From 141b6c3c5f7128ec45fdf753cadde62ec03e1776 Mon Sep 17 00:00:00 2001 From: kevinschaper Date: Thu, 17 Oct 2024 20:22:38 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20monarch-?= =?UTF-8?q?initiative/monarch-app@43c3200837f82a943e0b0040c18d72c241ddaa4c?= =?UTF-8?q?=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- docs/Data-Model/Association/index.html | 178 ++- docs/Data-Model/AssociationCount/index.html | 14 +- .../AssociationCountList/index.html | 22 +- docs/Data-Model/AssociationResults/index.html | 22 +- .../AssociationTableResults/index.html | 22 +- .../AssociationTypeMapping/index.html | 46 +- docs/Data-Model/Boolean/index.html | 32 + .../index.html | 22 +- docs/Data-Model/CompactAssociation/index.html | 4 +- .../CompactAssociationResults/index.html | 22 +- docs/Data-Model/Curie/index.html | 28 + docs/Data-Model/Date/index.html | 32 + docs/Data-Model/DateOrDatetime/index.html | 28 + 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28 + docs/Data-Model/match_target_label/index.html | 28 + docs/Data-Model/metadata/index.html | 28 + docs/Data-Model/metric/index.html | 28 + docs/Data-Model/name/index.html | 47 +- docs/Data-Model/namespace/index.html | 36 +- docs/Data-Model/negated/index.html | 28 + docs/Data-Model/neo4j/index.html | 28 + docs/Data-Model/node_hierarchy/index.html | 28 + docs/Data-Model/object/index.html | 28 + .../Data-Model/object_best_matches/index.html | 30 +- docs/Data-Model/object_category/index.html | 28 + docs/Data-Model/object_closure/index.html | 30 +- .../object_closure_label/index.html | 30 +- docs/Data-Model/object_id/index.html | 36 +- .../object_information_content/index.html | 28 + docs/Data-Model/object_label/index.html | 50 +- docs/Data-Model/object_namespace/index.html | 28 + docs/Data-Model/object_source/index.html | 28 + docs/Data-Model/object_taxon/index.html | 28 + docs/Data-Model/object_taxon_label/index.html | 28 + docs/Data-Model/object_termset/index.html | 30 +- docs/Data-Model/offset/index.html | 48 +- docs/Data-Model/onset_qualifier/index.html | 28 + .../onset_qualifier_category/index.html | 28 + .../onset_qualifier_closure/index.html | 30 +- .../onset_qualifier_closure_label/index.html | 30 +- .../onset_qualifier_label/index.html | 28 + .../onset_qualifier_namespace/index.html | 28 + docs/Data-Model/original_object/index.html | 28 + docs/Data-Model/original_subject/index.html | 28 + .../Data-Model/overlap_coefficient/index.html | 28 + docs/Data-Model/pathway/index.html | 28 + docs/Data-Model/phenodigm_score/index.html | 28 + docs/Data-Model/predicate/index.html | 30 +- docs/Data-Model/predicate_id/index.html | 28 + .../primary_knowledge_source/index.html | 28 + docs/Data-Model/provided_by/index.html | 44 +- docs/Data-Model/provided_by_link/index.html | 36 +- docs/Data-Model/publications/index.html | 30 +- docs/Data-Model/publications_links/index.html | 30 +- docs/Data-Model/qc_report/index.html | 28 + docs/Data-Model/qualifier/index.html | 30 +- docs/Data-Model/qualifier_category/index.html | 28 + docs/Data-Model/qualifier_closure/index.html | 30 +- .../qualifier_closure_label/index.html | 30 +- docs/Data-Model/qualifier_label/index.html | 28 + .../Data-Model/qualifier_namespace/index.html | 28 + docs/Data-Model/qualifiers/index.html | 30 +- .../Data-Model/qualifiers_category/index.html | 28 + docs/Data-Model/qualifiers_closure/index.html | 30 +- .../qualifiers_closure_label/index.html | 30 +- docs/Data-Model/qualifiers_label/index.html | 28 + .../qualifiers_namespace/index.html | 28 + docs/Data-Model/score/index.html | 32 +- docs/Data-Model/sex_qualifier/index.html | 28 + .../sex_qualifier_category/index.html | 28 + .../sex_qualifier_closure/index.html | 30 +- .../sex_qualifier_closure_label/index.html | 30 +- .../Data-Model/sex_qualifier_label/index.html | 28 + .../sex_qualifier_namespace/index.html | 28 + docs/Data-Model/similarity/index.html | 28 + docs/Data-Model/solr/index.html | 28 + docs/Data-Model/sqlite/index.html | 28 + docs/Data-Model/stage_qualifier/index.html | 28 + .../stage_qualifier_category/index.html | 28 + .../stage_qualifier_closure/index.html | 30 +- .../stage_qualifier_closure_label/index.html | 30 +- .../stage_qualifier_label/index.html | 28 + .../stage_qualifier_namespace/index.html | 28 + docs/Data-Model/start/index.html | 28 + docs/Data-Model/sub_classes/index.html | 30 +- docs/Data-Model/subject/index.html | 28 + .../subject_best_matches/index.html | 30 +- docs/Data-Model/subject_category/index.html | 28 + docs/Data-Model/subject_closure/index.html | 30 +- .../subject_closure_label/index.html | 30 +- docs/Data-Model/subject_id/index.html | 36 +- .../subject_information_content/index.html | 28 + docs/Data-Model/subject_label/index.html | 50 +- docs/Data-Model/subject_namespace/index.html | 28 + docs/Data-Model/subject_source/index.html | 28 + docs/Data-Model/subject_taxon/index.html | 28 + .../Data-Model/subject_taxon_label/index.html | 28 + docs/Data-Model/subject_termset/index.html | 30 +- docs/Data-Model/subsumed_by_score/index.html | 28 + docs/Data-Model/subsumes_score/index.html | 28 + docs/Data-Model/super_classes/index.html | 30 +- docs/Data-Model/symbol/index.html | 36 +- docs/Data-Model/symmetric/index.html | 28 + docs/Data-Model/synonym/index.html | 38 +- docs/Data-Model/text/index.html | 28 + docs/Data-Model/tokens/index.html | 30 +- docs/Data-Model/total/index.html | 48 +- docs/Data-Model/union_count/index.html | 28 + docs/Data-Model/uri/index.html | 36 +- docs/Data-Model/url/index.html | 28 + docs/Data-Model/version/index.html | 28 + docs/Data-Model/xref/index.html | 38 +- docs/search/search_index.json | 2 +- docs/sitemap.xml | 516 ++++---- docs/sitemap.xml.gz | Bin 1706 -> 1745 bytes 222 files changed, 13162 insertions(+), 856 deletions(-) create mode 100644 docs/Data-Model/disease_context_qualifier/index.html create mode 100644 docs/Data-Model/disease_context_qualifier_category/index.html create mode 100644 docs/Data-Model/disease_context_qualifier_closure/index.html create mode 100644 docs/Data-Model/disease_context_qualifier_closure_label/index.html create mode 100644 docs/Data-Model/disease_context_qualifier_label/index.html create mode 100644 docs/Data-Model/disease_context_qualifier_namespace/index.html diff --git a/docs/Data-Model/Association/index.html b/docs/Data-Model/Association/index.html index 4633d9b5c..738208a44 100644 --- a/docs/Data-Model/Association/index.html +++ b/docs/Data-Model/Association/index.html @@ -1041,6 +1041,18 @@

Class: Association

Association : category + Association : disease_context_qualifier + + Association : disease_context_qualifier_category + + Association : disease_context_qualifier_closure + + Association : disease_context_qualifier_closure_label + + Association : disease_context_qualifier_label + + Association : disease_context_qualifier_namespace + Association : evidence_count Association : frequency_qualifier @@ -1674,6 +1686,42 @@

Slots

Field containing stage_qualifier name and the names of all of it's ancestors direct + +disease_context_qualifier +0..1
String +A context qualifier representing a disease or condition in which a relationsh... +direct + + +disease_context_qualifier_label +0..1
String +The name of the disease_context_qualifier entity +direct + + +disease_context_qualifier_namespace +0..1
String +The namespace/prefix of the disease_context_qualifier entity +direct + + +disease_context_qualifier_category +0..1
String +The category of the disease_context_qualifier entity +direct + + +disease_context_qualifier_closure +*
String +Field containing disease_context_qualifier id and the ids of all of it's ance... +direct + + +disease_context_qualifier_closure_label +*
String +Field containing disease_context_qualifier name and the names of all of it's ... +direct +

Usages

@@ -1808,6 +1856,12 @@

Direct

- stage_qualifier_category - stage_qualifier_closure - stage_qualifier_closure_label +- disease_context_qualifier +- disease_context_qualifier_label +- disease_context_qualifier_namespace +- disease_context_qualifier_category +- disease_context_qualifier_closure +- disease_context_qualifier_closure_label @@ -1838,7 +1892,6 @@

Induced

name: category from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: false alias: category owner: Association domain_of: @@ -1848,6 +1901,7 @@

Induced

- AssociationTypeMapping - Entity range: string + multivalued: false subject: name: subject from_schema: https://w3id.org/monarch/monarch-py @@ -1895,12 +1949,12 @@

Induced

description: Field containing subject id and the ids of all of it's ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: subject_closure owner: Association domain_of: - Association range: string + multivalued: true subject_label: name: subject_label description: The name of the subject entity @@ -1921,12 +1975,12 @@

Induced

description: Field containing subject name and the names of all of it's ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: subject_closure_label owner: Association domain_of: - Association range: string + multivalued: true subject_taxon: name: subject_taxon from_schema: https://w3id.org/monarch/monarch-py @@ -1951,7 +2005,6 @@

Induced

name: predicate from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: false alias: predicate owner: Association domain_of: @@ -1959,6 +2012,7 @@

Induced

- CompactAssociation range: string required: true + multivalued: false object: name: object from_schema: https://w3id.org/monarch/monarch-py @@ -2005,12 +2059,12 @@

Induced

description: Field containing object id and the ids of all of it's ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: object_closure owner: Association domain_of: - Association range: string + multivalued: true object_label: name: object_label description: The name of the object entity @@ -2031,12 +2085,12 @@

Induced

description: Field containing object name and the names of all of it's ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: object_closure_label owner: Association domain_of: - Association range: string + multivalued: true object_taxon: name: object_taxon from_schema: https://w3id.org/monarch/monarch-py @@ -2070,12 +2124,12 @@

Induced

name: aggregator_knowledge_source from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: aggregator_knowledge_source owner: Association domain_of: - Association range: string + multivalued: true negated: name: negated from_schema: https://w3id.org/monarch/monarch-py @@ -2117,13 +2171,13 @@

Induced

from_schema: https://w3id.org/monarch/monarch-py rank: 1000 slot_uri: biolink:knowledge_level - multivalued: false alias: knowledge_level owner: Association domain_of: - Association range: string required: true + multivalued: false agent_type: name: agent_type description: Describes the high-level category of agent who originally generated @@ -2134,34 +2188,34 @@

Induced

from_schema: https://w3id.org/monarch/monarch-py rank: 1000 slot_uri: biolink:agent_type - multivalued: false alias: agent_type owner: Association domain_of: - Association range: string required: true + multivalued: false has_evidence: name: has_evidence from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: has_evidence owner: Association domain_of: - Association range: string + multivalued: true has_evidence_links: name: has_evidence_links description: List of ExpandedCuries with id and url for evidence from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: has_evidence_links owner: Association domain_of: - Association range: ExpandedCurie + multivalued: true inlined: true inlined_as_list: true has_count: @@ -2242,23 +2296,23 @@

Induced

name: publications from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: publications owner: Association domain_of: - Association range: string + multivalued: true publications_links: name: publications_links description: List of ExpandedCuries with id and url for publications from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: publications_links owner: Association domain_of: - Association range: ExpandedCurie + multivalued: true inlined: true inlined_as_list: true frequency_qualifier: @@ -2301,12 +2355,12 @@

Induced

name: qualifiers from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: qualifiers owner: Association domain_of: - Association range: string + multivalued: true qualifiers_label: name: qualifiers_label description: The name of the frequency_qualifier entity @@ -2345,34 +2399,34 @@

Induced

ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: qualifiers_closure owner: Association domain_of: - Association range: string + multivalued: true qualifiers_closure_label: name: qualifiers_closure_label description: Field containing frequency_qualifier name and the names of all of it's ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: qualifiers_closure_label owner: Association domain_of: - Association range: string + multivalued: true qualifier: name: qualifier from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: qualifier owner: Association domain_of: - Association range: string + multivalued: true qualifier_label: name: qualifier_label description: The name of the frequency_qualifier entity @@ -2411,24 +2465,24 @@

Induced

ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: qualifier_closure owner: Association domain_of: - Association range: string + multivalued: true qualifier_closure_label: name: qualifier_closure_label description: Field containing frequency_qualifier name and the names of all of it's ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: qualifier_closure_label owner: Association domain_of: - Association range: string + multivalued: true frequency_qualifier_label: name: frequency_qualifier_label description: The name of the frequency_qualifier entity @@ -2467,24 +2521,24 @@

Induced

ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: frequency_qualifier_closure owner: Association domain_of: - Association range: string + multivalued: true frequency_qualifier_closure_label: name: frequency_qualifier_closure_label description: Field containing frequency_qualifier name and the names of all of it's ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: frequency_qualifier_closure_label owner: Association domain_of: - Association range: string + multivalued: true onset_qualifier_label: name: onset_qualifier_label description: The name of the onset_qualifier entity @@ -2522,24 +2576,24 @@

Induced

description: Field containing onset_qualifier id and the ids of all of it's ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: onset_qualifier_closure owner: Association domain_of: - Association range: string + multivalued: true onset_qualifier_closure_label: name: onset_qualifier_closure_label description: Field containing onset_qualifier name and the names of all of it's ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: onset_qualifier_closure_label owner: Association domain_of: - Association range: string + multivalued: true sex_qualifier_label: name: sex_qualifier_label description: The name of the sex_qualifier entity @@ -2577,24 +2631,24 @@

Induced

description: Field containing sex_qualifier id and the ids of all of it's ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: sex_qualifier_closure owner: Association domain_of: - Association range: string + multivalued: true sex_qualifier_closure_label: name: sex_qualifier_closure_label description: Field containing sex_qualifier name and the names of all of it's ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: sex_qualifier_closure_label owner: Association domain_of: - Association range: string + multivalued: true stage_qualifier_label: name: stage_qualifier_label description: The name of the stage_qualifier entity @@ -2632,24 +2686,94 @@

Induced

description: Field containing stage_qualifier id and the ids of all of it's ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: stage_qualifier_closure owner: Association domain_of: - Association range: string + multivalued: true stage_qualifier_closure_label: name: stage_qualifier_closure_label description: Field containing stage_qualifier name and the names of all of it's ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: stage_qualifier_closure_label owner: Association domain_of: - Association range: string + multivalued: true + disease_context_qualifier: + name: disease_context_qualifier + description: A context qualifier representing a disease or condition in which + a relationship expressed in an association took place. + examples: + - value: MONDO:0004979 + - value: MONDO:0005148 + from_schema: https://w3id.org/monarch/monarch-py + rank: 1000 + alias: disease_context_qualifier + owner: Association + domain_of: + - Association + range: string + disease_context_qualifier_label: + name: disease_context_qualifier_label + description: The name of the disease_context_qualifier entity + from_schema: https://w3id.org/monarch/monarch-py + rank: 1000 + is_a: name + alias: disease_context_qualifier_label + owner: Association + domain_of: + - Association + range: string + disease_context_qualifier_namespace: + name: disease_context_qualifier_namespace + description: The namespace/prefix of the disease_context_qualifier entity + from_schema: https://w3id.org/monarch/monarch-py + rank: 1000 + alias: disease_context_qualifier_namespace + owner: Association + domain_of: + - Association + range: string + disease_context_qualifier_category: + name: disease_context_qualifier_category + description: The category of the disease_context_qualifier entity + from_schema: https://w3id.org/monarch/monarch-py + rank: 1000 + is_a: category + alias: disease_context_qualifier_category + owner: Association + domain_of: + - Association + range: string + disease_context_qualifier_closure: + name: disease_context_qualifier_closure + description: Field containing disease_context_qualifier id and the ids of all + of it's ancestors + from_schema: https://w3id.org/monarch/monarch-py + rank: 1000 + alias: disease_context_qualifier_closure + owner: Association + domain_of: + - Association + range: string + multivalued: true + disease_context_qualifier_closure_label: + name: disease_context_qualifier_closure_label + description: Field containing disease_context_qualifier name and the names of + all of it's ancestors + from_schema: https://w3id.org/monarch/monarch-py + rank: 1000 + alias: disease_context_qualifier_closure_label + owner: Association + domain_of: + - Association + range: string + multivalued: true diff --git a/docs/Data-Model/AssociationCount/index.html b/docs/Data-Model/AssociationCount/index.html index 619b697b9..aacb48914 100644 --- a/docs/Data-Model/AssociationCount/index.html +++ b/docs/Data-Model/AssociationCount/index.html @@ -1142,12 +1142,6 @@

Direct

category: name: category multivalued: false - domain_of: - - Association - - AssociationCount - - CompactAssociation - - AssociationTypeMapping - - Entity @@ -1160,18 +1154,11 @@

Induced

category: name: category multivalued: false - domain_of: - - Association - - AssociationCount - - CompactAssociation - - AssociationTypeMapping - - Entity attributes: category: name: category from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: false alias: category owner: AssociationCount domain_of: @@ -1181,6 +1168,7 @@

Induced

- AssociationTypeMapping - Entity range: string + multivalued: false label: name: label from_schema: https://w3id.org/monarch/monarch-py diff --git a/docs/Data-Model/AssociationCountList/index.html b/docs/Data-Model/AssociationCountList/index.html index 7708298cd..b9d58da00 100644 --- a/docs/Data-Model/AssociationCountList/index.html +++ b/docs/Data-Model/AssociationCountList/index.html @@ -1081,16 +1081,6 @@

Direct

slot_usage: items: name: items - domain_of: - - AssociationCountList - - AssociationResults - - CompactAssociationResults - - AssociationTableResults - - CategoryGroupedAssociationResults - - EntityResults - - HistoPheno - - MappingResults - - SearchResults range: AssociationCount @@ -1103,16 +1093,6 @@

Induced

slot_usage: items: name: items - domain_of: - - AssociationCountList - - AssociationResults - - CompactAssociationResults - - AssociationTableResults - - CategoryGroupedAssociationResults - - EntityResults - - HistoPheno - - MappingResults - - SearchResults range: AssociationCount attributes: items: @@ -1120,7 +1100,6 @@

Induced

description: A collection of items, with the type to be overriden by slot_usage from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: items owner: AssociationCountList domain_of: @@ -1135,6 +1114,7 @@

Induced

- SearchResults range: AssociationCount required: true + multivalued: true inlined: true inlined_as_list: true diff --git a/docs/Data-Model/AssociationResults/index.html b/docs/Data-Model/AssociationResults/index.html index 7a8f22166..f7f092aa7 100644 --- a/docs/Data-Model/AssociationResults/index.html +++ b/docs/Data-Model/AssociationResults/index.html @@ -1122,16 +1122,6 @@

Direct

slot_usage: items: name: items - domain_of: - - AssociationCountList - - AssociationResults - - CompactAssociationResults - - AssociationTableResults - - CategoryGroupedAssociationResults - - EntityResults - - HistoPheno - - MappingResults - - SearchResults range: Association @@ -1144,16 +1134,6 @@

Induced

slot_usage: items: name: items - domain_of: - - AssociationCountList - - AssociationResults - - CompactAssociationResults - - AssociationTableResults - - CategoryGroupedAssociationResults - - EntityResults - - HistoPheno - - MappingResults - - SearchResults range: Association attributes: items: @@ -1161,7 +1141,6 @@

Induced

description: A collection of items, with the type to be overriden by slot_usage from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: items owner: AssociationResults domain_of: @@ -1176,6 +1155,7 @@

Induced

- SearchResults range: Association required: true + multivalued: true inlined: true inlined_as_list: true limit: diff --git a/docs/Data-Model/AssociationTableResults/index.html b/docs/Data-Model/AssociationTableResults/index.html index e8d94adad..a6b5ff440 100644 --- a/docs/Data-Model/AssociationTableResults/index.html +++ b/docs/Data-Model/AssociationTableResults/index.html @@ -1122,16 +1122,6 @@

Direct

slot_usage: items: name: items - domain_of: - - AssociationCountList - - AssociationResults - - CompactAssociationResults - - AssociationTableResults - - CategoryGroupedAssociationResults - - EntityResults - - HistoPheno - - MappingResults - - SearchResults range: DirectionalAssociation @@ -1144,16 +1134,6 @@

Induced

slot_usage: items: name: items - domain_of: - - AssociationCountList - - AssociationResults - - CompactAssociationResults - - AssociationTableResults - - CategoryGroupedAssociationResults - - EntityResults - - HistoPheno - - MappingResults - - SearchResults range: DirectionalAssociation attributes: items: @@ -1161,7 +1141,6 @@

Induced

description: A collection of items, with the type to be overriden by slot_usage from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: items owner: AssociationTableResults domain_of: @@ -1176,6 +1155,7 @@

Induced

- SearchResults range: DirectionalAssociation required: true + multivalued: true inlined: true inlined_as_list: true limit: diff --git a/docs/Data-Model/AssociationTypeMapping/index.html b/docs/Data-Model/AssociationTypeMapping/index.html index c87bfa157..16c8a05b9 100644 --- a/docs/Data-Model/AssociationTypeMapping/index.html +++ b/docs/Data-Model/AssociationTypeMapping/index.html @@ -1105,41 +1105,21 @@

Direct

name: subject_label description: A label to describe the subjects of the association type as a whole for use in the UI - domain_of: - - Association - - CompactAssociation - - AssociationTypeMapping - - Mapping - - TermPairwiseSimilarity object_label: name: object_label description: A label to describe the objects of the association type as a whole for use in the UI - domain_of: - - Association - - CompactAssociation - - AssociationTypeMapping - - Mapping - - TermPairwiseSimilarity symmetric: name: symmetric description: Whether the association type is symmetric, meaning that the subject and object labels should be interchangeable ifabsent: 'False' - domain_of: - - AssociationTypeMapping required: true category: name: category description: The biolink category to use in queries for this association type - multivalued: false - domain_of: - - Association - - AssociationCount - - CompactAssociation - - AssociationTypeMapping - - Entity required: true + multivalued: false @@ -1154,41 +1134,21 @@

Induced

name: subject_label description: A label to describe the subjects of the association type as a whole for use in the UI - domain_of: - - Association - - CompactAssociation - - AssociationTypeMapping - - Mapping - - TermPairwiseSimilarity object_label: name: object_label description: A label to describe the objects of the association type as a whole for use in the UI - domain_of: - - Association - - CompactAssociation - - AssociationTypeMapping - - Mapping - - TermPairwiseSimilarity symmetric: name: symmetric description: Whether the association type is symmetric, meaning that the subject and object labels should be interchangeable ifabsent: 'False' - domain_of: - - AssociationTypeMapping required: true category: name: category description: The biolink category to use in queries for this association type - multivalued: false - domain_of: - - Association - - AssociationCount - - CompactAssociation - - AssociationTypeMapping - - Entity required: true + multivalued: false attributes: subject_label: name: subject_label @@ -1240,7 +1200,6 @@

Induced

description: The biolink category to use in queries for this association type from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: false alias: category owner: AssociationTypeMapping domain_of: @@ -1251,6 +1210,7 @@

Induced

- Entity range: string required: true + multivalued: false diff --git a/docs/Data-Model/Boolean/index.html b/docs/Data-Model/Boolean/index.html index 52abe9c7f..ba4b15b31 100644 --- a/docs/Data-Model/Boolean/index.html +++ b/docs/Data-Model/Boolean/index.html @@ -938,6 +938,15 @@ + + +
  • + + + Mappings + + +
    • @@ -977,6 +986,29 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfxsd:boolean
    nativehttps://w3id.org/monarch/monarch-py/:boolean
    exactschema:Boolean
    diff --git a/docs/Data-Model/CategoryGroupedAssociationResults/index.html b/docs/Data-Model/CategoryGroupedAssociationResults/index.html index 71f7b0cfb..825980b6d 100644 --- a/docs/Data-Model/CategoryGroupedAssociationResults/index.html +++ b/docs/Data-Model/CategoryGroupedAssociationResults/index.html @@ -1159,16 +1159,6 @@

    Direct

    slot_usage: items: name: items - domain_of: - - AssociationCountList - - AssociationResults - - CompactAssociationResults - - AssociationTableResults - - CategoryGroupedAssociationResults - - EntityResults - - HistoPheno - - MappingResults - - SearchResults range: Association @@ -1181,16 +1171,6 @@

    Induced

    slot_usage: items: name: items - domain_of: - - AssociationCountList - - AssociationResults - - CompactAssociationResults - - AssociationTableResults - - CategoryGroupedAssociationResults - - EntityResults - - HistoPheno - - MappingResults - - SearchResults range: Association attributes: counterpart_category: @@ -1209,7 +1189,6 @@

    Induced

    description: A collection of items, with the type to be overriden by slot_usage from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: items owner: CategoryGroupedAssociationResults domain_of: @@ -1224,6 +1203,7 @@

    Induced

    - SearchResults range: Association required: true + multivalued: true inlined: true inlined_as_list: true limit: diff --git a/docs/Data-Model/CompactAssociation/index.html b/docs/Data-Model/CompactAssociation/index.html index 522f8b7d4..43cd59599 100644 --- a/docs/Data-Model/CompactAssociation/index.html +++ b/docs/Data-Model/CompactAssociation/index.html @@ -1164,7 +1164,6 @@

    Induced

    name: category from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: false alias: category owner: CompactAssociation domain_of: @@ -1174,6 +1173,7 @@

    Induced

    - AssociationTypeMapping - Entity range: string + multivalued: false subject: name: subject from_schema: https://w3id.org/monarch/monarch-py @@ -1205,7 +1205,6 @@

    Induced

    name: predicate from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: false alias: predicate owner: CompactAssociation domain_of: @@ -1213,6 +1212,7 @@

    Induced

    - CompactAssociation range: string required: true + multivalued: false object: name: object from_schema: https://w3id.org/monarch/monarch-py diff --git a/docs/Data-Model/CompactAssociationResults/index.html b/docs/Data-Model/CompactAssociationResults/index.html index 22c3aaa02..e9a83f138 100644 --- a/docs/Data-Model/CompactAssociationResults/index.html +++ b/docs/Data-Model/CompactAssociationResults/index.html @@ -1122,16 +1122,6 @@

    Direct

    slot_usage: items: name: items - domain_of: - - AssociationCountList - - AssociationResults - - CompactAssociationResults - - AssociationTableResults - - CategoryGroupedAssociationResults - - EntityResults - - HistoPheno - - MappingResults - - SearchResults range: CompactAssociation @@ -1144,16 +1134,6 @@

    Induced

    slot_usage: items: name: items - domain_of: - - AssociationCountList - - AssociationResults - - CompactAssociationResults - - AssociationTableResults - - CategoryGroupedAssociationResults - - EntityResults - - HistoPheno - - MappingResults - - SearchResults range: CompactAssociation attributes: items: @@ -1161,7 +1141,6 @@

    Induced

    description: A collection of items, with the type to be overriden by slot_usage from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: items owner: CompactAssociationResults domain_of: @@ -1176,6 +1155,7 @@

    Induced

    - SearchResults range: CompactAssociation required: true + multivalued: true inlined: true inlined_as_list: true limit: diff --git a/docs/Data-Model/Curie/index.html b/docs/Data-Model/Curie/index.html index 7674c6f7d..cb90e947f 100644 --- a/docs/Data-Model/Curie/index.html +++ b/docs/Data-Model/Curie/index.html @@ -947,6 +947,15 @@ + + +
  • + + + Mappings + + +
    • @@ -991,6 +1000,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfxsd:string
    nativehttps://w3id.org/monarch/monarch-py/:curie
    diff --git a/docs/Data-Model/Date/index.html b/docs/Data-Model/Date/index.html index 22f231e73..4a3543f01 100644 --- a/docs/Data-Model/Date/index.html +++ b/docs/Data-Model/Date/index.html @@ -938,6 +938,15 @@ + + +
  • + + + Mappings + + +
    • @@ -977,6 +986,29 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfxsd:date
    nativehttps://w3id.org/monarch/monarch-py/:date
    exactschema:Date
    diff --git a/docs/Data-Model/DateOrDatetime/index.html b/docs/Data-Model/DateOrDatetime/index.html index 592f6eb46..37dfb4252 100644 --- a/docs/Data-Model/DateOrDatetime/index.html +++ b/docs/Data-Model/DateOrDatetime/index.html @@ -938,6 +938,15 @@ + + +
  • + + + Mappings + + +
    • @@ -977,6 +986,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selflinkml:DateOrDatetime
    nativehttps://w3id.org/monarch/monarch-py/:date_or_datetime
    diff --git a/docs/Data-Model/Datetime/index.html b/docs/Data-Model/Datetime/index.html index b0ea97fb8..8d112ca95 100644 --- a/docs/Data-Model/Datetime/index.html +++ b/docs/Data-Model/Datetime/index.html @@ -938,6 +938,15 @@ + + +
  • + + + Mappings + + +
    • @@ -977,6 +986,29 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfxsd:dateTime
    nativehttps://w3id.org/monarch/monarch-py/:datetime
    exactschema:DateTime
    diff --git a/docs/Data-Model/Decimal/index.html b/docs/Data-Model/Decimal/index.html index fe1530613..976c1d479 100644 --- a/docs/Data-Model/Decimal/index.html +++ b/docs/Data-Model/Decimal/index.html @@ -938,6 +938,15 @@ + + +
  • + + + Mappings + + +
    • @@ -974,6 +983,29 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfxsd:decimal
    nativehttps://w3id.org/monarch/monarch-py/:decimal
    broadschema:Number
    diff --git a/docs/Data-Model/DirectionalAssociation/index.html b/docs/Data-Model/DirectionalAssociation/index.html index edb479a32..c38ecffad 100644 --- a/docs/Data-Model/DirectionalAssociation/index.html +++ b/docs/Data-Model/DirectionalAssociation/index.html @@ -1051,6 +1051,18 @@

    Class: DirectionalAssociation

    click AssociationDirectionEnum href "../AssociationDirectionEnum" + DirectionalAssociation : disease_context_qualifier + + DirectionalAssociation : disease_context_qualifier_category + + DirectionalAssociation : disease_context_qualifier_closure + + DirectionalAssociation : disease_context_qualifier_closure_label + + DirectionalAssociation : disease_context_qualifier_label + + DirectionalAssociation : disease_context_qualifier_namespace + DirectionalAssociation : evidence_count DirectionalAssociation : frequency_qualifier @@ -1690,6 +1702,42 @@

    Slots

    Field containing stage_qualifier name and the names of all of it's ancestors Association + +disease_context_qualifier +0..1
    String +A context qualifier representing a disease or condition in which a relationsh... +Association + + +disease_context_qualifier_label +0..1
    String +The name of the disease_context_qualifier entity +Association + + +disease_context_qualifier_namespace +0..1
    String +The namespace/prefix of the disease_context_qualifier entity +Association + + +disease_context_qualifier_category +0..1
    String +The category of the disease_context_qualifier entity +Association + + +disease_context_qualifier_closure +*
    String +Field containing disease_context_qualifier id and the ids of all of it's ance... +Association + + +disease_context_qualifier_closure_label +*
    String +Field containing disease_context_qualifier name and the names of all of it's ... +Association +

    Usages

    @@ -1792,7 +1840,6 @@

    Induced

    name: category from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: false alias: category owner: DirectionalAssociation domain_of: @@ -1802,6 +1849,7 @@

    Induced

    - AssociationTypeMapping - Entity range: string + multivalued: false subject: name: subject from_schema: https://w3id.org/monarch/monarch-py @@ -1849,12 +1897,12 @@

    Induced

    description: Field containing subject id and the ids of all of it's ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: subject_closure owner: DirectionalAssociation domain_of: - Association range: string + multivalued: true subject_label: name: subject_label description: The name of the subject entity @@ -1875,12 +1923,12 @@

    Induced

    description: Field containing subject name and the names of all of it's ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: subject_closure_label owner: DirectionalAssociation domain_of: - Association range: string + multivalued: true subject_taxon: name: subject_taxon from_schema: https://w3id.org/monarch/monarch-py @@ -1905,7 +1953,6 @@

    Induced

    name: predicate from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: false alias: predicate owner: DirectionalAssociation domain_of: @@ -1913,6 +1960,7 @@

    Induced

    - CompactAssociation range: string required: true + multivalued: false object: name: object from_schema: https://w3id.org/monarch/monarch-py @@ -1959,12 +2007,12 @@

    Induced

    description: Field containing object id and the ids of all of it's ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: object_closure owner: DirectionalAssociation domain_of: - Association range: string + multivalued: true object_label: name: object_label description: The name of the object entity @@ -1985,12 +2033,12 @@

    Induced

    description: Field containing object name and the names of all of it's ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: object_closure_label owner: DirectionalAssociation domain_of: - Association range: string + multivalued: true object_taxon: name: object_taxon from_schema: https://w3id.org/monarch/monarch-py @@ -2024,12 +2072,12 @@

    Induced

    name: aggregator_knowledge_source from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: aggregator_knowledge_source owner: DirectionalAssociation domain_of: - Association range: string + multivalued: true negated: name: negated from_schema: https://w3id.org/monarch/monarch-py @@ -2071,13 +2119,13 @@

    Induced

    from_schema: https://w3id.org/monarch/monarch-py rank: 1000 slot_uri: biolink:knowledge_level - multivalued: false alias: knowledge_level owner: DirectionalAssociation domain_of: - Association range: string required: true + multivalued: false agent_type: name: agent_type description: Describes the high-level category of agent who originally generated @@ -2088,34 +2136,34 @@

    Induced

    from_schema: https://w3id.org/monarch/monarch-py rank: 1000 slot_uri: biolink:agent_type - multivalued: false alias: agent_type owner: DirectionalAssociation domain_of: - Association range: string required: true + multivalued: false has_evidence: name: has_evidence from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: has_evidence owner: DirectionalAssociation domain_of: - Association range: string + multivalued: true has_evidence_links: name: has_evidence_links description: List of ExpandedCuries with id and url for evidence from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: has_evidence_links owner: DirectionalAssociation domain_of: - Association range: ExpandedCurie + multivalued: true inlined: true inlined_as_list: true has_count: @@ -2196,23 +2244,23 @@

    Induced

    name: publications from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: publications owner: DirectionalAssociation domain_of: - Association range: string + multivalued: true publications_links: name: publications_links description: List of ExpandedCuries with id and url for publications from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: publications_links owner: DirectionalAssociation domain_of: - Association range: ExpandedCurie + multivalued: true inlined: true inlined_as_list: true frequency_qualifier: @@ -2255,12 +2303,12 @@

    Induced

    name: qualifiers from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: qualifiers owner: DirectionalAssociation domain_of: - Association range: string + multivalued: true qualifiers_label: name: qualifiers_label description: The name of the frequency_qualifier entity @@ -2299,34 +2347,34 @@

    Induced

    ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: qualifiers_closure owner: DirectionalAssociation domain_of: - Association range: string + multivalued: true qualifiers_closure_label: name: qualifiers_closure_label description: Field containing frequency_qualifier name and the names of all of it's ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: qualifiers_closure_label owner: DirectionalAssociation domain_of: - Association range: string + multivalued: true qualifier: name: qualifier from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: qualifier owner: DirectionalAssociation domain_of: - Association range: string + multivalued: true qualifier_label: name: qualifier_label description: The name of the frequency_qualifier entity @@ -2365,24 +2413,24 @@

    Induced

    ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: qualifier_closure owner: DirectionalAssociation domain_of: - Association range: string + multivalued: true qualifier_closure_label: name: qualifier_closure_label description: Field containing frequency_qualifier name and the names of all of it's ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: qualifier_closure_label owner: DirectionalAssociation domain_of: - Association range: string + multivalued: true frequency_qualifier_label: name: frequency_qualifier_label description: The name of the frequency_qualifier entity @@ -2421,24 +2469,24 @@

    Induced

    ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: frequency_qualifier_closure owner: DirectionalAssociation domain_of: - Association range: string + multivalued: true frequency_qualifier_closure_label: name: frequency_qualifier_closure_label description: Field containing frequency_qualifier name and the names of all of it's ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: frequency_qualifier_closure_label owner: DirectionalAssociation domain_of: - Association range: string + multivalued: true onset_qualifier_label: name: onset_qualifier_label description: The name of the onset_qualifier entity @@ -2476,24 +2524,24 @@

    Induced

    description: Field containing onset_qualifier id and the ids of all of it's ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: onset_qualifier_closure owner: DirectionalAssociation domain_of: - Association range: string + multivalued: true onset_qualifier_closure_label: name: onset_qualifier_closure_label description: Field containing onset_qualifier name and the names of all of it's ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: onset_qualifier_closure_label owner: DirectionalAssociation domain_of: - Association range: string + multivalued: true sex_qualifier_label: name: sex_qualifier_label description: The name of the sex_qualifier entity @@ -2531,24 +2579,24 @@

    Induced

    description: Field containing sex_qualifier id and the ids of all of it's ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: sex_qualifier_closure owner: DirectionalAssociation domain_of: - Association range: string + multivalued: true sex_qualifier_closure_label: name: sex_qualifier_closure_label description: Field containing sex_qualifier name and the names of all of it's ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: sex_qualifier_closure_label owner: DirectionalAssociation domain_of: - Association range: string + multivalued: true stage_qualifier_label: name: stage_qualifier_label description: The name of the stage_qualifier entity @@ -2586,24 +2634,94 @@

    Induced

    description: Field containing stage_qualifier id and the ids of all of it's ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: stage_qualifier_closure owner: DirectionalAssociation domain_of: - Association range: string + multivalued: true stage_qualifier_closure_label: name: stage_qualifier_closure_label description: Field containing stage_qualifier name and the names of all of it's ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: stage_qualifier_closure_label owner: DirectionalAssociation domain_of: - Association range: string + multivalued: true + disease_context_qualifier: + name: disease_context_qualifier + description: A context qualifier representing a disease or condition in which + a relationship expressed in an association took place. + examples: + - value: MONDO:0004979 + - value: MONDO:0005148 + from_schema: https://w3id.org/monarch/monarch-py + rank: 1000 + alias: disease_context_qualifier + owner: DirectionalAssociation + domain_of: + - Association + range: string + disease_context_qualifier_label: + name: disease_context_qualifier_label + description: The name of the disease_context_qualifier entity + from_schema: https://w3id.org/monarch/monarch-py + rank: 1000 + is_a: name + alias: disease_context_qualifier_label + owner: DirectionalAssociation + domain_of: + - Association + range: string + disease_context_qualifier_namespace: + name: disease_context_qualifier_namespace + description: The namespace/prefix of the disease_context_qualifier entity + from_schema: https://w3id.org/monarch/monarch-py + rank: 1000 + alias: disease_context_qualifier_namespace + owner: DirectionalAssociation + domain_of: + - Association + range: string + disease_context_qualifier_category: + name: disease_context_qualifier_category + description: The category of the disease_context_qualifier entity + from_schema: https://w3id.org/monarch/monarch-py + rank: 1000 + is_a: category + alias: disease_context_qualifier_category + owner: DirectionalAssociation + domain_of: + - Association + range: string + disease_context_qualifier_closure: + name: disease_context_qualifier_closure + description: Field containing disease_context_qualifier id and the ids of all + of it's ancestors + from_schema: https://w3id.org/monarch/monarch-py + rank: 1000 + alias: disease_context_qualifier_closure + owner: DirectionalAssociation + domain_of: + - Association + range: string + multivalued: true + disease_context_qualifier_closure_label: + name: disease_context_qualifier_closure_label + description: Field containing disease_context_qualifier name and the names of + all of it's ancestors + from_schema: https://w3id.org/monarch/monarch-py + rank: 1000 + alias: disease_context_qualifier_closure_label + owner: DirectionalAssociation + domain_of: + - Association + range: string + multivalued: true diff --git a/docs/Data-Model/Double/index.html b/docs/Data-Model/Double/index.html index 4e04343ae..d86925067 100644 --- a/docs/Data-Model/Double/index.html +++ b/docs/Data-Model/Double/index.html @@ -938,6 +938,15 @@ + + +
  • + + + Mappings + + +
    • @@ -974,6 +983,29 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfxsd:double
    nativehttps://w3id.org/monarch/monarch-py/:double
    closeschema:Float
    diff --git a/docs/Data-Model/Entity/index.html b/docs/Data-Model/Entity/index.html index e459ee59d..0e95c58b4 100644 --- a/docs/Data-Model/Entity/index.html +++ b/docs/Data-Model/Entity/index.html @@ -1364,7 +1364,6 @@

    Induced

    name: category from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: false alias: category owner: Entity domain_of: @@ -1374,6 +1373,7 @@

    Induced

    - AssociationTypeMapping - Entity range: string + multivalued: false name: name: name from_schema: https://w3id.org/monarch/monarch-py @@ -1420,12 +1420,12 @@

    Induced

    name: xref from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: xref owner: Entity domain_of: - Entity range: string + multivalued: true provided_by: name: provided_by from_schema: https://w3id.org/monarch/monarch-py @@ -1472,12 +1472,12 @@

    Induced

    name: synonym from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: synonym owner: Entity domain_of: - Entity range: string + multivalued: true uri: name: uri description: The URI of the entity @@ -1513,12 +1513,12 @@

    Induced

    this entity from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: has_phenotype owner: Entity domain_of: - Entity range: string + multivalued: true inlined: true inlined_as_list: true has_phenotype_label: @@ -1527,12 +1527,12 @@

    Induced

    entity from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: has_phenotype_label owner: Entity domain_of: - Entity range: string + multivalued: true inlined: true inlined_as_list: true has_phenotype_closure: @@ -1541,12 +1541,12 @@

    Induced

    this entity expanded to include all ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: has_phenotype_closure owner: Entity domain_of: - Entity range: string + multivalued: true inlined: true inlined_as_list: true has_phenotype_closure_label: @@ -1555,12 +1555,12 @@

    Induced

    entity expanded to include all ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: has_phenotype_closure_label owner: Entity domain_of: - Entity range: string + multivalued: true inlined: true inlined_as_list: true has_phenotype_count: diff --git a/docs/Data-Model/EntityResults/index.html b/docs/Data-Model/EntityResults/index.html index fe3a977ce..a924b0a2d 100644 --- a/docs/Data-Model/EntityResults/index.html +++ b/docs/Data-Model/EntityResults/index.html @@ -1122,16 +1122,6 @@

    Direct

    slot_usage: items: name: items - domain_of: - - AssociationCountList - - AssociationResults - - CompactAssociationResults - - AssociationTableResults - - CategoryGroupedAssociationResults - - EntityResults - - HistoPheno - - MappingResults - - SearchResults range: Entity @@ -1144,16 +1134,6 @@

    Induced

    slot_usage: items: name: items - domain_of: - - AssociationCountList - - AssociationResults - - CompactAssociationResults - - AssociationTableResults - - CategoryGroupedAssociationResults - - EntityResults - - HistoPheno - - MappingResults - - SearchResults range: Entity attributes: items: @@ -1161,7 +1141,6 @@

    Induced

    description: A collection of items, with the type to be overriden by slot_usage from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: items owner: EntityResults domain_of: @@ -1176,6 +1155,7 @@

    Induced

    - SearchResults range: Entity required: true + multivalued: true inlined: true inlined_as_list: true limit: diff --git a/docs/Data-Model/FacetField/index.html b/docs/Data-Model/FacetField/index.html index fa84a442f..0740a5c18 100644 --- a/docs/Data-Model/FacetField/index.html +++ b/docs/Data-Model/FacetField/index.html @@ -1139,12 +1139,12 @@

    Induced

    description: Collection of FacetValue label/value instances belonging to a FacetField from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: facet_values owner: FacetField domain_of: - FacetField range: FacetValue + multivalued: true inlined: true inlined_as_list: true diff --git a/docs/Data-Model/Float/index.html b/docs/Data-Model/Float/index.html index 20141d483..30ac65ff7 100644 --- a/docs/Data-Model/Float/index.html +++ b/docs/Data-Model/Float/index.html @@ -938,6 +938,15 @@ + + +
  • + + + Mappings + + +
    • @@ -974,6 +983,29 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfxsd:float
    nativehttps://w3id.org/monarch/monarch-py/:float
    exactschema:Float
    diff --git a/docs/Data-Model/HistoPheno/index.html b/docs/Data-Model/HistoPheno/index.html index 8461980b2..b9ea6fed4 100644 --- a/docs/Data-Model/HistoPheno/index.html +++ b/docs/Data-Model/HistoPheno/index.html @@ -1088,16 +1088,6 @@

    Direct

    slot_usage: items: name: items - domain_of: - - AssociationCountList - - AssociationResults - - CompactAssociationResults - - AssociationTableResults - - CategoryGroupedAssociationResults - - EntityResults - - HistoPheno - - MappingResults - - SearchResults range: HistoBin @@ -1109,16 +1099,6 @@

    Induced

    slot_usage: items: name: items - domain_of: - - AssociationCountList - - AssociationResults - - CompactAssociationResults - - AssociationTableResults - - CategoryGroupedAssociationResults - - EntityResults - - HistoPheno - - MappingResults - - SearchResults range: HistoBin attributes: id: @@ -1144,7 +1124,6 @@

    Induced

    description: A collection of items, with the type to be overriden by slot_usage from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: items owner: HistoPheno domain_of: @@ -1159,6 +1138,7 @@

    Induced

    - SearchResults range: HistoBin required: true + multivalued: true inlined: true inlined_as_list: true diff --git a/docs/Data-Model/Integer/index.html b/docs/Data-Model/Integer/index.html index 686ca0450..90231b428 100644 --- a/docs/Data-Model/Integer/index.html +++ b/docs/Data-Model/Integer/index.html @@ -938,6 +938,15 @@ + + +
  • + + + Mappings + + +
    • @@ -974,6 +983,29 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfxsd:integer
    nativehttps://w3id.org/monarch/monarch-py/:integer
    exactschema:Integer
    diff --git a/docs/Data-Model/ItemCount/index.html b/docs/Data-Model/ItemCount/index.html index 5b3a29e85..b58a319aa 100644 --- a/docs/Data-Model/ItemCount/index.html +++ b/docs/Data-Model/ItemCount/index.html @@ -938,6 +938,15 @@ + + +
  • + + + Mappings + + +
    • @@ -976,6 +985,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:ItemCount
    nativehttps://w3id.org/monarch/monarch-py/:ItemCount
    diff --git a/docs/Data-Model/Jsonpath/index.html b/docs/Data-Model/Jsonpath/index.html index 971be67e7..18d8f3593 100644 --- a/docs/Data-Model/Jsonpath/index.html +++ b/docs/Data-Model/Jsonpath/index.html @@ -938,6 +938,15 @@ + + +
  • + + + Mappings + + +
    • @@ -977,6 +986,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfxsd:string
    nativehttps://w3id.org/monarch/monarch-py/:jsonpath
    diff --git a/docs/Data-Model/Jsonpointer/index.html b/docs/Data-Model/Jsonpointer/index.html index a1a56e7d0..6cfb7b6db 100644 --- a/docs/Data-Model/Jsonpointer/index.html +++ b/docs/Data-Model/Jsonpointer/index.html @@ -938,6 +938,15 @@ + + +
  • + + + Mappings + + +
    • @@ -977,6 +986,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfxsd:string
    nativehttps://w3id.org/monarch/monarch-py/:jsonpointer
    diff --git a/docs/Data-Model/MappingResults/index.html b/docs/Data-Model/MappingResults/index.html index a7954ba22..10772e4ad 100644 --- a/docs/Data-Model/MappingResults/index.html +++ b/docs/Data-Model/MappingResults/index.html @@ -1124,16 +1124,6 @@

    Direct

    slot_usage: items: name: items - domain_of: - - AssociationCountList - - AssociationResults - - CompactAssociationResults - - AssociationTableResults - - CategoryGroupedAssociationResults - - EntityResults - - HistoPheno - - MappingResults - - SearchResults range: Mapping @@ -1147,16 +1137,6 @@

    Induced

    slot_usage: items: name: items - domain_of: - - AssociationCountList - - AssociationResults - - CompactAssociationResults - - AssociationTableResults - - CategoryGroupedAssociationResults - - EntityResults - - HistoPheno - - MappingResults - - SearchResults range: Mapping attributes: items: @@ -1164,7 +1144,6 @@

    Induced

    description: A collection of items, with the type to be overriden by slot_usage from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: items owner: MappingResults domain_of: @@ -1179,6 +1158,7 @@

    Induced

    - SearchResults range: Mapping required: true + multivalued: true inlined: true inlined_as_list: true limit: diff --git a/docs/Data-Model/MultiEntityAssociationResults/index.html b/docs/Data-Model/MultiEntityAssociationResults/index.html index bbfbefa8b..389e8783e 100644 --- a/docs/Data-Model/MultiEntityAssociationResults/index.html +++ b/docs/Data-Model/MultiEntityAssociationResults/index.html @@ -1178,13 +1178,13 @@

    Induced

    name: associated_categories from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: associated_categories owner: MultiEntityAssociationResults domain_of: - MultiEntityAssociationResults range: CategoryGroupedAssociationResults required: true + multivalued: true inlined: true inlined_as_list: true limit: diff --git a/docs/Data-Model/Ncname/index.html b/docs/Data-Model/Ncname/index.html index 5e8317e9b..e84f8817c 100644 --- a/docs/Data-Model/Ncname/index.html +++ b/docs/Data-Model/Ncname/index.html @@ -938,6 +938,15 @@ + + +
  • + + + Mappings + + +
    • @@ -977,6 +986,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfxsd:string
    nativehttps://w3id.org/monarch/monarch-py/:ncname
    diff --git a/docs/Data-Model/NegativeLogValue/index.html b/docs/Data-Model/NegativeLogValue/index.html index e7ae18ccb..473e165c4 100644 --- a/docs/Data-Model/NegativeLogValue/index.html +++ b/docs/Data-Model/NegativeLogValue/index.html @@ -938,6 +938,15 @@ + + +
  • + + + Mappings + + +
    • @@ -976,6 +985,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:NegativeLogValue
    nativehttps://w3id.org/monarch/monarch-py/:NegativeLogValue
    diff --git a/docs/Data-Model/Node/index.html b/docs/Data-Model/Node/index.html index 8c1eda480..c85958769 100644 --- a/docs/Data-Model/Node/index.html +++ b/docs/Data-Model/Node/index.html @@ -1419,12 +1419,12 @@

    Induced

    description: A list of genes that are known to be causally associated with a disease from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: causal_gene owner: Node domain_of: - Node range: Entity + multivalued: true inlined: true inlined_as_list: true causes_disease: @@ -1433,12 +1433,12 @@

    Induced

    a gene from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: causes_disease owner: Node domain_of: - Node range: Entity + multivalued: true inlined: true inlined_as_list: true mappings: @@ -1446,12 +1446,12 @@

    Induced

    description: List of ExpandedCuries with id and url for mapped entities from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: mappings owner: Node domain_of: - Node range: ExpandedCurie + multivalued: true inlined: true inlined_as_list: true external_links: @@ -1459,12 +1459,12 @@

    Induced

    description: ExpandedCurie with id and url for xrefs from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: external_links owner: Node domain_of: - Node range: ExpandedCurie + multivalued: true inlined: true inlined_as_list: true provided_by_link: @@ -1483,13 +1483,13 @@

    Induced

    name: association_counts from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: association_counts owner: Node domain_of: - Node range: AssociationCount required: true + multivalued: true inlined: true inlined_as_list: true node_hierarchy: @@ -1524,7 +1524,6 @@

    Induced

    name: category from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: false alias: category owner: Node domain_of: @@ -1534,6 +1533,7 @@

    Induced

    - AssociationTypeMapping - Entity range: string + multivalued: false name: name: name from_schema: https://w3id.org/monarch/monarch-py @@ -1580,12 +1580,12 @@

    Induced

    name: xref from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: xref owner: Node domain_of: - Entity range: string + multivalued: true provided_by: name: provided_by from_schema: https://w3id.org/monarch/monarch-py @@ -1609,12 +1609,12 @@

    Induced

    name: synonym from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: synonym owner: Node domain_of: - Entity range: string + multivalued: true uri: name: uri description: The URI of the entity @@ -1650,12 +1650,12 @@

    Induced

    this entity from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: has_phenotype owner: Node domain_of: - Entity range: string + multivalued: true inlined: true inlined_as_list: true has_phenotype_label: @@ -1664,12 +1664,12 @@

    Induced

    entity from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: has_phenotype_label owner: Node domain_of: - Entity range: string + multivalued: true inlined: true inlined_as_list: true has_phenotype_closure: @@ -1678,12 +1678,12 @@

    Induced

    this entity expanded to include all ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: has_phenotype_closure owner: Node domain_of: - Entity range: string + multivalued: true inlined: true inlined_as_list: true has_phenotype_closure_label: @@ -1692,12 +1692,12 @@

    Induced

    entity expanded to include all ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: has_phenotype_closure_label owner: Node domain_of: - Entity range: string + multivalued: true inlined: true inlined_as_list: true has_phenotype_count: diff --git a/docs/Data-Model/NodeHierarchy/index.html b/docs/Data-Model/NodeHierarchy/index.html index 111bbd7f8..b80ce0b93 100644 --- a/docs/Data-Model/NodeHierarchy/index.html +++ b/docs/Data-Model/NodeHierarchy/index.html @@ -1132,26 +1132,26 @@

