:0007370", "UPHENO:0001002", - "BFO:0000020", - "HP:0000736", - "BFO:0000003", + "HP:0012429", + "UPHENO:0076791", + "UPHENO:0087518", + "UPHENO:0076799", + "UPHENO:0080079", + "UPHENO:0087902", "BFO:0000002", - "UPHENO:0001001", - "UPHENO:0049622", - "UPHENO:0001003", + "UPHENO:0011580", + "HP:0001273", "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", + "HP:0002977", + "UPHENO:0008622", + "UPHENO:0087750", + "HP:0000707", + "UPHENO:0001003", + "UPHENO:0076692", + "UPHENO:0076702", + "HP:0033725", + "UPHENO:0087415", + "HP:0001274", + "UPHENO:0026028", + "BFO:0000020", + "UPHENO:0015280", + "UPHENO:0081562", + "UPHENO:0081435", + "HP:0012639", + "UPHENO:0020888", + "UPHENO:0085804", + "UPHENO:0080200", + "UPHENO:0006910", + "UPHENO:0008523", + "UPHENO:0004523", "PATO:0000001", - "HP:0000001", "UPHENO:0001005", - "HP:0000707", - "HP:0011446", - "BFO:0000001", - "GO:0032501", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0001016", + "UPHENO:0087032", + "UPHENO:0087531", + "HP:0002011", + "HP:0002500", + "UPHENO:0076805", + "UPHENO:0011498", + "UPHENO:0080204", + "UPHENO:0085805", + "UPHENO:0002536", + "UPHENO:0076807", + "UPHENO:0025935", + "UPHENO:0001001", + "HP:0000118", + "UPHENO:0020584", ], - "object_label": "Short attention span (HPO)", + "object_label": "Agenesis of corpus callosum", "object_closure_label": [ - "abnormality of anatomical entity physiology", - "abnormal anatomical entity", - "Abnormality of higher mental function (HPO)", + "All", + "Abnormal cerebral morphology", + "abnormal anatomical entity morphology", + "aplasia or hypoplasia of anatomical entity", + "abnormal brain white matter morphology", + "abnormal phenotype by ontology source", + "abnormal brain commissure morphology", + "abnormal cerebral hemisphere morphology", + "abnormal dorsal telencephalic commissure morphology", + "abnormal number of anatomical enitites of type corpus callosum", + "Abnormal corpus callosum morphology", + "Abnormality of brain morphology", + "absent anatomical entity in the multicellular organism", "quality", - "multicellular organismal process", + "Phenotypic abnormality", + "abnormal number of anatomical entities of type anatomical entity in independent continuant", + "absent anatomical entity", + "abnormal nervous system", + "continuant", + "abnormal telencephalon morphology", + "abnormal nervous system morphology", "abnormal anatomical entity", + "Aplasia/Hypoplasia involving the central nervous system", + "Agenesis of corpus callosum", + "absent anatomical entity in the independent continuant", "specifically dependent continuant", + "Abnormality of the nervous system", "phenotype by ontology source", - "abnormal nervous system", - "occurrent", - "continuant", - "material anatomical entity", - "nervous system", - "All (HPO)", - "abnormal phenotype by ontology source", - "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", - "abnormal response to stimulus", - "continuant", - "abnormality of anatomical entity physiology", - "multicellular anatomical structure", - "anatomical system", - "attention behavior", + "Morphological central nervous system abnormality", + "Abnormal cerebral white matter morphology", + "abnormal brain morphology", + "abnormal number of anatomical enitites of type anatomical entity", + "Abnormal forebrain morphology", + "Aplasia/Hypoplasia of the cerebrum", + "abnormal anatomical entity morphology in the brain", + "Abnormal nervous system morphology", + "abnormal forebrain morphology", + "abnormal corpus callosum morphology", + "absent anatomical entity in the brain", + "absent corpus callosum", + "Abnormal cerebral subcortex morphology", + "aplasia or hypoplasia of corpus callosum", + "absent anatomical entity in the nervous system", + "abnormal anatomical entity", + "abnormal cerebral subcortex morphology", + "Aplasia/Hypoplasia of the corpus callosum", + "absent anatomical entity in the central nervous system", + "Thin corpus callosum", + "abnormal axon tract morphology", + "Phenotypic abnormality", + "Aplasia/Hypoplasia of the cerebral white matter", + "abnormal central nervous system morphology", + "abnormal forebrain morphology", + "aplasia or hypoplasia of telencephalon", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal cerebral hemisphere white matter morphology", + "abnormal anatomical entity morphology", + "entity", ], "object_taxon": None, "object_taxon_label": None, @@ -2051,16 +1635,16 @@ def associations(): "negated": None, "pathway": None, "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:0000736", + "has_evidence": ["ECO:0000501"], + "has_evidence_links": [{"id": "ECO:0000501", "url": "http://purl.obolibrary.org/obo/ECO_0000501"}], + "grouping_key": "MONDO:0013154🍪🍪biolink:has_phenotype🍪HP:0001274", "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": None}], + "publications": ["PMID:15894594"], + "publications_links": [{"id": "PMID:15894594", "url": "http://identifiers.org/pubmed/15894594"}], "qualifiers": [], "frequency_qualifier": "HP:0040282", "onset_qualifier": None, @@ -2071,11 +1655,11 @@ def associations(): "qualifiers_category": None, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_label": "Frequent", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -2093,178 +1677,178 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:4e02df87-842a-11ee-884f-6be035239f90", + "id": "uuid:89e159d6-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013154", + "original_subject": "OMIM:613150", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0018939", + "MONDO:0019052", + "MONDO:0018282", "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", + "MONDO:0013154", "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:0000171", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0015286", + "MONDO:0016155", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000020", + "MONDO:0700071", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", "BFO:0000001", + "MONDO:0002320", ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "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", + "disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "muscular dystrophy-dystroglycanopathy, type A", + "neuromuscular disease", + "muscle-eye-brain disease", + "skeletal muscle disorder", + "entity", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "continuant", + "myopathy", + "congenital muscular dystrophy", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome", + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "metabolic disease", + "qualitative or quantitative defects of alpha-dystroglycan", + "disease", + "myopathy caused by variation in POMT2", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0001622", + "object": "HP:0007260", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "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", - "UPHENO:0001001", + "HP:0000001", + "HP:0002060", + "HP:0100547", + "UPHENO:0081603", + "HP:0012443", + "HP:0002538", "UPHENO:0001002", - "BFO:0000020", - "UPHENO:0001003", - "BFO:0000001", + "UPHENO:0076791", + "UPHENO:0087518", + "UPHENO:0076799", + "HP:0001339", "UPHENO:0001005", - "UPHENO:0049940", - "BFO:0000015", - "UBERON:0000061", - "UBERON:0000468", + "BFO:0000001", + "UPHENO:0075696", + "HP:0000707", + "UPHENO:0001003", + "UPHENO:0076692", + "UPHENO:0049643", + "UPHENO:0076702", + "UPHENO:0015280", + "UPHENO:0081435", + "HP:0012639", + "UPHENO:0020888", + "UPHENO:0049587", + "HP:0002269", "BFO:0000002", - "UPHENO:0049440", - "BFO:0000004", - "UBERON:0000922", - "HP:0001622", - "HP:0000118", - "UPHENO:0049449", - "HP:0001787", + "BFO:0000020", + "HP:0002536", + "UPHENO:0004523", "PATO:0000001", - "UBERON:0000323", - "HP:0000001", - "UPHENO:0075949", - "GO:0032501", - "GO:0022414", - "UBERON:0010000", + "UPHENO:0049852", + "UPHENO:0087531", + "HP:0002011", + "HP:0007260", + "UPHENO:0076805", + "UPHENO:0050121", + "UPHENO:0049855", + "UPHENO:0002536", + "UPHENO:0001001", + "HP:0000118", + "UPHENO:0049634", + "UPHENO:0020584", ], - "object_label": "Premature birth (HPO)", + "object_label": "Type II lissencephaly", "object_closure_label": [ - "Phenotypic abnormality", - "specifically dependent continuant", + "All", + "Abnormal cerebral morphology", + "continuant", + "abnormal cell motility", + "abnormal anatomical entity morphology", + "Lissencephaly", + "abnormal cerebral hemisphere morphology", + "Abnormality of brain morphology", "quality", - "multicellular organismal process", - "reproductive process", + "abnormal neuron migration", "abnormal phenotype by ontology source", - "premature biological_process", + "Phenotypic abnormality", + "Abnormal cortical gyration", + "abnormal nervous system", + "Abnormality of neuronal migration", + "abnormal telencephalon morphology", + "abnormal cell migration", + "abnormal nervous system morphology", + "abnormal anatomical entity", + "Abnormality of the nervous system", "phenotype by ontology source", - "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", - "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", + "phenotype", + "Morphological central nervous system abnormality", + "Type II lissencephaly", + "abnormal brain morphology", + "abnormal cellular process", + "Abnormal forebrain morphology", + "abnormal cerebral cortex morphology", + "abnormal anatomical entity morphology in the brain", + "Abnormal nervous system morphology", + "abnormal forebrain morphology", + "Abnormal cerebral cortex morphology", + "abnormal locomotion", "abnormal anatomical entity", - "independent continuant", - "multicellular anatomical structure", - "late embryo", + "Phenotypic abnormality", + "abnormal central nervous system morphology", + "abnormal forebrain morphology", + "specifically dependent continuant", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "entity", ], "object_taxon": None, "object_taxon_label": None, @@ -2273,18 +1857,18 @@ def associations(): "negated": None, "pathway": None, "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:0001622", + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0013154🍪🍪biolink:has_phenotype🍪HP:0007260", "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": None}], + "publications": ["PMID:15894594"], + "publications_links": [{"id": "PMID:15894594", "url": "http://identifiers.org/pubmed/15894594"}], "qualifiers": [], - "frequency_qualifier": "HP:0040282", + "frequency_qualifier": "HP:0040280", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, @@ -2293,11 +1877,11 @@ def associations(): "qualifiers_category": None, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_label": "Obligate", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Obligate"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -2315,200 +1899,180 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:4e02df88-842a-11ee-884f-6be035239f90", + "id": "uuid:89e159da-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013154", + "original_subject": "OMIM:613150", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0018939", + "MONDO:0019052", + "MONDO:0018282", "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", + "MONDO:0013154", "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:0000171", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0015286", + "MONDO:0016155", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000020", + "MONDO:0700071", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", "BFO:0000001", + "MONDO:0002320", ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "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", + "disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "muscular dystrophy-dystroglycanopathy, type A", + "neuromuscular disease", + "muscle-eye-brain disease", + "skeletal muscle disorder", + "entity", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "continuant", + "myopathy", + "congenital muscular dystrophy", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome", + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "metabolic disease", + "qualitative or quantitative defects of alpha-dystroglycan", + "disease", + "myopathy caused by variation in POMT2", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0001883", + "object": "HP:0000659", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "PR:000050567", - "UBERON:0000465", - "RO:0002577", - "BFO:0000001", - "BFO:0000040", - "UBERON:0001062", - "UBERON:0000154", + "HP:0000315", + "HP:0000001", + "HP:0000234", + "UPHENO:0021670", + "HP:0000593", "UPHENO:0001002", - "BFO:0000020", - "UPHENO:0081575", - "BFO:0000002", - "UBERON:0002101", - "UBERON:0004709", - "UPHENO:0001001", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "UBERON:0000061", - "UBERON:0008784", - "UBERON:0002470", + "UPHENO:0076957", + "UPHENO:0087597", + "UPHENO:0075997", + "UPHENO:0072814", "UPHENO:0001005", - "UPHENO:0081581", + "UPHENO:0075696", + "HP:0000152", + "UPHENO:0087907", + "UPHENO:0002910", + "UPHENO:0001003", "UPHENO:0076692", - "UPHENO:0003070", - "UPHENO:0002830", - "BFO:0000004", - "UBERON:0004708", - "UBERON:0000475", - "UBERON:0000468", - "UBERON:0010709", - "HP:0001883", - "BFO:0000002", - "HP:0001760", - "HP:0040064", + "HP:0004328", + "UPHENO:0015280", + "HP:0000271", + "UPHENO:0088049", + "UPHENO:0071309", + "UPHENO:0071334", + "UPHENO:0021474", + "UPHENO:0002844", + "HP:0007700", + "BFO:0000020", + "HP:0000659", + "HP:0012372", + "UPHENO:0087472", + "HP:0000478", + "UPHENO:0087924", + "UPHENO:0002764", + "UPHENO:0003020", + "UPHENO:0002536", "PATO:0000001", - "UBERON:0002103", - "UBERON:0010707", - "UBERON:0000026", - "UBERON:0010758", - "UBERON:0006058", - "UBERON:0002387", - "HP:0002814", - "HP:0005656", + "UPHENO:0001001", + "UPHENO:0086589", "HP:0000118", - "UBERON:0015212", - "UBERON:0010538", - "HP:0000001", - "UBERON:0010000", - "UBERON:0000978", - "UBERON:0002529", + "BFO:0000002", + "UPHENO:0021038", + "UPHENO:0020584", + "BFO:0000001", ], - "object_label": "Talipes (HPO)", + "object_label": "Peters anomaly", "object_closure_label": [ + "Abnormality of the orbital region", + "All", + "Ocular anterior segment dysgenesis", + "abnormal anatomical entity morphology", + "abnormal orbital region", + "abnormally formed anatomical entity in independent continuant", + "abnormal craniocervical region", + "Abnormal eye morphology", + "abnormal face morphology", "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)", + "Phenotypic abnormality", "continuant", - "appendage", - "subdivision of organism along appendicular axis", - "Abnormality of the lower limb (HPO)", - "Phenotypic abnormality (HPO)", + "Peters anomaly", "entity", - "lateral structure", - "leg", - "limb segment", + "abnormally formed anterior chamber of eyeball", + "abnormal camera-type eye morphology", + "abnormal head", + "malformed anatomical entity", + "abnormal anterior segment of eyeball morphology", + "abnormal anatomical entity", + "Abnormality of the eye", + "abnormal camera-type eye morphology", + "phenotype by ontology source", + "phenotype", + "abnormal craniocervical region morphology", + "Abnormality of the head", + "abnormal anterior chamber of eyeball morphology", + "abnormal anterior segment of eyeball morphology", + "abnormally formed anatomical entity", + "quality", + "Abnormal anterior chamber morphology", + "Abnormality of head or neck", + "abnormal head morphology", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity", + "Abnormal anterior eye segment morphology", "Phenotypic abnormality", - "abnormal pes morphology", + "specifically dependent continuant", + "abnormal anatomical entity morphology in the independent continuant", + "Abnormality of the face", + "abnormal anterior chamber of eyeball 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", - "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, @@ -2517,16 +2081,16 @@ def associations(): "negated": None, "pathway": None, "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:0001883", + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0013154🍪🍪biolink:has_phenotype🍪HP:0000659", "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": None}], + "publications": ["PMID:15894594"], + "publications_links": [{"id": "PMID:15894594", "url": "http://identifiers.org/pubmed/15894594"}], "qualifiers": [], "frequency_qualifier": "HP:0040282", "onset_qualifier": None, @@ -2537,11 +2101,11 @@ def associations(): "qualifiers_category": None, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_label": "Frequent", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -2559,166 +2123,174 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:4e02df8e-842a-11ee-884f-6be035239f90", + "id": "uuid:89e159df-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013154", + "original_subject": "OMIM:613150", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0018939", + "MONDO:0019052", + "MONDO:0018282", "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", + "MONDO:0013154", "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:0000171", + "MONDO:0020120", "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", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0015286", + "MONDO:0016155", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000020", + "MONDO:0700071", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", + "BFO:0000001", + "MONDO:0002320", + ], + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "subject_closure_label": [ "nervous system disorder", - "heart disorder", - "myotonic dystrophy type 1", - "progressive muscular dystrophy", "musculoskeletal system disorder", - "hereditary disease", - "eye disorder", + "disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "muscular dystrophy-dystroglycanopathy, type A", + "neuromuscular disease", + "muscle-eye-brain disease", + "skeletal muscle disorder", + "entity", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "continuant", + "myopathy", + "congenital muscular dystrophy", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome", + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "metabolic disease", + "qualitative or quantitative defects of alpha-dystroglycan", + "disease", + "myopathy caused by variation in POMT2", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0011098", + "object": "HP:0002951", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "UBERON:0000465", - "UPHENO:0082875", - "HP:0011442", - "HP:0002186", - "UPHENO:0004523", - "BFO:0000001", - "BFO:0000040", - "UBERON:0001062", + "HP:0000001", + "HP:0012443", + "HP:0011283", + "HP:0002951", "UPHENO:0001002", + "UPHENO:0076791", + "UPHENO:0081601", + "HP:0001317", + "UPHENO:0080079", + "UPHENO:0076720", + "UPHENO:0081573", + "UPHENO:0080089", + "BFO:0000001", + "UPHENO:0075696", + "HP:0002977", + "HP:0000707", + "UPHENO:0001003", + "UPHENO:0076692", + "UPHENO:0076702", + "UPHENO:0086932", + "UPHENO:0015280", + "UPHENO:0020013", + "UPHENO:0081435", + "HP:0012639", + "HP:0002334", "BFO:0000002", - "UPHENO:0001001", "BFO:0000020", - "UPHENO:0001003", + "UPHENO:0086586", + "UPHENO:0004523", + "PATO:0000001", + "HP:0011282", + "HP:0002011", + "UPHENO:0076805", "UPHENO:0002536", - "BFO:0000001", - "UBERON:0000061", - "UPHENO:0075696", + "UPHENO:0001001", "UPHENO:0001005", - "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:0000467", - "UBERON:0001016", + "HP:0006817", + "HP:0007360", + "UPHENO:0020584", ], - "object_label": "Speech apraxia (HPO)", + "object_label": "Partial absence of cerebellar vermis", "object_closure_label": [ - "abnormality of anatomical entity physiology", - "specifically dependent continuant", - "Abnormality of higher mental function (HPO)", + "All", + "continuant", + "Aplasia/Hypoplasia of the cerebellar vermis", + "Aplasia/Hypoplasia of the cerebellum", + "aplasia or hypoplasia of cerebellum", + "abnormal anatomical entity morphology", + "aplasia or hypoplasia of anatomical entity", + "abnormal cerebellum morphology", + "abnormal cerebellar vermis morphology", + "Abnormality of brain morphology", + "Abnormal metencephalon morphology", "quality", + "Abnormal hindbrain morphology", + "Phenotypic abnormality", + "abnormal cerebellar cortex morphology", + "abnormal nervous system", + "Abnormal cerebellum morphology", + "abnormal nervous system morphology", + "abnormal hindbrain morphology", "abnormal anatomical entity", - "abnormal phenotype by ontology source", + "Aplasia/Hypoplasia involving the central nervous system", + "Abnormality of the nervous system", "phenotype by ontology source", + "phenotype", + "abnormal phenotype by ontology source", + "Morphological central nervous system abnormality", + "abnormal brain morphology", + "abnormal anatomical entity morphology in the brain", + "Abnormal nervous system morphology", + "Partial absence of cerebellar vermis", "abnormal anatomical entity", - "abnormal nervous system", - "continuant", - "material anatomical entity", - "nervous system", - "All (HPO)", - "continuant", - "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "entity", + "Abnormal cerebellar vermis morphology", "Phenotypic abnormality", - "abnormality of nervous system physiology", - "anatomical structure", - "multicellular organism", - "phenotype", - "Speech apraxia (HPO)", + "abnormal central nervous system morphology", + "abnormal metencephalon morphology", + "specifically dependent continuant", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal hindbrain morphology", + "abnormal anatomical entity morphology", "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", ], "object_taxon": None, "object_taxon_label": None, @@ -2727,16 +2299,16 @@ def associations(): "negated": None, "pathway": None, "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:0011098", + "has_evidence": ["ECO:0000501"], + "has_evidence_links": [{"id": "ECO:0000501", "url": "http://purl.obolibrary.org/obo/ECO_0000501"}], + "grouping_key": "MONDO:0013154🍪🍪biolink:has_phenotype🍪HP:0002951", "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": None}], + "publications": ["PMID:15894594"], + "publications_links": [{"id": "PMID:15894594", "url": "http://identifiers.org/pubmed/15894594"}], "qualifiers": [], "frequency_qualifier": "HP:0040282", "onset_qualifier": None, @@ -2747,11 +2319,11 @@ def associations(): "qualifiers_category": None, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_label": "Frequent", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -2769,170 +2341,186 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:4e02df90-842a-11ee-884f-6be035239f90", + "id": "uuid:89e159e0-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013154", + "original_subject": "OMIM:613150", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0018939", + "MONDO:0019052", + "MONDO:0018282", "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", + "MONDO:0013154", "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:0000171", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0015286", + "MONDO:0016155", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000020", + "MONDO:0700071", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", "BFO:0000001", + "MONDO:0002320", ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "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", + "disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "muscular dystrophy-dystroglycanopathy, type A", + "neuromuscular disease", + "muscle-eye-brain disease", + "skeletal muscle disorder", + "entity", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "continuant", + "myopathy", + "congenital muscular dystrophy", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome", + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "metabolic disease", + "qualitative or quantitative defects of alpha-dystroglycan", + "disease", + "myopathy caused by variation in POMT2", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0011710", + "object": "HP:0000175", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "UPHENO:0002536", - "PR:000050567", - "UBERON:0000465", - "UPHENO:0082875", - "UPHENO:0080362", - "BFO:0000040", - "UBERON:0001062", - "HP:0030956", - "HP:0001626", - "HP:0031546", - "BFO:0000002", - "UPHENO:0001001", + "HP:0000001", + "HP:0000163", + "HP:0000234", + "UPHENO:0033635", "UPHENO:0001002", - "UPHENO:0001003", + "UPHENO:0033572", + "UPHENO:0087585", + "UPHENO:0076786", + "UPHENO:0076760", + "HP:0025033", + "HP:0002664", + "HP:0000175", + "HP:0000202", + "BFO:0000001", "UPHENO:0075696", - "UPHENO:0001005", - "BFO:0000020", - "HP:0011710", - "UPHENO:0002406", - "BFO:0000004", - "UBERON:0004535", - "UBERON:0000061", - "UBERON:0000468", - "HP:0012722", - "HP:0000118", + "HP:0000152", + "UPHENO:0087907", + "UPHENO:0002910", + "UPHENO:0076800", + "UPHENO:0001003", + "UPHENO:0076692", + "UPHENO:0002828", + "UPHENO:0002833", + "HP:0000309", + "UPHENO:0015280", + "HP:0000271", + "HP:0025031", + "UPHENO:0076803", + "UPHENO:0002844", "BFO:0000002", - "UPHENO:0002332", + "BFO:0000020", + "HP:0011793", + "UPHENO:0086824", + "HP:0000174", "PATO:0000001", - "HP:0000001", - "HP:0011025", - "BFO:0000001", - "BFO:0000001", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0001009", + "UPHENO:0087472", + "UPHENO:0002764", + "HP:0031816", + "HP:0000153", + "UPHENO:0002536", + "UPHENO:0001001", + "UPHENO:0086589", + "UPHENO:0001005", + "HP:0000118", + "UPHENO:0075655", + "UPHENO:0020584", ], - "object_label": "Bundle branch block (HPO)", + "object_label": "Cleft palate", "object_closure_label": [ - "abnormality of anatomical entity physiology", - "Phenotypic abnormality", - "Abnormal cardiovascular system physiology (HPO)", + "All", + "Abnormal oral cavity morphology", + "continuant", + "abnormal opening of the anatomical entity", + "Orofacial cleft", + "abnormal anatomical entity morphology", + "abnormal craniocervical region", + "Neoplasm", + "Cleft palate", "quality", - "entity", + "abnormal face morphology", + "Phenotypic abnormality", + "Abnormality of digestive system morphology", + "Neoplasm by anatomical site", + "abnormal roof of mouth morphology", + "Abnormal palate morphology", + "abnormal head", + "abnormal oral cavity morphology", + "abnormal secondary palate morphology", "abnormal anatomical entity", - "abnormal phenotype by ontology source", + "abnormal digestive system", + "Abnormal midface morphology", "phenotype by ontology source", - "continuant", - "protein-containing material entity", - "material anatomical entity", - "circulatory system", - "All (HPO)", - "Cardiac conduction abnormality (HPO)", - "Phenotypic abnormality (HPO)", - "continuant", - "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 craniocervical region morphology", + "abnormal phenotype by ontology source", + "Abnormal oral morphology", + "Abnormality of the mouth", + "Abnormality of the head", + "abnormal incomplete closing of the secondary palate", + "Abnormality of head or neck", + "abnormal head morphology", + "abnormal face", + "abnormal mouth morphology", "abnormal anatomical entity", - "Heart block (HPO)", - "multicellular anatomical structure", - "anatomical system", + "Abnormality of the digestive system", + "abnormal digestive system morphology", + "abnormal mouth", + "Phenotypic abnormality", + "abnormal incomplete closing of the anatomical entity", + "abnormal midface morphology", + "specifically dependent continuant", + "abnormal anatomical entity morphology in the independent continuant", + "Abnormality of the face", + "abnormal anatomical entity morphology", + "entity", ], "object_taxon": None, "object_taxon_label": None, @@ -2941,16 +2529,16 @@ def associations(): "negated": None, "pathway": None, "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", + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0013154🍪🍪biolink:has_phenotype🍪HP:0000175", "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": None}], + "publications": ["PMID:15894594"], + "publications_links": [{"id": "PMID:15894594", "url": "http://identifiers.org/pubmed/15894594"}], "qualifiers": [], "frequency_qualifier": "HP:0040282", "onset_qualifier": None, @@ -2961,11 +2549,11 @@ def associations(): "qualifiers_category": None, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_label": "Frequent", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": ["Frequency (HPO)", "Frequent (HPO)", "All (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -2983,170 +2571,180 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:4e02dfa2-842a-11ee-884f-6be035239f90", + "id": "uuid:89e159e3-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013154", + "original_subject": "OMIM:613150", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0018939", + "MONDO:0019052", + "MONDO:0018282", "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", + "MONDO:0013154", "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:0000171", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0015286", + "MONDO:0016155", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000020", + "MONDO:0700071", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", "BFO:0000001", + "MONDO:0002320", ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "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", + "disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "muscular dystrophy-dystroglycanopathy, type A", + "neuromuscular disease", + "muscle-eye-brain disease", + "skeletal muscle disorder", + "entity", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "continuant", + "myopathy", + "congenital muscular dystrophy", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome", + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "metabolic disease", + "qualitative or quantitative defects of alpha-dystroglycan", + "disease", + "myopathy caused by variation in POMT2", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0001513", + "object": "HP:0001321", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "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:0000001", + "HP:0012443", + "HP:0011283", "UPHENO:0001002", - "UPHENO:0001003", + "UPHENO:0081099", + "UPHENO:0076791", + "UPHENO:0081601", + "HP:0001317", + "UPHENO:0080079", + "UPHENO:0076720", + "HP:0001321", + "UPHENO:0081091", + "UPHENO:0080089", "BFO:0000001", - "UBERON:0000061", "UPHENO:0075696", - "UPHENO:0001005", - "BFO:0000020", - "BFO:0000015", - "BFO:0000004", - "HP:0001507", + "HP:0002977", + "HP:0000707", + "UPHENO:0001003", + "UPHENO:0076692", + "UPHENO:0076702", + "UPHENO:0086932", + "UPHENO:0015280", + "UPHENO:0020013", + "UPHENO:0081435", + "HP:0012639", + "UPHENO:0012541", + "UPHENO:0068971", "BFO:0000002", + "BFO:0000020", + "UPHENO:0081790", + "UPHENO:0004523", + "HP:0011282", + "HP:0002011", + "UPHENO:0076805", + "UPHENO:0068984", "UPHENO:0002536", - "HP:0000118", - "UPHENO:0010795", - "HP:0004323", - "UPHENO:0010763", "PATO:0000001", - "HP:0000001", - "HP:0004324", - "UPHENO:0008312", - "GO:0040007", - "UBERON:0010000", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0000118", + "UPHENO:0075195", + "HP:0007360", + "UPHENO:0020584", ], - "object_label": "Obesity (HPO)", + "object_label": "Cerebellar hypoplasia", "object_closure_label": [ + "All", + "continuant", + "abnormal size of anatomical entity", + "Aplasia/Hypoplasia of the cerebellum", + "anatomical entity hypoplasia", + "aplasia or hypoplasia of cerebellum", + "abnormal anatomical entity morphology", + "aplasia or hypoplasia of anatomical entity", + "abnormal cerebellum morphology", + "Cerebellar hypoplasia", + "Abnormality of brain morphology", + "Abnormal metencephalon morphology", + "Abnormal hindbrain morphology", "Phenotypic abnormality", + "anatomical entity hypoplasia in independent continuant", + "abnormal nervous system", + "decreased size of the anatomical entity", + "Abnormal cerebellum morphology", + "abnormal nervous system morphology", + "abnormal hindbrain morphology", "abnormal anatomical entity", - "increased multicellular organism mass", + "Aplasia/Hypoplasia involving the central nervous system", + "Abnormality of the nervous system", + "phenotype by ontology source", + "phenotype", + "abnormal phenotype by ontology source", + "Morphological central nervous system abnormality", + "abnormal brain morphology", + "abnormal anatomical entity morphology in the brain", + "Abnormal nervous system morphology", "quality", - "growth", + "decreased size of the cerebellum", "abnormal anatomical entity", - "abnormal phenotype by ontology source", - "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", - "biological_process", - "increased anatomical entity mass", + "decreased size of the anatomical entity in the independent continuant", + "Phenotypic abnormality", + "cerebellum hypoplasia", + "abnormal central nervous system morphology", + "abnormal metencephalon morphology", "specifically dependent continuant", - "anatomical structure", - "phenotype", - "Increased body weight (HPO)", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal hindbrain morphology", + "abnormal anatomical entity morphology", "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", ], "object_taxon": None, "object_taxon_label": None, @@ -3155,18 +2753,18 @@ def associations(): "negated": None, "pathway": None, "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:0001513", + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0013154🍪🍪biolink:has_phenotype🍪HP:0001321", "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": None}], + "publications": ["PMID:15894594"], + "publications_links": [{"id": "PMID:15894594", "url": "http://identifiers.org/pubmed/15894594"}], "qualifiers": [], - "frequency_qualifier": "HP:0040284", + "frequency_qualifier": "HP:0040282", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, @@ -3175,11 +2773,11 @@ def associations(): "qualifiers_category": None, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Very rare (HPO)", + "frequency_qualifier_label": "Frequent", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040279", "HP:0000001", "HP:0040284"], - "frequency_qualifier_closure_label": ["Very rare (HPO)", "Frequency (HPO)", "All (HPO)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -3197,186 +2795,130 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:4e02df92-842a-11ee-884f-6be035239f90", + "id": "uuid:89e159e5-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013154", + "original_subject": "OMIM:613150", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0018939", + "MONDO:0019052", + "MONDO:0018282", "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", + "MONDO:0013154", "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:0000171", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0015286", + "MONDO:0016155", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000020", + "MONDO:0700071", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", "BFO:0000001", + "MONDO:0002320", ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "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", + "disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "muscular dystrophy-dystroglycanopathy, type A", + "neuromuscular disease", + "muscle-eye-brain disease", + "skeletal muscle disorder", + "entity", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "continuant", + "myopathy", + "congenital muscular dystrophy", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome", + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "metabolic disease", + "qualitative or quantitative defects of alpha-dystroglycan", + "disease", + "myopathy caused by variation in POMT2", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0000729", + "object": "HP:0003560", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "UPHENO:0002536", + "HP:0000001", + "UPHENO:0001002", + "UPHENO:0076710", + "HP:0003011", "BFO:0000001", - "GO:0008150", - "UBERON:0000465", - "NBO:0000313", - "UPHENO:0082875", - "UPHENO:0004523", - "UPHENO:0049587", - "BFO:0000040", - "GO:0007610", - "UBERON:0000468", - "BFO:0000020", - "BFO:0000003", + "UPHENO:0001003", + "UPHENO:0076692", + "HP:0011805", + "HP:0003560", "BFO:0000002", + "BFO:0000020", + "PATO:0000001", + "UPHENO:0002816", + "UPHENO:0002536", "UPHENO:0001001", - "UPHENO:0049622", - "UPHENO:0001002", - "UPHENO:0001003", - "BFO:0000001", - "UBERON:0001062", - "UBERON:0000061", - "UPHENO:0075696", "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:0079826", - "PATO:0000001", - "HP:0000001", - "HP:0000707", - "HP:0011446", - "GO:0032501", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0001016", + "HP:0033127", ], - "object_label": "Autistic behavior (HPO)", + "object_label": "Muscular dystrophy", "object_closure_label": [ - "abnormality of anatomical entity physiology", - "Phenotypic abnormality", - "Abnormality of higher mental function (HPO)", + "All", + "continuant", + "Abnormality of the musculoskeletal system", + "abnormal anatomical entity morphology", "quality", - "multicellular organismal process", - "abnormal anatomical entity", - "abnormal phenotype by ontology source", - "specifically dependent continuant", + "Phenotypic abnormality", + "Abnormality of the musculature", + "abnormal muscle organ morphology", + "Abnormal skeletal muscle morphology", + "Muscular dystrophy", "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", "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 phenotype by ontology source", + "abnormal musculature", "abnormal anatomical entity", - "independent continuant", - "multicellular anatomical structure", - "anatomical system", + "Phenotypic abnormality", + "specifically dependent continuant", + "entity", ], "object_taxon": None, "object_taxon_label": None, @@ -3385,18 +2927,18 @@ def