    Induced

    name: super_classes from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: super_classes owner: NodeHierarchy domain_of: - NodeHierarchy range: Entity required: true + multivalued: true inlined: true inlined_as_list: true sub_classes: name: sub_classes from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: sub_classes owner: NodeHierarchy domain_of: - NodeHierarchy range: Entity required: true + multivalued: true inlined: true inlined_as_list: true diff --git a/docs/Data-Model/Nodeidentifier/index.html b/docs/Data-Model/Nodeidentifier/index.html index 81ea60095..16fd1738c 100644 --- a/docs/Data-Model/Nodeidentifier/index.html +++ b/docs/Data-Model/Nodeidentifier/index.html @@ -938,6 +938,15 @@ + + +
  • + + + Mappings + + +
    • @@ -977,6 +986,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfshex:nonLiteral
    nativehttps://w3id.org/monarch/monarch-py/:nodeidentifier
    diff --git a/docs/Data-Model/NonNegativeFloat/index.html b/docs/Data-Model/NonNegativeFloat/index.html index 977be3efa..940bbe169 100644 --- a/docs/Data-Model/NonNegativeFloat/index.html +++ b/docs/Data-Model/NonNegativeFloat/index.html @@ -938,6 +938,15 @@ + + +
  • + + + Mappings + + +
    • @@ -976,6 +985,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:NonNegativeFloat
    nativehttps://w3id.org/monarch/monarch-py/:NonNegativeFloat
    diff --git a/docs/Data-Model/Objectidentifier/index.html b/docs/Data-Model/Objectidentifier/index.html index fc06d2005..4be00032c 100644 --- a/docs/Data-Model/Objectidentifier/index.html +++ b/docs/Data-Model/Objectidentifier/index.html @@ -947,6 +947,15 @@ + + +
  • + + + Mappings + + +
    • @@ -990,6 +999,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfshex:iri
    nativehttps://w3id.org/monarch/monarch-py/:objectidentifier
    diff --git a/docs/Data-Model/SearchResult/index.html b/docs/Data-Model/SearchResult/index.html index ed642b0e4..0669f085a 100644 --- a/docs/Data-Model/SearchResult/index.html +++ b/docs/Data-Model/SearchResult/index.html @@ -1288,18 +1288,9 @@

    Direct

    slot_usage: category: name: category - domain_of: - - Association - - AssociationCount - - CompactAssociation - - AssociationTypeMapping - - Entity required: true name: name: name - domain_of: - - Entity - - MultiEntityAssociationResults required: true @@ -1312,18 +1303,9 @@

    Induced

    slot_usage: category: name: category - domain_of: - - Association - - AssociationCount - - CompactAssociation - - AssociationTypeMapping - - Entity required: true name: name: name - domain_of: - - Entity - - MultiEntityAssociationResults required: true attributes: highlight: @@ -1369,7 +1351,6 @@

    Induced

    name: category from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: false alias: category owner: SearchResult domain_of: @@ -1380,6 +1361,7 @@

    Induced

    - Entity range: string required: true + multivalued: false name: name: name from_schema: https://w3id.org/monarch/monarch-py @@ -1427,12 +1409,12 @@

    Induced

    name: xref from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: xref owner: SearchResult domain_of: - Entity range: string + multivalued: true provided_by: name: provided_by from_schema: https://w3id.org/monarch/monarch-py @@ -1479,12 +1461,12 @@

    Induced

    name: synonym from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: synonym owner: SearchResult domain_of: - Entity range: string + multivalued: true uri: name: uri description: The URI of the entity @@ -1520,12 +1502,12 @@

    Induced

    this entity from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: has_phenotype owner: SearchResult domain_of: - Entity range: string + multivalued: true inlined: true inlined_as_list: true has_phenotype_label: @@ -1534,12 +1516,12 @@

    Induced

    entity from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: has_phenotype_label owner: SearchResult domain_of: - Entity range: string + multivalued: true inlined: true inlined_as_list: true has_phenotype_closure: @@ -1548,12 +1530,12 @@

    Induced

    this entity expanded to include all ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: has_phenotype_closure owner: SearchResult domain_of: - Entity range: string + multivalued: true inlined: true inlined_as_list: true has_phenotype_closure_label: @@ -1562,12 +1544,12 @@

    Induced

    entity expanded to include all ancestors from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: has_phenotype_closure_label owner: SearchResult domain_of: - Entity range: string + multivalued: true inlined: true inlined_as_list: true has_phenotype_count: diff --git a/docs/Data-Model/SearchResults/index.html b/docs/Data-Model/SearchResults/index.html index e15efec4f..52d98e98e 100644 --- a/docs/Data-Model/SearchResults/index.html +++ b/docs/Data-Model/SearchResults/index.html @@ -1154,16 +1154,6 @@

    Direct

    slot_usage: items: name: items - domain_of: - - AssociationCountList - - AssociationResults - - CompactAssociationResults - - AssociationTableResults - - CategoryGroupedAssociationResults - - EntityResults - - HistoPheno - - MappingResults - - SearchResults range: SearchResult @@ -1176,16 +1166,6 @@

    Induced

    slot_usage: items: name: items - domain_of: - - AssociationCountList - - AssociationResults - - CompactAssociationResults - - AssociationTableResults - - CategoryGroupedAssociationResults - - EntityResults - - HistoPheno - - MappingResults - - SearchResults range: SearchResult attributes: items: @@ -1193,7 +1173,6 @@

    Induced

    description: A collection of items, with the type to be overriden by slot_usage from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: items owner: SearchResults domain_of: @@ -1208,6 +1187,7 @@

    Induced

    - SearchResults range: SearchResult required: true + multivalued: true inlined: true inlined_as_list: true facet_fields: @@ -1215,12 +1195,12 @@

    Induced

    description: Collection of facet field responses with the field values and counts from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: facet_fields owner: SearchResults domain_of: - SearchResults range: FacetField + multivalued: true inlined: true inlined_as_list: true facet_queries: @@ -1229,12 +1209,12 @@

    Induced

    and counts from_schema: https://w3id.org/monarch/monarch-py rank: 1000 - multivalued: true alias: facet_queries owner: SearchResults domain_of: - SearchResults range: FacetValue + multivalued: true inlined: true inlined_as_list: true limit: diff --git a/docs/Data-Model/SemsimSearchResult/index.html b/docs/Data-Model/SemsimSearchResult/index.html index 5cb46d3ca..8a04796f1 100644 --- a/docs/Data-Model/SemsimSearchResult/index.html +++ b/docs/Data-Model/SemsimSearchResult/index.html @@ -1104,10 +1104,6 @@

    Direct

    slot_usage: subject: name: subject - domain_of: - - Association - - CompactAssociation - - SemsimSearchResult range: Entity inlined: true @@ -1120,10 +1116,6 @@

    Induced

    slot_usage: subject: name: subject - domain_of: - - Association - - CompactAssociation - - SemsimSearchResult range: Entity inlined: true attributes: diff --git a/docs/Data-Model/Sparqlpath/index.html b/docs/Data-Model/Sparqlpath/index.html index a9ff40d0c..6f24c36cb 100644 --- a/docs/Data-Model/Sparqlpath/index.html +++ b/docs/Data-Model/Sparqlpath/index.html @@ -938,6 +938,15 @@ + + +
  • + + + Mappings + + +
    • @@ -977,6 +986,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfxsd:string
    nativehttps://w3id.org/monarch/monarch-py/:sparqlpath
    diff --git a/docs/Data-Model/String/index.html b/docs/Data-Model/String/index.html index 597b113ca..50d39c343 100644 --- a/docs/Data-Model/String/index.html +++ b/docs/Data-Model/String/index.html @@ -938,6 +938,15 @@ + + +
  • + + + Mappings + + +
    • @@ -974,6 +983,29 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfxsd:string
    nativehttps://w3id.org/monarch/monarch-py/:string
    exactschema:Text
    diff --git a/docs/Data-Model/TermSetPairwiseSimilarity/index.html b/docs/Data-Model/TermSetPairwiseSimilarity/index.html index 4f70ebc39..8e2467415 100644 --- a/docs/Data-Model/TermSetPairwiseSimilarity/index.html +++ b/docs/Data-Model/TermSetPairwiseSimilarity/index.html @@ -1213,45 +1213,45 @@

    Induced

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+            
    
+              
    
+                
+                  
+
+  
+  
+
+
+
    Slot: disease_context_qualifier
    
+
    A context qualifier representing a disease or condition in which a relationship expressed in an association took place.
    
+
    URI: https://w3id.org/monarch/monarch-py/:disease_context_qualifier
    
+
+
+
    Applicable Classes
    
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
    NameDescriptionModifies Slot
    DirectionalAssociationAn association that gives it's direction relative to a specified entityno
    Associationno
    
+
    Properties
    
+
+
    Examples
    
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
    Value
    MONDO:0004979
    MONDO:0005148
    
+
    Identifier and Mapping Information
    
+
    Schema Source
    
+
+
    Mappings
    
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:disease_context_qualifier
    nativehttps://w3id.org/monarch/monarch-py/:disease_context_qualifier
    
+
    LinkML Source
    
+
    
+
    name: disease_context_qualifier
+description: A context qualifier representing a disease or condition in which a relationship
+  expressed in an association took place.
+examples:
+- value: MONDO:0004979
+- value: MONDO:0005148
+from_schema: https://w3id.org/monarch/monarch-py
+rank: 1000
+alias: disease_context_qualifier
+domain_of:
+- Association
+range: string
+
    
+
    
+
+
+
+
+
+
+
+
+
+
+
+
+                
+              
    
+            
    
+          
+          
+
+        
    
+        
+      
    
+      
+        
+      
+    
    
+    
    
+      
    
+    
    
+    
+    
+    
+    
+    
+      
+      
+    
+  
+
\ No newline at end of file
diff --git a/docs/Data-Model/disease_context_qualifier_category/index.html b/docs/Data-Model/disease_context_qualifier_category/index.html
new file mode 100644
index 000000000..561793687
--- /dev/null
+++ b/docs/Data-Model/disease_context_qualifier_category/index.html
@@ -0,0 +1,1158 @@
+
+
+
+  
+    
+      
+      
+      
+      
+      
+        
+      
+      
+      
+      
+      
+      
+    
+    
+      
+        Slot: disease_context_qualifier_category - monarch-py
+      
+    
+    
+      
+      
+        
+        
+      
+      
+
+
+    
+    
+      
+    
+    
+      
+        
+        
+        
+        
+        
+      
+    
+    
+      
+    
+    
+    
+      
+
+    
+    
+    
+  
+  
+  
+    
+    
+      
+    
+    
+    
+    
+    
+  
+    
+    
+    
+    
+    
+    
    
+      
+    
    
+    
+    
+      
+
+  
+
+
    
+  
+  
+    
+      
+
+    
+  
+
    
+    
+    
    
+      
+      
+        
+      
+      
    
+        
    
+          
+            
+              
+              
    
+                
    
+                  
    
+                    
+
+
+  
+
+
+
+                  
    
+                
    
+              
    
+            
+            
+              
+              
    
+                
    
+                  
    
+                    
+
+
+                  
    
+                
    
+              
    
+            
+          
+          
+            
    
+              
    
+                
+                  
+
+  
+  
+
+
+
    Slot: disease_context_qualifier_category
    
+
    The category of the disease_context_qualifier entity
    
+
    URI: https://w3id.org/monarch/monarch-py/:disease_context_qualifier_category
    
+
    Inheritance
    
+
      
+
    • category
        
+
      • disease_context_qualifier_category
        • 
+
      
+
      • 
+
    
+
    Applicable Classes
    
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
    NameDescriptionModifies Slot
    DirectionalAssociationAn association that gives it's direction relative to a specified entityno
    Associationno
    
+
    Properties
    
+
+
    Identifier and Mapping Information
    
+
    Schema Source
    
+
+
    Mappings
    
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:disease_context_qualifier_category
    nativehttps://w3id.org/monarch/monarch-py/:disease_context_qualifier_category
    
+
    LinkML Source
    
+
    
+
    name: disease_context_qualifier_category
+description: The category of the disease_context_qualifier entity
+from_schema: https://w3id.org/monarch/monarch-py
+rank: 1000
+is_a: category
+alias: disease_context_qualifier_category
+domain_of:
+- Association
+range: string
+
    
+
    
+
+
+
+
+
+
+
+
+
+
+
+
+                
+              
    
+            
    
+          
+          
+
+        
    
+        
+      
    
+      
+        
+      
+    
    
+    
    
+      
    
+    
    
+    
+    
+    
+    
+    
+      
+      
+    
+  
+
\ No newline at end of file
diff --git a/docs/Data-Model/disease_context_qualifier_closure/index.html b/docs/Data-Model/disease_context_qualifier_closure/index.html
new file mode 100644
index 000000000..c374bac93
--- /dev/null
+++ b/docs/Data-Model/disease_context_qualifier_closure/index.html
@@ -0,0 +1,1150 @@
+
+
+
+  
+    
+      
+      
+      
+      
+      
+        
+      
+      
+      
+      
+      
+      
+    
+    
+      
+        Slot: disease_context_qualifier_closure - monarch-py
+      
+    
+    
+      
+      
+        
+        
+      
+      
+
+
+    
+    
+      
+    
+    
+      
+        
+        
+        
+        
+        
+      
+    
+    
+      
+    
+    
+    
+      
+
+    
+    
+    
+  
+  
+  
+    
+    
+      
+    
+    
+    
+    
+    
+  
+    
+    
+    
+    
+    
+    
    
+      
+    
    
+    
+    
+      
+
+  
+
+
    
+  
+  
+    
+      
+
+    
+  
+
    
+    
+    
    
+      
+      
+        
+      
+      
    
+        
    
+          
+            
+              
+              
    
+                
    
+                  
    
+                    
+
+
+  
+
+
+
+                  
    
+                
    
+              
    
+            
+            
+              
+              
    
+                
    
+                  
    
+                    
+
+
+                  
    
+                
    
+              
    
+            
+          
+          
+            
    
+              
    
+                
+                  
+
+  
+  
+
+
+
    Slot: disease_context_qualifier_closure
    
+
    Field containing disease_context_qualifier id and the ids of all of it's ancestors
    
+
    URI: https://w3id.org/monarch/monarch-py/:disease_context_qualifier_closure
    
+
+
+
    Applicable Classes
    
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
    NameDescriptionModifies Slot
    DirectionalAssociationAn association that gives it's direction relative to a specified entityno
    Associationno
    
+
    Properties
    
+
      
+
    • 
+
      Range: String
      
+
      • 
+
    • 
+
      Multivalued: True
      
+
      • 
+
    
+
    Identifier and Mapping Information
    
+
    Schema Source
    
+
+
    Mappings
    
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:disease_context_qualifier_closure
    nativehttps://w3id.org/monarch/monarch-py/:disease_context_qualifier_closure
    
+
    LinkML Source
    
+
    
+
    name: disease_context_qualifier_closure
+description: Field containing disease_context_qualifier id and the ids of all of it's
+  ancestors
+from_schema: https://w3id.org/monarch/monarch-py
+rank: 1000
+alias: disease_context_qualifier_closure
+domain_of:
+- Association
+range: string
+multivalued: true
+
    
+
    
+
+
+
+
+
+
+
+
+
+
+
+
+                
+              
    
+            
    
+          
+          
+
+        
    
+        
+      
    
+      
+        
+      
+    
    
+    
    
+      
    
+    
    
+    
+    
+    
+    
+    
+      
+      
+    
+  
+
\ No newline at end of file
diff --git a/docs/Data-Model/disease_context_qualifier_closure_label/index.html b/docs/Data-Model/disease_context_qualifier_closure_label/index.html
new file mode 100644
index 000000000..c41669a99
--- /dev/null
+++ b/docs/Data-Model/disease_context_qualifier_closure_label/index.html
@@ -0,0 +1,1150 @@
+
+
+
+  
+    
+      
+      
+      
+      
+      
+        
+      
+      
+      
+      
+      
+      
+    
+    
+      
+        Slot: disease_context_qualifier_closure_label - monarch-py
+      
+    
+    
+      
+      
+        
+        
+      
+      
+
+
+    
+    
+      
+    
+    
+      
+        
+        
+        
+        
+        
+      
+    
+    
+      
+    
+    
+    
+      
+
+    
+    
+    
+  
+  
+  
+    
+    
+      
+    
+    
+    
+    
+    
+  
+    
+    
+    
+    
+    
+    
    
+      
+    
    
+    
+    
+      
+
+  
+
+
    
+  
+  
+    
+      
+
+    
+  
+
    
+    
+    
    
+      
+      
+        
+      
+      
    
+        
    
+          
+            
+              
+              
    
+                
    
+                  
    
+                    
+
+
+  
+
+
+
+                  
    
+                
    
+              
    
+            
+            
+              
+              
    
+                
    
+                  
    
+                    
+
+
+                  
    
+                
    
+              
    
+            
+          
+          
+            
    
+              
    
+                
+                  
+
+  
+  
+
+
+
    Slot: disease_context_qualifier_closure_label
    
+
    Field containing disease_context_qualifier name and the names of all of it's ancestors
    
+
    URI: https://w3id.org/monarch/monarch-py/:disease_context_qualifier_closure_label
    
+
+
+
    Applicable Classes
    
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
    NameDescriptionModifies Slot
    DirectionalAssociationAn association that gives it's direction relative to a specified entityno
    Associationno
    
+
    Properties
    
+
      
+
    • 
+
      Range: String
      
+
      • 
+
    • 
+
      Multivalued: True
      
+
      • 
+
    
+
    Identifier and Mapping Information
    
+
    Schema Source
    
+
+
    Mappings
    
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:disease_context_qualifier_closure_label
    nativehttps://w3id.org/monarch/monarch-py/:disease_context_qualifier_closure_label
    
+
    LinkML Source
    
+
    
+
    name: disease_context_qualifier_closure_label
+description: Field containing disease_context_qualifier name and the names of all
+  of it's ancestors
+from_schema: https://w3id.org/monarch/monarch-py
+rank: 1000
+alias: disease_context_qualifier_closure_label
+domain_of:
+- Association
+range: string
+multivalued: true
+
    
+
    
+
+
+
+
+
+
+
+
+
+
+
+
+                
+              
    
+            
    
+          
+          
+
+        
    
+        
+      
    
+      
+        
+      
+    
    
+    
    
+      
    
+    
    
+    
+    
+    
+    
+    
+      
+      
+    
+  
+
\ No newline at end of file
diff --git a/docs/Data-Model/disease_context_qualifier_label/index.html b/docs/Data-Model/disease_context_qualifier_label/index.html
new file mode 100644
index 000000000..aa266f309
--- /dev/null
+++ b/docs/Data-Model/disease_context_qualifier_label/index.html
@@ -0,0 +1,1158 @@
+
+
+
+  
+    
+      
+      
+      
+      
+      
+        
+      
+      
+      
+      
+      
+      
+    
+    
+      
+        Slot: disease_context_qualifier_label - monarch-py
+      
+    
+    
+      
+      
+        
+        
+      
+      
+
+
+    
+    
+      
+    
+    
+      
+        
+        
+        
+        
+        
+      
+    
+    
+      
+    
+    
+    
+      
+
+    
+    
+    
+  
+  
+  
+    
+    
+      
+    
+    
+    
+    
+    
+  
+    
+    
+    
+    
+    
+    
    
+      
+    
    
+    
+    
+      
+
+  
+
+
    
+  
+  
+    
+      
+
+    
+  
+
    
+    
+    
    
+      
+      
+        
+      
+      
    
+        
    
+          
+            
+              
+              
    
+                
    
+                  
    
+                    
+
+
+  
+
+
+
+                  
    
+                
    
+              
    
+            
+            
+              
+              
    
+                
    
+                  
    
+                    
+
+
+                  
    
+                
    
+              
    
+            
+          
+          
+            
    
+              
    
+                
+                  
+
+  
+  
+
+
+
    Slot: disease_context_qualifier_label
    
+
    The name of the disease_context_qualifier entity
    
+
    URI: https://w3id.org/monarch/monarch-py/:disease_context_qualifier_label
    
+
    Inheritance
    
+
      
+
    • name
        
+
      • disease_context_qualifier_label
        • 
+
      
+
      • 
+
    
+
    Applicable Classes
    
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
    NameDescriptionModifies Slot
    DirectionalAssociationAn association that gives it's direction relative to a specified entityno
    Associationno
    
+
    Properties
    
+
+
    Identifier and Mapping Information
    
+
    Schema Source
    
+
+
    Mappings
    
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:disease_context_qualifier_label
    nativehttps://w3id.org/monarch/monarch-py/:disease_context_qualifier_label
    
+
    LinkML Source
    
+
    
+
    name: disease_context_qualifier_label
+description: The name of the disease_context_qualifier entity
+from_schema: https://w3id.org/monarch/monarch-py
+rank: 1000
+is_a: name
+alias: disease_context_qualifier_label
+domain_of:
+- Association
+range: string
+
    
+
    
+
+
+
+
+
+
+
+
+
+
+
+
+                
+              
    
+            
    
+          
+          
+
+        
    
+        
+      
    
+      
+        
+      
+    
    
+    
    
+      
    
+    
    
+    
+    
+    
+    
+    
+      
+      
+    
+  
+
\ No newline at end of file
diff --git a/docs/Data-Model/disease_context_qualifier_namespace/index.html b/docs/Data-Model/disease_context_qualifier_namespace/index.html
new file mode 100644
index 000000000..6d1158d8d
--- /dev/null
+++ b/docs/Data-Model/disease_context_qualifier_namespace/index.html
@@ -0,0 +1,1143 @@
+
+
+
+  
+    
+      
+      
+      
+      
+      
+        
+      
+      
+      
+      
+      
+      
+    
+    
+      
+        Slot: disease_context_qualifier_namespace - monarch-py
+      
+    
+    
+      
+      
+        
+        
+      
+      
+
+
+    
+    
+      
+    
+    
+      
+        
+        
+        
+        
+        
+      
+    
+    
+      
+    
+    
+    
+      
+
+    
+    
+    
+  
+  
+  
+    
+    
+      
+    
+    
+    
+    
+    
+  
+    
+    
+    
+    
+    
+    
    
+      
+    
    
+    
+    
+      
+
+  
+
+
    
+  
+  
+    
+      
+
+    
+  
+
    
+    
+    
    
+      
+      
+        
+      
+      
    
+        
    
+          
+            
+              
+              
    
+                
    
+                  
    
+                    
+
+
+  
+
+
+
+                  
    
+                
    
+              
    
+            
+            
+              
+              
    
+                
    
+                  
    
+                    
+
+
+                  
    
+                
    
+              
    
+            
+          
+          
+            
    
+              
    
+                
+                  
+
+  
+  
+
+
+
    Slot: disease_context_qualifier_namespace
    
+
    The namespace/prefix of the disease_context_qualifier entity
    
+
    URI: https://w3id.org/monarch/monarch-py/:disease_context_qualifier_namespace
    
+
+
+
    Applicable Classes
    
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
    NameDescriptionModifies Slot
    DirectionalAssociationAn association that gives it's direction relative to a specified entityno
    Associationno
    
+
    Properties
    
+
+
    Identifier and Mapping Information
    
+
    Schema Source
    
+
+
    Mappings
    
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:disease_context_qualifier_namespace
    nativehttps://w3id.org/monarch/monarch-py/:disease_context_qualifier_namespace
    
+
    LinkML Source
    
+
    
+
    name: disease_context_qualifier_namespace
+description: The namespace/prefix of the disease_context_qualifier entity
+from_schema: https://w3id.org/monarch/monarch-py
+rank: 1000
+alias: disease_context_qualifier_namespace
+domain_of:
+- Association
+range: string
+
    
+
    
+
+
+
+
+
+
+
+
+
+
+
+
+                
+              
    
+            
    
+          
+          
+
+        
    
+        
+      
    
+      
+        
+      
+    
    
+    
    
+      
    
+    
    
+    
+    
+    
+    
+    
+      
+      
+    
+  
+
\ No newline at end of file
diff --git a/docs/Data-Model/end/index.html b/docs/Data-Model/end/index.html
index d8c37072d..3e1a4921c 100644
--- a/docs/Data-Model/end/index.html
+++ b/docs/Data-Model/end/index.html
@@ -956,6 +956,15 @@
       
     
   
+
    • + +
  • + + + Mappings + + +
  • @@ -1016,6 +1025,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:end
    nativehttps://w3id.org/monarch/monarch-py/:end

    LinkML Source

    name: end
diff --git a/docs/Data-Model/evidence_count/index.html b/docs/Data-Model/evidence_count/index.html
index abf54515b..1c6f4abbd 100644
--- a/docs/Data-Model/evidence_count/index.html
+++ b/docs/Data-Model/evidence_count/index.html
@@ -956,6 +956,15 @@
       
     
   
+
    • + +
  • + + + Mappings + + +
  • @@ -1021,6 +1030,25 @@

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index d88c391b3..e4f5127d3 100644
--- a/docs/Data-Model/id/index.html
+++ b/docs/Data-Model/id/index.html
@@ -956,6 +956,15 @@
       
     
   
+
    • + +
  • + + + Mappings + + +
  • @@ -1000,12 +1009,17 @@

    Applicable Classes

    -HistoBin +DirectionalAssociation +An association that gives it's direction relative to a specified entity +no + + +HistoPheno no -MultiEntityAssociationResults +Association no @@ -1015,18 +1029,18 @@

    Applicable Classes

    no -DirectionalAssociation -An association that gives it's direction relative to a specified entity +Node +UI container class extending Entity with additional information no -SearchResult +TermInfo no -TermInfo - +ExpandedCurie +A curie bundled along with its expanded url no @@ -1035,22 +1049,17 @@

    Applicable Classes

    no -ExpandedCurie -A curie bundled along with its expanded url -no - - -Node -UI container class extending Entity with additional information +HistoBin + no -Association +MultiEntityAssociationResults no -HistoPheno +SearchResult no @@ -1070,6 +1079,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:id
    nativehttps://w3id.org/monarch/monarch-py/:id

    LinkML Source

    name: id
diff --git a/docs/Data-Model/in_taxon/index.html b/docs/Data-Model/in_taxon/index.html
index a1ea74943..75de821af 100644
--- a/docs/Data-Model/in_taxon/index.html
+++ b/docs/Data-Model/in_taxon/index.html
@@ -965,6 +965,15 @@
       
     
   
+
    • + +
  • + + + Mappings + + +
  • @@ -1016,8 +1025,8 @@

    Applicable Classes

    -Entity -Represents an Entity in the Monarch KG data model +SearchResult + no @@ -1026,8 +1035,8 @@

    Applicable Classes

    no -SearchResult - +Entity +Represents an Entity in the Monarch KG data model no @@ -1041,6 +1050,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:in_taxon
    nativehttps://w3id.org/monarch/monarch-py/:in_taxon

    LinkML Source

    name: in_taxon
diff --git a/docs/Data-Model/in_taxon_label/index.html b/docs/Data-Model/in_taxon_label/index.html
index d3160ef73..90d85e38a 100644
--- a/docs/Data-Model/in_taxon_label/index.html
+++ b/docs/Data-Model/in_taxon_label/index.html
@@ -965,6 +965,15 @@
       
     
   
+
    • + +
  • + + + Mappings + + +
  • @@ -1016,8 +1025,8 @@

    Applicable Classes

    -Entity -Represents an Entity in the Monarch KG data model +SearchResult + no @@ -1026,8 +1035,8 @@

    Applicable Classes

    no -SearchResult - +Entity +Represents an Entity in the Monarch KG data model no @@ -1041,6 +1050,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:in_taxon_label
    nativehttps://w3id.org/monarch/monarch-py/:in_taxon_label

    LinkML Source

    name: in_taxon_label
diff --git a/docs/Data-Model/index.html b/docs/Data-Model/index.html
index e2d5757f2..b06b6c4a2 100644
--- a/docs/Data-Model/index.html
+++ b/docs/Data-Model/index.html
@@ -1305,6 +1305,30 @@ 
    Slots
    
 The directionality of the association relative to a given entity for an assoc...
 
 
+disease_context_qualifier
+A context qualifier representing a disease or condition in which a relationsh...
+
+
+disease_context_qualifier_category
+The category of the disease_context_qualifier entity
+
+
+disease_context_qualifier_closure
+Field containing disease_context_qualifier id and the ids of all of it's ance...
+
+
+disease_context_qualifier_closure_label
+Field containing disease_context_qualifier name and the names of all of it's ...
+
+
+disease_context_qualifier_label
+The name of the disease_context_qualifier entity
+
+
+disease_context_qualifier_namespace
+The namespace/prefix of the disease_context_qualifier entity
+
+
 end
 end position of the annotation
 
diff --git a/docs/Data-Model/information_content/index.html b/docs/Data-Model/information_content/index.html
index f3ab6c5e2..199ac9ac3 100644
--- a/docs/Data-Model/information_content/index.html
+++ b/docs/Data-Model/information_content/index.html
@@ -965,6 +965,15 @@
       
     
   
+
    • + +
  • + + + Mappings + + +
  • @@ -996,6 +1005,9 @@

    Slot: information_content

    The IC is the negative log of the probability of the concept

    +
      +
    • NOTE: this is an abstract slot and should not be populated directly
      • +

    URI: https://w3id.org/monarch/monarch-py/:information_content

    Inheritance

    +
    • + +
  • + + + Mappings + + +
  • @@ -1015,6 +1024,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:inheritance
    nativehttps://w3id.org/monarch/monarch-py/:inheritance

    LinkML Source

    name: inheritance
diff --git a/docs/Data-Model/intersection_count/index.html b/docs/Data-Model/intersection_count/index.html
index 6efe7fd83..d232e641a 100644
--- a/docs/Data-Model/intersection_count/index.html
+++ b/docs/Data-Model/intersection_count/index.html
@@ -956,6 +956,15 @@
       
     
   
+
    • + +
  • + + + Mappings + + +
  • @@ -1003,6 +1012,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:intersection_count
    nativehttps://w3id.org/monarch/monarch-py/:intersection_count

    LinkML Source

    name: intersection_count
diff --git a/docs/Data-Model/iri/index.html b/docs/Data-Model/iri/index.html
index 71c1dd887..32140b547 100644
--- a/docs/Data-Model/iri/index.html
+++ b/docs/Data-Model/iri/index.html
@@ -956,6 +956,15 @@
       
     
   
+
    • + +
  • + + + Mappings + + +
  • @@ -1000,8 +1009,8 @@

    Applicable Classes

    -Entity -Represents an Entity in the Monarch KG data model +SearchResult + no @@ -1010,8 +1019,8 @@

    Applicable Classes

    no -SearchResult - +Entity +Represents an Entity in the Monarch KG data model no @@ -1025,6 +1034,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:iri
    nativehttps://w3id.org/monarch/monarch-py/:iri

    LinkML Source

    name: iri
diff --git a/docs/Data-Model/items/index.html b/docs/Data-Model/items/index.html
index 9dd42ab3c..a0b6bb8c1 100644
--- a/docs/Data-Model/items/index.html
+++ b/docs/Data-Model/items/index.html
@@ -956,6 +956,15 @@
       
     
   
+
    • + +
  • + + + Mappings + + +
  • @@ -1001,32 +1010,32 @@

    Applicable Classes

    -AssociationTableResults - +MappingResults +SSSOM Mappings returned as a results collection yes -CompactAssociationResults +CategoryGroupedAssociationResults yes -MappingResults -SSSOM Mappings returned as a results collection +HistoPheno + yes -AssociationResults +EntityResults yes -CategoryGroupedAssociationResults +AssociationResults yes -EntityResults +CompactAssociationResults yes @@ -1036,12 +1045,12 @@

    Applicable Classes

    yes -SearchResults +AssociationTableResults yes -HistoPheno +SearchResults yes @@ -1064,13 +1073,31 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:items
    nativehttps://w3id.org/monarch/monarch-py/:items

    LinkML Source

    name: items
 description: A collection of items, with the type to be overriden by slot_usage
 from_schema: https://w3id.org/monarch/monarch-py
 rank: 1000
-multivalued: true
 alias: items
 domain_of:
 - AssociationCountList
@@ -1084,6 +1111,7 @@ 
    LinkML Source
    
 - SearchResults
 range: string
 required: true
+multivalued: true
 inlined: true
 inlined_as_list: true
    diff --git a/docs/Data-Model/jaccard_similarity/index.html b/docs/Data-Model/jaccard_similarity/index.html index 5aff71ad8..b963fd971 100644 --- a/docs/Data-Model/jaccard_similarity/index.html +++ b/docs/Data-Model/jaccard_similarity/index.html @@ -965,6 +965,15 @@ +
    • + +
  • + + + Mappings + + +
  • @@ -1030,6 +1039,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:jaccard_similarity
    nativehttps://w3id.org/monarch/monarch-py/:jaccard_similarity

    LinkML Source

    name: jaccard_similarity
diff --git a/docs/Data-Model/kg/index.html b/docs/Data-Model/kg/index.html
index d7e705463..0f9f3677e 100644
--- a/docs/Data-Model/kg/index.html
+++ b/docs/Data-Model/kg/index.html
@@ -965,6 +965,15 @@
       
     
   
+
    • + +
  • + + + Mappings + + +
  • @@ -1029,6 +1038,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:kg
    nativehttps://w3id.org/monarch/monarch-py/:kg

    LinkML Source

    name: kg
diff --git a/docs/Data-Model/knowledge_level/index.html b/docs/Data-Model/knowledge_level/index.html
index 850e93a5e..77d98baf1 100644
--- a/docs/Data-Model/knowledge_level/index.html
+++ b/docs/Data-Model/knowledge_level/index.html
@@ -956,6 +956,15 @@
       
     
   
+
    • + +
  • + + + Mappings + + +
  • @@ -1026,6 +1035,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfbiolink:knowledge_level
    nativehttps://w3id.org/monarch/monarch-py/:knowledge_level

    LinkML Source

    name: knowledge_level
@@ -1038,12 +1066,12 @@ 
    LinkML Source
    
 from_schema: https://w3id.org/monarch/monarch-py
 rank: 1000
 slot_uri: biolink:knowledge_level
-multivalued: false
 alias: knowledge_level
 domain_of:
 - Association
 range: string
 required: true
+multivalued: false
    diff --git a/docs/Data-Model/knowledge_source/index.html b/docs/Data-Model/knowledge_source/index.html index ffc66b2cc..b1d7613ee 100644 --- a/docs/Data-Model/knowledge_source/index.html +++ b/docs/Data-Model/knowledge_source/index.html @@ -947,6 +947,15 @@ +
    • + +
  • + + + Mappings + + +
  • @@ -994,14 +1003,33 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:knowledge_source
    nativehttps://w3id.org/monarch/monarch-py/:knowledge_source

    LinkML Source

    name: knowledge_source
 from_schema: https://w3id.org/monarch/monarch-py
 rank: 1000
-multivalued: true
 alias: knowledge_source
 range: string
+multivalued: true
    diff --git a/docs/Data-Model/label/index.html b/docs/Data-Model/label/index.html index 99c376436..2433025ee 100644 --- a/docs/Data-Model/label/index.html +++ b/docs/Data-Model/label/index.html @@ -956,6 +956,15 @@ +
    • + +
  • + + + Mappings + + +
  • @@ -1000,27 +1009,27 @@

    Applicable Classes

    -HistoBin +FacetValue no -FacetField +TermInfo no -FacetValue +AssociationCount no -AssociationCount +FacetField no -TermInfo +HistoBin no @@ -1040,6 +1049,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:label
    nativehttps://w3id.org/monarch/monarch-py/:label

    LinkML Source

    name: label
diff --git a/docs/Data-Model/limit/index.html b/docs/Data-Model/limit/index.html
index 5602462de..641355c00 100644
--- a/docs/Data-Model/limit/index.html
+++ b/docs/Data-Model/limit/index.html
@@ -956,6 +956,15 @@
       
     
   
+
    • + +
  • + + + Mappings + + +
  • @@ -1001,37 +1010,37 @@

    Applicable Classes

    -AssociationTableResults - +MappingResults +SSSOM Mappings returned as a results collection no -CompactAssociationResults +CategoryGroupedAssociationResults no -MappingResults -SSSOM Mappings returned as a results collection +Results + no -AssociationResults +EntityResults no -CategoryGroupedAssociationResults +AssociationResults no -EntityResults +CompactAssociationResults no -MultiEntityAssociationResults +AssociationTableResults no @@ -1041,7 +1050,7 @@

    Applicable Classes

    no -Results +MultiEntityAssociationResults no @@ -1061,6 +1070,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:limit
    nativehttps://w3id.org/monarch/monarch-py/:limit

    LinkML Source

    name: limit
diff --git a/docs/Data-Model/mapping_justification/index.html b/docs/Data-Model/mapping_justification/index.html
index 016dede6e..35b11cf28 100644
--- a/docs/Data-Model/mapping_justification/index.html
+++ b/docs/Data-Model/mapping_justification/index.html
@@ -956,6 +956,15 @@
       
     
   
+
    • + +
  • + + + Mappings + + +
  • @@ -1015,6 +1024,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:mapping_justification
    nativehttps://w3id.org/monarch/monarch-py/:mapping_justification

    LinkML Source

    name: mapping_justification
diff --git a/docs/Data-Model/mappings/index.html b/docs/Data-Model/mappings/index.html
index c347f0e7d..14caa4422 100644
--- a/docs/Data-Model/mappings/index.html
+++ b/docs/Data-Model/mappings/index.html
@@ -956,6 +956,15 @@
       
     
   
+
    • + +
  • + + + Mappings + + +
  • @@ -1021,17 +1030,36 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:mappings
    nativehttps://w3id.org/monarch/monarch-py/:mappings

    LinkML Source

    name: mappings
 description: List of ExpandedCuries with id and url for mapped entities
 from_schema: https://w3id.org/monarch/monarch-py
 rank: 1000
-multivalued: true
 alias: mappings
 domain_of:
 - Node
 range: ExpandedCurie
+multivalued: true
 inlined: true
 inlined_as_list: true
    diff --git a/docs/Data-Model/match_source/index.html b/docs/Data-Model/match_source/index.html index 33482f0a3..1fb0e81a9 100644 --- a/docs/Data-Model/match_source/index.html +++ b/docs/Data-Model/match_source/index.html @@ -965,6 +965,15 @@ +
    • + +
  • + + + Mappings + + +
  • @@ -1033,6 +1042,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:match_source
    nativehttps://w3id.org/monarch/monarch-py/:match_source

    LinkML Source

    name: match_source
diff --git a/docs/Data-Model/match_source_label/index.html b/docs/Data-Model/match_source_label/index.html
index de90b1563..88332a356 100644
--- a/docs/Data-Model/match_source_label/index.html
+++ b/docs/Data-Model/match_source_label/index.html
@@ -956,6 +956,15 @@
       
     
   
+
    • + +
  • + + + Mappings + + +
  • @@ -1015,6 +1024,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:match_source_label
    nativehttps://w3id.org/monarch/monarch-py/:match_source_label

    LinkML Source

    name: match_source_label
diff --git a/docs/Data-Model/match_subsumer/index.html b/docs/Data-Model/match_subsumer/index.html
index 763b0a1d3..f8d2fd5f5 100644
--- a/docs/Data-Model/match_subsumer/index.html
+++ b/docs/Data-Model/match_subsumer/index.html
@@ -956,6 +956,15 @@
       
     
   
+
    • + +
  • + + + Mappings + + +
  • @@ -1015,6 +1024,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:match_subsumer
    nativehttps://w3id.org/monarch/monarch-py/:match_subsumer

    LinkML Source

    name: match_subsumer
diff --git a/docs/Data-Model/match_subsumer_label/index.html b/docs/Data-Model/match_subsumer_label/index.html
index e27f5f765..9da89c076 100644
--- a/docs/Data-Model/match_subsumer_label/index.html
+++ b/docs/Data-Model/match_subsumer_label/index.html
@@ -956,6 +956,15 @@
       
     
   
+
    • + +
  • + + + Mappings + + +
  • @@ -1015,6 +1024,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:match_subsumer_label
    nativehttps://w3id.org/monarch/monarch-py/:match_subsumer_label

    LinkML Source

    name: match_subsumer_label
diff --git a/docs/Data-Model/match_target/index.html b/docs/Data-Model/match_target/index.html
index 7e7c80ddf..2fa22d2f5 100644
--- a/docs/Data-Model/match_target/index.html
+++ b/docs/Data-Model/match_target/index.html
@@ -956,6 +956,15 @@
       
     
   
+
    • + +
  • + + + Mappings + + +
  • @@ -1016,6 +1025,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:match_target
    nativehttps://w3id.org/monarch/monarch-py/:match_target

    LinkML Source

    name: match_target
diff --git a/docs/Data-Model/match_target_label/index.html b/docs/Data-Model/match_target_label/index.html
index f3a8eb504..ba8629f4f 100644
--- a/docs/Data-Model/match_target_label/index.html
+++ b/docs/Data-Model/match_target_label/index.html
@@ -956,6 +956,15 @@
       
     
   
+
    • + +
  • + + + Mappings + + +
  • @@ -1015,6 +1024,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:match_target_label
    nativehttps://w3id.org/monarch/monarch-py/:match_target_label

    LinkML Source

    name: match_target_label
diff --git a/docs/Data-Model/metadata/index.html b/docs/Data-Model/metadata/index.html
index d6c34c909..11c9ba114 100644
--- a/docs/Data-Model/metadata/index.html
+++ b/docs/Data-Model/metadata/index.html
@@ -965,6 +965,15 @@
       
     
   
+
    • + +
  • + + + Mappings + + +
  • @@ -1029,6 +1038,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:metadata
    nativehttps://w3id.org/monarch/monarch-py/:metadata

    LinkML Source

    name: metadata
diff --git a/docs/Data-Model/metric/index.html b/docs/Data-Model/metric/index.html
index 73f070199..75bb69de8 100644
--- a/docs/Data-Model/metric/index.html
+++ b/docs/Data-Model/metric/index.html
@@ -956,6 +956,15 @@
       
     
   
+
    • + +
  • + + + Mappings + + +
  • @@ -1015,6 +1024,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:metric
    nativehttps://w3id.org/monarch/monarch-py/:metric

    LinkML Source

    name: metric
diff --git a/docs/Data-Model/name/index.html b/docs/Data-Model/name/index.html
index 72c63d791..61dea44eb 100644
--- a/docs/Data-Model/name/index.html
+++ b/docs/Data-Model/name/index.html
@@ -965,6 +965,15 @@
       
     
   
+
    • + +
  • + + + Mappings + + +
  • @@ -1007,6 +1016,7 @@

    Inheritance

  • onset_qualifier_label
  • sex_qualifier_label
  • stage_qualifier_label
    • +
  • disease_context_qualifier_label
    • @@ -1021,13 +1031,8 @@

    Applicable Classes

    -Entity -Represents an Entity in the Monarch KG data model -no - - -Node -UI container class extending Entity with additional information +MultiEntityAssociationResults + no @@ -1036,8 +1041,13 @@

    Applicable Classes

    yes -MultiEntityAssociationResults - +Node +UI container class extending Entity with additional information +no + + +Entity +Represents an Entity in the Monarch KG data model no @@ -1051,6 +1061,25 @@

    Schema Source

    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:name
    nativehttps://w3id.org/monarch/monarch-py/:name

    LinkML Source

    name: name
diff --git a/docs/Data-Model/namespace/index.html b/docs/Data-Model/namespace/index.html
index 033d58c67..6dd99bd71 100644
--- a/docs/Data-Model/namespace/index.html
+++ b/docs/Data-Model/namespace/index.html
@@ -956,6 +956,15 @@
       
     
   
+
+      
+        
  • 
+  
+    
+      Mappings
+    
+  
+  
 
    • 
       
         
  • 
@@ -1001,8 +1010,8 @@ 
    Applicable Classes
    
 
 
 
-Entity
-Represents an Entity in the Monarch KG data model
+SearchResult
+
 no
 
 
@@ -1011,8 +1020,8 @@ 
    Applicable Classes
    
 no
 
 
-SearchResult
-
+Entity
+Represents an Entity in the Monarch KG data model
 no
 
 
@@ -1026,6 +1035,25 @@ 
    Schema Source
    
 
+
    Mappings
    
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
    Mapping TypeMapped Value
    selfhttps://w3id.org/monarch/monarch-py/:namespace
    nativehttps://w3id.org/monarch/monarch-py/:namespace
    
 
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index a8e944352..476acd4fe 100644
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diff --git a/docs/search/search_index.json b/docs/search/search_index.json
index bbde40800..714d1a4c2 100644
--- a/docs/search/search_index.json
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    monarch-py is a Python library for interacting with and querying the Monarch knowledge graph, with implementations for Solr and SQLite backends.
     
    This means the same API methods can be used regardless of the implementation.
     
    This library provides a collection of interfaces for graph operations such as retrieving entities and browsing associations.
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    Requires Python 3.8 or higher
     
    This library is available via pip or pipx:
     
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    Full usage instructions here
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    $ monarch sql entity MONDO:0012933\n{\n    \"id\": \"MONDO:0012933\",\n    \"category\": [\n        \"biolink:Disease\"\n    ],\n    \"name\": \"breast-ovarian cancer, familial, susceptibility to, 2\",\n    \"description\": \"Any hereditary breast ovarian cancer syndrome in which the cause of the disease is a mutation in the BRCA2 gene.\",\n    \"xref\": [],\n    \"provided_by\": \"phenio_nodes\",\n    \"in_taxon\": null,\n    \"source\": null,\n    \"symbol\": null,\n    \"type\": null,\n    \"synonym\": []\n}\n$ monarch associations --subject MONDO:0012933 --limit 5\n{\n    \"limit\": 5,\n    \"offset\": 0,\n    \"total\": 5,\n    \"associations\": [\n        ... # List of Associations\n    ]\n}\n
    "},{"location":"#basic-example-as-a-module","title":"Basic Example - As a Module","text":"
    >>> from monarch_py.implementations.solr.solr_implementation import SolrImplementation\n>>> si = SolrImplementation()\n>>> entity = si.get_entity(\"MONDO:0007947\")\n>>> print(entity.name)\n\"Marfan syndrome\"\n\n>>> response = si.get_associations(predicate=\"biolink:has_phenotype\")\n>>> print(response.total > 600000)\nTrue\n>>> print(\"biolink:has_phenotype\" in response.associations[0].predicate)\nTrue\n
    "},{"location":"API-Reference/","title":"API Reference","text":"
    This section outlines the monarch-py API.  
     
    Here you can find detailed documentation and source code for its interfaces and implementations. 
    "},{"location":"API-Reference/#interfaces","title":"Interfaces","text":""},{"location":"API-Reference/#src.monarch_py.interfaces.entity_interface.EntityInterface","title":"EntityInterface","text":"
                   Bases: ABC
     
    Abstract interface for entities in the Monarch KG
    "},{"location":"API-Reference/#src.monarch_py.interfaces.entity_interface.EntityInterface.get_entity","title":"get_entity  abstractmethod","text":"
    Retrieve a specific entity by exact ID match, with optional extras
     
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     Name Type Description Default id str 
    id of the entity to search for.
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    Whether to get a count of associations for the entity. Defaults to False.
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    Whether to get the entity's heirarchy in the data model. Defaults to False.
     False 
    Raises:
     Type Description NotImplementedError 
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    Returns:
     Name Type Description Entity Entity 
    Dataclass representing results of an entity search.
    "},{"location":"API-Reference/#src.monarch_py.interfaces.association_interface.AssociationInterface","title":"AssociationInterface","text":"
                   Bases: ABC
     
    Abstract interface for associations in the Monarch KG
    "},{"location":"API-Reference/#src.monarch_py.interfaces.association_interface.AssociationInterface.get_associations","title":"get_associations  abstractmethod","text":"
    Retrieve paginated association records, with filter options
     
    Parameters:
     Name Type Description Default category str 
    Filter to only associations matching the specified category. Defaults to None.
     None predicate str 
    Filter to only associations matching the specified predicate. Defaults to None.
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    Filter to only associations matching the specified subject. Defaults to None.
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     None entity str 
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     None offset int 
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     0 limit int 
    Limit results to specified number. Defaults to 20.
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    Raises:
     Type Description NotImplementedError 
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    Returns:
     Type Description AssociationResults 
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    "},{"location":"API-Reference/#src.monarch_py.interfaces.search_interface.SearchInterface","title":"SearchInterface","text":"
                   Bases: ABC
     
    Abstract interface for searching the Monarch KG in a Lucene way
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    Parameters:
     Name Type Description Default q str 
    Query string to match against
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    Returns:
     Name Type Description SearchResults SearchResults 
    Dataclass representing results of a generic entity search.
    "},{"location":"API-Reference/#src.monarch_py.interfaces.search_interface.SearchInterface.get_association_counts","title":"get_association_counts","text":"
    Get counts of associations for a given entity Args:     entity (str): Entity to get association counts for Returns:     List[FacetValue]: List of FacetValue objects representing the counts of associations for the given entity
    "},{"location":"API-Reference/#src.monarch_py.interfaces.search_interface.SearchInterface.get_association_facets","title":"get_association_facets","text":"
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    Parameters:
     Name Type Description Default entity str 
    Entity to get associations for
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    Category of associations to return
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    Query string to match against
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     0 limit int 
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     5 
    Returns:
     Name Type Description AssociationResults AssociationTableResults 
    Dataclass representing results of an association search.
    "},{"location":"API-Reference/#src.monarch_py.interfaces.search_interface.SearchInterface.search","title":"search  abstractmethod","text":"
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                   Bases: EntityInterface, AssociationInterface, SearchInterface, GroundingInterface
     
    Implementation of Monarch Interfaces for Solr endpoint
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    Retrieve paginated association records, with filter options
     
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    Filter to only associations matching the specified predicates. Defaults to None.
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    Filter to only associations matching the specified subjects. Defaults to None.
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    Limit results to specified number. Defaults to 20.
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    Returns:
     Name Type Description AssociationResults Union[AssociationResults, CompactAssociation] 
    Dataclass representing results of an association search.
    "},{"location":"API-Reference/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_counterpart_entities","title":"get_counterpart_entities","text":"
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    The entity to get associations for
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    an entity ID occurring in the object. Defaults to None.
     None"},{"location":"API-Reference/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_entity","title":"get_entity","text":"
    Retrieve a specific entity by exact ID match, with optional extras
     
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     Name Type Description Default id str 
    id of the entity to search for.
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    Whether to include association counts and hierarchy in the response.
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    Returns:
     Name Type Description Entity Optional[Union[Node, Entity]] 
    Dataclass representing results of an entity search.
     Node Optional[Union[Node, Entity]] 
    Dataclass representing results of an entity search with extra=True.
    "},{"location":"API-Reference/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_histopheno","title":"get_histopheno","text":"
    Get histopheno counts for a given subject_closure
    "},{"location":"API-Reference/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_multi_entity_associations","title":"get_multi_entity_associations","text":"
    Get associations between multiple entities and counterparts of a given category
     
    Parameters:
     Name Type Description Default entity List[str] 
    List of entity IDs to get associations for
     required counterpart_category List[str] 
    List of categories of counterpart entity to get associations for. Defaults to None.
     None offset int 
    Result offset, for pagination. Defaults to 0.
     0 limit int 
    Limit results to specified number. Defaults to 20.
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     20"},{"location":"API-Reference/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.ground_entity","title":"ground_entity","text":"
    Grounds a single entity
     
    Parameters:
     Name Type Description Default text str 
    Text to ground
     required 
    Returns:
     Name Type Description Entity List[Entity] 
    Dataclass representing a single entity
    "},{"location":"API-Reference/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.search","title":"search","text":"
    Search for entities by label, with optional filters
     
    Parameters:
     Name Type Description Default q str 
    Query string. Defaults to \":\".
     '*:*' offset int 
    Result offset, for pagination. Defaults to 0.
     0 limit int 
    Limit results to specified number. Defaults to 20.
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     None facet_queries List[str] 
    List of queries to include facet counts for. Defaults to None.
     None filter_queries List[str] 
    List of queries to filter results by. Defaults to None.
     None sort str 
    Sort results by the specified field. Defaults to None.
     None 
    Returns:
     Name Type Description SearchResults SearchResults 
    Dataclass representing results of a search.
    "},{"location":"API-Reference/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.solr_is_available","title":"solr_is_available","text":"
    Check if the Solr instance is available
    "},{"location":"API-Reference/#src.monarch_py.implementations.sql.sql_implementation.SQLImplementation","title":"SQLImplementation  dataclass","text":"
                   Bases: EntityInterface, AssociationInterface
     
    Implementation of Monarch Interfaces for SQL endpoint
    "},{"location":"API-Reference/#src.monarch_py.implementations.sql.sql_implementation.SQLImplementation.get_associations","title":"get_associations","text":"
    Retrieve paginated association records, with filter options
     
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    Filter to only associations matching the specified category. Defaults to None.
     None predicate str 
    Filter to only associations matching the specified predicate. Defaults to None.
     None subject str 
    Filter to only associations matching the specified subject. Defaults to None.
     None object str 
    Filter to only associations matching the specified object. Defaults to None.
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    Filter to only associations with the specified term ID as an ancestor of the subject. Defaults to None.
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    Filter to only associations the specified term ID as an ancestor of the object. Defaults to None.
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    Filter to only associations where the specified entity is the subject or the object. Defaults to None.
     None association_type str 
    Filter to only associations matching the specified association label. Defaults to None.
     required compact bool 
    Whether to return compact or full association records. Defaults to False.
     False offset int 
    Result offset, for pagination. Defaults to 0.
     0 limit int 
    Limit results to specified number. Defaults to 20.
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    Returns:
     Name Type Description AssociationResults Union[AssociationResults, CompactAssociationResults] 
    Dataclass representing results of an association search.
    "},{"location":"API-Reference/#src.monarch_py.implementations.sql.sql_implementation.SQLImplementation.get_entity","title":"get_entity","text":"
    Retrieve a specific entity by exact ID match, writh optional extras
     
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     Name Type Description Default id str 
    id of the entity to search for.
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     required get_hierarchy bool 
    Whether to get the entity hierarchy. Defaults to False.
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    Returns:
     Name Type Description Entity Entity 
    Dataclass representing results of an entity search.
    "},{"location":"Data-Model/","title":"monarch-py","text":"
    Data models for the Monarch Initiative data access library
     
    URI: https://w3id.org/monarch/monarch-py
     
    Name: monarch-py
    "},{"location":"Data-Model/#classes","title":"Classes","text":"Class Description Association None DirectionalAssociation An association that gives it's direction relative to a specified entity AssociationCountList Container class for a list of association counts AssociationTypeMapping A data class to hold the necessary information to produce association type counts for given  entities with appropriate directional labels BestMatch None CompactAssociation None Entity Represents an Entity in the Monarch KG data model Node UI container class extending Entity with additional information SearchResult None ExpandedCurie A curie bundled along with its expanded url FacetField None FacetValue None AssociationCount None HistoBin None HistoPheno None Mapping A minimal class to hold a SSSOM mapping NodeHierarchy None PairwiseSimilarity Abstract grouping for representing individual pairwise similarities TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms Release A class to hold information about a release of the Monarch KG Results None AssociationResults None AssociationTableResults None CategoryGroupedAssociationResults None CompactAssociationResults None EntityResults None MappingResults SSSOM Mappings returned as a results collection MultiEntityAssociationResults None SearchResults None SemsimSearchResult None TermInfo None TextAnnotationResult None"},{"location":"Data-Model/#slots","title":"Slots","text":"Slot Description agent_type Describes the high-level category of agent who originally generated a  statem... aggregator_knowledge_source ancestor_id the most recent common ancestor of the two compared entities ancestor_information_content The IC of the object ancestor_label the name or label of the ancestor concept ancestor_source associated_categories association_counts average_score best_score category causal_gene A list of genes that are known to be causally associated with a disease causes_disease A list of diseases that are known to be causally associated with a gene cosine_similarity the dot product of two node embeddings divided by the product of their length... count count of documents counterpart_category The category of the counterpart entity in a given association,  eg deprecated A boolean flag indicating that an entity is no longer considered current or v... description dice_similarity direction The directionality of the association relative to a given entity for an assoc... end end position of the annotation evidence_count count of supporting documents, evidence codes, and sources supplying evidence external_links ExpandedCurie with id and url for xrefs facet_fields Collection of facet field responses with the field values and counts facet_queries Collection of facet query responses with the query string values and counts facet_values Collection of FacetValue label/value instances belonging to a FacetField frequency_qualifier frequency_qualifier_category The category of the frequency_qualifier entity frequency_qualifier_closure Field containing frequency_qualifier id and the ids of all of it's ancestors frequency_qualifier_closure_label Field containing frequency_qualifier name and the names of all of it's ancest... frequency_qualifier_label The name of the frequency_qualifier entity frequency_qualifier_namespace The namespace/prefix of the frequency_qualifier entity full_name The long form name of an entity graph_stats grouping_key A concatenation of fields used to group associations with the same essential/... has_count count of out of has_total representing a frequency has_evidence has_evidence_links List of ExpandedCuries with id and url for evidence has_percentage percentage, which may be calculated from has_count and has_total, as 100 * qu... has_phenotype A list of phenotype identifiers that are known to be associated with this ent... has_phenotype_closure A list of phenotype identifiers that are known to be associated with this ent... has_phenotype_closure_label A list of phenotype labels that are known to be associated with this entity e... has_phenotype_count A count of the number of phenotypes that are known to be associated with this... has_phenotype_label A list of phenotype labels that are known to be associated with this entity has_quotient quotient, which should be 1/100 of has_percentage has_total total, devided by has_count, representing a frequency highlight matching text snippet containing html tags id in_taxon The biolink taxon that the entity is in the closure of in_taxon_label The label of the biolink taxon that the entity is in the closure of information_content The IC is the negative log of the probability of the concept inheritance intersection_count iri items A collection of items, with the type to be overriden by slot_usage jaccard_similarity The number of concepts in the intersection divided by the number in the union kg knowledge_level Describes the level of knowledge expressed in a statement, based on the reaso... knowledge_source label limit number of items to return in a response mapping_justification mappings List of ExpandedCuries with id and url for mapped entities match_source match_source_label match_subsumer match_subsumer_label match_target the entity matches match_target_label metadata metric name namespace The namespace/prefix portion of this entity's identifier negated neo4j node_hierarchy object object_best_matches object_category The category of the object entity object_closure Field containing object id and the ids of all of it's ancestors object_closure_label Field containing object name and the names of all of it's ancestors object_id object_information_content The IC of the object object_label The name of the object entity object_namespace The namespace/prefix of the object entity object_source the source for the second entity object_taxon object_taxon_label object_termset offset offset into the total number of items onset_qualifier onset_qualifier_category The category of the onset_qualifier entity onset_qualifier_closure Field containing onset_qualifier id and the ids of all of it's ancestors onset_qualifier_closure_label Field containing onset_qualifier name and the names of all of it's ancestors onset_qualifier_label The name of the onset_qualifier entity onset_qualifier_namespace The namespace/prefix of the onset_qualifier entity original_object original_subject overlap_coefficient pathway phenodigm_score the geometric mean of the jaccard similarity and the information content predicate predicate_id primary_knowledge_source provided_by provided_by_link A link to the docs for the knowledge source that provided the node/edge publications publications_links List of ExpandedCuries with id and url for publications qc_report qualifier qualifier_category The category of the frequency_qualifier entity qualifier_closure Field containing frequency_qualifier id and the ids of all of it's ancestors qualifier_closure_label Field containing frequency_qualifier name and the names of all of it's ancest... qualifier_label The name of the frequency_qualifier entity qualifier_namespace The namespace/prefix of the frequency_qualifier entity qualifiers qualifiers_category The category of the frequency_qualifier entity qualifiers_closure Field containing frequency_qualifier id and the ids of all of it's ancestors qualifiers_closure_label Field containing frequency_qualifier name and the names of all of it's ancest... qualifiers_label The name of the frequency_qualifier entity qualifiers_namespace The namespace/prefix of the frequency_qualifier entity score sex_qualifier sex_qualifier_category The category of the sex_qualifier entity sex_qualifier_closure Field containing sex_qualifier id and the ids of all of it's ancestors sex_qualifier_closure_label Field containing sex_qualifier name and the names of all of it's ancestors sex_qualifier_label The name of the sex_qualifier entity sex_qualifier_namespace The namespace/prefix of the sex_qualifier entity similarity solr sqlite stage_qualifier stage_qualifier_category The category of the stage_qualifier entity stage_qualifier_closure Field containing stage_qualifier id and the ids of all of it's ancestors stage_qualifier_closure_label Field containing stage_qualifier name and the names of all of it's ancestors stage_qualifier_label The name of the stage_qualifier entity stage_qualifier_namespace The namespace/prefix of the stage_qualifier entity start start position of the annotation sub_classes subject subject_best_matches subject_category The category of the subject entity subject_closure Field containing subject id and the ids of all of it's ancestors subject_closure_label Field containing subject name and the names of all of it's ancestors subject_id subject_information_content The IC of the subject subject_label The name of the subject entity subject_namespace The namespace/prefix of the subject entity subject_source the source for the first entity subject_taxon subject_taxon_label subject_termset subsumed_by_score subsumes_score super_classes symbol symmetric Whether the association type is symmetric, i synonym text text without tokens tokens A collection of entities or concepts total total number of items matching a query union_count uri The URI of the entity url version xref"},{"location":"Data-Model/#enumerations","title":"Enumerations","text":"Enumeration Description AssociationDirectionEnum The directionality of an association as it relates to a specified entity, wit..."},{"location":"Data-Model/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer ItemCount Jsonpath A string encoding a JSON Path Jsonpointer A string encoding a JSON Pointer Ncname Prefix part of CURIE NegativeLogValue Nodeidentifier A URI, CURIE or BNODE that represents a node in a model NonNegativeFloat Objectidentifier A URI or CURIE that represents an object in the model Sparqlpath A string encoding a SPARQL Property Path String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE ZeroToOne"},{"location":"Data-Model/#subsets","title":"Subsets","text":"Subset Description"},{"location":"Data-Model/Association/","title":"Class: Association","text":"
    URI: https://w3id.org/monarch/monarch-py/:Association
     
     classDiagram\n    class Association\n    click Association href \"../Association\"\n      Association <|-- DirectionalAssociation\n        click DirectionalAssociation href \"../DirectionalAssociation\"\n\n      Association : agent_type\n\n      Association : aggregator_knowledge_source\n\n      Association : category\n\n      Association : evidence_count\n\n      Association : frequency_qualifier\n\n      Association : frequency_qualifier_category\n\n      Association : frequency_qualifier_closure\n\n      Association : frequency_qualifier_closure_label\n\n      Association : frequency_qualifier_label\n\n      Association : frequency_qualifier_namespace\n\n      Association : grouping_key\n\n      Association : has_count\n\n      Association : has_evidence\n\n      Association : has_evidence_links\n\n\n\n\n    Association --> \"*\" ExpandedCurie : has_evidence_links\n    click ExpandedCurie href \"../ExpandedCurie\"\n\n\n      Association : has_percentage\n\n      Association : has_quotient\n\n      Association : has_total\n\n      Association : id\n\n      Association : knowledge_level\n\n      Association : negated\n\n      Association : object\n\n      Association : object_category\n\n      Association : object_closure\n\n      Association : object_closure_label\n\n      Association : object_label\n\n      Association : object_namespace\n\n      Association : object_taxon\n\n      Association : object_taxon_label\n\n      Association : onset_qualifier\n\n      Association : onset_qualifier_category\n\n      Association : onset_qualifier_closure\n\n      Association : onset_qualifier_closure_label\n\n      Association : onset_qualifier_label\n\n      Association : onset_qualifier_namespace\n\n      Association : original_object\n\n      Association : original_subject\n\n      Association : pathway\n\n      Association : predicate\n\n      Association : primary_knowledge_source\n\n      Association : provided_by\n\n      Association : provided_by_link\n\n\n\n\n    Association --> \"0..1\" ExpandedCurie : provided_by_link\n    click ExpandedCurie href \"../ExpandedCurie\"\n\n\n      Association : publications\n\n      Association : publications_links\n\n\n\n\n    Association --> \"*\" ExpandedCurie : publications_links\n    click ExpandedCurie href \"../ExpandedCurie\"\n\n\n      Association : qualifier\n\n      Association : qualifier_category\n\n      Association : qualifier_closure\n\n      Association : qualifier_closure_label\n\n      Association : qualifier_label\n\n      Association : qualifier_namespace\n\n      Association : qualifiers\n\n      Association : qualifiers_category\n\n      Association : qualifiers_closure\n\n      Association : qualifiers_closure_label\n\n      Association : qualifiers_label\n\n      Association : qualifiers_namespace\n\n      Association : sex_qualifier\n\n      Association : sex_qualifier_category\n\n      Association : sex_qualifier_closure\n\n      Association : sex_qualifier_closure_label\n\n      Association : sex_qualifier_label\n\n      Association : sex_qualifier_namespace\n\n      Association : stage_qualifier\n\n      Association : stage_qualifier_category\n\n      Association : stage_qualifier_closure\n\n      Association : stage_qualifier_closure_label\n\n      Association : stage_qualifier_label\n\n      Association : stage_qualifier_namespace\n\n      Association : subject\n\n      Association : subject_category\n\n      Association : subject_closure\n\n      Association : subject_closure_label\n\n      Association : subject_label\n\n      Association : subject_namespace\n\n      Association : subject_taxon\n\n      Association : subject_taxon_label\n
    "},{"location":"Data-Model/Association/#inheritance","title":"Inheritance","text":"
       
    • Association
         
      • DirectionalAssociation
        •  
       
      •  
    "},{"location":"Data-Model/Association/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1  String direct category 0..1  String direct subject 1  String direct original_subject 0..1  String direct subject_namespace 0..1  String The namespace/prefix of the subject entity direct subject_category 0..1  String The category of the subject entity direct subject_closure *  String Field containing subject id and the ids of all of it's ancestors direct subject_label 0..1  String The name of the subject entity direct subject_closure_label *  String Field containing subject name and the names of all of it's ancestors direct subject_taxon 0..1  String direct subject_taxon_label 0..1  String direct predicate 1  String direct object 1  String direct original_object 0..1  String direct object_namespace 0..1  String The namespace/prefix of the object entity direct object_category 0..1  String The category of the object entity direct object_closure *  String Field containing object id and the ids of all of it's ancestors direct object_label 0..1  String The name of the object entity direct object_closure_label *  String Field containing object name and the names of all of it's ancestors direct object_taxon 0..1  String direct object_taxon_label 0..1  String direct primary_knowledge_source 0..1  String direct aggregator_knowledge_source *  String direct negated 0..1  Boolean direct pathway 0..1  String direct evidence_count 0..1  Integer count of supporting documents, evidence codes, and sources supplying evidence direct knowledge_level 1  String Describes the level of knowledge expressed in a statement, based on the reaso... direct agent_type 1  String Describes the high-level category of agent who originally generated a  statem... direct has_evidence *  String direct has_evidence_links *  ExpandedCurie List of ExpandedCuries with id and url for evidence direct has_count 0..1  Integer count of out of has_total representing a frequency direct has_total 0..1  Integer total, devided by has_count, representing a frequency direct has_percentage 0..1  Float percentage, which may be calculated from has_count and has_total, as 100 * qu... direct has_quotient 0..1  Float quotient, which should be 1/100 of has_percentage direct grouping_key 0..1  String A concatenation of fields used to group associations with the same essential/... direct provided_by 0..1  String direct provided_by_link 0..1  ExpandedCurie A link to the docs for the knowledge source that provided the node/edge direct publications *  String direct publications_links *  ExpandedCurie List of ExpandedCuries with id and url for publications direct frequency_qualifier 0..1  String direct onset_qualifier 0..1  String direct sex_qualifier 0..1  String direct stage_qualifier 0..1  String direct qualifiers *  String direct qualifiers_label 0..1  String The name of the frequency_qualifier entity direct qualifiers_namespace 0..1  String The namespace/prefix of the frequency_qualifier entity direct qualifiers_category 0..1  String The category of the frequency_qualifier entity direct qualifiers_closure *  String Field containing frequency_qualifier id and the ids of all of it's ancestors direct qualifiers_closure_label *  String Field containing frequency_qualifier name and the names of all of it's ancest... direct qualifier *  String direct qualifier_label 0..1  String The name of the frequency_qualifier entity direct qualifier_namespace 0..1  String The namespace/prefix of the frequency_qualifier entity direct qualifier_category 0..1  String The category of the frequency_qualifier entity direct qualifier_closure *  String Field containing frequency_qualifier id and the ids of all of it's ancestors direct qualifier_closure_label *  String Field containing frequency_qualifier name and the names of all of it's ancest... direct frequency_qualifier_label 0..1  String The name of the frequency_qualifier entity direct frequency_qualifier_namespace 0..1  String The namespace/prefix of the frequency_qualifier entity direct frequency_qualifier_category 0..1  String The category of the frequency_qualifier entity direct frequency_qualifier_closure *  String Field containing frequency_qualifier id and the ids of all of it's ancestors direct frequency_qualifier_closure_label *  String Field containing frequency_qualifier name and the names of all of it's ancest... direct onset_qualifier_label 0..1  String The name of the onset_qualifier entity direct onset_qualifier_namespace 0..1  String The namespace/prefix of the onset_qualifier entity direct onset_qualifier_category 0..1  String The category of the onset_qualifier entity direct onset_qualifier_closure *  String Field containing onset_qualifier id and the ids of all of it's ancestors direct onset_qualifier_closure_label *  String Field containing onset_qualifier name and the names of all of it's ancestors direct sex_qualifier_label 0..1  String The name of the sex_qualifier entity direct sex_qualifier_namespace 0..1  String The namespace/prefix of the sex_qualifier entity direct sex_qualifier_category 0..1  String The category of the sex_qualifier entity direct sex_qualifier_closure *  String Field containing sex_qualifier id and the ids of all of it's ancestors direct sex_qualifier_closure_label *  String Field containing sex_qualifier name and the names of all of it's ancestors direct stage_qualifier_label 0..1  String The name of the stage_qualifier entity direct stage_qualifier_namespace 0..1  String The namespace/prefix of the stage_qualifier entity direct stage_qualifier_category 0..1  String The category of the stage_qualifier entity direct stage_qualifier_closure *  String Field containing stage_qualifier id and the ids of all of it's ancestors direct stage_qualifier_closure_label *  String Field containing stage_qualifier name and the names of all of it's ancestors direct"},{"location":"Data-Model/Association/#usages","title":"Usages","text":"used by used in type used AssociationResults items range Association CategoryGroupedAssociationResults items range Association"},{"location":"Data-Model/Association/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Association/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Association/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:Association native https://w3id.org/monarch/monarch-py/:Association"},{"location":"Data-Model/Association/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/Association/#direct","title":"Direct","text":"
    name: Association\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- id\n- category\n- subject\n- original_subject\n- subject_namespace\n- subject_category\n- subject_closure\n- subject_label\n- subject_closure_label\n- subject_taxon\n- subject_taxon_label\n- predicate\n- object\n- original_object\n- object_namespace\n- object_category\n- object_closure\n- object_label\n- object_closure_label\n- object_taxon\n- object_taxon_label\n- primary_knowledge_source\n- aggregator_knowledge_source\n- negated\n- pathway\n- evidence_count\n- knowledge_level\n- agent_type\n- has_evidence\n- has_evidence_links\n- has_count\n- has_total\n- has_percentage\n- has_quotient\n- grouping_key\n- provided_by\n- provided_by_link\n- publications\n- publications_links\n- frequency_qualifier\n- onset_qualifier\n- sex_qualifier\n- stage_qualifier\n- qualifiers\n- qualifiers_label\n- qualifiers_namespace\n- qualifiers_category\n- qualifiers_closure\n- qualifiers_closure_label\n- qualifier\n- qualifier_label\n- qualifier_namespace\n- qualifier_category\n- qualifier_closure\n- qualifier_closure_label\n- frequency_qualifier_label\n- frequency_qualifier_namespace\n- frequency_qualifier_category\n- frequency_qualifier_closure\n- frequency_qualifier_closure_label\n- onset_qualifier_label\n- onset_qualifier_namespace\n- onset_qualifier_category\n- onset_qualifier_closure\n- onset_qualifier_closure_label\n- sex_qualifier_label\n- sex_qualifier_namespace\n- sex_qualifier_category\n- sex_qualifier_closure\n- sex_qualifier_closure_label\n- stage_qualifier_label\n- stage_qualifier_namespace\n- stage_qualifier_category\n- stage_qualifier_closure\n- stage_qualifier_closure_label\n
    "},{"location":"Data-Model/Association/#induced","title":"Induced","text":"
    name: Association\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  id:\n    name: id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Association\n    domain_of:\n    - Association\n    - ExpandedCurie\n    - Entity\n    - HistoPheno\n    - HistoBin\n    - Mapping\n    - MultiEntityAssociationResults\n    - TermInfo\n    range: string\n    required: true\n  category:\n    name: category\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: false\n    alias: category\n    owner: Association\n    domain_of:\n    - Association\n    - AssociationCount\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Entity\n    range: string\n  subject:\n    name: subject\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: subject\n    owner: Association\n    domain_of:\n    - Association\n    - CompactAssociation\n    - SemsimSearchResult\n    range: string\n    required: true\n  original_subject:\n    name: original_subject\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: original_subject\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  subject_namespace:\n    name: subject_namespace\n    description: The namespace/prefix of the subject entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: subject_namespace\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  subject_category:\n    name: subject_category\n    description: The category of the subject entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: subject_category\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  subject_closure:\n    name: subject_closure\n    description: Field containing subject id and the ids of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: subject_closure\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  subject_label:\n    name: subject_label\n    description: The name of the subject entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: subject_label\n    owner: Association\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n  subject_closure_label:\n    name: subject_closure_label\n    description: Field containing subject name and the names of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: subject_closure_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  subject_taxon:\n    name: subject_taxon\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: in_taxon\n    alias: subject_taxon\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  subject_taxon_label:\n    name: subject_taxon_label\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: in_taxon_label\n    alias: subject_taxon_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: false\n    alias: predicate\n    owner: Association\n    domain_of:\n    - Association\n    - CompactAssociation\n    range: string\n    required: true\n  object:\n    name: object\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: object\n    owner: Association\n    domain_of:\n    - Association\n    - CompactAssociation\n    range: string\n    required: true\n  original_object:\n    name: original_object\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: original_object\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  object_namespace:\n    name: object_namespace\n    description: The namespace/prefix of the object entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: object_namespace\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  object_category:\n    name: object_category\n    description: The category of the object entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: object_category\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  object_closure:\n    name: object_closure\n    description: Field containing object id and the ids of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: object_closure\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  object_label:\n    name: object_label\n    description: The name of the object entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: object_label\n    owner: Association\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n  object_closure_label:\n    name: object_closure_label\n    description: Field containing object name and the names of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: object_closure_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  object_taxon:\n    name: object_taxon\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: in_taxon\n    alias: object_taxon\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  object_taxon_label:\n    name: object_taxon_label\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: in_taxon_label\n    alias: object_taxon_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  primary_knowledge_source:\n    name: primary_knowledge_source\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: primary_knowledge_source\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  aggregator_knowledge_source:\n    name: aggregator_knowledge_source\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: aggregator_knowledge_source\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  negated:\n    name: negated\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: negated\n    owner: Association\n    domain_of:\n    - Association\n    - CompactAssociation\n    range: boolean\n  pathway:\n    name: pathway\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: pathway\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  evidence_count:\n    name: evidence_count\n    description: count of supporting documents, evidence codes, and sources supplying\n      evidence\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: evidence_count\n    owner: Association\n    domain_of:\n    - Association\n    range: integer\n  knowledge_level:\n    name: knowledge_level\n    description: Describes the level of knowledge expressed in a statement, based\n      on the reasoning or analysis methods used to generate the statement, or the\n      scope or specificity of what the statement expresses to be true.\n    notes:\n    - The range in this schema is represented as a string, but is constrained  to\n      values from biolink:KnowledgeLevelEnum at ingest time\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    slot_uri: biolink:knowledge_level\n    multivalued: false\n    alias: knowledge_level\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n    required: true\n  agent_type:\n    name: agent_type\n    description: Describes the high-level category of agent who originally generated\n      a  statement of knowledge or other type of information.\n    notes:\n    - The range in this schema is represented as a string, but is constrained  to\n      values from biolink:AgentTypeEnum at ingest time\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    slot_uri: biolink:agent_type\n    multivalued: false\n    alias: agent_type\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n    required: true\n  has_evidence:\n    name: has_evidence\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: has_evidence\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  has_evidence_links:\n    name: has_evidence_links\n    description: List of ExpandedCuries with id and url for evidence\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: has_evidence_links\n    owner: Association\n    domain_of:\n    - Association\n    range: ExpandedCurie\n    inlined: true\n    inlined_as_list: true\n  has_count:\n    name: has_count\n    description: count of out of has_total representing a frequency\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_count\n    owner: Association\n    domain_of:\n    - Association\n    range: integer\n  has_total:\n    name: has_total\n    description: total, devided by has_count, representing a frequency\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_total\n    owner: Association\n    domain_of:\n    - Association\n    range: integer\n  has_percentage:\n    name: has_percentage\n    description: percentage, which may be calculated from has_count and has_total,\n      as 100 * quotient or provided directly, rounded to the integer level\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_percentage\n    owner: Association\n    domain_of:\n    - Association\n    range: float\n  has_quotient:\n    name: has_quotient\n    description: quotient, which should be 1/100 of has_percentage\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_quotient\n    owner: Association\n    domain_of:\n    - Association\n    range: float\n  grouping_key:\n    name: grouping_key\n    description: A concatenation of fields used to group associations with the same\n      essential/defining properties\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: grouping_key\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  provided_by:\n    name: provided_by\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: provided_by\n    owner: Association\n    domain_of:\n    - Association\n    - Entity\n    range: string\n  provided_by_link:\n    name: provided_by_link\n    description: A link to the docs for the knowledge source that provided the node/edge.\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: provided_by_link\n    owner: Association\n    domain_of:\n    - Association\n    - Node\n    range: ExpandedCurie\n    inlined: true\n  publications:\n    name: publications\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: publications\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  publications_links:\n    name: publications_links\n    description: List of ExpandedCuries with id and url for publications\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: publications_links\n    owner: Association\n    domain_of:\n    - Association\n    range: ExpandedCurie\n    inlined: true\n    inlined_as_list: true\n  frequency_qualifier:\n    name: frequency_qualifier\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: frequency_qualifier\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  onset_qualifier:\n    name: onset_qualifier\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: onset_qualifier\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  sex_qualifier:\n    name: sex_qualifier\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: sex_qualifier\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  stage_qualifier:\n    name: stage_qualifier\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: stage_qualifier\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  qualifiers:\n    name: qualifiers\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: qualifiers\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  qualifiers_label:\n    name: qualifiers_label\n    description: The name of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: qualifiers_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  qualifiers_namespace:\n    name: qualifiers_namespace\n    description: The namespace/prefix of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: qualifiers_namespace\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  qualifiers_category:\n    name: qualifiers_category\n    description: The category of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: qualifiers_category\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  qualifiers_closure:\n    name: qualifiers_closure\n    description: Field containing frequency_qualifier id and the ids of all of it's\n      ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: qualifiers_closure\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  qualifiers_closure_label:\n    name: qualifiers_closure_label\n    description: Field containing frequency_qualifier name and the names of all of\n      it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: qualifiers_closure_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  qualifier:\n    name: qualifier\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: qualifier\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  qualifier_label:\n    name: qualifier_label\n    description: The name of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: qualifier_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  qualifier_namespace:\n    name: qualifier_namespace\n    description: The namespace/prefix of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: qualifier_namespace\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  qualifier_category:\n    name: qualifier_category\n    description: The category of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: qualifier_category\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  qualifier_closure:\n    name: qualifier_closure\n    description: Field containing frequency_qualifier id and the ids of all of it's\n      ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: qualifier_closure\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  qualifier_closure_label:\n    name: qualifier_closure_label\n    description: Field containing frequency_qualifier name and the names of all of\n      it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: qualifier_closure_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  frequency_qualifier_label:\n    name: frequency_qualifier_label\n    description: The name of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: frequency_qualifier_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  frequency_qualifier_namespace:\n    name: frequency_qualifier_namespace\n    description: The namespace/prefix of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: frequency_qualifier_namespace\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  frequency_qualifier_category:\n    name: frequency_qualifier_category\n    description: The category of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: frequency_qualifier_category\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  frequency_qualifier_closure:\n    name: frequency_qualifier_closure\n    description: Field containing frequency_qualifier id and the ids of all of it's\n      ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: frequency_qualifier_closure\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  frequency_qualifier_closure_label:\n    name: frequency_qualifier_closure_label\n    description: Field containing frequency_qualifier name and the names of all of\n      it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: frequency_qualifier_closure_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  onset_qualifier_label:\n    name: onset_qualifier_label\n    description: The name of the onset_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: onset_qualifier_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  onset_qualifier_namespace:\n    name: onset_qualifier_namespace\n    description: The namespace/prefix of the onset_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: onset_qualifier_namespace\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  onset_qualifier_category:\n    name: onset_qualifier_category\n    description: The category of the onset_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: onset_qualifier_category\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  onset_qualifier_closure:\n    name: onset_qualifier_closure\n    description: Field containing onset_qualifier id and the ids of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: onset_qualifier_closure\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  onset_qualifier_closure_label:\n    name: onset_qualifier_closure_label\n    description: Field containing onset_qualifier name and the names of all of it's\n      ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: onset_qualifier_closure_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  sex_qualifier_label:\n    name: sex_qualifier_label\n    description: The name of the sex_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: sex_qualifier_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  sex_qualifier_namespace:\n    name: sex_qualifier_namespace\n    description: The namespace/prefix of the sex_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: sex_qualifier_namespace\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  sex_qualifier_category:\n    name: sex_qualifier_category\n    description: The category of the sex_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: sex_qualifier_category\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  sex_qualifier_closure:\n    name: sex_qualifier_closure\n    description: Field containing sex_qualifier id and the ids of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: sex_qualifier_closure\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  sex_qualifier_closure_label:\n    name: sex_qualifier_closure_label\n    description: Field containing sex_qualifier name and the names of all of it's\n      ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: sex_qualifier_closure_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  stage_qualifier_label:\n    name: stage_qualifier_label\n    description: The name of the stage_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: stage_qualifier_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  stage_qualifier_namespace:\n    name: stage_qualifier_namespace\n    description: The namespace/prefix of the stage_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: stage_qualifier_namespace\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  stage_qualifier_category:\n    name: stage_qualifier_category\n    description: The category of the stage_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: stage_qualifier_category\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  stage_qualifier_closure:\n    name: stage_qualifier_closure\n    description: Field containing stage_qualifier id and the ids of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: stage_qualifier_closure\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  stage_qualifier_closure_label:\n    name: stage_qualifier_closure_label\n    description: Field containing stage_qualifier name and the names of all of it's\n      ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: stage_qualifier_closure_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n
    "},{"location":"Data-Model/AssociationCount/","title":"Class: AssociationCount","text":"
    URI: https://w3id.org/monarch/monarch-py/:AssociationCount
     
     classDiagram\n    class AssociationCount\n    click AssociationCount href \"../AssociationCount\"\n      FacetValue <|-- AssociationCount\n        click FacetValue href \"../FacetValue\"\n\n      AssociationCount : category\n\n      AssociationCount : count\n\n      AssociationCount : label\n
    "},{"location":"Data-Model/AssociationCount/#inheritance","title":"Inheritance","text":"
       
    • FacetValue
         
      • AssociationCount
        •  
       
      •  
    "},{"location":"Data-Model/AssociationCount/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance category 0..1  String direct label 1  String FacetValue count 0..1  Integer count of documents FacetValue"},{"location":"Data-Model/AssociationCount/#usages","title":"Usages","text":"used by used in type used AssociationCountList items range AssociationCount Node association_counts range AssociationCount"},{"location":"Data-Model/AssociationCount/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/AssociationCount/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/AssociationCount/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:AssociationCount native https://w3id.org/monarch/monarch-py/:AssociationCount"},{"location":"Data-Model/AssociationCount/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/AssociationCount/#direct","title":"Direct","text":"
    name: AssociationCount\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: FacetValue\nslots:\n- category\nslot_usage:\n  category:\n    name: category\n    multivalued: false\n    domain_of:\n    - Association\n    - AssociationCount\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Entity\n
    "},{"location":"Data-Model/AssociationCount/#induced","title":"Induced","text":"
    name: AssociationCount\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: FacetValue\nslot_usage:\n  category:\n    name: category\n    multivalued: false\n    domain_of:\n    - Association\n    - AssociationCount\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Entity\nattributes:\n  category:\n    name: category\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: false\n    alias: category\n    owner: AssociationCount\n    domain_of:\n    - Association\n    - AssociationCount\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Entity\n    range: string\n  label:\n    name: label\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: label\n    owner: AssociationCount\n    domain_of:\n    - FacetValue\n    - FacetField\n    - TermInfo\n    range: string\n    required: true\n  count:\n    name: count\n    description: count of documents\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: count\n    owner: AssociationCount\n    domain_of:\n    - FacetValue\n    range: integer\n
    "},{"location":"Data-Model/AssociationCountList/","title":"Class: AssociationCountList","text":"
    Container class for a list of association counts
     
    URI: https://w3id.org/monarch/monarch-py/:AssociationCountList
     
     classDiagram\n    class AssociationCountList\n    click AssociationCountList href \"../AssociationCountList\"\n      AssociationCountList : items\n\n\n\n\n    AssociationCountList --> \"1..*\" AssociationCount : items\n    click AssociationCount href \"../AssociationCount\"\n
    "},{"location":"Data-Model/AssociationCountList/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance items 1..*  AssociationCount A collection of items, with the type to be overriden by slot_usage direct"},{"location":"Data-Model/AssociationCountList/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/AssociationCountList/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/AssociationCountList/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:AssociationCountList native https://w3id.org/monarch/monarch-py/:AssociationCountList"},{"location":"Data-Model/AssociationCountList/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/AssociationCountList/#direct","title":"Direct","text":"
    name: AssociationCountList\ndescription: Container class for a list of association counts\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- items\nslot_usage:\n  items:\n    name: items\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: AssociationCount\n
    "},{"location":"Data-Model/AssociationCountList/#induced","title":"Induced","text":"
    name: AssociationCountList\ndescription: Container class for a list of association counts\nfrom_schema: https://w3id.org/monarch/monarch-py\nslot_usage:\n  items:\n    name: items\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: AssociationCount\nattributes:\n  items:\n    name: items\n    description: A collection of items, with the type to be overriden by slot_usage\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: items\n    owner: AssociationCountList\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: AssociationCount\n    required: true\n    inlined: true\n    inlined_as_list: true\n
    "},{"location":"Data-Model/AssociationDirectionEnum/","title":"Enum: AssociationDirectionEnum","text":"
    The directionality of an association as it relates to a specified entity, with edges being categorized as incoming or outgoing
     
    URI: AssociationDirectionEnum
    "},{"location":"Data-Model/AssociationDirectionEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description incoming None An association for which a specified entity is the object or part of the obje... outgoing None An association for which a specified entity is the subject or part of the sub..."},{"location":"Data-Model/AssociationDirectionEnum/#slots","title":"Slots","text":"Name Description direction The directionality of the association relative to a given entity for an assoc..."},{"location":"Data-Model/AssociationDirectionEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/AssociationDirectionEnum/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/AssociationDirectionEnum/#linkml-source","title":"LinkML Source","text":"
    name: AssociationDirectionEnum\ndescription: The directionality of an association as it relates to a specified entity,\n  with edges being categorized as incoming or outgoing\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\npermissible_values:\n  incoming:\n    text: incoming\n    description: An association for which a specified entity is the object or part\n      of the object closure\n  outgoing:\n    text: outgoing\n    description: An association for which a specified entity is the subject or part\n      of the subject closure\n
    "},{"location":"Data-Model/AssociationResults/","title":"Class: AssociationResults","text":"
    URI: https://w3id.org/monarch/monarch-py/:AssociationResults
     
     classDiagram\n    class AssociationResults\n    click AssociationResults href \"../AssociationResults\"\n      Results <|-- AssociationResults\n        click Results href \"../Results\"\n\n      AssociationResults : items\n\n\n\n\n    AssociationResults --> \"1..*\" Association : items\n    click Association href \"../Association\"\n\n\n      AssociationResults : limit\n\n      AssociationResults : offset\n\n      AssociationResults : total\n
    "},{"location":"Data-Model/AssociationResults/#inheritance","title":"Inheritance","text":"
       
    • Results
         
      • AssociationResults
        •  
       
      •  
    "},{"location":"Data-Model/AssociationResults/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance items 1..*  Association A collection of items, with the type to be overriden by slot_usage direct limit 1  Integer number of items to return in a response Results offset 1  Integer offset into the total number of items Results total 1  Integer total number of items matching a query Results"},{"location":"Data-Model/AssociationResults/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/AssociationResults/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/AssociationResults/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:AssociationResults native https://w3id.org/monarch/monarch-py/:AssociationResults"},{"location":"Data-Model/AssociationResults/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/AssociationResults/#direct","title":"Direct","text":"
    name: AssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- items\nslot_usage:\n  items:\n    name: items\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: Association\n
    "},{"location":"Data-Model/AssociationResults/#induced","title":"Induced","text":"
    name: AssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n  items:\n    name: items\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: Association\nattributes:\n  items:\n    name: items\n    description: A collection of items, with the type to be overriden by slot_usage\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: items\n    owner: AssociationResults\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: Association\n    required: true\n    inlined: true\n    inlined_as_list: true\n  limit:\n    name: limit\n    description: number of items to return in a response\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: limit\n    owner: AssociationResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  offset:\n    name: offset\n    description: offset into the total number of items\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: offset\n    owner: AssociationResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  total:\n    name: total\n    description: total number of items matching a query\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: total\n    owner: AssociationResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n
    "},{"location":"Data-Model/AssociationTableResults/","title":"Class: AssociationTableResults","text":"
    URI: https://w3id.org/monarch/monarch-py/:AssociationTableResults
     
     classDiagram\n    class AssociationTableResults\n    click AssociationTableResults href \"../AssociationTableResults\"\n      Results <|-- AssociationTableResults\n        click Results href \"../Results\"\n\n      AssociationTableResults : items\n\n\n\n\n    AssociationTableResults --> \"1..*\" DirectionalAssociation : items\n    click DirectionalAssociation href \"../DirectionalAssociation\"\n\n\n      AssociationTableResults : limit\n\n      AssociationTableResults : offset\n\n      AssociationTableResults : total\n
    "},{"location":"Data-Model/AssociationTableResults/#inheritance","title":"Inheritance","text":"
       
    • Results
         
      • AssociationTableResults
        •  
       
      •  
    "},{"location":"Data-Model/AssociationTableResults/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance items 1..*  DirectionalAssociation A collection of items, with the type to be overriden by slot_usage direct limit 1  Integer number of items to return in a response Results offset 1  Integer offset into the total number of items Results total 1  Integer total number of items matching a query Results"},{"location":"Data-Model/AssociationTableResults/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/AssociationTableResults/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/AssociationTableResults/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:AssociationTableResults native https://w3id.org/monarch/monarch-py/:AssociationTableResults"},{"location":"Data-Model/AssociationTableResults/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/AssociationTableResults/#direct","title":"Direct","text":"
    name: AssociationTableResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- items\nslot_usage:\n  items:\n    name: items\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: DirectionalAssociation\n
    "},{"location":"Data-Model/AssociationTableResults/#induced","title":"Induced","text":"
    name: AssociationTableResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n  items:\n    name: items\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: DirectionalAssociation\nattributes:\n  items:\n    name: items\n    description: A collection of items, with the type to be overriden by slot_usage\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: items\n    owner: AssociationTableResults\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: DirectionalAssociation\n    required: true\n    inlined: true\n    inlined_as_list: true\n  limit:\n    name: limit\n    description: number of items to return in a response\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: limit\n    owner: AssociationTableResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  offset:\n    name: offset\n    description: offset into the total number of items\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: offset\n    owner: AssociationTableResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  total:\n    name: total\n    description: total number of items matching a query\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: total\n    owner: AssociationTableResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n
    "},{"location":"Data-Model/AssociationTypeMapping/","title":"Class: AssociationTypeMapping","text":"
    A data class to hold the necessary information to produce association type counts for given  entities with appropriate directional labels
     
    URI: https://w3id.org/monarch/monarch-py/:AssociationTypeMapping
     
     classDiagram\n    class AssociationTypeMapping\n    click AssociationTypeMapping href \"../AssociationTypeMapping\"\n      AssociationTypeMapping : category\n\n      AssociationTypeMapping : object_label\n\n      AssociationTypeMapping : subject_label\n\n      AssociationTypeMapping : symmetric\n
    "},{"location":"Data-Model/AssociationTypeMapping/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_label 0..1  String A label to describe the subjects of the association type as a whole for use i... direct object_label 0..1  String A label to describe the objects of the association type as a whole for use in... direct symmetric 1  Boolean Whether the association type is symmetric, meaning that the subject and objec... direct category 1  String The biolink category to use in queries for this association type direct"},{"location":"Data-Model/AssociationTypeMapping/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/AssociationTypeMapping/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/AssociationTypeMapping/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:AssociationTypeMapping native https://w3id.org/monarch/monarch-py/:AssociationTypeMapping"},{"location":"Data-Model/AssociationTypeMapping/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/AssociationTypeMapping/#direct","title":"Direct","text":"
    name: AssociationTypeMapping\ndescription: A data class to hold the necessary information to produce association\n  type counts for given  entities with appropriate directional labels\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- subject_label\n- object_label\n- symmetric\n- category\nslot_usage:\n  subject_label:\n    name: subject_label\n    description: A label to describe the subjects of the association type as a whole\n      for use in the UI\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n  object_label:\n    name: object_label\n    description: A label to describe the objects of the association type as a whole\n      for use in the UI\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n  symmetric:\n    name: symmetric\n    description: Whether the association type is symmetric, meaning that the subject\n      and object labels should be interchangeable\n    ifabsent: 'False'\n    domain_of:\n    - AssociationTypeMapping\n    required: true\n  category:\n    name: category\n    description: The biolink category to use in queries for this association type\n    multivalued: false\n    domain_of:\n    - Association\n    - AssociationCount\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Entity\n    required: true\n
    "},{"location":"Data-Model/AssociationTypeMapping/#induced","title":"Induced","text":"
    name: AssociationTypeMapping\ndescription: A data class to hold the necessary information to produce association\n  type counts for given  entities with appropriate directional labels\nfrom_schema: https://w3id.org/monarch/monarch-py\nslot_usage:\n  subject_label:\n    name: subject_label\n    description: A label to describe the subjects of the association type as a whole\n      for use in the UI\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n  object_label:\n    name: object_label\n    description: A label to describe the objects of the association type as a whole\n      for use in the UI\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n  symmetric:\n    name: symmetric\n    description: Whether the association type is symmetric, meaning that the subject\n      and object labels should be interchangeable\n    ifabsent: 'False'\n    domain_of:\n    - AssociationTypeMapping\n    required: true\n  category:\n    name: category\n    description: The biolink category to use in queries for this association type\n    multivalued: false\n    domain_of:\n    - Association\n    - AssociationCount\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Entity\n    required: true\nattributes:\n  subject_label:\n    name: subject_label\n    description: A label to describe the subjects of the association type as a whole\n      for use in the UI\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: subject_label\n    owner: AssociationTypeMapping\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n  object_label:\n    name: object_label\n    description: A label to describe the objects of the association type as a whole\n      for use in the UI\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: object_label\n    owner: AssociationTypeMapping\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n  symmetric:\n    name: symmetric\n    description: Whether the association type is symmetric, meaning that the subject\n      and object labels should be interchangeable\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    ifabsent: 'False'\n    alias: symmetric\n    owner: AssociationTypeMapping\n    domain_of:\n    - AssociationTypeMapping\n    range: boolean\n    required: true\n  category:\n    name: category\n    description: The biolink category to use in queries for this association type\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: false\n    alias: category\n    owner: AssociationTypeMapping\n    domain_of:\n    - Association\n    - AssociationCount\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Entity\n    range: string\n    required: true\n
    "},{"location":"Data-Model/BestMatch/","title":"Class: BestMatch","text":"
    URI: https://w3id.org/monarch/monarch-py/:BestMatch
     
     classDiagram\n    class BestMatch\n    click BestMatch href \"../BestMatch\"\n      BestMatch : match_source\n\n      BestMatch : match_source_label\n\n      BestMatch : match_subsumer\n\n      BestMatch : match_subsumer_label\n\n      BestMatch : match_target\n\n      BestMatch : match_target_label\n\n      BestMatch : score\n\n      BestMatch : similarity\n\n\n\n\n    BestMatch --> \"1\" TermPairwiseSimilarity : similarity\n    click TermPairwiseSimilarity href \"../TermPairwiseSimilarity\"\n
    "},{"location":"Data-Model/BestMatch/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance match_source 1  String direct match_source_label 0..1  String direct match_target 0..1  String the entity matches direct match_target_label 0..1  String direct score 1  Float direct match_subsumer 0..1  Uriorcurie direct match_subsumer_label 0..1  String direct similarity 1  TermPairwiseSimilarity direct"},{"location":"Data-Model/BestMatch/#usages","title":"Usages","text":"used by used in type used TermSetPairwiseSimilarity subject_best_matches range BestMatch TermSetPairwiseSimilarity object_best_matches range BestMatch"},{"location":"Data-Model/BestMatch/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/BestMatch/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/BestMatch/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:BestMatch native https://w3id.org/monarch/monarch-py/:BestMatch"},{"location":"Data-Model/BestMatch/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/BestMatch/#direct","title":"Direct","text":"
    name: BestMatch\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  match_source:\n    name: match_source\n    comments:\n    - note that the match_source is either the subject or the object\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    rank: 1000\n    identifier: true\n    domain_of:\n    - BestMatch\n    required: true\n  match_source_label:\n    name: match_source_label\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    rank: 1000\n    domain_of:\n    - BestMatch\n  match_target:\n    name: match_target\n    description: the entity matches\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    rank: 1000\n    domain_of:\n    - BestMatch\n  match_target_label:\n    name: match_target_label\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    rank: 1000\n    domain_of:\n    - BestMatch\n  score:\n    name: score\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    domain_of:\n    - SearchResult\n    - BestMatch\n    - SemsimSearchResult\n    range: float\n    required: true\n  match_subsumer:\n    name: match_subsumer\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    rank: 1000\n    domain_of:\n    - BestMatch\n    range: uriorcurie\n  match_subsumer_label:\n    name: match_subsumer_label\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    rank: 1000\n    domain_of:\n    - BestMatch\n  similarity:\n    name: similarity\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    domain_of:\n    - BestMatch\n    - SemsimSearchResult\n    range: TermPairwiseSimilarity\n    required: true\n
    "},{"location":"Data-Model/BestMatch/#induced","title":"Induced","text":"
    name: BestMatch\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  match_source:\n    name: match_source\n    comments:\n    - note that the match_source is either the subject or the object\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    rank: 1000\n    identifier: true\n    alias: match_source\n    owner: BestMatch\n    domain_of:\n    - BestMatch\n    range: string\n    required: true\n  match_source_label:\n    name: match_source_label\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    rank: 1000\n    alias: match_source_label\n    owner: BestMatch\n    domain_of:\n    - BestMatch\n    range: string\n  match_target:\n    name: match_target\n    description: the entity matches\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    rank: 1000\n    alias: match_target\n    owner: BestMatch\n    domain_of:\n    - BestMatch\n    range: string\n  match_target_label:\n    name: match_target_label\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    rank: 1000\n    alias: match_target_label\n    owner: BestMatch\n    domain_of:\n    - BestMatch\n    range: string\n  score:\n    name: score\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    alias: score\n    owner: BestMatch\n    domain_of:\n    - SearchResult\n    - BestMatch\n    - SemsimSearchResult\n    range: float\n    required: true\n  match_subsumer:\n    name: match_subsumer\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    rank: 1000\n    alias: match_subsumer\n    owner: BestMatch\n    domain_of:\n    - BestMatch\n    range: uriorcurie\n  match_subsumer_label:\n    name: match_subsumer_label\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    rank: 1000\n    alias: match_subsumer_label\n    owner: BestMatch\n    domain_of:\n    - BestMatch\n    range: string\n  similarity:\n    name: similarity\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    alias: similarity\n    owner: BestMatch\n    domain_of:\n    - BestMatch\n    - SemsimSearchResult\n    range: TermPairwiseSimilarity\n    required: true\n
    "},{"location":"Data-Model/Boolean/","title":"Type: Boolean","text":"
    A binary (true or false) value
     
    URI: xsd:boolean
     
       
    •  
      base: Bool
       
      •  
    •  
      uri: xsd:boolean
       
      •  
    •  
      repr: bool
       
      •  
    "},{"location":"Data-Model/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Boolean/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/CategoryGroupedAssociationResults/","title":"Class: CategoryGroupedAssociationResults","text":"
    URI: https://w3id.org/monarch/monarch-py/:CategoryGroupedAssociationResults
     
     classDiagram\n    class CategoryGroupedAssociationResults\n    click CategoryGroupedAssociationResults href \"../CategoryGroupedAssociationResults\"\n      Results <|-- CategoryGroupedAssociationResults\n        click Results href \"../Results\"\n\n      CategoryGroupedAssociationResults : counterpart_category\n\n      CategoryGroupedAssociationResults : items\n\n\n\n\n    CategoryGroupedAssociationResults --> \"1..*\" Association : items\n    click Association href \"../Association\"\n\n\n      CategoryGroupedAssociationResults : limit\n\n      CategoryGroupedAssociationResults : offset\n\n      CategoryGroupedAssociationResults : total\n
    "},{"location":"Data-Model/CategoryGroupedAssociationResults/#inheritance","title":"Inheritance","text":"
       
    • Results
         
      • CategoryGroupedAssociationResults
        •  
       
      •  
    "},{"location":"Data-Model/CategoryGroupedAssociationResults/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance counterpart_category 0..1  String The category of the counterpart entity in a given association,  eg direct items 1..*  Association A collection of items, with the type to be overriden by slot_usage direct limit 1  Integer number of items to return in a response Results offset 1  Integer offset into the total number of items Results total 1  Integer total number of items matching a query Results"},{"location":"Data-Model/CategoryGroupedAssociationResults/#usages","title":"Usages","text":"used by used in type used MultiEntityAssociationResults associated_categories range CategoryGroupedAssociationResults"},{"location":"Data-Model/CategoryGroupedAssociationResults/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/CategoryGroupedAssociationResults/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/CategoryGroupedAssociationResults/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:CategoryGroupedAssociationResults native https://w3id.org/monarch/monarch-py/:CategoryGroupedAssociationResults"},{"location":"Data-Model/CategoryGroupedAssociationResults/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/CategoryGroupedAssociationResults/#direct","title":"Direct","text":"
    name: CategoryGroupedAssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- counterpart_category\n- items\nslot_usage:\n  items:\n    name: items\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: Association\n
    "},{"location":"Data-Model/CategoryGroupedAssociationResults/#induced","title":"Induced","text":"
    name: CategoryGroupedAssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n  items:\n    name: items\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: Association\nattributes:\n  counterpart_category:\n    name: counterpart_category\n    description: The category of the counterpart entity in a given association,  eg.\n      the category of the entity that is not the subject\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: counterpart_category\n    owner: CategoryGroupedAssociationResults\n    domain_of:\n    - CategoryGroupedAssociationResults\n    range: string\n  items:\n    name: items\n    description: A collection of items, with the type to be overriden by slot_usage\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: items\n    owner: CategoryGroupedAssociationResults\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: Association\n    required: true\n    inlined: true\n    inlined_as_list: true\n  limit:\n    name: limit\n    description: number of items to return in a response\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: limit\n    owner: CategoryGroupedAssociationResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  offset:\n    name: offset\n    description: offset into the total number of items\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: offset\n    owner: CategoryGroupedAssociationResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  total:\n    name: total\n    description: total number of items matching a query\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: total\n    owner: CategoryGroupedAssociationResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n
    "},{"location":"Data-Model/CompactAssociation/","title":"Class: CompactAssociation","text":"
    URI: https://w3id.org/monarch/monarch-py/:CompactAssociation
     
     classDiagram\n    class CompactAssociation\n    click CompactAssociation href \"../CompactAssociation\"\n      CompactAssociation : category\n\n      CompactAssociation : negated\n\n      CompactAssociation : object\n\n      CompactAssociation : object_label\n\n      CompactAssociation : predicate\n\n      CompactAssociation : subject\n\n      CompactAssociation : subject_label\n
    "},{"location":"Data-Model/CompactAssociation/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance category 0..1  String direct subject 1  String direct subject_label 0..1  String The name of the subject entity direct predicate 1  String direct object 1  String direct object_label 0..1  String The name of the object entity direct negated 0..1  Boolean direct"},{"location":"Data-Model/CompactAssociation/#usages","title":"Usages","text":"used by used in type used CompactAssociationResults items range CompactAssociation"},{"location":"Data-Model/CompactAssociation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/CompactAssociation/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/CompactAssociation/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:CompactAssociation native https://w3id.org/monarch/monarch-py/:CompactAssociation"},{"location":"Data-Model/CompactAssociation/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/CompactAssociation/#direct","title":"Direct","text":"
    name: CompactAssociation\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- category\n- subject\n- subject_label\n- predicate\n- object\n- object_label\n- negated\n
    "},{"location":"Data-Model/CompactAssociation/#induced","title":"Induced","text":"
    name: CompactAssociation\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  category:\n    name: category\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: false\n    alias: category\n    owner: CompactAssociation\n    domain_of:\n    - Association\n    - AssociationCount\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Entity\n    range: string\n  subject:\n    name: subject\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: subject\n    owner: CompactAssociation\n    domain_of:\n    - Association\n    - CompactAssociation\n    - SemsimSearchResult\n    range: string\n    required: true\n  subject_label:\n    name: subject_label\n    description: The name of the subject entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: subject_label\n    owner: CompactAssociation\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: false\n    alias: predicate\n    owner: CompactAssociation\n    domain_of:\n    - Association\n    - CompactAssociation\n    range: string\n    required: true\n  object:\n    name: object\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: object\n    owner: CompactAssociation\n    domain_of:\n    - Association\n    - CompactAssociation\n    range: string\n    required: true\n  object_label:\n    name: object_label\n    description: The name of the object entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: object_label\n    owner: CompactAssociation\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n  negated:\n    name: negated\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: negated\n    owner: CompactAssociation\n    domain_of:\n    - Association\n    - CompactAssociation\n    range: boolean\n
    "},{"location":"Data-Model/CompactAssociationResults/","title":"Class: CompactAssociationResults","text":"
    URI: https://w3id.org/monarch/monarch-py/:CompactAssociationResults
     
     classDiagram\n    class CompactAssociationResults\n    click CompactAssociationResults href \"../CompactAssociationResults\"\n      Results <|-- CompactAssociationResults\n        click Results href \"../Results\"\n\n      CompactAssociationResults : items\n\n\n\n\n    CompactAssociationResults --> \"1..*\" CompactAssociation : items\n    click CompactAssociation href \"../CompactAssociation\"\n\n\n      CompactAssociationResults : limit\n\n      CompactAssociationResults : offset\n\n      CompactAssociationResults : total\n
    "},{"location":"Data-Model/CompactAssociationResults/#inheritance","title":"Inheritance","text":"
       