associations(): "negated": None, "pathway": None, "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:0000729", + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0013154🍪🍪biolink:has_phenotype🍪HP:0003560", "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": None}], + "publications": ["PMID:15894594"], + "publications_links": [{"id": "PMID:15894594", "url": "http://identifiers.org/pubmed/15894594"}], "qualifiers": [], - "frequency_qualifier": "HP:0040283", + "frequency_qualifier": "HP:0040280", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, @@ -3405,11 +2947,11 @@ def associations(): "qualifiers_category": None, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_label": "Obligate", "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)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Obligate"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -3427,194 +2969,176 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:4e02df94-842a-11ee-884f-6be035239f90", + "id": "uuid:89e159e8-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013154", + "original_subject": "OMIM:613150", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0018939", + "MONDO:0019052", + "MONDO:0018282", "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", + "MONDO:0013154", "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:0000171", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0015286", + "MONDO:0016155", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000020", + "MONDO:0700071", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", "BFO:0000001", + "MONDO:0002320", ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "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", + "disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "muscular dystrophy-dystroglycanopathy, type A", + "neuromuscular disease", + "muscle-eye-brain disease", + "skeletal muscle disorder", + "entity", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "continuant", + "myopathy", + "congenital muscular dystrophy", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome", + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "metabolic disease", + "qualitative or quantitative defects of alpha-dystroglycan", + "disease", + "myopathy caused by variation in POMT2", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0000752", + "object": "HP:0000568", "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:0004523", - "BFO:0000040", - "UBERON:0001062", - "GO:0007610", - "NBO:0000568", - "BFO:0000003", - "BFO:0000002", - "UPHENO:0001001", - "UPHENO:0049622", + "HP:0000315", + "HP:0000001", + "UPHENO:0075219", + "HP:0000234", + "UPHENO:0075997", + "UPHENO:0080079", + "UPHENO:0001005", "UPHENO:0001002", - "UPHENO:0001003", - "BFO:0000001", - "UBERON:0000061", - "HP:0000752", + "BFO:0000002", "UPHENO:0075696", - "UPHENO:0001005", + "HP:0000152", + "UPHENO:0087907", + "UPHENO:0002910", + "UPHENO:0001003", + "UPHENO:0076692", + "HP:0000568", + "UPHENO:0015280", + "HP:0000271", + "UPHENO:0012541", + "UPHENO:0080209", + "UPHENO:0068971", + "UPHENO:0021474", + "UPHENO:0002844", "BFO:0000020", - "UPHENO:0002433", - "HP:0012638", - "NBO:0000644", - "BFO:0000015", - "BFO:0000004", - "UBERON:0000468", - "UPHENO:0049586", - "BFO:0000002", + "HP:0008056", + "PATO:0000001", + "HP:0012372", + "UPHENO:0087472", + "HP:0000478", + "HP:0100887", + "UPHENO:0087924", + "UPHENO:0002764", + "UPHENO:0003020", "UPHENO:0002536", - "HP:0000708", - "NBO:0000243", - "UPHENO:0080585", + "UPHENO:0069523", + "UPHENO:0001001", + "UPHENO:0086589", "HP:0000118", - "UPHENO:0002332", - "UPHENO:0079826", - "PATO:0000001", - "HP:0000001", - "HP:0000707", - "HP:0011446", + "UPHENO:0075195", + "UPHENO:0020584", "BFO:0000001", - "GO:0032501", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0001016", ], - "object_label": "Hyperactivity (HPO)", + "object_label": "Microphthalmia", "object_closure_label": [ - "abnormality of anatomical entity physiology", - "Phenotypic abnormality", - "abnormal anatomical entity", - "Abnormality of higher mental function (HPO)", + "Abnormality of the orbital region", + "All", + "abnormal size of eyeball of camera-type eye", + "abnormal size of anatomical entity", + "abnormal anatomical entity morphology", + "abnormal orbital region", + "aplasia or hypoplasia of anatomical entity", + "abnormal craniocervical region", "quality", - "multicellular organismal process", - "Hyperactivity (HPO)", - "abnormal anatomical entity", + "Abnormal eye morphology", + "abnormal face 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", + "Phenotypic abnormality", + "Phenotypic abnormality", + "Aplasia/Hypoplasia affecting the eye", "entity", - "hyperactivity", - "biological_process", - "specifically dependent continuant", - "abnormality of nervous system physiology", - "anatomical structure", - "multicellular organism", + "aplasia or hypoplasia of eyeball of camera-type eye", + "decreased size of the anatomical entity", + "abnormal camera-type eye morphology", + "abnormal head", + "continuant", + "abnormal anatomical entity", + "Abnormality of the eye", + "Abnormality of globe size", + "abnormal camera-type eye morphology", + "Microphthalmia", + "phenotype by ontology source", "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", + "abnormal craniocervical region morphology", + "Abnormality of the head", + "Abnormality of head or neck", + "abnormal head morphology", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity", + "decreased size of the eyeball of camera-type eye", + "decreased size of the anatomical entity in the independent continuant", + "specifically dependent continuant", + "abnormal anatomical entity morphology in the independent continuant", + "Abnormality of the face", + "abnormal anatomical entity morphology", ], "object_taxon": None, "object_taxon_label": None, @@ -3623,18 +3147,18 @@ def associations(): "negated": None, "pathway": None, "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:0000752", + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0013154🍪🍪biolink:has_phenotype🍪HP:0000568", "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": None}], + "publications": ["PMID:15894594"], + "publications_links": [{"id": "PMID:15894594", "url": "http://identifiers.org/pubmed/15894594"}], "qualifiers": [], - "frequency_qualifier": "HP:0040283", + "frequency_qualifier": "HP:0040282", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, @@ -3643,11 +3167,11 @@ def associations(): "qualifiers_category": None, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_label": "Frequent", "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)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -3665,156 +3189,194 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:4e02df96-842a-11ee-884f-6be035239f90", + "id": "uuid:89e159ea-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013154", + "original_subject": "OMIM:613150", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0018939", + "MONDO:0019052", + "MONDO:0018282", "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", + "MONDO:0013154", "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:0000171", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0015286", + "MONDO:0016155", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000020", + "MONDO:0700071", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", "BFO:0000001", + "MONDO:0002320", ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "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", + "disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "muscular dystrophy-dystroglycanopathy, type A", + "neuromuscular disease", + "muscle-eye-brain disease", + "skeletal muscle disorder", + "entity", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "continuant", + "myopathy", + "congenital muscular dystrophy", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome", + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "metabolic disease", + "qualitative or quantitative defects of alpha-dystroglycan", + "disease", + "myopathy caused by variation in POMT2", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0001558", + "object": "HP:0000204", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0001197", - "UBERON:0000465", - "HP:0034059", - "BFO:0000040", - "UBERON:0001062", - "BFO:0000002", - "UPHENO:0001001", + "HP:0000001", + "HP:0000163", + "HP:0000177", + "HP:0000234", + "UPHENO:0087551", + "UPHENO:0033572", + "UPHENO:0087585", + "UPHENO:0076786", "UPHENO:0001002", - "BFO:0000020", - "UPHENO:0001003", + "BFO:0000002", + "HP:0025033", + "HP:0002664", + "UPHENO:0033642", + "HP:0000202", "BFO:0000001", + "UPHENO:0075696", + "HP:0000152", + "UPHENO:0087907", + "UPHENO:0002910", + "UPHENO:0001003", + "UPHENO:0076692", + "UPHENO:0020955", + "UPHENO:0002828", + "UPHENO:0002833", + "HP:0000309", + "HP:0410030", + "BFO:0000020", + "UPHENO:0015280", + "HP:0000271", + "HP:0000159", + "HP:0025031", + "UPHENO:0076803", + "UPHENO:0002844", + "HP:0011793", + "UPHENO:0087472", + "UPHENO:0076800", + "UPHENO:0033637", "UPHENO:0001005", - "HP:0001558", - "BFO:0000004", - "UBERON:0000061", - "UBERON:0000468", - "BFO:0000002", + "UPHENO:0087554", + "HP:0000204", + "UPHENO:0002764", + "HP:0031816", + "HP:0000153", "UPHENO:0002536", - "HP:0001557", - "UBERON:0000922", - "HP:0000118", - "HP:0034057", "PATO:0000001", - "UBERON:0000323", - "HP:0000001", - "UPHENO:0075949", - "BFO:0000001", - "UBERON:0010000", + "UPHENO:0001001", + "UPHENO:0086589", + "HP:0000118", + "UPHENO:0075655", + "UPHENO:0020584", ], - "object_label": "Decreased fetal movement (HPO)", + "object_label": "Cleft upper lip", "object_closure_label": [ + "All", + "Abnormal oral cavity morphology", + "Abnormal upper lip morphology", + "abnormal opening of the anatomical entity", + "Orofacial cleft", + "abnormal anatomical entity morphology", + "abnormal lip morphology", + "abnormal phenotype by ontology source", + "abnormal upper lip morphology", + "Cleft upper lip", + "abnormal craniocervical region", + "Neoplasm", + "abnormal incomplete closing of the upper lip", + "abnormal lip morphology", + "abnormal face morphology", "Phenotypic abnormality", - "specifically dependent continuant", + "Phenotypic abnormality", + "Abnormality of digestive system morphology", + "Neoplasm by anatomical site", + "abnormal head", + "continuant", + "abnormal oral cavity morphology", "abnormal anatomical entity", - "quality", - "abnormal phenotype by ontology source", + "abnormal mouth morphology", + "abnormal incomplete closing of the lip", + "abnormal digestive system", + "Abnormal midface morphology", + "Cleft lip", + "specifically dependent continuant", "phenotype by ontology source", - "continuant", - "material anatomical entity", - "All (HPO)", - "continuant", - "embryo", - "Phenotypic abnormality (HPO)", - "abnormal late embryo", - "Fetal anomaly (HPO)", - "entity", - "entity", - "Decreased fetal movement (HPO)", - "multicellular organism", + "Abnormal lip morphology", "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", + "abnormal craniocervical region morphology", + "Abnormal oral morphology", + "Abnormality of the mouth", + "Abnormality of the head", + "quality", + "Abnormality of head or neck", + "abnormal head morphology", + "abnormal face", + "abnormal anatomical entity", + "Abnormality of the digestive system", + "abnormal digestive system morphology", + "abnormal mouth", + "abnormal incomplete closing of the anatomical entity", + "abnormal midface morphology", + "abnormal anatomical entity morphology in the independent continuant", + "Abnormality of the face", + "abnormal anatomical entity morphology", + "entity", ], "object_taxon": None, "object_taxon_label": None, @@ -3823,18 +3385,18 @@ def associations(): "negated": None, "pathway": None, "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:0001558", + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0013154🍪🍪biolink:has_phenotype🍪HP:0000204", "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": None}], + "publications": ["PMID:15894594"], + "publications_links": [{"id": "PMID:15894594", "url": "http://identifiers.org/pubmed/15894594"}], "qualifiers": [], - "frequency_qualifier": "HP:0040283", + "frequency_qualifier": "HP:0040282", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, @@ -3843,11 +3405,11 @@ def associations(): "qualifiers_category": None, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_label": "Frequent", "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)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -3865,158 +3427,172 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:4e02df97-842a-11ee-884f-6be035239f90", + "id": "uuid:89e159ed-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013154", + "original_subject": "OMIM:613150", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0018939", + "MONDO:0019052", + "MONDO:0018282", "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", + "MONDO:0013154", "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:0000171", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0015286", + "MONDO:0016155", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000020", + "MONDO:0700071", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", "BFO:0000001", + "MONDO:0002320", ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "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", + "disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "muscular dystrophy-dystroglycanopathy, type A", + "neuromuscular disease", + "muscle-eye-brain disease", + "skeletal muscle disorder", + "entity", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "continuant", + "myopathy", + "congenital muscular dystrophy", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome", + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "metabolic disease", + "qualitative or quantitative defects of alpha-dystroglycan", + "disease", + "myopathy caused by variation in POMT2", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0001561", + "object": "HP:0003557", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0001197", - "UPHENO:0075852", - "UPHENO:0002536", - "UBERON:0000465", - "BFO:0000001", - "BFO:0000040", - "BFO:0000002", - "UPHENO:0001001", + "HP:0000001", + "HP:0004303", + "HP:0025461", + "UPHENO:0088180", + "UPHENO:0086172", "UPHENO:0001002", - "UPHENO:0001003", - "BFO:0000001", - "UBERON:0001062", - "UBERON:0000061", - "UBERON:0000463", + "HP:0003557", + "UPHENO:0076710", + "UPHENO:0084928", + "UPHENO:0085097", "UPHENO:0001005", + "BFO:0000002", + "HP:0003011", + "UPHENO:0006889", + "UPHENO:0075696", + "UPHENO:0080626", + "UPHENO:0001003", + "UPHENO:0076692", + "UPHENO:0077801", + "UPHENO:0085135", + "HP:0011805", "BFO:0000020", - "BFO:0000004", - "UBERON:0000173", - "UBERON:0000468", - "HP:0001561", - "UBERON:0000922", - "HP:0000118", + "UPHENO:0015280", + "HP:0012084", + "UPHENO:0086462", + "UPHENO:0087047", + "HP:0025354", + "UPHENO:0085099", + "UPHENO:0002816", + "UPHENO:0002536", "PATO:0000001", - "UBERON:0000323", - "HP:0000001", - "BFO:0000002", - "UPHENO:0075949", - "HP:0001560", - "UBERON:0010000", + "UPHENO:0001001", + "UPHENO:0067691", + "HP:0000118", + "UPHENO:0075195", + "HP:0033127", + "UPHENO:0086457", + "UPHENO:0020584", + "BFO:0000001", ], - "object_label": "Polyhydramnios (HPO)", + "object_label": "Increased variability in muscle fiber diameter", "object_closure_label": [ - "Phenotypic abnormality", - "Abnormality of the amniotic fluid (HPO)", - "quality", + "All", + "Abnormal muscle fiber morphology", + "abnormal size of anatomical entity", + "Abnormality of the musculoskeletal system", + "abnormal anatomical entity morphology", + "abnormal size of cell", + "abnormal cell morphology", + "abnormal muscle cell morphology", + "abnormal skeletal muscle tissue morphology", + "abnormal cellular_component", + "abnormal cell of skeletal muscle morphology", "abnormal phenotype by ontology source", - "phenotype by ontology source", - "continuant", - "material anatomical entity", - "All (HPO)", - "embryo", - "Phenotypic abnormality (HPO)", - "abnormal late embryo", + "Phenotypic abnormality", + "Abnormality of the musculature", + "Abnormality of skeletal muscle fiber size", + "abnormal size of skeletal muscle fiber", "entity", + "continuant", + "Increased variability in muscle fiber diameter", + "abnormal muscle organ morphology", + "abnormal anatomical entity", + "Abnormal skeletal muscle morphology", "specifically dependent continuant", - "anatomical entity", - "anatomical structure", - "organism substance", - "amniotic fluid", - "multicellular organism", + "phenotype by ontology source", "phenotype", - "continuant", - "entity", - "independent continuant", - "Abnormality of prenatal development or birth (HPO)", - "abnormal amniotic fluid", - "material entity", - "Polyhydramnios (HPO)", + "abnormal morphology of cellular_component", + "Abnormal cellular phenotype", + "quality", + "abnormal cell", + "abnormal size of cellular_component", + "Abnormal cell morphology", + "abnormal cell of skeletal muscle morphology", + "abnormal musculature", "abnormal anatomical entity", - "multicellular anatomical structure", - "late embryo", + "abnormal myotube morphology", + "Phenotypic abnormality", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal size of cell of skeletal muscle", + "abnormal anatomical entity morphology", ], "object_taxon": None, "object_taxon_label": None, @@ -4025,18 +3601,18 @@ def associations(): "negated": None, "pathway": None, "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:0001561", + "has_evidence": ["ECO:0000501"], + "has_evidence_links": [{"id": "ECO:0000501", "url": "http://purl.obolibrary.org/obo/ECO_0000501"}], + "grouping_key": "MONDO:0013154🍪🍪biolink:has_phenotype🍪HP:0003557", "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": None}], + "publications": ["PMID:15894594"], + "publications_links": [{"id": "PMID:15894594", "url": "http://identifiers.org/pubmed/15894594"}], "qualifiers": [], - "frequency_qualifier": "HP:0040283", + "frequency_qualifier": "HP:0040280", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, @@ -4045,11 +3621,11 @@ def associations(): "qualifiers_category": None, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_label": "Obligate", "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)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Obligate"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -4067,296 +3643,158 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:4e02df98-842a-11ee-884f-6be035239f90", + "id": "uuid:89ed09a8-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0011925", + "original_subject": "OMIM:607855", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", "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:0100228", "MONDO:0019056", - "MONDO:0004994", - "MONDO:0004995", - "MONDO:0700223", - "MONDO:0003382", - "BFO:0000016", + "BFO:0000001", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", - "BFO:0000001", + "MONDO:0019950", + "BFO:0000017", + "MONDO:0020121", + "BFO:0000002", + "BFO:0000020", + "MONDO:0011925", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0700223", + "MONDO:0002081", + "MONDO:0002320", ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "congenital merosin-deficient muscular dystrophy 1A", "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", + "continuant", "musculoskeletal system disorder", - "hereditary disease", - "eye disorder", + "disease", + "LAMA2-related muscular dystrophy", + "congenital merosin-deficient muscular dystrophy 1A", + "neuromuscular disease", + "skeletal muscle disorder", + "congenital nervous system disorder", "muscular dystrophy", + "myopathy", + "congenital muscular dystrophy", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome", + "human disease", + "hereditary skeletal muscle disorder", + "disposition", + "disease", + "hereditary disease", + "muscle tissue disorder", + "specifically dependent continuant", + "entity", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0001643", + "object": "HP:0001371", "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", + "HP:0000001", + "HP:0034430", + "HP:0000924", + "HP:0011843", + "UPHENO:0082875", + "UPHENO:0081440", + "UPHENO:0076710", + "UPHENO:0088186", + "HP:0001371", + "UPHENO:0001005", "BFO:0000002", - "UBERON:0013768", - "UBERON:0003509", - "UBERON:0003513", - "UBERON:0011695", - "UBERON:0004716", - "UBERON:0004145", - "UBERON:0005985", - "UBERON:0002049", - "UBERON:0002201", - "UBERON:0006876", - "UPHENO:0001001", + "HP:0003011", + "UPHENO:0076703", + "UPHENO:0002332", "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "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:0000477", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0004111", - "UBERON:0004573", - "UBERON:0003498", - "HP:0011603", - "UPHENO:0020351", - "HP:0030680", - "UPHENO:0076765", - "BFO:0000002", - "HP:0025015", - "HP:0002597", - "UPHENO:0076810", - "HP:0033353", + "HP:0003549", + "HP:0011842", + "HP:0011805", + "UPHENO:0001002", + "UPHENO:0021425", + "UPHENO:0015280", + "UPHENO:0002964", + "UPHENO:0046759", + "UPHENO:0002712", + "UPHENO:0012541", + "UPHENO:0068971", + "BFO:0000020", + "UPHENO:0031839", + "UPHENO:0046505", + "UPHENO:0075696", + "UPHENO:0087888", + "HP:0034392", + "UPHENO:0002816", + "UPHENO:0002536", "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", + "UPHENO:0001001", + "HP:0011729", + "HP:0100261", "HP:0000118", - "UPHENO:0075655", + "UPHENO:0075195", + "HP:0033127", "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", + "BFO:0000001", ], - "object_label": "Patent ductus arteriosus (HPO)", + "object_label": "Flexion contracture", "object_closure_label": [ - "abnormal blood vessel morphology", - "abnormal anatomical entity", - "specifically dependent continuant", - "phenotype by ontology source", + "All", + "abnormal size of anatomical entity", + "Abnormality of the musculoskeletal system", + "abnormal anatomical entity morphology", + "Flexion contracture", + "decreased length of anatomical entity", "abnormal anatomical entity", - "continuant", - "protein-containing material entity", - "material anatomical entity", - "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", + "Phenotypic abnormality", + "Abnormality of the musculature", + "abnormality of anatomical entity physiology", + "decreased length of anatomical entity in independent continuant", "entity", - "structure with developmental contribution from neural crest", - "thoracic cavity element", - "primary circulatory organ", - "abnormal coronary vessel morphology", - "Abnormality of the cardiovascular system (HPO)", + "decreased size of the anatomical entity", + "continuant", + "abnormality of musculoskeletal system physiology", + "abnormal muscle organ morphology", + "abnormal anatomical entity length", + "abnormal tendon morphology", + "Abnormal skeletal morphology", + "Abnormal skeletal muscle morphology", "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", - "anatomical conduit", - "systemic artery", - "heart blood vessel", - "heart plus pericardium", + "abnormal tendon morphology", + "phenotype by ontology source", + "abnormal connective tissue", + "Abnormal musculoskeletal physiology", "phenotype", - "abnormal incomplete closing of the ductus arteriosus", + "Abnormality of joint mobility", + "Abnormal tendon morphology", + "Joint contracture", + "decreased length of tendon", + "quality", + "abnormality of anatomical entity physiology", + "abnormal skeletal system morphology", + "Abnormal joint physiology", + "Abnormality of the skeletal system", + "abnormal musculature", + "abnormal anatomical entity", + "decreased size of the anatomical entity in the independent continuant", + "Abnormality of connective tissue", + "specifically dependent continuant", "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", - "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", - "mesoderm-derived structure", - "artery", - "thoracic segment blood vessel", - "heart", - "heart vasculature", + "abnormal skeletal system", + "abnormal anatomical entity morphology", ], "object_taxon": None, "object_taxon_label": None, @@ -4365,18 +3803,18 @@ def associations(): "negated": None, "pathway": None, "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:0001643", + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0011925🍪🍪biolink:has_phenotype🍪HP:0001371", "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": None}], + "publications": ["PMID:12552556"], + "publications_links": [{"id": "PMID:12552556", "url": "http://identifiers.org/pubmed/12552556"}], "qualifiers": [], - "frequency_qualifier": "HP:0040283", + "frequency_qualifier": "HP:0040282", "onset_qualifier": None, "sex_qualifier": None, "stage_qualifier": None, @@ -4385,11 +3823,11 @@ def associations(): "qualifiers_category": None, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_label": "Frequent", "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)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -4407,218 +3845,170 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:4e02df99-842a-11ee-884f-6be035239f90", + "id": "uuid:89e15869-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013904", + "original_subject": "OMIM:614830", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0019052", "MONDO:0000001", - "MONDO:0020121", + "MONDO:0005336", + "OGMS:0000031", + "MONDO:0700069", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0000171", + "MONDO:0020120", + "MONDO:0700096", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0700075", + "MONDO:0024322", "BFO:0000017", - "MONDO:0008056", - "MONDO:0035646", + "MONDO:0013904", + "MONDO:0015286", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000002", + "BFO:0000020", "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:0005066", "MONDO:0700223", - "MONDO:0003382", - "BFO:0000016", - "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", - "OGMS:0000031", - "BFO:0000001", + "MONDO:0002081", + "MONDO:0002320", ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", "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", + "continuant", "musculoskeletal system disorder", - "hereditary disease", - "eye disorder", + "muscular dystrophy-dystroglycanopathy, type A", + "myopathy caused by variation in POMGNT2", + "neuromuscular disease", + "skeletal muscle disorder", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "myopathy", + "disease", + "congenital muscular dystrophy", + "congenital muscular dystrophy caused by variation in POMGNT2", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome", + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", + "metabolic disease", + "disease", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "entity", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0001671", + "object": "HP:0000568", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "PR:000050567", - "UBERON:0000465", - "UPHENO:0019888", - "UPHENO:0080362", - "HP:0001627", - "UPHENO:0015280", - "BFO:0000040", - "UBERON:0001062", - "UBERON:0000468", - "UBERON:0011676", - "UBERON:0013701", - "HP:0001626", + "HP:0000315", + "HP:0000001", + "UPHENO:0075219", + "HP:0000234", + "UPHENO:0075997", + "UPHENO:0080079", + "UPHENO:0001005", "UPHENO:0001002", - "BFO:0000020", - "UPHENO:0015324", - "HP:0001671", "BFO:0000002", - "UPHENO:0001001", + "UPHENO:0075696", + "HP:0000152", + "UPHENO:0087907", + "UPHENO:0002910", "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", + "HP:0000568", + "UPHENO:0015280", + "HP:0000271", + "UPHENO:0012541", + "UPHENO:0080209", + "UPHENO:0068971", + "UPHENO:0021474", + "UPHENO:0002844", + "BFO:0000020", + "HP:0008056", + "PATO:0000001", + "HP:0012372", + "UPHENO:0087472", + "HP:0000478", + "HP:0100887", + "UPHENO:0087924", + "UPHENO:0002764", + "UPHENO:0003020", "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", + "UPHENO:0069523", + "UPHENO:0001001", + "UPHENO:0086589", "HP:0000118", + "UPHENO:0075195", "UPHENO:0020584", - "PATO:0000001", - "UBERON:0003037", - "UBERON:0010314", - "HP:0000001", - "UPHENO:0001005", "BFO:0000001", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0004120", - "UBERON:0001009", - "UBERON:0005178", - "UBERON:0007100", ], - "object_label": "Abnormal cardiac septum morphology (HPO)", + "object_label": "Microphthalmia", "object_closure_label": [ - "abnormal anatomical entity", + "Abnormality of the orbital region", + "All", + "abnormal size of eyeball of camera-type eye", + "abnormal size of anatomical entity", + "abnormal anatomical entity morphology", + "abnormal orbital region", + "aplasia or hypoplasia of anatomical entity", + "abnormal craniocervical region", "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)", + "Abnormal eye morphology", + "abnormal face morphology", "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)", - "abnormal anatomical entity morphology", - "entity", - "entity", - "septum", - "structure with developmental contribution from neural crest", - "thoracic cavity element", - "primary circulatory organ", - "Abnormality of the cardiovascular system (HPO)", "Phenotypic abnormality", - "abnormal cardiovascular system morphology", - "abnormal anatomical entity morphology", - "organism subdivision", - "organ", - "heart plus pericardium", + "Phenotypic abnormality", + "Aplasia/Hypoplasia affecting the eye", + "entity", + "aplasia or hypoplasia of eyeball of camera-type eye", + "decreased size of the anatomical entity", + "abnormal camera-type eye morphology", + "abnormal head", + "continuant", + "abnormal anatomical entity", + "Abnormality of the eye", + "Abnormality of globe size", + "abnormal camera-type eye morphology", + "Microphthalmia", + "phenotype by ontology source", "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", - "anatomical entity", - "cardiovascular system", - "anatomical structure", + "abnormal craniocervical region morphology", + "Abnormality of the head", + "Abnormality of head or neck", + "abnormal head morphology", + "abnormal face", + "abnormal eyeball of camera-type eye", "abnormal anatomical entity", - "abnormal cardiac septum morphology", - "abnormal cardiovascular system", - "Abnormal heart morphology (HPO)", - "abnormal heart morphology", - "multicellular anatomical structure", - "anatomical system", - "mesoderm-derived structure", - "cardiac septum", - "heart", + "decreased size of the eyeball of camera-type eye", + "decreased size of the anatomical entity in the independent continuant", + "specifically dependent continuant", + "abnormal anatomical entity morphology in the independent continuant", + "Abnormality of the face", + "abnormal anatomical entity morphology", ], "object_taxon": None, "object_taxon_label": None, @@ -4627,16 +4017,16 @@ def associations(): "negated": None, "pathway": None, "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:0001671", + "has_evidence": ["ECO:0000269"], + "has_evidence_links": [{"id": "ECO:0000269", "url": "http://purl.obolibrary.org/obo/ECO_0000269"}], + "grouping_key": "MONDO:0013904🍪🍪biolink:has_phenotype🍪HP:0000568", "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": None}], + "publications": ["PMID:22958903"], + "publications_links": [{"id": "PMID:22958903", "url": "http://identifiers.org/pubmed/22958903"}], "qualifiers": [], "frequency_qualifier": "HP:0040283", "onset_qualifier": None, @@ -4647,11 +4037,11 @@ def associations(): "qualifiers_category": None, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_label": "Occasional", "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)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040283"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Occasional"], "onset_qualifier_label": None, "onset_qualifier_namespace": None, "onset_qualifier_category": None, @@ -4669,172 +4059,196 @@ def associations(): "stage_qualifier_closure_label": [], }, { - "id": "uuid:4e02df9a-842a-11ee-884f-6be035239f90", + "id": "uuid:89e159d4-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013154", + "original_subject": "OMIM:613150", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0018939", + "MONDO:0019052", + "MONDO:0018282", "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", + "MONDO:0013154", "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:0000171", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0015286", + "MONDO:0016155", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000020", + "MONDO:0700071", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", "BFO:0000001", + "MONDO:0002320", ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "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", + "disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "muscular dystrophy-dystroglycanopathy, type A", + "neuromuscular disease", + "muscle-eye-brain disease", + "skeletal muscle disorder", + "entity", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "continuant", + "myopathy", + "congenital muscular dystrophy", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome", + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "metabolic disease", + "qualitative or quantitative defects of alpha-dystroglycan", + "disease", + "myopathy caused by variation in POMT2", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", ], "subject_taxon": None, "subject_taxon_label": None, "predicate": "biolink:has_phenotype", - "object": "HP:0002014", + "object": "HP:0002084", "original_object": None, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "UPHENO:0002443", - "UPHENO:0002536", - "UBERON:0000465", - "UPHENO:0082875", - "HP:0002664", - "BFO:0000001", - "BFO:0000040", - "UBERON:0001062", + "HP:0000001", + "HP:0000924", + "UPHENO:0050108", + "UPHENO:0081436", + "HP:0000234", + "UPHENO:0020641", + "UPHENO:0087665", + "UPHENO:0076791", + "UPHENO:0087089", + "HP:0011815", + "UPHENO:0001005", "UPHENO:0001002", - "BFO:0000020", - "HP:0011793", - "HP:0011458", - "BFO:0000002", - "UBERON:0001988", - "UPHENO:0001001", - "UPHENO:0002833", - "UPHENO:0001003", - "UBERON:0000463", + "BFO:0000001", "UPHENO:0075696", - "HP:0002014", - "HP:0025031", - "BFO:0000004", - "UBERON:0000061", - "UBERON:0000174", - "UBERON:0000468", - "BFO:0000002", - "HP:0025032", + "UPHENO:0051077", + "UPHENO:0076703", + "HP:0000152", + "UPHENO:0087907", + "HP:0000929", + "HP:0000707", + "UPHENO:0001003", + "UPHENO:0076692", + "UPHENO:0022529", + "UPHENO:0076702", + "UPHENO:0087363", + "UPHENO:0051003", + "HP:0011842", + "UPHENO:0088123", + "HP:0045005", + "UPHENO:0015280", + "HP:0034237", + "UPHENO:0002964", + "HP:0012639", + "UPHENO:0049587", + "UPHENO:0002844", + "BFO:0000020", + "HP:0002084", + "HP:0410043", + "UPHENO:0004523", "PATO:0000001", + "UPHENO:0002764", + "HP:0002011", + "UPHENO:0002536", + "UPHENO:0081566", + "UPHENO:0001001", + "UPHENO:0086589", "HP:0000118", - "UPHENO:0002332", - "HP:0000001", - "UPHENO:0001005", - "BFO:0000001", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0001007", + "BFO:0000002", + "HP:0009121", + "HP:0033127", + "UPHENO:0020584", ], - "object_label": "Diarrhea (HPO)", + "object_label": "Encephalocele", "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)", + "All", + "Abnormal axial skeleton morphology", + "Abnormality of the musculoskeletal system", + "abnormal anatomical entity morphology", + "abnormal craniocervical region", + "Abnormal skull morphology", + "abnormal neural tube morphology", + "quality", "abnormal phenotype by ontology source", - "continuant", - "feces", - "Phenotypic abnormality (HPO)", "Phenotypic abnormality", - "Neoplasm by anatomical site (HPO)", - "Abdominal symptom (HPO)", - "quality", - "organism substance", - "excreta", - "multicellular organism", + "Phenotypic abnormality", + "continuant", + "Encephalocele", + "Abnormal neural tube morphology", + "abnormal nervous system", + "abnormal head", + "abnormal axial skeleton plus cranial skeleton morphology", + "Cephalocele", + "abnormal postcranial axial skeleton morphology", + "abnormal nervous system morphology", + "abnormal neural tube morphology", + "abnormal anatomical entity", + "abnormal neural tube closure", + "abnormal tube formation", + "Abnormal skeletal morphology", + "abnormal embryonic tissue morphology", + "Neural tube defect", + "Abnormality of the nervous system", + "phenotype by ontology source", + "abnormal biological_process", "phenotype", - "Neoplasm (HPO)", - "entity", - "independent continuant", - "abnormality of digestive system physiology", - "Abnormality of the digestive system (HPO)", - "material entity", - "anatomical entity", - "anatomical structure", - "abnormality of anatomical entity physiology", + "abnormal craniocervical region morphology", + "Morphological central nervous system abnormality", + "abnormal developmental process", + "abnormal development of anatomical entity", + "Abnormality of the head", + "Abnormal nervous system morphology", + "abnormal embryo morphology", + "abnormal skeletal system morphology", + "Abnormality of head or neck", + "abnormal head morphology", + "Abnormality of the skeletal system", "abnormal anatomical entity", - "multicellular anatomical structure", - "anatomical system", + "abnormal skull morphology", + "abnormal central nervous system morphology", + "specifically dependent continuant", + "abnormal anatomical entity morphology in the independent continuant", + "Open neural tube defect", + "abnormal skeletal system", + "abnormal anatomical entity morphology", + "entity", ], "object_taxon": None, "object_taxon_label": None, @@ -4845,14 +4259,14 @@ 