    • Results
         
      • CompactAssociationResults
        •  
       
      •  
    "},{"location":"Data-Model/CompactAssociationResults/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance items 1..*  CompactAssociation A collection of items, with the type to be overriden by slot_usage direct limit 1  Integer number of items to return in a response Results offset 1  Integer offset into the total number of items Results total 1  Integer total number of items matching a query Results"},{"location":"Data-Model/CompactAssociationResults/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/CompactAssociationResults/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/CompactAssociationResults/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:CompactAssociationResults native https://w3id.org/monarch/monarch-py/:CompactAssociationResults"},{"location":"Data-Model/CompactAssociationResults/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/CompactAssociationResults/#direct","title":"Direct","text":"
    name: CompactAssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- items\nslot_usage:\n  items:\n    name: items\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: CompactAssociation\n
    "},{"location":"Data-Model/CompactAssociationResults/#induced","title":"Induced","text":"
    name: CompactAssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n  items:\n    name: items\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: CompactAssociation\nattributes:\n  items:\n    name: items\n    description: A collection of items, with the type to be overriden by slot_usage\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: items\n    owner: CompactAssociationResults\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: CompactAssociation\n    required: true\n    inlined: true\n    inlined_as_list: true\n  limit:\n    name: limit\n    description: number of items to return in a response\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: limit\n    owner: CompactAssociationResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  offset:\n    name: offset\n    description: offset into the total number of items\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: offset\n    owner: CompactAssociationResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  total:\n    name: total\n    description: total number of items matching a query\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: total\n    owner: CompactAssociationResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n
    "},{"location":"Data-Model/Curie/","title":"Type: Curie","text":"
    a compact URI
     
    URI: xsd:string
     
       
    •  
      base: Curie
       
      •  
    •  
      uri: xsd:string
       
      •  
    •  
      repr: str
       
      •  
    "},{"location":"Data-Model/Curie/#comments","title":"Comments","text":"
       
    • in RDF serializations this MUST be expanded to a URI
      •  
    • in non-RDF serializations MAY be serialized as the compact representation
      •  
    "},{"location":"Data-Model/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Curie/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Date/","title":"Type: Date","text":"
    a date (year, month and day) in an idealized calendar
     
    URI: xsd:date
     
       
    •  
      base: XSDDate
       
      •  
    •  
      uri: xsd:date
       
      •  
    •  
      repr: str
       
      •  
    "},{"location":"Data-Model/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Date/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/DateOrDatetime/","title":"Type: DateOrDatetime","text":"
    Either a date or a datetime
     
    URI: linkml:DateOrDatetime
     
       
    •  
      base: str
       
      •  
    •  
      uri: linkml:DateOrDatetime
       
      •  
    •  
      repr: str
       
      •  
    "},{"location":"Data-Model/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/DateOrDatetime/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Datetime/","title":"Type: Datetime","text":"
    The combination of a date and time
     
    URI: xsd:dateTime
     
       
    •  
      base: XSDDateTime
       
      •  
    •  
      uri: xsd:dateTime
       
      •  
    •  
      repr: str
       
      •  
    "},{"location":"Data-Model/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Datetime/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Decimal/","title":"Type: Decimal","text":"
    A real number with arbitrary precision that conforms to the xsd:decimal specification
     
    URI: xsd:decimal
     
       
    •  
      base: Decimal
       
      •  
    •  
      uri: xsd:decimal
       
      •  
    "},{"location":"Data-Model/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Decimal/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/DirectionalAssociation/","title":"Class: DirectionalAssociation","text":"
    An association that gives it's direction relative to a specified entity
     
    URI: https://w3id.org/monarch/monarch-py/:DirectionalAssociation
     
     classDiagram\n    class DirectionalAssociation\n    click DirectionalAssociation href \"../DirectionalAssociation\"\n      Association <|-- DirectionalAssociation\n        click Association href \"../Association\"\n\n      DirectionalAssociation : agent_type\n\n      DirectionalAssociation : aggregator_knowledge_source\n\n      DirectionalAssociation : category\n\n      DirectionalAssociation : direction\n\n\n\n\n    DirectionalAssociation --> \"1\" AssociationDirectionEnum : direction\n    click AssociationDirectionEnum href \"../AssociationDirectionEnum\"\n\n\n      DirectionalAssociation : evidence_count\n\n      DirectionalAssociation : frequency_qualifier\n\n      DirectionalAssociation : frequency_qualifier_category\n\n      DirectionalAssociation : frequency_qualifier_closure\n\n      DirectionalAssociation : frequency_qualifier_closure_label\n\n      DirectionalAssociation : frequency_qualifier_label\n\n      DirectionalAssociation : frequency_qualifier_namespace\n\n      DirectionalAssociation : grouping_key\n\n      DirectionalAssociation : has_count\n\n      DirectionalAssociation : has_evidence\n\n      DirectionalAssociation : has_evidence_links\n\n\n\n\n    DirectionalAssociation --> \"*\" ExpandedCurie : has_evidence_links\n    click ExpandedCurie href \"../ExpandedCurie\"\n\n\n      DirectionalAssociation : has_percentage\n\n      DirectionalAssociation : has_quotient\n\n      DirectionalAssociation : has_total\n\n      DirectionalAssociation : id\n\n      DirectionalAssociation : knowledge_level\n\n      DirectionalAssociation : negated\n\n      DirectionalAssociation : object\n\n      DirectionalAssociation : object_category\n\n      DirectionalAssociation : object_closure\n\n      DirectionalAssociation : object_closure_label\n\n      DirectionalAssociation : object_label\n\n      DirectionalAssociation : object_namespace\n\n      DirectionalAssociation : object_taxon\n\n      DirectionalAssociation : object_taxon_label\n\n      DirectionalAssociation : onset_qualifier\n\n      DirectionalAssociation : onset_qualifier_category\n\n      DirectionalAssociation : onset_qualifier_closure\n\n      DirectionalAssociation : onset_qualifier_closure_label\n\n      DirectionalAssociation : onset_qualifier_label\n\n      DirectionalAssociation : onset_qualifier_namespace\n\n      DirectionalAssociation : original_object\n\n      DirectionalAssociation : original_subject\n\n      DirectionalAssociation : pathway\n\n      DirectionalAssociation : predicate\n\n      DirectionalAssociation : primary_knowledge_source\n\n      DirectionalAssociation : provided_by\n\n      DirectionalAssociation : provided_by_link\n\n\n\n\n    DirectionalAssociation --> \"0..1\" ExpandedCurie : provided_by_link\n    click ExpandedCurie href \"../ExpandedCurie\"\n\n\n      DirectionalAssociation : publications\n\n      DirectionalAssociation : publications_links\n\n\n\n\n    DirectionalAssociation --> \"*\" ExpandedCurie : publications_links\n    click ExpandedCurie href \"../ExpandedCurie\"\n\n\n      DirectionalAssociation : qualifier\n\n      DirectionalAssociation : qualifier_category\n\n      DirectionalAssociation : qualifier_closure\n\n      DirectionalAssociation : qualifier_closure_label\n\n      DirectionalAssociation : qualifier_label\n\n      DirectionalAssociation : qualifier_namespace\n\n      DirectionalAssociation : qualifiers\n\n      DirectionalAssociation : qualifiers_category\n\n      DirectionalAssociation : qualifiers_closure\n\n      DirectionalAssociation : qualifiers_closure_label\n\n      DirectionalAssociation : qualifiers_label\n\n      DirectionalAssociation : qualifiers_namespace\n\n      DirectionalAssociation : sex_qualifier\n\n      DirectionalAssociation : sex_qualifier_category\n\n      DirectionalAssociation : sex_qualifier_closure\n\n      DirectionalAssociation : sex_qualifier_closure_label\n\n      DirectionalAssociation : sex_qualifier_label\n\n      DirectionalAssociation : sex_qualifier_namespace\n\n      DirectionalAssociation : stage_qualifier\n\n      DirectionalAssociation : stage_qualifier_category\n\n      DirectionalAssociation : stage_qualifier_closure\n\n      DirectionalAssociation : stage_qualifier_closure_label\n\n      DirectionalAssociation : stage_qualifier_label\n\n      DirectionalAssociation : stage_qualifier_namespace\n\n      DirectionalAssociation : subject\n\n      DirectionalAssociation : subject_category\n\n      DirectionalAssociation : subject_closure\n\n      DirectionalAssociation : subject_closure_label\n\n      DirectionalAssociation : subject_label\n\n      DirectionalAssociation : subject_namespace\n\n      DirectionalAssociation : subject_taxon\n\n      DirectionalAssociation : subject_taxon_label\n
    "},{"location":"Data-Model/DirectionalAssociation/#inheritance","title":"Inheritance","text":"
       
    • Association
         
      • DirectionalAssociation
        •  
       
      •  
    "},{"location":"Data-Model/DirectionalAssociation/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance direction 1  AssociationDirectionEnum The directionality of the association relative to a given entity for an assoc... direct id 1  String Association category 0..1  String Association subject 1  String Association original_subject 0..1  String Association subject_namespace 0..1  String The namespace/prefix of the subject entity Association subject_category 0..1  String The category of the subject entity Association subject_closure *  String Field containing subject id and the ids of all of it's ancestors Association subject_label 0..1  String The name of the subject entity Association subject_closure_label *  String Field containing subject name and the names of all of it's ancestors Association subject_taxon 0..1  String Association subject_taxon_label 0..1  String Association predicate 1  String Association object 1  String Association original_object 0..1  String Association object_namespace 0..1  String The namespace/prefix of the object entity Association object_category 0..1  String The category of the object entity Association object_closure *  String Field containing object id and the ids of all of it's ancestors Association object_label 0..1  String The name of the object entity Association object_closure_label *  String Field containing object name and the names of all of it's ancestors Association object_taxon 0..1  String Association object_taxon_label 0..1  String Association primary_knowledge_source 0..1  String Association aggregator_knowledge_source *  String Association negated 0..1  Boolean Association pathway 0..1  String Association evidence_count 0..1  Integer count of supporting documents, evidence codes, and sources supplying evidence Association knowledge_level 1  String Describes the level of knowledge expressed in a statement, based on the reaso... Association agent_type 1  String Describes the high-level category of agent who originally generated a  statem... Association has_evidence *  String Association has_evidence_links *  ExpandedCurie List of ExpandedCuries with id and url for evidence Association has_count 0..1  Integer count of out of has_total representing a frequency Association has_total 0..1  Integer total, devided by has_count, representing a frequency Association has_percentage 0..1  Float percentage, which may be calculated from has_count and has_total, as 100 * qu... Association has_quotient 0..1  Float quotient, which should be 1/100 of has_percentage Association grouping_key 0..1  String A concatenation of fields used to group associations with the same essential/... Association provided_by 0..1  String Association provided_by_link 0..1  ExpandedCurie A link to the docs for the knowledge source that provided the node/edge Association publications *  String Association publications_links *  ExpandedCurie List of ExpandedCuries with id and url for publications Association frequency_qualifier 0..1  String Association onset_qualifier 0..1  String Association sex_qualifier 0..1  String Association stage_qualifier 0..1  String Association qualifiers *  String Association qualifiers_label 0..1  String The name of the frequency_qualifier entity Association qualifiers_namespace 0..1  String The namespace/prefix of the frequency_qualifier entity Association qualifiers_category 0..1  String The category of the frequency_qualifier entity Association qualifiers_closure *  String Field containing frequency_qualifier id and the ids of all of it's ancestors Association qualifiers_closure_label *  String Field containing frequency_qualifier name and the names of all of it's ancest... Association qualifier *  String Association qualifier_label 0..1  String The name of the frequency_qualifier entity Association qualifier_namespace 0..1  String The namespace/prefix of the frequency_qualifier entity Association qualifier_category 0..1  String The category of the frequency_qualifier entity Association qualifier_closure *  String Field containing frequency_qualifier id and the ids of all of it's ancestors Association qualifier_closure_label *  String Field containing frequency_qualifier name and the names of all of it's ancest... Association frequency_qualifier_label 0..1  String The name of the frequency_qualifier entity Association frequency_qualifier_namespace 0..1  String The namespace/prefix of the frequency_qualifier entity Association frequency_qualifier_category 0..1  String The category of the frequency_qualifier entity Association frequency_qualifier_closure *  String Field containing frequency_qualifier id and the ids of all of it's ancestors Association frequency_qualifier_closure_label *  String Field containing frequency_qualifier name and the names of all of it's ancest... Association onset_qualifier_label 0..1  String The name of the onset_qualifier entity Association onset_qualifier_namespace 0..1  String The namespace/prefix of the onset_qualifier entity Association onset_qualifier_category 0..1  String The category of the onset_qualifier entity Association onset_qualifier_closure *  String Field containing onset_qualifier id and the ids of all of it's ancestors Association onset_qualifier_closure_label *  String Field containing onset_qualifier name and the names of all of it's ancestors Association sex_qualifier_label 0..1  String The name of the sex_qualifier entity Association sex_qualifier_namespace 0..1  String The namespace/prefix of the sex_qualifier entity Association sex_qualifier_category 0..1  String The category of the sex_qualifier entity Association sex_qualifier_closure *  String Field containing sex_qualifier id and the ids of all of it's ancestors Association sex_qualifier_closure_label *  String Field containing sex_qualifier name and the names of all of it's ancestors Association stage_qualifier_label 0..1  String The name of the stage_qualifier entity Association stage_qualifier_namespace 0..1  String The namespace/prefix of the stage_qualifier entity Association stage_qualifier_category 0..1  String The category of the stage_qualifier entity Association stage_qualifier_closure *  String Field containing stage_qualifier id and the ids of all of it's ancestors Association stage_qualifier_closure_label *  String Field containing stage_qualifier name and the names of all of it's ancestors Association"},{"location":"Data-Model/DirectionalAssociation/#usages","title":"Usages","text":"used by used in type used AssociationTableResults items range DirectionalAssociation"},{"location":"Data-Model/DirectionalAssociation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/DirectionalAssociation/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/DirectionalAssociation/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:DirectionalAssociation native https://w3id.org/monarch/monarch-py/:DirectionalAssociation"},{"location":"Data-Model/DirectionalAssociation/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/DirectionalAssociation/#direct","title":"Direct","text":"
    name: DirectionalAssociation\ndescription: An association that gives it's direction relative to a specified entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Association\nslots:\n- direction\n
    "},{"location":"Data-Model/DirectionalAssociation/#induced","title":"Induced","text":"
    name: DirectionalAssociation\ndescription: An association that gives it's direction relative to a specified entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Association\nattributes:\n  direction:\n    name: direction\n    description: The directionality of the association relative to a given entity\n      for an association_count. If the entity is the subject or in the subject closure,\n      the direction is forwards, if it is the object or in the object closure, the\n      direction is backwards.\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: direction\n    owner: DirectionalAssociation\n    domain_of:\n    - DirectionalAssociation\n    range: AssociationDirectionEnum\n    required: true\n  id:\n    name: id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    - ExpandedCurie\n    - Entity\n    - HistoPheno\n    - HistoBin\n    - Mapping\n    - MultiEntityAssociationResults\n    - TermInfo\n    range: string\n    required: true\n  category:\n    name: category\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: false\n    alias: category\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    - AssociationCount\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Entity\n    range: string\n  subject:\n    name: subject\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: subject\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    - CompactAssociation\n    - SemsimSearchResult\n    range: string\n    required: true\n  original_subject:\n    name: original_subject\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: original_subject\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  subject_namespace:\n    name: subject_namespace\n    description: The namespace/prefix of the subject entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: subject_namespace\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  subject_category:\n    name: subject_category\n    description: The category of the subject entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: subject_category\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  subject_closure:\n    name: subject_closure\n    description: Field containing subject id and the ids of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: subject_closure\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  subject_label:\n    name: subject_label\n    description: The name of the subject entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: subject_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n  subject_closure_label:\n    name: subject_closure_label\n    description: Field containing subject name and the names of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: subject_closure_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  subject_taxon:\n    name: subject_taxon\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: in_taxon\n    alias: subject_taxon\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  subject_taxon_label:\n    name: subject_taxon_label\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: in_taxon_label\n    alias: subject_taxon_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: false\n    alias: predicate\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    - CompactAssociation\n    range: string\n    required: true\n  object:\n    name: object\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: object\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    - CompactAssociation\n    range: string\n    required: true\n  original_object:\n    name: original_object\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: original_object\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  object_namespace:\n    name: object_namespace\n    description: The namespace/prefix of the object entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: object_namespace\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  object_category:\n    name: object_category\n    description: The category of the object entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: object_category\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  object_closure:\n    name: object_closure\n    description: Field containing object id and the ids of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: object_closure\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  object_label:\n    name: object_label\n    description: The name of the object entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: object_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n  object_closure_label:\n    name: object_closure_label\n    description: Field containing object name and the names of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: object_closure_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  object_taxon:\n    name: object_taxon\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: in_taxon\n    alias: object_taxon\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  object_taxon_label:\n    name: object_taxon_label\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: in_taxon_label\n    alias: object_taxon_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  primary_knowledge_source:\n    name: primary_knowledge_source\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: primary_knowledge_source\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  aggregator_knowledge_source:\n    name: aggregator_knowledge_source\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: aggregator_knowledge_source\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  negated:\n    name: negated\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: negated\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    - CompactAssociation\n    range: boolean\n  pathway:\n    name: pathway\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: pathway\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  evidence_count:\n    name: evidence_count\n    description: count of supporting documents, evidence codes, and sources supplying\n      evidence\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: evidence_count\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: integer\n  knowledge_level:\n    name: knowledge_level\n    description: Describes the level of knowledge expressed in a statement, based\n      on the reasoning or analysis methods used to generate the statement, or the\n      scope or specificity of what the statement expresses to be true.\n    notes:\n    - The range in this schema is represented as a string, but is constrained  to\n      values from biolink:KnowledgeLevelEnum at ingest time\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    slot_uri: biolink:knowledge_level\n    multivalued: false\n    alias: knowledge_level\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n    required: true\n  agent_type:\n    name: agent_type\n    description: Describes the high-level category of agent who originally generated\n      a  statement of knowledge or other type of information.\n    notes:\n    - The range in this schema is represented as a string, but is constrained  to\n      values from biolink:AgentTypeEnum at ingest time\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    slot_uri: biolink:agent_type\n    multivalued: false\n    alias: agent_type\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n    required: true\n  has_evidence:\n    name: has_evidence\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: has_evidence\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  has_evidence_links:\n    name: has_evidence_links\n    description: List of ExpandedCuries with id and url for evidence\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: has_evidence_links\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: ExpandedCurie\n    inlined: true\n    inlined_as_list: true\n  has_count:\n    name: has_count\n    description: count of out of has_total representing a frequency\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_count\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: integer\n  has_total:\n    name: has_total\n    description: total, devided by has_count, representing a frequency\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_total\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: integer\n  has_percentage:\n    name: has_percentage\n    description: percentage, which may be calculated from has_count and has_total,\n      as 100 * quotient or provided directly, rounded to the integer level\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_percentage\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: float\n  has_quotient:\n    name: has_quotient\n    description: quotient, which should be 1/100 of has_percentage\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_quotient\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: float\n  grouping_key:\n    name: grouping_key\n    description: A concatenation of fields used to group associations with the same\n      essential/defining properties\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: grouping_key\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  provided_by:\n    name: provided_by\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: provided_by\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    - Entity\n    range: string\n  provided_by_link:\n    name: provided_by_link\n    description: A link to the docs for the knowledge source that provided the node/edge.\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: provided_by_link\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    - Node\n    range: ExpandedCurie\n    inlined: true\n  publications:\n    name: publications\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: publications\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  publications_links:\n    name: publications_links\n    description: List of ExpandedCuries with id and url for publications\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: publications_links\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: ExpandedCurie\n    inlined: true\n    inlined_as_list: true\n  frequency_qualifier:\n    name: frequency_qualifier\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: frequency_qualifier\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  onset_qualifier:\n    name: onset_qualifier\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: onset_qualifier\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  sex_qualifier:\n    name: sex_qualifier\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: sex_qualifier\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  stage_qualifier:\n    name: stage_qualifier\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: stage_qualifier\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  qualifiers:\n    name: qualifiers\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: qualifiers\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  qualifiers_label:\n    name: qualifiers_label\n    description: The name of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: qualifiers_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  qualifiers_namespace:\n    name: qualifiers_namespace\n    description: The namespace/prefix of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: qualifiers_namespace\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  qualifiers_category:\n    name: qualifiers_category\n    description: The category of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: qualifiers_category\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  qualifiers_closure:\n    name: qualifiers_closure\n    description: Field containing frequency_qualifier id and the ids of all of it's\n      ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: qualifiers_closure\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  qualifiers_closure_label:\n    name: qualifiers_closure_label\n    description: Field containing frequency_qualifier name and the names of all of\n      it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: qualifiers_closure_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  qualifier:\n    name: qualifier\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: qualifier\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  qualifier_label:\n    name: qualifier_label\n    description: The name of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: qualifier_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  qualifier_namespace:\n    name: qualifier_namespace\n    description: The namespace/prefix of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: qualifier_namespace\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  qualifier_category:\n    name: qualifier_category\n    description: The category of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: qualifier_category\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  qualifier_closure:\n    name: qualifier_closure\n    description: Field containing frequency_qualifier id and the ids of all of it's\n      ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: qualifier_closure\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  qualifier_closure_label:\n    name: qualifier_closure_label\n    description: Field containing frequency_qualifier name and the names of all of\n      it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: qualifier_closure_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  frequency_qualifier_label:\n    name: frequency_qualifier_label\n    description: The name of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: frequency_qualifier_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  frequency_qualifier_namespace:\n    name: frequency_qualifier_namespace\n    description: The namespace/prefix of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: frequency_qualifier_namespace\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  frequency_qualifier_category:\n    name: frequency_qualifier_category\n    description: The category of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: frequency_qualifier_category\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  frequency_qualifier_closure:\n    name: frequency_qualifier_closure\n    description: Field containing frequency_qualifier id and the ids of all of it's\n      ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: frequency_qualifier_closure\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  frequency_qualifier_closure_label:\n    name: frequency_qualifier_closure_label\n    description: Field containing frequency_qualifier name and the names of all of\n      it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: frequency_qualifier_closure_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  onset_qualifier_label:\n    name: onset_qualifier_label\n    description: The name of the onset_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: onset_qualifier_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  onset_qualifier_namespace:\n    name: onset_qualifier_namespace\n    description: The namespace/prefix of the onset_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: onset_qualifier_namespace\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  onset_qualifier_category:\n    name: onset_qualifier_category\n    description: The category of the onset_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: onset_qualifier_category\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  onset_qualifier_closure:\n    name: onset_qualifier_closure\n    description: Field containing onset_qualifier id and the ids of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: onset_qualifier_closure\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  onset_qualifier_closure_label:\n    name: onset_qualifier_closure_label\n    description: Field containing onset_qualifier name and the names of all of it's\n      ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: onset_qualifier_closure_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  sex_qualifier_label:\n    name: sex_qualifier_label\n    description: The name of the sex_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: sex_qualifier_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  sex_qualifier_namespace:\n    name: sex_qualifier_namespace\n    description: The namespace/prefix of the sex_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: sex_qualifier_namespace\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  sex_qualifier_category:\n    name: sex_qualifier_category\n    description: The category of the sex_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: sex_qualifier_category\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  sex_qualifier_closure:\n    name: sex_qualifier_closure\n    description: Field containing sex_qualifier id and the ids of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: sex_qualifier_closure\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  sex_qualifier_closure_label:\n    name: sex_qualifier_closure_label\n    description: Field containing sex_qualifier name and the names of all of it's\n      ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: sex_qualifier_closure_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  stage_qualifier_label:\n    name: stage_qualifier_label\n    description: The name of the stage_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: stage_qualifier_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  stage_qualifier_namespace:\n    name: stage_qualifier_namespace\n    description: The namespace/prefix of the stage_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: stage_qualifier_namespace\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  stage_qualifier_category:\n    name: stage_qualifier_category\n    description: The category of the stage_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: stage_qualifier_category\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  stage_qualifier_closure:\n    name: stage_qualifier_closure\n    description: Field containing stage_qualifier id and the ids of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: stage_qualifier_closure\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  stage_qualifier_closure_label:\n    name: stage_qualifier_closure_label\n    description: Field containing stage_qualifier name and the names of all of it's\n      ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: stage_qualifier_closure_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n
    "},{"location":"Data-Model/Double/","title":"Type: Double","text":"
    A real number that conforms to the xsd:double specification
     
    URI: xsd:double
     
       
    •  
      base: float
       
      •  
    •  
      uri: xsd:double
       
      •  
    "},{"location":"Data-Model/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Double/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Entity/","title":"Class: Entity","text":"
    Represents an Entity in the Monarch KG data model
     
    URI: https://w3id.org/monarch/monarch-py/:Entity
     
     classDiagram\n    class Entity\n    click Entity href \"../Entity\"\n      Entity <|-- Node\n        click Node href \"../Node\"\n      Entity <|-- SearchResult\n        click SearchResult href \"../SearchResult\"\n\n      Entity : category\n\n      Entity : deprecated\n\n      Entity : description\n\n      Entity : full_name\n\n      Entity : has_phenotype\n\n      Entity : has_phenotype_closure\n\n      Entity : has_phenotype_closure_label\n\n      Entity : has_phenotype_count\n\n      Entity : has_phenotype_label\n\n      Entity : id\n\n      Entity : in_taxon\n\n      Entity : in_taxon_label\n\n      Entity : iri\n\n      Entity : name\n\n      Entity : namespace\n\n      Entity : provided_by\n\n      Entity : symbol\n\n      Entity : synonym\n\n      Entity : uri\n\n      Entity : xref\n
    "},{"location":"Data-Model/Entity/#inheritance","title":"Inheritance","text":"
       
    • Entity
         
      • Node
        •  
      • SearchResult
        •  
       
      •  
    "},{"location":"Data-Model/Entity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1  String direct category 0..1  String direct name 0..1  String direct full_name 0..1  String The long form name of an entity direct deprecated 0..1  Boolean A boolean flag indicating that an entity is no longer considered current or v... direct description 0..1  String direct xref *  String direct provided_by 0..1  String direct in_taxon 0..1  String The biolink taxon that the entity is in the closure of direct in_taxon_label 0..1  String The label of the biolink taxon that the entity is in the closure of direct symbol 0..1  String direct synonym *  String direct uri 0..1  String The URI of the entity direct iri 0..1  String direct namespace 0..1  String The namespace/prefix portion of this entity's identifier direct has_phenotype *  String A list of phenotype identifiers that are known to be associated with this ent... direct has_phenotype_label *  String A list of phenotype labels that are known to be associated with this entity direct has_phenotype_closure *  String A list of phenotype identifiers that are known to be associated with this ent... direct has_phenotype_closure_label *  String A list of phenotype labels that are known to be associated with this entity e... direct has_phenotype_count 0..1  Integer A count of the number of phenotypes that are known to be associated with this... direct"},{"location":"Data-Model/Entity/#usages","title":"Usages","text":"used by used in type used EntityResults items range Entity Node inheritance range Entity Node causal_gene range Entity Node causes_disease range Entity NodeHierarchy super_classes range Entity NodeHierarchy sub_classes range Entity TextAnnotationResult tokens range Entity SemsimSearchResult subject range Entity"},{"location":"Data-Model/Entity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Entity/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Entity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:Entity native https://w3id.org/monarch/monarch-py/:Entity"},{"location":"Data-Model/Entity/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/Entity/#direct","title":"Direct","text":"
    name: Entity\ndescription: Represents an Entity in the Monarch KG data model\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- id\n- category\n- name\n- full_name\n- deprecated\n- description\n- xref\n- provided_by\n- in_taxon\n- in_taxon_label\n- symbol\n- synonym\n- uri\n- iri\n- namespace\n- has_phenotype\n- has_phenotype_label\n- has_phenotype_closure\n- has_phenotype_closure_label\n- has_phenotype_count\n
    "},{"location":"Data-Model/Entity/#induced","title":"Induced","text":"
    name: Entity\ndescription: Represents an Entity in the Monarch KG data model\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  id:\n    name: id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Entity\n    domain_of:\n    - Association\n    - ExpandedCurie\n    - Entity\n    - HistoPheno\n    - HistoBin\n    - Mapping\n    - MultiEntityAssociationResults\n    - TermInfo\n    range: string\n    required: true\n  category:\n    name: category\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: false\n    alias: category\n    owner: Entity\n    domain_of:\n    - Association\n    - AssociationCount\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Entity\n    range: string\n  name:\n    name: name\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: name\n    owner: Entity\n    domain_of:\n    - Entity\n    - MultiEntityAssociationResults\n    range: string\n  full_name:\n    name: full_name\n    description: The long form name of an entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: full_name\n    owner: Entity\n    domain_of:\n    - Entity\n    range: string\n  deprecated:\n    name: deprecated\n    description: A boolean flag indicating that an entity is no longer considered\n      current or valid.\n    from_schema: https://w3id.org/monarch/monarch-py\n    exact_mappings:\n    - oboInOwl:ObsoleteClass\n    rank: 1000\n    alias: deprecated\n    owner: Entity\n    domain_of:\n    - Entity\n    range: boolean\n  description:\n    name: description\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: description\n    owner: Entity\n    domain_of:\n    - Entity\n    range: string\n  xref:\n    name: xref\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: xref\n    owner: Entity\n    domain_of:\n    - Entity\n    range: string\n  provided_by:\n    name: provided_by\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: provided_by\n    owner: Entity\n    domain_of:\n    - Association\n    - Entity\n    range: string\n  in_taxon:\n    name: in_taxon\n    description: The biolink taxon that the entity is in the closure of.\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: in_taxon\n    owner: Entity\n    domain_of:\n    - Entity\n    - Node\n    range: string\n  in_taxon_label:\n    name: in_taxon_label\n    description: The label of the biolink taxon that the entity is in the closure\n      of.\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: in_taxon_label\n    owner: Entity\n    domain_of:\n    - Entity\n    - Node\n    range: string\n  symbol:\n    name: symbol\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: symbol\n    owner: Entity\n    domain_of:\n    - Entity\n    range: string\n  synonym:\n    name: synonym\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: synonym\n    owner: Entity\n    domain_of:\n    - Entity\n    range: string\n  uri:\n    name: uri\n    description: The URI of the entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: uri\n    owner: Entity\n    domain_of:\n    - Entity\n    range: string\n  iri:\n    name: iri\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: iri\n    owner: Entity\n    domain_of:\n    - Entity\n    range: string\n  namespace:\n    name: namespace\n    description: The namespace/prefix portion of this entity's identifier\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: namespace\n    owner: Entity\n    domain_of:\n    - Entity\n    range: string\n  has_phenotype:\n    name: has_phenotype\n    description: A list of phenotype identifiers that are known to be associated with\n      this entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: has_phenotype\n    owner: Entity\n    domain_of:\n    - Entity\n    range: string\n    inlined: true\n    inlined_as_list: true\n  has_phenotype_label:\n    name: has_phenotype_label\n    description: A list of phenotype labels that are known to be associated with this\n      entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: has_phenotype_label\n    owner: Entity\n    domain_of:\n    - Entity\n    range: string\n    inlined: true\n    inlined_as_list: true\n  has_phenotype_closure:\n    name: has_phenotype_closure\n    description: A list of phenotype identifiers that are known to be associated with\n      this entity expanded to include all ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: has_phenotype_closure\n    owner: Entity\n    domain_of:\n    - Entity\n    range: string\n    inlined: true\n    inlined_as_list: true\n  has_phenotype_closure_label:\n    name: has_phenotype_closure_label\n    description: A list of phenotype labels that are known to be associated with this\n      entity expanded to include all ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: has_phenotype_closure_label\n    owner: Entity\n    domain_of:\n    - Entity\n    range: string\n    inlined: true\n    inlined_as_list: true\n  has_phenotype_count:\n    name: has_phenotype_count\n    description: A count of the number of phenotypes that are known to be associated\n      with this entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_phenotype_count\n    owner: Entity\n    domain_of:\n    - Entity\n    range: integer\n
    "},{"location":"Data-Model/EntityResults/","title":"Class: EntityResults","text":"
    URI: https://w3id.org/monarch/monarch-py/:EntityResults
     
     classDiagram\n    class EntityResults\n    click EntityResults href \"../EntityResults\"\n      Results <|-- EntityResults\n        click Results href \"../Results\"\n\n      EntityResults : items\n\n\n\n\n    EntityResults --> \"1..*\" Entity : items\n    click Entity href \"../Entity\"\n\n\n      EntityResults : limit\n\n      EntityResults : offset\n\n      EntityResults : total\n
    "},{"location":"Data-Model/EntityResults/#inheritance","title":"Inheritance","text":"
       
    • Results
         
      • EntityResults
        •  
       
      •  
    "},{"location":"Data-Model/EntityResults/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance items 1..*  Entity A collection of items, with the type to be overriden by slot_usage direct limit 1  Integer number of items to return in a response Results offset 1  Integer offset into the total number of items Results total 1  Integer total number of items matching a query Results"},{"location":"Data-Model/EntityResults/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/EntityResults/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/EntityResults/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:EntityResults native https://w3id.org/monarch/monarch-py/:EntityResults"},{"location":"Data-Model/EntityResults/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/EntityResults/#direct","title":"Direct","text":"
    name: EntityResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- items\nslot_usage:\n  items:\n    name: items\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: Entity\n
    "},{"location":"Data-Model/EntityResults/#induced","title":"Induced","text":"
    name: EntityResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n  items:\n    name: items\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: Entity\nattributes:\n  items:\n    name: items\n    description: A collection of items, with the type to be overriden by slot_usage\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: items\n    owner: EntityResults\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: Entity\n    required: true\n    inlined: true\n    inlined_as_list: true\n  limit:\n    name: limit\n    description: number of items to return in a response\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: limit\n    owner: EntityResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  offset:\n    name: offset\n    description: offset into the total number of items\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: offset\n    owner: EntityResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  total:\n    name: total\n    description: total number of items matching a query\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: total\n    owner: EntityResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n
    "},{"location":"Data-Model/ExpandedCurie/","title":"Class: ExpandedCurie","text":"
    A curie bundled along with its expanded url
     
    URI: https://w3id.org/monarch/monarch-py/:ExpandedCurie
     
     classDiagram\n    class ExpandedCurie\n    click ExpandedCurie href \"../ExpandedCurie\"\n      ExpandedCurie : id\n\n      ExpandedCurie : url\n
    "},{"location":"Data-Model/ExpandedCurie/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1  String direct url 0..1  String direct"},{"location":"Data-Model/ExpandedCurie/#usages","title":"Usages","text":"used by used in type used Association has_evidence_links range ExpandedCurie Association provided_by_link range ExpandedCurie Association publications_links range ExpandedCurie DirectionalAssociation has_evidence_links range ExpandedCurie DirectionalAssociation provided_by_link range ExpandedCurie DirectionalAssociation publications_links range ExpandedCurie Node mappings range ExpandedCurie Node external_links range ExpandedCurie Node provided_by_link range ExpandedCurie"},{"location":"Data-Model/ExpandedCurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/ExpandedCurie/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/ExpandedCurie/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:ExpandedCurie native https://w3id.org/monarch/monarch-py/:ExpandedCurie"},{"location":"Data-Model/ExpandedCurie/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/ExpandedCurie/#direct","title":"Direct","text":"
    name: ExpandedCurie\ndescription: A curie bundled along with its expanded url\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- id\n- url\n
    "},{"location":"Data-Model/ExpandedCurie/#induced","title":"Induced","text":"
    name: ExpandedCurie\ndescription: A curie bundled along with its expanded url\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  id:\n    name: id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ExpandedCurie\n    domain_of:\n    - Association\n    - ExpandedCurie\n    - Entity\n    - HistoPheno\n    - HistoBin\n    - Mapping\n    - MultiEntityAssociationResults\n    - TermInfo\n    range: string\n    required: true\n  url:\n    name: url\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: url\n    owner: ExpandedCurie\n    domain_of:\n    - ExpandedCurie\n    - Release\n    range: string\n
    "},{"location":"Data-Model/FacetField/","title":"Class: FacetField","text":"
    URI: https://w3id.org/monarch/monarch-py/:FacetField
     
     classDiagram\n    class FacetField\n    click FacetField href \"../FacetField\"\n      FacetField : facet_values\n\n\n\n\n    FacetField --> \"*\" FacetValue : facet_values\n    click FacetValue href \"../FacetValue\"\n\n\n      FacetField : label\n
    "},{"location":"Data-Model/FacetField/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance label 1  String direct facet_values *  FacetValue Collection of FacetValue label/value instances belonging to a FacetField direct"},{"location":"Data-Model/FacetField/#usages","title":"Usages","text":"used by used in type used SearchResults facet_fields range FacetField"},{"location":"Data-Model/FacetField/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/FacetField/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/FacetField/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:FacetField native https://w3id.org/monarch/monarch-py/:FacetField"},{"location":"Data-Model/FacetField/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/FacetField/#direct","title":"Direct","text":"
    name: FacetField\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- label\n- facet_values\n
    "},{"location":"Data-Model/FacetField/#induced","title":"Induced","text":"
    name: FacetField\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  label:\n    name: label\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: label\n    owner: FacetField\n    domain_of:\n    - FacetValue\n    - FacetField\n    - TermInfo\n    range: string\n    required: true\n  facet_values:\n    name: facet_values\n    description: Collection of FacetValue label/value instances belonging to a FacetField\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: facet_values\n    owner: FacetField\n    domain_of:\n    - FacetField\n    range: FacetValue\n    inlined: true\n    inlined_as_list: true\n
    "},{"location":"Data-Model/FacetValue/","title":"Class: FacetValue","text":"
    URI: https://w3id.org/monarch/monarch-py/:FacetValue
     
     classDiagram\n    class FacetValue\n    click FacetValue href \"../FacetValue\"\n      FacetValue <|-- AssociationCount\n        click AssociationCount href \"../AssociationCount\"\n      FacetValue <|-- HistoBin\n        click HistoBin href \"../HistoBin\"\n\n      FacetValue : count\n\n      FacetValue : label\n
    "},{"location":"Data-Model/FacetValue/#inheritance","title":"Inheritance","text":"
       
    • FacetValue
         
      • AssociationCount
        •  
      • HistoBin
        •  
       
      •  
    "},{"location":"Data-Model/FacetValue/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance label 1  String direct count 0..1  Integer count of documents direct"},{"location":"Data-Model/FacetValue/#usages","title":"Usages","text":"used by used in type used FacetField facet_values range FacetValue SearchResults facet_queries range FacetValue"},{"location":"Data-Model/FacetValue/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/FacetValue/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/FacetValue/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:FacetValue native https://w3id.org/monarch/monarch-py/:FacetValue"},{"location":"Data-Model/FacetValue/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/FacetValue/#direct","title":"Direct","text":"
    name: FacetValue\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- label\n- count\n
    "},{"location":"Data-Model/FacetValue/#induced","title":"Induced","text":"
    name: FacetValue\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  label:\n    name: label\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: label\n    owner: FacetValue\n    domain_of:\n    - FacetValue\n    - FacetField\n    - TermInfo\n    range: string\n    required: true\n  count:\n    name: count\n    description: count of documents\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: count\n    owner: FacetValue\n    domain_of:\n    - FacetValue\n    range: integer\n
    "},{"location":"Data-Model/Float/","title":"Type: Float","text":"
    A real number that conforms to the xsd:float specification
     
    URI: xsd:float
     
       
    •  
      base: float
       
      •  
    •  
      uri: xsd:float
       
      •  
    "},{"location":"Data-Model/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Float/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/HistoBin/","title":"Class: HistoBin","text":"
    URI: https://w3id.org/monarch/monarch-py/:HistoBin
     
     classDiagram\n    class HistoBin\n    click HistoBin href \"../HistoBin\"\n      FacetValue <|-- HistoBin\n        click FacetValue href \"../FacetValue\"\n\n      HistoBin : count\n\n      HistoBin : id\n\n      HistoBin : label\n
    "},{"location":"Data-Model/HistoBin/#inheritance","title":"Inheritance","text":"
       
    • FacetValue
         
      • HistoBin
        •  
       
      •  
    "},{"location":"Data-Model/HistoBin/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1  String direct label 1  String FacetValue count 0..1  Integer count of documents FacetValue"},{"location":"Data-Model/HistoBin/#usages","title":"Usages","text":"used by used in type used HistoPheno items range HistoBin"},{"location":"Data-Model/HistoBin/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/HistoBin/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/HistoBin/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:HistoBin native https://w3id.org/monarch/monarch-py/:HistoBin"},{"location":"Data-Model/HistoBin/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/HistoBin/#direct","title":"Direct","text":"
    name: HistoBin\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: FacetValue\nslots:\n- id\n
    "},{"location":"Data-Model/HistoBin/#induced","title":"Induced","text":"
    name: HistoBin\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: FacetValue\nattributes:\n  id:\n    name: id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: HistoBin\n    domain_of:\n    - Association\n    - ExpandedCurie\n    - Entity\n    - HistoPheno\n    - HistoBin\n    - Mapping\n    - MultiEntityAssociationResults\n    - TermInfo\n    range: string\n    required: true\n  label:\n    name: label\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: label\n    owner: HistoBin\n    domain_of:\n    - FacetValue\n    - FacetField\n    - TermInfo\n    range: string\n    required: true\n  count:\n    name: count\n    description: count of documents\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: count\n    owner: HistoBin\n    domain_of:\n    - FacetValue\n    range: integer\n
    "},{"location":"Data-Model/HistoPheno/","title":"Class: HistoPheno","text":"
    URI: https://w3id.org/monarch/monarch-py/:HistoPheno
     
     classDiagram\n    class HistoPheno\n    click HistoPheno href \"../HistoPheno\"\n      HistoPheno : id\n\n      HistoPheno : items\n\n\n\n\n    HistoPheno --> \"1..*\" HistoBin : items\n    click HistoBin href \"../HistoBin\"\n
    "},{"location":"Data-Model/HistoPheno/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1  String direct items 1..*  HistoBin A collection of items, with the type to be overriden by slot_usage direct"},{"location":"Data-Model/HistoPheno/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/HistoPheno/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/HistoPheno/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:HistoPheno native https://w3id.org/monarch/monarch-py/:HistoPheno"},{"location":"Data-Model/HistoPheno/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/HistoPheno/#direct","title":"Direct","text":"
    name: HistoPheno\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- id\n- items\nslot_usage:\n  items:\n    name: items\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: HistoBin\n
    "},{"location":"Data-Model/HistoPheno/#induced","title":"Induced","text":"
    name: HistoPheno\nfrom_schema: https://w3id.org/monarch/monarch-py\nslot_usage:\n  items:\n    name: items\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: HistoBin\nattributes:\n  id:\n    name: id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: HistoPheno\n    domain_of:\n    - Association\n    - ExpandedCurie\n    - Entity\n    - HistoPheno\n    - HistoBin\n    - Mapping\n    - MultiEntityAssociationResults\n    - TermInfo\n    range: string\n    required: true\n  items:\n    name: items\n    description: A collection of items, with the type to be overriden by slot_usage\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: items\n    owner: HistoPheno\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: HistoBin\n    required: true\n    inlined: true\n    inlined_as_list: true\n
    "},{"location":"Data-Model/Integer/","title":"Type: Integer","text":"
    An integer
     
    URI: xsd:integer
     
       
    •  
      base: int
       
      •  
    •  
      uri: xsd:integer
       
      •  
    "},{"location":"Data-Model/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Integer/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/ItemCount/","title":"Type: ItemCount","text":"
    URI: xsd:integer
     
       
    •  
      base: int
       
      •  
    •  
      uri: xsd:integer
       
      •  
    •  
      typeof: integer
       
      •  
    "},{"location":"Data-Model/ItemCount/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/ItemCount/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Jsonpath/","title":"Type: Jsonpath","text":"
    A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.
     
    URI: xsd:string
     
       
    •  
      base: str
       
      •  
    •  
      uri: xsd:string
       
      •  
    •  
      repr: str
       
      •  
    "},{"location":"Data-Model/Jsonpath/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Jsonpath/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Jsonpointer/","title":"Type: Jsonpointer","text":"
    A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.
     
    URI: xsd:string
     
       
    •  
      base: str
       
      •  
    •  
      uri: xsd:string
       
      •  
    •  
      repr: str
       
      •  
    "},{"location":"Data-Model/Jsonpointer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Jsonpointer/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Mapping/","title":"Class: Mapping","text":"
    A minimal class to hold a SSSOM mapping
     
    URI: https://w3id.org/monarch/monarch-py/:Mapping
     
     classDiagram\n    class Mapping\n    click Mapping href \"../Mapping\"\n      Mapping : id\n\n      Mapping : mapping_justification\n\n      Mapping : object_id\n\n      Mapping : object_label\n\n      Mapping : predicate_id\n\n      Mapping : subject_id\n\n      Mapping : subject_label\n
    "},{"location":"Data-Model/Mapping/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_id 1  String direct subject_label 0..1  String The name of the subject entity direct predicate_id 1  String direct object_id 1  String direct object_label 0..1  String The name of the object entity direct mapping_justification 0..1  String direct id 1  String direct"},{"location":"Data-Model/Mapping/#usages","title":"Usages","text":"used by used in type used MappingResults items range Mapping"},{"location":"Data-Model/Mapping/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Mapping/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Mapping/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:Mapping native https://w3id.org/monarch/monarch-py/:Mapping"},{"location":"Data-Model/Mapping/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/Mapping/#direct","title":"Direct","text":"
    name: Mapping\ndescription: A minimal class to hold a SSSOM mapping\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- subject_id\n- subject_label\n- predicate_id\n- object_id\n- object_label\n- mapping_justification\n- id\n
    "},{"location":"Data-Model/Mapping/#induced","title":"Induced","text":"
    name: Mapping\ndescription: A minimal class to hold a SSSOM mapping\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  subject_id:\n    name: subject_id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: subject_id\n    owner: Mapping\n    domain_of:\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n    required: true\n  subject_label:\n    name: subject_label\n    description: The name of the subject entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: subject_label\n    owner: Mapping\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n  predicate_id:\n    name: predicate_id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: predicate_id\n    owner: Mapping\n    domain_of:\n    - Mapping\n    range: string\n    required: true\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: object_id\n    owner: Mapping\n    domain_of:\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n    required: true\n  object_label:\n    name: object_label\n    description: The name of the object entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: object_label\n    owner: Mapping\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n  mapping_justification:\n    name: mapping_justification\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: mapping_justification\n    owner: Mapping\n    domain_of:\n    - Mapping\n    range: string\n  id:\n    name: id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Mapping\n    domain_of:\n    - Association\n    - ExpandedCurie\n    - Entity\n    - HistoPheno\n    - HistoBin\n    - Mapping\n    - MultiEntityAssociationResults\n    - TermInfo\n    range: string\n    required: true\n
    "},{"location":"Data-Model/MappingResults/","title":"Class: MappingResults","text":"
    SSSOM Mappings returned as a results collection
     
    URI: https://w3id.org/monarch/monarch-py/:MappingResults
     
     classDiagram\n    class MappingResults\n    click MappingResults href \"../MappingResults\"\n      Results <|-- MappingResults\n        click Results href \"../Results\"\n\n      MappingResults : items\n\n\n\n\n    MappingResults --> \"1..*\" Mapping : items\n    click Mapping href \"../Mapping\"\n\n\n      MappingResults : limit\n\n      MappingResults : offset\n\n      MappingResults : total\n
    "},{"location":"Data-Model/MappingResults/#inheritance","title":"Inheritance","text":"
       
    • Results
         
      • MappingResults
        •  
       
      •  
    "},{"location":"Data-Model/MappingResults/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance items 1..*  Mapping A collection of items, with the type to be overriden by slot_usage direct limit 1  Integer number of items to return in a response Results offset 1  Integer offset into the total number of items Results total 1  Integer total number of items matching a query Results"},{"location":"Data-Model/MappingResults/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/MappingResults/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/MappingResults/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:MappingResults native https://w3id.org/monarch/monarch-py/:MappingResults"},{"location":"Data-Model/MappingResults/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/MappingResults/#direct","title":"Direct","text":"
    name: MappingResults\ndescription: SSSOM Mappings returned as a results collection\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- items\nslot_usage:\n  items:\n    name: items\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: Mapping\n
    "},{"location":"Data-Model/MappingResults/#induced","title":"Induced","text":"
    name: MappingResults\ndescription: SSSOM Mappings returned as a results collection\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n  items:\n    name: items\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: Mapping\nattributes:\n  items:\n    name: items\n    description: A collection of items, with the type to be overriden by slot_usage\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: items\n    owner: MappingResults\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: Mapping\n    required: true\n    inlined: true\n    inlined_as_list: true\n  limit:\n    name: limit\n    description: number of items to return in a response\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: limit\n    owner: MappingResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  offset:\n    name: offset\n    description: offset into the total number of items\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: offset\n    owner: MappingResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  total:\n    name: total\n    description: total number of items matching a query\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: total\n    owner: MappingResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n
    "},{"location":"Data-Model/MultiEntityAssociationResults/","title":"Class: MultiEntityAssociationResults","text":"
    URI: https://w3id.org/monarch/monarch-py/:MultiEntityAssociationResults
     
     classDiagram\n    class MultiEntityAssociationResults\n    click MultiEntityAssociationResults href \"../MultiEntityAssociationResults\"\n      Results <|-- MultiEntityAssociationResults\n        click Results href \"../Results\"\n\n      MultiEntityAssociationResults : associated_categories\n\n\n\n\n    MultiEntityAssociationResults --> \"1..*\" CategoryGroupedAssociationResults : associated_categories\n    click CategoryGroupedAssociationResults href \"../CategoryGroupedAssociationResults\"\n\n\n      MultiEntityAssociationResults : id\n\n      MultiEntityAssociationResults : limit\n\n      MultiEntityAssociationResults : name\n\n      MultiEntityAssociationResults : offset\n\n      MultiEntityAssociationResults : total\n
    "},{"location":"Data-Model/MultiEntityAssociationResults/#inheritance","title":"Inheritance","text":"
       
    • Results
         
      • MultiEntityAssociationResults
        •  
       
      •  
    "},{"location":"Data-Model/MultiEntityAssociationResults/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1  String direct name 0..1  String direct associated_categories 1..*  CategoryGroupedAssociationResults direct limit 1  Integer number of items to return in a response Results offset 1  Integer offset into the total number of items Results total 1  Integer total number of items matching a query Results"},{"location":"Data-Model/MultiEntityAssociationResults/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/MultiEntityAssociationResults/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/MultiEntityAssociationResults/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:MultiEntityAssociationResults native https://w3id.org/monarch/monarch-py/:MultiEntityAssociationResults"},{"location":"Data-Model/MultiEntityAssociationResults/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/MultiEntityAssociationResults/#direct","title":"Direct","text":"
    name: MultiEntityAssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- id\n- name\n- associated_categories\n
    "},{"location":"Data-Model/MultiEntityAssociationResults/#induced","title":"Induced","text":"
    name: MultiEntityAssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nattributes:\n  id:\n    name: id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MultiEntityAssociationResults\n    domain_of:\n    - Association\n    - ExpandedCurie\n    - Entity\n    - HistoPheno\n    - HistoBin\n    - Mapping\n    - MultiEntityAssociationResults\n    - TermInfo\n    range: string\n    required: true\n  name:\n    name: name\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: name\n    owner: MultiEntityAssociationResults\n    domain_of:\n    - Entity\n    - MultiEntityAssociationResults\n    range: string\n  associated_categories:\n    name: associated_categories\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: associated_categories\n    owner: MultiEntityAssociationResults\n    domain_of:\n    - MultiEntityAssociationResults\n    range: CategoryGroupedAssociationResults\n    required: true\n    inlined: true\n    inlined_as_list: true\n  limit:\n    name: limit\n    description: number of items to return in a response\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: limit\n    owner: MultiEntityAssociationResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  offset:\n    name: offset\n    description: offset into the total number of items\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: offset\n    owner: MultiEntityAssociationResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  total:\n    name: total\n    description: total number of items matching a query\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: total\n    owner: MultiEntityAssociationResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n
    "},{"location":"Data-Model/Ncname/","title":"Type: Ncname","text":"
    Prefix part of CURIE
     
    URI: xsd:string
     
       
    •  
      base: NCName
       
      •  
    •  
      uri: xsd:string
       
      •  
    •  
      repr: str
       
      •  
    "},{"location":"Data-Model/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Ncname/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/NegativeLogValue/","title":"Type: NegativeLogValue","text":"
    URI: xsd:float
     
       
    •  
      base: float
       
      •  
    •  
      uri: xsd:float
       
      •  
    •  
      typeof: float
       
      •  
    "},{"location":"Data-Model/NegativeLogValue/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/NegativeLogValue/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Node/","title":"Class: Node","text":"
    UI container class extending Entity with additional information
     
    URI: https://w3id.org/monarch/monarch-py/:Node
     
     classDiagram\n    class Node\n    click Node href \"../Node\"\n      Entity <|-- Node\n        click Entity href \"../Entity\"\n\n      Node : association_counts\n\n\n\n\n    Node --> \"1..*\" AssociationCount : association_counts\n    click AssociationCount href \"../AssociationCount\"\n\n\n      Node : category\n\n      Node : causal_gene\n\n\n\n\n    Node --> \"*\" Entity : causal_gene\n    click Entity href \"../Entity\"\n\n\n      Node : causes_disease\n\n\n\n\n    Node --> \"*\" Entity : causes_disease\n    click Entity href \"../Entity\"\n\n\n      Node : deprecated\n\n      Node : description\n\n      Node : external_links\n\n\n\n\n    Node --> \"*\" ExpandedCurie : external_links\n    click ExpandedCurie href \"../ExpandedCurie\"\n\n\n      Node : full_name\n\n      Node : has_phenotype\n\n      Node : has_phenotype_closure\n\n      Node : has_phenotype_closure_label\n\n      Node : has_phenotype_count\n\n      Node : has_phenotype_label\n\n      Node : id\n\n      Node : in_taxon\n\n      Node : in_taxon_label\n\n      Node : inheritance\n\n\n\n\n    Node --> \"0..1\" Entity : inheritance\n    click Entity href \"../Entity\"\n\n\n      Node : iri\n\n      Node : mappings\n\n\n\n\n    Node --> \"*\" ExpandedCurie : mappings\n    click ExpandedCurie href \"../ExpandedCurie\"\n\n\n      Node : name\n\n      Node : namespace\n\n      Node : node_hierarchy\n\n\n\n\n    Node --> \"0..1\" NodeHierarchy : node_hierarchy\n    click NodeHierarchy href \"../NodeHierarchy\"\n\n\n      Node : provided_by\n\n      Node : provided_by_link\n\n\n\n\n    Node --> \"0..1\" ExpandedCurie : provided_by_link\n    click ExpandedCurie href \"../ExpandedCurie\"\n\n\n      Node : symbol\n\n      Node : synonym\n\n      Node : uri\n\n      Node : xref\n
    "},{"location":"Data-Model/Node/#inheritance","title":"Inheritance","text":"
       
    • Entity
         
      • Node
        •  
       
      •  
    "},{"location":"Data-Model/Node/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance in_taxon 0..1  String The biolink taxon that the entity is in the closure of direct in_taxon_label 0..1  String The label of the biolink taxon that the entity is in the closure of direct inheritance 0..1  Entity direct causal_gene *  Entity A list of genes that are known to be causally associated with a disease direct causes_disease *  Entity A list of diseases that are known to be causally associated with a gene direct mappings *  ExpandedCurie List of ExpandedCuries with id and url for mapped entities direct external_links *  ExpandedCurie ExpandedCurie with id and url for xrefs direct provided_by_link 0..1  ExpandedCurie A link to the docs for the knowledge source that provided the node/edge direct association_counts 1..*  AssociationCount direct node_hierarchy 0..1  NodeHierarchy direct id 1  String Entity category 0..1  String Entity name 0..1  String Entity full_name 0..1  String The long form name of an entity Entity deprecated 0..1  Boolean A boolean flag indicating that an entity is no longer considered current or v... Entity description 0..1  String Entity xref *  String Entity provided_by 0..1  String Entity symbol 0..1  String Entity synonym *  String Entity uri 0..1  String The URI of the entity Entity iri 0..1  String Entity namespace 0..1  String The namespace/prefix portion of this entity's identifier Entity has_phenotype *  String A list of phenotype identifiers that are known to be associated with this ent... Entity has_phenotype_label *  String A list of phenotype labels that are known to be associated with this entity Entity has_phenotype_closure *  String A list of phenotype identifiers that are known to be associated with this ent... Entity has_phenotype_closure_label *  String A list of phenotype labels that are known to be associated with this entity e... Entity has_phenotype_count 0..1  Integer A count of the number of phenotypes that are known to be associated with this... Entity"},{"location":"Data-Model/Node/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Node/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Node/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:Node native https://w3id.org/monarch/monarch-py/:Node"},{"location":"Data-Model/Node/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/Node/#direct","title":"Direct","text":"
    name: Node\ndescription: UI container class extending Entity with additional information\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Entity\nslots:\n- in_taxon\n- in_taxon_label\n- inheritance\n- causal_gene\n- causes_disease\n- mappings\n- external_links\n- provided_by_link\n- association_counts\n- node_hierarchy\n
    "},{"location":"Data-Model/Node/#induced","title":"Induced","text":"
    name: Node\ndescription: UI container class extending Entity with additional information\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Entity\nattributes:\n  in_taxon:\n    name: in_taxon\n    description: The biolink taxon that the entity is in the closure of.\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: in_taxon\n    owner: Node\n    domain_of:\n    - Entity\n    - Node\n    range: string\n  in_taxon_label:\n    name: in_taxon_label\n    description: The label of the biolink taxon that the entity is in the closure\n      of.\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: in_taxon_label\n    owner: Node\n    domain_of:\n    - Entity\n    - Node\n    range: string\n  inheritance:\n    name: inheritance\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: inheritance\n    owner: Node\n    domain_of:\n    - Node\n    range: Entity\n    inlined: true\n  causal_gene:\n    name: causal_gene\n    description: A list of genes that are known to be causally associated with a disease\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: causal_gene\n    owner: Node\n    domain_of:\n    - Node\n    range: Entity\n    inlined: true\n    inlined_as_list: true\n  causes_disease:\n    name: causes_disease\n    description: A list of diseases that are known to be causally associated with\n      a gene\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: causes_disease\n    owner: Node\n    domain_of:\n    - Node\n    range: Entity\n    inlined: true\n    inlined_as_list: true\n  mappings:\n    name: mappings\n    description: List of ExpandedCuries with id and url for mapped entities\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: mappings\n    owner: Node\n    domain_of:\n    - Node\n    range: ExpandedCurie\n    inlined: true\n    inlined_as_list: true\n  external_links:\n    name: external_links\n    description: ExpandedCurie with id and url for xrefs\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: external_links\n    owner: Node\n    domain_of:\n    - Node\n    range: ExpandedCurie\n    inlined: true\n    inlined_as_list: true\n  provided_by_link:\n    name: provided_by_link\n    description: A link to the docs for the knowledge source that provided the node/edge.\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: provided_by_link\n    owner: Node\n    domain_of:\n    - Association\n    - Node\n    range: ExpandedCurie\n    inlined: true\n  association_counts:\n    name: association_counts\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: association_counts\n    owner: Node\n    domain_of:\n    - Node\n    range: AssociationCount\n    required: true\n    inlined: true\n    inlined_as_list: true\n  node_hierarchy:\n    name: node_hierarchy\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: node_hierarchy\n    owner: Node\n    domain_of:\n    - Node\n    range: NodeHierarchy\n    inlined: true\n  id:\n    name: id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Node\n    domain_of:\n    - Association\n    - ExpandedCurie\n    - Entity\n    - HistoPheno\n    - HistoBin\n    - Mapping\n    - MultiEntityAssociationResults\n    - TermInfo\n    range: string\n    required: true\n  category:\n    name: category\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: false\n    alias: category\n    owner: Node\n    domain_of:\n    - Association\n    - AssociationCount\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Entity\n    range: string\n  name:\n    name: name\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: name\n    owner: Node\n    domain_of:\n    - Entity\n    - MultiEntityAssociationResults\n    range: string\n  full_name:\n    name: full_name\n    description: The long form name of an entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: full_name\n    owner: Node\n    domain_of:\n    - Entity\n    range: string\n  deprecated:\n    name: deprecated\n    description: A boolean flag indicating that an entity is no longer considered\n      current or valid.\n    from_schema: https://w3id.org/monarch/monarch-py\n    exact_mappings:\n    - oboInOwl:ObsoleteClass\n    rank: 1000\n    alias: deprecated\n    owner: Node\n    domain_of:\n    - Entity\n    range: boolean\n  description:\n    name: description\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: description\n    owner: Node\n    domain_of:\n    - Entity\n    range: string\n  xref:\n    name: xref\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: xref\n    owner: Node\n    domain_of:\n    - Entity\n    range: string\n  provided_by:\n    name: provided_by\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: provided_by\n    owner: Node\n    domain_of:\n    - Association\n    - Entity\n    range: string\n  symbol:\n    name: symbol\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: symbol\n    owner: Node\n    domain_of:\n    - Entity\n    range: string\n  synonym:\n    name: synonym\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: synonym\n    owner: Node\n    domain_of:\n    - Entity\n    range: string\n  uri:\n    name: uri\n    description: The URI of the entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: uri\n    owner: Node\n    domain_of:\n    - Entity\n    range: string\n  iri:\n    name: iri\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: iri\n    owner: Node\n    domain_of:\n    - Entity\n    range: string\n  namespace:\n    name: namespace\n    description: The namespace/prefix portion of this entity's identifier\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: namespace\n    owner: Node\n    domain_of:\n    - Entity\n    range: string\n  has_phenotype:\n    name: has_phenotype\n    description: A list of phenotype identifiers that are known to be associated with\n      this entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: has_phenotype\n    owner: Node\n    domain_of:\n    - Entity\n    range: string\n    inlined: true\n    inlined_as_list: true\n  has_phenotype_label:\n    name: has_phenotype_label\n    description: A list of phenotype labels that are known to be associated with this\n      entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: has_phenotype_label\n    owner: Node\n    domain_of:\n    - Entity\n    range: string\n    inlined: true\n    inlined_as_list: true\n  has_phenotype_closure:\n    name: has_phenotype_closure\n    description: A list of phenotype identifiers that are known to be associated with\n      this entity expanded to include all ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: has_phenotype_closure\n    owner: Node\n    domain_of:\n    - Entity\n    range: string\n    inlined: true\n    inlined_as_list: true\n  has_phenotype_closure_label:\n    name: has_phenotype_closure_label\n    description: A list of phenotype labels that are known to be associated with this\n      entity expanded to include all ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: has_phenotype_closure_label\n    owner: Node\n    domain_of:\n    - Entity\n    range: string\n    inlined: true\n    inlined_as_list: true\n  has_phenotype_count:\n    name: has_phenotype_count\n    description: A count of the number of phenotypes that are known to be associated\n      with this entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_phenotype_count\n    owner: Node\n    domain_of:\n    - Entity\n    range: integer\n
    "},{"location":"Data-Model/NodeHierarchy/","title":"Class: NodeHierarchy","text":"
    URI: https://w3id.org/monarch/monarch-py/:NodeHierarchy
     
     classDiagram\n    class NodeHierarchy\n    click NodeHierarchy href \"../NodeHierarchy\"\n      NodeHierarchy : sub_classes\n\n\n\n\n    NodeHierarchy --> \"1..*\" Entity : sub_classes\n    click Entity href \"../Entity\"\n\n\n      NodeHierarchy : super_classes\n\n\n\n\n    NodeHierarchy --> \"1..*\" Entity : super_classes\n    click Entity href \"../Entity\"\n
    "},{"location":"Data-Model/NodeHierarchy/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance super_classes 1..*  Entity direct sub_classes 1..*  Entity direct"},{"location":"Data-Model/NodeHierarchy/#usages","title":"Usages","text":"used by used in type used Node node_hierarchy range NodeHierarchy"},{"location":"Data-Model/NodeHierarchy/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/NodeHierarchy/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/NodeHierarchy/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:NodeHierarchy native https://w3id.org/monarch/monarch-py/:NodeHierarchy"},{"location":"Data-Model/NodeHierarchy/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/NodeHierarchy/#direct","title":"Direct","text":"
    name: NodeHierarchy\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- super_classes\n- sub_classes\n
    "},{"location":"Data-Model/NodeHierarchy/#induced","title":"Induced","text":"
    name: NodeHierarchy\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  super_classes:\n    name: super_classes\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: super_classes\n    owner: NodeHierarchy\n    domain_of:\n    - NodeHierarchy\n    range: Entity\n    required: true\n    inlined: true\n    inlined_as_list: true\n  sub_classes:\n    name: sub_classes\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: sub_classes\n    owner: NodeHierarchy\n    domain_of:\n    - NodeHierarchy\n    range: Entity\n    required: true\n    inlined: true\n    inlined_as_list: true\n
    "},{"location":"Data-Model/Nodeidentifier/","title":"Type: Nodeidentifier","text":"
    A URI, CURIE or BNODE that represents a node in a model.
     
    URI: shex:nonLiteral
     
       
    •  
      base: NodeIdentifier
       
      •  
    •  
      uri: shex:nonLiteral
       
      •  
    •  
      repr: str
       
      •  
    "},{"location":"Data-Model/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Nodeidentifier/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/NonNegativeFloat/","title":"Type: NonNegativeFloat","text":"
    URI: xsd:float
     
       
    •  
      base: float
       
      •  
    •  
      uri: xsd:float
       
      •  
    •  
      typeof: float
       
      •  
    "},{"location":"Data-Model/NonNegativeFloat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/NonNegativeFloat/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Objectidentifier/","title":"Type: Objectidentifier","text":"
    A URI or CURIE that represents an object in the model.
     
    URI: shex:iri
     
       
    •  
      base: ElementIdentifier
       
      •  
    •  
      uri: shex:iri
       
      •  
    •  
      repr: str
       
      •  
    "},{"location":"Data-Model/Objectidentifier/#comments","title":"Comments","text":"
       
    • Used for inheritance and type checking
      •  
    "},{"location":"Data-Model/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Objectidentifier/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/PairwiseSimilarity/","title":"Class: PairwiseSimilarity","text":"
    Abstract grouping for representing individual pairwise similarities
     
       
    • NOTE: this is an abstract class and should not be instantiated directly
      •  
     
    URI: https://w3id.org/monarch/monarch-py/:PairwiseSimilarity
     
     classDiagram\n    class PairwiseSimilarity\n    click PairwiseSimilarity href \"../PairwiseSimilarity\"\n      PairwiseSimilarity <|-- TermPairwiseSimilarity\n        click TermPairwiseSimilarity href \"../TermPairwiseSimilarity\"\n      PairwiseSimilarity <|-- TermSetPairwiseSimilarity\n        click TermSetPairwiseSimilarity href \"../TermSetPairwiseSimilarity\"\n
    "},{"location":"Data-Model/PairwiseSimilarity/#inheritance","title":"Inheritance","text":"
       
    • PairwiseSimilarity
         
      • TermPairwiseSimilarity
        •  
      • TermSetPairwiseSimilarity
        •  
       
      •  
    "},{"location":"Data-Model/PairwiseSimilarity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"Data-Model/PairwiseSimilarity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/PairwiseSimilarity/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/PairwiseSimilarity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:PairwiseSimilarity native https://w3id.org/monarch/monarch-py/:PairwiseSimilarity"},{"location":"Data-Model/PairwiseSimilarity/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/PairwiseSimilarity/#direct","title":"Direct","text":"
    name: PairwiseSimilarity\ndescription: Abstract grouping for representing individual pairwise similarities\nfrom_schema: https://w3id.org/monarch/monarch-py\nabstract: true\n
    "},{"location":"Data-Model/PairwiseSimilarity/#induced","title":"Induced","text":"
    name: PairwiseSimilarity\ndescription: Abstract grouping for representing individual pairwise similarities\nfrom_schema: https://w3id.org/monarch/monarch-py\nabstract: true\n
    "},{"location":"Data-Model/Release/","title":"Class: Release","text":"
    A class to hold information about a release of the Monarch KG
     
    URI: https://w3id.org/monarch/monarch-py/:Release
     
     classDiagram\n    class Release\n    click Release href \"../Release\"\n      Release : graph_stats\n\n      Release : kg\n\n      Release : metadata\n\n      Release : neo4j\n\n      Release : qc_report\n\n      Release : solr\n\n      Release : sqlite\n\n      Release : url\n\n      Release : version\n
    "},{"location":"Data-Model/Release/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance version 0..1  String direct url 0..1  String direct kg 0..1  String direct sqlite 0..1  String direct solr 0..1  String direct neo4j 0..1  String direct metadata 0..1  String direct graph_stats 0..1  String direct qc_report 0..1  String direct"},{"location":"Data-Model/Release/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Release/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Release/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:Release native https://w3id.org/monarch/monarch-py/:Release"},{"location":"Data-Model/Release/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/Release/#direct","title":"Direct","text":"
    name: Release\ndescription: A class to hold information about a release of the Monarch KG\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- version\n- url\n- kg\n- sqlite\n- solr\n- neo4j\n- metadata\n- graph_stats\n- qc_report\n
    "},{"location":"Data-Model/Release/#induced","title":"Induced","text":"
    name: Release\ndescription: A class to hold information about a release of the Monarch KG\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  version:\n    name: version\n    id_prefixes:\n    - string\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: version\n    owner: Release\n    domain_of:\n    - Release\n    range: string\n  url:\n    name: url\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: url\n    owner: Release\n    domain_of:\n    - ExpandedCurie\n    - Release\n    range: string\n  kg:\n    name: kg\n    id_prefixes:\n    - string\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: kg\n    owner: Release\n    domain_of:\n    - Release\n    range: string\n  sqlite:\n    name: sqlite\n    id_prefixes:\n    - string\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: sqlite\n    owner: Release\n    domain_of:\n    - Release\n    range: string\n  solr:\n    name: solr\n    id_prefixes:\n    - string\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: solr\n    owner: Release\n    domain_of:\n    - Release\n    range: string\n  neo4j:\n    name: neo4j\n    id_prefixes:\n    - string\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: neo4j\n    owner: Release\n    domain_of:\n    - Release\n    range: string\n  metadata:\n    name: metadata\n    id_prefixes:\n    - string\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: metadata\n    owner: Release\n    domain_of:\n    - Release\n    range: string\n  graph_stats:\n    name: graph_stats\n    id_prefixes:\n    - string\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: graph_stats\n    owner: Release\n    domain_of:\n    - Release\n    range: string\n  qc_report:\n    name: qc_report\n    id_prefixes:\n    - string\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: qc_report\n    owner: Release\n    domain_of:\n    - Release\n    range: string\n
    "},{"location":"Data-Model/Results/","title":"Class: Results","text":"
       
    • NOTE: this is an abstract class and should not be instantiated directly
      •  
     
    URI: https://w3id.org/monarch/monarch-py/:Results
     
     classDiagram\n    class Results\n    click Results href \"../Results\"\n      Results <|-- AssociationResults\n        click AssociationResults href \"../AssociationResults\"\n      Results <|-- CompactAssociationResults\n        click CompactAssociationResults href \"../CompactAssociationResults\"\n      Results <|-- AssociationTableResults\n        click AssociationTableResults href \"../AssociationTableResults\"\n      Results <|-- CategoryGroupedAssociationResults\n        click CategoryGroupedAssociationResults href \"../CategoryGroupedAssociationResults\"\n      Results <|-- EntityResults\n        click EntityResults href \"../EntityResults\"\n      Results <|-- MappingResults\n        click MappingResults href \"../MappingResults\"\n      Results <|-- MultiEntityAssociationResults\n        click MultiEntityAssociationResults href \"../MultiEntityAssociationResults\"\n      Results <|-- SearchResults\n        click SearchResults href \"../SearchResults\"\n\n      Results : limit\n\n      Results : offset\n\n      Results : total\n
    "},{"location":"Data-Model/Results/#inheritance","title":"Inheritance","text":"
       
    • Results
         
      • AssociationResults
        •  
      • CompactAssociationResults
        •  
      • AssociationTableResults
        •  
      • CategoryGroupedAssociationResults
        •  
      • EntityResults
        •  
      • MappingResults
        •  
      • MultiEntityAssociationResults
        •  
      • SearchResults
        •  
       
      •  
    "},{"location":"Data-Model/Results/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance limit 1  Integer number of items to return in a response direct offset 1  Integer offset into the total number of items direct total 1  Integer total number of items matching a query direct"},{"location":"Data-Model/Results/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Results/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Results/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:Results native https://w3id.org/monarch/monarch-py/:Results"},{"location":"Data-Model/Results/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/Results/#direct","title":"Direct","text":"
    name: Results\nfrom_schema: https://w3id.org/monarch/monarch-py\nabstract: true\nslots:\n- limit\n- offset\n- total\n
    "},{"location":"Data-Model/Results/#induced","title":"Induced","text":"
    name: Results\nfrom_schema: https://w3id.org/monarch/monarch-py\nabstract: true\nattributes:\n  limit:\n    name: limit\n    description: number of items to return in a response\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: limit\n    owner: Results\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  offset:\n    name: offset\n    description: offset into the total number of items\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: offset\n    owner: Results\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  total:\n    name: total\n    description: total number of items matching a query\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: total\n    owner: Results\n    domain_of:\n    - Results\n    range: integer\n    required: true\n
    "},{"location":"Data-Model/SearchResult/","title":"Class: SearchResult","text":"
    URI: https://w3id.org/monarch/monarch-py/:SearchResult
     
     classDiagram\n    class SearchResult\n    click SearchResult href \"../SearchResult\"\n      Entity <|-- SearchResult\n        click Entity href \"../Entity\"\n\n      SearchResult : category\n\n      SearchResult : deprecated\n\n      SearchResult : description\n\n      SearchResult : full_name\n\n      SearchResult : has_phenotype\n\n      SearchResult : has_phenotype_closure\n\n      SearchResult : has_phenotype_closure_label\n\n      SearchResult : has_phenotype_count\n\n      SearchResult : has_phenotype_label\n\n      SearchResult : highlight\n\n      SearchResult : id\n\n      SearchResult : in_taxon\n\n      SearchResult : in_taxon_label\n\n      SearchResult : iri\n\n      SearchResult : name\n\n      SearchResult : namespace\n\n      SearchResult : provided_by\n\n      SearchResult : score\n\n      SearchResult : symbol\n\n      SearchResult : synonym\n\n      SearchResult : uri\n\n      SearchResult : xref\n
    "},{"location":"Data-Model/SearchResult/#inheritance","title":"Inheritance","text":"
       
    • Entity
         
      • SearchResult
        •  
       
      •  
    "},{"location":"Data-Model/SearchResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance highlight 0..1  String matching text snippet containing html tags direct score 0..1  Float direct id 1  String Entity category 1  String Entity name 1  String Entity full_name 0..1  String The long form name of an entity Entity deprecated 0..1  Boolean A boolean flag indicating that an entity is no longer considered current or v... Entity description 0..1  String Entity xref *  String Entity provided_by 0..1  String Entity in_taxon 0..1  String The biolink taxon that the entity is in the closure of Entity in_taxon_label 0..1  String The label of the biolink taxon that the entity is in the closure of Entity symbol 0..1  String Entity synonym *  String Entity uri 0..1  String The URI of the entity Entity iri 0..1  String Entity namespace 0..1  String The namespace/prefix portion of this entity's identifier Entity has_phenotype *  String A list of phenotype identifiers that are known to be associated with this ent... Entity has_phenotype_label *  String A list of phenotype labels that are known to be associated with this entity Entity has_phenotype_closure *  String A list of phenotype identifiers that are known to be associated with this ent... Entity has_phenotype_closure_label *  String A list of phenotype labels that are known to be associated with this entity e... Entity has_phenotype_count 0..1  Integer A count of the number of phenotypes that are known to be associated with this... Entity"},{"location":"Data-Model/SearchResult/#usages","title":"Usages","text":"used by used in type used SearchResults items range SearchResult"},{"location":"Data-Model/SearchResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/SearchResult/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/SearchResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:SearchResult native https://w3id.org/monarch/monarch-py/:SearchResult"},{"location":"Data-Model/SearchResult/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/SearchResult/#direct","title":"Direct","text":"
    name: SearchResult\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Entity\nslots:\n- highlight\n- score\nslot_usage:\n  category:\n    name: category\n    domain_of:\n    - Association\n    - AssociationCount\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Entity\n    required: true\n  name:\n    name: name\n    domain_of:\n    - Entity\n    - MultiEntityAssociationResults\n    required: true\n
    "},{"location":"Data-Model/SearchResult/#induced","title":"Induced","text":"
    name: SearchResult\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Entity\nslot_usage:\n  category:\n    name: category\n    domain_of:\n    - Association\n    - AssociationCount\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Entity\n    required: true\n  name:\n    name: name\n    domain_of:\n    - Entity\n    - MultiEntityAssociationResults\n    required: true\nattributes:\n  highlight:\n    name: highlight\n    description: matching text snippet containing html tags\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: highlight\n    owner: SearchResult\n    domain_of:\n    - SearchResult\n    range: string\n  score:\n    name: score\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: score\n    owner: SearchResult\n    domain_of:\n    - SearchResult\n    - BestMatch\n    - SemsimSearchResult\n    range: float\n  id:\n    name: id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: SearchResult\n    domain_of:\n    - Association\n    - ExpandedCurie\n    - Entity\n    - HistoPheno\n    - HistoBin\n    - Mapping\n    - MultiEntityAssociationResults\n    - TermInfo\n    range: string\n    required: true\n  category:\n    name: category\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: false\n    alias: category\n    owner: SearchResult\n    domain_of:\n    - Association\n    - AssociationCount\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Entity\n    range: string\n    required: true\n  name:\n    name: name\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: name\n    owner: SearchResult\n    domain_of:\n    - Entity\n    - MultiEntityAssociationResults\n    range: string\n    required: true\n  full_name:\n    name: full_name\n    description: The long form name of an entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: full_name\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: string\n  deprecated:\n    name: deprecated\n    description: A boolean flag indicating that an entity is no longer considered\n      current or valid.\n    from_schema: https://w3id.org/monarch/monarch-py\n    exact_mappings:\n    - oboInOwl:ObsoleteClass\n    rank: 1000\n    alias: deprecated\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: boolean\n  description:\n    name: description\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: description\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: string\n  xref:\n    name: xref\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: xref\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: string\n  provided_by:\n    name: provided_by\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: provided_by\n    owner: SearchResult\n    domain_of:\n    - Association\n    - Entity\n    range: string\n  in_taxon:\n    name: in_taxon\n    description: The biolink taxon that the entity is in the closure of.\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: in_taxon\n    owner: SearchResult\n    domain_of:\n    - Entity\n    - Node\n    range: string\n  in_taxon_label:\n    name: in_taxon_label\n    description: The label of the biolink taxon that the entity is in the closure\n      of.\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: in_taxon_label\n    owner: SearchResult\n    domain_of:\n    - Entity\n    - Node\n    range: string\n  symbol:\n    name: symbol\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: symbol\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: string\n  synonym:\n    name: synonym\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: synonym\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: string\n  uri:\n    name: uri\n    description: The URI of the entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: uri\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: string\n  iri:\n    name: iri\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: iri\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: string\n  namespace:\n    name: namespace\n    description: The namespace/prefix portion of this entity's identifier\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: namespace\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: string\n  has_phenotype:\n    name: has_phenotype\n    description: A list of phenotype identifiers that are known to be associated with\n      this entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: has_phenotype\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: string\n    inlined: true\n    inlined_as_list: true\n  has_phenotype_label:\n    name: has_phenotype_label\n    description: A list of phenotype labels that are known to be associated with this\n      entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: has_phenotype_label\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: string\n    inlined: true\n    inlined_as_list: true\n  has_phenotype_closure:\n    name: has_phenotype_closure\n    description: A list of phenotype identifiers that are known to be associated with\n      this entity expanded to include all ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: has_phenotype_closure\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: string\n    inlined: true\n    inlined_as_list: true\n  has_phenotype_closure_label:\n    name: has_phenotype_closure_label\n    description: A list of phenotype labels that are known to be associated with this\n      entity expanded to include all ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: has_phenotype_closure_label\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: string\n    inlined: true\n    inlined_as_list: true\n  has_phenotype_count:\n    name: has_phenotype_count\n    description: A count of the number of phenotypes that are known to be associated\n      with this entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_phenotype_count\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: integer\n
    "},{"location":"Data-Model/SearchResults/","title":"Class: SearchResults","text":"
    URI: https://w3id.org/monarch/monarch-py/:SearchResults
     
     classDiagram\n    class SearchResults\n    click SearchResults href \"../SearchResults\"\n      Results <|-- SearchResults\n        click Results href \"../Results\"\n\n      SearchResults : facet_fields\n\n\n\n\n    SearchResults --> \"*\" FacetField : facet_fields\n    click FacetField href \"../FacetField\"\n\n\n      SearchResults : facet_queries\n\n\n\n\n    SearchResults --> \"*\" FacetValue : facet_queries\n    click FacetValue href \"../FacetValue\"\n\n\n      SearchResults : items\n\n\n\n\n    SearchResults --> \"1..*\" SearchResult : items\n    click SearchResult href \"../SearchResult\"\n\n\n      SearchResults : limit\n\n      SearchResults : offset\n\n      SearchResults : total\n
    "},{"location":"Data-Model/SearchResults/#inheritance","title":"Inheritance","text":"
       
    • Results
         
      • SearchResults
        •  
       
      •  
    "},{"location":"Data-Model/SearchResults/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance items 1..*  SearchResult A collection of items, with the type to be overriden by slot_usage direct facet_fields *  FacetField Collection of facet field responses with the field values and counts direct facet_queries *  FacetValue Collection of facet query responses with the query string values and counts direct limit 1  Integer number of items to return in a response Results offset 1  Integer offset into the total number of items Results total 1  Integer total number of items matching a query Results"},{"location":"Data-Model/SearchResults/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/SearchResults/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/SearchResults/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:SearchResults native https://w3id.org/monarch/monarch-py/:SearchResults"},{"location":"Data-Model/SearchResults/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/SearchResults/#direct","title":"Direct","text":"
    name: SearchResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- items\n- facet_fields\n- facet_queries\nslot_usage:\n  items:\n    name: items\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: SearchResult\n
    "},{"location":"Data-Model/SearchResults/#induced","title":"Induced","text":"
    name: SearchResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n  items:\n    name: items\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: SearchResult\nattributes:\n  items:\n    name: items\n    description: A collection of items, with the type to be overriden by slot_usage\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: items\n    owner: SearchResults\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: SearchResult\n    required: true\n    inlined: true\n    inlined_as_list: true\n  facet_fields:\n    name: facet_fields\n    description: Collection of facet field responses with the field values and counts\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: facet_fields\n    owner: SearchResults\n    domain_of:\n    - SearchResults\n    range: FacetField\n    inlined: true\n    inlined_as_list: true\n  facet_queries:\n    name: facet_queries\n    description: Collection of facet query responses with the query string values\n      and counts\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: facet_queries\n    owner: SearchResults\n    domain_of:\n    - SearchResults\n    range: FacetValue\n    inlined: true\n    inlined_as_list: true\n  limit:\n    name: limit\n    description: number of items to return in a response\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: limit\n    owner: SearchResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  offset:\n    name: offset\n    description: offset into the total number of items\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: offset\n    owner: SearchResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  total:\n    name: total\n    description: total number of items matching a query\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: total\n    owner: SearchResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n
    "},{"location":"Data-Model/SemsimSearchResult/","title":"Class: SemsimSearchResult","text":"
    URI: https://w3id.org/monarch/monarch-py/:SemsimSearchResult
     
     classDiagram\n    class SemsimSearchResult\n    click SemsimSearchResult href \"../SemsimSearchResult\"\n      SemsimSearchResult : score\n\n      SemsimSearchResult : similarity\n\n\n\n\n    SemsimSearchResult --> \"0..1\" TermSetPairwiseSimilarity : similarity\n    click TermSetPairwiseSimilarity href \"../TermSetPairwiseSimilarity\"\n\n\n      SemsimSearchResult : subject\n\n\n\n\n    SemsimSearchResult --> \"1\" Entity : subject\n    click Entity href \"../Entity\"\n
    "},{"location":"Data-Model/SemsimSearchResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 1  Entity direct score 0..1  Float direct similarity 0..1  TermSetPairwiseSimilarity direct"},{"location":"Data-Model/SemsimSearchResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/SemsimSearchResult/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/SemsimSearchResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:SemsimSearchResult native https://w3id.org/monarch/monarch-py/:SemsimSearchResult"},{"location":"Data-Model/SemsimSearchResult/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/SemsimSearchResult/#direct","title":"Direct","text":"
    name: SemsimSearchResult\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- subject\n- score\n- similarity\nslot_usage:\n  subject:\n    name: subject\n    domain_of:\n    - Association\n    - CompactAssociation\n    - SemsimSearchResult\n    range: Entity\n    inlined: true\n
    "},{"location":"Data-Model/SemsimSearchResult/#induced","title":"Induced","text":"
    name: SemsimSearchResult\nfrom_schema: https://w3id.org/monarch/monarch-py\nslot_usage:\n  subject:\n    name: subject\n    domain_of:\n    - Association\n    - CompactAssociation\n    - SemsimSearchResult\n    range: Entity\n    inlined: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: subject\n    owner: SemsimSearchResult\n    domain_of:\n    - Association\n    - CompactAssociation\n    - SemsimSearchResult\n    range: Entity\n    required: true\n    inlined: true\n  score:\n    name: score\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: score\n    owner: SemsimSearchResult\n    domain_of:\n    - SearchResult\n    - BestMatch\n    - SemsimSearchResult\n    range: float\n  similarity:\n    name: similarity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: similarity\n    owner: SemsimSearchResult\n    domain_of:\n    - BestMatch\n    - SemsimSearchResult\n    range: TermSetPairwiseSimilarity\n
    "},{"location":"Data-Model/Sparqlpath/","title":"Type: Sparqlpath","text":"
    A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.
     
    URI: xsd:string
     
       
    •  
      base: str
       
      •  
    •  
      uri: xsd:string
       
      •  
    •  
      repr: str
       
      •  
    "},{"location":"Data-Model/Sparqlpath/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Sparqlpath/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/String/","title":"Type: String","text":"
    A character string
     
    URI: xsd:string
     
       
    •  
      base: str
       
      •  
    •  
      uri: xsd:string
       
      •  
    "},{"location":"Data-Model/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/String/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/TermInfo/","title":"Class: TermInfo","text":"
    URI: https://w3id.org/monarch/monarch-py/:TermInfo
     
     classDiagram\n    class TermInfo\n    click TermInfo href \"../TermInfo\"\n      TermInfo : id\n\n      TermInfo : label\n
    "},{"location":"Data-Model/TermInfo/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1  String direct label 0..1  String direct"},{"location":"Data-Model/TermInfo/#usages","title":"Usages","text":"used by used in type used TermSetPairwiseSimilarity subject_termset range TermInfo TermSetPairwiseSimilarity object_termset range TermInfo"},{"location":"Data-Model/TermInfo/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/TermInfo/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/TermInfo/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:TermInfo native https://w3id.org/monarch/monarch-py/:TermInfo"},{"location":"Data-Model/TermInfo/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/TermInfo/#direct","title":"Direct","text":"
    name: TermInfo\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  id:\n    name: id\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    identifier: true\n    domain_of:\n    - Association\n    - ExpandedCurie\n    - Entity\n    - HistoPheno\n    - HistoBin\n    - Mapping\n    - MultiEntityAssociationResults\n    - TermInfo\n    required: true\n  label:\n    name: label\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    slot_uri: rdfs:label\n    domain_of:\n    - FacetValue\n    - FacetField\n    - TermInfo\n
    "},{"location":"Data-Model/TermInfo/#induced","title":"Induced","text":"
    name: TermInfo\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  id:\n    name: id\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    identifier: true\n    alias: id\n    owner: TermInfo\n    domain_of:\n    - Association\n    - ExpandedCurie\n    - Entity\n    - HistoPheno\n    - HistoBin\n    - Mapping\n    - MultiEntityAssociationResults\n    - TermInfo\n    range: string\n    required: true\n  label:\n    name: label\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    slot_uri: rdfs:label\n    alias: label\n    owner: TermInfo\n    domain_of:\n    - FacetValue\n    - FacetField\n    - TermInfo\n    range: string\n
    "},{"location":"Data-Model/TermPairwiseSimilarity/","title":"Class: TermPairwiseSimilarity","text":"
    A simple pairwise similarity between two atomic concepts/terms
     
    URI: https://w3id.org/monarch/monarch-py/:TermPairwiseSimilarity
     
     classDiagram\n    class TermPairwiseSimilarity\n    click TermPairwiseSimilarity href \"../TermPairwiseSimilarity\"\n      PairwiseSimilarity <|-- TermPairwiseSimilarity\n        click PairwiseSimilarity href \"../PairwiseSimilarity\"\n\n      TermPairwiseSimilarity : ancestor_id\n\n      TermPairwiseSimilarity : ancestor_information_content\n\n      TermPairwiseSimilarity : ancestor_label\n\n      TermPairwiseSimilarity : ancestor_source\n\n      TermPairwiseSimilarity : cosine_similarity\n\n      TermPairwiseSimilarity : dice_similarity\n\n      TermPairwiseSimilarity : jaccard_similarity\n\n      TermPairwiseSimilarity : object_id\n\n      TermPairwiseSimilarity : object_information_content\n\n      TermPairwiseSimilarity : object_label\n\n      TermPairwiseSimilarity : object_source\n\n      TermPairwiseSimilarity : phenodigm_score\n\n      TermPairwiseSimilarity : subject_id\n\n      TermPairwiseSimilarity : subject_information_content\n\n      TermPairwiseSimilarity : subject_label\n\n      TermPairwiseSimilarity : subject_source\n
    "},{"location":"Data-Model/TermPairwiseSimilarity/#inheritance","title":"Inheritance","text":"
       
    • PairwiseSimilarity
         
      • TermPairwiseSimilarity
        •  
       
      •  
    "},{"location":"Data-Model/TermPairwiseSimilarity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_id 1  String direct subject_label 0..1  String The name of the subject entity direct subject_source 0..1  String the source for the first entity direct object_id 1  String direct object_label 0..1  String The name of the object entity direct object_source 0..1  String the source for the second entity direct ancestor_id 0..1  Uriorcurie the most recent common ancestor of the two compared entities direct ancestor_label 0..1  String the name or label of the ancestor concept direct ancestor_source 0..1  String direct object_information_content 0..1  NegativeLogValue The IC of the object direct subject_information_content 0..1  NegativeLogValue The IC of the subject direct ancestor_information_content 0..1  NegativeLogValue The IC of the object direct jaccard_similarity 0..1  ZeroToOne The number of concepts in the intersection divided by the number in the union direct cosine_similarity 0..1  Float the dot product of two node embeddings divided by the product of their length... direct dice_similarity 0..1  ZeroToOne direct phenodigm_score 0..1  NonNegativeFloat the geometric mean of the jaccard similarity and the information content direct"},{"location":"Data-Model/TermPairwiseSimilarity/#usages","title":"Usages","text":"used by used in type used BestMatch similarity range TermPairwiseSimilarity"},{"location":"Data-Model/TermPairwiseSimilarity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/TermPairwiseSimilarity/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/TermPairwiseSimilarity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:TermPairwiseSimilarity native https://w3id.org/monarch/monarch-py/:TermPairwiseSimilarity"},{"location":"Data-Model/TermPairwiseSimilarity/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/TermPairwiseSimilarity/#direct","title":"Direct","text":"
    name: TermPairwiseSimilarity\ndescription: A simple pairwise similarity between two atomic concepts/terms\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: PairwiseSimilarity\nslots:\n- subject_id\n- subject_label\n- subject_source\n- object_id\n- object_label\n- object_source\n- ancestor_id\n- ancestor_label\n- ancestor_source\n- object_information_content\n- subject_information_content\n- ancestor_information_content\n- jaccard_similarity\n- cosine_similarity\n- dice_similarity\n- phenodigm_score\n
    "},{"location":"Data-Model/TermPairwiseSimilarity/#induced","title":"Induced","text":"
    name: TermPairwiseSimilarity\ndescription: A simple pairwise similarity between two atomic concepts/terms\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: PairwiseSimilarity\nattributes:\n  subject_id:\n    name: subject_id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: subject_id\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n    required: true\n  subject_label:\n    name: subject_label\n    description: The name of the subject entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: subject_label\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n  subject_source:\n    name: subject_source\n    description: the source for the first entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    slot_uri: sssom:subject_source\n    alias: subject_source\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - TermPairwiseSimilarity\n    range: string\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: object_id\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n    required: true\n  object_label:\n    name: object_label\n    description: The name of the object entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: object_label\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n  object_source:\n    name: object_source\n    description: the source for the second entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    slot_uri: sssom:object_source\n    alias: object_source\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - TermPairwiseSimilarity\n    range: string\n  ancestor_id:\n    name: ancestor_id\n    description: the most recent common ancestor of the two compared entities. If\n      there are multiple MRCAs then the most informative one is selected\n    todos:\n    - decide on what to do when there are multiple possible ancestos\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: ancestor_id\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - TermPairwiseSimilarity\n    range: uriorcurie\n  ancestor_label:\n    name: ancestor_label\n    description: the name or label of the ancestor concept\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: ancestor_label\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - TermPairwiseSimilarity\n    range: string\n  ancestor_source:\n    name: ancestor_source\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: ancestor_source\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - TermPairwiseSimilarity\n    range: string\n  object_information_content:\n    name: object_information_content\n    description: The IC of the object\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: information_content\n    alias: object_information_content\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - TermPairwiseSimilarity\n    range: NegativeLogValue\n  subject_information_content:\n    name: subject_information_content\n    description: The IC of the subject\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: information_content\n    alias: subject_information_content\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - TermPairwiseSimilarity\n    range: NegativeLogValue\n  ancestor_information_content:\n    name: ancestor_information_content\n    description: The IC of the object\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: information_content\n    alias: ancestor_information_content\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - TermPairwiseSimilarity\n    range: NegativeLogValue\n  jaccard_similarity:\n    name: jaccard_similarity\n    description: The number of concepts in the intersection divided by the number\n      in the union\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: score\n    alias: jaccard_similarity\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - TermPairwiseSimilarity\n    range: ZeroToOne\n  cosine_similarity:\n    name: cosine_similarity\n    description: the dot product of two node embeddings divided by the product of\n      their lengths\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: score\n    alias: cosine_similarity\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - TermPairwiseSimilarity\n    range: float\n  dice_similarity:\n    name: dice_similarity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: score\n    alias: dice_similarity\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - TermPairwiseSimilarity\n    range: ZeroToOne\n  phenodigm_score:\n    name: phenodigm_score\n    description: the geometric mean of the jaccard similarity and the information\n      content\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: score\n    alias: phenodigm_score\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - TermPairwiseSimilarity\n    range: NonNegativeFloat\n    equals_expression: sqrt({jaccard_similarity} * {information_content})\n
    "},{"location":"Data-Model/TermSetPairwiseSimilarity/","title":"Class: TermSetPairwiseSimilarity","text":"
    A simple pairwise similarity between two sets of concepts/terms
     
    URI: https://w3id.org/monarch/monarch-py/:TermSetPairwiseSimilarity
     
     classDiagram\n    class TermSetPairwiseSimilarity\n    click TermSetPairwiseSimilarity href \"../TermSetPairwiseSimilarity\"\n      PairwiseSimilarity <|-- TermSetPairwiseSimilarity\n        click PairwiseSimilarity href \"../PairwiseSimilarity\"\n\n      TermSetPairwiseSimilarity : average_score\n\n      TermSetPairwiseSimilarity : best_score\n\n      TermSetPairwiseSimilarity : metric\n\n      TermSetPairwiseSimilarity : object_best_matches\n\n\n\n\n    TermSetPairwiseSimilarity --> \"*\" BestMatch : object_best_matches\n    click BestMatch href \"../BestMatch\"\n\n\n      TermSetPairwiseSimilarity : object_termset\n\n\n\n\n    TermSetPairwiseSimilarity --> \"*\" TermInfo : object_termset\n    click TermInfo href \"../TermInfo\"\n\n\n      TermSetPairwiseSimilarity : subject_best_matches\n\n\n\n\n    TermSetPairwiseSimilarity --> \"*\" BestMatch : subject_best_matches\n    click BestMatch href \"../BestMatch\"\n\n\n      TermSetPairwiseSimilarity : subject_termset\n\n\n\n\n    TermSetPairwiseSimilarity --> \"*\" TermInfo : subject_termset\n    click TermInfo href \"../TermInfo\"\n
    "},{"location":"Data-Model/TermSetPairwiseSimilarity/#inheritance","title":"Inheritance","text":"
       
    • PairwiseSimilarity
         
      • TermSetPairwiseSimilarity
        •  
       
      •  
    "},{"location":"Data-Model/TermSetPairwiseSimilarity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_termset *  TermInfo direct object_termset *  TermInfo direct subject_best_matches *  BestMatch direct object_best_matches *  BestMatch direct average_score 0..1  Float direct best_score 0..1  Float direct metric 0..1  Uriorcurie direct"},{"location":"Data-Model/TermSetPairwiseSimilarity/#usages","title":"Usages","text":"used by used in type used SemsimSearchResult similarity range TermSetPairwiseSimilarity"},{"location":"Data-Model/TermSetPairwiseSimilarity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/TermSetPairwiseSimilarity/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/TermSetPairwiseSimilarity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:TermSetPairwiseSimilarity native https://w3id.org/monarch/monarch-py/:TermSetPairwiseSimilarity"},{"location":"Data-Model/TermSetPairwiseSimilarity/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/TermSetPairwiseSimilarity/#direct","title":"Direct","text":"
    name: TermSetPairwiseSimilarity\ndescription: A simple pairwise similarity between two sets of concepts/terms\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: PairwiseSimilarity\nslots:\n- subject_termset\n- object_termset\n- subject_best_matches\n- object_best_matches\n- average_score\n- best_score\n- metric\n
    "},{"location":"Data-Model/TermSetPairwiseSimilarity/#induced","title":"Induced","text":"
    name: TermSetPairwiseSimilarity\ndescription: A simple pairwise similarity between two sets of concepts/terms\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: PairwiseSimilarity\nattributes:\n  subject_termset:\n    name: subject_termset\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: subject_termset\n    owner: TermSetPairwiseSimilarity\n    domain_of:\n    - TermSetPairwiseSimilarity\n    range: TermInfo\n    inlined: true\n  object_termset:\n    name: object_termset\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: object_termset\n    owner: TermSetPairwiseSimilarity\n    domain_of:\n    - TermSetPairwiseSimilarity\n    range: TermInfo\n    inlined: true\n  subject_best_matches:\n    name: subject_best_matches\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: subject_best_matches\n    owner: TermSetPairwiseSimilarity\n    domain_of:\n    - TermSetPairwiseSimilarity\n    range: BestMatch\n    inlined: true\n  object_best_matches:\n    name: object_best_matches\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: object_best_matches\n    owner: TermSetPairwiseSimilarity\n    domain_of:\n    - TermSetPairwiseSimilarity\n    range: BestMatch\n    inlined: true\n  average_score:\n    name: average_score\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: average_score\n    owner: TermSetPairwiseSimilarity\n    domain_of:\n    - TermSetPairwiseSimilarity\n    range: float\n    required: false\n  best_score:\n    name: best_score\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: best_score\n    owner: TermSetPairwiseSimilarity\n    domain_of:\n    - TermSetPairwiseSimilarity\n    range: float\n    required: false\n  metric:\n    name: metric\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: metric\n    owner: TermSetPairwiseSimilarity\n    domain_of:\n    - TermSetPairwiseSimilarity\n    range: uriorcurie\n
    "},{"location":"Data-Model/TextAnnotationResult/","title":"Class: TextAnnotationResult","text":"
    URI: https://w3id.org/monarch/monarch-py/:TextAnnotationResult
     
     classDiagram\n    class TextAnnotationResult\n    click TextAnnotationResult href \"../TextAnnotationResult\"\n      TextAnnotationResult : end\n\n      TextAnnotationResult : start\n\n      TextAnnotationResult : text\n\n      TextAnnotationResult : tokens\n\n\n\n\n    TextAnnotationResult --> \"*\" Entity : tokens\n    click Entity href \"../Entity\"\n
    "},{"location":"Data-Model/TextAnnotationResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance text 0..1  String text without tokens direct tokens *  Entity A collection of entities or concepts direct start 0..1  Integer start position of the annotation direct end 0..1  Integer end position of the annotation direct"},{"location":"Data-Model/TextAnnotationResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/TextAnnotationResult/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/TextAnnotationResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:TextAnnotationResult native https://w3id.org/monarch/monarch-py/:TextAnnotationResult"},{"location":"Data-Model/TextAnnotationResult/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/TextAnnotationResult/#direct","title":"Direct","text":"
    name: TextAnnotationResult\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- text\n- tokens\n- start\n- end\n
    "},{"location":"Data-Model/TextAnnotationResult/#induced","title":"Induced","text":"
    name: TextAnnotationResult\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  text:\n    name: text\n    description: text without tokens\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: text\n    owner: TextAnnotationResult\n    domain_of:\n    - TextAnnotationResult\n    range: string\n    inlined: true\n  tokens:\n    name: tokens\n    description: A collection of entities or concepts\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    multivalued: true\n    alias: tokens\n    owner: TextAnnotationResult\n    domain_of:\n    - TextAnnotationResult\n    range: Entity\n    inlined: true\n    inlined_as_list: true\n  start:\n    name: start\n    description: start position of the annotation\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: start\n    owner: TextAnnotationResult\n    domain_of:\n    - TextAnnotationResult\n    range: integer\n  end:\n    name: end\n    description: end position of the annotation\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: end\n    owner: TextAnnotationResult\n    domain_of:\n    - TextAnnotationResult\n    range: integer\n
    "},{"location":"Data-Model/Time/","title":"Type: Time","text":"
    A time object represents a (local) time of day, independent of any particular day
     
    URI: xsd:time
     
       
    •  
      base: XSDTime
       
      •  
    •  
      uri: xsd:time
       
      •  
    •  
      repr: str
       
      •  
    "},{"location":"Data-Model/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Time/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Uri/","title":"Type: Uri","text":"
    a complete URI
     
    URI: xsd:anyURI
     
       
    •  
      base: URI
       
      •  
    •  
      uri: xsd:anyURI
       
      •  
    •  
      repr: str
       
      •  
    "},{"location":"Data-Model/Uri/#comments","title":"Comments","text":"
       
    • in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node
      •  
    "},{"location":"Data-Model/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Uri/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Uriorcurie/","title":"Type: Uriorcurie","text":"
    a URI or a CURIE
     
    URI: xsd:anyURI
     
       
    •  
      base: URIorCURIE
       
      •  
    •  
      uri: xsd:anyURI
       
      •  
    •  
      repr: str
       
      •  
    "},{"location":"Data-Model/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Uriorcurie/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/ZeroToOne/","title":"Type: ZeroToOne","text":"
    URI: xsd:float
     
       
    •  
      base: float
       
      •  
    •  
      uri: xsd:float
       
      •  
    •  
      typeof: float
       
      •  
    "},{"location":"Data-Model/ZeroToOne/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/ZeroToOne/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/agent_type/","title":"Slot: agent_type","text":"
    Describes the high-level category of agent who originally generated a  statement of knowledge or other type of information.
     