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:0035646🍪🍪biolink:has_phenotype🍪HP:0002014", + "grouping_key": "MONDO:0013154🍪🍪biolink:has_phenotype🍪HP:0002084", "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": None}], + "publications": ["OMIM:613150"], + "publications_links": [{"id": "OMIM:613150", "url": "http://identifiers.org/mim/613150"}], "qualifiers": [], "frequency_qualifier": "HP:0040283", "onset_qualifier": None, @@ -4863,11 +4277,11 @@ def associations(): "qualifiers_category": None, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_label": "Occasional", "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)"], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040283"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Occasional"], "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 cc784db31..4ada732f0 100644 --- a/backend/tests/fixtures/autocomplete.py +++ b/backend/tests/fixtures/autocomplete.py @@ -6,29 +6,8 @@ def autocomplete(): return { "limit": 10, "offset": 0, - "total": 230, + "total": 216, "items": [ - { - "id": "MONDO:0054748", - "category": "biolink:Disease", - "name": "Fanconi anemia, complementation group S", - "full_name": None, - "deprecated": None, - "description": None, - "xref": [], - "provided_by": "phenio_nodes", - "in_taxon": None, - "in_taxon_label": None, - "symbol": None, - "synonym": [ - "FANCS", - "Fanconi anemia, complementation GROUP S", - "Fanconi anemia, complementation group S", - ], - "uri": None, - "highlight": None, - "score": None, - }, { "id": "MONDO:0009215", "category": "biolink:Disease", @@ -464,54 +443,54 @@ def autocomplete(): "score": None, }, { - "id": "MONDO:0012186", + "id": "MONDO:0009213", "category": "biolink:Disease", - "name": "Fanconi anemia complementation group I", + "name": "Fanconi anemia complementation group C", "full_name": None, "deprecated": None, - "description": "Fanconi anemia caused by mutations in the FANCI gene, encoding Fanconi anemia group I protein.", + "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", "in_taxon": None, "in_taxon_label": None, "symbol": None, "synonym": [ - "FANCI", - "Fanconi Anemia, complementation Group 1", - "Fanconi Anemia, complementation group type 1", - "Fanconi anaemia complementation group type I", - "Fanconi anemia complementation group I", - "Fanconi anemia complementation group type I", - "Fanconi anemia, complementation group I", + "FA3", + "FACC", + "FANCC", + "Fanconi Anemia, complementation group type C", + "Fanconi anaemia complementation group type C", + "Fanconi anemia complementation group C", + "Fanconi anemia complementation group type C", + "Fanconi anemia, complementation group C", + "Fanconi pancytopenia type 3", + "Fanconi pancytopenia, type 3", + "facc", ], "uri": None, "highlight": None, "score": None, }, { - "id": "MONDO:0009213", + "id": "MONDO:0012186", "category": "biolink:Disease", - "name": "Fanconi anemia complementation group C", + "name": "Fanconi anemia complementation group I", "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.", + "description": "Fanconi anemia caused by mutations in the FANCI gene, encoding Fanconi anemia group I protein.", "xref": [], "provided_by": "phenio_nodes", "in_taxon": None, "in_taxon_label": None, "symbol": None, "synonym": [ - "FA3", - "FACC", - "FANCC", - "Fanconi Anemia, complementation group type C", - "Fanconi anaemia complementation group type C", - "Fanconi anemia complementation group C", - "Fanconi anemia complementation group type C", - "Fanconi anemia, complementation group C", - "Fanconi pancytopenia type 3", - "Fanconi pancytopenia, type 3", - "facc", + "FANCI", + "Fanconi Anemia, complementation Group 1", + "Fanconi Anemia, complementation group type 1", + "Fanconi anaemia complementation group type I", + "Fanconi anemia complementation group I", + "Fanconi anemia complementation group type I", + "Fanconi anemia, complementation group I", ], "uri": None, "highlight": None, @@ -568,6 +547,30 @@ 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 anaemia 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_response.py b/backend/tests/fixtures/autocomplete_response.py index 648c5e672..44d9c54e3 100644 --- a/backend/tests/fixtures/autocomplete_response.py +++ b/backend/tests/fixtures/autocomplete_response.py @@ -20,25 +20,13 @@ def autocomplete_response(): }, }, "response": { - "num_found": 230, + "num_found": 216, "start": 0, "docs": [ - { - "id": "MONDO:0054748", - "category": "biolink:Disease", - "name": "Fanconi anemia, complementation group S", - "provided_by": "phenio_nodes", - "synonym": [ - "FANCS", - "Fanconi anemia, complementation GROUP S", - "Fanconi anemia, complementation group S", - ], - }, { "id": "MONDO:0009215", "category": "biolink:Disease", "name": "Fanconi anemia complementation group A", - "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.", "provided_by": "phenio_nodes", "synonym": [ "Estren-Dameshek variant of Fanconi Anaemia", @@ -58,12 +46,12 @@ def autocomplete_response(): "Fanconi anemia complementation group type A", "Fanconi anemia, complementation group A", ], + "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.", }, { "id": "MONDO:0013566", "category": "biolink:Disease", "name": "Fanconi anemia complementation group L", - "description": "Any Fanconi anemia in which the cause of the disease is a mutation in the FANCL gene.", "provided_by": "phenio_nodes", "synonym": [ "FANCL", @@ -78,12 +66,12 @@ def autocomplete_response(): "Fanconi anemia complementation group type L", "Fanconi anemia, complementation group L", ], + "description": "Any Fanconi anemia in which the cause of the disease is a mutation in the FANCL gene.", }, { "id": "MONDO:0010953", "category": "biolink:Disease", "name": "Fanconi anemia complementation group E", - "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.", "provided_by": "phenio_nodes", "synonym": [ "FANCE", @@ -98,12 +86,12 @@ def autocomplete_response(): "Fanconi anemia, complementation group E", "face", ], + "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.", }, { "id": "MONDO:0001083", "category": "biolink:Disease", "name": "Fanconi renotubular syndrome", - "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.", "provided_by": "phenio_nodes", "synonym": [ "De toni-Fanconi syndrome", @@ -119,12 +107,12 @@ def autocomplete_response(): "infantile nephropathic cystinosis", "toni-debre-Fanconi syndrome", ], + "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.", }, { "id": "MONDO:0019391", "category": "biolink:Disease", "name": "Fanconi anemia", - "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.", "provided_by": "phenio_nodes", "synonym": [ "Fanconi anemia", @@ -136,12 +124,12 @@ def autocomplete_response(): "pancytopenia, congenital", "primary erythroid hypoplasia", ], + "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.", }, { "id": "MONDO:0013248", "category": "biolink:Disease", "name": "Fanconi anemia complementation group O", - "description": "Any Fanconi anemia in which the cause of the disease is a mutation in the RAD51C gene.", "provided_by": "phenio_nodes", "synonym": [ "FANCO", @@ -158,12 +146,12 @@ def autocomplete_response(): "Rad51C Fanconi anaemia", "Rad51C Fanconi anemia", ], + "description": "Any Fanconi anemia in which the cause of the disease is a mutation in the RAD51C gene.", }, { "id": "MONDO:0013499", "category": "biolink:Disease", "name": "Fanconi anemia complementation group P", - "description": "Any Fanconi anemia in which the cause of the disease is a mutation in the SLX4 gene.", "provided_by": "phenio_nodes", "synonym": [ "FANCP", @@ -180,6 +168,7 @@ def autocomplete_response(): "Slx4 Fanconi anaemia", "Slx4 Fanconi anemia", ], + "description": "Any Fanconi anemia in which the cause of the disease is a mutation in the SLX4 gene.", }, { "id": "MONDO:0024525", @@ -203,7 +192,6 @@ def autocomplete_response(): "id": "MONDO:0014985", "category": "biolink:Disease", "name": "Fanconi anemia complementation group V", - "description": "Any Fanconi anemia in which the cause of the disease is a mutation in the MAD2L2 gene.", "provided_by": "phenio_nodes", "synonym": [ "FANCV", @@ -218,12 +206,12 @@ def autocomplete_response(): "MAD2L2 Fanconi anaemia", "MAD2L2 Fanconi anemia", ], + "description": "Any Fanconi anemia in which the cause of the disease is a mutation in the MAD2L2 gene.", }, { "id": "MONDO:0012565", "category": "biolink:Disease", "name": "Fanconi anemia complementation group N", - "description": "Any Fanconi anemia in which the cause of the disease is a mutation in the PALB2 gene.", "provided_by": "phenio_nodes", "synonym": [ "FANCN", @@ -237,12 +225,12 @@ def autocomplete_response(): "PALB2 Fanconi anaemia", "PALB2 Fanconi anemia", ], + "description": "Any Fanconi anemia in which the cause of the disease is a mutation in the PALB2 gene.", }, { "id": "MONDO:0014986", "category": "biolink:Disease", "name": "Fanconi anemia complementation group R", - "description": "Any Fanconi anemia in which the cause of the disease is a mutation in the RAD51 gene.", "provided_by": "phenio_nodes", "synonym": [ "FANCR", @@ -256,12 +244,12 @@ def autocomplete_response(): "RAD51 Fanconi anaemia", "RAD51 Fanconi anemia", ], + "description": "Any Fanconi anemia in which the cause of the disease is a mutation in the RAD51 gene.", }, { "id": "MONDO:0014987", "category": "biolink:Disease", "name": "Fanconi anemia complementation group U", - "description": "Any Fanconi anemia in which the cause of the disease is a mutation in the XRCC2 gene.", "provided_by": "phenio_nodes", "synonym": [ "FANCU", @@ -275,12 +263,12 @@ def autocomplete_response(): "XRCC2 Fanconi anaemia", "XRCC2 Fanconi anemia", ], + "description": "Any Fanconi anemia in which the cause of the disease is a mutation in the XRCC2 gene.", }, { "id": "MONDO:0014108", "category": "biolink:Disease", "name": "Fanconi anemia complementation group Q", - "description": "Any Fanconi anemia in which the cause of the disease is a mutation in the ERCC4 gene.", "provided_by": "phenio_nodes", "synonym": [ "ERCC4 Fanconi anaemia", @@ -293,12 +281,12 @@ def autocomplete_response(): "Fanconi anemia complementation group type Q", "Fanconi anemia, complementation group Q", ], + "description": "Any Fanconi anemia in which the cause of the disease is a mutation in the ERCC4 gene.", }, { "id": "MONDO:0014638", "category": "biolink:Disease", "name": "Fanconi anemia complementation group T", - "description": "Any Fanconi anemia in which the cause of the disease is a mutation in the UBE2T gene.", "provided_by": "phenio_nodes", "synonym": [ "FANCT", @@ -311,12 +299,12 @@ def autocomplete_response(): "UBE2T Fanconi anaemia", "UBE2T Fanconi anemia", ], + "description": "Any Fanconi anemia in which the cause of the disease is a mutation in the UBE2T gene.", }, { "id": "MONDO:0010351", "category": "biolink:Disease", "name": "Fanconi anemia complementation group B", - "description": "Fanconi anemia caused by mutations of the FANCB gene. This gene encodes the protein for complementation group B.", "provided_by": "phenio_nodes", "synonym": [ "FA2", @@ -331,28 +319,12 @@ def autocomplete_response(): "Fanconi pancytopenia type 2", "Fanconi pancytopenia, type 2", ], - }, - { - "id": "MONDO:0012186", - "category": "biolink:Disease", - "name": "Fanconi anemia complementation group I", - "description": "Fanconi anemia caused by mutations in the FANCI gene, encoding Fanconi anemia group I protein.", - "provided_by": "phenio_nodes", - "synonym": [ - "FANCI", - "Fanconi Anemia, complementation Group 1", - "Fanconi Anemia, complementation group type 1", - "Fanconi anaemia complementation group type I", - "Fanconi anemia complementation group I", - "Fanconi anemia complementation group type I", - "Fanconi anemia, complementation group I", - ], + "description": "Fanconi anemia caused by mutations of the FANCB gene. This gene encodes the protein for complementation group B.", }, { "id": "MONDO:0009213", "category": "biolink:Disease", "name": "Fanconi anemia complementation group C", - "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.", "provided_by": "phenio_nodes", "synonym": [ "FA3", @@ -367,12 +339,28 @@ def autocomplete_response(): "Fanconi pancytopenia, type 3", "facc", ], + "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.", + }, + { + "id": "MONDO:0012186", + "category": "biolink:Disease", + "name": "Fanconi anemia complementation group I", + "provided_by": "phenio_nodes", + "synonym": [ + "FANCI", + "Fanconi Anemia, complementation Group 1", + "Fanconi Anemia, complementation group type 1", + "Fanconi anaemia complementation group type I", + "Fanconi anemia complementation group I", + "Fanconi anemia complementation group type I", + "Fanconi anemia, complementation group I", + ], + "description": "Fanconi anemia caused by mutations in the FANCI gene, encoding Fanconi anemia group I protein.", }, { "id": "MONDO:0009214", "category": "biolink:Disease", "name": "Fanconi anemia complementation group D2", - "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.", "provided_by": "phenio_nodes", "synonym": [ "FA4", @@ -385,12 +373,12 @@ def autocomplete_response(): "Fanconi pancytopenia type 4", "Fanconi pancytopenia, type 4", ], + "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.", }, { "id": "MONDO:0011325", "category": "biolink:Disease", "name": "Fanconi anemia complementation group F", - "description": "Fanconi anemia caused by mutations of the FANCF gene. This gene encodes a polypeptide with homology to the prokaryotic RNA-binding protein ROM.", "provided_by": "phenio_nodes", "synonym": [ "FANCF", @@ -400,6 +388,22 @@ def autocomplete_response(): "Fanconi anemia complementation group type F", "Fanconi anemia, complementation group F", ], + "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 anaemia 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.", }, ], }, diff --git a/backend/tests/fixtures/entity_response.py b/backend/tests/fixtures/entity_response.py index 2d447a450..9fe0fa04c 100644 --- a/backend/tests/fixtures/entity_response.py +++ b/backend/tests/fixtures/entity_response.py @@ -7,6 +7,6 @@ def entity_response(): "id": "MONDO:0020121", "category": "biolink:Disease", "name": "muscular dystrophy", - "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.", "provided_by": "phenio_nodes", + "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.", } diff --git a/backend/tests/fixtures/histopheno.py b/backend/tests/fixtures/histopheno.py index 290113ed9..108fb1d7c 100644 --- a/backend/tests/fixtures/histopheno.py +++ b/backend/tests/fixtures/histopheno.py @@ -6,23 +6,23 @@ def histopheno(): return { "id": "MONDO:0020121", "items": [ - {"label": "musculature", "count": 1756, "id": "HP:0003011"}, - {"label": "nervous_system", "count": 1130, "id": "HP:0000707"}, - {"label": "head_neck", "count": 602, "id": "HP:0000152"}, - {"label": "skeletal_system", "count": 493, "id": "HP:0000924"}, - {"label": "respiratory", "count": 320, "id": "HP:0002086"}, - {"label": "eye", "count": 300, "id": "HP:0000478"}, - {"label": "metabolism_homeostasis", "count": 221, "id": "HP:0001939"}, - {"label": "cardiovascular_system", "count": 185, "id": "HP:0001626"}, - {"label": "blood", "count": 184, "id": "HP:0001871"}, - {"label": "connective_tissue", "count": 165, "id": "HP:0003549"}, - {"label": "neoplasm", "count": 150, "id": "HP:0002664"}, - {"label": "digestive_system", "count": 144, "id": "HP:0025031"}, - {"label": "integument", "count": 48, "id": "HP:0001574"}, + {"label": "musculature", "count": 1686, "id": "HP:0003011"}, + {"label": "nervous_system", "count": 1077, "id": "HP:0000707"}, + {"label": "head_neck", "count": 583, "id": "HP:0000152"}, + {"label": "skeletal_system", "count": 472, "id": "HP:0000924"}, + {"label": "eye", "count": 289, "id": "HP:0000478"}, + {"label": "metabolism_homeostasis", "count": 215, "id": "HP:0001939"}, + {"label": "cardiovascular_system", "count": 178, "id": "HP:0001626"}, + {"label": "blood", "count": 177, "id": "HP:0001871"}, + {"label": "connective_tissue", "count": 161, "id": "HP:0003549"}, + {"label": "respiratory", "count": 150, "id": "HP:0002086"}, + {"label": "neoplasm", "count": 149, "id": "HP:0002664"}, + {"label": "digestive_system", "count": 143, "id": "HP:0025031"}, + {"label": "integument", "count": 47, "id": "HP:0001574"}, {"label": "genitourinary_system", "count": 44, "id": "HP:0000119"}, - {"label": "growth", "count": 33, "id": "HP:0001507"}, + {"label": "growth", "count": 32, "id": "HP:0001507"}, {"label": "ear", "count": 28, "id": "HP:0000598"}, - {"label": "endocrine", "count": 26, "id": "HP:0000818"}, + {"label": "endocrine", "count": 25, "id": "HP:0000818"}, {"label": "immune_system", "count": 22, "id": "HP:0002715"}, {"label": "prenatal_or_birth", "count": 21, "id": "HP:0001197"}, {"label": "breast", "count": 1, "id": "HP:0000769"}, diff --git a/backend/tests/fixtures/histopheno_response.py b/backend/tests/fixtures/histopheno_response.py index 67fb5632e..83da0ef38 100644 --- a/backend/tests/fixtures/histopheno_response.py +++ b/backend/tests/fixtures/histopheno_response.py @@ -40,29 +40,29 @@ def histopheno_response(): "facet": "true", }, }, - "response": {"num_found": 4563, "start": 0, "docs": []}, + "response": {"num_found": 4361, "start": 0, "docs": []}, "facet_counts": { "facet_fields": {}, "facet_queries": { - 'object_closure:"HP:0000924"': 493, - 'object_closure:"HP:0000707"': 1130, - 'object_closure:"HP:0000152"': 602, - 'object_closure:"HP:0001574"': 48, - 'object_closure:"HP:0000478"': 300, - 'object_closure:"HP:0001626"': 185, - 'object_closure:"HP:0001939"': 221, + 'object_closure:"HP:0000924"': 472, + 'object_closure:"HP:0000707"': 1077, + 'object_closure:"HP:0000152"': 583, + 'object_closure:"HP:0001574"': 47, + 'object_closure:"HP:0000478"': 289, + 'object_closure:"HP:0001626"': 178, + 'object_closure:"HP:0001939"': 215, 'object_closure:"HP:0000119"': 44, - 'object_closure:"HP:0025031"': 144, - 'object_closure:"HP:0002664"': 150, - 'object_closure:"HP:0001871"': 184, + 'object_closure:"HP:0025031"': 143, + 'object_closure:"HP:0002664"': 149, + 'object_closure:"HP:0001871"': 177, 'object_closure:"HP:0002715"': 22, - 'object_closure:"HP:0000818"': 26, - 'object_closure:"HP:0003011"': 1756, - 'object_closure:"HP:0002086"': 320, + 'object_closure:"HP:0000818"': 25, + 'object_closure:"HP:0003011"': 1686, + 'object_closure:"HP:0002086"': 150, 'object_closure:"HP:0000598"': 28, - 'object_closure:"HP:0003549"': 165, + 'object_closure:"HP:0003549"': 161, 'object_closure:"HP:0001197"': 21, - 'object_closure:"HP:0001507"': 33, + 'object_closure:"HP:0001507"': 32, 'object_closure:"HP:0000769"': 1, }, }, diff --git a/backend/tests/fixtures/mapping_response.py b/backend/tests/fixtures/mapping_response.py index 92ee42cb3..55356a33c 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": "074f33ef-cab8-46e9-b535-5c637220dcd1", + "id": "63d84b9a-93bc-4d4a-9c2c-755a444f7d7c", }, { "subject_id": "MONDO:0020121", @@ -38,24 +38,25 @@ def mapping_response(): "object_id": "ICD10CM:G71.0", "object_label": "Muscular dystrophy", "mapping_justification": "semapv:UnspecifiedMatching", - "id": "575115b8-67a4-482d-88e7-1b1b60fdd99a", + "id": "1e7e3e71-c912-443f-b92f-c7a828543070", }, { "subject_id": "MONDO:0020121", "subject_label": "muscular dystrophy", "predicate_id": "skos:exactMatch", - "object_id": "MESH:D009136", + "object_id": "NCIT:C84910", + "object_label": "Muscular Dystrophy", "mapping_justification": "semapv:UnspecifiedMatching", - "id": "a2f1233e-1951-4f40-9a79-60f591a24bb5", + "id": "8b7a5c87-d896-4daf-ac51-6ad53ef838a7", }, { "subject_id": "MONDO:0020121", "subject_label": "muscular dystrophy", "predicate_id": "skos:exactMatch", - "object_id": "NCIT:C84910", - "object_label": "Muscular Dystrophy", + "object_id": "Orphanet:98473", + "object_label": "Muscular dystrophy", "mapping_justification": "semapv:UnspecifiedMatching", - "id": "73eaeaef-9868-4e50-a4ed-aee537a830ae", + "id": "74d9dc89-0a38-41fd-8f0f-9b89e1085824", }, { "subject_id": "MONDO:0020121", @@ -63,7 +64,7 @@ def mapping_response(): "predicate_id": "skos:exactMatch", "object_id": "SCTID:73297009", "mapping_justification": "semapv:UnspecifiedMatching", - "id": "3f7aa4af-411c-47fe-9b3a-d8248484ea2d", + "id": "f93de036-44d8-43fd-b5b6-9753b75f79b0", }, { "subject_id": "MONDO:0020121", @@ -71,15 +72,15 @@ def mapping_response(): "predicate_id": "skos:exactMatch", "object_id": "UMLS:C0026850", "mapping_justification": "semapv:UnspecifiedMatching", - "id": "f8d6fe34-2d2a-4ace-a314-f4def3070e3a", + "id": "d5cbdd21-5791-4b49-ae6f-42b8f226e3bf", }, { "subject_id": "MONDO:0020121", "subject_label": "muscular dystrophy", "predicate_id": "skos:exactMatch", - "object_id": "Orphanet:98473", + "object_id": "mesh:D009136", "mapping_justification": "semapv:UnspecifiedMatching", - "id": "63588ca1-4204-4143-88b3-152b31ea0c41", + "id": "573ffaec-5e44-47a3-affc-1019df4b4ef9", }, ], }, diff --git a/backend/tests/fixtures/mappings.py b/backend/tests/fixtures/mappings.py index 9badad32a..0150e0a00 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": "074f33ef-cab8-46e9-b535-5c637220dcd1", + "id": "63d84b9a-93bc-4d4a-9c2c-755a444f7d7c", }, { "subject_id": "MONDO:0020121", @@ -24,25 +24,25 @@ def mappings(): "object_id": "ICD10CM:G71.0", "object_label": "Muscular dystrophy", "mapping_justification": "semapv:UnspecifiedMatching", - "id": "575115b8-67a4-482d-88e7-1b1b60fdd99a", + "id": "1e7e3e71-c912-443f-b92f-c7a828543070", }, { "subject_id": "MONDO:0020121", "subject_label": "muscular dystrophy", "predicate_id": "skos:exactMatch", - "object_id": "MESH:D009136", - "object_label": None, + "object_id": "NCIT:C84910", + "object_label": "Muscular Dystrophy", "mapping_justification": "semapv:UnspecifiedMatching", - "id": "a2f1233e-1951-4f40-9a79-60f591a24bb5", + "id": "8b7a5c87-d896-4daf-ac51-6ad53ef838a7", }, { "subject_id": "MONDO:0020121", "subject_label": "muscular dystrophy", "predicate_id": "skos:exactMatch", - "object_id": "NCIT:C84910", - "object_label": "Muscular Dystrophy", + "object_id": "Orphanet:98473", + "object_label": "Muscular dystrophy", "mapping_justification": "semapv:UnspecifiedMatching", - "id": "73eaeaef-9868-4e50-a4ed-aee537a830ae", + "id": "74d9dc89-0a38-41fd-8f0f-9b89e1085824", }, { "subject_id": "MONDO:0020121", @@ -51,7 +51,7 @@ def mappings(): "object_id": "SCTID:73297009", "object_label": None, "mapping_justification": "semapv:UnspecifiedMatching", - "id": "3f7aa4af-411c-47fe-9b3a-d8248484ea2d", + "id": "f93de036-44d8-43fd-b5b6-9753b75f79b0", }, { "subject_id": "MONDO:0020121", @@ -60,16 +60,16 @@ def mappings(): "object_id": "UMLS:C0026850", "object_label": None, "mapping_justification": "semapv:UnspecifiedMatching", - "id": "f8d6fe34-2d2a-4ace-a314-f4def3070e3a", + "id": "d5cbdd21-5791-4b49-ae6f-42b8f226e3bf", }, { "subject_id": "MONDO:0020121", "subject_label": "muscular dystrophy", "predicate_id": "skos:exactMatch", - "object_id": "Orphanet:98473", + "object_id": "mesh:D009136", "object_label": None, "mapping_justification": "semapv:UnspecifiedMatching", - "id": "63588ca1-4204-4143-88b3-152b31ea0c41", + "id": "573ffaec-5e44-47a3-affc-1019df4b4ef9", }, ], } diff --git a/backend/tests/fixtures/node.py b/backend/tests/fixtures/node.py index 6f094d3af..4353e9069 100644 --- a/backend/tests/fixtures/node.py +++ b/backend/tests/fixtures/node.py @@ -21,13 +21,13 @@ def node(): "causal_gene": [], "causes_disease": [], "mappings": [ - {"id": "DOID:9884", "url": None}, + {"id": "DOID:9884", "url": "http://purl.obolibrary.org/obo/DOID_9884"}, {"id": "ICD10CM:G71.0", "url": "https://icd.codes/icd10cm/G71.0"}, - {"id": "MESH:D009136", "url": None}, - {"id": "NCIT:C84910", "url": None}, - {"id": "SCTID:73297009", "url": None}, - {"id": "UMLS:C0026850", "url": None}, + {"id": "NCIT:C84910", "url": "http://purl.obolibrary.org/obo/NCIT_C84910"}, {"id": "Orphanet:98473", "url": None}, + {"id": "SCTID:73297009", "url": "http://identifiers.org/snomedct/73297009"}, + {"id": "UMLS:C0026850", "url": "http://identifiers.org/umls/C0026850"}, + {"id": "mesh:D009136", "url": None}, ], "external_links": [], "provided_by_link": { @@ -35,9 +35,9 @@ def node(): "url": "https://monarch-initiative.github.io/monarch-ingest/Sources/phenio/#", }, "association_counts": [ - {"label": "Phenotypes", "count": 4027, "category": "biolink:DiseaseToPhenotypicFeatureAssociation"}, + {"label": "Phenotypes", "count": 3879, "category": "biolink:DiseaseToPhenotypicFeatureAssociation"}, {"label": "Causal Genes", "count": 124, "category": "biolink:CausalGeneToDiseaseAssociation"}, - {"label": "Correlated Genes", "count": 151, "category": "biolink:CorrelatedGeneToDiseaseAssociation"}, + {"label": "Correlated Genes", "count": 139, "category": "biolink:CorrelatedGeneToDiseaseAssociation"}, ], "node_hierarchy": { "super_classes": [ @@ -89,9 +89,9 @@ def node(): ], "sub_classes": [ { - "id": "MONDO:0008028", + "id": "MONDO:0016106", "category": "biolink:Disease", - "name": "muscular dystrophy, Barnes type", + "name": "progressive muscular dystrophy", "full_name": None, "deprecated": None, "description": None, @@ -104,9 +104,9 @@ def node(): "uri": None, }, { - "id": "MONDO:0010675", + "id": "MONDO:0018949", "category": "biolink:Disease", - "name": "muscular dystrophy, cardiac type", + "name": "distal myopathy", "full_name": None, "deprecated": None, "description": None, @@ -119,9 +119,9 @@ def node(): "uri": None, }, { - "id": "MONDO:0010676", + "id": "MONDO:0019950", "category": "biolink:Disease", - "name": "muscular dystrophy, Hemizygous lethal type", + "name": "congenital muscular dystrophy", "full_name": None, "deprecated": None, "description": None, @@ -134,9 +134,9 @@ def node(): "uri": None, }, { - "id": "MONDO:0010677", + "id": "MONDO:0023204", "category": "biolink:Disease", - "name": "muscular dystrophy, Mabry type", + "name": "Fukuda-Miyanomae-Nakata syndrome", "full_name": None, "deprecated": None, "description": None, @@ -149,9 +149,9 @@ def node(): "uri": None, }, { - "id": "MONDO:0010678", + "id": "MONDO:0100228", "category": "biolink:Disease", - "name": "muscular dystrophy, progressive Pectorodorsal", + "name": "LAMA2-related muscular dystrophy", "full_name": None, "deprecated": None, "description": None, @@ -164,9 +164,9 @@ def node(): "uri": None, }, { - "id": "MONDO:0019950", + "id": "MONDO:0008028", "category": "biolink:Disease", - "name": "congenital muscular dystrophy", + "name": "muscular dystrophy, Barnes type", "full_name": None, "deprecated": None, "description": None, @@ -179,9 +179,9 @@ def node(): "uri": None, }, { - "id": "MONDO:0023204", + "id": "MONDO:0010311", "category": "biolink:Disease", - "name": "Fukuda-Miyanomae-Nakata syndrome", + "name": "Becker muscular dystrophy", "full_name": None, "deprecated": None, "description": None, @@ -194,9 +194,9 @@ def node(): "uri": None, }, { - "id": "MONDO:0100228", + "id": "MONDO:0010675", "category": "biolink:Disease", - "name": "LAMA2-related muscular dystrophy", + "name": "muscular dystrophy, cardiac type", "full_name": None, "deprecated": None, "description": None, @@ -209,9 +209,9 @@ def node(): "uri": None, }, { - "id": "MONDO:0018949", + "id": "MONDO:0010676", "category": "biolink:Disease", - "name": "distal myopathy", + "name": "muscular dystrophy, Hemizygous lethal type", "full_name": None, "deprecated": None, "description": None, @@ -224,9 +224,39 @@ def node(): "uri": None, }, { - "id": "MONDO:0016106", + "id": "MONDO:0010677", "category": "biolink:Disease", - "name": "progressive muscular dystrophy", + "name": "muscular dystrophy, Mabry type", + "full_name": None, + "deprecated": None, + "description": None, + "xref": [], + "provided_by": None, + "in_taxon": None, + "in_taxon_label": None, + "symbol": None, + "synonym": [], + "uri": None, + }, + { + "id": "MONDO:0010678", + "category": "biolink:Disease", + "name": "muscular dystrophy, progressive Pectorodorsal", + "full_name": None, + "deprecated": None, + "description": None, + "xref": [], + "provided_by": None, + "in_taxon": None, + "in_taxon_label": None, + "symbol": None, + "synonym": [], + "uri": None, + }, + { + "id": "MONDO:0010679", + "category": "biolink:Disease", + "name": "Duchenne muscular dystrophy", "full_name": None, "deprecated": None, "description": None, diff --git a/backend/tests/fixtures/phenotype_explorer_search.py b/backend/tests/fixtures/phenotype_explorer_search.py index 4f06444c9..1f96b6356 100644 --- a/backend/tests/fixtures/phenotype_explorer_search.py +++ b/backend/tests/fixtures/phenotype_explorer_search.py @@ -219,8 +219,8 @@ def phenotype_explorer_search(): "HP:0002104": BestMatch( match_source="HP:0002104", match_source_label="Apnea (HPO)", - match_target="ZP:0018569", - match_target_label="myeloid cell development absent, abnormal (ZPO)", + match_target="ZP:0018568", + match_target_label="primitive hemopoiesis absent, abnormal (ZPO)", score=9.08524944639702, match_subsumer=None, match_subsumer_label=None, @@ -228,7 +228,7 @@ def phenotype_explorer_search(): subject_id="HP:0002104", subject_label=None, subject_source=None, - object_id="ZP:0018569", + object_id="ZP:0018568", object_label=None, object_source=None, ancestor_id="UPHENO:0034024", @@ -237,17 +237,17 @@ def phenotype_explorer_search(): object_information_content=None, subject_information_content=None, ancestor_information_content=9.08524944639702, - jaccard_similarity=0.34615384615384615, + jaccard_similarity=0.3333333333333333, cosine_similarity=None, dice_similarity=None, - phenodigm_score=1.773384910034319, + phenodigm_score=1.7402346054863809, ), ), "HP:0012378": BestMatch( match_source="HP:0012378", match_source_label="Fatigue (HPO)", - match_target="ZP:0018569", - match_target_label="myeloid cell development absent, abnormal (ZPO)", + match_target="ZP:0018568", + match_target_label="primitive hemopoiesis absent, abnormal (ZPO)", score=1.6836208034928104, match_subsumer=None, match_subsumer_label=None, @@ -255,7 +255,7 @@ def phenotype_explorer_search(): subject_id="HP:0012378", subject_label=None, subject_source=None, - object_id="ZP:0018569", + object_id="ZP:0018568", object_label=None, object_source=None, ancestor_id="UPHENO:0001005", @@ -264,10 +264,10 @@ def phenotype_explorer_search(): object_information_content=None, subject_information_content=None, ancestor_information_content=1.6836208034928104, - jaccard_similarity=0.47058823529411764, + jaccard_similarity=0.4444444444444444, cosine_similarity=None, dice_similarity=None, - phenodigm_score=0.8901079388591847, + phenodigm_score=0.8650294287846346, ), ), }, @@ -368,8 +368,8 @@ def phenotype_explorer_search(): "HP:0002104": BestMatch( match_source="HP:0002104", match_source_label="Apnea (HPO)", - match_target="ZP:0018569", - match_target_label="myeloid cell development absent, abnormal (ZPO)", + match_target="ZP:0018568", + match_target_label="primitive hemopoiesis absent, abnormal (ZPO)", score=9.08524944639702, match_subsumer=None, match_subsumer_label=None, @@ -377,7 +377,7 @@ def phenotype_explorer_search(): subject_id="HP:0002104", subject_label=None, subject_source=None, - object_id="ZP:0018569", + object_id="ZP:0018568", object_label=None, object_source=None, ancestor_id="UPHENO:0034024", @@ -386,10 +386,10 @@ def phenotype_explorer_search(): object_information_content=None, subject_information_content=None, ancestor_information_content=9.08524944639702, - jaccard_similarity=0.34615384615384615, + jaccard_similarity=0.3333333333333333, cosine_similarity=None, dice_similarity=None, - phenodigm_score=1.773384910034319, + phenodigm_score=1.7402346054863809, ), ), "HP:0012378": BestMatch( @@ -461,8 +461,8 @@ def phenotype_explorer_search(): "ZP:0018569": TermInfo(id="ZP:0018569", label="myeloid cell development absent, abnormal (ZPO)"), }, object_termset={ - "HP:0012378": TermInfo(id="HP:0012378", label="Fatigue (HPO)"), "HP:0002104": TermInfo(id="HP:0002104", label="Apnea (HPO)"), + "HP:0012378": TermInfo(id="HP:0012378", label="Fatigue (HPO)"), }, subject_best_matches={ "ZP:0018568": BestMatch( @@ -524,8 +524,8 @@ def phenotype_explorer_search(): "HP:0002104": BestMatch( match_source="HP:0002104", match_source_label="Apnea (HPO)", - match_target="ZP:0018569", - match_target_label="myeloid cell development absent, abnormal (ZPO)", + match_target="ZP:0018568", + match_target_label="primitive hemopoiesis absent, abnormal (ZPO)", score=9.08524944639702, match_subsumer=None, match_subsumer_label=None, @@ -533,7 +533,7 @@ def phenotype_explorer_search(): subject_id="HP:0002104", subject_label=None, subject_source=None, - object_id="ZP:0018569", + object_id="ZP:0018568", object_label=None, object_source=None, ancestor_id="UPHENO:0034024", @@ -542,17 +542,17 @@ def phenotype_explorer_search(): object_information_content=None, subject_information_content=None, ancestor_information_content=9.08524944639702, - jaccard_similarity=0.34615384615384615, + jaccard_similarity=0.3333333333333333, cosine_similarity=None, dice_similarity=None, - phenodigm_score=1.773384910034319, + phenodigm_score=1.7402346054863809, ), ), "HP:0012378": BestMatch( match_source="HP:0012378", match_source_label="Fatigue (HPO)", - match_target="ZP:0018569", - match_target_label="myeloid cell development absent, abnormal (ZPO)", + match_target="ZP:0018568", + match_target_label="primitive hemopoiesis absent, abnormal (ZPO)", score=1.6836208034928104, match_subsumer=None, match_subsumer_label=None, @@ -560,7 +560,7 @@ def phenotype_explorer_search(): subject_id="HP:0012378", subject_label=None, subject_source=None, - object_id="ZP:0018569", + object_id="ZP:0018568", object_label=None, object_source=None, ancestor_id="UPHENO:0001005", @@ -569,10 +569,10 @@ def phenotype_explorer_search(): object_information_content=None, subject_information_content=None, ancestor_information_content=1.6836208034928104, - jaccard_similarity=0.47058823529411764, + jaccard_similarity=0.4444444444444444, cosine_similarity=None, dice_similarity=None, - phenodigm_score=0.8901079388591847, + phenodigm_score=0.8650294287846346, ), ), }, @@ -606,8 +606,8 @@ def phenotype_explorer_search(): score=7.234842285670967, similarity=TermSetPairwiseSimilarity( subject_termset={ - "ZP:0018569": TermInfo(id="ZP:0018569", label="myeloid cell development absent, abnormal (ZPO)"), "ZP:0018568": TermInfo(id="ZP:0018568", label="primitive hemopoiesis absent, abnormal (ZPO)"), + "ZP:0018569": TermInfo(id="ZP:0018569", label="myeloid cell development absent, abnormal (ZPO)"), }, object_termset={ "HP:0002104": TermInfo(id="HP:0002104", label="Apnea (HPO)"), @@ -749,8 +749,8 @@ def phenotype_explorer_search(): score=5.412148503540145, similarity=TermSetPairwiseSimilarity( subject_termset={ - "ZP:0000945": TermInfo(id="ZP:0000945", label="pigment cell quality, abnormal (ZPO)"), "ZP:0100294": TermInfo(id="ZP:0100294", label="visual perception absent, abnormal (ZPO)"), + "ZP:0000945": TermInfo(id="ZP:0000945", label="pigment cell quality, abnormal (ZPO)"), }, object_termset={ "HP:0012378": TermInfo(id="HP:0012378", label="Fatigue (HPO)"), @@ -892,19 +892,19 @@ def phenotype_explorer_search(): score=5.384435124944915, similarity=TermSetPairwiseSimilarity( subject_termset={ - "ZP:0015039": TermInfo(id="ZP:0015039", label="visual behavior absent, abnormal (ZPO)"), "ZP:0001841": TermInfo(id="ZP:0001841", label="visual behavior quality, abnormal (ZPO)"), + "ZP:0015039": TermInfo(id="ZP:0015039", label="visual behavior absent, abnormal (ZPO)"), }, object_termset={ - "HP:0012378": TermInfo(id="HP:0012378", label="Fatigue (HPO)"), "HP:0002104": TermInfo(id="HP:0002104", label="Apnea (HPO)"), + "HP:0012378": TermInfo(id="HP:0012378", label="Fatigue (HPO)"), }, subject_best_matches={ "ZP:0001841": BestMatch( match_source="ZP:0001841", match_source_label="visual behavior quality, abnormal (ZPO)", - match_target="HP:0012378", - match_target_label="Fatigue (HPO)", + match_target="HP:0002104", + match_target_label="Apnea (HPO)", score=1.6836208034928104, match_subsumer=None, match_subsumer_label=None, @@ -912,7 +912,7 @@ def phenotype_explorer_search(): subject_id="ZP:0001841", subject_label=None, subject_source=None, - object_id="HP:0012378", + object_id="HP:0002104", object_label=None, object_source=None, ancestor_id="UPHENO:0001005", @@ -921,10 +921,10 @@ def phenotype_explorer_search(): object_information_content=None, subject_information_content=None, ancestor_information_content=1.6836208034928104, - jaccard_similarity=0.47058823529411764, + jaccard_similarity=0.2962962962962963, cosine_similarity=None, dice_similarity=None, - phenodigm_score=0.8901079388591847, + phenodigm_score=0.7062935710045181, ), ), "ZP:0015039": BestMatch( @@ -1038,8 +1038,8 @@ def phenotype_explorer_search(): "ZP:0021445": TermInfo(id="ZP:0021445", label="gill increased amount, abnormal (ZPO)") }, object_termset={ - "HP:0012378": TermInfo(id="HP:0012378", label="Fatigue (HPO)"), "HP:0002104": TermInfo(id="HP:0002104", label="Apnea (HPO)"), + "HP:0012378": TermInfo(id="HP:0012378", label="Fatigue (HPO)"), }, subject_best_matches={ "ZP:0021445": BestMatch( diff --git a/backend/tests/fixtures/search.py b/backend/tests/fixtures/search.py index 6e5d5cc55..58b561c31 100644 --- a/backend/tests/fixtures/search.py +++ b/backend/tests/fixtures/search.py @@ -6,7 +6,7 @@ def search(): return { "limit": 20, "offset": 0, - "total": 115, + "total": 101, "items": [ { "id": "MONDO:0019391", diff --git a/backend/tests/fixtures/search_response.py b/backend/tests/fixtures/search_response.py index 4b21b7f4b..2cee41619 100644 --- a/backend/tests/fixtures/search_response.py +++ b/backend/tests/fixtures/search_response.py @@ -21,14 +21,13 @@ def search_response(): }, }, "response": { - "num_found": 115, + "num_found": 101, "start": 0, "docs": [ { "id": "MONDO:0019391", "category": "biolink:Disease", "name": "Fanconi anemia", - "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.", "provided_by": "phenio_nodes", "synonym": [ "Fanconi anemia", @@ -40,12 +39,12 @@ def search_response(): "pancytopenia, congenital", "primary erythroid hypoplasia", ], + "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.", }, { "id": "MONDO:0001083", "category": "biolink:Disease", "name": "Fanconi renotubular syndrome", - "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.", "provided_by": "phenio_nodes", "synonym": [ "De toni-Fanconi syndrome", @@ -61,44 +60,44 @@ def search_response(): "infantile nephropathic cystinosis", "toni-debre-Fanconi syndrome", ], + "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.", }, { "id": "MONDO:0007600", "category": "biolink:Disease", "name": "primary Fanconi syndrome", - "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.", "provided_by": "phenio_nodes", "synonym": ["FRTS1", "Fanconi renotubular syndrome 1", "primary Fanconi renotubular syndrome"], + "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.", }, { "id": "MONDO:0009217", "category": "biolink:Disease", "name": "Fanconi-like syndrome", - "description": "A syndrome characterized by pancytopenia, immune deficiency and cutaneous malignancies.", "provided_by": "phenio_nodes", "synonym": ["Fanconi-like syndrome"], + "description": "A syndrome characterized by pancytopenia, immune deficiency and cutaneous malignancies.", }, { "id": "MONDO:0060778", "category": "biolink:Disease", "name": "adult Fanconi syndrome", - "description": "Probably related to a recessive gene, this is Fanconi Syndrome, characterized by adult onset.", "provided_by": "phenio_nodes", "synonym": ["adult Fanconi syndrome", "adult Fanconi's syndrome"], + "description": "Probably related to a recessive gene, this is Fanconi Syndrome, characterized by adult onset.", }, { "id": "MONDO:0060779", "category": "biolink:Disease", "name": "acquired Fanconi syndrome", - "description": "Fanconi Syndrome caused by exposure to noxious agents.", "provided_by": "phenio_nodes", "synonym": ["acquired Fanconi syndrome"], + "description": "Fanconi Syndrome caused by exposure to noxious agents.", }, { "id": "MONDO:0013247", "category": "biolink:Disease", "name": "Fanconi renotubular syndrome 2", - "description": "Any Fanconi syndrome in which the cause of the disease is a mutation in the SLC34A1 gene.", "provided_by": "phenio_nodes", "synonym": [ "FRTS2", @@ -107,12 +106,12 @@ def search_response(): "Fanconi syndrome caused by mutation in SLC34A1", "SLC34A1 Fanconi syndrome", ], + "description": "Any Fanconi syndrome in which the cause of the disease is a mutation in the SLC34A1 gene.", }, { "id": "MONDO:0014275", "category": "biolink:Disease", "name": "Fanconi renotubular syndrome 3", - "description": "Any Fanconi syndrome in which the cause of the disease is a mutation in the EHHADH gene.", "provided_by": "phenio_nodes", "synonym": [ "EHHADH Fanconi syndrome", @@ -121,6 +120,7 @@ def search_response(): "Fanconi renotubular syndrome type 3", "Fanconi syndrome caused by mutation in EHHADH", ], + "description": "Any Fanconi syndrome in which the cause of the disease is a mutation in the EHHADH gene.", }, { "id": "MONDO:0024525", @@ -156,15 +156,14 @@ def search_response(): "id": "MONDO:0100238", "category": "biolink:Disease", "name": "inherited Fanconi renotubular syndrome", - "description": "An instance of Fanconi renotubular syndrome that is inherited.", "provided_by": "phenio_nodes", "synonym": ["hereditary Fanconi renotubular syndrome"], + "description": "An instance of Fanconi renotubular syndrome that is inherited.", }, { "id": "MONDO:0009213", "category": "biolink:Disease", "name": "Fanconi anemia complementation group C", - "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.", "provided_by": "phenio_nodes", "synonym": [ "FA3", @@ -179,12 +178,12 @@ def search_response(): "Fanconi pancytopenia, type 3", "facc", ], + "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.", }, { "id": "MONDO:0009214", "category": "biolink:Disease", "name": "Fanconi anemia complementation group D2", - "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.", "provided_by": "phenio_nodes", "synonym": [ "FA4", @@ -197,12 +196,12 @@ def search_response(): "Fanconi pancytopenia type 4", "Fanconi pancytopenia, type 4", ], + "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.", }, { "id": "MONDO:0009215", "category": "biolink:Disease", "name": "Fanconi anemia complementation group A", - "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.", "provided_by": "phenio_nodes", "synonym": [ "Estren-Dameshek variant of Fanconi Anaemia", @@ -222,12 +221,12 @@ def search_response(): "Fanconi anemia complementation group type A", "Fanconi anemia, complementation group A", ], + "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.", }, { "id": "MONDO:0010351", "category": "biolink:Disease", "name": "Fanconi anemia complementation group B", - "description": "Fanconi anemia caused by mutations of the FANCB gene. This gene encodes the protein for complementation group B.", "provided_by": "phenio_nodes", "synonym": [ "FA2", @@ -242,12 +241,12 @@ def search_response(): "Fanconi pancytopenia type 2", "Fanconi pancytopenia, type 2", ], + "description": "Fanconi anemia caused by mutations of the FANCB gene. This gene encodes the protein for complementation group B.", }, { "id": "MONDO:0010953", "category": "biolink:Disease", "name": "Fanconi anemia complementation group E", - "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.", "provided_by": "phenio_nodes", "synonym": [ "FANCE", @@ -262,12 +261,12 @@ def search_response(): "Fanconi anemia, complementation group E", "face", ], + "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.", }, { "id": "MONDO:0011325", "category": "biolink:Disease", "name": "Fanconi anemia complementation group F", - "description": "Fanconi anemia caused by mutations of the FANCF gene. This gene encodes a polypeptide with homology to the prokaryotic RNA-binding protein ROM.", "provided_by": "phenio_nodes", "synonym": [ "FANCF", @@ -277,12 +276,12 @@ def search_response(): "Fanconi anemia complementation group type F", "Fanconi anemia, complementation group F", ], + "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:0011584", "category": "biolink:Disease", "name": "Fanconi anemia complementation group D1", - "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.", "provided_by": "phenio_nodes", "synonym": [ "FAD1", @@ -292,12 +291,12 @@ def search_response(): "Fanconi anemia, complementation group D1", "inherited cancer-predisposing syndrome due to biallelic BRCA2 mutations", ], + "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.", }, { "id": "MONDO:0012186", "category": "biolink:Disease", "name": "Fanconi anemia complementation group I", - "description": "Fanconi anemia caused by mutations in the FANCI gene, encoding Fanconi anemia group I protein.", "provided_by": "phenio_nodes", "synonym": [ "FANCI", @@ -308,12 +307,12 @@ def search_response(): "Fanconi anemia complementation group type I", "Fanconi anemia, complementation group I", ], + "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", - "description": "Fanconi anemia caused by mutations in the BRIP1 gene, encoding Fanconi anemia group J protein.", "provided_by": "phenio_nodes", "synonym": [ "FANCJ", @@ -323,6 +322,7 @@ def search_response(): "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.", }, ], }, diff --git a/frontend/fixtures/association-counts.json b/frontend/fixtures/association-counts.json index 207c58a9c..e85d8e815 100644 --- a/frontend/fixtures/association-counts.json +++ b/frontend/fixtures/association-counts.json @@ -2,7 +2,7 @@ "items": [ { "label": "Phenotypes", - "count": 4027, + "count": 3879, "category": "biolink:DiseaseToPhenotypicFeatureAssociation" }, { @@ -12,7 +12,7 @@ }, { "label": "Correlated Genes", - "count": 151, + "count": 139, "category": "biolink:CorrelatedGeneToDiseaseAssociation" } ] diff --git a/frontend/fixtures/association-table.json b/frontend/fixtures/association-table.json index 557c1160a..26bf26754 100644 --- a/frontend/fixtures/association-table.json +++ b/frontend/fixtures/association-table.json @@ -1,73 +1,61 @@ { "limit": 5, "offset": 0, - "total": 4027, + "total": 3879, "items": [ { - "id": "uuid:4677e7a0-842a-11ee-884f-6be035239f90", + "id": "uuid:8b925f4a-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0020793", "original_subject": "OMIM:164310", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018949", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", "MONDO:0000001", + "MONDO:0016106", + "MONDO:0005336", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0020120", + "MONDO:0700096", + "OGMS:0000031", + "BFO:0000017", + "MONDO:0018949", "MONDO:0025193", "MONDO:0020121", + "BFO:0000002", "MONDO:0020793", - "MONDO:0003847", - "BFO:0000001", "BFO:0000020", - "MONDO:0016106", - "MONDO:0005336", - "MONDO:0000462", - "BFO:0000017", + "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0002081", - "MONDO:0005328", - "BFO:0000002", - "MONDO:0005071", - "MONDO:0020120", - "MONDO:0019056", "MONDO:0700223", - "MONDO:0003382", - "BFO:0000016", - "MONDO:0700096", - "MONDO:0024458", - "OGMS:0000031" + "MONDO:0002081" ], "subject_label": "oculopharyngodistal myopathy 1", "subject_closure_label": [ - "eyelids malposition disorder", + "nervous system disorder", + "continuant", + "oculopharyngodistal myopathy 1", + "musculoskeletal system disorder", "disease", + "neuromuscular disease", + "skeletal muscle disorder", + "oculopharyngodistal myopathy", + "muscular dystrophy", + "progressive muscular dystrophy", + "myopathy", "realizable entity", - "disease", - "specifically dependent continuant", - "muscle tissue disorder", - "disorder of orbital region", + "human disease", "hereditary skeletal muscle disorder", - "continuant", - "eye adnexa disorder", - "eyelid disorder", "disposition", - "human disease", - "disorder of visual system", - "myopathy", - "distal myopathy", - "nervous system disorder", - "entity", - "progressive muscular dystrophy", - "musculoskeletal system disorder", + "disease", "hereditary disease", - "eye disorder", - "oculopharyngodistal myopathy", - "muscular dystrophy", - "oculopharyngodistal myopathy 1", - "skeletal muscle disorder", - "neuromuscular disease" + "muscle tissue disorder", + "distal myopathy", + "specifically dependent continuant", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, @@ -77,87 +65,55 @@ "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "UPHENO:0002816", - "BFO:0000001", - "UBERON:0000465", + "HP:0000001", "UPHENO:0082875", - "BFO:0000040", - "UBERON:0011216", "HP:0001324", "UPHENO:0080555", - "HP:0011804", - "BFO:0000002", - "UPHENO:0001001", - "UPHENO:0001002", - "BFO:0000020", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "UBERON:0001062", "UPHENO:0001005", - "HP:0033127", - "BFO:0000004", - "UBERON:0000061", - "UBERON:0000062", - "UBERON:0000468", - "UPHENO:0075696", + "UPHENO:0001002", "HP:0003011", - "UPHENO:0002320", - "HP:0000118", - "BFO:0000002", + "UPHENO:0075696", "UPHENO:0002332", + "UPHENO:0001003", + "UPHENO:0080556", + "UPHENO:0002320", + "BFO:0000020", "HP:0002460", + "UPHENO:0002816", + "UPHENO:0002536", + "HP:0011804", "PATO:0000001", - "UBERON:0010000", - "HP:0000001", - "UPHENO:0080556", - "UBERON:0000467", - "UBERON:0005090", - "UBERON:0001630", - "UBERON:0000383", - "UBERON:0001015" + "UPHENO:0001001", + "HP:0000118", + "BFO:0000002", + "HP:0033127", + "BFO:0000001" ], - "object_label": "Distal muscle weakness (HPO)", + "object_label": "Distal muscle weakness", "object_closure_label": [ - "abnormality of anatomical entity physiology", - "Phenotypic abnormality", - "specifically dependent continuant", - "quality", + "All", + "Abnormality of the musculoskeletal system", "abnormal phenotype by ontology source", - "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)", + "Phenotypic abnormality", + "Phenotypic abnormality", "continuant", - "decreased muscle organ strength", - "Distal muscle weakness (HPO)", + "Abnormality of the musculature", + "abnormality of anatomical entity physiology", + "Distal muscle weakness", "entity", - "multicellular anatomical structure", - "Muscle weakness (HPO)", - "anatomical entity", - "organ", - "multicellular organism", - "phenotype", - "independent continuant", + "abnormality of muscle organ physiology", "decreased anatomical entity strength", - "Abnormality of the musculoskeletal system (HPO)", - "entity", - "material entity", - "anatomical structure", - "musculature of body", - "musculature", "abnormal anatomical entity", + "phenotype by ontology source", + "phenotype", + "Abnormal muscle physiology", + "quality", "abnormality of anatomical entity physiology", - "anatomical system", - "muscle structure" + "abnormal musculature", + "abnormal anatomical entity", + "Muscle weakness", + "specifically dependent continuant", + "decreased muscle organ strength" ], "object_taxon": null, "object_taxon_label": null, @@ -183,15 +139,15 @@ "publications_links": [ { "id": "PMID:21242490", - "url": null + "url": "http://identifiers.org/pubmed/21242490" }, { "id": "PMID:32493488", - "url": null + "url": "http://identifiers.org/pubmed/32493488" }, { "id": "PMID:31332380", - "url": null + "url": "http://identifiers.org/pubmed/31332380" } ], "qualifiers": [], @@ -204,15 +160,11 @@ "qualifiers_category": null, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_label": "Frequent", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": [ - "Frequency (HPO)", - "Frequent (HPO)", - "All (HPO)" - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -231,70 +183,58 @@ "direction": "outgoing" }, { - "id": "uuid:4677e7b1-842a-11ee-884f-6be035239f90", + "id": "uuid:8b925f5b-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0020793", "original_subject": "OMIM:164310", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0018949", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", "MONDO:0000001", + "MONDO:0016106", + "MONDO:0005336", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0020120", + "MONDO:0700096", + "OGMS:0000031", + "BFO:0000017", + "MONDO:0018949", "MONDO:0025193", "MONDO:0020121", + "BFO:0000002", "MONDO:0020793", - "MONDO:0003847", - "BFO:0000001", "BFO:0000020", - "MONDO:0016106", - "MONDO:0005336", - "MONDO:0000462", - "BFO:0000017", + "MONDO:0003847", "MONDO:0003939", - "MONDO:0002022", - "MONDO:0002081", - "MONDO:0005328", - "BFO:0000002", - "MONDO:0005071", - "MONDO:0020120", - "MONDO:0019056", "MONDO:0700223", - "MONDO:0003382", - "BFO:0000016", - "MONDO:0700096", - "MONDO:0024458", - "OGMS:0000031" + "MONDO:0002081" ], "subject_label": "oculopharyngodistal myopathy 1", "subject_closure_label": [ - "eyelids malposition disorder", + "nervous system disorder", + "continuant", + "oculopharyngodistal myopathy 1", + "musculoskeletal system disorder", "disease", + "neuromuscular disease", + "skeletal muscle disorder", + "oculopharyngodistal myopathy", + "muscular dystrophy", + "progressive muscular dystrophy", + "myopathy", "realizable entity", - "disease", - "specifically dependent continuant", - "muscle tissue disorder", - "disorder of orbital region", + "human disease", "hereditary skeletal muscle disorder", - "continuant", - "eye adnexa disorder", - "eyelid disorder", "disposition", - "human disease", - "disorder of visual system", - "myopathy", - "distal myopathy", - "nervous system disorder", - "entity", - "progressive muscular dystrophy", - "musculoskeletal system disorder", + "disease", "hereditary disease", - "eye disorder", - "oculopharyngodistal myopathy", - "muscular dystrophy", - "oculopharyngodistal myopathy 1", - "skeletal muscle disorder", - "neuromuscular disease" + "muscle tissue disorder", + "distal myopathy", + "specifically dependent continuant", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, @@ -304,141 +244,71 @@ "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "UPHENO:0002443", + "HP:0000001", "UPHENO:0002471", "HP:0025270", - "UPHENO:0002536", - "UBERON:0000465", - "RO:0002577", + "UPHENO:0002725", + "UPHENO:0002433", "UPHENO:0082875", "HP:0002664", - "UPHENO:0004523", "BFO:0000001", - "BFO:0000040", - "UBERON:0001062", - "UBERON:0011676", - "UBERON:0013701", - "BFO:0000020", - "HP:0011793", - "BFO:0000002", - "UBERON:0005409", - "UPHENO:0001001", + "UPHENO:0075696", + "UPHENO:0002332", + "HP:0000707", + "UPHENO:0001003", + "HP:0011024", + "UPHENO:0002443", "UPHENO:0002833", "HP:0002015", "UPHENO:0001002", - "UPHENO:0001003", - "UPHENO:0075696", - "UPHENO:0002433", "HP:0025031", "UPHENO:0002474", "HP:0012638", - "BFO:0000004", - "UBERON:0000061", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0004111", - "UBERON:0000468", - "HP:0011024", - "UPHENO:0002725", + "UPHENO:0001001", + "HP:0012719", "BFO:0000002", + "BFO:0000020", + "HP:0011793", + "UPHENO:0004523", "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", + "UPHENO:0002536", "PATO:0000001", - "UBERON:0001555", - "UBERON:0004921", - "HP:0000001", - "HP:0012719", "UPHENO:0001005", - "HP:0000707", - "BFO:0000001", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0000064", - "UBERON:0001007", - "UBERON:0001016", - "UBERON:0013522", - "UBERON:0005178", - "UBERON:0004908" + "HP:0000118" ], - "object_label": "Dysphagia (HPO)", + "object_label": "Dysphagia", "object_closure_label": [ + "All", + "abnormality of alimentary part of gastrointestinal system physiology", + "Abnormal esophagus physiology", + "continuant", + "Neoplasm", + "Phenotypic abnormality", "abnormality of anatomical entity physiology", + "Neoplasm by anatomical site", + "abnormal nervous system", + "phenotype", + "Functional abnormality of the gastrointestinal tract", + "abnormal anatomical entity", "abnormal digestive system", - "Dysphagia (HPO)", + "Dysphagia", "Phenotypic abnormality", - "quality", - "abnormal anatomical entity", - "specifically dependent continuant", - "Abnormality of digestive system physiology (HPO)", + "Abnormality of the nervous system", "phenotype by ontology source", - "abnormal nervous system", - "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", + "quality", + "abnormality of anatomical entity physiology", "abnormal alimentary part of gastrointestinal system", - "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "entity", - "thoracic cavity element", - "upper digestive tract", "abnormality of nervous system physiology", - "Neoplasm by anatomical site (HPO)", - "organism subdivision", - "organ", - "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", - "Abnormality of the gastrointestinal tract (HPO)", - "abnormality of anatomical entity physiology", + "Abnormality of digestive system physiology", "abnormal anatomical entity", - "multicellular anatomical structure", - "anatomical system", - "digestive tract", - "subdivision of digestive tract" + "Abnormality of the digestive system", + "abnormality of esophagus physiology", + "Abnormal nervous system physiology", + "Abnormality of the gastrointestinal tract", + "abnormality of digestive system physiology", + "specifically dependent continuant", + "entity" ], "object_taxon": null, "object_taxon_label": null, @@ -464,15 +334,15 @@ "publications_links": [ { "id": "PMID:21242490", - "url": null + "url": "http://identifiers.org/pubmed/21242490" }, { "id": "PMID:32493488", - "url": null + "url": "http://identifiers.org/pubmed/32493488" }, { "id": "PMID:31332380", - "url": null + "url": "http://identifiers.org/pubmed/31332380" } ], "qualifiers": [], @@ -485,15 +355,11 @@ "qualifiers_category": null, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_label": "Frequent", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": [ - "Frequency (HPO)", - "Frequent (HPO)", - "All (HPO)" - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -512,84 +378,84 @@ "direction": "outgoing" }, { - "id": "uuid:42ef70e0-842a-11ee-884f-6be035239f90", + "id": "uuid:8904bb34-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0013049", "original_subject": "OMIM:612937", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0016333", - "MONDO:0002320", + "MONDO:0004994", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0019052", "MONDO:0000001", - "MONDO:0013049", - "MONDO:0020121", - "MONDO:0003847", - "BFO:0000001", - "MONDO:0018276", - "BFO:0000020", "MONDO:0005336", - "MONDO:0019052", - "MONDO:0005500", - "MONDO:0005066", - "MONDO:0024322", - "BFO:0000017", - "MONDO:0003939", - "MONDO:0002081", - "MONDO:0005021", - "MONDO:0019950", + "OGMS:0000031", "BFO:0000002", "MONDO:0005217", - "MONDO:0015286", - "MONDO:0005071", + "MONDO:0019056", + "BFO:0000001", "MONDO:0005267", "MONDO:0020120", - "MONDO:0019056", - "MONDO:0004994", - "MONDO:0004995", - "MONDO:0700223", - "BFO:0000016", "MONDO:0700096", - "MONDO:0000591", + "MONDO:0005021", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0024322", + "BFO:0000017", "MONDO:0017749", - "OGMS:0000031" + "MONDO:0015286", + "MONDO:0020121", + "MONDO:0004995", + "BFO:0000020", + "MONDO:0000591", + "MONDO:0013049", + "MONDO:0016333", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005500", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", + "MONDO:0002320" ], "subject_label": "DPM3-congenital disorder of glycosylation", "subject_closure_label": [ + "cardiomyopathy", + "nervous system disorder", + "musculoskeletal system disorder", + "dilated cardiomyopathy", + "neuromuscular disease", + "familial cardiomyopathy", + "skeletal muscle disorder", + "intrinsic cardiomyopathy", + "congenital nervous system disorder", + "muscular dystrophy", + "cardiovascular disorder", + "continuant", + "myopathy", "disease", + "congenital muscular dystrophy", + "DPM3-congenital disorder of glycosylation", "disorder of glycosylation", "realizable entity", - "disorder of multiple glycosylation", - "disease", - "specifically dependent continuant", - "familial cardiomyopathy", - "muscle tissue disorder", - "cardiomyopathy", - "cardiovascular disorder", + "human disease", + "congenital disorder of glycosylation", "hereditary skeletal muscle disorder", - "continuant", - "inborn errors of metabolism", + "disposition", + "disorder of multiple glycosylation", "congenital disorder of glycosylation type I", "metabolic disease", - "disposition", - "human disease", - "intrinsic cardiomyopathy", - "muscular dystrophy-dystroglycanopathy", - "myopathy", - "dilated cardiomyopathy", - "nervous system disorder", + "disease", "heart disorder", - "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" + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "muscular dystrophy-dystroglycanopathy", + "specifically dependent continuant", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, @@ -599,203 +465,71 @@ "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:0004536", - "UPHENO:0051668", - "HP:0001871", - "UPHENO:0077821", + "HP:0000001", + "HP:0011021", + "UPHENO:0051763", + "UPHENO:0004459", "BFO:0000001", - "GO:0008150", - "BFO:0000040", - "UBERON:0000468", + "HP:0004364", "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:0002193", - "UBERON:0002390", - "UBERON:0000179", - "UPHENO:0001001", - "UPHENO:0051763", - "UPHENO:0051801", - "UPHENO:0001003", "UPHENO:0081547", "UPHENO:0077826", - "BFO:0000001", - "UBERON:0001062", - "UBERON:0000061", - "UBERON:0000463", - "CHEBI:50047", - "CHEBI:37622", - "CHEBI:33256", - "UPHENO:0075696", - "UPHENO:0076286", - "HP:0040081", - "HP:0002795", - "HP:0012415", + "HP:0032180", + "UPHENO:0076289", + "HP:0001871", + "UPHENO:0001003", + "UPHENO:0051801", + "HP:0001939", "UPHENO:0051612", "UPHENO:0051804", - "BFO:0000015", - "BFO:0000004", - "GO:0032991", - "CHEBI:23367", - "UBERON:0000178", - "UBERON:0004120", - "UBERON:0006314", - "GO:0061695", - "CHEBI:16670", - "CHEBI:33302", - "CHEBI:33304", - "CHEBI:33582", - "GO:0002185", - "CHEBI:15841", - "CHEBI:51143", - "CHEBI:25806", - "CHEBI:36962", - "CHEBI:50860", - "UPHENO:0077817", - "UPHENO:0076289", - "UPHENO:0002448", - "UPHENO:0002536", - "HP:0032180", + "UPHENO:0077821", + "BFO:0000020", + "HP:0010876", "PATO:0000001", - "CHEBI:138675", - "UPHENO:0077825", - "HP:0000118", - "UPHENO:0004459", - "UPHENO:0002332", - "HP:0500165", - "HP:0000001", - "HP:0011021", - "UPHENO:0001005", + "UPHENO:0051668", "BFO:0000002", - "HP:0010876", - "HP:0001939", - "GO:0008152", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0001004" + "UPHENO:0046284", + "UPHENO:0002536", + "HP:0003236", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0000118", + "UPHENO:0076286", + "HP:0040081" ], - "object_label": "Elevated circulating creatine kinase concentration (HPO)", + "object_label": "Elevated circulating creatine kinase concentration", "object_closure_label": [ - "Abnormal circulating nitrogen compound concentration (HPO)", - "abnormality of anatomical entity physiology", - "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 role bodily fluid level", - "abnormal blood nitrogen molecular entity level", - "occurrent", - "continuant", - "cellular_component", - "chemical entity", - "protein-containing material entity", - "material anatomical entity", - "transferase complex", - "macromolecule", - "p-block molecular entity", - "respiratory system", - "All (HPO)", - "Abnormality of circulating enzyme level (HPO)", - "abnormal phenotype by ontology source", - "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", + "All", + "Abnormality of circulating enzyme level", "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)", + "abnormal independent continuant nitrogen molecular entity level", + "abnormal role blood level", + "Abnormal circulating creatine kinase concentration", + "Abnormality of blood and blood-forming tissues", "entity", - "Phenotypic abnormality", - "abnormal independent continuant gas molecular entity level", "quality", - "anatomical entity", - "anatomical structure", - "organism substance", - "mesoderm-derived structure", - "bodily fluid", - "transferase complex, transferring phosphorus-containing groups", - "peptide", - "pnictogen molecular entity", - "chalcogen molecular entity", - "carbon group molecular entity", - "carboxamide", - "primary amide", - "organic amino compound", + "Phenotypic abnormality", + "Abnormal circulating protein concentration", + "abnormal role bodily fluid level", + "abnormal blood nitrogen molecular entity level", + "Abnormal circulating metabolite concentration", + "abnormal role independent continuant level", + "abnormal independent continuant chemical entity level", + "phenotype by ontology source", "phenotype", + "abnormal phenotype by ontology source", "continuant", - "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 hematopoietic system", + "Abnormality of metabolism/homeostasis", + "Elevated circulating creatine kinase concentration", + "Abnormal circulating nitrogen compound concentration", + "abnormal chemical entity level", + "abnormal anatomical entity", "abnormal blood protein polypeptide chain level", "abnormal blood chemical entity level", - "biological_process", - "material entity", - "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", - "gas molecular entity", - "creatine kinase complex", - "polypeptide", - "nitrogen molecular entity", - "oxygen molecular entity", - "organochalcogen compound", - "organic molecular entity" + "Phenotypic abnormality", + "specifically dependent continuant", + "abnormal independent continuant protein polypeptide chain level" ], "object_taxon": null, "object_taxon_label": null, @@ -821,11 +555,11 @@ "publications_links": [ { "id": "PMID:19576565", - "url": null + "url": "http://identifiers.org/pubmed/19576565" }, { "id": "PMID:28803818", - "url": null + "url": "http://identifiers.org/pubmed/28803818" } ], "qualifiers": [], @@ -838,15 +572,11 @@ "qualifiers_category": null, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_label": "Obligate", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040279", "HP:0000001", "HP:0040280"], - "frequency_qualifier_closure_label": [ - "Obligate (HPO)", - "Frequency (HPO)", - "All (HPO)" - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Obligate"], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -865,64 +595,64 @@ "direction": "outgoing" }, { - "id": "uuid:476a1081-842a-11ee-884f-6be035239f90", + "id": "uuid:8c422f2b-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0009681", "original_subject": "OMIM:254090", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0002320", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0000355", "MONDO:0000001", - "MONDO:0020121", - "MONDO:0019952", - "MONDO:0003847", "MONDO:0005336", - "MONDO:0000355", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0020120", + "MONDO:0700096", + "OGMS:0000031", + "MONDO:0019950", "BFO:0000017", - "MONDO:0100225", + "MONDO:0016139", + "MONDO:0020121", + "MONDO:0019952", "BFO:0000020", + "MONDO:0100225", + "MONDO:0009681", + "MONDO:0003847", "MONDO:0003939", - "MONDO:0002081", - "MONDO:0019950", - "MONDO:0005071", - "BFO:0000002", - "MONDO:0020120", - "MONDO:0019056", "MONDO:0700223", - "BFO:0000016", - "MONDO:0016139", - "MONDO:0700096", - "MONDO:0009681", - "OGMS:0000031", - "BFO:0000001" + "BFO:0000002", + "MONDO:0002081", + "MONDO:0002320" ], "subject_label": "Ullrich congenital muscular dystrophy 1", "subject_closure_label": [ + "nervous system disorder", + "congenital myopathy", + "musculoskeletal system disorder", "disease", - "realizable entity", - "collagen 6-related myopathy", - "specifically dependent continuant", + "neuromuscular disease", + "continuant", + "skeletal muscle disorder", "Ullrich congenital muscular dystrophy 1", + "congenital nervous system disorder", + "muscular dystrophy", + "myopathy", + "congenital muscular dystrophy", + "realizable entity", + "human disease", + "hereditary skeletal muscle disorder", + "disposition", "disease", + "hereditary disease", "muscle tissue disorder", - "hereditary skeletal muscle disorder", "Ullrich congenital muscular dystrophy", - "continuant", - "disposition", + "specifically dependent continuant", + "collagen 6-related myopathy", "qualitative or quantitative protein defects in neuromuscular diseases", - "human disease", - "entity", - "myopathy", - "nervous system disorder", - "musculoskeletal system disorder", - "hereditary disease", - "congenital nervous system disorder", - "congenital muscular dystrophy", - "muscular dystrophy", - "congenital myopathy", - "skeletal muscle disorder", - "neuromuscular disease" + "entity" ], "subject_taxon": null, "subject_taxon_label": null, @@ -932,91 +662,55 @@ "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0011729", + "HP:0000001", + "HP:0020152", + "HP:0034430", + "HP:0000924", "HP:0011843", - "UBERON:0000465", "UPHENO:0082875", - "HP:0001388", - "BFO:0000001", - "BFO:0000040", - "UBERON:0011216", - "UBERON:0034921", "UPHENO:0001002", - "BFO:0000020", - "BFO:0000002", - "UPHENO:0001001", - "UPHENO:0002964", - "UPHENO:0001003", "UPHENO:0081440", + "HP:0001388", "BFO:0000001", - "UBERON:0001062", - "UBERON:0000061", - "UBERON:0034925", "UPHENO:0075696", - "UPHENO:0001005", - "HP:0033127", - "BFO:0000004", - "UBERON:0004770", - "UBERON:0000468", - "HP:0034430", - "HP:0000924", + "UPHENO:0002332", + "UPHENO:0001003", + "UPHENO:0002964", + "BFO:0000020", + "PATO:0000001", "BFO:0000002", "UPHENO:0002536", + "UPHENO:0001001", + "HP:0011729", + "UPHENO:0001005", "HP:0000118", - "UPHENO:0002332", - "PATO:0000001", - "UBERON:0000982", - "HP:0000001", - "HP:0020152", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0002204", - "UBERON:0004905", - "UBERON:0001434" + "HP:0033127" ], - "object_label": "Distal joint laxity (HPO)", + "object_label": "Distal joint laxity", "object_closure_label": [ - "abnormality of anatomical entity physiology", - "Joint laxity (HPO)", - "abnormal skeletal system", - "abnormal anatomical entity", + "All", + "Distal joint laxity", + "Abnormality of the musculoskeletal system", + "Joint laxity", "quality", + "Phenotypic abnormality", + "abnormality of anatomical entity physiology", + "abnormality of musculoskeletal system physiology", "abnormal anatomical entity", - "abnormal phenotype by ontology source", - "specifically dependent continuant", "phenotype by ontology source", - "abnormality of musculoskeletal system physiology", - "continuant", - "material anatomical entity", - "musculoskeletal system", - "All (HPO)", - "Distal joint laxity (HPO)", + "Abnormal musculoskeletal physiology", + "phenotype", + "Abnormality of joint mobility", + "abnormal phenotype by ontology source", "continuant", - "organ system subdivision", - "multi organ part structure", + "abnormality of anatomical entity physiology", "Abnormal joint physiology", - "Abnormality of the skeletal system (HPO)", - "Phenotypic abnormality (HPO)", - "entity", + "Abnormality of the skeletal system", + "abnormal anatomical 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", - "abnormality of anatomical entity physiology", - "multicellular anatomical structure", - "anatomical system", - "skeletal joint" + "specifically dependent continuant", + "abnormal skeletal system", + "entity" ], "object_taxon": null, "object_taxon_label": null, @@ -1042,11 +736,11 @@ "publications_links": [ { "id": "PMID:16258657", - "url": null + "url": "http://identifiers.org/pubmed/16258657" }, { "id": "OMIM:254090", - "url": null + "url": "http://identifiers.org/mim/254090" } ], "qualifiers": [], @@ -1059,15 +753,11 @@ "qualifiers_category": null, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_label": "Obligate", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040279", "HP:0000001", "HP:0040280"], - "frequency_qualifier_closure_label": [ - "Obligate (HPO)", - "Frequency (HPO)", - "All (HPO)" - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Obligate"], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -1086,66 +776,66 @@ "direction": "outgoing" }, { - "id": "uuid:46170673-842a-11ee-884f-6be035239f90", + "id": "uuid:8b4c43bf-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", "subject": "MONDO:0009676", "original_subject": "OMIM:253601", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0016145", + "MONDO:0005071", + "MONDO:0006025", + "BFO:0000016", + "MONDO:0009676", "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:0016971", - "MONDO:0005071", - "MONDO:0020120", + "MONDO:0000429", "MONDO:0019056", - "MONDO:0700223", - "BFO:0000016", - "MONDO:0016139", + "BFO:0000001", + "MONDO:0020120", "MONDO:0700096", "OGMS:0000031", - "BFO:0000001" + "MONDO:0016145", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0016971", + "MONDO:0020121", + "BFO:0000002", + "BFO:0000020", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0700223", + "MONDO:0002081", + "MONDO:0015152" ], "subject_label": "autosomal recessive limb-girdle muscular dystrophy type 2B", "subject_closure_label": [ - "disease", - "realizable entity", - "disease", - "specifically dependent continuant", - "muscle tissue disorder", - "hereditary skeletal muscle disorder", + "nervous system disorder", "continuant", - "limb-girdle muscular dystrophy", - "disposition", - "qualitative or quantitative protein defects in neuromuscular diseases", - "human disease", - "entity", + "musculoskeletal system disorder", + "disease", "autosomal genetic disease", - "autosomal recessive disease", - "myopathy", - "nervous system disorder", + "neuromuscular disease", "autosomal recessive limb-girdle muscular dystrophy type 2B", + "skeletal muscle disorder", "autosomal recessive limb-girdle muscular dystrophy", - "qualitative or quantitative defects of dysferlin", + "limb-girdle muscular dystrophy", + "muscular dystrophy", "progressive muscular dystrophy", - "musculoskeletal system disorder", + "myopathy", + "realizable entity", + "human disease", + "hereditary skeletal muscle disorder", + "disposition", + "disease", + "autosomal recessive disease", "hereditary disease", - "muscular dystrophy", - "skeletal muscle disorder", - "neuromuscular disease" + "muscle tissue disorder", + "qualitative or quantitative defects of dysferlin", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, @@ -1155,87 +845,55 @@ "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "UPHENO:0002816", - "UPHENO:0002536", - "UBERON:0000465", + "HP:0000001", "UPHENO:0082875", - "BFO:0000040", - "UBERON:0001062", - "UBERON:0011216", "UPHENO:0001002", "HP:0001324", "UPHENO:0080555", - "HP:0011804", - "BFO:0000002", - "UPHENO:0001001", - "HP:0003701", - "UPHENO:0001003", + "HP:0003011", "BFO:0000001", - "BFO:0000020", - "HP:0033127", - "BFO:0000004", - "UBERON:0000061", - "UBERON:0000062", - "UBERON:0000468", "UPHENO:0075696", - "BFO:0000002", - "HP:0003011", - "UPHENO:0002320", - "HP:0000118", "UPHENO:0002332", + "UPHENO:0001003", + "HP:0003701", + "UPHENO:0080556", + "UPHENO:0002320", + "UPHENO:0001001", + "BFO:0000002", + "BFO:0000020", "PATO:0000001", - "HP:0000001", + "UPHENO:0002816", + "UPHENO:0002536", + "HP:0011804", "UPHENO:0001005", - "UPHENO:0080556", - "BFO:0000001", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0005090", - "UBERON:0001630", - "UBERON:0000383", - "UBERON:0001015" + "HP:0000118", + "HP:0033127" ], - "object_label": "Proximal muscle weakness (HPO)", + "object_label": "Proximal muscle weakness", "object_closure_label": [ - "abnormality of anatomical entity physiology", - "Proximal muscle weakness (HPO)", - "quality", - "Abnormality of the musculature (HPO)", - "phenotype by ontology source", - "continuant", - "material anatomical entity", - "muscle organ", - "All (HPO)", - "abnormal phenotype by ontology source", + "All", "continuant", - "abnormal musculature", - "Abnormal