    URI: biolink:agent_type
    "},{"location":"Data-Model/agent_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/agent_type/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/agent_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/agent_type/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/agent_type/#linkml-source","title":"LinkML Source","text":"
    name: agent_type\ndescription: Describes the high-level category of agent who originally generated a  statement\n  of knowledge or other type of information.\nnotes:\n- The range in this schema is represented as a string, but is constrained  to values\n  from biolink:AgentTypeEnum at ingest time\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nslot_uri: biolink:agent_type\nmultivalued: false\nalias: agent_type\ndomain_of:\n- Association\nrange: string\nrequired: true\n
    "},{"location":"Data-Model/aggregator_knowledge_source/","title":"Slot: aggregator_knowledge_source","text":"
    URI: https://w3id.org/monarch/monarch-py/:aggregator_knowledge_source
    "},{"location":"Data-Model/aggregator_knowledge_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/aggregator_knowledge_source/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/aggregator_knowledge_source/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/aggregator_knowledge_source/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/aggregator_knowledge_source/#linkml-source","title":"LinkML Source","text":"
    name: aggregator_knowledge_source\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: aggregator_knowledge_source\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/ancestor_id/","title":"Slot: ancestor_id","text":"
    the most recent common ancestor of the two compared entities. If there are multiple MRCAs then the most informative one is selected
     
    URI: https://w3id.org/monarch/monarch-py/:ancestor_id
    "},{"location":"Data-Model/ancestor_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/ancestor_id/#properties","title":"Properties","text":"
       
    • Range: Uriorcurie
      •  
    "},{"location":"Data-Model/ancestor_id/#todos","title":"TODOs","text":"
       
    • decide on what to do when there are multiple possible ancestos
      •  
    "},{"location":"Data-Model/ancestor_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/ancestor_id/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/ancestor_id/#linkml-source","title":"LinkML Source","text":"
    name: ancestor_id\ndescription: the most recent common ancestor of the two compared entities. If there\n  are multiple MRCAs then the most informative one is selected\ntodos:\n- decide on what to do when there are multiple possible ancestos\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: ancestor_id\ndomain_of:\n- TermPairwiseSimilarity\nrange: uriorcurie\n
    "},{"location":"Data-Model/ancestor_information_content/","title":"Slot: ancestor_information_content","text":"
    The IC of the object
     
    URI: https://w3id.org/monarch/monarch-py/:ancestor_information_content
    "},{"location":"Data-Model/ancestor_information_content/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • information_content
           
        • ancestor_information_content
          •  
         
        •  
       
      •  
    "},{"location":"Data-Model/ancestor_information_content/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/ancestor_information_content/#properties","title":"Properties","text":"
       
    • Range: NegativeLogValue
      •  
    "},{"location":"Data-Model/ancestor_information_content/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/ancestor_information_content/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/ancestor_information_content/#linkml-source","title":"LinkML Source","text":"
    name: ancestor_information_content\ndescription: The IC of the object\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: information_content\nalias: ancestor_information_content\ndomain_of:\n- TermPairwiseSimilarity\nrange: NegativeLogValue\n
    "},{"location":"Data-Model/ancestor_label/","title":"Slot: ancestor_label","text":"
    the name or label of the ancestor concept
     
    URI: https://w3id.org/monarch/monarch-py/:ancestor_label
    "},{"location":"Data-Model/ancestor_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/ancestor_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/ancestor_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/ancestor_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/ancestor_label/#linkml-source","title":"LinkML Source","text":"
    name: ancestor_label\ndescription: the name or label of the ancestor concept\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: ancestor_label\ndomain_of:\n- TermPairwiseSimilarity\nrange: string\n
    "},{"location":"Data-Model/ancestor_source/","title":"Slot: ancestor_source","text":"
    URI: https://w3id.org/monarch/monarch-py/:ancestor_source
    "},{"location":"Data-Model/ancestor_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/ancestor_source/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/ancestor_source/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/ancestor_source/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/ancestor_source/#linkml-source","title":"LinkML Source","text":"
    name: ancestor_source\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: ancestor_source\ndomain_of:\n- TermPairwiseSimilarity\nrange: string\n
    "},{"location":"Data-Model/associated_categories/","title":"Slot: associated_categories","text":"
    URI: https://w3id.org/monarch/monarch-py/:associated_categories
    "},{"location":"Data-Model/associated_categories/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MultiEntityAssociationResults no"},{"location":"Data-Model/associated_categories/#properties","title":"Properties","text":"
       
    •  
      Range: CategoryGroupedAssociationResults
       
      •  
    •  
      Multivalued: True
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/associated_categories/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/associated_categories/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/associated_categories/#linkml-source","title":"LinkML Source","text":"
    name: associated_categories\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: associated_categories\ndomain_of:\n- MultiEntityAssociationResults\nrange: CategoryGroupedAssociationResults\nrequired: true\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/association_counts/","title":"Slot: association_counts","text":"
    URI: https://w3id.org/monarch/monarch-py/:association_counts
    "},{"location":"Data-Model/association_counts/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/association_counts/#properties","title":"Properties","text":"
       
    •  
      Range: AssociationCount
       
      •  
    •  
      Multivalued: True
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/association_counts/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/association_counts/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/association_counts/#linkml-source","title":"LinkML Source","text":"
    name: association_counts\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: association_counts\ndomain_of:\n- Node\nrange: AssociationCount\nrequired: true\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/average_score/","title":"Slot: average_score","text":"
    URI: https://w3id.org/monarch/monarch-py/:average_score
    "},{"location":"Data-Model/average_score/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/average_score/#properties","title":"Properties","text":"
       
    • Range: Float
      •  
    "},{"location":"Data-Model/average_score/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/average_score/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/average_score/#linkml-source","title":"LinkML Source","text":"
    name: average_score\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: average_score\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: float\nrequired: false\n
    "},{"location":"Data-Model/best_score/","title":"Slot: best_score","text":"
    URI: https://w3id.org/monarch/monarch-py/:best_score
    "},{"location":"Data-Model/best_score/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/best_score/#properties","title":"Properties","text":"
       
    • Range: Float
      •  
    "},{"location":"Data-Model/best_score/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/best_score/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/best_score/#linkml-source","title":"LinkML Source","text":"
    name: best_score\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: best_score\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: float\nrequired: false\n
    "},{"location":"Data-Model/category/","title":"Slot: category","text":"
    URI: https://w3id.org/monarch/monarch-py/:category
    "},{"location":"Data-Model/category/#inheritance","title":"Inheritance","text":"
       
    • category
         
      • subject_category
        •  
      • object_category
        •  
      • qualifiers_category
        •  
      • qualifier_category
        •  
      • frequency_qualifier_category
        •  
      • onset_qualifier_category
        •  
      • sex_qualifier_category
        •  
      • stage_qualifier_category
        •  
       
      •  
    "},{"location":"Data-Model/category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AssociationTypeMapping A data class to hold the necessary information to produce association type co... yes Entity Represents an Entity in the Monarch KG data model no AssociationCount yes DirectionalAssociation An association that gives it's direction relative to a specified entity no SearchResult yes Node UI container class extending Entity with additional information no CompactAssociation no Association no"},{"location":"Data-Model/category/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/category/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/category/#linkml-source","title":"LinkML Source","text":"
    name: category\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: false\nalias: category\ndomain_of:\n- Association\n- AssociationCount\n- CompactAssociation\n- AssociationTypeMapping\n- Entity\nrange: string\n
    "},{"location":"Data-Model/causal_gene/","title":"Slot: causal_gene","text":"
    A list of genes that are known to be causally associated with a disease
     
    URI: https://w3id.org/monarch/monarch-py/:causal_gene
    "},{"location":"Data-Model/causal_gene/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/causal_gene/#properties","title":"Properties","text":"
       
    •  
      Range: Entity
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/causal_gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/causal_gene/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/causal_gene/#linkml-source","title":"LinkML Source","text":"
    name: causal_gene\ndescription: A list of genes that are known to be causally associated with a disease\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: causal_gene\ndomain_of:\n- Node\nrange: Entity\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/causes_disease/","title":"Slot: causes_disease","text":"
    A list of diseases that are known to be causally associated with a gene
     
    URI: https://w3id.org/monarch/monarch-py/:causes_disease
    "},{"location":"Data-Model/causes_disease/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/causes_disease/#properties","title":"Properties","text":"
       
    •  
      Range: Entity
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/causes_disease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/causes_disease/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/causes_disease/#linkml-source","title":"LinkML Source","text":"
    name: causes_disease\ndescription: A list of diseases that are known to be causally associated with a gene\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: causes_disease\ndomain_of:\n- Node\nrange: Entity\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/cosine_similarity/","title":"Slot: cosine_similarity","text":"
    the dot product of two node embeddings divided by the product of their lengths
     
    URI: https://w3id.org/monarch/monarch-py/:cosine_similarity
    "},{"location":"Data-Model/cosine_similarity/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • cosine_similarity
        •  
       
      •  
    "},{"location":"Data-Model/cosine_similarity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/cosine_similarity/#properties","title":"Properties","text":"
       
    • Range: Float
      •  
    "},{"location":"Data-Model/cosine_similarity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/cosine_similarity/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/cosine_similarity/#linkml-source","title":"LinkML Source","text":"
    name: cosine_similarity\ndescription: the dot product of two node embeddings divided by the product of their\n  lengths\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: cosine_similarity\ndomain_of:\n- TermPairwiseSimilarity\nrange: float\n
    "},{"location":"Data-Model/count/","title":"Slot: count","text":"
    count of documents
     
    URI: https://w3id.org/monarch/monarch-py/:count
    "},{"location":"Data-Model/count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FacetValue no AssociationCount no HistoBin no"},{"location":"Data-Model/count/#properties","title":"Properties","text":"
       
    • Range: Integer
      •  
    "},{"location":"Data-Model/count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/count/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/count/#linkml-source","title":"LinkML Source","text":"
    name: count\ndescription: count of documents\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: count\ndomain_of:\n- FacetValue\nrange: integer\n
    "},{"location":"Data-Model/counterpart_category/","title":"Slot: counterpart_category","text":"
    The category of the counterpart entity in a given association,  eg. the category of the entity that is not the subject
     
    URI: https://w3id.org/monarch/monarch-py/:counterpart_category
    "},{"location":"Data-Model/counterpart_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CategoryGroupedAssociationResults no"},{"location":"Data-Model/counterpart_category/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/counterpart_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/counterpart_category/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/counterpart_category/#linkml-source","title":"LinkML Source","text":"
    name: counterpart_category\ndescription: The category of the counterpart entity in a given association,  eg. the\n  category of the entity that is not the subject\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: counterpart_category\ndomain_of:\n- CategoryGroupedAssociationResults\nrange: string\n
    "},{"location":"Data-Model/deprecated/","title":"Slot: deprecated","text":"
    A boolean flag indicating that an entity is no longer considered current or valid.
     
    URI: https://w3id.org/monarch/monarch-py/:deprecated
    "},{"location":"Data-Model/deprecated/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Entity Represents an Entity in the Monarch KG data model no Node UI container class extending Entity with additional information no SearchResult no"},{"location":"Data-Model/deprecated/#properties","title":"Properties","text":"
       
    • Range: Boolean
      •  
    "},{"location":"Data-Model/deprecated/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/deprecated/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/deprecated/#linkml-source","title":"LinkML Source","text":"
    name: deprecated\ndescription: A boolean flag indicating that an entity is no longer considered current\n  or valid.\nfrom_schema: https://w3id.org/monarch/monarch-py\nexact_mappings:\n- oboInOwl:ObsoleteClass\nrank: 1000\nalias: deprecated\ndomain_of:\n- Entity\nrange: boolean\n
    "},{"location":"Data-Model/description/","title":"Slot: description","text":"
    URI: https://w3id.org/monarch/monarch-py/:description
    "},{"location":"Data-Model/description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Entity Represents an Entity in the Monarch KG data model no Node UI container class extending Entity with additional information no SearchResult no"},{"location":"Data-Model/description/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/description/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/description/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/description/#linkml-source","title":"LinkML Source","text":"
    name: description\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: description\ndomain_of:\n- Entity\nrange: string\n
    "},{"location":"Data-Model/dice_similarity/","title":"Slot: dice_similarity","text":"
    URI: https://w3id.org/monarch/monarch-py/:dice_similarity
    "},{"location":"Data-Model/dice_similarity/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • dice_similarity
        •  
       
      •  
    "},{"location":"Data-Model/dice_similarity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/dice_similarity/#properties","title":"Properties","text":"
       
    • Range: ZeroToOne
      •  
    "},{"location":"Data-Model/dice_similarity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/dice_similarity/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/dice_similarity/#linkml-source","title":"LinkML Source","text":"
    name: dice_similarity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: dice_similarity\ndomain_of:\n- TermPairwiseSimilarity\nrange: ZeroToOne\n
    "},{"location":"Data-Model/direction/","title":"Slot: direction","text":"
    The directionality of the association relative to a given entity for an association_count. If the entity is the subject or in the subject closure, the direction is forwards, if it is the object or in the object closure, the direction is backwards.
     
    URI: https://w3id.org/monarch/monarch-py/:direction
    "},{"location":"Data-Model/direction/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/direction/#properties","title":"Properties","text":"
       
    •  
      Range: AssociationDirectionEnum
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/direction/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/direction/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/direction/#linkml-source","title":"LinkML Source","text":"
    name: direction\ndescription: The directionality of the association relative to a given entity for\n  an association_count. If the entity is the subject or in the subject closure, the\n  direction is forwards, if it is the object or in the object closure, the direction\n  is backwards.\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: direction\ndomain_of:\n- DirectionalAssociation\nrange: AssociationDirectionEnum\nrequired: true\n
    "},{"location":"Data-Model/end/","title":"Slot: end","text":"
    end position of the annotation
     
    URI: https://w3id.org/monarch/monarch-py/:end
    "},{"location":"Data-Model/end/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextAnnotationResult no"},{"location":"Data-Model/end/#properties","title":"Properties","text":"
       
    • Range: Integer
      •  
    "},{"location":"Data-Model/end/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/end/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/end/#linkml-source","title":"LinkML Source","text":"
    name: end\ndescription: end position of the annotation\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: end\ndomain_of:\n- TextAnnotationResult\nrange: integer\n
    "},{"location":"Data-Model/evidence_count/","title":"Slot: evidence_count","text":"
    count of supporting documents, evidence codes, and sources supplying evidence
     
    URI: https://w3id.org/monarch/monarch-py/:evidence_count
    "},{"location":"Data-Model/evidence_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/evidence_count/#properties","title":"Properties","text":"
       
    • Range: Integer
      •  
    "},{"location":"Data-Model/evidence_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/evidence_count/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/evidence_count/#linkml-source","title":"LinkML Source","text":"
    name: evidence_count\ndescription: count of supporting documents, evidence codes, and sources supplying\n  evidence\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: evidence_count\ndomain_of:\n- Association\nrange: integer\n
    "},{"location":"Data-Model/external_links/","title":"Slot: external_links","text":"
    ExpandedCurie with id and url for xrefs
     
    URI: https://w3id.org/monarch/monarch-py/:external_links
    "},{"location":"Data-Model/external_links/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/external_links/#properties","title":"Properties","text":"
       
    •  
      Range: ExpandedCurie
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/external_links/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/external_links/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/external_links/#linkml-source","title":"LinkML Source","text":"
    name: external_links\ndescription: ExpandedCurie with id and url for xrefs\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: external_links\ndomain_of:\n- Node\nrange: ExpandedCurie\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/facet_fields/","title":"Slot: facet_fields","text":"
    Collection of facet field responses with the field values and counts
     
    URI: https://w3id.org/monarch/monarch-py/:facet_fields
    "},{"location":"Data-Model/facet_fields/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResults no"},{"location":"Data-Model/facet_fields/#properties","title":"Properties","text":"
       
    •  
      Range: FacetField
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/facet_fields/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/facet_fields/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/facet_fields/#linkml-source","title":"LinkML Source","text":"
    name: facet_fields\ndescription: Collection of facet field responses with the field values and counts\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: facet_fields\ndomain_of:\n- SearchResults\nrange: FacetField\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/facet_queries/","title":"Slot: facet_queries","text":"
    Collection of facet query responses with the query string values and counts
     
    URI: https://w3id.org/monarch/monarch-py/:facet_queries
    "},{"location":"Data-Model/facet_queries/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResults no"},{"location":"Data-Model/facet_queries/#properties","title":"Properties","text":"
       
    •  
      Range: FacetValue
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/facet_queries/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/facet_queries/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/facet_queries/#linkml-source","title":"LinkML Source","text":"
    name: facet_queries\ndescription: Collection of facet query responses with the query string values and\n  counts\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: facet_queries\ndomain_of:\n- SearchResults\nrange: FacetValue\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/facet_values/","title":"Slot: facet_values","text":"
    Collection of FacetValue label/value instances belonging to a FacetField
     
    URI: https://w3id.org/monarch/monarch-py/:facet_values
    "},{"location":"Data-Model/facet_values/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FacetField no"},{"location":"Data-Model/facet_values/#properties","title":"Properties","text":"
       
    •  
      Range: FacetValue
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/facet_values/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/facet_values/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/facet_values/#linkml-source","title":"LinkML Source","text":"
    name: facet_values\ndescription: Collection of FacetValue label/value instances belonging to a FacetField\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: facet_values\ndomain_of:\n- FacetField\nrange: FacetValue\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/frequency_qualifier/","title":"Slot: frequency_qualifier","text":"
    URI: https://w3id.org/monarch/monarch-py/:frequency_qualifier
    "},{"location":"Data-Model/frequency_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/frequency_qualifier/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/frequency_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/frequency_qualifier/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/frequency_qualifier/#linkml-source","title":"LinkML Source","text":"
    name: frequency_qualifier\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: frequency_qualifier\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/frequency_qualifier_category/","title":"Slot: frequency_qualifier_category","text":"
    The category of the frequency_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:frequency_qualifier_category
    "},{"location":"Data-Model/frequency_qualifier_category/#inheritance","title":"Inheritance","text":"
       
    • category
         
      • frequency_qualifier_category
        •  
       
      •  
    "},{"location":"Data-Model/frequency_qualifier_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/frequency_qualifier_category/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/frequency_qualifier_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/frequency_qualifier_category/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/frequency_qualifier_category/#linkml-source","title":"LinkML Source","text":"
    name: frequency_qualifier_category\ndescription: The category of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: frequency_qualifier_category\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/frequency_qualifier_closure/","title":"Slot: frequency_qualifier_closure","text":"
    Field containing frequency_qualifier id and the ids of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:frequency_qualifier_closure
    "},{"location":"Data-Model/frequency_qualifier_closure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/frequency_qualifier_closure/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/frequency_qualifier_closure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/frequency_qualifier_closure/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/frequency_qualifier_closure/#linkml-source","title":"LinkML Source","text":"
    name: frequency_qualifier_closure\ndescription: Field containing frequency_qualifier id and the ids of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: frequency_qualifier_closure\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/frequency_qualifier_closure_label/","title":"Slot: frequency_qualifier_closure_label","text":"
    Field containing frequency_qualifier name and the names of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:frequency_qualifier_closure_label
    "},{"location":"Data-Model/frequency_qualifier_closure_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/frequency_qualifier_closure_label/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/frequency_qualifier_closure_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/frequency_qualifier_closure_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/frequency_qualifier_closure_label/#linkml-source","title":"LinkML Source","text":"
    name: frequency_qualifier_closure_label\ndescription: Field containing frequency_qualifier name and the names of all of it's\n  ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: frequency_qualifier_closure_label\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/frequency_qualifier_label/","title":"Slot: frequency_qualifier_label","text":"
    The name of the frequency_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:frequency_qualifier_label
    "},{"location":"Data-Model/frequency_qualifier_label/#inheritance","title":"Inheritance","text":"
       
    • name
         
      • frequency_qualifier_label
        •  
       
      •  
    "},{"location":"Data-Model/frequency_qualifier_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/frequency_qualifier_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/frequency_qualifier_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/frequency_qualifier_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/frequency_qualifier_label/#linkml-source","title":"LinkML Source","text":"
    name: frequency_qualifier_label\ndescription: The name of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: frequency_qualifier_label\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/frequency_qualifier_namespace/","title":"Slot: frequency_qualifier_namespace","text":"
    The namespace/prefix of the frequency_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:frequency_qualifier_namespace
    "},{"location":"Data-Model/frequency_qualifier_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/frequency_qualifier_namespace/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/frequency_qualifier_namespace/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/frequency_qualifier_namespace/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/frequency_qualifier_namespace/#linkml-source","title":"LinkML Source","text":"
    name: frequency_qualifier_namespace\ndescription: The namespace/prefix of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: frequency_qualifier_namespace\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/full_name/","title":"Slot: full_name","text":"
    The long form name of an entity
     
    URI: https://w3id.org/monarch/monarch-py/:full_name
    "},{"location":"Data-Model/full_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Entity Represents an Entity in the Monarch KG data model no Node UI container class extending Entity with additional information no SearchResult no"},{"location":"Data-Model/full_name/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/full_name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/full_name/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/full_name/#linkml-source","title":"LinkML Source","text":"
    name: full_name\ndescription: The long form name of an entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: full_name\ndomain_of:\n- Entity\nrange: string\n
    "},{"location":"Data-Model/graph_stats/","title":"Slot: graph_stats","text":"
    URI: https://w3id.org/monarch/monarch-py/:graph_stats
    "},{"location":"Data-Model/graph_stats/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/graph_stats/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/graph_stats/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/graph_stats/#valid-id-prefixes","title":"Valid ID Prefixes","text":"
    Instances of this class should have identifiers with one of the following prefixes:
     
       
    • string
      •  
    "},{"location":"Data-Model/graph_stats/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/graph_stats/#linkml-source","title":"LinkML Source","text":"
    name: graph_stats\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: graph_stats\ndomain_of:\n- Release\nrange: string\n
    "},{"location":"Data-Model/grouping_key/","title":"Slot: grouping_key","text":"
    A concatenation of fields used to group associations with the same essential/defining properties
     
    URI: https://w3id.org/monarch/monarch-py/:grouping_key
    "},{"location":"Data-Model/grouping_key/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/grouping_key/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/grouping_key/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/grouping_key/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/grouping_key/#linkml-source","title":"LinkML Source","text":"
    name: grouping_key\ndescription: A concatenation of fields used to group associations with the same essential/defining\n  properties\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: grouping_key\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/has_count/","title":"Slot: has_count","text":"
    count of out of has_total representing a frequency
     
    URI: https://w3id.org/monarch/monarch-py/:has_count
    "},{"location":"Data-Model/has_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/has_count/#properties","title":"Properties","text":"
       
    • Range: Integer
      •  
    "},{"location":"Data-Model/has_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/has_count/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/has_count/#linkml-source","title":"LinkML Source","text":"
    name: has_count\ndescription: count of out of has_total representing a frequency\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_count\ndomain_of:\n- Association\nrange: integer\n
    "},{"location":"Data-Model/has_evidence/","title":"Slot: has_evidence","text":"
    URI: https://w3id.org/monarch/monarch-py/:has_evidence
    "},{"location":"Data-Model/has_evidence/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/has_evidence/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/has_evidence/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/has_evidence/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/has_evidence/#linkml-source","title":"LinkML Source","text":"
    name: has_evidence\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: has_evidence\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/has_evidence_links/","title":"Slot: has_evidence_links","text":"
    List of ExpandedCuries with id and url for evidence
     
    URI: https://w3id.org/monarch/monarch-py/:has_evidence_links
    "},{"location":"Data-Model/has_evidence_links/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/has_evidence_links/#properties","title":"Properties","text":"
       
    •  
      Range: ExpandedCurie
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/has_evidence_links/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/has_evidence_links/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/has_evidence_links/#linkml-source","title":"LinkML Source","text":"
    name: has_evidence_links\ndescription: List of ExpandedCuries with id and url for evidence\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: has_evidence_links\ndomain_of:\n- Association\nrange: ExpandedCurie\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/has_percentage/","title":"Slot: has_percentage","text":"
    percentage, which may be calculated from has_count and has_total, as 100 * quotient or provided directly, rounded to the integer level
     
    URI: https://w3id.org/monarch/monarch-py/:has_percentage
    "},{"location":"Data-Model/has_percentage/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/has_percentage/#properties","title":"Properties","text":"
       
    • Range: Float
      •  
    "},{"location":"Data-Model/has_percentage/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/has_percentage/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/has_percentage/#linkml-source","title":"LinkML Source","text":"
    name: has_percentage\ndescription: percentage, which may be calculated from has_count and has_total, as\n  100 * quotient or provided directly, rounded to the integer level\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_percentage\ndomain_of:\n- Association\nrange: float\n
    "},{"location":"Data-Model/has_phenotype/","title":"Slot: has_phenotype","text":"
    A list of phenotype identifiers that are known to be associated with this entity
     
    URI: https://w3id.org/monarch/monarch-py/:has_phenotype
    "},{"location":"Data-Model/has_phenotype/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Entity Represents an Entity in the Monarch KG data model no Node UI container class extending Entity with additional information no SearchResult no"},{"location":"Data-Model/has_phenotype/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/has_phenotype/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/has_phenotype/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/has_phenotype/#linkml-source","title":"LinkML Source","text":"
    name: has_phenotype\ndescription: A list of phenotype identifiers that are known to be associated with\n  this entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: has_phenotype\ndomain_of:\n- Entity\nrange: string\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/has_phenotype_closure/","title":"Slot: has_phenotype_closure","text":"
    A list of phenotype identifiers that are known to be associated with this entity expanded to include all ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:has_phenotype_closure
    "},{"location":"Data-Model/has_phenotype_closure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Entity Represents an Entity in the Monarch KG data model no Node UI container class extending Entity with additional information no SearchResult no"},{"location":"Data-Model/has_phenotype_closure/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/has_phenotype_closure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/has_phenotype_closure/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/has_phenotype_closure/#linkml-source","title":"LinkML Source","text":"
    name: has_phenotype_closure\ndescription: A list of phenotype identifiers that are known to be associated with\n  this entity expanded to include all ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: has_phenotype_closure\ndomain_of:\n- Entity\nrange: string\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/has_phenotype_closure_label/","title":"Slot: has_phenotype_closure_label","text":"
    A list of phenotype labels that are known to be associated with this entity expanded to include all ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:has_phenotype_closure_label
    "},{"location":"Data-Model/has_phenotype_closure_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Entity Represents an Entity in the Monarch KG data model no Node UI container class extending Entity with additional information no SearchResult no"},{"location":"Data-Model/has_phenotype_closure_label/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/has_phenotype_closure_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/has_phenotype_closure_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/has_phenotype_closure_label/#linkml-source","title":"LinkML Source","text":"
    name: has_phenotype_closure_label\ndescription: A list of phenotype labels that are known to be associated with this\n  entity expanded to include all ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: has_phenotype_closure_label\ndomain_of:\n- Entity\nrange: string\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/has_phenotype_count/","title":"Slot: has_phenotype_count","text":"
    A count of the number of phenotypes that are known to be associated with this entity
     
    URI: https://w3id.org/monarch/monarch-py/:has_phenotype_count
    "},{"location":"Data-Model/has_phenotype_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Entity Represents an Entity in the Monarch KG data model no Node UI container class extending Entity with additional information no SearchResult no"},{"location":"Data-Model/has_phenotype_count/#properties","title":"Properties","text":"
       
    • Range: Integer
      •  
    "},{"location":"Data-Model/has_phenotype_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/has_phenotype_count/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/has_phenotype_count/#linkml-source","title":"LinkML Source","text":"
    name: has_phenotype_count\ndescription: A count of the number of phenotypes that are known to be associated with\n  this entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_phenotype_count\ndomain_of:\n- Entity\nrange: integer\n
    "},{"location":"Data-Model/has_phenotype_label/","title":"Slot: has_phenotype_label","text":"
    A list of phenotype labels that are known to be associated with this entity
     
    URI: https://w3id.org/monarch/monarch-py/:has_phenotype_label
    "},{"location":"Data-Model/has_phenotype_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Entity Represents an Entity in the Monarch KG data model no Node UI container class extending Entity with additional information no SearchResult no"},{"location":"Data-Model/has_phenotype_label/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/has_phenotype_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/has_phenotype_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/has_phenotype_label/#linkml-source","title":"LinkML Source","text":"
    name: has_phenotype_label\ndescription: A list of phenotype labels that are known to be associated with this\n  entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: has_phenotype_label\ndomain_of:\n- Entity\nrange: string\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/has_quotient/","title":"Slot: has_quotient","text":"
    quotient, which should be 1/100 of has_percentage
     
    URI: https://w3id.org/monarch/monarch-py/:has_quotient
    "},{"location":"Data-Model/has_quotient/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/has_quotient/#properties","title":"Properties","text":"
       
    • Range: Float
      •  
    "},{"location":"Data-Model/has_quotient/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/has_quotient/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/has_quotient/#linkml-source","title":"LinkML Source","text":"
    name: has_quotient\ndescription: quotient, which should be 1/100 of has_percentage\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_quotient\ndomain_of:\n- Association\nrange: float\n
    "},{"location":"Data-Model/has_total/","title":"Slot: has_total","text":"
    total, devided by has_count, representing a frequency
     
    URI: https://w3id.org/monarch/monarch-py/:has_total
    "},{"location":"Data-Model/has_total/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/has_total/#properties","title":"Properties","text":"
       
    • Range: Integer
      •  
    "},{"location":"Data-Model/has_total/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/has_total/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/has_total/#linkml-source","title":"LinkML Source","text":"
    name: has_total\ndescription: total, devided by has_count, representing a frequency\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_total\ndomain_of:\n- Association\nrange: integer\n
    "},{"location":"Data-Model/highlight/","title":"Slot: highlight","text":"
    matching text snippet containing html tags
     
    URI: https://w3id.org/monarch/monarch-py/:highlight
    "},{"location":"Data-Model/highlight/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no"},{"location":"Data-Model/highlight/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/highlight/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/highlight/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/highlight/#linkml-source","title":"LinkML Source","text":"
    name: highlight\ndescription: matching text snippet containing html tags\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: highlight\ndomain_of:\n- SearchResult\nrange: string\n
    "},{"location":"Data-Model/id/","title":"Slot: id","text":"
    URI: https://w3id.org/monarch/monarch-py/:id
    "},{"location":"Data-Model/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot HistoBin no MultiEntityAssociationResults no Entity Represents an Entity in the Monarch KG data model no DirectionalAssociation An association that gives it's direction relative to a specified entity no SearchResult no TermInfo no Mapping A minimal class to hold a SSSOM mapping no ExpandedCurie A curie bundled along with its expanded url no Node UI container class extending Entity with additional information no Association no HistoPheno no"},{"location":"Data-Model/id/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/id/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/id/#linkml-source","title":"LinkML Source","text":"
    name: id\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nidentifier: true\nalias: id\ndomain_of:\n- Association\n- ExpandedCurie\n- Entity\n- HistoPheno\n- HistoBin\n- Mapping\n- MultiEntityAssociationResults\n- TermInfo\nrange: string\nrequired: true\n
    "},{"location":"Data-Model/in_taxon/","title":"Slot: in_taxon","text":"
    The biolink taxon that the entity is in the closure of.
     
    URI: https://w3id.org/monarch/monarch-py/:in_taxon
    "},{"location":"Data-Model/in_taxon/#inheritance","title":"Inheritance","text":"
       
    • in_taxon
         
      • subject_taxon
        •  
      • object_taxon
        •  
       
      •  
    "},{"location":"Data-Model/in_taxon/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Entity Represents an Entity in the Monarch KG data model no Node UI container class extending Entity with additional information no SearchResult no"},{"location":"Data-Model/in_taxon/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/in_taxon/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/in_taxon/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/in_taxon/#linkml-source","title":"LinkML Source","text":"
    name: in_taxon\ndescription: The biolink taxon that the entity is in the closure of.\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: in_taxon\ndomain_of:\n- Entity\n- Node\nrange: string\n
    "},{"location":"Data-Model/in_taxon_label/","title":"Slot: in_taxon_label","text":"
    The label of the biolink taxon that the entity is in the closure of.
     
    URI: https://w3id.org/monarch/monarch-py/:in_taxon_label
    "},{"location":"Data-Model/in_taxon_label/#inheritance","title":"Inheritance","text":"
       
    • in_taxon_label
         
      • subject_taxon_label
        •  
      • object_taxon_label
        •  
       
      •  
    "},{"location":"Data-Model/in_taxon_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Entity Represents an Entity in the Monarch KG data model no Node UI container class extending Entity with additional information no SearchResult no"},{"location":"Data-Model/in_taxon_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/in_taxon_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/in_taxon_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/in_taxon_label/#linkml-source","title":"LinkML Source","text":"
    name: in_taxon_label\ndescription: The label of the biolink taxon that the entity is in the closure of.\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: in_taxon_label\ndomain_of:\n- Entity\n- Node\nrange: string\n
    "},{"location":"Data-Model/information_content/","title":"Slot: information_content","text":"
    The IC is the negative log of the probability of the concept
     
    URI: https://w3id.org/monarch/monarch-py/:information_content
    "},{"location":"Data-Model/information_content/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • information_content
           
        • subject_information_content
          •  
        • object_information_content
          •  
        • ancestor_information_content
          •  
         
        •  
       
      •  
    "},{"location":"Data-Model/information_content/#properties","title":"Properties","text":"
       
    • Range: NegativeLogValue
      •  
    "},{"location":"Data-Model/information_content/#aliases","title":"Aliases","text":"
       
    • IC
      •  
    "},{"location":"Data-Model/information_content/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/information_content/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/information_content/#linkml-source","title":"LinkML Source","text":"
    name: information_content\ndescription: The IC is the negative log of the probability of the concept\nfrom_schema: https://w3id.org/monarch/monarch-py\naliases:\n- IC\nrank: 1000\nis_a: score\nabstract: true\nalias: information_content\nrange: NegativeLogValue\n
    "},{"location":"Data-Model/inheritance/","title":"Slot: inheritance","text":"
    URI: https://w3id.org/monarch/monarch-py/:inheritance
    "},{"location":"Data-Model/inheritance/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/inheritance/#properties","title":"Properties","text":"
       
    • Range: Entity
      •  
    "},{"location":"Data-Model/inheritance/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/inheritance/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/inheritance/#linkml-source","title":"LinkML Source","text":"
    name: inheritance\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: inheritance\ndomain_of:\n- Node\nrange: Entity\ninlined: true\n
    "},{"location":"Data-Model/intersection_count/","title":"Slot: intersection_count","text":"
    URI: https://w3id.org/monarch/monarch-py/:intersection_count
    "},{"location":"Data-Model/intersection_count/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • intersection_count
        •  
       
      •  
    "},{"location":"Data-Model/intersection_count/#properties","title":"Properties","text":"
       
    • Range: ItemCount
      •  
    "},{"location":"Data-Model/intersection_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/intersection_count/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/intersection_count/#linkml-source","title":"LinkML Source","text":"
    name: intersection_count\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: intersection_count\nrange: ItemCount\n
    "},{"location":"Data-Model/iri/","title":"Slot: iri","text":"
    URI: https://w3id.org/monarch/monarch-py/:iri
    "},{"location":"Data-Model/iri/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Entity Represents an Entity in the Monarch KG data model no Node UI container class extending Entity with additional information no SearchResult no"},{"location":"Data-Model/iri/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/iri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/iri/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/iri/#linkml-source","title":"LinkML Source","text":"
    name: iri\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: iri\ndomain_of:\n- Entity\nrange: string\n
    "},{"location":"Data-Model/items/","title":"Slot: items","text":"
    A collection of items, with the type to be overriden by slot_usage
     
    URI: https://w3id.org/monarch/monarch-py/:items
    "},{"location":"Data-Model/items/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AssociationTableResults yes CompactAssociationResults yes MappingResults SSSOM Mappings returned as a results collection yes AssociationResults yes CategoryGroupedAssociationResults yes EntityResults yes AssociationCountList Container class for a list of association counts yes SearchResults yes HistoPheno yes"},{"location":"Data-Model/items/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/items/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/items/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/items/#linkml-source","title":"LinkML Source","text":"
    name: items\ndescription: A collection of items, with the type to be overriden by slot_usage\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: items\ndomain_of:\n- AssociationCountList\n- AssociationResults\n- CompactAssociationResults\n- AssociationTableResults\n- CategoryGroupedAssociationResults\n- EntityResults\n- HistoPheno\n- MappingResults\n- SearchResults\nrange: string\nrequired: true\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/jaccard_similarity/","title":"Slot: jaccard_similarity","text":"
    The number of concepts in the intersection divided by the number in the union
     
    URI: https://w3id.org/monarch/monarch-py/:jaccard_similarity
    "},{"location":"Data-Model/jaccard_similarity/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • jaccard_similarity
        •  
       
      •  
    "},{"location":"Data-Model/jaccard_similarity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/jaccard_similarity/#properties","title":"Properties","text":"
       
    • Range: ZeroToOne
      •  
    "},{"location":"Data-Model/jaccard_similarity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/jaccard_similarity/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/jaccard_similarity/#linkml-source","title":"LinkML Source","text":"
    name: jaccard_similarity\ndescription: The number of concepts in the intersection divided by the number in the\n  union\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: jaccard_similarity\ndomain_of:\n- TermPairwiseSimilarity\nrange: ZeroToOne\n
    "},{"location":"Data-Model/kg/","title":"Slot: kg","text":"
    URI: https://w3id.org/monarch/monarch-py/:kg
    "},{"location":"Data-Model/kg/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/kg/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/kg/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/kg/#valid-id-prefixes","title":"Valid ID Prefixes","text":"
    Instances of this class should have identifiers with one of the following prefixes:
     
       
    • string
      •  
    "},{"location":"Data-Model/kg/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/kg/#linkml-source","title":"LinkML Source","text":"
    name: kg\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: kg\ndomain_of:\n- Release\nrange: string\n
    "},{"location":"Data-Model/knowledge_level/","title":"Slot: knowledge_level","text":"
    Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true.
     
    URI: biolink:knowledge_level
    "},{"location":"Data-Model/knowledge_level/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/knowledge_level/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/knowledge_level/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/knowledge_level/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/knowledge_level/#linkml-source","title":"LinkML Source","text":"
    name: knowledge_level\ndescription: Describes the level of knowledge expressed in a statement, based on the\n  reasoning or analysis methods used to generate the statement, or the scope or specificity\n  of what the statement expresses to be true.\nnotes:\n- The range in this schema is represented as a string, but is constrained  to values\n  from biolink:KnowledgeLevelEnum at ingest time\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nslot_uri: biolink:knowledge_level\nmultivalued: false\nalias: knowledge_level\ndomain_of:\n- Association\nrange: string\nrequired: true\n
    "},{"location":"Data-Model/knowledge_source/","title":"Slot: knowledge_source","text":"
    URI: https://w3id.org/monarch/monarch-py/:knowledge_source
    "},{"location":"Data-Model/knowledge_source/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/knowledge_source/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/knowledge_source/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/knowledge_source/#linkml-source","title":"LinkML Source","text":"
    name: knowledge_source\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: knowledge_source\nrange: string\n
    "},{"location":"Data-Model/label/","title":"Slot: label","text":"
    URI: https://w3id.org/monarch/monarch-py/:label
    "},{"location":"Data-Model/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot HistoBin no FacetField no FacetValue no AssociationCount no TermInfo no"},{"location":"Data-Model/label/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/label/#linkml-source","title":"LinkML Source","text":"
    name: label\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: label\ndomain_of:\n- FacetValue\n- FacetField\n- TermInfo\nrange: string\nrequired: true\n
    "},{"location":"Data-Model/limit/","title":"Slot: limit","text":"
    number of items to return in a response
     
    URI: https://w3id.org/monarch/monarch-py/:limit
    "},{"location":"Data-Model/limit/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AssociationTableResults no CompactAssociationResults no MappingResults SSSOM Mappings returned as a results collection no AssociationResults no CategoryGroupedAssociationResults no EntityResults no MultiEntityAssociationResults no SearchResults no Results no"},{"location":"Data-Model/limit/#properties","title":"Properties","text":"
       
    •  
      Range: Integer
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/limit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/limit/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/limit/#linkml-source","title":"LinkML Source","text":"
    name: limit\ndescription: number of items to return in a response\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: limit\ndomain_of:\n- Results\nrange: integer\nrequired: true\n
    "},{"location":"Data-Model/mapping_justification/","title":"Slot: mapping_justification","text":"
    URI: https://w3id.org/monarch/monarch-py/:mapping_justification
    "},{"location":"Data-Model/mapping_justification/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Mapping A minimal class to hold a SSSOM mapping no"},{"location":"Data-Model/mapping_justification/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/mapping_justification/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/mapping_justification/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/mapping_justification/#linkml-source","title":"LinkML Source","text":"
    name: mapping_justification\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: mapping_justification\ndomain_of:\n- Mapping\nrange: string\n
    "},{"location":"Data-Model/mappings/","title":"Slot: mappings","text":"
    List of ExpandedCuries with id and url for mapped entities
     
    URI: https://w3id.org/monarch/monarch-py/:mappings
    "},{"location":"Data-Model/mappings/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/mappings/#properties","title":"Properties","text":"
       
    •  
      Range: ExpandedCurie
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/mappings/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/mappings/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/mappings/#linkml-source","title":"LinkML Source","text":"
    name: mappings\ndescription: List of ExpandedCuries with id and url for mapped entities\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: mappings\ndomain_of:\n- Node\nrange: ExpandedCurie\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/match_source/","title":"Slot: match_source","text":"
    URI: https://w3id.org/monarch/monarch-py/:match_source
    "},{"location":"Data-Model/match_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no"},{"location":"Data-Model/match_source/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/match_source/#comments","title":"Comments","text":"
       
    • note that the match_source is either the subject or the object
      •  
    "},{"location":"Data-Model/match_source/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/match_source/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/match_source/#linkml-source","title":"LinkML Source","text":"
    name: match_source\ncomments:\n- note that the match_source is either the subject or the object\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nidentifier: true\nalias: match_source\nowner: BestMatch\ndomain_of:\n- BestMatch\nrange: string\nrequired: true\n
    "},{"location":"Data-Model/match_source_label/","title":"Slot: match_source_label","text":"
    URI: https://w3id.org/monarch/monarch-py/:match_source_label
    "},{"location":"Data-Model/match_source_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no"},{"location":"Data-Model/match_source_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/match_source_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/match_source_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/match_source_label/#linkml-source","title":"LinkML Source","text":"
    name: match_source_label\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: match_source_label\nowner: BestMatch\ndomain_of:\n- BestMatch\nrange: string\n
    "},{"location":"Data-Model/match_subsumer/","title":"Slot: match_subsumer","text":"
    URI: https://w3id.org/monarch/monarch-py/:match_subsumer
    "},{"location":"Data-Model/match_subsumer/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no"},{"location":"Data-Model/match_subsumer/#properties","title":"Properties","text":"
       
    • Range: Uriorcurie
      •  
    "},{"location":"Data-Model/match_subsumer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/match_subsumer/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/match_subsumer/#linkml-source","title":"LinkML Source","text":"
    name: match_subsumer\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: match_subsumer\nowner: BestMatch\ndomain_of:\n- BestMatch\nrange: uriorcurie\n
    "},{"location":"Data-Model/match_subsumer_label/","title":"Slot: match_subsumer_label","text":"
    URI: https://w3id.org/monarch/monarch-py/:match_subsumer_label
    "},{"location":"Data-Model/match_subsumer_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no"},{"location":"Data-Model/match_subsumer_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/match_subsumer_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/match_subsumer_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/match_subsumer_label/#linkml-source","title":"LinkML Source","text":"
    name: match_subsumer_label\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: match_subsumer_label\nowner: BestMatch\ndomain_of:\n- BestMatch\nrange: string\n
    "},{"location":"Data-Model/match_target/","title":"Slot: match_target","text":"
    the entity matches
     
    URI: https://w3id.org/monarch/monarch-py/:match_target
    "},{"location":"Data-Model/match_target/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no"},{"location":"Data-Model/match_target/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/match_target/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/match_target/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/match_target/#linkml-source","title":"LinkML Source","text":"
    name: match_target\ndescription: the entity matches\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: match_target\nowner: BestMatch\ndomain_of:\n- BestMatch\nrange: string\n
    "},{"location":"Data-Model/match_target_label/","title":"Slot: match_target_label","text":"
    URI: https://w3id.org/monarch/monarch-py/:match_target_label
    "},{"location":"Data-Model/match_target_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no"},{"location":"Data-Model/match_target_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/match_target_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/match_target_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/match_target_label/#linkml-source","title":"LinkML Source","text":"
    name: match_target_label\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: match_target_label\nowner: BestMatch\ndomain_of:\n- BestMatch\nrange: string\n
    "},{"location":"Data-Model/metadata/","title":"Slot: metadata","text":"
    URI: https://w3id.org/monarch/monarch-py/:metadata
    "},{"location":"Data-Model/metadata/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/metadata/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/metadata/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/metadata/#valid-id-prefixes","title":"Valid ID Prefixes","text":"
    Instances of this class should have identifiers with one of the following prefixes:
     
       
    • string
      •  
    "},{"location":"Data-Model/metadata/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/metadata/#linkml-source","title":"LinkML Source","text":"
    name: metadata\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: metadata\ndomain_of:\n- Release\nrange: string\n
    "},{"location":"Data-Model/metric/","title":"Slot: metric","text":"
    URI: https://w3id.org/monarch/monarch-py/:metric
    "},{"location":"Data-Model/metric/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/metric/#properties","title":"Properties","text":"
       
    • Range: Uriorcurie
      •  
    "},{"location":"Data-Model/metric/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/metric/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/metric/#linkml-source","title":"LinkML Source","text":"
    name: metric\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: metric\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: uriorcurie\n
    "},{"location":"Data-Model/monarch-py/","title":"monarch-py","text":"
    Data models for the Monarch Initiative data access library
     
    URI: https://w3id.org/monarch/monarch-py
    "},{"location":"Data-Model/name/","title":"Slot: name","text":"
    URI: https://w3id.org/monarch/monarch-py/:name
    "},{"location":"Data-Model/name/#inheritance","title":"Inheritance","text":"
       
    • name
         
      • subject_label
        •  
      • object_label
        •  
      • qualifiers_label
        •  
      • qualifier_label
        •  
      • frequency_qualifier_label
        •  
      • onset_qualifier_label
        •  
      • sex_qualifier_label
        •  
      • stage_qualifier_label
        •  
       
      •  
    "},{"location":"Data-Model/name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Entity Represents an Entity in the Monarch KG data model no Node UI container class extending Entity with additional information no SearchResult yes MultiEntityAssociationResults no"},{"location":"Data-Model/name/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/name/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/name/#linkml-source","title":"LinkML Source","text":"
    name: name\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: name\ndomain_of:\n- Entity\n- MultiEntityAssociationResults\nrange: string\n
    "},{"location":"Data-Model/namespace/","title":"Slot: namespace","text":"
    The namespace/prefix portion of this entity's identifier
     
    URI: https://w3id.org/monarch/monarch-py/:namespace
    "},{"location":"Data-Model/namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Entity Represents an Entity in the Monarch KG data model no Node UI container class extending Entity with additional information no SearchResult no"},{"location":"Data-Model/namespace/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/namespace/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/namespace/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/namespace/#linkml-source","title":"LinkML Source","text":"
    name: namespace\ndescription: The namespace/prefix portion of this entity's identifier\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: namespace\ndomain_of:\n- Entity\nrange: string\n
    "},{"location":"Data-Model/negated/","title":"Slot: negated","text":"
    URI: https://w3id.org/monarch/monarch-py/:negated
    "},{"location":"Data-Model/negated/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no CompactAssociation no Association no"},{"location":"Data-Model/negated/#properties","title":"Properties","text":"
       
    • Range: Boolean
      •  
    "},{"location":"Data-Model/negated/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/negated/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/negated/#linkml-source","title":"LinkML Source","text":"
    name: negated\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: negated\ndomain_of:\n- Association\n- CompactAssociation\nrange: boolean\n
    "},{"location":"Data-Model/neo4j/","title":"Slot: neo4j","text":"
    URI: https://w3id.org/monarch/monarch-py/:neo4j
    "},{"location":"Data-Model/neo4j/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/neo4j/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/neo4j/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/neo4j/#valid-id-prefixes","title":"Valid ID Prefixes","text":"
    Instances of this class should have identifiers with one of the following prefixes:
     
       
    • string
      •  
    "},{"location":"Data-Model/neo4j/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/neo4j/#linkml-source","title":"LinkML Source","text":"
    name: neo4j\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: neo4j\ndomain_of:\n- Release\nrange: string\n
    "},{"location":"Data-Model/node_hierarchy/","title":"Slot: node_hierarchy","text":"
    URI: https://w3id.org/monarch/monarch-py/:node_hierarchy
    "},{"location":"Data-Model/node_hierarchy/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/node_hierarchy/#properties","title":"Properties","text":"
       
    • Range: NodeHierarchy
      •  
    "},{"location":"Data-Model/node_hierarchy/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/node_hierarchy/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/node_hierarchy/#linkml-source","title":"LinkML Source","text":"
    name: node_hierarchy\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: node_hierarchy\ndomain_of:\n- Node\nrange: NodeHierarchy\ninlined: true\n
    "},{"location":"Data-Model/object/","title":"Slot: object","text":"
    URI: https://w3id.org/monarch/monarch-py/:object
    "},{"location":"Data-Model/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no CompactAssociation no Association no"},{"location":"Data-Model/object/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/object/#linkml-source","title":"LinkML Source","text":"
    name: object\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: object\ndomain_of:\n- Association\n- CompactAssociation\nrange: string\nrequired: true\n
    "},{"location":"Data-Model/object_best_matches/","title":"Slot: object_best_matches","text":"
    URI: https://w3id.org/monarch/monarch-py/:object_best_matches
    "},{"location":"Data-Model/object_best_matches/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/object_best_matches/#properties","title":"Properties","text":"
       
    •  
      Range: BestMatch
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/object_best_matches/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object_best_matches/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/object_best_matches/#linkml-source","title":"LinkML Source","text":"
    name: object_best_matches\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: object_best_matches\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: BestMatch\ninlined: true\n
    "},{"location":"Data-Model/object_category/","title":"Slot: object_category","text":"
    The category of the object entity
     
    URI: https://w3id.org/monarch/monarch-py/:object_category
    "},{"location":"Data-Model/object_category/#inheritance","title":"Inheritance","text":"
       
    • category
         
      • object_category
        •  
       
      •  
    "},{"location":"Data-Model/object_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/object_category/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/object_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object_category/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/object_category/#linkml-source","title":"LinkML Source","text":"
    name: object_category\ndescription: The category of the object entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: object_category\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/object_closure/","title":"Slot: object_closure","text":"
    Field containing object id and the ids of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:object_closure
    "},{"location":"Data-Model/object_closure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/object_closure/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/object_closure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object_closure/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/object_closure/#linkml-source","title":"LinkML Source","text":"
    name: object_closure\ndescription: Field containing object id and the ids of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: object_closure\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/object_closure_label/","title":"Slot: object_closure_label","text":"
    Field containing object name and the names of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:object_closure_label
    "},{"location":"Data-Model/object_closure_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/object_closure_label/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/object_closure_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object_closure_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/object_closure_label/#linkml-source","title":"LinkML Source","text":"
    name: object_closure_label\ndescription: Field containing object name and the names of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: object_closure_label\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/object_id/","title":"Slot: object_id","text":"
    URI: https://w3id.org/monarch/monarch-py/:object_id
    "},{"location":"Data-Model/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no Mapping A minimal class to hold a SSSOM mapping no"},{"location":"Data-Model/object_id/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object_id/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/object_id/#linkml-source","title":"LinkML Source","text":"
    name: object_id\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: object_id\ndomain_of:\n- Mapping\n- TermPairwiseSimilarity\nrange: string\nrequired: true\n
    "},{"location":"Data-Model/object_information_content/","title":"Slot: object_information_content","text":"
    The IC of the object
     
    URI: https://w3id.org/monarch/monarch-py/:object_information_content
    "},{"location":"Data-Model/object_information_content/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • information_content
           
        • object_information_content
          •  
         
        •  
       
      •  
    "},{"location":"Data-Model/object_information_content/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/object_information_content/#properties","title":"Properties","text":"
       
    • Range: NegativeLogValue
      •  
    "},{"location":"Data-Model/object_information_content/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object_information_content/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/object_information_content/#linkml-source","title":"LinkML Source","text":"
    name: object_information_content\ndescription: The IC of the object\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: information_content\nalias: object_information_content\ndomain_of:\n- TermPairwiseSimilarity\nrange: NegativeLogValue\n
    "},{"location":"Data-Model/object_label/","title":"Slot: object_label","text":"
    The name of the object entity
     
    URI: https://w3id.org/monarch/monarch-py/:object_label
    "},{"location":"Data-Model/object_label/#inheritance","title":"Inheritance","text":"
       
    • name
         
      • object_label
        •  
       
      •  
    "},{"location":"Data-Model/object_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AssociationTypeMapping A data class to hold the necessary information to produce association type co... yes TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no DirectionalAssociation An association that gives it's direction relative to a specified entity no Mapping A minimal class to hold a SSSOM mapping no CompactAssociation no Association no"},{"location":"Data-Model/object_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/object_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/object_label/#linkml-source","title":"LinkML Source","text":"
    name: object_label\ndescription: The name of the object entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: object_label\ndomain_of:\n- Association\n- CompactAssociation\n- AssociationTypeMapping\n- Mapping\n- TermPairwiseSimilarity\nrange: string\n
    "},{"location":"Data-Model/object_namespace/","title":"Slot: object_namespace","text":"
    The namespace/prefix of the object entity
     
    URI: https://w3id.org/monarch/monarch-py/:object_namespace
    "},{"location":"Data-Model/object_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/object_namespace/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/object_namespace/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object_namespace/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/object_namespace/#linkml-source","title":"LinkML Source","text":"
    name: object_namespace\ndescription: The namespace/prefix of the object entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: object_namespace\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/object_source/","title":"Slot: object_source","text":"
    the source for the second entity
     
    URI: sssom:object_source
    "},{"location":"Data-Model/object_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/object_source/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/object_source/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object_source/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/object_source/#linkml-source","title":"LinkML Source","text":"
    name: object_source\ndescription: the source for the second entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nslot_uri: sssom:object_source\nalias: object_source\ndomain_of:\n- TermPairwiseSimilarity\nrange: string\n
    "},{"location":"Data-Model/object_taxon/","title":"Slot: object_taxon","text":"
    URI: https://w3id.org/monarch/monarch-py/:object_taxon
    "},{"location":"Data-Model/object_taxon/#inheritance","title":"Inheritance","text":"
       
    • in_taxon
         
      • object_taxon
        •  
       
      •  
    "},{"location":"Data-Model/object_taxon/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/object_taxon/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/object_taxon/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object_taxon/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/object_taxon/#linkml-source","title":"LinkML Source","text":"
    name: object_taxon\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: in_taxon\nalias: object_taxon\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/object_taxon_label/","title":"Slot: object_taxon_label","text":"
    URI: https://w3id.org/monarch/monarch-py/:object_taxon_label
    "},{"location":"Data-Model/object_taxon_label/#inheritance","title":"Inheritance","text":"
       
    • in_taxon_label
         
      • object_taxon_label
        •  
       
      •  
    "},{"location":"Data-Model/object_taxon_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/object_taxon_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/object_taxon_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object_taxon_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/object_taxon_label/#linkml-source","title":"LinkML Source","text":"
    name: object_taxon_label\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: in_taxon_label\nalias: object_taxon_label\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/object_termset/","title":"Slot: object_termset","text":"
    URI: https://w3id.org/monarch/monarch-py/:object_termset
    "},{"location":"Data-Model/object_termset/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/object_termset/#properties","title":"Properties","text":"
       
    •  
      Range: TermInfo
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/object_termset/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object_termset/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/object_termset/#linkml-source","title":"LinkML Source","text":"
    name: object_termset\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: object_termset\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: TermInfo\ninlined: true\n
    "},{"location":"Data-Model/offset/","title":"Slot: offset","text":"
    offset into the total number of items
     
    URI: https://w3id.org/monarch/monarch-py/:offset
    "},{"location":"Data-Model/offset/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AssociationTableResults no CompactAssociationResults no MappingResults SSSOM Mappings returned as a results collection no AssociationResults no CategoryGroupedAssociationResults no EntityResults no MultiEntityAssociationResults no SearchResults no Results no"},{"location":"Data-Model/offset/#properties","title":"Properties","text":"
       