muscle physiology (HPO)", - "organ system subdivision", - "abnormality of muscle organ physiology", - "Phenotypic abnormality (HPO)", - "decreased muscle organ strength", - "entity", - "entity", + "Abnormality of the musculoskeletal system", + "quality", "Phenotypic abnormality", - "Muscle weakness (HPO)", - "specifically dependent continuant", - "organ", - "multicellular organism", + "Abnormality of the musculature", + "abnormality of anatomical entity physiology", + "abnormality of muscle organ physiology", "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", + "Proximal muscle weakness", + "phenotype by ontology source", + "abnormal phenotype by ontology source", + "Abnormal muscle physiology", "abnormality of anatomical entity physiology", + "abnormal musculature", "abnormal anatomical entity", - "multicellular anatomical structure", - "anatomical system", - "muscle structure" + "Phenotypic abnormality", + "Muscle weakness", + "specifically dependent continuant", + "decreased muscle organ strength", + "entity" ], "object_taxon": null, "object_taxon_label": null, @@ -1261,11 +919,11 @@ "publications_links": [ { "id": "PMID:9731527", - "url": null + "url": "http://identifiers.org/pubmed/9731527" }, { "id": "PMID:9009996", - "url": null + "url": "http://identifiers.org/pubmed/9009996" } ], "qualifiers": [], @@ -1278,15 +936,11 @@ "qualifiers_category": null, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Obligate (HPO)", + "frequency_qualifier_label": "Obligate", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040279", "HP:0000001", "HP:0040280"], - "frequency_qualifier_closure_label": [ - "Obligate (HPO)", - "Frequency (HPO)", - "All (HPO)" - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Obligate"], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, diff --git a/frontend/fixtures/associations.json b/frontend/fixtures/associations.json index 7d30eeee4..20b6f41f5 100644 --- a/frontend/fixtures/associations.json +++ b/frontend/fixtures/associations.json @@ -1,135 +1,175 @@ { "limit": 20, "offset": 0, - "total": 4838, + "total": 4624, "items": [ { - "id": "uuid:4e12a2a1-842a-11ee-884f-6be035239f90", + "id": "uuid:89e15863-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035432", - "original_subject": "Orphanet:565899", + "subject": "MONDO:0013904", + "original_subject": "OMIM:614830", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0005071", + "BFO:0000016", + "MONDO:0019052", "MONDO:0000001", - "MONDO:0020121", - "MONDO:0003847", - "BFO:0000001", - "MONDO:0016106", "MONDO:0005336", + "OGMS:0000031", + "MONDO:0700069", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0000171", + "MONDO:0020120", + "MONDO:0700096", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0700075", + "MONDO:0024322", "BFO:0000017", - "MONDO:0003939", - "MONDO:0035432", - "BFO:0000020", - "MONDO:0002081", - "MONDO:0016971", - "MONDO:0005071", + "MONDO:0013904", + "MONDO:0015286", + "MONDO:0017741", + "MONDO:0020121", "BFO:0000002", - "MONDO:0020120", - "MONDO:0019056", + "BFO:0000020", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", "MONDO:0700223", - "BFO:0000016", - "MONDO:0700096", - "OGMS:0000031" + "MONDO:0002081", + "MONDO:0002320" ], - "subject_label": "POMGNT2-related limb-girdle muscular dystrophy R24", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", "subject_closure_label": [ + "nervous system disorder", + "continuant", + "musculoskeletal system disorder", + "muscular dystrophy-dystroglycanopathy, type A", + "myopathy caused by variation in POMGNT2", + "neuromuscular disease", + "skeletal muscle disorder", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", + "muscular dystrophy", + "myopathy", "disease", + "congenital muscular dystrophy", + "congenital muscular dystrophy caused by variation in POMGNT2", + "disorder of glycosylation", "realizable entity", - "disease", - "POMGNT2-related limb-girdle muscular dystrophy R24", - "muscle tissue disorder", + "human disease", + "congenital disorder of glycosylation", "hereditary skeletal muscle disorder", - "limb-girdle muscular dystrophy", - "continuant", "disposition", - "human disease", - "specifically dependent continuant", - "myopathy", - "nervous system disorder", - "entity", - "progressive muscular dystrophy", - "musculoskeletal system disorder", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", + "metabolic disease", + "disease", "hereditary disease", - "muscular dystrophy", - "skeletal muscle disorder", - "neuromuscular disease" + "muscle tissue disorder", + "inborn errors of metabolism", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0002465", + "object": "HP:0007260", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "UPHENO:0002536", - "BFO:0000001", - "UBERON:0000465", - "UPHENO:0082875", - "BFO:0000002", - "UPHENO:0004523", - "BFO:0000040", - "UBERON:0001062", + "HP:0000001", + "HP:0002060", + "HP:0100547", + "UPHENO:0081603", + "HP:0012443", + "HP:0002538", "UPHENO:0001002", - "BFO:0000020", - "BFO:0000002", - "UPHENO:0001001", - "UPHENO:0001003", + "UPHENO:0076791", + "UPHENO:0087518", + "UPHENO:0076799", + "HP:0001339", + "UPHENO:0001005", "BFO:0000001", "UPHENO:0075696", - "UPHENO:0002433", - "HP:0012638", - "BFO:0000004", - "UBERON:0000061", - "UBERON:0000468", - "HP:0002167", + "HP:0000707", + "UPHENO:0001003", + "UPHENO:0076692", + "UPHENO:0049643", + "UPHENO:0076702", + "UPHENO:0015280", + "UPHENO:0081435", + "HP:0012639", + "UPHENO:0020888", + "UPHENO:0049587", + "HP:0002269", + "BFO:0000002", + "BFO:0000020", + "HP:0002536", + "UPHENO:0004523", "PATO:0000001", + "UPHENO:0049852", + "UPHENO:0087531", + "HP:0002011", + "HP:0007260", + "UPHENO:0076805", + "UPHENO:0050121", + "UPHENO:0049855", + "UPHENO:0002536", + "UPHENO:0001001", "HP:0000118", - "UPHENO:0002332", - "HP:0000001", - "HP:0002465", - "UPHENO:0001005", - "HP:0000707", - "HP:0011446", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0001016" + "UPHENO:0049634", + "UPHENO:0020584" ], - "object_label": "Poor speech (HPO)", + "object_label": "Type II lissencephaly", "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", + "All", + "Abnormal cerebral morphology", "continuant", - "material anatomical entity", - "nervous system", - "All (HPO)", - "Poor speech (HPO)", + "abnormal cell motility", + "abnormal anatomical entity morphology", + "Lissencephaly", + "abnormal cerebral hemisphere morphology", + "Abnormality of brain morphology", + "quality", + "abnormal neuron migration", "abnormal phenotype by ontology source", - "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "entity", "Phenotypic abnormality", - "abnormality of nervous system physiology", - "quality", - "multicellular organism", + "Abnormal cortical gyration", + "abnormal nervous system", + "Abnormality of neuronal migration", + "abnormal telencephalon morphology", + "abnormal cell migration", + "abnormal nervous system morphology", + "abnormal anatomical entity", + "Abnormality of the nervous system", + "phenotype by ontology source", + "abnormal biological_process", "phenotype", - "independent continuant", - "entity", - "Abnormal nervous system physiology (HPO)", - "material entity", - "anatomical entity", - "anatomical structure", - "continuant", - "abnormality of anatomical entity physiology", + "Morphological central nervous system abnormality", + "Type II lissencephaly", + "abnormal brain morphology", + "abnormal cellular process", + "Abnormal forebrain morphology", + "abnormal cerebral cortex morphology", + "abnormal anatomical entity morphology in the brain", + "Abnormal nervous system morphology", + "abnormal forebrain morphology", + "Abnormal cerebral cortex morphology", + "abnormal locomotion", "abnormal anatomical entity", - "multicellular anatomical structure", - "anatomical system" + "Phenotypic abnormality", + "abnormal central nervous system morphology", + "abnormal forebrain morphology", + "specifically dependent continuant", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "entity" ], "object_taxon": null, "object_taxon_label": null, @@ -138,28 +178,28 @@ "negated": null, "pathway": null, "evidence_count": 2, - "has_evidence": ["ECO:0000304"], + "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { - "id": "ECO:0000304", - "url": "http://purl.obolibrary.org/obo/ECO_0000304" + "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], - "grouping_key": "MONDO:0035432🍪🍪biolink:has_phenotype🍪HP:0002465", + "grouping_key": "MONDO:0013904🍪🍪biolink:has_phenotype🍪HP:0007260", "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:565899"], + "publications": ["PMID:22958903"], "publications_links": [ { - "id": "orphanet:565899", - "url": null + "id": "PMID:22958903", + "url": "http://identifiers.org/pubmed/22958903" } ], "qualifiers": [], - "frequency_qualifier": "HP:0040282", + "frequency_qualifier": "HP:0040280", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, @@ -168,15 +208,11 @@ "qualifiers_category": null, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_label": "Obligate", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": [ - "Frequency (HPO)", - "Frequent (HPO)", - "All (HPO)" - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Obligate"], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -194,258 +230,174 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:4e12a2a3-842a-11ee-884f-6be035239f90", + "id": "uuid:89e15864-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035432", - "original_subject": "Orphanet:565899", + "subject": "MONDO:0013904", + "original_subject": "OMIM:614830", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0005071", + "BFO:0000016", + "MONDO:0019052", "MONDO:0000001", - "MONDO:0020121", - "MONDO:0003847", - "BFO:0000001", - "MONDO:0016106", "MONDO:0005336", + "OGMS:0000031", + "MONDO:0700069", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0000171", + "MONDO:0020120", + "MONDO:0700096", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0700075", + "MONDO:0024322", "BFO:0000017", - "MONDO:0003939", - "MONDO:0035432", - "BFO:0000020", - "MONDO:0002081", - "MONDO:0016971", - "MONDO:0005071", + "MONDO:0013904", + "MONDO:0015286", + "MONDO:0017741", + "MONDO:0020121", "BFO:0000002", - "MONDO:0020120", - "MONDO:0019056", + "BFO:0000020", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", "MONDO:0700223", - "BFO:0000016", - "MONDO:0700096", - "OGMS:0000031" + "MONDO:0002081", + "MONDO:0002320" ], - "subject_label": "POMGNT2-related limb-girdle muscular dystrophy R24", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", "subject_closure_label": [ + "nervous system disorder", + "continuant", + "musculoskeletal system disorder", + "muscular dystrophy-dystroglycanopathy, type A", + "myopathy caused by variation in POMGNT2", + "neuromuscular disease", + "skeletal muscle disorder", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", + "muscular dystrophy", + "myopathy", "disease", + "congenital muscular dystrophy", + "congenital muscular dystrophy caused by variation in POMGNT2", + "disorder of glycosylation", "realizable entity", - "disease", - "POMGNT2-related limb-girdle muscular dystrophy R24", - "muscle tissue disorder", + "human disease", + "congenital disorder of glycosylation", "hereditary skeletal muscle disorder", - "limb-girdle muscular dystrophy", - "continuant", "disposition", - "human disease", - "specifically dependent continuant", - "myopathy", - "nervous system disorder", - "entity", - "progressive muscular dystrophy", - "musculoskeletal system disorder", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", + "metabolic disease", + "disease", "hereditary disease", - "muscular dystrophy", - "skeletal muscle disorder", - "neuromuscular disease" + "muscle tissue disorder", + "inborn errors of metabolism", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0008981", + "object": "HP:0001321", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0008981", - "UPHENO:0084535", - "UPHENO:0002816", - "HP:0030236", - "PR:000050567", - "UBERON:0000465", - "RO:0002577", - "UPHENO:0015280", - "HP:0001437", - "BFO:0000040", - "UBERON:0001062", - "UBERON:0011216", - "UBERON:0000154", - "UBERON:0006067", + "HP:0000001", + "HP:0012443", + "HP:0011283", "UPHENO:0001002", - "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", + "UPHENO:0081099", + "UPHENO:0076791", + "UPHENO:0081601", + "HP:0001317", + "UPHENO:0080079", + "UPHENO:0076720", + "HP:0001321", + "UPHENO:0081091", + "UPHENO:0080089", "BFO:0000001", - "UBERON:0004482", - "UBERON:0001383", - "UBERON:0008784", - "UBERON:0002471", "UPHENO:0075696", - "UPHENO:0001005", - "HP:0009127", - "BFO:0000020", - "UPHENO:0001072", - "UPHENO:0081581", - "HP:0033127", + "HP:0002977", + "HP:0000707", "UPHENO:0001003", "UPHENO:0076692", - "UPHENO:0003070", - "UPHENO:0002830", - "BFO:0000004", - "UBERON:0004708", - "UBERON:0000061", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0000468", - "UBERON:0010709", - "HP:0002981", - "UPHENO:0065599", + "UPHENO:0076702", + "UPHENO:0086932", + "UPHENO:0015280", + "UPHENO:0020013", + "UPHENO:0081435", + "HP:0012639", + "UPHENO:0012541", + "UPHENO:0068971", "BFO:0000002", - "HP:0003011", + "BFO:0000020", + "UPHENO:0081790", + "UPHENO:0004523", + "HP:0011282", + "HP:0002011", + "UPHENO:0076805", + "UPHENO:0068984", "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", + "UPHENO:0001001", + "UPHENO:0001005", "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" + "UPHENO:0075195", + "HP:0007360", + "UPHENO:0020584" ], - "object_label": "Calf muscle hypertrophy (HPO)", + "object_label": "Cerebellar hypoplasia", "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", + "All", "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)", + "abnormal size of anatomical entity", + "Aplasia/Hypoplasia of the cerebellum", + "anatomical entity hypoplasia", + "aplasia or hypoplasia of cerebellum", "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", + "aplasia or hypoplasia of anatomical entity", + "abnormal cerebellum morphology", + "Cerebellar hypoplasia", + "Abnormality of brain morphology", + "Abnormal metencephalon morphology", + "Abnormal hindbrain morphology", "Phenotypic abnormality", - "Abnormality of the calf musculature (HPO)", - "specifically dependent continuant", - "abnormal anatomical entity morphology", - "abnormal leg", - "quality", - "organism subdivision", - "organ", - "multicellular organism", - "pelvic complex", - "musculature of lower limb", - "muscle of leg", - "lower limb segment", - "zeugopod", + "anatomical entity hypoplasia in independent continuant", + "abnormal nervous system", + "decreased size of the anatomical entity", + "Abnormal cerebellum morphology", + "abnormal nervous system morphology", + "abnormal hindbrain morphology", + "abnormal anatomical entity", + "Aplasia/Hypoplasia involving the central nervous system", + "Abnormality of the nervous system", + "phenotype by ontology source", "phenotype", - "abnormal hindlimb zeugopod", + "abnormal phenotype by ontology source", + "Morphological central nervous system abnormality", + "abnormal brain morphology", + "abnormal anatomical entity morphology in the brain", + "Abnormal nervous system morphology", + "quality", + "decreased size of the cerebellum", + "abnormal anatomical entity", + "decreased size of the anatomical entity in the independent continuant", + "Phenotypic abnormality", + "cerebellum hypoplasia", + "abnormal central nervous system morphology", + "abnormal metencephalon morphology", + "specifically dependent continuant", "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", - "muscle structure", - "skeletal musculature", - "hindlimb", - "appendage girdle complex", - "appendage musculature", - "musculature of pelvic complex", - "limb muscle", - "pelvic complex muscle", - "paired limb/fin segment" + "abnormal hindbrain morphology", + "abnormal anatomical entity morphology", + "entity" ], "object_taxon": null, "object_taxon_label": null, @@ -454,28 +406,28 @@ "negated": null, "pathway": null, "evidence_count": 2, - "has_evidence": ["ECO:0000304"], + "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { - "id": "ECO:0000304", - "url": "http://purl.obolibrary.org/obo/ECO_0000304" + "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], - "grouping_key": "MONDO:0035432🍪🍪biolink:has_phenotype🍪HP:0008981", + "grouping_key": "MONDO:0013904🍪🍪biolink:has_phenotype🍪HP:0001321", "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:565899"], + "publications": ["PMID:22958903"], "publications_links": [ { - "id": "orphanet:565899", - "url": null + "id": "PMID:22958903", + "url": "http://identifiers.org/pubmed/22958903" } ], "qualifiers": [], - "frequency_qualifier": "HP:0040282", + "frequency_qualifier": "HP:0040280", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, @@ -484,15 +436,11 @@ "qualifiers_category": null, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_label": "Obligate", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": [ - "Frequency (HPO)", - "Frequent (HPO)", - "All (HPO)" - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Obligate"], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -510,220 +458,134 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:4e12a2a4-842a-11ee-884f-6be035239f90", + "id": "uuid:89e15866-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035432", - "original_subject": "Orphanet:565899", + "subject": "MONDO:0013904", + "original_subject": "OMIM:614830", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ + "MONDO:0005071", + "BFO:0000016", + "MONDO:0019052", "MONDO:0000001", - "MONDO:0020121", - "MONDO:0003847", - "BFO:0000001", - "MONDO:0016106", "MONDO:0005336", + "OGMS:0000031", + "MONDO:0700069", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0000171", + "MONDO:0020120", + "MONDO:0700096", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0700075", + "MONDO:0024322", "BFO:0000017", - "MONDO:0003939", - "MONDO:0035432", - "BFO:0000020", - "MONDO:0002081", - "MONDO:0016971", - "MONDO:0005071", + "MONDO:0013904", + "MONDO:0015286", + "MONDO:0017741", + "MONDO:0020121", "BFO:0000002", - "MONDO:0020120", - "MONDO:0019056", + "BFO:0000020", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", "MONDO:0700223", - "BFO:0000016", - "MONDO:0700096", - "OGMS:0000031" + "MONDO:0002081", + "MONDO:0002320" ], - "subject_label": "POMGNT2-related limb-girdle muscular dystrophy R24", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", "subject_closure_label": [ + "nervous system disorder", + "continuant", + "musculoskeletal system disorder", + "muscular dystrophy-dystroglycanopathy, type A", + "myopathy caused by variation in POMGNT2", + "neuromuscular disease", + "skeletal muscle disorder", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", + "muscular dystrophy", + "myopathy", "disease", + "congenital muscular dystrophy", + "congenital muscular dystrophy caused by variation in POMGNT2", + "disorder of glycosylation", "realizable entity", - "disease", - "POMGNT2-related limb-girdle muscular dystrophy R24", - "muscle tissue disorder", + "human disease", + "congenital disorder of glycosylation", "hereditary skeletal muscle disorder", - "limb-girdle muscular dystrophy", - "continuant", "disposition", - "human disease", - "specifically dependent continuant", - "myopathy", - "nervous system disorder", - "entity", - "progressive muscular dystrophy", - "musculoskeletal system disorder", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", + "metabolic disease", + "disease", "hereditary disease", - "muscular dystrophy", - "skeletal muscle disorder", - "neuromuscular disease" + "muscle tissue disorder", + "inborn errors of metabolism", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0008994", + "object": "HP:0001252", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0008994", - "UPHENO:0002816", - "UPHENO:0002536", - "PR:000050567", - "UBERON:0000465", - "RO:0002577", + "HP:0000001", + "UPHENO:0082555", "UPHENO:0082875", - "HP:0001437", - "BFO:0000040", - "UBERON:0001062", - "UBERON:0011216", - "UBERON:0000154", - "UBERON:0000026", + "UPHENO:0001005", "UPHENO:0001002", - "HP:0001324", - "BFO:0000020", - "UPHENO:0080555", - "HP:0011804", "BFO:0000002", - "UBERON:0002101", - "UBERON:0004709", - "UBERON:0015212", - "UPHENO:0001001", - "HP:0003701", - "HP:0011805", - "UPHENO:0001003", - "UPHENO:0002647", + "HP:0003011", + "HP:0001252", "BFO:0000001", - "UBERON:0000061", - "UBERON:0004482", - "UBERON:0008784", "UPHENO:0075696", - "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", - "HP:0003011", - "UPHENO:0076710", - "HP:0040064", - "UBERON:0002103", - "UBERON:0010707", - "UBERON:0010758", - "UBERON:0006058", - "UPHENO:0002320", - "HP:0002814", - "HP:0000118", "UPHENO:0002332", + "UPHENO:0001003", + "UPHENO:0002320", + "BFO:0000020", "PATO:0000001", - "UBERON:0007271", - "UBERON:0014792", - "UBERON:0010538", - "HP:0000001", - "UPHENO:0002644", - "UPHENO:0080556", - "BFO:0000001", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0005090", - "UBERON:0001630", - "UBERON:0000383", - "UBERON:0001015", - "UBERON:0000978", - "UBERON:0007270", - "UBERON:0004480", - "UBERON:0002529" + "UPHENO:0002816", + "UPHENO:0002536", + "HP:0011804", + "UPHENO:0001001", + "HP:0003808", + "HP:0000118", + "HP:0033127", + "UPHENO:0082557" ], - "object_label": "Proximal muscle weakness in lower limbs (HPO)", + "object_label": "Hypotonia", "object_closure_label": [ - "abnormality of anatomical entity physiology", - "Proximal muscle weakness (HPO)", - "Abnormal skeletal muscle morphology (HPO)", + "All", + "decreased anatomical entity tone", + "Abnormality of the musculoskeletal system", + "Hypotonia", "quality", - "abnormal anatomical entity", "abnormal phenotype by ontology source", - "Abnormality of the musculature of the limbs (HPO)", - "specifically dependent continuant", - "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", - "organism subdivision", - "organ", - "multicellular organism", - "pelvic complex", - "musculature of lower limb", - "lower limb segment", + "Phenotypic abnormality", + "Abnormality of the musculature", + "abnormality of anatomical entity physiology", + "abnormality of muscle organ physiology", + "continuant", + "abnormal anatomical entity", + "phenotype by ontology source", "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", + "Abnormal muscle tone", + "Abnormal muscle physiology", "abnormality of anatomical entity physiology", + "abnormal musculature", "abnormal anatomical entity", - "abnormal muscle organ morphology", - "Abnormality of limbs (HPO)", - "multicellular anatomical structure", - "anatomical system", - "muscle structure", - "hindlimb", - "appendage girdle complex", - "appendage musculature", - "musculature of pelvic complex", - "paired limb/fin segment" + "specifically dependent continuant", + "decreased muscle organ tone", + "entity" ], "object_taxon": null, "object_taxon_label": null, @@ -732,24 +594,24 @@ "negated": null, "pathway": null, "evidence_count": 2, - "has_evidence": ["ECO:0000304"], + "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { - "id": "ECO:0000304", - "url": "http://purl.obolibrary.org/obo/ECO_0000304" + "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], - "grouping_key": "MONDO:0035432🍪🍪biolink:has_phenotype🍪HP:0008994", + "grouping_key": "MONDO:0013904🍪🍪biolink:has_phenotype🍪HP:0001252", "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:565899"], + "publications": ["PMID:22958903"], "publications_links": [ { - "id": "orphanet:565899", - "url": null + "id": "PMID:22958903", + "url": "http://identifiers.org/pubmed/22958903" } ], "qualifiers": [], @@ -762,15 +624,11 @@ "qualifiers_category": null, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_label": "Frequent", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": [ - "Frequency (HPO)", - "Frequent (HPO)", - "All (HPO)" - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -788,240 +646,124 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:4e02df81-842a-11ee-884f-6be035239f90", + "id": "uuid:89e15867-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013904", + "original_subject": "OMIM:614830", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0019052", "MONDO:0000001", - "MONDO:0020121", + "MONDO:0005336", + "OGMS:0000031", + "MONDO:0700069", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0000171", + "MONDO:0020120", + "MONDO:0700096", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0700075", + "MONDO:0024322", "BFO:0000017", - "MONDO:0008056", - "MONDO:0035646", + "MONDO:0013904", + "MONDO:0015286", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000002", + "BFO:0000020", "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:0005066", "MONDO:0700223", - "MONDO:0003382", - "BFO:0000016", - "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", - "OGMS:0000031", - "BFO:0000001" + "MONDO:0002081", + "MONDO:0002320" ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", "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", + "continuant", "musculoskeletal system disorder", - "hereditary disease", - "eye disorder", + "muscular dystrophy-dystroglycanopathy, type A", + "myopathy caused by variation in POMGNT2", + "neuromuscular disease", + "skeletal muscle disorder", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "myopathy", + "disease", + "congenital muscular dystrophy", + "congenital muscular dystrophy caused by variation in POMGNT2", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome" + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", + "metabolic disease", + "disease", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0000256", + "object": "HP:0003560", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000256", - "UPHENO:0002536", - "UPHENO:0081566", - "HP:0000240", - "UBERON:0000465", - "UPHENO:0075220", - "UPHENO:0001208", - "UPHENO:0002844", - "UPHENO:0015280", - "BFO:0000001", - "BFO:0000040", - "UBERON:0001062", - "UBERON:0011216", - "UBERON:0011676", - "UBERON:0013701", - "UPHENO:0075148", + "HP:0000001", "UPHENO:0001002", - "UPHENO:0075195", - "HP:0009121", - "BFO:0000002", - "UPHENO:0001001", - "HP:0011842", - "BFO:0000020", - "UPHENO:0002964", - "UPHENO:0001003", - "UPHENO:0021447", + "UPHENO:0076710", + "HP:0003011", "BFO:0000001", - "UBERON:0000061", - "UBERON:0034925", - "HP:0040194", - "UPHENO:0075696", - "UPHENO:0001005", - "UPHENO:0002764", - "UPHENO:0001072", - "UPHENO:0081581", - "HP:0033127", + "UPHENO:0001003", "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", + "HP:0011805", + "HP:0003560", "BFO:0000002", - "UPHENO:0020584", + "BFO:0000020", "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" + "UPHENO:0002816", + "UPHENO:0002536", + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0000118", + "HP:0033127" ], - "object_label": "Macrocephaly (HPO)", + "object_label": "Muscular dystrophy", "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", + "All", "continuant", - "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)", + "Abnormality of the musculoskeletal system", "abnormal anatomical entity morphology", - "entity", - "structure with developmental contribution from neural crest", - "abnormal size of head", + "quality", "Phenotypic abnormality", - "abnormal anatomical entity morphology", - "Abnormality of skull size (HPO)", - "anatomical structure", - "anatomical collection", - "skeleton", - "organism subdivision", - "multicellular organism", - "anterior region of body", + "Abnormality of the musculature", + "abnormal muscle organ morphology", + "Abnormal skeletal muscle morphology", + "Muscular dystrophy", + "phenotype by ontology source", "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", - "subdivision of skeleton", - "skeletal system", - "increased size of the head", - "abnormal head", + "abnormal phenotype by ontology source", + "abnormal musculature", "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" + "Phenotypic abnormality", + "specifically dependent continuant", + "entity" ], "object_taxon": null, "object_taxon_label": null, @@ -1030,28 +772,28 @@ "negated": null, "pathway": null, "evidence_count": 2, - "has_evidence": ["ECO:0000304"], + "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { - "id": "ECO:0000304", - "url": "http://purl.obolibrary.org/obo/ECO_0000304" + "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], - "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0000256", + "grouping_key": "MONDO:0013904🍪🍪biolink:has_phenotype🍪HP:0003560", "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": ["PMID:22958903"], "publications_links": [ { - "id": "orphanet:589821", - "url": null + "id": "PMID:22958903", + "url": "http://identifiers.org/pubmed/22958903" } ], "qualifiers": [], - "frequency_qualifier": "HP:0040281", + "frequency_qualifier": "HP:0040280", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, @@ -1060,15 +802,11 @@ "qualifiers_category": null, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Very frequent (HPO)", + "frequency_qualifier_label": "Obligate", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040281", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": [ - "Frequency (HPO)", - "All (HPO)", - "Very frequent (HPO)" - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Obligate"], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -1086,248 +824,176 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:4e02df82-842a-11ee-884f-6be035239f90", + "id": "uuid:89e1586b-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013904", + "original_subject": "OMIM:614830", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0019052", "MONDO:0000001", - "MONDO:0020121", + "MONDO:0005336", + "OGMS:0000031", + "MONDO:0700069", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0000171", + "MONDO:0020120", + "MONDO:0700096", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0700075", + "MONDO:0024322", "BFO:0000017", - "MONDO:0008056", - "MONDO:0035646", + "MONDO:0013904", + "MONDO:0015286", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000002", + "BFO:0000020", "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:0005066", "MONDO:0700223", - "MONDO:0003382", - "BFO:0000016", - "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", - "OGMS:0000031", - "BFO:0000001" + "MONDO:0002081", + "MONDO:0002320" ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", "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", + "continuant", "musculoskeletal system disorder", - "hereditary disease", - "eye disorder", + "muscular dystrophy-dystroglycanopathy, type A", + "myopathy caused by variation in POMGNT2", + "neuromuscular disease", + "skeletal muscle disorder", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "myopathy", + "disease", + "congenital muscular dystrophy", + "congenital muscular dystrophy caused by variation in POMGNT2", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome" + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", + "metabolic disease", + "disease", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0000297", + "object": "HP:0007973", "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:0001062", - "UBERON:0011216", - "UBERON:0011676", - "UBERON:0013701", - "UPHENO:0001002", - "HP:0011804", + "HP:0000315", + "HP:0000001", + "HP:0000234", + "UPHENO:0076782", + "UPHENO:0088038", + "UPHENO:0075997", "BFO:0000002", - "UBERON:0001630", - "UBERON:0002376", - "UBERON:0015789", - "UPHENO:0001001", - "HP:0011805", - "BFO:0000020", - "UPHENO:0001003", "BFO:0000001", - "UBERON:0000061", "UPHENO:0075696", - "UPHENO:0001005", - "UPHENO:0002764", - "UPHENO:0081581", - "HP:0033127", + "HP:0000152", + "UPHENO:0087907", + "UPHENO:0002910", + "UPHENO:0087596", + "HP:0000707", + "UPHENO:0001003", "UPHENO:0076692", - "BFO:0000004", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0000468", - "UBERON:0000153", + "HP:0007973", + "UPHENO:0076702", + "UPHENO:0001002", + "UPHENO:0021656", + "UPHENO:0015280", + "HP:0000271", + "HP:0012639", + "UPHENO:0021037", + "UPHENO:0021474", "UPHENO:0002844", - "BFO:0000002", - "HP:0003011", - "UPHENO:0076710", + "BFO:0000020", + "UPHENO:0004523", + "HP:0000479", + "HP:0012372", + "UPHENO:0087472", + "HP:0000478", + "UPHENO:0087924", + "UPHENO:0001005", + "HP:0001098", + "UPHENO:0002764", + "HP:0004329", + "UPHENO:0003020", + "UPHENO:0002536", "PATO:0000001", - "UPHENO:0002908", - "UBERON:0007811", - "UBERON:0001444", - "UBERON:0013702", - "UBERON:0000033", - "UPHENO:0002320", - "UPHENO:0082555", - "HP:0000152", + "UPHENO:0001001", + "UPHENO:0086589", "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" + "UPHENO:0020584" ], - "object_label": "Facial hypotonia (HPO)", + "object_label": "Retinal dysplasia", "object_closure_label": [ - "abnormality of anatomical entity physiology", - "abnormal head", - "Abnormal skeletal muscle morphology (HPO)", - "specifically dependent continuant", - "abnormal anatomical entity", + "Abnormality of the orbital region", + "All", + "abnormal anatomical entity morphology", + "abnormal orbital region", "abnormal phenotype by ontology source", + "Abnormal fundus 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)", + "Abnormal posterior eye segment morphology", + "abnormal posterior segment of eyeball morphology", + "abnormal retina morphology", + "Abnormal retinal morphology", + "Abnormal eye morphology", + "abnormal face morphology", + "Phenotypic abnormality", + "abnormal nervous system", + "abnormal posterior segment of eyeball morphology", + "abnormal camera-type eye morphology", + "abnormal head", "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", - "skeletal musculature of head", - "musculature of face", + "abnormal ocular fundus morphology", + "Retinal dysplasia", + "abnormal nervous system morphology", + "abnormal anatomical entity", + "Abnormality of the eye", + "abnormal camera-type eye morphology", "Phenotypic abnormality", - "abnormal anatomical entity morphology", - "quality", - "abnormal facial muscle", - "anatomical structure", - "organism subdivision", - "organ", - "multicellular organism", - "anterior region of body", + "abnormal ocular fundus morphology", + "Abnormality of the nervous system", + "phenotype by ontology source", "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", - "skeletal muscle organ", + "abnormal craniocervical region morphology", + "Abnormality of the head", + "Abnormal nervous system morphology", + "quality", + "Abnormality of head or neck", + "abnormal head morphology", "abnormal face", - "abnormality of anatomical entity physiology", - "Hypotonia (HPO)", + "abnormal eyeball of camera-type eye", "abnormal anatomical entity", - "abnormal muscle organ morphology", - "multicellular anatomical structure", - "anatomical system", - "muscle structure", - "skeletal musculature", - "mesoderm-derived structure", - "face", - "craniocervical region musculature", - "axial musculature", - "craniocervical muscle", - "facial muscle" + "specifically dependent continuant", + "abnormal anatomical entity morphology in the independent continuant", + "Abnormality of the face", + "abnormal anatomical entity morphology", + "entity" ], "object_taxon": null, "object_taxon_label": null, @@ -1336,28 +1002,28 @@ "negated": null, "pathway": null, "evidence_count": 2, - "has_evidence": ["ECO:0000304"], + "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { - "id": "ECO:0000304", - "url": "http://purl.obolibrary.org/obo/ECO_0000304" + "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], - "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0000297", + "grouping_key": "MONDO:0013904🍪🍪biolink:has_phenotype🍪HP:0007973", "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": ["PMID:22958903"], "publications_links": [ { - "id": "orphanet:589821", - "url": null + "id": "PMID:22958903", + "url": "http://identifiers.org/pubmed/22958903" } ], "qualifiers": [], - "frequency_qualifier": "HP:0040281", + "frequency_qualifier": "HP:0040282", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, @@ -1366,15 +1032,11 @@ "qualifiers_category": null, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Very frequent (HPO)", + "frequency_qualifier_label": "Frequent", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040281", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": [ - "Frequency (HPO)", - "All (HPO)", - "Very frequent (HPO)" - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -1392,264 +1054,142 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:4e02df83-842a-11ee-884f-6be035239f90", + "id": "uuid:89e1586c-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013904", + "original_subject": "OMIM:614830", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0019052", "MONDO:0000001", - "MONDO:0020121", + "MONDO:0005336", + "OGMS:0000031", + "MONDO:0700069", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0000171", + "MONDO:0020120", + "MONDO:0700096", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0700075", + "MONDO:0024322", "BFO:0000017", - "MONDO:0008056", - "MONDO:0035646", + "MONDO:0013904", + "MONDO:0015286", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000002", + "BFO:0000020", "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:0005066", "MONDO:0700223", - "MONDO:0003382", - "BFO:0000016", - "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", - "OGMS:0000031", - "BFO:0000001" + "MONDO:0002081", + "MONDO:0002320" ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", "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", + "continuant", "musculoskeletal system disorder", - "hereditary disease", - "eye disorder", + "muscular dystrophy-dystroglycanopathy, type A", + "myopathy caused by variation in POMGNT2", + "neuromuscular disease", + "skeletal muscle disorder", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "myopathy", + "disease", + "congenital muscular dystrophy", + "congenital muscular dystrophy caused by variation in POMGNT2", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome" + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", + "metabolic disease", + "disease", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0010804", + "object": "HP:0000501", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0000159", - "UPHENO:0076803", - "UBERON:0000465", - "UPHENO:0002910", - "UPHENO:0076800", - "UPHENO:0003064", - "BFO:0000002", - "HP:0002664", - "UPHENO:0015280", - "BFO:0000040", - "BFO:0000141", - "UBERON:0001062", - "UBERON:0011676", - "UBERON:0013701", - "UPHENO:0002828", + "HP:0000315", + "HP:0000001", + "HP:0000234", + "UPHENO:0082875", + "UPHENO:0075997", + "UPHENO:0075696", + "HP:0000152", + "HP:0000501", + "UPHENO:0002910", + "UPHENO:0002332", + "UPHENO:0001003", "UPHENO:0001002", - "BFO:0000020", - "HP:0011793", - "UPHENO:0076786", - "BFO:0000002", - "UBERON:0000167", + "HP:0000271", "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", - "HP:0011339", - "HP:0010804", - "UPHENO:0020584", - "PATO:0000001", - "UBERON:0010314", - "UBERON:0003102", - "UBERON:0010000", - "UBERON:0001555", - "UBERON:0001456", - "UBERON:0004921", - "HP:0000001", + "BFO:0000002", + "BFO:0000020", + "HP:0012373", + "HP:0000478", "UPHENO:0001005", - "HP:0031816", - "HP:0000153", - "HP:0000234", - "HP:0000271", - "BFO:0000001", - "UBERON:0000467", - "UBERON:0000064", - "UBERON:0001007", - "UBERON:0013522", - "UBERON:0000165" + "UPHENO:0002219", + "UPHENO:0002764", + "UPHENO:0003020", + "UPHENO:0002536", + "PATO:0000001", + "HP:0000118", + "BFO:0000001" ], - "object_label": "Tented upper lip vermilion (HPO)", + "object_label": "Glaucoma", "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", + "Abnormality of the orbital region", + "All", "continuant", - "material anatomical entity", - "organ part", - "digestive system", - "head", - "midface", - "All (HPO)", + "abnormal orbital region", "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", + "abnormality of camera-type eye physiology", + "abnormal craniocervical region", "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", + "abnormality of anatomical entity physiology", + "Abnormal eye physiology", + "entity", "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 head", + "abnormal anatomical entity", + "Abnormality of the eye", + "Phenotypic abnormality", + "phenotype by ontology source", + "Abnormality of the head", + "quality", + "abnormality of anatomical entity physiology", + "Abnormality of head or neck", + "Glaucoma", "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" + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity", + "specifically dependent continuant", + "Abnormality of the face" ], "object_taxon": null, "object_taxon_label": null, @@ -1658,28 +1198,28 @@ "negated": null, "pathway": null, "evidence_count": 2, - "has_evidence": ["ECO:0000304"], + "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { - "id": "ECO:0000304", - "url": "http://purl.obolibrary.org/obo/ECO_0000304" + "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], - "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0010804", + "grouping_key": "MONDO:0013904🍪🍪biolink:has_phenotype🍪HP:0000501", "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": ["PMID:22958903"], "publications_links": [ { - "id": "orphanet:589821", - "url": null + "id": "PMID:22958903", + "url": "http://identifiers.org/pubmed/22958903" } ], "qualifiers": [], - "frequency_qualifier": "HP:0040281", + "frequency_qualifier": "HP:0040282", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, @@ -1688,15 +1228,11 @@ "qualifiers_category": null, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Very frequent (HPO)", + "frequency_qualifier_label": "Frequent", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040281", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": [ - "Frequency (HPO)", - "All (HPO)", - "Very frequent (HPO)" - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -1714,178 +1250,182 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:4e02df84-842a-11ee-884f-6be035239f90", + "id": "uuid:89e159cd-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013154", + "original_subject": "OMIM:613150", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0018939", + "MONDO:0019052", + "MONDO:0018282", "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", + "MONDO:0013154", "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:0000171", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", - "BFO:0000001" + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0015286", + "MONDO:0016155", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000020", + "MONDO:0700071", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", + "BFO:0000001", + "MONDO:0002320" ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "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", + "disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "muscular dystrophy-dystroglycanopathy, type A", + "neuromuscular disease", + "muscle-eye-brain disease", + "skeletal muscle disorder", + "entity", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "continuant", + "myopathy", + "congenital muscular dystrophy", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome" + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "metabolic disease", + "qualitative or quantitative defects of alpha-dystroglycan", + "disease", + "myopathy caused by variation in POMT2", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0031843", + "object": "HP:0009917", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "UBERON:0000465", - "GO:0050877", - "UPHENO:0082875", - "UPHENO:0004523", - "GO:0008150", - "BFO:0000040", - "UBERON:0001062", - "GO:0003008", - "BFO:0000020", - "BFO:0000003", - "BFO:0000002", - "UPHENO:0001001", + "HP:0000315", + "HP:0000001", + "HP:0000234", + "HP:0000615", + "UPHENO:0021672", + "UPHENO:0021663", + "UPHENO:0087597", + "UPHENO:0075997", "UPHENO:0001002", - "HP:0031843", - "UPHENO:0001003", + "BFO:0000002", "BFO:0000001", - "UBERON:0000061", - "GO:0050890", - "UPHENO:0001005", - "UPHENO:0002433", - "HP:0100543", - "HP:0012638", - "BFO:0000015", - "UBERON:0000468", "UPHENO:0075696", - "BFO:0000002", + "HP:0000152", + "UPHENO:0087907", + "UPHENO:0002910", + "UPHENO:0001003", + "HP:0009917", + "UPHENO:0088042", + "UPHENO:0076692", + "UPHENO:0086817", + "HP:0004328", + "HP:0000553", + "UPHENO:0015280", + "HP:0000271", + "UPHENO:0088050", + "UPHENO:0021474", + "UPHENO:0002844", + "BFO:0000020", + "HP:0000525", + "PATO:0000001", + "HP:0012372", + "UPHENO:0087472", + "HP:0000478", + "UPHENO:0087924", + "UPHENO:0002764", + "UPHENO:0003020", "UPHENO:0002536", - "BFO:0000004", + "UPHENO:0001001", + "UPHENO:0086589", + "UPHENO:0001005", "HP:0000118", - "UPHENO:0002332", - "PATO:0000001", - "HP:0000001", - "HP:0000707", - "HP:0011446", - "BFO:0000001", - "GO:0032501", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0001016" + "UPHENO:0076804", + "UPHENO:0021038", + "UPHENO:0020584" ], - "object_label": "Bradyphrenia (HPO)", + "object_label": "Persistent pupillary membrane", "object_closure_label": [ - "abnormality of anatomical entity physiology", + "Abnormality of the orbital region", + "All", + "abnormal uvea morphology", + "Persistent pupillary membrane", + "abnormal pupil morphology", + "abnormal anatomical entity morphology", + "abnormal anterior uvea morphology", + "abnormal orbital region", + "abnormal craniocervical region", + "quality", + "Abnormal eye morphology", + "abnormal face morphology", "Phenotypic abnormality", - "Bradyphrenia (HPO)", + "Phenotypic abnormality", + "Abnormality iris morphology", + "abnormal camera-type eye morphology", + "abnormal head", + "continuant", + "abnormal iris morphology", + "abnormal pupil morphology", + "abnormal anterior segment of eyeball morphology", "abnormal anatomical entity", - "Abnormality of higher mental function (HPO)", - "quality", - "multicellular organismal process", - "abnormal phenotype by ontology source", - "specifically dependent continuant", + "Abnormality of the eye", + "abnormal camera-type eye morphology", "phenotype by ontology source", - "abnormal nervous system", - "occurrent", - "continuant", - "material anatomical entity", - "nervous system", - "All (HPO)", - "continuant", - "system process", - "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "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 craniocervical region morphology", + "abnormal phenotype by ontology source", + "Abnormality of the head", + "Abnormal pupil morphology", + "abnormal anterior segment of eyeball morphology", + "Abnormality of head or neck", + "abnormal head morphology", + "abnormal face", + "abnormal eyeball of camera-type eye", "abnormal anatomical entity", - "abnormality of anatomical entity physiology", - "independent continuant", - "multicellular anatomical structure", - "anatomical system" + "abnormal iris morphology", + "Abnormal anterior eye segment morphology", + "Abnormal uvea morphology", + "specifically dependent continuant", + "abnormal anatomical entity morphology in the independent continuant", + "Abnormality of the face", + "abnormal anatomical entity morphology", + "entity" ], "object_taxon": null, "object_taxon_label": null, @@ -1894,28 +1434,28 @@ "negated": null, "pathway": null, "evidence_count": 2, - "has_evidence": ["ECO:0000304"], + "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { - "id": "ECO:0000304", - "url": "http://purl.obolibrary.org/obo/ECO_0000304" + "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], - "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0031843", + "grouping_key": "MONDO:0013154🍪🍪biolink:has_phenotype🍪HP:0009917", "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": ["PMID:15894594"], "publications_links": [ { - "id": "orphanet:589821", - "url": null + "id": "PMID:15894594", + "url": "http://identifiers.org/pubmed/15894594" } ], "qualifiers": [], - "frequency_qualifier": "HP:0040281", + "frequency_qualifier": "HP:0040282", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, @@ -1924,15 +1464,11 @@ "qualifiers_category": null, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Very frequent (HPO)", + "frequency_qualifier_label": "Frequent", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040281", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": [ - "Frequency (HPO)", - "All (HPO)", - "Very frequent (HPO)" - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -1950,192 +1486,212 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:4e02df85-842a-11ee-884f-6be035239f90", + "id": "uuid:89e159d3-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013154", + "original_subject": "OMIM:613150", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0018939", + "MONDO:0019052", + "MONDO:0018282", "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", + "MONDO:0013154", "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:0000171", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", - "BFO:0000001" + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0015286", + "MONDO:0016155", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000020", + "MONDO:0700071", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", + "BFO:0000001", + "MONDO:0002320" ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "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", + "disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "muscular dystrophy-dystroglycanopathy, type A", + "neuromuscular disease", + "muscle-eye-brain disease", + "skeletal muscle disorder", + "entity", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "continuant", + "myopathy", + "congenital muscular dystrophy", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome" + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "metabolic disease", + "qualitative or quantitative defects of alpha-dystroglycan", + "disease", + "myopathy caused by variation in POMT2", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0000736", + "object": "HP:0001274", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "UBERON:0000465", - "NBO:0000313", - "NBO:0000308", - "UPHENO:0082875", - "BFO:0000002", - "UPHENO:0004523", - "UPHENO:0049587", - "GO:0008150", - "BFO:0000040", - "UBERON:0001062", - "GO:0007610", + "HP:0000001", + "HP:0002060", + "HP:0010993", + "HP:0100547", + "HP:0007364", + "HP:0012443", + "UPHENO:0026506", + "UPHENO:0021803", + "HP:0007370", "UPHENO:0001002", - "BFO:0000020", - "HP:0000736", - "BFO:0000003", + "HP:0012429", + "UPHENO:0076791", + "UPHENO:0087518", + "UPHENO:0076799", + "UPHENO:0080079", + "UPHENO:0087902", "BFO:0000002", - "UPHENO:0001001", - "UPHENO:0049622", - "UPHENO:0001003", + "UPHENO:0011580", + "HP:0001273", "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", + "HP:0002977", + "UPHENO:0008622", + "UPHENO:0087750", + "HP:0000707", + "UPHENO:0001003", + "UPHENO:0076692", + "UPHENO:0076702", + "HP:0033725", + "UPHENO:0087415", + "HP:0001274", + "UPHENO:0026028", + "BFO:0000020", + "UPHENO:0015280", + "UPHENO:0081562", + "UPHENO:0081435", + "HP:0012639", + "UPHENO:0020888", + "UPHENO:0085804", + "UPHENO:0080200", + "UPHENO:0006910", + "UPHENO:0008523", + "UPHENO:0004523", "PATO:0000001", - "HP:0000001", "UPHENO:0001005", - "HP:0000707", - "HP:0011446", - "BFO:0000001", - "GO:0032501", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0001016" + "UPHENO:0087032", + "UPHENO:0087531", + "HP:0002011", + "HP:0002500", + "UPHENO:0076805", + "UPHENO:0011498", + "UPHENO:0080204", + "UPHENO:0085805", + "UPHENO:0002536", + "UPHENO:0076807", + "UPHENO:0025935", + "UPHENO:0001001", + "HP:0000118", + "UPHENO:0020584" ], - "object_label": "Short attention span (HPO)", + "object_label": "Agenesis of corpus callosum", "object_closure_label": [ - "abnormality of anatomical entity physiology", - "abnormal anatomical entity", - "Abnormality of higher mental function (HPO)", + "All", + "Abnormal cerebral morphology", + "abnormal anatomical entity morphology", + "aplasia or hypoplasia of anatomical entity", + "abnormal brain white matter morphology", + "abnormal phenotype by ontology source", + "abnormal brain commissure morphology", + "abnormal cerebral hemisphere morphology", + "abnormal dorsal telencephalic commissure morphology", + "abnormal number of anatomical enitites of type corpus callosum", + "Abnormal corpus callosum morphology", + "Abnormality of brain morphology", + "absent anatomical entity in the multicellular organism", "quality", - "multicellular organismal process", + "Phenotypic abnormality", + "abnormal number of anatomical entities of type anatomical entity in independent continuant", + "absent anatomical entity", + "abnormal nervous system", + "continuant", + "abnormal telencephalon morphology", + "abnormal nervous system morphology", "abnormal anatomical entity", + "Aplasia/Hypoplasia involving the central nervous system", + "Agenesis of corpus callosum", + "absent anatomical entity in the independent continuant", "specifically dependent continuant", + "Abnormality of the nervous system", "phenotype by ontology source", - "abnormal nervous system", - "occurrent", - "continuant", - "material anatomical entity", - "nervous system", - "All (HPO)", - "abnormal phenotype by ontology source", - "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", - "abnormal response to stimulus", - "continuant", - "abnormality of anatomical entity physiology", - "multicellular anatomical structure", - "anatomical system", - "attention behavior" + "Morphological central nervous system abnormality", + "Abnormal cerebral white matter morphology", + "abnormal brain morphology", + "abnormal number of anatomical enitites of type anatomical entity", + "Abnormal forebrain morphology", + "Aplasia/Hypoplasia of the cerebrum", + "abnormal anatomical entity morphology in the brain", + "Abnormal nervous system morphology", + "abnormal forebrain morphology", + "abnormal corpus callosum morphology", + "absent anatomical entity in the brain", + "absent corpus callosum", + "Abnormal cerebral subcortex morphology", + "aplasia or hypoplasia of corpus callosum", + "absent anatomical entity in the nervous system", + "abnormal anatomical entity", + "abnormal cerebral subcortex morphology", + "Aplasia/Hypoplasia of the corpus callosum", + "absent anatomical entity in the central nervous system", + "Thin corpus callosum", + "abnormal axon tract morphology", + "Phenotypic abnormality", + "Aplasia/Hypoplasia of the cerebral white matter", + "abnormal central nervous system morphology", + "abnormal forebrain morphology", + "aplasia or hypoplasia of telencephalon", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal cerebral hemisphere white matter morphology", + "abnormal anatomical entity morphology", + "entity" ], "object_taxon": null, "object_taxon_label": null, @@ -2144,24 +1700,24 @@ "negated": null, "pathway": null, "evidence_count": 2, - "has_evidence": ["ECO:0000304"], + "has_evidence": ["ECO:0000501"], "has_evidence_links": [ { - "id": "ECO:0000304", - "url": "http://purl.obolibrary.org/obo/ECO_0000304" + "id": "ECO:0000501", + "url": "http://purl.obolibrary.org/obo/ECO_0000501" } ], - "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0000736", + "grouping_key": "MONDO:0013154🍪🍪biolink:has_phenotype🍪HP:0001274", "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": ["PMID:15894594"], "publications_links": [ { - "id": "orphanet:589821", - "url": null + "id": "PMID:15894594", + "url": "http://identifiers.org/pubmed/15894594" } ], "qualifiers": [], @@ -2174,15 +1730,11 @@ "qualifiers_category": null, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_label": "Frequent", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": [ - "Frequency (HPO)", - "Frequent (HPO)", - "All (HPO)" - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -2200,178 +1752,178 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:4e02df87-842a-11ee-884f-6be035239f90", + "id": "uuid:89e159d6-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013154", + "original_subject": "OMIM:613150", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0018939", + "MONDO:0019052", + "MONDO:0018282", "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", + "MONDO:0013154", "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:0000171", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", - "BFO:0000001" + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0015286", + "MONDO:0016155", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000020", + "MONDO:0700071", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", + "BFO:0000001", + "MONDO:0002320" ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "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", + "disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "muscular dystrophy-dystroglycanopathy, type A", + "neuromuscular disease", + "muscle-eye-brain disease", + "skeletal muscle disorder", + "entity", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "continuant", + "myopathy", + "congenital muscular dystrophy", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome" + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "metabolic disease", + "qualitative or quantitative defects of alpha-dystroglycan", + "disease", + "myopathy caused by variation in POMT2", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0001622", + "object": "HP:0007260", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "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", - "UPHENO:0001001", + "HP:0000001", + "HP:0002060", + "HP:0100547", + "UPHENO:0081603", + "HP:0012443", + "HP:0002538", "UPHENO:0001002", - "BFO:0000020", - "UPHENO:0001003", - "BFO:0000001", + "UPHENO:0076791", + "UPHENO:0087518", + "UPHENO:0076799", + "HP:0001339", "UPHENO:0001005", - "UPHENO:0049940", - "BFO:0000015", - "UBERON:0000061", - "UBERON:0000468", + "BFO:0000001", + "UPHENO:0075696", + "HP:0000707", + "UPHENO:0001003", + "UPHENO:0076692", + "UPHENO:0049643", + "UPHENO:0076702", + "UPHENO:0015280", + "UPHENO:0081435", + "HP:0012639", + "UPHENO:0020888", + "UPHENO:0049587", + "HP:0002269", "BFO:0000002", - "UPHENO:0049440", - "BFO:0000004", - "UBERON:0000922", - "HP:0001622", - "HP:0000118", - "UPHENO:0049449", - "HP:0001787", + "BFO:0000020", + "HP:0002536", + "UPHENO:0004523", "PATO:0000001", - "UBERON:0000323", - "HP:0000001", - "UPHENO:0075949", - "GO:0032501", - "GO:0022414", - "UBERON:0010000" + "UPHENO:0049852", + "UPHENO:0087531", + "HP:0002011", + "HP:0007260", + "UPHENO:0076805", + "UPHENO:0050121", + "UPHENO:0049855", + "UPHENO:0002536", + "UPHENO:0001001", + "HP:0000118", + "UPHENO:0049634", + "UPHENO:0020584" ], - "object_label": "Premature birth (HPO)", + "object_label": "Type II lissencephaly", "object_closure_label": [ - "Phenotypic abnormality", - "specifically dependent continuant", + "All", + "Abnormal cerebral morphology", + "continuant", + "abnormal cell motility", + "abnormal anatomical entity morphology", + "Lissencephaly", + "abnormal cerebral hemisphere morphology", + "Abnormality of brain morphology", "quality", - "multicellular organismal process", - "reproductive process", + "abnormal neuron migration", "abnormal phenotype by ontology source", - "premature biological_process", + "Phenotypic abnormality", + "Abnormal cortical gyration", + "abnormal nervous system", + "Abnormality of neuronal migration", + "abnormal telencephalon morphology", + "abnormal cell migration", + "abnormal nervous system morphology", + "abnormal anatomical entity", + "Abnormality of the nervous system", "phenotype by ontology source", - "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", - "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", + "phenotype", + "Morphological central nervous system abnormality", + "Type II lissencephaly", + "abnormal brain morphology", + "abnormal cellular process", + "Abnormal forebrain morphology", + "abnormal cerebral cortex morphology", + "abnormal anatomical entity morphology in the brain", + "Abnormal nervous system morphology", + "abnormal forebrain morphology", + "Abnormal cerebral cortex morphology", + "abnormal locomotion", "abnormal anatomical entity", - "independent continuant", - "multicellular anatomical structure", - "late embryo" + "Phenotypic abnormality", + "abnormal central nervous system morphology", + "abnormal forebrain morphology", + "specifically dependent continuant", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal anatomical entity morphology", + "entity" ], "object_taxon": null, "object_taxon_label": null, @@ -2380,28 +1932,28 @@ "negated": null, "pathway": null, "evidence_count": 2, - "has_evidence": ["ECO:0000304"], + "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { - "id": "ECO:0000304", - "url": "http://purl.obolibrary.org/obo/ECO_0000304" + "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], - "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001622", + "grouping_key": "MONDO:0013154🍪🍪biolink:has_phenotype🍪HP:0007260", "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": ["PMID:15894594"], "publications_links": [ { - "id": "orphanet:589821", - "url": null + "id": "PMID:15894594", + "url": "http://identifiers.org/pubmed/15894594" } ], "qualifiers": [], - "frequency_qualifier": "HP:0040282", + "frequency_qualifier": "HP:0040280", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, @@ -2410,15 +1962,11 @@ "qualifiers_category": null, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_label": "Obligate", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": [ - "Frequency (HPO)", - "Frequent (HPO)", - "All (HPO)" - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Obligate"], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -2436,200 +1984,180 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:4e02df88-842a-11ee-884f-6be035239f90", + "id": "uuid:89e159da-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013154", + "original_subject": "OMIM:613150", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0018939", + "MONDO:0019052", + "MONDO:0018282", "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", + "MONDO:0013154", "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:0000171", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", - "BFO:0000001" + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0015286", + "MONDO:0016155", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000020", + "MONDO:0700071", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", + "BFO:0000001", + "MONDO:0002320" ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "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", + "disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "muscular dystrophy-dystroglycanopathy, type A", + "neuromuscular disease", + "muscle-eye-brain disease", + "skeletal muscle disorder", + "entity", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "continuant", + "myopathy", + "congenital muscular dystrophy", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome" + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "metabolic disease", + "qualitative or quantitative defects of alpha-dystroglycan", + "disease", + "myopathy caused by variation in POMT2", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0001883", + "object": "HP:0000659", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "PR:000050567", - "UBERON:0000465", - "RO:0002577", - "BFO:0000001", - "BFO:0000040", - "UBERON:0001062", - "UBERON:0000154", + "HP:0000315", + "HP:0000001", + "HP:0000234", + "UPHENO:0021670", + "HP:0000593", "UPHENO:0001002", - "BFO:0000020", - "UPHENO:0081575", - "BFO:0000002", - "UBERON:0002101", - "UBERON:0004709", - "UPHENO:0001001", - "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "UBERON:0000061", - "UBERON:0008784", - "UBERON:0002470", + "UPHENO:0076957", + "UPHENO:0087597", + "UPHENO:0075997", + "UPHENO:0072814", "UPHENO:0001005", - "UPHENO:0081581", + "UPHENO:0075696", + "HP:0000152", + "UPHENO:0087907", + "UPHENO:0002910", + "UPHENO:0001003", "UPHENO:0076692", - "UPHENO:0003070", - "UPHENO:0002830", - "BFO:0000004", - "UBERON:0004708", - "UBERON:0000475", - "UBERON:0000468", - "UBERON:0010709", - "HP:0001883", - "BFO:0000002", - "HP:0001760", - "HP:0040064", + "HP:0004328", + "UPHENO:0015280", + "HP:0000271", + "UPHENO:0088049", + "UPHENO:0071309", + "UPHENO:0071334", + "UPHENO:0021474", + "UPHENO:0002844", + "HP:0007700", + "BFO:0000020", + "HP:0000659", + "HP:0012372", + "UPHENO:0087472", + "HP:0000478", + "UPHENO:0087924", + "UPHENO:0002764", + "UPHENO:0003020", + "UPHENO:0002536", "PATO:0000001", - "UBERON:0002103", - "UBERON:0010707", - "UBERON:0000026", - "UBERON:0010758", - "UBERON:0006058", - "UBERON:0002387", - "HP:0002814", - "HP:0005656", + "UPHENO:0001001", + "UPHENO:0086589", "HP:0000118", - "UBERON:0015212", - "UBERON:0010538", - "HP:0000001", - "UBERON:0010000", - "UBERON:0000978", - "UBERON:0002529" + "BFO:0000002", + "UPHENO:0021038", + "UPHENO:0020584", + "BFO:0000001" ], - "object_label": "Talipes (HPO)", + "object_label": "Peters anomaly", "object_closure_label": [ + "Abnormality of the orbital region", + "All", + "Ocular anterior segment dysgenesis", + "abnormal anatomical entity morphology", + "abnormal orbital region", + "abnormally formed anatomical entity in independent continuant", + "abnormal craniocervical region", + "Abnormal eye morphology", + "abnormal face morphology", "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)", + "Phenotypic abnormality", "continuant", - "appendage", - "subdivision of organism along appendicular axis", - "Abnormality of the lower limb (HPO)", - "Phenotypic abnormality (HPO)", + "Peters anomaly", "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", + "abnormally formed anterior chamber of eyeball", + "abnormal camera-type eye morphology", + "abnormal head", + "malformed anatomical entity", + "abnormal anterior segment of eyeball morphology", + "abnormal anatomical entity", + "Abnormality of the eye", + "abnormal camera-type eye morphology", + "phenotype by ontology source", "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", - "pelvic appendage", - "pes", - "Talipes (HPO)", - "Abnormality of limbs (HPO)", - "multicellular anatomical structure", - "hindlimb", - "appendage girdle complex", - "paired limb/fin segment" + "abnormal craniocervical region morphology", + "Abnormality of the head", + "abnormal anterior chamber of eyeball morphology", + "abnormal anterior segment of eyeball morphology", + "abnormally formed anatomical entity", + "quality", + "Abnormal anterior chamber morphology", + "Abnormality of head or neck", + "abnormal head morphology", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity", + "Abnormal anterior eye segment morphology", + "Phenotypic abnormality", + "specifically dependent continuant", + "abnormal anatomical entity morphology in the independent continuant", + "Abnormality of the face", + "abnormal anterior chamber of eyeball morphology", + "abnormal anatomical entity morphology" ], "object_taxon": null, "object_taxon_label": null, @@ -2638,24 +2166,24 @@ "negated": null, "pathway": null, "evidence_count": 2, - "has_evidence": ["ECO:0000304"], + "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { - "id": "ECO:0000304", - "url": "http://purl.obolibrary.org/obo/ECO_0000304" + "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], - "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001883", + "grouping_key": "MONDO:0013154🍪🍪biolink:has_phenotype🍪HP:0000659", "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": ["PMID:15894594"], "publications_links": [ { - "id": "orphanet:589821", - "url": null + "id": "PMID:15894594", + "url": "http://identifiers.org/pubmed/15894594" } ], "qualifiers": [], @@ -2668,15 +2196,11 @@ "qualifiers_category": null, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_label": "Frequent", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": [ - "Frequency (HPO)", - "Frequent (HPO)", - "All (HPO)" - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -2694,166 +2218,174 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:4e02df8e-842a-11ee-884f-6be035239f90", + "id": "uuid:89e159df-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013154", + "original_subject": "OMIM:613150", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0018939", + "MONDO:0019052", + "MONDO:0018282", "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", + "MONDO:0013154", "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:0000171", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", - "BFO:0000001" + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0015286", + "MONDO:0016155", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000020", + "MONDO:0700071", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", + "BFO:0000001", + "MONDO:0002320" ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "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", + "disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "muscular dystrophy-dystroglycanopathy, type A", + "neuromuscular disease", + "muscle-eye-brain disease", + "skeletal muscle disorder", + "entity", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "continuant", + "myopathy", + "congenital muscular dystrophy", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome" + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "metabolic disease", + "qualitative or quantitative defects of alpha-dystroglycan", + "disease", + "myopathy caused by variation in POMT2", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0011098", + "object": "HP:0002951", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "UBERON:0000465", - "UPHENO:0082875", - "HP:0011442", - "HP:0002186", - "UPHENO:0004523", - "BFO:0000001", - "BFO:0000040", - "UBERON:0001062", + "HP:0000001", + "HP:0012443", + "HP:0011283", + "HP:0002951", "UPHENO:0001002", + "UPHENO:0076791", + "UPHENO:0081601", + "HP:0001317", + "UPHENO:0080079", + "UPHENO:0076720", + "UPHENO:0081573", + "UPHENO:0080089", + "BFO:0000001", + "UPHENO:0075696", + "HP:0002977", + "HP:0000707", + "UPHENO:0001003", + "UPHENO:0076692", + "UPHENO:0076702", + "UPHENO:0086932", + "UPHENO:0015280", + "UPHENO:0020013", + "UPHENO:0081435", + "HP:0012639", + "HP:0002334", "BFO:0000002", - "UPHENO:0001001", "BFO:0000020", - "UPHENO:0001003", + "UPHENO:0086586", + "UPHENO:0004523", + "PATO:0000001", + "HP:0011282", + "HP:0002011", + "UPHENO:0076805", "UPHENO:0002536", - "BFO:0000001", - "UBERON:0000061", - "UPHENO:0075696", + "UPHENO:0001001", "UPHENO:0001005", - "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:0000467", - "UBERON:0001016" + "HP:0006817", + "HP:0007360", + "UPHENO:0020584" ], - "object_label": "Speech apraxia (HPO)", + "object_label": "Partial absence of cerebellar vermis", "object_closure_label": [ - "abnormality of anatomical entity physiology", - "specifically dependent continuant", - "Abnormality of higher mental function (HPO)", + "All", + "continuant", + "Aplasia/Hypoplasia of the cerebellar vermis", + "Aplasia/Hypoplasia of the cerebellum", + "aplasia or hypoplasia of cerebellum", + "abnormal anatomical entity morphology", + "aplasia or hypoplasia of anatomical entity", + "abnormal cerebellum morphology", + "abnormal cerebellar vermis morphology", + "Abnormality of brain morphology", + "Abnormal metencephalon morphology", "quality", + "Abnormal hindbrain morphology", + "Phenotypic abnormality", + "abnormal cerebellar cortex morphology", + "abnormal nervous system", + "Abnormal cerebellum morphology", + "abnormal nervous system morphology", + "abnormal hindbrain morphology", "abnormal anatomical entity", - "abnormal phenotype by ontology source", + "Aplasia/Hypoplasia involving the central nervous system", + "Abnormality of the nervous system", "phenotype by ontology source", + "phenotype", + "abnormal phenotype by ontology source", + "Morphological central nervous system abnormality", + "abnormal brain morphology", + "abnormal anatomical entity morphology in the brain", + "Abnormal nervous system morphology", + "Partial absence of cerebellar vermis", "abnormal anatomical entity", - "abnormal nervous system", - "continuant", - "material anatomical entity", - "nervous system", - "All (HPO)", - "continuant", - "Phenotypic abnormality (HPO)", - "Abnormality of the nervous system (HPO)", - "entity", + "Abnormal cerebellar vermis morphology", "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" + "abnormal central nervous system morphology", + "abnormal metencephalon morphology", + "specifically dependent continuant", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal hindbrain morphology", + "abnormal anatomical entity morphology", + "entity" ], "object_taxon": null, "object_taxon_label": null, @@ -2862,24 +2394,24 @@ "negated": null, "pathway": null, "evidence_count": 2, - "has_evidence": ["ECO:0000304"], + "has_evidence": ["ECO:0000501"], "has_evidence_links": [ { - "id": "ECO:0000304", - "url": "http://purl.obolibrary.org/obo/ECO_0000304" + "id": "ECO:0000501", + "url": "http://purl.obolibrary.org/obo/ECO_0000501" } ], - "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0011098", + "grouping_key": "MONDO:0013154🍪🍪biolink:has_phenotype🍪HP:0002951", "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": ["PMID:15894594"], "publications_links": [ { - "id": "orphanet:589821", - "url": null + "id": "PMID:15894594", + "url": "http://identifiers.org/pubmed/15894594" } ], "qualifiers": [], @@ -2892,15 +2424,11 @@ "qualifiers_category": null, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_label": "Frequent", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": [ - "Frequency (HPO)", - "Frequent (HPO)", - "All (HPO)" - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -2918,170 +2446,186 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:4e02df90-842a-11ee-884f-6be035239f90", + "id": "uuid:89e159e0-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013154", + "original_subject": "OMIM:613150", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0018939", + "MONDO:0019052", + "MONDO:0018282", "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", + "MONDO:0013154", "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:0000171", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", - "BFO:0000001" + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0015286", + "MONDO:0016155", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000020", + "MONDO:0700071", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", + "BFO:0000001", + "MONDO:0002320" ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "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", + "disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "muscular dystrophy-dystroglycanopathy, type A", + "neuromuscular disease", + "muscle-eye-brain disease", + "skeletal muscle disorder", + "entity", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "continuant", + "myopathy", + "congenital muscular dystrophy", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome" + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "metabolic disease", + "qualitative or quantitative defects of alpha-dystroglycan", + "disease", + "myopathy caused by variation in