    •  
      Range: Integer
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/offset/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/offset/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/offset/#linkml-source","title":"LinkML Source","text":"
    name: offset\ndescription: offset into the total number of items\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: offset\ndomain_of:\n- Results\nrange: integer\nrequired: true\n
    "},{"location":"Data-Model/onset_qualifier/","title":"Slot: onset_qualifier","text":"
    URI: https://w3id.org/monarch/monarch-py/:onset_qualifier
    "},{"location":"Data-Model/onset_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/onset_qualifier/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/onset_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/onset_qualifier/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/onset_qualifier/#linkml-source","title":"LinkML Source","text":"
    name: onset_qualifier\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: onset_qualifier\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/onset_qualifier_category/","title":"Slot: onset_qualifier_category","text":"
    The category of the onset_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:onset_qualifier_category
    "},{"location":"Data-Model/onset_qualifier_category/#inheritance","title":"Inheritance","text":"
       
    • category
         
      • onset_qualifier_category
        •  
       
      •  
    "},{"location":"Data-Model/onset_qualifier_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/onset_qualifier_category/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/onset_qualifier_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/onset_qualifier_category/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/onset_qualifier_category/#linkml-source","title":"LinkML Source","text":"
    name: onset_qualifier_category\ndescription: The category of the onset_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: onset_qualifier_category\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/onset_qualifier_closure/","title":"Slot: onset_qualifier_closure","text":"
    Field containing onset_qualifier id and the ids of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:onset_qualifier_closure
    "},{"location":"Data-Model/onset_qualifier_closure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/onset_qualifier_closure/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/onset_qualifier_closure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/onset_qualifier_closure/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/onset_qualifier_closure/#linkml-source","title":"LinkML Source","text":"
    name: onset_qualifier_closure\ndescription: Field containing onset_qualifier id and the ids of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: onset_qualifier_closure\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/onset_qualifier_closure_label/","title":"Slot: onset_qualifier_closure_label","text":"
    Field containing onset_qualifier name and the names of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:onset_qualifier_closure_label
    "},{"location":"Data-Model/onset_qualifier_closure_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/onset_qualifier_closure_label/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/onset_qualifier_closure_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/onset_qualifier_closure_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/onset_qualifier_closure_label/#linkml-source","title":"LinkML Source","text":"
    name: onset_qualifier_closure_label\ndescription: Field containing onset_qualifier name and the names of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: onset_qualifier_closure_label\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/onset_qualifier_label/","title":"Slot: onset_qualifier_label","text":"
    The name of the onset_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:onset_qualifier_label
    "},{"location":"Data-Model/onset_qualifier_label/#inheritance","title":"Inheritance","text":"
       
    • name
         
      • onset_qualifier_label
        •  
       
      •  
    "},{"location":"Data-Model/onset_qualifier_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/onset_qualifier_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/onset_qualifier_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/onset_qualifier_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/onset_qualifier_label/#linkml-source","title":"LinkML Source","text":"
    name: onset_qualifier_label\ndescription: The name of the onset_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: onset_qualifier_label\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/onset_qualifier_namespace/","title":"Slot: onset_qualifier_namespace","text":"
    The namespace/prefix of the onset_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:onset_qualifier_namespace
    "},{"location":"Data-Model/onset_qualifier_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/onset_qualifier_namespace/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/onset_qualifier_namespace/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/onset_qualifier_namespace/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/onset_qualifier_namespace/#linkml-source","title":"LinkML Source","text":"
    name: onset_qualifier_namespace\ndescription: The namespace/prefix of the onset_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: onset_qualifier_namespace\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/original_object/","title":"Slot: original_object","text":"
    URI: https://w3id.org/monarch/monarch-py/:original_object
    "},{"location":"Data-Model/original_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/original_object/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/original_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/original_object/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/original_object/#linkml-source","title":"LinkML Source","text":"
    name: original_object\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: original_object\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/original_subject/","title":"Slot: original_subject","text":"
    URI: https://w3id.org/monarch/monarch-py/:original_subject
    "},{"location":"Data-Model/original_subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/original_subject/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/original_subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/original_subject/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/original_subject/#linkml-source","title":"LinkML Source","text":"
    name: original_subject\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: original_subject\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/overlap_coefficient/","title":"Slot: overlap_coefficient","text":"
    URI: https://w3id.org/monarch/monarch-py/:overlap_coefficient
    "},{"location":"Data-Model/overlap_coefficient/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • overlap_coefficient
        •  
       
      •  
    "},{"location":"Data-Model/overlap_coefficient/#properties","title":"Properties","text":"
       
    • Range: ZeroToOne
      •  
    "},{"location":"Data-Model/overlap_coefficient/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/overlap_coefficient/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/overlap_coefficient/#linkml-source","title":"LinkML Source","text":"
    name: overlap_coefficient\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: overlap_coefficient\nrange: ZeroToOne\n
    "},{"location":"Data-Model/pathway/","title":"Slot: pathway","text":"
    URI: https://w3id.org/monarch/monarch-py/:pathway
    "},{"location":"Data-Model/pathway/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/pathway/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/pathway/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/pathway/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/pathway/#linkml-source","title":"LinkML Source","text":"
    name: pathway\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: pathway\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/phenodigm_score/","title":"Slot: phenodigm_score","text":"
    the geometric mean of the jaccard similarity and the information content
     
    URI: https://w3id.org/monarch/monarch-py/:phenodigm_score
    "},{"location":"Data-Model/phenodigm_score/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • phenodigm_score
        •  
       
      •  
    "},{"location":"Data-Model/phenodigm_score/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/phenodigm_score/#properties","title":"Properties","text":"
       
    • Range: NonNegativeFloat
      •  
    "},{"location":"Data-Model/phenodigm_score/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/phenodigm_score/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/phenodigm_score/#linkml-source","title":"LinkML Source","text":"
    name: phenodigm_score\ndescription: the geometric mean of the jaccard similarity and the information content\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: phenodigm_score\ndomain_of:\n- TermPairwiseSimilarity\nrange: NonNegativeFloat\nequals_expression: sqrt({jaccard_similarity} * {information_content})\n
    "},{"location":"Data-Model/predicate/","title":"Slot: predicate","text":"
    URI: https://w3id.org/monarch/monarch-py/:predicate
    "},{"location":"Data-Model/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no CompactAssociation no Association no"},{"location":"Data-Model/predicate/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/predicate/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/predicate/#linkml-source","title":"LinkML Source","text":"
    name: predicate\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: false\nalias: predicate\ndomain_of:\n- Association\n- CompactAssociation\nrange: string\nrequired: true\n
    "},{"location":"Data-Model/predicate_id/","title":"Slot: predicate_id","text":"
    URI: https://w3id.org/monarch/monarch-py/:predicate_id
    "},{"location":"Data-Model/predicate_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Mapping A minimal class to hold a SSSOM mapping no"},{"location":"Data-Model/predicate_id/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/predicate_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/predicate_id/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/predicate_id/#linkml-source","title":"LinkML Source","text":"
    name: predicate_id\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: predicate_id\ndomain_of:\n- Mapping\nrange: string\nrequired: true\n
    "},{"location":"Data-Model/primary_knowledge_source/","title":"Slot: primary_knowledge_source","text":"
    URI: https://w3id.org/monarch/monarch-py/:primary_knowledge_source
    "},{"location":"Data-Model/primary_knowledge_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/primary_knowledge_source/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/primary_knowledge_source/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/primary_knowledge_source/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/primary_knowledge_source/#linkml-source","title":"LinkML Source","text":"
    name: primary_knowledge_source\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: primary_knowledge_source\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/provided_by/","title":"Slot: provided_by","text":"
    URI: https://w3id.org/monarch/monarch-py/:provided_by
    "},{"location":"Data-Model/provided_by/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Entity Represents an Entity in the Monarch KG data model no DirectionalAssociation An association that gives it's direction relative to a specified entity no SearchResult no Node UI container class extending Entity with additional information no Association no"},{"location":"Data-Model/provided_by/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/provided_by/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/provided_by/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/provided_by/#linkml-source","title":"LinkML Source","text":"
    name: provided_by\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: provided_by\ndomain_of:\n- Association\n- Entity\nrange: string\n
    "},{"location":"Data-Model/provided_by_link/","title":"Slot: provided_by_link","text":"
    A link to the docs for the knowledge source that provided the node/edge.
     
    URI: https://w3id.org/monarch/monarch-py/:provided_by_link
    "},{"location":"Data-Model/provided_by_link/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Node UI container class extending Entity with additional information no Association no"},{"location":"Data-Model/provided_by_link/#properties","title":"Properties","text":"
       
    • Range: ExpandedCurie
      •  
    "},{"location":"Data-Model/provided_by_link/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/provided_by_link/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/provided_by_link/#linkml-source","title":"LinkML Source","text":"
    name: provided_by_link\ndescription: A link to the docs for the knowledge source that provided the node/edge.\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: provided_by_link\ndomain_of:\n- Association\n- Node\nrange: ExpandedCurie\ninlined: true\n
    "},{"location":"Data-Model/publications/","title":"Slot: publications","text":"
    URI: https://w3id.org/monarch/monarch-py/:publications
    "},{"location":"Data-Model/publications/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/publications/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/publications/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/publications/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/publications/#linkml-source","title":"LinkML Source","text":"
    name: publications\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: publications\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/publications_links/","title":"Slot: publications_links","text":"
    List of ExpandedCuries with id and url for publications
     
    URI: https://w3id.org/monarch/monarch-py/:publications_links
    "},{"location":"Data-Model/publications_links/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/publications_links/#properties","title":"Properties","text":"
       
    •  
      Range: ExpandedCurie
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/publications_links/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/publications_links/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/publications_links/#linkml-source","title":"LinkML Source","text":"
    name: publications_links\ndescription: List of ExpandedCuries with id and url for publications\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: publications_links\ndomain_of:\n- Association\nrange: ExpandedCurie\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/qc_report/","title":"Slot: qc_report","text":"
    URI: https://w3id.org/monarch/monarch-py/:qc_report
    "},{"location":"Data-Model/qc_report/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/qc_report/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/qc_report/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qc_report/#valid-id-prefixes","title":"Valid ID Prefixes","text":"
    Instances of this class should have identifiers with one of the following prefixes:
     
       
    • string
      •  
    "},{"location":"Data-Model/qc_report/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/qc_report/#linkml-source","title":"LinkML Source","text":"
    name: qc_report\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: qc_report\ndomain_of:\n- Release\nrange: string\n
    "},{"location":"Data-Model/qualifier/","title":"Slot: qualifier","text":"
    URI: https://w3id.org/monarch/monarch-py/:qualifier
    "},{"location":"Data-Model/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/qualifier/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifier/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/qualifier/#linkml-source","title":"LinkML Source","text":"
    name: qualifier\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: qualifier\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/qualifier_category/","title":"Slot: qualifier_category","text":"
    The category of the frequency_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:qualifier_category
    "},{"location":"Data-Model/qualifier_category/#inheritance","title":"Inheritance","text":"
       
    • category
         
      • qualifier_category
        •  
       
      •  
    "},{"location":"Data-Model/qualifier_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/qualifier_category/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/qualifier_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifier_category/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/qualifier_category/#linkml-source","title":"LinkML Source","text":"
    name: qualifier_category\ndescription: The category of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: qualifier_category\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/qualifier_closure/","title":"Slot: qualifier_closure","text":"
    Field containing frequency_qualifier id and the ids of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:qualifier_closure
    "},{"location":"Data-Model/qualifier_closure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/qualifier_closure/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/qualifier_closure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifier_closure/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/qualifier_closure/#linkml-source","title":"LinkML Source","text":"
    name: qualifier_closure\ndescription: Field containing frequency_qualifier id and the ids of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: qualifier_closure\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/qualifier_closure_label/","title":"Slot: qualifier_closure_label","text":"
    Field containing frequency_qualifier name and the names of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:qualifier_closure_label
    "},{"location":"Data-Model/qualifier_closure_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/qualifier_closure_label/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/qualifier_closure_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifier_closure_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/qualifier_closure_label/#linkml-source","title":"LinkML Source","text":"
    name: qualifier_closure_label\ndescription: Field containing frequency_qualifier name and the names of all of it's\n  ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: qualifier_closure_label\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/qualifier_label/","title":"Slot: qualifier_label","text":"
    The name of the frequency_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:qualifier_label
    "},{"location":"Data-Model/qualifier_label/#inheritance","title":"Inheritance","text":"
       
    • name
         
      • qualifier_label
        •  
       
      •  
    "},{"location":"Data-Model/qualifier_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/qualifier_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/qualifier_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifier_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/qualifier_label/#linkml-source","title":"LinkML Source","text":"
    name: qualifier_label\ndescription: The name of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: qualifier_label\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/qualifier_namespace/","title":"Slot: qualifier_namespace","text":"
    The namespace/prefix of the frequency_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:qualifier_namespace
    "},{"location":"Data-Model/qualifier_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/qualifier_namespace/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/qualifier_namespace/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifier_namespace/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/qualifier_namespace/#linkml-source","title":"LinkML Source","text":"
    name: qualifier_namespace\ndescription: The namespace/prefix of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: qualifier_namespace\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/qualifiers/","title":"Slot: qualifiers","text":"
    URI: https://w3id.org/monarch/monarch-py/:qualifiers
    "},{"location":"Data-Model/qualifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/qualifiers/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/qualifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifiers/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/qualifiers/#linkml-source","title":"LinkML Source","text":"
    name: qualifiers\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: qualifiers\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/qualifiers_category/","title":"Slot: qualifiers_category","text":"
    The category of the frequency_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:qualifiers_category
    "},{"location":"Data-Model/qualifiers_category/#inheritance","title":"Inheritance","text":"
       
    • category
         
      • qualifiers_category
        •  
       
      •  
    "},{"location":"Data-Model/qualifiers_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/qualifiers_category/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/qualifiers_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifiers_category/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/qualifiers_category/#linkml-source","title":"LinkML Source","text":"
    name: qualifiers_category\ndescription: The category of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: qualifiers_category\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/qualifiers_closure/","title":"Slot: qualifiers_closure","text":"
    Field containing frequency_qualifier id and the ids of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:qualifiers_closure
    "},{"location":"Data-Model/qualifiers_closure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/qualifiers_closure/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/qualifiers_closure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifiers_closure/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/qualifiers_closure/#linkml-source","title":"LinkML Source","text":"
    name: qualifiers_closure\ndescription: Field containing frequency_qualifier id and the ids of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: qualifiers_closure\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/qualifiers_closure_label/","title":"Slot: qualifiers_closure_label","text":"
    Field containing frequency_qualifier name and the names of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:qualifiers_closure_label
    "},{"location":"Data-Model/qualifiers_closure_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/qualifiers_closure_label/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/qualifiers_closure_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifiers_closure_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/qualifiers_closure_label/#linkml-source","title":"LinkML Source","text":"
    name: qualifiers_closure_label\ndescription: Field containing frequency_qualifier name and the names of all of it's\n  ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: qualifiers_closure_label\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/qualifiers_label/","title":"Slot: qualifiers_label","text":"
    The name of the frequency_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:qualifiers_label
    "},{"location":"Data-Model/qualifiers_label/#inheritance","title":"Inheritance","text":"
       
    • name
         
      • qualifiers_label
        •  
       
      •  
    "},{"location":"Data-Model/qualifiers_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/qualifiers_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/qualifiers_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifiers_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/qualifiers_label/#linkml-source","title":"LinkML Source","text":"
    name: qualifiers_label\ndescription: The name of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: qualifiers_label\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/qualifiers_namespace/","title":"Slot: qualifiers_namespace","text":"
    The namespace/prefix of the frequency_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:qualifiers_namespace
    "},{"location":"Data-Model/qualifiers_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/qualifiers_namespace/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/qualifiers_namespace/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifiers_namespace/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/qualifiers_namespace/#linkml-source","title":"LinkML Source","text":"
    name: qualifiers_namespace\ndescription: The namespace/prefix of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: qualifiers_namespace\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/score/","title":"Slot: score","text":"
    URI: https://w3id.org/monarch/monarch-py/:score
    "},{"location":"Data-Model/score/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • information_content
        •  
      • jaccard_similarity
        •  
      • cosine_similarity
        •  
      • dice_similarity
        •  
      • phenodigm_score
        •  
      • overlap_coefficient
        •  
      • subsumes_score
        •  
      • subsumed_by_score
        •  
      • intersection_count
        •  
      • union_count
        •  
       
      •  
    "},{"location":"Data-Model/score/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no BestMatch no SemsimSearchResult no"},{"location":"Data-Model/score/#properties","title":"Properties","text":"
       
    • Range: Float
      •  
    "},{"location":"Data-Model/score/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/score/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/score/#linkml-source","title":"LinkML Source","text":"
    name: score\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: score\ndomain_of:\n- SearchResult\n- BestMatch\n- SemsimSearchResult\nrange: float\n
    "},{"location":"Data-Model/sex_qualifier/","title":"Slot: sex_qualifier","text":"
    URI: https://w3id.org/monarch/monarch-py/:sex_qualifier
    "},{"location":"Data-Model/sex_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/sex_qualifier/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/sex_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/sex_qualifier/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/sex_qualifier/#linkml-source","title":"LinkML Source","text":"
    name: sex_qualifier\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: sex_qualifier\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/sex_qualifier_category/","title":"Slot: sex_qualifier_category","text":"
    The category of the sex_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:sex_qualifier_category
    "},{"location":"Data-Model/sex_qualifier_category/#inheritance","title":"Inheritance","text":"
       
    • category
         
      • sex_qualifier_category
        •  
       
      •  
    "},{"location":"Data-Model/sex_qualifier_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/sex_qualifier_category/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/sex_qualifier_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/sex_qualifier_category/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/sex_qualifier_category/#linkml-source","title":"LinkML Source","text":"
    name: sex_qualifier_category\ndescription: The category of the sex_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: sex_qualifier_category\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/sex_qualifier_closure/","title":"Slot: sex_qualifier_closure","text":"
    Field containing sex_qualifier id and the ids of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:sex_qualifier_closure
    "},{"location":"Data-Model/sex_qualifier_closure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/sex_qualifier_closure/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/sex_qualifier_closure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/sex_qualifier_closure/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/sex_qualifier_closure/#linkml-source","title":"LinkML Source","text":"
    name: sex_qualifier_closure\ndescription: Field containing sex_qualifier id and the ids of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: sex_qualifier_closure\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/sex_qualifier_closure_label/","title":"Slot: sex_qualifier_closure_label","text":"
    Field containing sex_qualifier name and the names of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:sex_qualifier_closure_label
    "},{"location":"Data-Model/sex_qualifier_closure_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/sex_qualifier_closure_label/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/sex_qualifier_closure_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/sex_qualifier_closure_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/sex_qualifier_closure_label/#linkml-source","title":"LinkML Source","text":"
    name: sex_qualifier_closure_label\ndescription: Field containing sex_qualifier name and the names of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: sex_qualifier_closure_label\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/sex_qualifier_label/","title":"Slot: sex_qualifier_label","text":"
    The name of the sex_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:sex_qualifier_label
    "},{"location":"Data-Model/sex_qualifier_label/#inheritance","title":"Inheritance","text":"
       
    • name
         
      • sex_qualifier_label
        •  
       
      •  
    "},{"location":"Data-Model/sex_qualifier_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/sex_qualifier_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/sex_qualifier_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/sex_qualifier_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/sex_qualifier_label/#linkml-source","title":"LinkML Source","text":"
    name: sex_qualifier_label\ndescription: The name of the sex_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: sex_qualifier_label\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/sex_qualifier_namespace/","title":"Slot: sex_qualifier_namespace","text":"
    The namespace/prefix of the sex_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:sex_qualifier_namespace
    "},{"location":"Data-Model/sex_qualifier_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/sex_qualifier_namespace/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/sex_qualifier_namespace/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/sex_qualifier_namespace/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/sex_qualifier_namespace/#linkml-source","title":"LinkML Source","text":"
    name: sex_qualifier_namespace\ndescription: The namespace/prefix of the sex_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: sex_qualifier_namespace\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/similarity/","title":"Slot: similarity","text":"
    URI: https://w3id.org/monarch/monarch-py/:similarity
    "},{"location":"Data-Model/similarity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no SemsimSearchResult no"},{"location":"Data-Model/similarity/#properties","title":"Properties","text":"
       
    • Range: TermSetPairwiseSimilarity
      •  
    "},{"location":"Data-Model/similarity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/similarity/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/similarity/#linkml-source","title":"LinkML Source","text":"
    name: similarity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: similarity\ndomain_of:\n- BestMatch\n- SemsimSearchResult\nrange: TermSetPairwiseSimilarity\n
    "},{"location":"Data-Model/solr/","title":"Slot: solr","text":"
    URI: https://w3id.org/monarch/monarch-py/:solr
    "},{"location":"Data-Model/solr/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/solr/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/solr/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/solr/#valid-id-prefixes","title":"Valid ID Prefixes","text":"
    Instances of this class should have identifiers with one of the following prefixes:
     
       
    • string
      •  
    "},{"location":"Data-Model/solr/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/solr/#linkml-source","title":"LinkML Source","text":"
    name: solr\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: solr\ndomain_of:\n- Release\nrange: string\n
    "},{"location":"Data-Model/sqlite/","title":"Slot: sqlite","text":"
    URI: https://w3id.org/monarch/monarch-py/:sqlite
    "},{"location":"Data-Model/sqlite/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/sqlite/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/sqlite/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/sqlite/#valid-id-prefixes","title":"Valid ID Prefixes","text":"
    Instances of this class should have identifiers with one of the following prefixes:
     
       
    • string
      •  
    "},{"location":"Data-Model/sqlite/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/sqlite/#linkml-source","title":"LinkML Source","text":"
    name: sqlite\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: sqlite\ndomain_of:\n- Release\nrange: string\n
    "},{"location":"Data-Model/stage_qualifier/","title":"Slot: stage_qualifier","text":"
    URI: https://w3id.org/monarch/monarch-py/:stage_qualifier
    "},{"location":"Data-Model/stage_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/stage_qualifier/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/stage_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/stage_qualifier/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/stage_qualifier/#linkml-source","title":"LinkML Source","text":"
    name: stage_qualifier\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: stage_qualifier\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/stage_qualifier_category/","title":"Slot: stage_qualifier_category","text":"
    The category of the stage_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:stage_qualifier_category
    "},{"location":"Data-Model/stage_qualifier_category/#inheritance","title":"Inheritance","text":"
       
    • category
         
      • stage_qualifier_category
        •  
       
      •  
    "},{"location":"Data-Model/stage_qualifier_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/stage_qualifier_category/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/stage_qualifier_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/stage_qualifier_category/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/stage_qualifier_category/#linkml-source","title":"LinkML Source","text":"
    name: stage_qualifier_category\ndescription: The category of the stage_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: stage_qualifier_category\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/stage_qualifier_closure/","title":"Slot: stage_qualifier_closure","text":"
    Field containing stage_qualifier id and the ids of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:stage_qualifier_closure
    "},{"location":"Data-Model/stage_qualifier_closure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/stage_qualifier_closure/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/stage_qualifier_closure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/stage_qualifier_closure/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/stage_qualifier_closure/#linkml-source","title":"LinkML Source","text":"
    name: stage_qualifier_closure\ndescription: Field containing stage_qualifier id and the ids of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: stage_qualifier_closure\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/stage_qualifier_closure_label/","title":"Slot: stage_qualifier_closure_label","text":"
    Field containing stage_qualifier name and the names of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:stage_qualifier_closure_label
    "},{"location":"Data-Model/stage_qualifier_closure_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/stage_qualifier_closure_label/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/stage_qualifier_closure_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/stage_qualifier_closure_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/stage_qualifier_closure_label/#linkml-source","title":"LinkML Source","text":"
    name: stage_qualifier_closure_label\ndescription: Field containing stage_qualifier name and the names of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: stage_qualifier_closure_label\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/stage_qualifier_label/","title":"Slot: stage_qualifier_label","text":"
    The name of the stage_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:stage_qualifier_label
    "},{"location":"Data-Model/stage_qualifier_label/#inheritance","title":"Inheritance","text":"
       
    • name
         
      • stage_qualifier_label
        •  
       
      •  
    "},{"location":"Data-Model/stage_qualifier_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/stage_qualifier_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/stage_qualifier_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/stage_qualifier_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/stage_qualifier_label/#linkml-source","title":"LinkML Source","text":"
    name: stage_qualifier_label\ndescription: The name of the stage_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: stage_qualifier_label\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/stage_qualifier_namespace/","title":"Slot: stage_qualifier_namespace","text":"
    The namespace/prefix of the stage_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:stage_qualifier_namespace
    "},{"location":"Data-Model/stage_qualifier_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/stage_qualifier_namespace/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/stage_qualifier_namespace/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/stage_qualifier_namespace/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/stage_qualifier_namespace/#linkml-source","title":"LinkML Source","text":"
    name: stage_qualifier_namespace\ndescription: The namespace/prefix of the stage_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: stage_qualifier_namespace\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/start/","title":"Slot: start","text":"
    start position of the annotation
     
    URI: https://w3id.org/monarch/monarch-py/:start
    "},{"location":"Data-Model/start/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextAnnotationResult no"},{"location":"Data-Model/start/#properties","title":"Properties","text":"
       
    • Range: Integer
      •  
    "},{"location":"Data-Model/start/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/start/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/start/#linkml-source","title":"LinkML Source","text":"
    name: start\ndescription: start position of the annotation\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: start\ndomain_of:\n- TextAnnotationResult\nrange: integer\n
    "},{"location":"Data-Model/sub_classes/","title":"Slot: sub_classes","text":"
    URI: https://w3id.org/monarch/monarch-py/:sub_classes
    "},{"location":"Data-Model/sub_classes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NodeHierarchy no"},{"location":"Data-Model/sub_classes/#properties","title":"Properties","text":"
       
    •  
      Range: Entity
       
      •  
    •  
      Multivalued: True
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/sub_classes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/sub_classes/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/sub_classes/#linkml-source","title":"LinkML Source","text":"
    name: sub_classes\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: sub_classes\ndomain_of:\n- NodeHierarchy\nrange: Entity\nrequired: true\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/subject/","title":"Slot: subject","text":"
    URI: https://w3id.org/monarch/monarch-py/:subject
    "},{"location":"Data-Model/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no CompactAssociation no Association no SemsimSearchResult yes"},{"location":"Data-Model/subject/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subject/#linkml-source","title":"LinkML Source","text":"
    name: subject\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: subject\ndomain_of:\n- Association\n- CompactAssociation\n- SemsimSearchResult\nrange: string\nrequired: true\n
    "},{"location":"Data-Model/subject_best_matches/","title":"Slot: subject_best_matches","text":"
    URI: https://w3id.org/monarch/monarch-py/:subject_best_matches
    "},{"location":"Data-Model/subject_best_matches/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/subject_best_matches/#properties","title":"Properties","text":"
       
    •  
      Range: BestMatch
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/subject_best_matches/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject_best_matches/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subject_best_matches/#linkml-source","title":"LinkML Source","text":"
    name: subject_best_matches\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: subject_best_matches\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: BestMatch\ninlined: true\n
    "},{"location":"Data-Model/subject_category/","title":"Slot: subject_category","text":"
    The category of the subject entity
     
    URI: https://w3id.org/monarch/monarch-py/:subject_category
    "},{"location":"Data-Model/subject_category/#inheritance","title":"Inheritance","text":"
       
    • category
         
      • subject_category
        •  
       
      •  
    "},{"location":"Data-Model/subject_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/subject_category/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/subject_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject_category/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subject_category/#linkml-source","title":"LinkML Source","text":"
    name: subject_category\ndescription: The category of the subject entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: subject_category\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/subject_closure/","title":"Slot: subject_closure","text":"
    Field containing subject id and the ids of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:subject_closure
    "},{"location":"Data-Model/subject_closure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/subject_closure/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/subject_closure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject_closure/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subject_closure/#linkml-source","title":"LinkML Source","text":"
    name: subject_closure\ndescription: Field containing subject id and the ids of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: subject_closure\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/subject_closure_label/","title":"Slot: subject_closure_label","text":"
    Field containing subject name and the names of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:subject_closure_label
    "},{"location":"Data-Model/subject_closure_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/subject_closure_label/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/subject_closure_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject_closure_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subject_closure_label/#linkml-source","title":"LinkML Source","text":"
    name: subject_closure_label\ndescription: Field containing subject name and the names of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: subject_closure_label\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/subject_id/","title":"Slot: subject_id","text":"
    URI: https://w3id.org/monarch/monarch-py/:subject_id
    "},{"location":"Data-Model/subject_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no Mapping A minimal class to hold a SSSOM mapping no"},{"location":"Data-Model/subject_id/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/subject_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject_id/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subject_id/#linkml-source","title":"LinkML Source","text":"
    name: subject_id\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: subject_id\ndomain_of:\n- Mapping\n- TermPairwiseSimilarity\nrange: string\nrequired: true\n
    "},{"location":"Data-Model/subject_information_content/","title":"Slot: subject_information_content","text":"
    The IC of the subject
     
    URI: https://w3id.org/monarch/monarch-py/:subject_information_content
    "},{"location":"Data-Model/subject_information_content/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • information_content
           
        • subject_information_content
          •  
         
        •  
       
      •  
    "},{"location":"Data-Model/subject_information_content/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/subject_information_content/#properties","title":"Properties","text":"
       
    • Range: NegativeLogValue
      •  
    "},{"location":"Data-Model/subject_information_content/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject_information_content/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subject_information_content/#linkml-source","title":"LinkML Source","text":"
    name: subject_information_content\ndescription: The IC of the subject\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: information_content\nalias: subject_information_content\ndomain_of:\n- TermPairwiseSimilarity\nrange: NegativeLogValue\n
    "},{"location":"Data-Model/subject_label/","title":"Slot: subject_label","text":"
    The name of the subject entity
     
    URI: https://w3id.org/monarch/monarch-py/:subject_label
    "},{"location":"Data-Model/subject_label/#inheritance","title":"Inheritance","text":"
       
    • name
         
      • subject_label
        •  
       
      •  
    "},{"location":"Data-Model/subject_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AssociationTypeMapping A data class to hold the necessary information to produce association type co... yes TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no DirectionalAssociation An association that gives it's direction relative to a specified entity no Mapping A minimal class to hold a SSSOM mapping no CompactAssociation no Association no"},{"location":"Data-Model/subject_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/subject_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subject_label/#linkml-source","title":"LinkML Source","text":"
    name: subject_label\ndescription: The name of the subject entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: subject_label\ndomain_of:\n- Association\n- CompactAssociation\n- AssociationTypeMapping\n- Mapping\n- TermPairwiseSimilarity\nrange: string\n
    "},{"location":"Data-Model/subject_namespace/","title":"Slot: subject_namespace","text":"
    The namespace/prefix of the subject entity
     
    URI: https://w3id.org/monarch/monarch-py/:subject_namespace
    "},{"location":"Data-Model/subject_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/subject_namespace/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/subject_namespace/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject_namespace/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subject_namespace/#linkml-source","title":"LinkML Source","text":"
    name: subject_namespace\ndescription: The namespace/prefix of the subject entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: subject_namespace\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/subject_source/","title":"Slot: subject_source","text":"
    the source for the first entity
     
    URI: sssom:subject_source
    "},{"location":"Data-Model/subject_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/subject_source/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/subject_source/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject_source/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subject_source/#linkml-source","title":"LinkML Source","text":"
    name: subject_source\ndescription: the source for the first entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nslot_uri: sssom:subject_source\nalias: subject_source\ndomain_of:\n- TermPairwiseSimilarity\nrange: string\n
    "},{"location":"Data-Model/subject_taxon/","title":"Slot: subject_taxon","text":"
    URI: https://w3id.org/monarch/monarch-py/:subject_taxon
    "},{"location":"Data-Model/subject_taxon/#inheritance","title":"Inheritance","text":"
       
    • in_taxon
         
      • subject_taxon
        •  
       
      •  
    "},{"location":"Data-Model/subject_taxon/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/subject_taxon/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/subject_taxon/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject_taxon/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subject_taxon/#linkml-source","title":"LinkML Source","text":"
    name: subject_taxon\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: in_taxon\nalias: subject_taxon\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/subject_taxon_label/","title":"Slot: subject_taxon_label","text":"
    URI: https://w3id.org/monarch/monarch-py/:subject_taxon_label
    "},{"location":"Data-Model/subject_taxon_label/#inheritance","title":"Inheritance","text":"
       
    • in_taxon_label
         
      • subject_taxon_label
        •  
       
      •  
    "},{"location":"Data-Model/subject_taxon_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/subject_taxon_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/subject_taxon_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject_taxon_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subject_taxon_label/#linkml-source","title":"LinkML Source","text":"
    name: subject_taxon_label\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: in_taxon_label\nalias: subject_taxon_label\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/subject_termset/","title":"Slot: subject_termset","text":"
    URI: https://w3id.org/monarch/monarch-py/:subject_termset
    "},{"location":"Data-Model/subject_termset/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/subject_termset/#properties","title":"Properties","text":"
       
    •  
      Range: TermInfo
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/subject_termset/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject_termset/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subject_termset/#linkml-source","title":"LinkML Source","text":"
    name: subject_termset\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: subject_termset\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: TermInfo\ninlined: true\n
    "},{"location":"Data-Model/subsumed_by_score/","title":"Slot: subsumed_by_score","text":"
    URI: https://w3id.org/monarch/monarch-py/:subsumed_by_score
    "},{"location":"Data-Model/subsumed_by_score/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • subsumed_by_score
        •  
       
      •  
    "},{"location":"Data-Model/subsumed_by_score/#properties","title":"Properties","text":"
       
    • Range: ZeroToOne
      •  
    "},{"location":"Data-Model/subsumed_by_score/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subsumed_by_score/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subsumed_by_score/#linkml-source","title":"LinkML Source","text":"
    name: subsumed_by_score\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: subsumed_by_score\nrange: ZeroToOne\n
    "},{"location":"Data-Model/subsumes_score/","title":"Slot: subsumes_score","text":"
    URI: https://w3id.org/monarch/monarch-py/:subsumes_score
    "},{"location":"Data-Model/subsumes_score/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • subsumes_score
        •  
       
      •  
    "},{"location":"Data-Model/subsumes_score/#properties","title":"Properties","text":"
       
    • Range: ZeroToOne
      •  
    "},{"location":"Data-Model/subsumes_score/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subsumes_score/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subsumes_score/#linkml-source","title":"LinkML Source","text":"
    name: subsumes_score\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: subsumes_score\nrange: ZeroToOne\n
    "},{"location":"Data-Model/super_classes/","title":"Slot: super_classes","text":"
    URI: https://w3id.org/monarch/monarch-py/:super_classes
    "},{"location":"Data-Model/super_classes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NodeHierarchy no"},{"location":"Data-Model/super_classes/#properties","title":"Properties","text":"
       
    •  
      Range: Entity
       
      •  
    •  
      Multivalued: True
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/super_classes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/super_classes/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/super_classes/#linkml-source","title":"LinkML Source","text":"
    name: super_classes\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: super_classes\ndomain_of:\n- NodeHierarchy\nrange: Entity\nrequired: true\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/symbol/","title":"Slot: symbol","text":"
    URI: https://w3id.org/monarch/monarch-py/:symbol
    "},{"location":"Data-Model/symbol/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Entity Represents an Entity in the Monarch KG data model no Node UI container class extending Entity with additional information no SearchResult no"},{"location":"Data-Model/symbol/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/symbol/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/symbol/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/symbol/#linkml-source","title":"LinkML Source","text":"
    name: symbol\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: symbol\ndomain_of:\n- Entity\nrange: string\n
    "},{"location":"Data-Model/symmetric/","title":"Slot: symmetric","text":"
    Whether the association type is symmetric, i.e. the subject and object labels are interchangeable.
     
    URI: https://w3id.org/monarch/monarch-py/:symmetric
    "},{"location":"Data-Model/symmetric/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AssociationTypeMapping A data class to hold the necessary information to produce association type co... yes"},{"location":"Data-Model/symmetric/#properties","title":"Properties","text":"
       
    • Range: Boolean
      •  
    "},{"location":"Data-Model/symmetric/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/symmetric/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/symmetric/#linkml-source","title":"LinkML Source","text":"
    name: symmetric\ndescription: Whether the association type is symmetric, i.e. the subject and object\n  labels are interchangeable.\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: symmetric\ndomain_of:\n- AssociationTypeMapping\nrange: boolean\n
    "},{"location":"Data-Model/synonym/","title":"Slot: synonym","text":"
    URI: https://w3id.org/monarch/monarch-py/:synonym
    "},{"location":"Data-Model/synonym/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Entity Represents an Entity in the Monarch KG data model no Node UI container class extending Entity with additional information no SearchResult no"},{"location":"Data-Model/synonym/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/synonym/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/synonym/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/synonym/#linkml-source","title":"LinkML Source","text":"
    name: synonym\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: synonym\ndomain_of:\n- Entity\nrange: string\n
    "},{"location":"Data-Model/text/","title":"Slot: text","text":"
    text without tokens
     
    URI: https://w3id.org/monarch/monarch-py/:text
    "},{"location":"Data-Model/text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextAnnotationResult no"},{"location":"Data-Model/text/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/text/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/text/#linkml-source","title":"LinkML Source","text":"
    name: text\ndescription: text without tokens\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: text\ndomain_of:\n- TextAnnotationResult\nrange: string\ninlined: true\n
    "},{"location":"Data-Model/tokens/","title":"Slot: tokens","text":"
    A collection of entities or concepts
     
    URI: https://w3id.org/monarch/monarch-py/:tokens
    "},{"location":"Data-Model/tokens/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextAnnotationResult no"},{"location":"Data-Model/tokens/#properties","title":"Properties","text":"
       
    •  
      Range: Entity
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/tokens/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/tokens/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/tokens/#linkml-source","title":"LinkML Source","text":"
    name: tokens\ndescription: A collection of entities or concepts\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: tokens\ndomain_of:\n- TextAnnotationResult\nrange: Entity\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/total/","title":"Slot: total","text":"
    total number of items matching a query
     
    URI: https://w3id.org/monarch/monarch-py/:total
    "},{"location":"Data-Model/total/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AssociationTableResults no CompactAssociationResults no MappingResults SSSOM Mappings returned as a results collection no AssociationResults no CategoryGroupedAssociationResults no EntityResults no MultiEntityAssociationResults no SearchResults no Results no"},{"location":"Data-Model/total/#properties","title":"Properties","text":"
       
    •  
      Range: Integer
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/total/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/total/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/total/#linkml-source","title":"LinkML Source","text":"
    name: total\ndescription: total number of items matching a query\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: total\ndomain_of:\n- Results\nrange: integer\nrequired: true\n
    "},{"location":"Data-Model/union_count/","title":"Slot: union_count","text":"
    URI: https://w3id.org/monarch/monarch-py/:union_count
    "},{"location":"Data-Model/union_count/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • union_count
        •  
       
      •  
    "},{"location":"Data-Model/union_count/#properties","title":"Properties","text":"
       
    • Range: ItemCount
      •  
    "},{"location":"Data-Model/union_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/union_count/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/union_count/#linkml-source","title":"LinkML Source","text":"
    name: union_count\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: union_count\nrange: ItemCount\n
    "},{"location":"Data-Model/uri/","title":"Slot: uri","text":"
    The URI of the entity
     
    URI: https://w3id.org/monarch/monarch-py/:uri
    "},{"location":"Data-Model/uri/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Entity Represents an Entity in the Monarch KG data model no Node UI container class extending Entity with additional information no SearchResult no"},{"location":"Data-Model/uri/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/uri/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/uri/#linkml-source","title":"LinkML Source","text":"
    name: uri\ndescription: The URI of the entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: uri\ndomain_of:\n- Entity\nrange: string\n
    "},{"location":"Data-Model/url/","title":"Slot: url","text":"
    URI: https://w3id.org/monarch/monarch-py/:url
    "},{"location":"Data-Model/url/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExpandedCurie A curie bundled along with its expanded url no Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/url/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/url/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/url/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/url/#linkml-source","title":"LinkML Source","text":"
    name: url\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: url\ndomain_of:\n- ExpandedCurie\n- Release\nrange: string\n
    "},{"location":"Data-Model/version/","title":"Slot: version","text":"
    URI: https://w3id.org/monarch/monarch-py/:version
    "},{"location":"Data-Model/version/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/version/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/version/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/version/#valid-id-prefixes","title":"Valid ID Prefixes","text":"
    Instances of this class should have identifiers with one of the following prefixes:
     
       
    • string
      •  
    "},{"location":"Data-Model/version/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/version/#linkml-source","title":"LinkML Source","text":"
    name: version\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: version\ndomain_of:\n- Release\nrange: string\n
    "},{"location":"Data-Model/xref/","title":"Slot: xref","text":"
    URI: https://w3id.org/monarch/monarch-py/:xref
    "},{"location":"Data-Model/xref/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Entity Represents an Entity in the Monarch KG data model no Node UI container class extending Entity with additional information no SearchResult no"},{"location":"Data-Model/xref/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/xref/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/xref/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/xref/#linkml-source","title":"LinkML Source","text":"
    name: xref\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nmultivalued: true\nalias: xref\ndomain_of:\n- Entity\nrange: string\n
    "},{"location":"FastAPI/","title":"Monarch-Py FastAPI","text":"
    A FastAPI is also available for browsing the knowledge graph produced by the Monarch Initiative, which wraps the monarch-py library.
     
    It is included automatically as part of monarch-py when installed via pip or pipx.
    "},{"location":"FastAPI/#running-the-api-server","title":"Running the API Server","text":"
    A local development server can be started with the command:
     
    monarch-api\n
     
    or using uvicorn:
     
    # Using uvicorn directly:\npoetry run uvicorn src.monarch_py.api.main:app --reload\n\n# Using the Makefile shortcut:\ncd <path-to>/monarch-app\nmake dev-api\n
     
    The API is then available at http://127.0.0.1:8000/v3/api.
     
    Swagger documentation is available at http://127.0.0.1:8000/v3/docs, and a ReDoc interface at http://127.0.0.1:8000/v3/redoc.
    "},{"location":"FastAPI/#documentation","title":"Documentation","text":"
    API Reference
     
    Data Response Model
    "},{"location":"FastAPI/Endpoints/","title":"Monarch API Endpoints","text":"
    This section contains API reference for the various endpoints provided by monarch-api.
    "},{"location":"FastAPI/Endpoints/#endpoints","title":"Endpoints:","text":"
       
    • Association 
      •  
    • Entity 
      •  
    • SemSim (Semantic Similarity)
      •  
    "},{"location":"FastAPI/Endpoints/association/","title":"Association Endpoints","text":""},{"location":"FastAPI/Endpoints/entity/","title":"Entity Endpoints","text":""},{"location":"FastAPI/Endpoints/semsim/","title":"SemSim Endpoints","text":""},{"location":"FastAPI/Endpoints/semsim/#src.monarch_py.api.semsim.autocomplete","title":"autocomplete","text":"
    Autocomplete for semantic similarity lookups, prioritizes entities which have direct phenotype associations. Note: This API endpoint is experimental and may evolve or disappear over time.
     
    Parameters:
     Name Type Description Default q str 
    Query string to autocomplete against
     Query(default='*:*', title='Query string to autocomplete against', examples=['fanc', 'ehler']) 
    Returns:
     Type Description SearchResults 
    SearchResults
    "},{"location":"Usage/","title":"Usage","text":"
    monarch-py can be used via command line, or as a Python module.
    "},{"location":"Usage/#cli","title":"CLI","text":""},{"location":"Usage/#overview","title":"Overview","text":"
    monarch-py can be used to query various implementations of the Monarch knowledge graph. The default, and more feature-rich, implementation is Solr, and is the default.
     
    Subcommands are available to specify the backend.
     
    For example: 
    # The following two commands are equivalent,\n# as both query the Solr KG\n$ monarch entity MONDO:0012933 \n$ monarch solr entity MONDO:0012933\n\n# Whereas the following specifies the SQL implementation\n$ monarch sql entity MONDO:0012933\n
     
    You can also use an environment variable to specify a Solr URL to query a different Solr instance. monarch-py checks for the MONARCH_SOLR_URL environment variable, and uses it if it exists. If not, it uses the default Solr URL of http://localhost:8983/solr.
    "},{"location":"Usage/#commands","title":"Commands","text":"
    CLI commands are listed here, or can be found by running monarch --help.
    "},{"location":"Usage/#module","title":"Module","text":"
    TBD
    "},{"location":"Usage/CLI/","title":"monarch","text":"
    Usage:
     
    $ monarch [OPTIONS] COMMAND [ARGS]...\n
     
    Options:
     
       
    • --version / --no-version
      •  
    • --quiet / --no-quiet: [default: no-quiet]
      •  
    • --debug / --no-debug: [default: no-debug]
      •  
    • --install-completion: Install completion for the current shell.
      •  
    • --show-completion: Show completion for the current shell, to copy it or customize the installation.
      •  
    • --help: Show this message and exit.
      •  
     
    Commands:
     
       
    • association-counts: Retrieve association counts for an entity...
      •  
    • association-table
      •  
    • associations: Paginate through associations
      •  
    • autocomplete: Return entity autcomplete matches for a...
      •  
    • compare: Compare two sets of phenotypes using...
      •  
    • entity: Retrieve an entity by ID
      •  
    • histopheno: Retrieve the histopheno data for an entity...
      •  
    • mappings
      •  
    • multi-entity-associations: Paginate through associations for multiple...
      •  
    • release: Retrieve metadata for a specific release
      •  
    • releases: List all available releases of the Monarch...
      •  
    • schema: Print the linkml schema for the data model
      •  
    • search: Search for entities
      •  
    • solr
      •  
    • sql
      •  
    • test: Test the CLI
      •  
    "},{"location":"Usage/CLI/#monarch-association-counts","title":"monarch association-counts","text":"
    Retrieve association counts for an entity by ID
     
    Args:     entity: The entity to get association counts for     fmt: The format of the output (json, yaml, tsv, table). Default JSON     output: The path to the output file. Default stdout
     
    Returns:     A list of association counts for the given entity containing association type, label and count
     
    Usage:
     
    $ monarch association-counts [OPTIONS] [ENTITY]\n
     
    Arguments:
     
       
    • [ENTITY]: The entity to get association counts for
      •  
     
    Options:
     
       
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-association-table","title":"monarch association-table","text":"
    Usage:
     
    $ monarch association-table [OPTIONS] ENTITY CATEGORY:{biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation}\n
     
    Arguments:
     
       
    • ENTITY: The entity to get associations for  [required]
      •  
    • CATEGORY:{biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation}: The association category to get associations for, ex. biolink:GeneToPhenotypicFeatureAssociation  [required]
      •  
     
    Options:
     
       
    • -q, --query TEXT
      •  
    • -t, --traverse-orthologs: Whether to traverse orthologs when getting associations
      •  
    • -s, --sort TEXT
      •  
    • -l, --limit INTEGER: [default: 5]
      •  
    • --offset INTEGER: [default: 0]
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-associations","title":"monarch associations","text":"
    Paginate through associations
     
    Args:     category: A comma-separated list of categories     subject: A comma-separated list of subjects     predicate: A comma-separated list of predicates     object: A comma-separated list of objects     entity: A comma-separated list of entities     limit: The number of associations to return     direct: Whether to exclude associations with subject/object as ancestors     offset: The offset of the first association to be retrieved     fmt: The format of the output (json, yaml, tsv, table)     output: The path to the output file (stdout if not specified)
     
    Usage:
     
    $ monarch associations [OPTIONS]\n
     
    Options:
     
       
    • -c, --category [biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation]: Category to get associations for
      •  
    • -s, --subject TEXT: Subject ID to get associations for
      •  
    • -p, --predicate [biolink:interacts_with|biolink:expressed_in|biolink:has_phenotype|biolink:is_sequence_variant_of|biolink:enables|biolink:actively_involved_in|biolink:orthologous_to|biolink:located_in|biolink:subclass_of|biolink:related_to|biolink:participates_in|biolink:acts_upstream_of_or_within|biolink:active_in|biolink:part_of|biolink:model_of|biolink:causes|biolink:acts_upstream_of|biolink:has_mode_of_inheritance|biolink:contributes_to|biolink:gene_associated_with_condition|biolink:treats_or_applied_or_studied_to_treat|biolink:colocalizes_with|biolink:acts_upstream_of_positive_effect|biolink:acts_upstream_of_or_within_positive_effect|biolink:acts_upstream_of_negative_effect|biolink:acts_upstream_of_or_within_negative_effect]: Predicate ID to get associations for
      •  
    • -o, --object TEXT: Object ID to get associations for
      •  
    • -e, --entity TEXT: Entity (subject or object) ID to get associations for
      •  
    • -d, --direct: Whether to exclude associations with subject/object as ancestors
      •  
    • -C, --compact: Whether to return a compact representation of the associations
      •  
    • -l, --limit INTEGER: The number of associations to return  [default: 20]
      •  
    • --offset INTEGER: The offset of the first association to be retrieved  [default: 0]
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-autocomplete","title":"monarch autocomplete","text":"
    Return entity autcomplete matches for a query string
     
    Args:     q: The query string to autocomplete against     fmt: The format of the output (json, yaml, tsv, table)     output: The path to the output file (stdout if not specified)
     
    Usage:
     
    $ monarch autocomplete [OPTIONS] [Q]\n
     
    Arguments:
     
       
    • [Q]: Query string to autocomplete against
      •  
     
    Options:
     
       
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-compare","title":"monarch compare","text":"
    Compare two sets of phenotypes using semantic similarity via SemSimian
     
    Usage:
     
    $ monarch compare [OPTIONS] SUBJECTS OBJECTS\n
     
    Arguments:
     
       
    • SUBJECTS: Comma separated list of subjects to compare  [required]
      •  
    • OBJECTS: Comma separated list of objects to compare  [required]
      •  
     
    Options:
     
       
    • -m, --metric [ancestor_information_content|jaccard_similarity|phenodigm_score]: The metric to use for comparison  [default: ancestor_information_content]
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-entity","title":"monarch entity","text":"
    Retrieve an entity by ID
     
    Args:     id: The identifier of the entity to be retrieved     fmt: The format of the output (json, yaml, tsv, table)     output: The path to the output file (stdout if not specified)
     
    Usage:
     
    $ monarch entity [OPTIONS] [ID]\n
     
    Arguments:
     
       
    • [ID]: The identifier of the entity to be retrieved
      •  
     
    Options:
     
       
    • -e, --extra: Include extra fields in the output (association_counts and node_hierarchy)
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-histopheno","title":"monarch histopheno","text":"
    Retrieve the histopheno data for an entity by ID
     
    Args:     subject: The subject of the association
     
    Optional Args:     fmt (str): The format of the output (json, yaml, tsv, table). Default JSON     output (str): The path to the output file. Default stdout
     
    Usage:
     
    $ monarch histopheno [OPTIONS] [SUBJECT]\n
     
    Arguments:
     
       
    • [SUBJECT]: The subject of the association
      •  
     
    Options:
     
       
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-mappings","title":"monarch mappings","text":"
    Usage:
     
    $ monarch mappings [OPTIONS]\n
     
    Options:
     
       
    • -e, --entity-id TEXT: entity ID to get mappings for
      •  
    • -s, --subject-id TEXT: subject ID to get mappings for
      •  
    • -p, --predicate-id [skos:exactMatch|skos:broadMatch]: predicate ID to get mappings for
      •  
    • -o, --object-id TEXT: object ID to get mappings for
      •  
    • -m, --mapping-justification TEXT: mapping justification to get mappings for
      •  
    • --offset INTEGER: The offset of the first mapping to be retrieved  [default: 0]
      •  
    • -l, --limit INTEGER: The number of mappings to return  [default: 20]
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-multi-entity-associations","title":"monarch multi-entity-associations","text":"
    Paginate through associations for multiple entities
     
    Args:     entity: A comma-separated list of entities     counterpart_category: A comma-separated list of counterpart categories     limit: The number of associations to return     offset: The offset of the first association to be retrieved     fmt: The format of the output (json, yaml, tsv, table)     output: The path to the output file (stdout if not specified)
     
    Usage:
     
    $ monarch multi-entity-associations [OPTIONS]\n
     
    Options:
     
       
    • -e, --entity TEXT: Comma-separated list of entities
      •  
    • -c, --counterpart-category TEXT
      •  
    • -l, --limit INTEGER: [default: 20]
      •  
    • --offset INTEGER: [default: 0]
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -o, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-release","title":"monarch release","text":"
    Retrieve metadata for a specific release
     
    Args:     release_ver: The release version to get metadata for     fmt: The format of the output (json, yaml, tsv, table)     output: The path to the output file (stdout if not specified)
     
    Usage:
     
    $ monarch release [OPTIONS] [RELEASE_VER]\n
     
    Arguments:
     
       
    • [RELEASE_VER]: The release version to get metadata for
      •  
     
    Options:
     
       
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-releases","title":"monarch releases","text":"
    List all available releases of the Monarch Knowledge Graph
     
    Usage:
     
    $ monarch releases [OPTIONS]\n
     
    Options:
     
       
    • --dev: Get dev releases of the KG (default is False)
      •  
    • -l, --limit INTEGER: The number of releases to return  [default: 0]
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-schema","title":"monarch schema","text":"
    Print the linkml schema for the data model
     
    Usage:
     
    $ monarch schema [OPTIONS]\n
     
    Options:
     
       
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-search","title":"monarch search","text":"
    Search for entities
     
    Args:     q: The query string to search for     category: The category of the entity     in_taxon_label: The taxon label to filter by     limit: The number of entities to return     offset: The offset of the first entity to be retrieved     fmt: The format of the output (json, yaml, tsv, table)     output: The path to the output file (stdout if not specified)
     
    Usage:
     
    $ monarch search [OPTIONS]\n
     
    Options:
     
       
    • -q, --query TEXT
      •  
    • -c, --category [biolink:SequenceVariant|biolink:Gene|biolink:Genotype|biolink:PhenotypicFeature|biolink:BiologicalProcessOrActivity|biolink:Disease|biolink:GrossAnatomicalStructure|biolink:Cell|biolink:Pathway|biolink:NamedThing|biolink:AnatomicalEntity|biolink:CellularComponent|biolink:MolecularEntity|biolink:BiologicalProcess|biolink:MacromolecularComplex|biolink:MolecularActivity|biolink:Protein|biolink:CellularOrganism|biolink:Vertebrate|biolink:Virus|biolink:BehavioralFeature|biolink:ChemicalEntity|biolink:LifeStage|biolink:PathologicalProcess|biolink:Drug|biolink:SmallMolecule|biolink:OrganismTaxon|biolink:InformationContentEntity|biolink:NucleicAcidEntity|biolink:EvidenceType|biolink:RNAProduct|biolink:Transcript|biolink:Fungus|biolink:Plant|biolink:ProcessedMaterial|biolink:Activity|biolink:Agent|biolink:ConfidenceLevel|biolink:Dataset|biolink:EnvironmentalFeature|biolink:GeneticInheritance|biolink:Haplotype|biolink:Invertebrate|biolink:Mammal|biolink:PopulationOfIndividualOrganisms|biolink:ProteinFamily|biolink:Publication|biolink:AccessibleDnaRegion|biolink:Bacterium|biolink:BiologicalSex|biolink:CellLine|biolink:ChemicalExposure|biolink:ChemicalMixture|biolink:DatasetDistribution|biolink:DiagnosticAid|biolink:DrugExposure|biolink:EnvironmentalProcess|biolink:Event|biolink:Exon|biolink:Genome|biolink:GenotypicSex|biolink:Human|biolink:IndividualOrganism|biolink:MaterialSample|biolink:MicroRNA|biolink:OrganismalEntity|biolink:Patent|biolink:PhenotypicSex|biolink:Polypeptide|biolink:ProteinDomain|biolink:ReagentTargetedGene|biolink:RegulatoryRegion|biolink:SiRNA|biolink:Snv|biolink:Study|biolink:StudyVariable|biolink:TranscriptionFactorBindingSite|biolink:Treatment|biolink:WebPage|biolink:Zygosity]
      •  
    • -t, --in-taxon-label TEXT
      •  
    • -ff, --facet-fields TEXT
      •  
    • --facet-queries TEXT
      •  
    • -l, --limit INTEGER: [default: 20]
      •  
    • --offset INTEGER: [default: 0]
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-solr","title":"monarch solr","text":"
    Usage:
     
    $ monarch solr [OPTIONS] COMMAND [ARGS]...\n
     
    Options:
     
       
    • --quiet / --no-quiet: [default: no-quiet]
      •  
    • --debug / --no-debug: [default: no-debug]
      •  
    • --help: Show this message and exit.
      •  
     
    Commands:
     
       
    • association-counts: Retrieve the association counts for a...
      •  
    • association-table
      •  
    • associations: Paginate through associations
      •  
    • autocomplete: Return entity autcomplete matches for a...
      •  
    • download: Download the Monarch Solr KG.
      •  
    • entity: Retrieve an entity by ID
      •  
    • histopheno: Retrieve the histopheno associations for a...
      •  
    • mappings
      •  
    • multi-entity-associations: Paginate through associations for multiple...
      •  
    • search: Search for entities
      •  
    • start: Starts a local Solr container.
      •  
    • status: Checks the status of the local Solr...
      •  
    • stop: Stops the local Solr container.
      •  
    "},{"location":"Usage/CLI/#monarch-solr-association-counts","title":"monarch solr association-counts","text":"
    Retrieve the association counts for a given entity
     
    Args:     entity (str): The entity to get association counts for
     
    Optional Args:     fmt (str): The format of the output (json, yaml, tsv, table). Default JSON     output (str): The path to the output file. Default stdout
     
    Usage:
     
    $ monarch solr association-counts [OPTIONS] [ENTITY]\n
     
    Arguments:
     
       
    • [ENTITY]: The entity to get association counts for
      •  
     
    Options:
     
       
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-solr-association-table","title":"monarch solr association-table","text":"
    Usage:
     
    $ monarch solr association-table [OPTIONS] ENTITY [CATEGORY]:[biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation]\n
     
    Arguments:
     
       
    • ENTITY: The entity to get associations for  [required]
      •  
    • [CATEGORY]:[biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation]: The association category to get associations for, ex. biolink:GeneToPhenotypicFeatureAssociation
      •  
     
    Options:
     
       
    • -t, --traverse-orthologs: Whether to traverse orthologs when getting associations
      •  
    • -q, --query TEXT
      •  
    • -s, --sort TEXT
      •  
    • -l, --limit INTEGER: [default: 5]
      •  
    • --offset INTEGER: [default: 0]
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-solr-associations","title":"monarch solr associations","text":"
    Paginate through associations
     
    Args:     category: The category of the association (multi-valued)     subject: The subject of the association (multi-valued)     predicate: The predicate of the association (multi-valued)     object: The object of the association (multi-valued)     entity: The entity (subject or object) of the association (multi-valued)     limit: The number of associations to return (default 20)     direct: Whether to exclude associations with subject/object as ancestors (default False)     offset: The offset of the first association to be retrieved     fmt: The format of the output (json, yaml, tsv, table) (default json)     output: The path to the output file (stdout if not specified) (default None)
     
    Usage:
     
    $ monarch solr associations [OPTIONS]\n
     
    Options:
     
       
    • -c, --category [biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation]: Category to get associations for
      •  
    • -s, --subject TEXT: Subject ID to get associations for
      •  
    • -p, --predicate [biolink:interacts_with|biolink:expressed_in|biolink:has_phenotype|biolink:is_sequence_variant_of|biolink:enables|biolink:actively_involved_in|biolink:orthologous_to|biolink:located_in|biolink:subclass_of|biolink:related_to|biolink:participates_in|biolink:acts_upstream_of_or_within|biolink:active_in|biolink:part_of|biolink:model_of|biolink:causes|biolink:acts_upstream_of|biolink:has_mode_of_inheritance|biolink:contributes_to|biolink:gene_associated_with_condition|biolink:treats_or_applied_or_studied_to_treat|biolink:colocalizes_with|biolink:acts_upstream_of_positive_effect|biolink:acts_upstream_of_or_within_positive_effect|biolink:acts_upstream_of_negative_effect|biolink:acts_upstream_of_or_within_negative_effect]: Predicate ID to get associations for
      •  
    • -o, --object TEXT: Object ID to get associations for
      •  
    • -e, --entity TEXT: Entity (subject or object) ID to get associations for
      •  
    • -d, --direct: Whether to exclude associations with subject/object as ancestors
      •  
    • -C, --compact: Whether to return a compact representation of the associations
      •  
    • -l, --limit INTEGER: The number of associations to return  [default: 20]
      •  
    • --offset INTEGER: The offset of the first association to be retrieved  [default: 0]
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-solr-autocomplete","title":"monarch solr autocomplete","text":"
    Return entity autcomplete matches for a query string
     
    Args:     q: The query string to autocomplete against     fmt: The format of the output (json, yaml, tsv, table)     output: The path to the output file (stdout if not specified)
     
    Usage:
     
    $ monarch solr autocomplete [OPTIONS] [Q]\n
     
    Arguments:
     
       
    • [Q]: Query string to autocomplete against
      •  
     
    Options:
     
       
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-solr-download","title":"monarch solr download","text":"
    Download the Monarch Solr KG.
     