POMT2", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0011710", + "object": "HP:0000175", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "UPHENO:0002536", - "PR:000050567", - "UBERON:0000465", - "UPHENO:0082875", - "UPHENO:0080362", - "BFO:0000040", - "UBERON:0001062", - "HP:0030956", - "HP:0001626", - "HP:0031546", - "BFO:0000002", - "UPHENO:0001001", + "HP:0000001", + "HP:0000163", + "HP:0000234", + "UPHENO:0033635", "UPHENO:0001002", - "UPHENO:0001003", + "UPHENO:0033572", + "UPHENO:0087585", + "UPHENO:0076786", + "UPHENO:0076760", + "HP:0025033", + "HP:0002664", + "HP:0000175", + "HP:0000202", + "BFO:0000001", "UPHENO:0075696", - "UPHENO:0001005", - "BFO:0000020", - "HP:0011710", - "UPHENO:0002406", - "BFO:0000004", - "UBERON:0004535", - "UBERON:0000061", - "UBERON:0000468", - "HP:0012722", - "HP:0000118", + "HP:0000152", + "UPHENO:0087907", + "UPHENO:0002910", + "UPHENO:0076800", + "UPHENO:0001003", + "UPHENO:0076692", + "UPHENO:0002828", + "UPHENO:0002833", + "HP:0000309", + "UPHENO:0015280", + "HP:0000271", + "HP:0025031", + "UPHENO:0076803", + "UPHENO:0002844", "BFO:0000002", - "UPHENO:0002332", + "BFO:0000020", + "HP:0011793", + "UPHENO:0086824", + "HP:0000174", "PATO:0000001", - "HP:0000001", - "HP:0011025", - "BFO:0000001", - "BFO:0000001", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0001009" + "UPHENO:0087472", + "UPHENO:0002764", + "HP:0031816", + "HP:0000153", + "UPHENO:0002536", + "UPHENO:0001001", + "UPHENO:0086589", + "UPHENO:0001005", + "HP:0000118", + "UPHENO:0075655", + "UPHENO:0020584" ], - "object_label": "Bundle branch block (HPO)", + "object_label": "Cleft palate", "object_closure_label": [ - "abnormality of anatomical entity physiology", - "Phenotypic abnormality", - "Abnormal cardiovascular system physiology (HPO)", + "All", + "Abnormal oral cavity morphology", + "continuant", + "abnormal opening of the anatomical entity", + "Orofacial cleft", + "abnormal anatomical entity morphology", + "abnormal craniocervical region", + "Neoplasm", + "Cleft palate", "quality", - "entity", + "abnormal face morphology", + "Phenotypic abnormality", + "Abnormality of digestive system morphology", + "Neoplasm by anatomical site", + "abnormal roof of mouth morphology", + "Abnormal palate morphology", + "abnormal head", + "abnormal oral cavity morphology", + "abnormal secondary palate morphology", "abnormal anatomical entity", - "abnormal phenotype by ontology source", + "abnormal digestive system", + "Abnormal midface morphology", "phenotype by ontology source", - "continuant", - "protein-containing material entity", - "material anatomical entity", - "circulatory system", - "All (HPO)", - "Cardiac conduction abnormality (HPO)", - "Phenotypic abnormality (HPO)", - "continuant", - "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 craniocervical region morphology", + "abnormal phenotype by ontology source", + "Abnormal oral morphology", + "Abnormality of the mouth", + "Abnormality of the head", + "abnormal incomplete closing of the secondary palate", + "Abnormality of head or neck", + "abnormal head morphology", + "abnormal face", + "abnormal mouth morphology", "abnormal anatomical entity", - "Heart block (HPO)", - "multicellular anatomical structure", - "anatomical system" + "Abnormality of the digestive system", + "abnormal digestive system morphology", + "abnormal mouth", + "Phenotypic abnormality", + "abnormal incomplete closing of the anatomical entity", + "abnormal midface morphology", + "specifically dependent continuant", + "abnormal anatomical entity morphology in the independent continuant", + "Abnormality of the face", + "abnormal anatomical entity morphology", + "entity" ], "object_taxon": null, "object_taxon_label": null, @@ -3090,24 +2634,24 @@ "negated": null, "pathway": null, "evidence_count": 2, - "has_evidence": ["ECO:0000304"], + "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { - "id": "ECO:0000304", - "url": "http://purl.obolibrary.org/obo/ECO_0000304" + "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], - "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0011710", + "grouping_key": "MONDO:0013154🍪🍪biolink:has_phenotype🍪HP:0000175", "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": ["PMID:15894594"], "publications_links": [ { - "id": "orphanet:589821", - "url": null + "id": "PMID:15894594", + "url": "http://identifiers.org/pubmed/15894594" } ], "qualifiers": [], @@ -3120,15 +2664,11 @@ "qualifiers_category": null, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Frequent (HPO)", + "frequency_qualifier_label": "Frequent", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040282", "HP:0040279", "HP:0000001"], - "frequency_qualifier_closure_label": [ - "Frequency (HPO)", - "Frequent (HPO)", - "All (HPO)" - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -3146,170 +2686,180 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:4e02dfa2-842a-11ee-884f-6be035239f90", + "id": "uuid:89e159e3-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013154", + "original_subject": "OMIM:613150", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0018939", + "MONDO:0019052", + "MONDO:0018282", "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", + "MONDO:0013154", "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:0000171", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", - "BFO:0000001" + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0015286", + "MONDO:0016155", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000020", + "MONDO:0700071", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", + "BFO:0000001", + "MONDO:0002320" ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "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", + "disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "muscular dystrophy-dystroglycanopathy, type A", + "neuromuscular disease", + "muscle-eye-brain disease", + "skeletal muscle disorder", + "entity", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "continuant", + "myopathy", + "congenital muscular dystrophy", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome" + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "metabolic disease", + "qualitative or quantitative defects of alpha-dystroglycan", + "disease", + "myopathy caused by variation in POMT2", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0001513", + "object": "HP:0001321", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "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:0000001", + "HP:0012443", + "HP:0011283", "UPHENO:0001002", - "UPHENO:0001003", + "UPHENO:0081099", + "UPHENO:0076791", + "UPHENO:0081601", + "HP:0001317", + "UPHENO:0080079", + "UPHENO:0076720", + "HP:0001321", + "UPHENO:0081091", + "UPHENO:0080089", "BFO:0000001", - "UBERON:0000061", "UPHENO:0075696", - "UPHENO:0001005", - "BFO:0000020", - "BFO:0000015", - "BFO:0000004", - "HP:0001507", + "HP:0002977", + "HP:0000707", + "UPHENO:0001003", + "UPHENO:0076692", + "UPHENO:0076702", + "UPHENO:0086932", + "UPHENO:0015280", + "UPHENO:0020013", + "UPHENO:0081435", + "HP:0012639", + "UPHENO:0012541", + "UPHENO:0068971", "BFO:0000002", + "BFO:0000020", + "UPHENO:0081790", + "UPHENO:0004523", + "HP:0011282", + "HP:0002011", + "UPHENO:0076805", + "UPHENO:0068984", "UPHENO:0002536", - "HP:0000118", - "UPHENO:0010795", - "HP:0004323", - "UPHENO:0010763", "PATO:0000001", - "HP:0000001", - "HP:0004324", - "UPHENO:0008312", - "GO:0040007", - "UBERON:0010000" + "UPHENO:0001001", + "UPHENO:0001005", + "HP:0000118", + "UPHENO:0075195", + "HP:0007360", + "UPHENO:0020584" ], - "object_label": "Obesity (HPO)", + "object_label": "Cerebellar hypoplasia", "object_closure_label": [ + "All", + "continuant", + "abnormal size of anatomical entity", + "Aplasia/Hypoplasia of the cerebellum", + "anatomical entity hypoplasia", + "aplasia or hypoplasia of cerebellum", + "abnormal anatomical entity morphology", + "aplasia or hypoplasia of anatomical entity", + "abnormal cerebellum morphology", + "Cerebellar hypoplasia", + "Abnormality of brain morphology", + "Abnormal metencephalon morphology", + "Abnormal hindbrain morphology", "Phenotypic abnormality", + "anatomical entity hypoplasia in independent continuant", + "abnormal nervous system", + "decreased size of the anatomical entity", + "Abnormal cerebellum morphology", + "abnormal nervous system morphology", + "abnormal hindbrain morphology", "abnormal anatomical entity", - "increased multicellular organism mass", + "Aplasia/Hypoplasia involving the central nervous system", + "Abnormality of the nervous system", + "phenotype by ontology source", + "phenotype", + "abnormal phenotype by ontology source", + "Morphological central nervous system abnormality", + "abnormal brain morphology", + "abnormal anatomical entity morphology in the brain", + "Abnormal nervous system morphology", "quality", - "growth", + "decreased size of the cerebellum", "abnormal anatomical entity", - "abnormal phenotype by ontology source", - "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", - "biological_process", - "increased anatomical entity mass", + "decreased size of the anatomical entity in the independent continuant", + "Phenotypic abnormality", + "cerebellum hypoplasia", + "abnormal central nervous system morphology", + "abnormal metencephalon morphology", "specifically dependent continuant", - "anatomical structure", - "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" + "abnormal anatomical entity morphology in the independent continuant", + "abnormal hindbrain morphology", + "abnormal anatomical entity morphology", + "entity" ], "object_taxon": null, "object_taxon_label": null, @@ -3318,28 +2868,28 @@ "negated": null, "pathway": null, "evidence_count": 2, - "has_evidence": ["ECO:0000304"], + "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { - "id": "ECO:0000304", - "url": "http://purl.obolibrary.org/obo/ECO_0000304" + "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], - "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001513", + "grouping_key": "MONDO:0013154🍪🍪biolink:has_phenotype🍪HP:0001321", "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": ["PMID:15894594"], "publications_links": [ { - "id": "orphanet:589821", - "url": null + "id": "PMID:15894594", + "url": "http://identifiers.org/pubmed/15894594" } ], "qualifiers": [], - "frequency_qualifier": "HP:0040284", + "frequency_qualifier": "HP:0040282", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, @@ -3348,15 +2898,11 @@ "qualifiers_category": null, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Very rare (HPO)", + "frequency_qualifier_label": "Frequent", "frequency_qualifier_namespace": "HP", "frequency_qualifier_category": "biolink:PhenotypicFeature", - "frequency_qualifier_closure": ["HP:0040279", "HP:0000001", "HP:0040284"], - "frequency_qualifier_closure_label": [ - "Very rare (HPO)", - "Frequency (HPO)", - "All (HPO)" - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -3374,186 +2920,130 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:4e02df92-842a-11ee-884f-6be035239f90", + "id": "uuid:89e159e5-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013154", + "original_subject": "OMIM:613150", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0018939", + "MONDO:0019052", + "MONDO:0018282", "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", + "MONDO:0013154", "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:0000171", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", - "BFO:0000001" + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0015286", + "MONDO:0016155", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000020", + "MONDO:0700071", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", + "BFO:0000001", + "MONDO:0002320" ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "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", + "disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "muscular dystrophy-dystroglycanopathy, type A", + "neuromuscular disease", + "muscle-eye-brain disease", + "skeletal muscle disorder", + "entity", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "continuant", + "myopathy", + "congenital muscular dystrophy", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome" + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "metabolic disease", + "qualitative or quantitative defects of alpha-dystroglycan", + "disease", + "myopathy caused by variation in POMT2", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0000729", + "object": "HP:0003560", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "UPHENO:0002536", + "HP:0000001", + "UPHENO:0001002", + "UPHENO:0076710", + "HP:0003011", "BFO:0000001", - "GO:0008150", - "UBERON:0000465", - "NBO:0000313", - "UPHENO:0082875", - "UPHENO:0004523", - "UPHENO:0049587", - "BFO:0000040", - "GO:0007610", - "UBERON:0000468", - "BFO:0000020", - "BFO:0000003", + "UPHENO:0001003", + "UPHENO:0076692", + "HP:0011805", + "HP:0003560", "BFO:0000002", + "BFO:0000020", + "PATO:0000001", + "UPHENO:0002816", + "UPHENO:0002536", "UPHENO:0001001", - "UPHENO:0049622", - "UPHENO:0001002", - "UPHENO:0001003", - "BFO:0000001", - "UBERON:0001062", - "UBERON:0000061", - "UPHENO:0075696", "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:0079826", - "PATO:0000001", - "HP:0000001", - "HP:0000707", - "HP:0011446", - "GO:0032501", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0001016" + "HP:0033127" ], - "object_label": "Autistic behavior (HPO)", + "object_label": "Muscular dystrophy", "object_closure_label": [ - "abnormality of anatomical entity physiology", - "Phenotypic abnormality", - "Abnormality of higher mental function (HPO)", + "All", + "continuant", + "Abnormality of the musculoskeletal system", + "abnormal anatomical entity morphology", "quality", - "multicellular organismal process", - "abnormal anatomical entity", - "abnormal phenotype by ontology source", - "specifically dependent continuant", + "Phenotypic abnormality", + "Abnormality of the musculature", + "abnormal muscle organ morphology", + "Abnormal skeletal muscle morphology", + "Muscular dystrophy", "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", "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 phenotype by ontology source", + "abnormal musculature", "abnormal anatomical entity", - "independent continuant", - "multicellular anatomical structure", - "anatomical system" + "Phenotypic abnormality", + "specifically dependent continuant", + "entity" ], "object_taxon": null, "object_taxon_label": null, @@ -3562,28 +3052,28 @@ "negated": null, "pathway": null, "evidence_count": 2, - "has_evidence": ["ECO:0000304"], + "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { - "id": "ECO:0000304", - "url": "http://purl.obolibrary.org/obo/ECO_0000304" + "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], - "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0000729", + "grouping_key": "MONDO:0013154🍪🍪biolink:has_phenotype🍪HP:0003560", "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": ["PMID:15894594"], "publications_links": [ { - "id": "orphanet:589821", - "url": null + "id": "PMID:15894594", + "url": "http://identifiers.org/pubmed/15894594" } ], "qualifiers": [], - "frequency_qualifier": "HP:0040283", + "frequency_qualifier": "HP:0040280", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, @@ -3592,15 +3082,11 @@ "qualifiers_category": null, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_label": "Obligate", "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)" - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Obligate"], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -3618,194 +3104,176 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:4e02df94-842a-11ee-884f-6be035239f90", + "id": "uuid:89e159e8-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013154", + "original_subject": "OMIM:613150", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0018939", + "MONDO:0019052", + "MONDO:0018282", "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", + "MONDO:0013154", "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:0000171", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", - "BFO:0000001" + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0015286", + "MONDO:0016155", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000020", + "MONDO:0700071", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", + "BFO:0000001", + "MONDO:0002320" ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "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", + "disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "muscular dystrophy-dystroglycanopathy, type A", + "neuromuscular disease", + "muscle-eye-brain disease", + "skeletal muscle disorder", + "entity", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "continuant", + "myopathy", + "congenital muscular dystrophy", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome" + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "metabolic disease", + "qualitative or quantitative defects of alpha-dystroglycan", + "disease", + "myopathy caused by variation in POMT2", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0000752", + "object": "HP:0000568", "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:0004523", - "BFO:0000040", - "UBERON:0001062", - "GO:0007610", - "NBO:0000568", - "BFO:0000003", - "BFO:0000002", - "UPHENO:0001001", - "UPHENO:0049622", + "HP:0000315", + "HP:0000001", + "UPHENO:0075219", + "HP:0000234", + "UPHENO:0075997", + "UPHENO:0080079", + "UPHENO:0001005", "UPHENO:0001002", - "UPHENO:0001003", - "BFO:0000001", - "UBERON:0000061", - "HP:0000752", + "BFO:0000002", "UPHENO:0075696", - "UPHENO:0001005", + "HP:0000152", + "UPHENO:0087907", + "UPHENO:0002910", + "UPHENO:0001003", + "UPHENO:0076692", + "HP:0000568", + "UPHENO:0015280", + "HP:0000271", + "UPHENO:0012541", + "UPHENO:0080209", + "UPHENO:0068971", + "UPHENO:0021474", + "UPHENO:0002844", "BFO:0000020", - "UPHENO:0002433", - "HP:0012638", - "NBO:0000644", - "BFO:0000015", - "BFO:0000004", - "UBERON:0000468", - "UPHENO:0049586", - "BFO:0000002", + "HP:0008056", + "PATO:0000001", + "HP:0012372", + "UPHENO:0087472", + "HP:0000478", + "HP:0100887", + "UPHENO:0087924", + "UPHENO:0002764", + "UPHENO:0003020", "UPHENO:0002536", - "HP:0000708", - "NBO:0000243", - "UPHENO:0080585", + "UPHENO:0069523", + "UPHENO:0001001", + "UPHENO:0086589", "HP:0000118", - "UPHENO:0002332", - "UPHENO:0079826", - "PATO:0000001", - "HP:0000001", - "HP:0000707", - "HP:0011446", - "BFO:0000001", - "GO:0032501", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0001016" + "UPHENO:0075195", + "UPHENO:0020584", + "BFO:0000001" ], - "object_label": "Hyperactivity (HPO)", + "object_label": "Microphthalmia", "object_closure_label": [ - "abnormality of anatomical entity physiology", - "Phenotypic abnormality", - "abnormal anatomical entity", - "Abnormality of higher mental function (HPO)", + "Abnormality of the orbital region", + "All", + "abnormal size of eyeball of camera-type eye", + "abnormal size of anatomical entity", + "abnormal anatomical entity morphology", + "abnormal orbital region", + "aplasia or hypoplasia of anatomical entity", + "abnormal craniocervical region", "quality", - "multicellular organismal process", - "Hyperactivity (HPO)", - "abnormal anatomical entity", + "Abnormal eye morphology", + "abnormal face 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", + "Phenotypic abnormality", + "Phenotypic abnormality", + "Aplasia/Hypoplasia affecting the eye", "entity", - "hyperactivity", - "biological_process", - "specifically dependent continuant", - "abnormality of nervous system physiology", - "anatomical structure", - "multicellular organism", + "aplasia or hypoplasia of eyeball of camera-type eye", + "decreased size of the anatomical entity", + "abnormal camera-type eye morphology", + "abnormal head", + "continuant", + "abnormal anatomical entity", + "Abnormality of the eye", + "Abnormality of globe size", + "abnormal camera-type eye morphology", + "Microphthalmia", + "phenotype by ontology source", "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" + "abnormal craniocervical region morphology", + "Abnormality of the head", + "Abnormality of head or neck", + "abnormal head morphology", + "abnormal face", + "abnormal eyeball of camera-type eye", + "abnormal anatomical entity", + "decreased size of the eyeball of camera-type eye", + "decreased size of the anatomical entity in the independent continuant", + "specifically dependent continuant", + "abnormal anatomical entity morphology in the independent continuant", + "Abnormality of the face", + "abnormal anatomical entity morphology" ], "object_taxon": null, "object_taxon_label": null, @@ -3814,28 +3282,28 @@ "negated": null, "pathway": null, "evidence_count": 2, - "has_evidence": ["ECO:0000304"], + "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { - "id": "ECO:0000304", - "url": "http://purl.obolibrary.org/obo/ECO_0000304" + "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], - "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0000752", + "grouping_key": "MONDO:0013154🍪🍪biolink:has_phenotype🍪HP:0000568", "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": ["PMID:15894594"], "publications_links": [ { - "id": "orphanet:589821", - "url": null + "id": "PMID:15894594", + "url": "http://identifiers.org/pubmed/15894594" } ], "qualifiers": [], - "frequency_qualifier": "HP:0040283", + "frequency_qualifier": "HP:0040282", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, @@ -3844,15 +3312,11 @@ "qualifiers_category": null, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_label": "Frequent", "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)" - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -3870,156 +3334,194 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:4e02df96-842a-11ee-884f-6be035239f90", + "id": "uuid:89e159ea-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013154", + "original_subject": "OMIM:613150", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0018939", + "MONDO:0019052", + "MONDO:0018282", "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", + "MONDO:0013154", "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:0000171", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", - "BFO:0000001" + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0015286", + "MONDO:0016155", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000020", + "MONDO:0700071", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", + "BFO:0000001", + "MONDO:0002320" ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "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", + "disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "muscular dystrophy-dystroglycanopathy, type A", + "neuromuscular disease", + "muscle-eye-brain disease", + "skeletal muscle disorder", + "entity", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "continuant", + "myopathy", + "congenital muscular dystrophy", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome" + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "metabolic disease", + "qualitative or quantitative defects of alpha-dystroglycan", + "disease", + "myopathy caused by variation in POMT2", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0001558", + "object": "HP:0000204", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0001197", - "UBERON:0000465", - "HP:0034059", - "BFO:0000040", - "UBERON:0001062", - "BFO:0000002", - "UPHENO:0001001", + "HP:0000001", + "HP:0000163", + "HP:0000177", + "HP:0000234", + "UPHENO:0087551", + "UPHENO:0033572", + "UPHENO:0087585", + "UPHENO:0076786", "UPHENO:0001002", - "BFO:0000020", - "UPHENO:0001003", + "BFO:0000002", + "HP:0025033", + "HP:0002664", + "UPHENO:0033642", + "HP:0000202", "BFO:0000001", + "UPHENO:0075696", + "HP:0000152", + "UPHENO:0087907", + "UPHENO:0002910", + "UPHENO:0001003", + "UPHENO:0076692", + "UPHENO:0020955", + "UPHENO:0002828", + "UPHENO:0002833", + "HP:0000309", + "HP:0410030", + "BFO:0000020", + "UPHENO:0015280", + "HP:0000271", + "HP:0000159", + "HP:0025031", + "UPHENO:0076803", + "UPHENO:0002844", + "HP:0011793", + "UPHENO:0087472", + "UPHENO:0076800", + "UPHENO:0033637", "UPHENO:0001005", - "HP:0001558", - "BFO:0000004", - "UBERON:0000061", - "UBERON:0000468", - "BFO:0000002", + "UPHENO:0087554", + "HP:0000204", + "UPHENO:0002764", + "HP:0031816", + "HP:0000153", "UPHENO:0002536", - "HP:0001557", - "UBERON:0000922", - "HP:0000118", - "HP:0034057", "PATO:0000001", - "UBERON:0000323", - "HP:0000001", - "UPHENO:0075949", - "BFO:0000001", - "UBERON:0010000" + "UPHENO:0001001", + "UPHENO:0086589", + "HP:0000118", + "UPHENO:0075655", + "UPHENO:0020584" ], - "object_label": "Decreased fetal movement (HPO)", + "object_label": "Cleft upper lip", "object_closure_label": [ + "All", + "Abnormal oral cavity morphology", + "Abnormal upper lip morphology", + "abnormal opening of the anatomical entity", + "Orofacial cleft", + "abnormal anatomical entity morphology", + "abnormal lip morphology", + "abnormal phenotype by ontology source", + "abnormal upper lip morphology", + "Cleft upper lip", + "abnormal craniocervical region", + "Neoplasm", + "abnormal incomplete closing of the upper lip", + "abnormal lip morphology", + "abnormal face morphology", "Phenotypic abnormality", - "specifically dependent continuant", + "Phenotypic abnormality", + "Abnormality of digestive system morphology", + "Neoplasm by anatomical site", + "abnormal head", + "continuant", + "abnormal oral cavity morphology", "abnormal anatomical entity", - "quality", - "abnormal phenotype by ontology source", + "abnormal mouth morphology", + "abnormal incomplete closing of the lip", + "abnormal digestive system", + "Abnormal midface morphology", + "Cleft lip", + "specifically dependent continuant", "phenotype by ontology source", - "continuant", - "material anatomical entity", - "All (HPO)", - "continuant", - "embryo", - "Phenotypic abnormality (HPO)", - "abnormal late embryo", - "Fetal anomaly (HPO)", - "entity", - "entity", - "Decreased fetal movement (HPO)", - "multicellular organism", + "Abnormal lip morphology", "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" + "abnormal craniocervical region morphology", + "Abnormal oral morphology", + "Abnormality of the mouth", + "Abnormality of the head", + "quality", + "Abnormality of head or neck", + "abnormal head morphology", + "abnormal face", + "abnormal anatomical entity", + "Abnormality of the digestive system", + "abnormal digestive system morphology", + "abnormal mouth", + "abnormal incomplete closing of the anatomical entity", + "abnormal midface morphology", + "abnormal anatomical entity morphology in the independent continuant", + "Abnormality of the face", + "abnormal anatomical entity morphology", + "entity" ], "object_taxon": null, "object_taxon_label": null, @@ -4028,28 +3530,28 @@ "negated": null, "pathway": null, "evidence_count": 2, - "has_evidence": ["ECO:0000304"], + "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { - "id": "ECO:0000304", - "url": "http://purl.obolibrary.org/obo/ECO_0000304" + "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], - "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001558", + "grouping_key": "MONDO:0013154🍪🍪biolink:has_phenotype🍪HP:0000204", "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": ["PMID:15894594"], "publications_links": [ { - "id": "orphanet:589821", - "url": null + "id": "PMID:15894594", + "url": "http://identifiers.org/pubmed/15894594" } ], "qualifiers": [], - "frequency_qualifier": "HP:0040283", + "frequency_qualifier": "HP:0040282", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, @@ -4058,15 +3560,11 @@ "qualifiers_category": null, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_label": "Frequent", "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)" - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -4084,158 +3582,172 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:4e02df97-842a-11ee-884f-6be035239f90", + "id": "uuid:89e159ed-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013154", + "original_subject": "OMIM:613150", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0018939", + "MONDO:0019052", + "MONDO:0018282", "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", + "MONDO:0013154", "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:0000171", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", - "BFO:0000001" + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0015286", + "MONDO:0016155", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000020", + "MONDO:0700071", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", + "BFO:0000001", + "MONDO:0002320" ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "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", + "disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "muscular dystrophy-dystroglycanopathy, type A", + "neuromuscular disease", + "muscle-eye-brain disease", + "skeletal muscle disorder", + "entity", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "continuant", + "myopathy", + "congenital muscular dystrophy", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome" + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "metabolic disease", + "qualitative or quantitative defects of alpha-dystroglycan", + "disease", + "myopathy caused by variation in POMT2", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0001561", + "object": "HP:0003557", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "HP:0001197", - "UPHENO:0075852", - "UPHENO:0002536", - "UBERON:0000465", - "BFO:0000001", - "BFO:0000040", - "BFO:0000002", - "UPHENO:0001001", + "HP:0000001", + "HP:0004303", + "HP:0025461", + "UPHENO:0088180", + "UPHENO:0086172", "UPHENO:0001002", - "UPHENO:0001003", - "BFO:0000001", - "UBERON:0001062", - "UBERON:0000061", - "UBERON:0000463", + "HP:0003557", + "UPHENO:0076710", + "UPHENO:0084928", + "UPHENO:0085097", "UPHENO:0001005", + "BFO:0000002", + "HP:0003011", + "UPHENO:0006889", + "UPHENO:0075696", + "UPHENO:0080626", + "UPHENO:0001003", + "UPHENO:0076692", + "UPHENO:0077801", + "UPHENO:0085135", + "HP:0011805", "BFO:0000020", - "BFO:0000004", - "UBERON:0000173", - "UBERON:0000468", - "HP:0001561", - "UBERON:0000922", - "HP:0000118", + "UPHENO:0015280", + "HP:0012084", + "UPHENO:0086462", + "UPHENO:0087047", + "HP:0025354", + "UPHENO:0085099", + "UPHENO:0002816", + "UPHENO:0002536", "PATO:0000001", - "UBERON:0000323", - "HP:0000001", - "BFO:0000002", - "UPHENO:0075949", - "HP:0001560", - "UBERON:0010000" + "UPHENO:0001001", + "UPHENO:0067691", + "HP:0000118", + "UPHENO:0075195", + "HP:0033127", + "UPHENO:0086457", + "UPHENO:0020584", + "BFO:0000001" ], - "object_label": "Polyhydramnios (HPO)", + "object_label": "Increased variability in muscle fiber diameter", "object_closure_label": [ - "Phenotypic abnormality", - "Abnormality of the amniotic fluid (HPO)", - "quality", + "All", + "Abnormal muscle fiber morphology", + "abnormal size of anatomical entity", + "Abnormality of the musculoskeletal system", + "abnormal anatomical entity morphology", + "abnormal size of cell", + "abnormal cell morphology", + "abnormal muscle cell morphology", + "abnormal skeletal muscle tissue morphology", + "abnormal cellular_component", + "abnormal cell of skeletal muscle morphology", "abnormal phenotype by ontology source", - "phenotype by ontology source", - "continuant", - "material anatomical entity", - "All (HPO)", - "embryo", - "Phenotypic abnormality (HPO)", - "abnormal late embryo", + "Phenotypic abnormality", + "Abnormality of the musculature", + "Abnormality of skeletal muscle fiber size", + "abnormal size of skeletal muscle fiber", "entity", + "continuant", + "Increased variability in muscle fiber diameter", + "abnormal muscle organ morphology", + "abnormal anatomical entity", + "Abnormal skeletal muscle morphology", "specifically dependent continuant", - "anatomical entity", - "anatomical structure", - "organism substance", - "amniotic fluid", - "multicellular organism", + "phenotype by ontology source", "phenotype", - "continuant", - "entity", - "independent continuant", - "Abnormality of prenatal development or birth (HPO)", - "abnormal amniotic fluid", - "material entity", - "Polyhydramnios (HPO)", + "abnormal morphology of cellular_component", + "Abnormal cellular phenotype", + "quality", + "abnormal cell", + "abnormal size of cellular_component", + "Abnormal cell morphology", + "abnormal cell of skeletal muscle morphology", + "abnormal musculature", "abnormal anatomical entity", - "multicellular anatomical structure", - "late embryo" + "abnormal myotube morphology", + "Phenotypic abnormality", + "abnormal anatomical entity morphology in the independent continuant", + "abnormal size of cell of skeletal muscle", + "abnormal anatomical entity morphology" ], "object_taxon": null, "object_taxon_label": null, @@ -4244,28 +3756,28 @@ "negated": null, "pathway": null, "evidence_count": 2, - "has_evidence": ["ECO:0000304"], + "has_evidence": ["ECO:0000501"], "has_evidence_links": [ { - "id": "ECO:0000304", - "url": "http://purl.obolibrary.org/obo/ECO_0000304" + "id": "ECO:0000501", + "url": "http://purl.obolibrary.org/obo/ECO_0000501" } ], - "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001561", + "grouping_key": "MONDO:0013154🍪🍪biolink:has_phenotype🍪HP:0003557", "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": ["PMID:15894594"], "publications_links": [ { - "id": "orphanet:589821", - "url": null + "id": "PMID:15894594", + "url": "http://identifiers.org/pubmed/15894594" } ], "qualifiers": [], - "frequency_qualifier": "HP:0040283", + "frequency_qualifier": "HP:0040280", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, @@ -4274,15 +3786,11 @@ "qualifiers_category": null, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_label": "Obligate", "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)" - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040280", "HP:0040279"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Obligate"], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -4300,296 +3808,158 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:4e02df98-842a-11ee-884f-6be035239f90", + "id": "uuid:89ed09a8-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0011925", + "original_subject": "OMIM:607855", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", "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:0100228", "MONDO:0019056", - "MONDO:0004994", - "MONDO:0004995", - "MONDO:0700223", - "MONDO:0003382", - "BFO:0000016", + "BFO:0000001", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", - "BFO:0000001" + "MONDO:0019950", + "BFO:0000017", + "MONDO:0020121", + "BFO:0000002", + "BFO:0000020", + "MONDO:0011925", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0700223", + "MONDO:0002081", + "MONDO:0002320" ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "congenital merosin-deficient muscular dystrophy 1A", "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", + "continuant", "musculoskeletal system disorder", - "hereditary disease", - "eye disorder", + "disease", + "LAMA2-related muscular dystrophy", + "congenital merosin-deficient muscular dystrophy 1A", + "neuromuscular disease", + "skeletal muscle disorder", + "congenital nervous system disorder", "muscular dystrophy", + "myopathy", + "congenital muscular dystrophy", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome" + "human disease", + "hereditary skeletal muscle disorder", + "disposition", + "disease", + "hereditary disease", + "muscle tissue disorder", + "specifically dependent continuant", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0001643", + "object": "HP:0001371", "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", + "HP:0000001", + "HP:0034430", + "HP:0000924", + "HP:0011843", + "UPHENO:0082875", + "UPHENO:0081440", + "UPHENO:0076710", + "UPHENO:0088186", + "HP:0001371", + "UPHENO:0001005", "BFO:0000002", - "UBERON:0013768", - "UBERON:0003509", - "UBERON:0003513", - "UBERON:0011695", - "UBERON:0004716", - "UBERON:0004145", - "UBERON:0005985", - "UBERON:0002049", - "UBERON:0002201", - "UBERON:0006876", - "UPHENO:0001001", + "HP:0003011", + "UPHENO:0076703", + "UPHENO:0002332", "UPHENO:0001003", - "UPHENO:0002536", - "BFO:0000001", - "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:0000477", - "UBERON:0000475", - "UBERON:0000062", - "UBERON:0004111", - "UBERON:0004573", - "UBERON:0003498", - "HP:0011603", - "UPHENO:0020351", - "HP:0030680", - "UPHENO:0076765", - "BFO:0000002", - "HP:0025015", - "HP:0002597", - "UPHENO:0076810", - "HP:0033353", + "HP:0003549", + "HP:0011842", + "HP:0011805", + "UPHENO:0001002", + "UPHENO:0021425", + "UPHENO:0015280", + "UPHENO:0002964", + "UPHENO:0046759", + "UPHENO:0002712", + "UPHENO:0012541", + "UPHENO:0068971", + "BFO:0000020", + "UPHENO:0031839", + "UPHENO:0046505", + "UPHENO:0075696", + "UPHENO:0087888", + "HP:0034392", + "UPHENO:0002816", + "UPHENO:0002536", "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", + "UPHENO:0001001", + "HP:0011729", + "HP:0100261", "HP:0000118", - "UPHENO:0075655", + "UPHENO:0075195", + "HP:0033127", "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" + "BFO:0000001" ], - "object_label": "Patent ductus arteriosus (HPO)", + "object_label": "Flexion contracture", "object_closure_label": [ - "abnormal blood vessel morphology", - "abnormal anatomical entity", - "specifically dependent continuant", - "phenotype by ontology source", + "All", + "abnormal size of anatomical entity", + "Abnormality of the musculoskeletal system", + "abnormal anatomical entity morphology", + "Flexion contracture", + "decreased length of anatomical entity", "abnormal anatomical entity", - "continuant", - "protein-containing material entity", - "material anatomical entity", - "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", + "Phenotypic abnormality", + "Abnormality of the musculature", + "abnormality of anatomical entity physiology", + "decreased length of anatomical entity in independent continuant", "entity", - "structure with developmental contribution from neural crest", - "thoracic cavity element", - "primary circulatory organ", - "abnormal coronary vessel morphology", - "Abnormality of the cardiovascular system (HPO)", + "decreased size of the anatomical entity", + "continuant", + "abnormality of musculoskeletal system physiology", + "abnormal muscle organ morphology", + "abnormal anatomical entity length", + "abnormal tendon morphology", + "Abnormal skeletal morphology", + "Abnormal skeletal muscle morphology", "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", - "anatomical conduit", - "systemic artery", - "heart blood vessel", - "heart plus pericardium", + "abnormal tendon morphology", + "phenotype by ontology source", + "abnormal connective tissue", + "Abnormal musculoskeletal physiology", "phenotype", - "abnormal incomplete closing of the ductus arteriosus", + "Abnormality of joint mobility", + "Abnormal tendon morphology", + "Joint contracture", + "decreased length of tendon", + "quality", + "abnormality of anatomical entity physiology", + "abnormal skeletal system morphology", + "Abnormal joint physiology", + "Abnormality of the skeletal system", + "abnormal musculature", + "abnormal anatomical entity", + "decreased size of the anatomical entity in the independent continuant", + "Abnormality of connective tissue", + "specifically dependent continuant", "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", - "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", - "mesoderm-derived structure", - "artery", - "thoracic segment blood vessel", - "heart", - "heart vasculature" + "abnormal skeletal system", + "abnormal anatomical entity morphology" ], "object_taxon": null, "object_taxon_label": null, @@ -4598,28 +3968,28 @@ "negated": null, "pathway": null, "evidence_count": 2, - "has_evidence": ["ECO:0000304"], + "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { - "id": "ECO:0000304", - "url": "http://purl.obolibrary.org/obo/ECO_0000304" + "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], - "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001643", + "grouping_key": "MONDO:0011925🍪🍪biolink:has_phenotype🍪HP:0001371", "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": ["PMID:12552556"], "publications_links": [ { - "id": "orphanet:589821", - "url": null + "id": "PMID:12552556", + "url": "http://identifiers.org/pubmed/12552556" } ], "qualifiers": [], - "frequency_qualifier": "HP:0040283", + "frequency_qualifier": "HP:0040282", "onset_qualifier": null, "sex_qualifier": null, "stage_qualifier": null, @@ -4628,15 +3998,11 @@ "qualifiers_category": null, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_label": "Frequent", "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)" - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040282"], + "frequency_qualifier_closure_label": ["All", "Frequent", "Frequency"], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -4654,218 +4020,170 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:4e02df99-842a-11ee-884f-6be035239f90", + "id": "uuid:89e15869-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013904", + "original_subject": "OMIM:614830", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0019052", "MONDO:0000001", - "MONDO:0020121", + "MONDO:0005336", + "OGMS:0000031", + "MONDO:0700069", + "MONDO:0019056", + "BFO:0000001", + "MONDO:0000171", + "MONDO:0020120", + "MONDO:0700096", + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0700075", + "MONDO:0024322", "BFO:0000017", - "MONDO:0008056", - "MONDO:0035646", + "MONDO:0013904", + "MONDO:0015286", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000002", + "BFO:0000020", "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:0005066", "MONDO:0700223", - "MONDO:0003382", - "BFO:0000016", - "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", - "OGMS:0000031", - "BFO:0000001" + "MONDO:0002081", + "MONDO:0002320" ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", "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", + "continuant", "musculoskeletal system disorder", - "hereditary disease", - "eye disorder", + "muscular dystrophy-dystroglycanopathy, type A", + "myopathy caused by variation in POMGNT2", + "neuromuscular disease", + "skeletal muscle disorder", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "myopathy", + "disease", + "congenital muscular dystrophy", + "congenital muscular dystrophy caused by variation in POMGNT2", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome" + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8", + "metabolic disease", + "disease", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "entity" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0001671", + "object": "HP:0000568", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "PR:000050567", - "UBERON:0000465", - "UPHENO:0019888", - "UPHENO:0080362", - "HP:0001627", - "UPHENO:0015280", - "BFO:0000040", - "UBERON:0001062", - "UBERON:0000468", - "UBERON:0011676", - "UBERON:0013701", - "HP:0001626", + "HP:0000315", + "HP:0000001", + "UPHENO:0075219", + "HP:0000234", + "UPHENO:0075997", + "UPHENO:0080079", + "UPHENO:0001005", "UPHENO:0001002", - "BFO:0000020", - "UPHENO:0015324", - "HP:0001671", "BFO:0000002", - "UPHENO:0001001", + "UPHENO:0075696", + "HP:0000152", + "UPHENO:0087907", + "UPHENO:0002910", "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", + "HP:0000568", + "UPHENO:0015280", + "HP:0000271", + "UPHENO:0012541", + "UPHENO:0080209", + "UPHENO:0068971", + "UPHENO:0021474", + "UPHENO:0002844", + "BFO:0000020", + "HP:0008056", + "PATO:0000001", + "HP:0012372", + "UPHENO:0087472", + "HP:0000478", + "HP:0100887", + "UPHENO:0087924", + "UPHENO:0002764", + "UPHENO:0003020", "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", + "UPHENO:0069523", + "UPHENO:0001001", + "UPHENO:0086589", "HP:0000118", + "UPHENO:0075195", "UPHENO:0020584", - "PATO:0000001", - "UBERON:0003037", - "UBERON:0010314", - "HP:0000001", - "UPHENO:0001005", - "BFO:0000001", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0004120", - "UBERON:0001009", - "UBERON:0005178", - "UBERON:0007100" + "BFO:0000001" ], - "object_label": "Abnormal cardiac septum morphology (HPO)", + "object_label": "Microphthalmia", "object_closure_label": [ - "abnormal anatomical entity", + "Abnormality of the orbital region", + "All", + "abnormal size of eyeball of camera-type eye", + "abnormal size of anatomical entity", + "abnormal anatomical entity morphology", + "abnormal orbital region", + "aplasia or hypoplasia of anatomical entity", + "abnormal craniocervical region", "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)", + "Abnormal eye morphology", + "abnormal face morphology", "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)", - "abnormal anatomical entity morphology", - "entity", - "entity", - "septum", - "structure with developmental contribution from neural crest", - "thoracic cavity element", - "primary circulatory organ", - "Abnormality of the cardiovascular system (HPO)", "Phenotypic abnormality", - "abnormal cardiovascular system morphology", - "abnormal anatomical entity morphology", - "organism subdivision", - "organ", - "heart plus pericardium", + "Phenotypic abnormality", + "Aplasia/Hypoplasia affecting the eye", + "entity", + "aplasia or hypoplasia of eyeball of camera-type eye", + "decreased size of the anatomical entity", + "abnormal camera-type eye morphology", + "abnormal head", + "continuant", + "abnormal anatomical entity", + "Abnormality of the eye", + "Abnormality of globe size", + "abnormal camera-type eye morphology", + "Microphthalmia", + "phenotype by ontology source", "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", - "anatomical entity", - "cardiovascular system", - "anatomical structure", + "abnormal craniocervical region morphology", + "Abnormality of the head", + "Abnormality of head or neck", + "abnormal head morphology", + "abnormal face", + "abnormal eyeball of camera-type eye", "abnormal anatomical entity", - "abnormal cardiac septum morphology", - "abnormal cardiovascular system", - "Abnormal heart morphology (HPO)", - "abnormal heart morphology", - "multicellular anatomical structure", - "anatomical system", - "mesoderm-derived structure", - "cardiac septum", - "heart" + "decreased size of the eyeball of camera-type eye", + "decreased size of the anatomical entity in the independent continuant", + "specifically dependent continuant", + "abnormal anatomical entity morphology in the independent continuant", + "Abnormality of the face", + "abnormal anatomical entity morphology" ], "object_taxon": null, "object_taxon_label": null, @@ -4874,24 +4192,24 @@ "negated": null, "pathway": null, "evidence_count": 2, - "has_evidence": ["ECO:0000304"], + "has_evidence": ["ECO:0000269"], "has_evidence_links": [ { - "id": "ECO:0000304", - "url": "http://purl.obolibrary.org/obo/ECO_0000304" + "id": "ECO:0000269", + "url": "http://purl.obolibrary.org/obo/ECO_0000269" } ], - "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0001671", + "grouping_key": "MONDO:0013904🍪🍪biolink:has_phenotype🍪HP:0000568", "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": ["PMID:22958903"], "publications_links": [ { - "id": "orphanet:589821", - "url": null + "id": "PMID:22958903", + "url": "http://identifiers.org/pubmed/22958903" } ], "qualifiers": [], @@ -4904,15 +4222,11 @@ "qualifiers_category": null, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_label": "Occasional", "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)" - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040283"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Occasional"], "onset_qualifier_label": null, "onset_qualifier_namespace": null, "onset_qualifier_category": null, @@ -4930,172 +4244,196 @@ "stage_qualifier_closure_label": [] }, { - "id": "uuid:4e02df9a-842a-11ee-884f-6be035239f90", + "id": "uuid:89e159d4-ae6f-11ee-9f7a-f78bc2e9ee32", "category": "biolink:DiseaseToPhenotypicFeatureAssociation", - "subject": "MONDO:0035646", - "original_subject": "Orphanet:589821", + "subject": "MONDO:0013154", + "original_subject": "OMIM:613150", "subject_namespace": "MONDO", "subject_category": "biolink:Disease", "subject_closure": [ - "MONDO:0024573", - "MONDO:0020158", + "MONDO:0005071", + "BFO:0000016", + "MONDO:0018939", + "MONDO:0019052", + "MONDO:0018282", "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", + "MONDO:0013154", "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:0000171", + "MONDO:0020120", "MONDO:0700096", - "MONDO:0000591", - "MONDO:0024458", "OGMS:0000031", - "BFO:0000001" + "MONDO:0019950", + "MONDO:0018276", + "MONDO:0045010", + "MONDO:0024322", + "BFO:0000017", + "MONDO:0016139", + "MONDO:0015286", + "MONDO:0016155", + "MONDO:0017741", + "MONDO:0020121", + "BFO:0000020", + "MONDO:0700071", + "MONDO:0003847", + "MONDO:0003939", + "MONDO:0005066", + "MONDO:0700223", + "MONDO:0002081", + "BFO:0000001", + "MONDO:0002320" ], - "subject_label": "congenital-onset Steinert myotonic dystrophy", + "subject_label": "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", "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", + "disease", + "muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2", + "muscular dystrophy-dystroglycanopathy, type A", + "neuromuscular disease", + "muscle-eye-brain disease", + "skeletal muscle disorder", + "entity", + "congenital nervous system disorder", + "disorder of protein O-glycosylation", "muscular dystrophy", + "continuant", + "myopathy", + "congenital muscular dystrophy", + "disorder of glycosylation", "realizable entity", - "skeletal muscle disorder", - "neuromuscular disease", - "myotonic syndrome" + "human disease", + "congenital disorder of glycosylation", + "hereditary skeletal muscle disorder", + "disposition", + "metabolic disease", + "qualitative or quantitative defects of alpha-dystroglycan", + "disease", + "myopathy caused by variation in POMT2", + "hereditary disease", + "muscle tissue disorder", + "inborn errors of metabolism", + "qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan", + "muscular dystrophy-dystroglycanopathy", + "glycoprotein metabolism disease", + "specifically dependent continuant", + "qualitative or quantitative protein defects in neuromuscular diseases" ], "subject_taxon": null, "subject_taxon_label": null, "predicate": "biolink:has_phenotype", - "object": "HP:0002014", + "object": "HP:0002084", "original_object": null, "object_namespace": "HP", "object_category": "biolink:PhenotypicFeature", "object_closure": [ - "UPHENO:0002443", - "UPHENO:0002536", - "UBERON:0000465", - "UPHENO:0082875", - "HP:0002664", - "BFO:0000001", - "BFO:0000040", - "UBERON:0001062", + "HP:0000001", + "HP:0000924", + "UPHENO:0050108", + "UPHENO:0081436", + "HP:0000234", + "UPHENO:0020641", + "UPHENO:0087665", + "UPHENO:0076791", + "UPHENO:0087089", + "HP:0011815", + "UPHENO:0001005", "UPHENO:0001002", - "BFO:0000020", - "HP:0011793", - "HP:0011458", - "BFO:0000002", - "UBERON:0001988", - "UPHENO:0001001", - "UPHENO:0002833", - "UPHENO:0001003", - "UBERON:0000463", + "BFO:0000001", "UPHENO:0075696", - "HP:0002014", - "HP:0025031", - "BFO:0000004", - "UBERON:0000061", - "UBERON:0000174", - "UBERON:0000468", - "BFO:0000002", - "HP:0025032", + "UPHENO:0051077", + "UPHENO:0076703", + "HP:0000152", + "UPHENO:0087907", + "HP:0000929", + "HP:0000707", + "UPHENO:0001003", + "UPHENO:0076692", + "UPHENO:0022529", + "UPHENO:0076702", + "UPHENO:0087363", + "UPHENO:0051003", + "HP:0011842", + "UPHENO:0088123", + "HP:0045005", + "UPHENO:0015280", + "HP:0034237", + "UPHENO:0002964", + "HP:0012639", + "UPHENO:0049587", + "UPHENO:0002844", + "BFO:0000020", + "HP:0002084", + "HP:0410043", + "UPHENO:0004523", "PATO:0000001", + "UPHENO:0002764", + "HP:0002011", + "UPHENO:0002536", + "UPHENO:0081566", + "UPHENO:0001001", + "UPHENO:0086589", "HP:0000118", - "UPHENO:0002332", - "HP:0000001", - "UPHENO:0001005", - "BFO:0000001", - "UBERON:0010000", - "UBERON:0000467", - "UBERON:0001007" + "BFO:0000002", + "HP:0009121", + "HP:0033127", + "UPHENO:0020584" ], - "object_label": "Diarrhea (HPO)", + "object_label": "Encephalocele", "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)", + "All", + "Abnormal axial skeleton morphology", + "Abnormality of the musculoskeletal system", + "abnormal anatomical entity morphology", + "abnormal craniocervical region", + "Abnormal skull morphology", + "abnormal neural tube morphology", + "quality", "abnormal phenotype by ontology source", - "continuant", - "feces", - "Phenotypic abnormality (HPO)", "Phenotypic abnormality", - "Neoplasm by anatomical site (HPO)", - "Abdominal symptom (HPO)", - "quality", - "organism substance", - "excreta", - "multicellular organism", + "Phenotypic abnormality", + "continuant", + "Encephalocele", + "Abnormal neural tube morphology", + "abnormal nervous system", + "abnormal head", + "abnormal axial skeleton plus cranial skeleton morphology", + "Cephalocele", + "abnormal postcranial axial skeleton morphology", + "abnormal nervous system morphology", + "abnormal neural tube morphology", + "abnormal anatomical entity", + "abnormal neural tube closure", + "abnormal tube formation", + "Abnormal skeletal morphology", + "abnormal embryonic tissue morphology", + "Neural tube defect", + "Abnormality of the nervous system", + "phenotype by ontology source", + "abnormal biological_process", "phenotype", - "Neoplasm (HPO)", - "entity", - "independent continuant", - "abnormality of digestive system physiology", - "Abnormality of the digestive system (HPO)", - "material entity", - "anatomical entity", - "anatomical structure", - "abnormality of anatomical entity physiology", + "abnormal craniocervical region morphology", + "Morphological central nervous system abnormality", + "abnormal developmental process", + "abnormal development of anatomical entity", + "Abnormality of the head", + "Abnormal nervous system morphology", + "abnormal embryo morphology", + "abnormal skeletal system morphology", + "Abnormality of head or neck", + "abnormal head morphology", + "Abnormality of the skeletal system", "abnormal anatomical entity", - "multicellular anatomical structure", - "anatomical system" + "abnormal skull morphology", + "abnormal central nervous system morphology", + "specifically dependent continuant", + "abnormal anatomical entity morphology in the independent continuant", + "Open neural tube defect", + "abnormal skeletal system", + "abnormal anatomical entity morphology", + "entity" ], "object_taxon": null, "object_taxon_label": null, @@ -5111,17 +4449,17 @@ "url": "http://purl.obolibrary.org/obo/ECO_0000304" } ], - "grouping_key": "MONDO:0035646🍪🍪biolink:has_phenotype🍪HP:0002014", + "grouping_key": "MONDO:0013154🍪🍪biolink:has_phenotype🍪HP:0002084", "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": ["OMIM:613150"], "publications_links": [ { - "id": "orphanet:589821", - "url": null + "id": "OMIM:613150", + "url": "http://identifiers.org/mim/613150" } ], "qualifiers": [], @@ -5134,15 +4472,11 @@ "qualifiers_category": null, "qualifiers_closure": [], "qualifiers_closure_label": [], - "frequency_qualifier_label": "Occasional (HPO)", + "frequency_qualifier_label": "Occasional", "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)" - ], + "frequency_qualifier_closure": ["HP:0000001", "HP:0040279", "HP:0040283"], + "frequency_qualifier_closure_label": ["All", "Frequency", "Occasional"], "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 85ebc76ee..2891db4f5 100644 --- a/frontend/fixtures/autocomplete.json +++ b/frontend/fixtures/autocomplete.json @@ -1,29 +1,8 @@ { "limit": 10, "offset": 0, - "total": 230, + "total": 216, "items": [ - { - "id": "MONDO:0054748", - "category": "biolink:Disease", - "name": "Fanconi anemia, complementation group S", - "full_name": null, - "deprecated": null, - "description": null, - "xref": [], - "provided_by": "phenio_nodes", - "in_taxon": null, - "in_taxon_label": null, - "symbol": null, - "synonym": [ - "FANCS", - "Fanconi anemia, complementation GROUP S", - "Fanconi anemia, complementation group S" - ], - "uri": null, - "highlight": null, - "score": null - }, { "id": "MONDO:0009215", "category": "biolink:Disease", @@ -459,54 +438,54 @@ "score": null }, { - "id": "MONDO:0012186", + "id": "MONDO:0009213", "category": "biolink:Disease", - "name": "Fanconi anemia complementation group I", + "name": "Fanconi anemia complementation group C", "full_name": null, "deprecated": null, - "description": "Fanconi anemia caused by mutations in the FANCI gene, encoding Fanconi anemia group I protein.", + "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", "in_taxon": null, "in_taxon_label": null, "symbol": null, "synonym": [ - "FANCI", - "Fanconi Anemia, complementation Group 1", - "Fanconi Anemia, complementation group type 1", - "Fanconi anaemia complementation group type I", - "Fanconi anemia complementation group I", - "Fanconi anemia complementation group type I", - "Fanconi anemia, complementation group I" + "FA3", + "FACC", + "FANCC", + "Fanconi Anemia, complementation group type C", + "Fanconi anaemia complementation group type C", + "Fanconi anemia complementation group C", + "Fanconi anemia complementation group type C", + "Fanconi anemia, complementation group C", + "Fanconi pancytopenia type 3", + "Fanconi pancytopenia, type 3", + "facc" ], "uri": null, "highlight": null, "score": null }, { - "id": "MONDO:0009213", + "id": "MONDO:0012186", "category": "biolink:Disease", - "name": "Fanconi anemia complementation group C", + "name": "Fanconi anemia complementation group I", "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.", + "description": "Fanconi anemia caused by mutations in the FANCI gene, encoding Fanconi anemia group I protein.", "xref": [], "provided_by": "phenio_nodes", "in_taxon": null, "in_taxon_label": null, "symbol": null, "synonym": [ - "FA3", - "FACC", - "FANCC", - "Fanconi Anemia, complementation group type C", - "Fanconi anaemia complementation group type C", - "Fanconi anemia complementation group C", - "Fanconi anemia complementation group type C", - "Fanconi anemia, complementation group C", - "Fanconi pancytopenia type 3", - "Fanconi pancytopenia, type 3", - "facc" + "FANCI", + "Fanconi Anemia, complementation Group 1", + "Fanconi Anemia, complementation group type 1", + "Fanconi anaemia complementation group type I", + "Fanconi anemia complementation group I", + "Fanconi anemia complementation group type I", + "Fanconi anemia, complementation group I" ], "uri": null, "highlight": null, @@ -562,6 +541,30 @@ "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 anaemia 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/histopheno.json b/frontend/fixtures/histopheno.json index 1cecaea78..4e5840723 100644 --- a/frontend/fixtures/histopheno.json +++ b/frontend/fixtures/histopheno.json @@ -3,67 +3,67 @@ "items": [ { "label": "musculature", - "count": 1756, + "count": 1686, "id": "HP:0003011" }, { "label": "nervous_system", - "count": 1130, + "count": 1077, "id": "HP:0000707" }, { "label": "head_neck", - "count": 602, + "count": 583, "id": "HP:0000152" }, { "label": "skeletal_system", - "count": 493, + "count": 472, "id": "HP:0000924" }, - { - "label": "respiratory", - "count": 320, - "id": "HP:0002086" - }, { "label": "eye", - "count": 300, + "count": 289, "id": "HP:0000478" }, { "label": "metabolism_homeostasis", - "count": 221, + "count": 215, "id": "HP:0001939" }, { "label": "cardiovascular_system", - "count": 185, + "count": 178, "id": "HP:0001626" }, { "label": "blood", - "count": 184, + "count": 177, "id": "HP:0001871" }, { "label": "connective_tissue", - "count": 165, + "count": 161, "id": "HP:0003549" }, { - "label": "neoplasm", + "label": "respiratory", "count": 150, + "id": "HP:0002086" + }, + { + "label": "neoplasm", + "count": 149, "id": "HP:0002664" }, { "label": "digestive_system", - "count": 144, + "count": 143, "id": "HP:0025031" }, { "label": "integument", - "count": 48, + "count": 47, "id": "HP:0001574" }, { @@ -73,7 +73,7 @@ }, { "label": "growth", - "count": 33, + "count": 32, "id": "HP:0001507" }, { @@ -83,7 +83,7 @@ }, { "label": "endocrine", - "count": 26, + "count": 25, "id": "HP:0000818" }, { diff --git a/frontend/fixtures/mappings.json b/frontend/fixtures/mappings.json index aa55cfae2..5fe60103d 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": "074f33ef-cab8-46e9-b535-5c637220dcd1" + "id": "63d84b9a-93bc-4d4a-9c2c-755a444f7d7c" }, { "subject_id": "MONDO:0020121", @@ -19,25 +19,25 @@ "object_id": "ICD10CM:G71.0", "object_label": "Muscular dystrophy", "mapping_justification": "semapv:UnspecifiedMatching", - "id": "575115b8-67a4-482d-88e7-1b1b60fdd99a" + "id": "1e7e3e71-c912-443f-b92f-c7a828543070" }, { "subject_id": "MONDO:0020121", "subject_label": "muscular dystrophy", "predicate_id": "skos:exactMatch", - "object_id": "MESH:D009136", - "object_label": null, + "object_id": "NCIT:C84910", + "object_label": "Muscular Dystrophy", "mapping_justification": "semapv:UnspecifiedMatching", - "id": "a2f1233e-1951-4f40-9a79-60f591a24bb5" + "id": "8b7a5c87-d896-4daf-ac51-6ad53ef838a7" }, { "subject_id": "MONDO:0020121", "subject_label": "muscular dystrophy", "predicate_id": "skos:exactMatch", - "object_id": "NCIT:C84910", - "object_label": "Muscular Dystrophy", + "object_id": "Orphanet:98473", + "object_label": "Muscular dystrophy", "mapping_justification": "semapv:UnspecifiedMatching", - "id": "73eaeaef-9868-4e50-a4ed-aee537a830ae" + "id": "74d9dc89-0a38-41fd-8f0f-9b89e1085824" }, { "subject_id": "MONDO:0020121", @@ -46,7 +46,7 @@ "object_id": "SCTID:73297009", "object_label": null, "mapping_justification": "semapv:UnspecifiedMatching", - "id": "3f7aa4af-411c-47fe-9b3a-d8248484ea2d" + "id": "f93de036-44d8-43fd-b5b6-9753b75f79b0" }, { "subject_id": "MONDO:0020121", @@ -55,16 +55,16 @@ "object_id": "UMLS:C0026850", "object_label": null, "mapping_justification": "semapv:UnspecifiedMatching", - "id": "f8d6fe34-2d2a-4ace-a314-f4def3070e3a" + "id": "d5cbdd21-5791-4b49-ae6f-42b8f226e3bf" }, { "subject_id": "MONDO:0020121", "subject_label": "muscular dystrophy", "predicate_id": "skos:exactMatch", - "object_id": "Orphanet:98473", + "object_id": "mesh:D009136", "object_label": null, "mapping_justification": "semapv:UnspecifiedMatching", - "id": "63588ca1-4204-4143-88b3-152b31ea0c41" + "id": "573ffaec-5e44-47a3-affc-1019df4b4ef9" } ] } diff --git a/frontend/fixtures/node.json b/frontend/fixtures/node.json index ba46228a1..4fda19ca9 100644 --- a/frontend/fixtures/node.json +++ b/frontend/fixtures/node.json @@ -18,30 +18,30 @@ "mappings": [ { "id": "DOID:9884", - "url": null + "url": "http://purl.obolibrary.org/obo/DOID_9884" }, { "id": "ICD10CM:G71.0", "url": "https://icd.codes/icd10cm/G71.0" }, { - "id": "MESH:D009136", - "url": null + "id": "NCIT:C84910", + "url": "http://purl.obolibrary.org/obo/NCIT_C84910" }, { - "id": "NCIT:C84910", + "id": "Orphanet:98473", "url": null }, { "id": "SCTID:73297009", - "url": null + "url": "http://identifiers.org/snomedct/73297009" }, { "id": "UMLS:C0026850", - "url": null + "url": "http://identifiers.org/umls/C0026850" }, { - "id": "Orphanet:98473", + "id": "mesh:D009136", "url": null } ], @@ -53,7 +53,7 @@ "association_counts": [ { "label": "Phenotypes", - "count": 4027, + "count": 3879, "category": "biolink:DiseaseToPhenotypicFeatureAssociation" }, { @@ -63,7 +63,7 @@ }, { "label": "Correlated Genes", - "count": 151, + "count": 139, "category": "biolink:CorrelatedGeneToDiseaseAssociation" } ], @@ -117,9 +117,9 @@ ], "sub_classes": [ { - "id": "MONDO:0008028", + "id": "MONDO:0016106", "category": "biolink:Disease", - "name": "muscular dystrophy, Barnes type", + "name": "progressive muscular dystrophy", "full_name": null, "deprecated": null, "description": null, @@ -132,9 +132,9 @@ "uri": null }, { - "id": "MONDO:0010675", + "id": "MONDO:0018949", "category": "biolink:Disease", - "name": "muscular dystrophy, cardiac type", + "name": "distal myopathy", "full_name": null, "deprecated": null, "description": null, @@ -147,9 +147,9 @@ "uri": null }, { - "id": "MONDO:0010676", + "id": "MONDO:0019950", "category": "biolink:Disease", - "name": "muscular dystrophy, Hemizygous lethal type", + "name": "congenital muscular dystrophy", "full_name": null, "deprecated": null, "description": null, @@ -162,9 +162,9 @@ "uri": null }, { - "id": "MONDO:0010677", + "id": "MONDO:0023204", "category": "biolink:Disease", - "name": "muscular dystrophy, Mabry type", + "name": "Fukuda-Miyanomae-Nakata syndrome", "full_name": null, "deprecated": null, "description": null, @@ -177,9 +177,9 @@ "uri": null }, { - "id": "MONDO:0010678", + "id": "MONDO:0100228", "category": "biolink:Disease", - "name": "muscular dystrophy, progressive Pectorodorsal", + "name": "LAMA2-related muscular dystrophy", "full_name": null, "deprecated": null, "description": null, @@ -192,9 +192,9 @@ "uri": null }, { - "id": "MONDO:0019950", + "id": "MONDO:0008028", "category": "biolink:Disease", - "name": "congenital muscular dystrophy", + "name": "muscular dystrophy, Barnes type", "full_name": null, "deprecated": null, "description": null, @@ -207,9 +207,9 @@ "uri": null }, { - "id": "MONDO:0023204", + "id": "MONDO:0010311", "category": "biolink:Disease", - "name": "Fukuda-Miyanomae-Nakata syndrome", + "name": "Becker muscular dystrophy", "full_name": null, "deprecated": null, "description": null, @@ -222,9 +222,9 @@ "uri": null }, { - "id": "MONDO:0100228", + "id": "MONDO:0010675", "category": "biolink:Disease", - "name": "LAMA2-related muscular dystrophy", + "name": "muscular dystrophy, cardiac type", "full_name": null, "deprecated": null, "description": null, @@ -237,9 +237,9 @@ "uri": null }, { - "id": "MONDO:0018949", + "id": "MONDO:0010676", "category": "biolink:Disease", - "name": "distal myopathy", + "name": "muscular dystrophy, Hemizygous lethal type", "full_name": null, "deprecated": null, "description": null, @@ -252,9 +252,39 @@ "uri": null }, { - "id": "MONDO:0016106", + "id": "MONDO:0010677", "category": "biolink:Disease", - "name": "progressive muscular dystrophy", + "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": [], + "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": [], + "uri": null + }, + { + "id": "MONDO:0010679", + "category": "biolink:Disease", + "name": "Duchenne muscular dystrophy", "full_name": null, "deprecated": null, "description": null, diff --git a/frontend/fixtures/phenotype-explorer-search.json b/frontend/fixtures/phenotype-explorer-search.json index f8686fa53..a3327ca0d 100644 --- a/frontend/fixtures/phenotype-explorer-search.json +++ b/frontend/fixtures/phenotype-explorer-search.json @@ -242,8 +242,8 @@ "HP:0002104": { "match_source": "HP:0002104", "match_source_label": "Apnea (HPO)", - "match_target": "ZP:0018569", - "match_target_label": "myeloid cell development absent, abnormal (ZPO)", + "match_target": "ZP:0018568", + "match_target_label": "primitive hemopoiesis absent, abnormal (ZPO)", "score": 9.08524944639702, "match_subsumer": null, "match_subsumer_label": null, @@ -251,7 +251,7 @@ "subject_id": "HP:0002104", "subject_label": null, "subject_source": null, - "object_id": "ZP:0018569", + "object_id": "ZP:0018568", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0034024", @@ -260,17 +260,17 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 9.08524944639702, - "jaccard_similarity": 0.34615384615384615, + "jaccard_similarity": 0.3333333333333333, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.773384910034319 + "phenodigm_score": 1.7402346054863809 } }, "HP:0012378": { "match_source": "HP:0012378", "match_source_label": "Fatigue (HPO)", - "match_target": "ZP:0018569", - "match_target_label": "myeloid cell development absent, abnormal (ZPO)", + "match_target": "ZP:0018568", + "match_target_label": "primitive hemopoiesis absent, abnormal (ZPO)", "score": 1.6836208034928104, "match_subsumer": null, "match_subsumer_label": null, @@ -278,7 +278,7 @@ "subject_id": "HP:0012378", "subject_label": null, "subject_source": null, - "object_id": "ZP:0018569", + "object_id": "ZP:0018568", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0001005", @@ -287,10 +287,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 1.6836208034928104, - "jaccard_similarity": 0.47058823529411764, + "jaccard_similarity": 0.4444444444444444, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 0.8901079388591847 + "phenodigm_score": 0.8650294287846346 } } }, @@ -403,8 +403,8 @@ "HP:0002104": { "match_source": "HP:0002104", "match_source_label": "Apnea (HPO)", - "match_target": "ZP:0018569", - "match_target_label": "myeloid cell development absent, abnormal (ZPO)", + "match_target": "ZP:0018568", + "match_target_label": "primitive hemopoiesis absent, abnormal (ZPO)", "score": 9.08524944639702, "match_subsumer": null, "match_subsumer_label": null, @@ -412,7 +412,7 @@ "subject_id": "HP:0002104", "subject_label": null, "subject_source": null, - "object_id": "ZP:0018569", + "object_id": "ZP:0018568", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0034024", @@ -421,10 +421,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 9.08524944639702, - "jaccard_similarity": 0.34615384615384615, + "jaccard_similarity": 0.3333333333333333, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.773384910034319 + "phenodigm_score": 1.7402346054863809 } }, "HP:0012378": { @@ -502,13 +502,13 @@ } }, "object_termset": { - "HP:0012378": { - "id": "HP:0012378", - "label": "Fatigue (HPO)" - }, "HP:0002104": { "id": "HP:0002104", "label": "Apnea (HPO)" + }, + "HP:0012378": { + "id": "HP:0012378", + "label": "Fatigue (HPO)" } }, "subject_best_matches": { @@ -571,8 +571,8 @@ "HP:0002104": { "match_source": "HP:0002104", "match_source_label": "Apnea (HPO)", - "match_target": "ZP:0018569", - "match_target_label": "myeloid cell development absent, abnormal (ZPO)", + "match_target": "ZP:0018568", + "match_target_label": "primitive hemopoiesis absent, abnormal (ZPO)", "score": 9.08524944639702, "match_subsumer": null, "match_subsumer_label": null, @@ -580,7 +580,7 @@ "subject_id": "HP:0002104", "subject_label": null, "subject_source": null, - "object_id": "ZP:0018569", + "object_id": "ZP:0018568", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0034024", @@ -589,17 +589,17 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 9.08524944639702, - "jaccard_similarity": 0.34615384615384615, + "jaccard_similarity": 0.3333333333333333, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.773384910034319 + "phenodigm_score": 1.7402346054863809 } }, "HP:0012378": { "match_source": "HP:0012378", "match_source_label": "Fatigue (HPO)", - "match_target": "ZP:0018569", - "match_target_label": "myeloid cell development absent, abnormal (ZPO)", + "match_target": "ZP:0018568", + "match_target_label": "primitive hemopoiesis absent, abnormal (ZPO)", "score": 1.6836208034928104, "match_subsumer": null, "match_subsumer_label": null, @@ -607,7 +607,7 @@ "subject_id": "HP:0012378", "subject_label": null, "subject_source": null, - "object_id": "ZP:0018569", + "object_id": "ZP:0018568", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0001005", @@ -616,10 +616,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 1.6836208034928104, - "jaccard_similarity": 0.47058823529411764, + "jaccard_similarity": 0.4444444444444444, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 0.8901079388591847 + "phenodigm_score": 0.8650294287846346 } } }, @@ -660,13 +660,13 @@ "score": 7.234842285670967, "similarity": { "subject_termset": { - "ZP:0018569": { - "id": "ZP:0018569", - "label": "myeloid cell development absent, abnormal (ZPO)" - }, "ZP:0018568": { "id": "ZP:0018568", "label": "primitive hemopoiesis absent, abnormal (ZPO)" + }, + "ZP:0018569": { + "id": "ZP:0018569", + "label": "myeloid cell development absent, abnormal (ZPO)" } }, "object_termset": { @@ -815,13 +815,13 @@ "score": 5.412148503540145, "similarity": { "subject_termset": { - "ZP:0000945": { - "id": "ZP:0000945", - "label": "pigment cell quality, abnormal (ZPO)" - }, "ZP:0100294": { "id": "ZP:0100294", "label": "visual perception absent, abnormal (ZPO)" + }, + "ZP:0000945": { + "id": "ZP:0000945", + "label": "pigment cell quality, abnormal (ZPO)" } }, "object_termset": { @@ -970,31 +970,31 @@ "score": 5.384435124944915, "similarity": { "subject_termset": { - "ZP:0015039": { - "id": "ZP:0015039", - "label": "visual behavior absent, abnormal (ZPO)" - }, "ZP:0001841": { "id": "ZP:0001841", "label": "visual behavior quality, abnormal (ZPO)" + }, + "ZP:0015039": { + "id": "ZP:0015039", + "label": "visual behavior absent, abnormal (ZPO)" } }, "object_termset": { - "HP:0012378": { - "id": "HP:0012378", - "label": "Fatigue (HPO)" - }, "HP:0002104": { "id": "HP:0002104", "label": "Apnea (HPO)" + }, + "HP:0012378": { + "id": "HP:0012378", + "label": "Fatigue (HPO)" } }, "subject_best_matches": { "ZP:0001841": { "match_source": "ZP:0001841", "match_source_label": "visual behavior quality, abnormal (ZPO)", - "match_target": "HP:0012378", - "match_target_label": "Fatigue (HPO)", + "match_target": "HP:0002104", + "match_target_label": "Apnea (HPO)", "score": 1.6836208034928104, "match_subsumer": null, "match_subsumer_label": null, @@ -1002,7 +1002,7 @@ "subject_id": "ZP:0001841", "subject_label": null, "subject_source": null, - "object_id": "HP:0012378", + "object_id": "HP:0002104", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0001005", @@ -1011,10 +1011,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 1.6836208034928104, - "jaccard_similarity": 0.47058823529411764, + "jaccard_similarity": 0.2962962962962963, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 0.8901079388591847 + "phenodigm_score": 0.7062935710045181 } }, "ZP:0015039": { @@ -1136,13 +1136,13 @@ } }, "object_termset": { - "HP:0012378": { - "id": "HP:0012378", - "label": "Fatigue (HPO)" - }, "HP:0002104": { "id": "HP:0002104", "label": "Apnea (HPO)" + }, + "HP:0012378": { + "id": "HP:0012378", + "label": "Fatigue (HPO)" } }, "subject_best_matches": { diff --git a/frontend/fixtures/search.json b/frontend/fixtures/search.json index 745cd65b1..8d4eaff18 100644 --- a/frontend/fixtures/search.json +++ b/frontend/fixtures/search.json @@ -1,7 +1,7 @@ { "limit": 20, "offset": 0, - "total": 115, + "total": 101, "items": [ { "id": "MONDO:0019391", diff --git a/frontend/src/pages/metadata.json b/frontend/src/pages/metadata.json index 11c74dad4..4312d91ff 100644 --- a/frontend/src/pages/metadata.json +++ b/frontend/src/pages/metadata.json @@ -3,12 +3,12 @@ { "label": "Genes", "icon": "category-gene", - "count": 558400 + "count": 558432 }, { "label": "Phenotypes", "icon": "category-phenotypic-quality", - "count": 117141 + "count": 123266 }, { "label": "Diseases", @@ -18,29 +18,29 @@ { "label": "Total Nodes", "icon": "node", - "count": 860203 + "count": 844639 } ], "association": [ { "label": "Gene to Disease", "icon": "association-gene-to-disease", - "count": 15032 + "count": 15123 }, { "label": "Gene to Phenotype", "icon": "association-gene-to-phenotype", - "count": 882741 + "count": 915761 }, { "label": "Disease to Phenotype", "icon": "association-disease-to-phenotype", - "count": 240274 + "count": 241389 }, { "label": "Total Associations", "icon": "association", - "count": 10052263 + "count": 11430197 } ] }