    Usage:
     
    $ monarch solr download [OPTIONS]\n
     
    Options:
     
       
    • --version TEXT: [default: latest]
      •  
    • --overwrite / --no-overwrite: [default: no-overwrite]
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-solr-entity","title":"monarch solr entity","text":"
    Retrieve an entity by ID
     
    Args:     id (str): The identifier of the entity to be retrieved
     
    Optional Args:     fmt (str): The format of the output (json, yaml, tsv, table). Default JSON     output (str): The path to the output file. Default stdout
     
    Usage:
     
    $ monarch solr entity [OPTIONS] [ID]\n
     
    Arguments:
     
       
    • [ID]: The identifier of the entity to be retrieved
      •  
     
    Options:
     
       
    • -e, --extra: Include extra fields in the output (association_counts and node_hierarchy)
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-solr-histopheno","title":"monarch solr histopheno","text":"
    Retrieve the histopheno associations for a given subject
     
    Args:     subject (str): The subject of the association
     
    Optional Args:     fmt (str): The format of the output (json, yaml, tsv, table). Default JSON     output (str): The path to the output file. Default stdout
     
    Usage:
     
    $ monarch solr histopheno [OPTIONS] [SUBJECT]\n
     
    Arguments:
     
       
    • [SUBJECT]: The subject of the association
      •  
     
    Options:
     
       
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: JSON]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-solr-mappings","title":"monarch solr mappings","text":"
    Usage:
     
    $ monarch solr mappings [OPTIONS]\n
     
    Options:
     
       
    • -e, --entity-id TEXT: entity ID to get mappings for
      •  
    • -s, --subject-id TEXT: subject ID to get mappings for
      •  
    • -p, --predicate-id [skos:exactMatch|skos:broadMatch]: predicate ID to get mappings for
      •  
    • -o, --object-id TEXT: object ID to get mappings for
      •  
    • -m, --mapping-justification TEXT: mapping justification to get mappings for
      •  
    • --offset INTEGER: The offset of the first mapping to be retrieved  [default: 0]
      •  
    • -l, --limit INTEGER: The number of mappings to return  [default: 20]
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-solr-multi-entity-associations","title":"monarch solr multi-entity-associations","text":"
    Paginate through associations for multiple entities
     
    Args:     entity: A comma-separated list of entities     counterpart_category: A comma-separated list of counterpart categories     limit: The number of associations to return     offset: The offset of the first association to be retrieved     fmt: The format of the output (json, yaml, tsv, table)     output: The path to the output file (stdout if not specified)
     
    Usage:
     
    $ monarch solr multi-entity-associations [OPTIONS]\n
     
    Options:
     
       
    • -e, --entity TEXT: Entity ID to get associations for
      •  
    • -c, --counterpart-category TEXT: Counterpart category to get associations for
      •  
    • -l, --limit INTEGER: [default: 20]
      •  
    • --offset INTEGER: [default: 0]
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-solr-search","title":"monarch solr search","text":"
    Search for entities
     
    Optional Args:     q: The query string to search for     category: The category of the entity     in_taxon_label: The taxon label to filter on     facet_fields: The fields to facet on     facet_queries: The queries to facet on     limit: The number of entities to return     offset: The offset of the first entity to be retrieved     fmt (str): The format of the output (json, yaml, tsv, table). Default JSON     output (str): The path to the output file. Default stdout
     
    Usage:
     
    $ monarch solr search [OPTIONS]\n
     
    Options:
     
       
    • -q, --query TEXT: [default: :]
      •  
    • -c, --category [biolink:SequenceVariant|biolink:Gene|biolink:Genotype|biolink:PhenotypicFeature|biolink:BiologicalProcessOrActivity|biolink:Disease|biolink:GrossAnatomicalStructure|biolink:Cell|biolink:Pathway|biolink:NamedThing|biolink:AnatomicalEntity|biolink:CellularComponent|biolink:MolecularEntity|biolink:BiologicalProcess|biolink:MacromolecularComplex|biolink:MolecularActivity|biolink:Protein|biolink:CellularOrganism|biolink:Vertebrate|biolink:Virus|biolink:BehavioralFeature|biolink:ChemicalEntity|biolink:LifeStage|biolink:PathologicalProcess|biolink:Drug|biolink:SmallMolecule|biolink:OrganismTaxon|biolink:InformationContentEntity|biolink:NucleicAcidEntity|biolink:EvidenceType|biolink:RNAProduct|biolink:Transcript|biolink:Fungus|biolink:Plant|biolink:ProcessedMaterial|biolink:Activity|biolink:Agent|biolink:ConfidenceLevel|biolink:Dataset|biolink:EnvironmentalFeature|biolink:GeneticInheritance|biolink:Haplotype|biolink:Invertebrate|biolink:Mammal|biolink:PopulationOfIndividualOrganisms|biolink:ProteinFamily|biolink:Publication|biolink:AccessibleDnaRegion|biolink:Bacterium|biolink:BiologicalSex|biolink:CellLine|biolink:ChemicalExposure|biolink:ChemicalMixture|biolink:DatasetDistribution|biolink:DiagnosticAid|biolink:DrugExposure|biolink:EnvironmentalProcess|biolink:Event|biolink:Exon|biolink:Genome|biolink:GenotypicSex|biolink:Human|biolink:IndividualOrganism|biolink:MaterialSample|biolink:MicroRNA|biolink:OrganismalEntity|biolink:Patent|biolink:PhenotypicSex|biolink:Polypeptide|biolink:ProteinDomain|biolink:ReagentTargetedGene|biolink:RegulatoryRegion|biolink:SiRNA|biolink:Snv|biolink:Study|biolink:StudyVariable|biolink:TranscriptionFactorBindingSite|biolink:Treatment|biolink:WebPage|biolink:Zygosity]
      •  
    • -t, --in-taxon-label TEXT
      •  
    • -ff, --facet-fields TEXT
      •  
    • --facet-queries TEXT
      •  
    • -l, --limit INTEGER: [default: 20]
      •  
    • --offset INTEGER: [default: 0]
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-solr-start","title":"monarch solr start","text":"
    Starts a local Solr container.
     
    Usage:
     
    $ monarch solr start [OPTIONS]\n
     
    Options:
     
       
    • --update / --no-update: [default: no-update]
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-solr-status","title":"monarch solr status","text":"
    Checks the status of the local Solr container.
     
    Usage:
     
    $ monarch solr status [OPTIONS]\n
     
    Options:
     
       
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-solr-stop","title":"monarch solr stop","text":"
    Stops the local Solr container.
     
    Usage:
     
    $ monarch solr stop [OPTIONS]\n
     
    Options:
     
       
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-sql","title":"monarch sql","text":"
    Usage:
     
    $ monarch sql [OPTIONS] COMMAND [ARGS]...\n
     
    Options:
     
       
    • --quiet / --no-quiet: [default: no-quiet]
      •  
    • --debug / --no-debug: [default: no-debug]
      •  
    • --help: Show this message and exit.
      •  
     
    Commands:
     
       
    • associations: Paginate through associations
      •  
    • entity: Retrieve an entity by ID
      •  
    "},{"location":"Usage/CLI/#monarch-sql-associations","title":"monarch sql associations","text":"
    Paginate through associations
     
    Args:     category: A comma-separated list of categories     subject: A comma-separated list of subjects     predicate: A comma-separated list of predicates     object: A comma-separated list of objects     entity: A comma-separated list of entities     direct: Whether to exclude associations with subject/object as ancestors     compact: Whether to return a compact representation of the associations     limit: The number of associations to return     offset: The offset of the first association to be retrieved     fmt: The format of the output (json, yaml, tsv, table)     output: The path to the output file (stdout if not specified)
     
    Usage:
     
    $ monarch sql associations [OPTIONS]\n
     
    Options:
     
       
    • -c, --category [biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation]: Category to get associations for
      •  
    • -s, --subject TEXT: Subject ID to get associations for
      •  
    • -p, --predicate [biolink:interacts_with|biolink:expressed_in|biolink:has_phenotype|biolink:is_sequence_variant_of|biolink:enables|biolink:actively_involved_in|biolink:orthologous_to|biolink:located_in|biolink:subclass_of|biolink:related_to|biolink:participates_in|biolink:acts_upstream_of_or_within|biolink:active_in|biolink:part_of|biolink:model_of|biolink:causes|biolink:acts_upstream_of|biolink:has_mode_of_inheritance|biolink:contributes_to|biolink:gene_associated_with_condition|biolink:treats_or_applied_or_studied_to_treat|biolink:colocalizes_with|biolink:acts_upstream_of_positive_effect|biolink:acts_upstream_of_or_within_positive_effect|biolink:acts_upstream_of_negative_effect|biolink:acts_upstream_of_or_within_negative_effect]: Predicate ID to get associations for
      •  
    • -o, --object TEXT: Object ID to get associations for
      •  
    • -e, --entity TEXT: Entity (subject or object) ID to get associations for
      •  
    • -d, --direct: Whether to exclude associations with subject/object as ancestors
      •  
    • -C, --compact: Whether to return a compact representation of the associations
      •  
    • -l, --limit INTEGER: The number of associations to return  [default: 20]
      •  
    • --offset INTEGER: The offset of the first association to be retrieved  [default: 0]
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -o, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-sql-entity","title":"monarch sql entity","text":"
    Retrieve an entity by ID
     
    Args:     id (str): The identifier of the entity to be retrieved     update (bool): = Whether to re-download the Monarch KG. Default False     fmt (str): The format of the output (json, yaml, tsv, table). Default JSON     output (str): The path to the output file. Default stdout
     
    Usage:
     
    $ monarch sql entity [OPTIONS] [ID]\n
     
    Arguments:
     
       
    • [ID]: The identifier of the entity to be retrieved
      •  
     
    Options:
     
       
    • -e, --extra: Include extra fields in the output (association_counts and node_hierarchy)
      •  
    • -u, --update: Whether to re-download the Monarch KG
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -o, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-test","title":"monarch test","text":"
    Test the CLI
     
    Usage:
     
    $ monarch test [OPTIONS]\n
     
    Options:
     
       
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/Implementations/","title":"Implementations","text":"
    monarch-py provides implementations of the abstract Interfaces for different Monarch KG endpoints/backends.
    "},{"location":"Usage/Implementations/#implementations_1","title":"Implementations:","text":""},{"location":"Usage/Implementations/#solr","title":"Solr","text":""},{"location":"Usage/Implementations/#sqlite","title":"SQLite","text":""},{"location":"Usage/Implementations/SQL/","title":"SQL","text":""},{"location":"Usage/Implementations/SQL/#src.monarch_py.implementations.sql.sql_implementation.SQLImplementation","title":"SQLImplementation  dataclass","text":"
                   Bases: EntityInterface, AssociationInterface
     
    Implementation of Monarch Interfaces for SQL endpoint
    "},{"location":"Usage/Implementations/SQL/#src.monarch_py.implementations.sql.sql_implementation.SQLImplementation.get_associations","title":"get_associations","text":"
    Retrieve paginated association records, with filter options
     
    Parameters:
     Name Type Description Default category str 
    Filter to only associations matching the specified category. Defaults to None.
     None predicate str 
    Filter to only associations matching the specified predicate. Defaults to None.
     None subject str 
    Filter to only associations matching the specified subject. Defaults to None.
     None object str 
    Filter to only associations matching the specified object. Defaults to None.
     None subject_closure str 
    Filter to only associations with the specified term ID as an ancestor of the subject. Defaults to None.
     None object_closure str 
    Filter to only associations the specified term ID as an ancestor of the object. Defaults to None.
     None entity str 
    Filter to only associations where the specified entity is the subject or the object. Defaults to None.
     None association_type str 
    Filter to only associations matching the specified association label. Defaults to None.
     required compact bool 
    Whether to return compact or full association records. Defaults to False.
     False offset int 
    Result offset, for pagination. Defaults to 0.
     0 limit int 
    Limit results to specified number. Defaults to 20.
     20 
    Returns:
     Name Type Description AssociationResults Union[AssociationResults, CompactAssociationResults] 
    Dataclass representing results of an association search.
    "},{"location":"Usage/Implementations/SQL/#src.monarch_py.implementations.sql.sql_implementation.SQLImplementation.get_entity","title":"get_entity","text":"
    Retrieve a specific entity by exact ID match, writh optional extras
     
    Parameters:
     Name Type Description Default id str 
    id of the entity to search for.
     required get_association_counts bool 
    Whether to get association counts. Defaults to False.
     required get_hierarchy bool 
    Whether to get the entity hierarchy. Defaults to False.
     required 
    Returns:
     Name Type Description Entity Entity 
    Dataclass representing results of an entity search.
    "},{"location":"Usage/Implementations/Solr/","title":"Solr","text":""},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation","title":"SolrImplementation  dataclass","text":"
                   Bases: EntityInterface, AssociationInterface, SearchInterface, GroundingInterface
     
    Implementation of Monarch Interfaces for Solr endpoint
    "},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_association_counts","title":"get_association_counts","text":"
    Get list of association counts for a given entity
    "},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_associations","title":"get_associations","text":"
    Retrieve paginated association records, with filter options
     
    Parameters:
     Name Type Description Default category List[AssociationCategory] 
    Filter to only associations matching the specified categories. Defaults to None.
     None predicate List[AssociationPredicate] 
    Filter to only associations matching the specified predicates. Defaults to None.
     None subject Optional[List[str]] 
    Filter to only associations matching the specified subjects. Defaults to None.
     None object Optional[List[str]] 
    Filter to only associations matching the specified objects. Defaults to None.
     None subject_closure Optional[str] 
    Filter to only associations with the specified term ID as an ancestor of the subject. Defaults to None
     None object_closure Optional[str] 
    Filter to only associations with the specified term ID as an ancestor of the object. Defaults to None
     None entity Optional[List[str]] 
    Filter to only associations where the specified entities are the subject or the object. Defaults to None.
     None q Optional[str] 
    Query string to search within matches. Defaults to None.
     None compact bool 
    Return compact results with fewer fields. Defaults to False.
     False offset int 
    Result offset, for pagination. Defaults to 0.
     0 limit int 
    Limit results to specified number. Defaults to 20.
     20 
    Returns:
     Name Type Description AssociationResults Union[AssociationResults, CompactAssociation] 
    Dataclass representing results of an association search.
    "},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_counterpart_entities","title":"get_counterpart_entities","text":"
    Get a list of entities directly associated with this_entity fetched from associations in the Solr index
     
    Parameters:
     Name Type Description Default this_entity Entity 
    The entity to get associations for
     required entity str 
    an entity ID occurring in either the subject or object. Defaults to None.
     None subject str 
    an entity ID occurring in the subject. Defaults to None.
     None predicate str 
    a predicate value. Defaults to None.
     None object str 
    an entity ID occurring in the object. Defaults to None.
     None"},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_entity","title":"get_entity","text":"
    Retrieve a specific entity by exact ID match, with optional extras
     
    Parameters:
     Name Type Description Default id str 
    id of the entity to search for.
     required extra bool 
    Whether to include association counts and hierarchy in the response.
     required 
    Returns:
     Name Type Description Entity Optional[Union[Node, Entity]] 
    Dataclass representing results of an entity search.
     Node Optional[Union[Node, Entity]] 
    Dataclass representing results of an entity search with extra=True.
    "},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_histopheno","title":"get_histopheno","text":"
    Get histopheno counts for a given subject_closure
    "},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_multi_entity_associations","title":"get_multi_entity_associations","text":"
    Get associations between multiple entities and counterparts of a given category
     
    Parameters:
     Name Type Description Default entity List[str] 
    List of entity IDs to get associations for
     required counterpart_category List[str] 
    List of categories of counterpart entity to get associations for. Defaults to None.
     None offset int 
    Result offset, for pagination. Defaults to 0.
     0 limit int 
    Limit results to specified number. Defaults to 20.
     required limit_per_group int 
    Limit results to specified number per group. Defaults to 20.
     20"},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.ground_entity","title":"ground_entity","text":"
    Grounds a single entity
     
    Parameters:
     Name Type Description Default text str 
    Text to ground
     required 
    Returns:
     Name Type Description Entity List[Entity] 
    Dataclass representing a single entity
    "},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.search","title":"search","text":"
    Search for entities by label, with optional filters
     
    Parameters:
     Name Type Description Default q str 
    Query string. Defaults to \":\".
     '*:*' offset int 
    Result offset, for pagination. Defaults to 0.
     0 limit int 
    Limit results to specified number. Defaults to 20.
     20 category List[str] 
    Filter to only entities matching the specified categories. Defaults to None.
     None in_taxon_label List[str] 
    Filter to only entities matching the specified taxon label. Defaults to None.
     None facet_fields List[str] 
    List of fields to include facet counts for. Defaults to None.
     None facet_queries List[str] 
    List of queries to include facet counts for. Defaults to None.
     None filter_queries List[str] 
    List of queries to filter results by. Defaults to None.
     None sort str 
    Sort results by the specified field. Defaults to None.
     None 
    Returns:
     Name Type Description SearchResults SearchResults 
    Dataclass representing results of a search.
    "},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.solr_is_available","title":"solr_is_available","text":"
    Check if the Solr instance is available
    "},{"location":"Usage/Interfaces/","title":"Interfaces","text":"
    monarch-py provides a collection of interfaces that abstractify implementation details, and provide a coherent set of graph operations.  
     
    Developers can code according to the interface, mostly ignoring whether the implementation is a relational database, a local file, etc. 
    "},{"location":"Usage/Interfaces/#interface","title":"Interface","text":"
       
    • Entity
      •  
    • Association
      •  
    • Query
      •  
    • Search
      •  
    "},{"location":"Usage/Interfaces/Association/","title":"Association","text":""},{"location":"Usage/Interfaces/Association/#src.monarch_py.interfaces.association_interface.AssociationInterface","title":"AssociationInterface","text":"
                   Bases: ABC
     
    Abstract interface for associations in the Monarch KG
    "},{"location":"Usage/Interfaces/Association/#src.monarch_py.interfaces.association_interface.AssociationInterface.get_associations","title":"get_associations  abstractmethod","text":"
    Retrieve paginated association records, with filter options
     
    Parameters:
     Name Type Description Default category str 
    Filter to only associations matching the specified category. Defaults to None.
     None predicate str 
    Filter to only associations matching the specified predicate. Defaults to None.
     None subject str 
    Filter to only associations matching the specified subject. Defaults to None.
     None subject_closure str 
    Filter to only associations with the specified term ID as an ancestor of the subject. Defaults to None
     None object str 
    Filter to only associations matching the specified object. Defaults to None.
     None object_closure str 
    Filter to only associations with the specified term ID as an ancestor of the object. Defaults to None
     None entity str 
    Filter to only associations where the specified entity is the subject or the object. Defaults to None.
     None offset int 
    Result offset, for pagination. Defaults to 0.
     0 limit int 
    Limit results to specified number. Defaults to 20.
     20 
    Raises:
     Type Description NotImplementedError 
    Use a specific implementation (see the documentation for a list of implementations)
     
    Returns:
     Type Description AssociationResults 
    AssociationResults: Dataclass representing results of an association search.
    "},{"location":"Usage/Interfaces/Entity/","title":"Entity","text":""},{"location":"Usage/Interfaces/Entity/#src.monarch_py.interfaces.entity_interface.EntityInterface","title":"EntityInterface","text":"
                   Bases: ABC
     
    Abstract interface for entities in the Monarch KG
    "},{"location":"Usage/Interfaces/Entity/#src.monarch_py.interfaces.entity_interface.EntityInterface.get_entity","title":"get_entity  abstractmethod","text":"
    Retrieve a specific entity by exact ID match, with optional extras
     
    Parameters:
     Name Type Description Default id str 
    id of the entity to search for.
     required get_association_counts bool 
    Whether to get a count of associations for the entity. Defaults to False.
     False get_hierarchy bool 
    Whether to get the entity's heirarchy in the data model. Defaults to False.
     False 
    Raises:
     Type Description NotImplementedError 
    Use a specific implementation (see the documentation for a list of implementations)
     
    Returns:
     Name Type Description Entity Entity 
    Dataclass representing results of an entity search.
    "},{"location":"Usage/Interfaces/Query/","title":"Query","text":""},{"location":"Usage/Interfaces/Query/#src.monarch_py.interfaces.query_interface.QueryInterface","title":"QueryInterface","text":"
                   Bases: ABC
     
    Abstract interface for querying the Monarch KG in a SQL way
    "},{"location":"Usage/Interfaces/Query/#src.monarch_py.interfaces.query_interface.QueryInterface.query","title":"query  abstractmethod","text":"
    Parameters:
     Name Type Description Default q str 
    Query string to match against
     required category str 
    Limit results to only this category
     required taxon str 
    Limit results to only this taxon
     required offset int 
    Offset of the first result to return, defaults to 0
     required limit int 
    Limit the number of results to return, defaults to 20
     required 
    Raises:
     Type Description NotImplementedError 
    Use a specific implementation (see the documentation for a list of implementations)
     
    Returns:
     Name Type Description EntityResults EntityResults 
    Dataclass representing results of a generic entity search.
    "},{"location":"Usage/Interfaces/Search/","title":"Search","text":""},{"location":"Usage/Interfaces/Search/#src.monarch_py.interfaces.search_interface.SearchInterface","title":"SearchInterface","text":"
                   Bases: ABC
     
    Abstract interface for searching the Monarch KG in a Lucene way
    "},{"location":"Usage/Interfaces/Search/#src.monarch_py.interfaces.search_interface.SearchInterface.autocomplete","title":"autocomplete","text":"
    Parameters:
     Name Type Description Default q str 
    Query string to match against
     required 
    Raises:
     Type Description NotImplementedError 
    Use a specific implementation (see the documentation for a list of implementations)
     
    Returns:
     Name Type Description SearchResults SearchResults 
    Dataclass representing results of a generic entity search.
    "},{"location":"Usage/Interfaces/Search/#src.monarch_py.interfaces.search_interface.SearchInterface.get_association_counts","title":"get_association_counts","text":"
    Get counts of associations for a given entity Args:     entity (str): Entity to get association counts for Returns:     List[FacetValue]: List of FacetValue objects representing the counts of associations for the given entity
    "},{"location":"Usage/Interfaces/Search/#src.monarch_py.interfaces.search_interface.SearchInterface.get_association_facets","title":"get_association_facets","text":"
    Get facet counts and facet query counts for associations Args:     facet_fields (List[str]): Facet fields to return counts for     facet_queries (List[str]): Facet queries to return counts for     category (str): Filter to only associations matching the specified category     predicate (str): Filter to only associations matching the specified predicate     subject (str): Filter to only associations matching the specified subject     subject_closure (str): Filter to only associations with the specified term ID as an ancestor of the subject     object (str): Filter to only associations matching the specified object     object_closure (str): Filter to only associations with the specified term ID as an ancestor of the object     entity (str): Filter to only associations where the specified entity is the subject or the object Returns:     SearchResults: Dataclass representing results of a search, with zero rows returned but total count     and faceting information populated
    "},{"location":"Usage/Interfaces/Search/#src.monarch_py.interfaces.search_interface.SearchInterface.get_association_table","title":"get_association_table","text":"
    Get associations for an entity matching a specified type, with optional search and sort parameters
     
    Parameters:
     Name Type Description Default entity str 
    Entity to get associations for
     required category str 
    Category of associations to return
     required query str 
    Query string to match against
     None sort str 
    Sort order, defaults to None
     None offset int 
    Offset of the first result to return, defaults to 0
     0 limit int 
    Limit the number of results to return, defaults to 20
     5 
    Returns:
     Name Type Description AssociationResults AssociationTableResults 
    Dataclass representing results of an association search.
    "},{"location":"Usage/Interfaces/Search/#src.monarch_py.interfaces.search_interface.SearchInterface.search","title":"search  abstractmethod","text":"
    Parameters:
     Name Type Description Default q str 
    Query string to match against
     required category str 
    Limit results to only this category
     None taxon str 
    Limit results to only this taxon
     required offset int 
    Offset of the first result to return, defaults to 0
     0 limit int 
    Limit the number of results to return, defaults to 20
     20 
    Raises:
     Type Description NotImplementedError 
    Use a specific implementation (see the documentation for a list of implementations)
     
    Returns:
     Name Type Description EntityResults SearchResults 
    Dataclass representing results of a generic entity search.
    "}]}
\ No newline at end of file
+{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"]},"docs":[{"location":"","title":"monarch-py","text":""},{"location":"#introduction","title":"Introduction","text":"
    monarch-py is a Python library for interacting with and querying the Monarch knowledge graph, with implementations for Solr and SQLite backends.
     
    This means the same API methods can be used regardless of the implementation.
     
    This library provides a collection of interfaces for graph operations such as retrieving entities and browsing associations.
    "},{"location":"#installation","title":"Installation","text":"
    Requires Python 3.8 or higher
     
    This library is available via pip or pipx:
     
    pip install monarch-py\n
    "},{"location":"#usage","title":"Usage","text":"
    Full usage instructions here
    "},{"location":"#basic-example-cli","title":"Basic Example - CLI","text":"
    $ monarch sql entity MONDO:0012933\n{\n    \"id\": \"MONDO:0012933\",\n    \"category\": [\n        \"biolink:Disease\"\n    ],\n    \"name\": \"breast-ovarian cancer, familial, susceptibility to, 2\",\n    \"description\": \"Any hereditary breast ovarian cancer syndrome in which the cause of the disease is a mutation in the BRCA2 gene.\",\n    \"xref\": [],\n    \"provided_by\": \"phenio_nodes\",\n    \"in_taxon\": null,\n    \"source\": null,\n    \"symbol\": null,\n    \"type\": null,\n    \"synonym\": []\n}\n$ monarch associations --subject MONDO:0012933 --limit 5\n{\n    \"limit\": 5,\n    \"offset\": 0,\n    \"total\": 5,\n    \"associations\": [\n        ... # List of Associations\n    ]\n}\n
    "},{"location":"#basic-example-as-a-module","title":"Basic Example - As a Module","text":"
    >>> from monarch_py.implementations.solr.solr_implementation import SolrImplementation\n>>> si = SolrImplementation()\n>>> entity = si.get_entity(\"MONDO:0007947\")\n>>> print(entity.name)\n\"Marfan syndrome\"\n\n>>> response = si.get_associations(predicate=\"biolink:has_phenotype\")\n>>> print(response.total > 600000)\nTrue\n>>> print(\"biolink:has_phenotype\" in response.associations[0].predicate)\nTrue\n
    "},{"location":"API-Reference/","title":"API Reference","text":"
    This section outlines the monarch-py API.  
     
    Here you can find detailed documentation and source code for its interfaces and implementations. 
    "},{"location":"API-Reference/#interfaces","title":"Interfaces","text":""},{"location":"API-Reference/#src.monarch_py.interfaces.entity_interface.EntityInterface","title":"EntityInterface","text":"
                   Bases: ABC
     
    Abstract interface for entities in the Monarch KG
    "},{"location":"API-Reference/#src.monarch_py.interfaces.entity_interface.EntityInterface.get_entity","title":"get_entity  abstractmethod","text":"
    Retrieve a specific entity by exact ID match, with optional extras
     
    Parameters:
     Name Type Description Default id str 
    id of the entity to search for.
     required get_association_counts bool 
    Whether to get a count of associations for the entity. Defaults to False.
     False get_hierarchy bool 
    Whether to get the entity's heirarchy in the data model. Defaults to False.
     False 
    Raises:
     Type Description NotImplementedError 
    Use a specific implementation (see the documentation for a list of implementations)
     
    Returns:
     Name Type Description Entity Entity 
    Dataclass representing results of an entity search.
    "},{"location":"API-Reference/#src.monarch_py.interfaces.association_interface.AssociationInterface","title":"AssociationInterface","text":"
                   Bases: ABC
     
    Abstract interface for associations in the Monarch KG
    "},{"location":"API-Reference/#src.monarch_py.interfaces.association_interface.AssociationInterface.get_associations","title":"get_associations  abstractmethod","text":"
    Retrieve paginated association records, with filter options
     
    Parameters:
     Name Type Description Default category str 
    Filter to only associations matching the specified category. Defaults to None.
     None predicate str 
    Filter to only associations matching the specified predicate. Defaults to None.
     None subject str 
    Filter to only associations matching the specified subject. Defaults to None.
     None subject_closure str 
    Filter to only associations with the specified term ID as an ancestor of the subject. Defaults to None
     None object str 
    Filter to only associations matching the specified object. Defaults to None.
     None object_closure str 
    Filter to only associations with the specified term ID as an ancestor of the object. Defaults to None
     None entity str 
    Filter to only associations where the specified entity is the subject or the object. Defaults to None.
     None offset int 
    Result offset, for pagination. Defaults to 0.
     0 limit int 
    Limit results to specified number. Defaults to 20.
     20 
    Raises:
     Type Description NotImplementedError 
    Use a specific implementation (see the documentation for a list of implementations)
     
    Returns:
     Type Description AssociationResults 
    AssociationResults: Dataclass representing results of an association search.
    "},{"location":"API-Reference/#src.monarch_py.interfaces.search_interface.SearchInterface","title":"SearchInterface","text":"
                   Bases: ABC
     
    Abstract interface for searching the Monarch KG in a Lucene way
    "},{"location":"API-Reference/#src.monarch_py.interfaces.search_interface.SearchInterface.autocomplete","title":"autocomplete","text":"
    Parameters:
     Name Type Description Default q str 
    Query string to match against
     required 
    Raises:
     Type Description NotImplementedError 
    Use a specific implementation (see the documentation for a list of implementations)
     
    Returns:
     Name Type Description SearchResults SearchResults 
    Dataclass representing results of a generic entity search.
    "},{"location":"API-Reference/#src.monarch_py.interfaces.search_interface.SearchInterface.get_association_counts","title":"get_association_counts","text":"
    Get counts of associations for a given entity Args:     entity (str): Entity to get association counts for Returns:     List[FacetValue]: List of FacetValue objects representing the counts of associations for the given entity
    "},{"location":"API-Reference/#src.monarch_py.interfaces.search_interface.SearchInterface.get_association_facets","title":"get_association_facets","text":"
    Get facet counts and facet query counts for associations Args:     facet_fields (List[str]): Facet fields to return counts for     facet_queries (List[str]): Facet queries to return counts for     category (str): Filter to only associations matching the specified category     predicate (str): Filter to only associations matching the specified predicate     subject (str): Filter to only associations matching the specified subject     subject_closure (str): Filter to only associations with the specified term ID as an ancestor of the subject     object (str): Filter to only associations matching the specified object     object_closure (str): Filter to only associations with the specified term ID as an ancestor of the object     entity (str): Filter to only associations where the specified entity is the subject or the object Returns:     SearchResults: Dataclass representing results of a search, with zero rows returned but total count     and faceting information populated
    "},{"location":"API-Reference/#src.monarch_py.interfaces.search_interface.SearchInterface.get_association_table","title":"get_association_table","text":"
    Get associations for an entity matching a specified type, with optional search and sort parameters
     
    Parameters:
     Name Type Description Default entity str 
    Entity to get associations for
     required category str 
    Category of associations to return
     required query str 
    Query string to match against
     None sort str 
    Sort order, defaults to None
     None offset int 
    Offset of the first result to return, defaults to 0
     0 limit int 
    Limit the number of results to return, defaults to 20
     5 
    Returns:
     Name Type Description AssociationResults AssociationTableResults 
    Dataclass representing results of an association search.
    "},{"location":"API-Reference/#src.monarch_py.interfaces.search_interface.SearchInterface.search","title":"search  abstractmethod","text":"
    Parameters:
     Name Type Description Default q str 
    Query string to match against
     required category str 
    Limit results to only this category
     None taxon str 
    Limit results to only this taxon
     required offset int 
    Offset of the first result to return, defaults to 0
     0 limit int 
    Limit the number of results to return, defaults to 20
     20 
    Raises:
     Type Description NotImplementedError 
    Use a specific implementation (see the documentation for a list of implementations)
     
    Returns:
     Name Type Description EntityResults SearchResults 
    Dataclass representing results of a generic entity search.
    "},{"location":"API-Reference/#implementations","title":"Implementations","text":""},{"location":"API-Reference/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation","title":"SolrImplementation  dataclass","text":"
                   Bases: EntityInterface, AssociationInterface, SearchInterface, GroundingInterface
     
    Implementation of Monarch Interfaces for Solr endpoint
    "},{"location":"API-Reference/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_association_counts","title":"get_association_counts","text":"
    Get list of association counts for a given entity
    "},{"location":"API-Reference/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_associations","title":"get_associations","text":"
    Retrieve paginated association records, with filter options
     
    Parameters:
     Name Type Description Default category List[AssociationCategory] 
    Filter to only associations matching the specified categories. Defaults to None.
     None predicate List[AssociationPredicate] 
    Filter to only associations matching the specified predicates. Defaults to None.
     None subject Optional[List[str]] 
    Filter to only associations matching the specified subjects. Defaults to None.
     None object Optional[List[str]] 
    Filter to only associations matching the specified objects. Defaults to None.
     None subject_closure Optional[str] 
    Filter to only associations with the specified term ID as an ancestor of the subject. Defaults to None
     None object_closure Optional[str] 
    Filter to only associations with the specified term ID as an ancestor of the object. Defaults to None
     None entity Optional[List[str]] 
    Filter to only associations where the specified entities are the subject or the object. Defaults to None.
     None q Optional[str] 
    Query string to search within matches. Defaults to None.
     None compact bool 
    Return compact results with fewer fields. Defaults to False.
     False offset int 
    Result offset, for pagination. Defaults to 0.
     0 limit int 
    Limit results to specified number. Defaults to 20.
     20 
    Returns:
     Name Type Description AssociationResults Union[AssociationResults, CompactAssociation] 
    Dataclass representing results of an association search.
    "},{"location":"API-Reference/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_counterpart_entities","title":"get_counterpart_entities","text":"
    Get a list of entities directly associated with this_entity fetched from associations in the Solr index
     
    Parameters:
     Name Type Description Default this_entity Entity 
    The entity to get associations for
     required entity str 
    an entity ID occurring in either the subject or object. Defaults to None.
     None subject str 
    an entity ID occurring in the subject. Defaults to None.
     None predicate str 
    a predicate value. Defaults to None.
     None object str 
    an entity ID occurring in the object. Defaults to None.
     None"},{"location":"API-Reference/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_entity","title":"get_entity","text":"
    Retrieve a specific entity by exact ID match, with optional extras
     
    Parameters:
     Name Type Description Default id str 
    id of the entity to search for.
     required extra bool 
    Whether to include association counts and hierarchy in the response.
     required 
    Returns:
     Name Type Description Entity Optional[Union[Node, Entity]] 
    Dataclass representing results of an entity search.
     Node Optional[Union[Node, Entity]] 
    Dataclass representing results of an entity search with extra=True.
    "},{"location":"API-Reference/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_histopheno","title":"get_histopheno","text":"
    Get histopheno counts for a given subject_closure
    "},{"location":"API-Reference/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_multi_entity_associations","title":"get_multi_entity_associations","text":"
    Get associations between multiple entities and counterparts of a given category
     
    Parameters:
     Name Type Description Default entity List[str] 
    List of entity IDs to get associations for
     required counterpart_category List[str] 
    List of categories of counterpart entity to get associations for. Defaults to None.
     None offset int 
    Result offset, for pagination. Defaults to 0.
     0 limit int 
    Limit results to specified number. Defaults to 20.
     required limit_per_group int 
    Limit results to specified number per group. Defaults to 20.
     20"},{"location":"API-Reference/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.ground_entity","title":"ground_entity","text":"
    Grounds a single entity
     
    Parameters:
     Name Type Description Default text str 
    Text to ground
     required 
    Returns:
     Name Type Description Entity List[Entity] 
    Dataclass representing a single entity
    "},{"location":"API-Reference/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.search","title":"search","text":"
    Search for entities by label, with optional filters
     
    Parameters:
     Name Type Description Default q str 
    Query string. Defaults to \":\".
     '*:*' offset int 
    Result offset, for pagination. Defaults to 0.
     0 limit int 
    Limit results to specified number. Defaults to 20.
     20 category List[str] 
    Filter to only entities matching the specified categories. Defaults to None.
     None in_taxon_label List[str] 
    Filter to only entities matching the specified taxon label. Defaults to None.
     None facet_fields List[str] 
    List of fields to include facet counts for. Defaults to None.
     None facet_queries List[str] 
    List of queries to include facet counts for. Defaults to None.
     None filter_queries List[str] 
    List of queries to filter results by. Defaults to None.
     None sort str 
    Sort results by the specified field. Defaults to None.
     None 
    Returns:
     Name Type Description SearchResults SearchResults 
    Dataclass representing results of a search.
    "},{"location":"API-Reference/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.solr_is_available","title":"solr_is_available","text":"
    Check if the Solr instance is available
    "},{"location":"API-Reference/#src.monarch_py.implementations.sql.sql_implementation.SQLImplementation","title":"SQLImplementation  dataclass","text":"
                   Bases: EntityInterface, AssociationInterface
     
    Implementation of Monarch Interfaces for SQL endpoint
    "},{"location":"API-Reference/#src.monarch_py.implementations.sql.sql_implementation.SQLImplementation.get_associations","title":"get_associations","text":"
    Retrieve paginated association records, with filter options
     
    Parameters:
     Name Type Description Default category str 
    Filter to only associations matching the specified category. Defaults to None.
     None predicate str 
    Filter to only associations matching the specified predicate. Defaults to None.
     None subject str 
    Filter to only associations matching the specified subject. Defaults to None.
     None object str 
    Filter to only associations matching the specified object. Defaults to None.
     None subject_closure str 
    Filter to only associations with the specified term ID as an ancestor of the subject. Defaults to None.
     None object_closure str 
    Filter to only associations the specified term ID as an ancestor of the object. Defaults to None.
     None entity str 
    Filter to only associations where the specified entity is the subject or the object. Defaults to None.
     None association_type str 
    Filter to only associations matching the specified association label. Defaults to None.
     required compact bool 
    Whether to return compact or full association records. Defaults to False.
     False offset int 
    Result offset, for pagination. Defaults to 0.
     0 limit int 
    Limit results to specified number. Defaults to 20.
     20 
    Returns:
     Name Type Description AssociationResults Union[AssociationResults, CompactAssociationResults] 
    Dataclass representing results of an association search.
    "},{"location":"API-Reference/#src.monarch_py.implementations.sql.sql_implementation.SQLImplementation.get_entity","title":"get_entity","text":"
    Retrieve a specific entity by exact ID match, writh optional extras
     
    Parameters:
     Name Type Description Default id str 
    id of the entity to search for.
     required get_association_counts bool 
    Whether to get association counts. Defaults to False.
     required get_hierarchy bool 
    Whether to get the entity hierarchy. Defaults to False.
     required 
    Returns:
     Name Type Description Entity Entity 
    Dataclass representing results of an entity search.
    "},{"location":"Data-Model/","title":"monarch-py","text":"
    Data models for the Monarch Initiative data access library
     
    URI: https://w3id.org/monarch/monarch-py
     
    Name: monarch-py
    "},{"location":"Data-Model/#classes","title":"Classes","text":"Class Description Association None DirectionalAssociation An association that gives it's direction relative to a specified entity AssociationCountList Container class for a list of association counts AssociationTypeMapping A data class to hold the necessary information to produce association type counts for given  entities with appropriate directional labels BestMatch None CompactAssociation None Entity Represents an Entity in the Monarch KG data model Node UI container class extending Entity with additional information SearchResult None ExpandedCurie A curie bundled along with its expanded url FacetField None FacetValue None AssociationCount None HistoBin None HistoPheno None Mapping A minimal class to hold a SSSOM mapping NodeHierarchy None PairwiseSimilarity Abstract grouping for representing individual pairwise similarities TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms Release A class to hold information about a release of the Monarch KG Results None AssociationResults None AssociationTableResults None CategoryGroupedAssociationResults None CompactAssociationResults None EntityResults None MappingResults SSSOM Mappings returned as a results collection MultiEntityAssociationResults None SearchResults None SemsimSearchResult None TermInfo None TextAnnotationResult None"},{"location":"Data-Model/#slots","title":"Slots","text":"Slot Description agent_type Describes the high-level category of agent who originally generated a  statem... aggregator_knowledge_source ancestor_id the most recent common ancestor of the two compared entities ancestor_information_content The IC of the object ancestor_label the name or label of the ancestor concept ancestor_source associated_categories association_counts average_score best_score category causal_gene A list of genes that are known to be causally associated with a disease causes_disease A list of diseases that are known to be causally associated with a gene cosine_similarity the dot product of two node embeddings divided by the product of their length... count count of documents counterpart_category The category of the counterpart entity in a given association,  eg deprecated A boolean flag indicating that an entity is no longer considered current or v... description dice_similarity direction The directionality of the association relative to a given entity for an assoc... disease_context_qualifier A context qualifier representing a disease or condition in which a relationsh... disease_context_qualifier_category The category of the disease_context_qualifier entity disease_context_qualifier_closure Field containing disease_context_qualifier id and the ids of all of it's ance... disease_context_qualifier_closure_label Field containing disease_context_qualifier name and the names of all of it's ... disease_context_qualifier_label The name of the disease_context_qualifier entity disease_context_qualifier_namespace The namespace/prefix of the disease_context_qualifier entity end end position of the annotation evidence_count count of supporting documents, evidence codes, and sources supplying evidence external_links ExpandedCurie with id and url for xrefs facet_fields Collection of facet field responses with the field values and counts facet_queries Collection of facet query responses with the query string values and counts facet_values Collection of FacetValue label/value instances belonging to a FacetField frequency_qualifier frequency_qualifier_category The category of the frequency_qualifier entity frequency_qualifier_closure Field containing frequency_qualifier id and the ids of all of it's ancestors frequency_qualifier_closure_label Field containing frequency_qualifier name and the names of all of it's ancest... frequency_qualifier_label The name of the frequency_qualifier entity frequency_qualifier_namespace The namespace/prefix of the frequency_qualifier entity full_name The long form name of an entity graph_stats grouping_key A concatenation of fields used to group associations with the same essential/... has_count count of out of has_total representing a frequency has_evidence has_evidence_links List of ExpandedCuries with id and url for evidence has_percentage percentage, which may be calculated from has_count and has_total, as 100 * qu... has_phenotype A list of phenotype identifiers that are known to be associated with this ent... has_phenotype_closure A list of phenotype identifiers that are known to be associated with this ent... has_phenotype_closure_label A list of phenotype labels that are known to be associated with this entity e... has_phenotype_count A count of the number of phenotypes that are known to be associated with this... has_phenotype_label A list of phenotype labels that are known to be associated with this entity has_quotient quotient, which should be 1/100 of has_percentage has_total total, devided by has_count, representing a frequency highlight matching text snippet containing html tags id in_taxon The biolink taxon that the entity is in the closure of in_taxon_label The label of the biolink taxon that the entity is in the closure of information_content The IC is the negative log of the probability of the concept inheritance intersection_count iri items A collection of items, with the type to be overriden by slot_usage jaccard_similarity The number of concepts in the intersection divided by the number in the union kg knowledge_level Describes the level of knowledge expressed in a statement, based on the reaso... knowledge_source label limit number of items to return in a response mapping_justification mappings List of ExpandedCuries with id and url for mapped entities match_source match_source_label match_subsumer match_subsumer_label match_target the entity matches match_target_label metadata metric name namespace The namespace/prefix portion of this entity's identifier negated neo4j node_hierarchy object object_best_matches object_category The category of the object entity object_closure Field containing object id and the ids of all of it's ancestors object_closure_label Field containing object name and the names of all of it's ancestors object_id object_information_content The IC of the object object_label The name of the object entity object_namespace The namespace/prefix of the object entity object_source the source for the second entity object_taxon object_taxon_label object_termset offset offset into the total number of items onset_qualifier onset_qualifier_category The category of the onset_qualifier entity onset_qualifier_closure Field containing onset_qualifier id and the ids of all of it's ancestors onset_qualifier_closure_label Field containing onset_qualifier name and the names of all of it's ancestors onset_qualifier_label The name of the onset_qualifier entity onset_qualifier_namespace The namespace/prefix of the onset_qualifier entity original_object original_subject overlap_coefficient pathway phenodigm_score the geometric mean of the jaccard similarity and the information content predicate predicate_id primary_knowledge_source provided_by provided_by_link A link to the docs for the knowledge source that provided the node/edge publications publications_links List of ExpandedCuries with id and url for publications qc_report qualifier qualifier_category The category of the frequency_qualifier entity qualifier_closure Field containing frequency_qualifier id and the ids of all of it's ancestors qualifier_closure_label Field containing frequency_qualifier name and the names of all of it's ancest... qualifier_label The name of the frequency_qualifier entity qualifier_namespace The namespace/prefix of the frequency_qualifier entity qualifiers qualifiers_category The category of the frequency_qualifier entity qualifiers_closure Field containing frequency_qualifier id and the ids of all of it's ancestors qualifiers_closure_label Field containing frequency_qualifier name and the names of all of it's ancest... qualifiers_label The name of the frequency_qualifier entity qualifiers_namespace The namespace/prefix of the frequency_qualifier entity score sex_qualifier sex_qualifier_category The category of the sex_qualifier entity sex_qualifier_closure Field containing sex_qualifier id and the ids of all of it's ancestors sex_qualifier_closure_label Field containing sex_qualifier name and the names of all of it's ancestors sex_qualifier_label The name of the sex_qualifier entity sex_qualifier_namespace The namespace/prefix of the sex_qualifier entity similarity solr sqlite stage_qualifier stage_qualifier_category The category of the stage_qualifier entity stage_qualifier_closure Field containing stage_qualifier id and the ids of all of it's ancestors stage_qualifier_closure_label Field containing stage_qualifier name and the names of all of it's ancestors stage_qualifier_label The name of the stage_qualifier entity stage_qualifier_namespace The namespace/prefix of the stage_qualifier entity start start position of the annotation sub_classes subject subject_best_matches subject_category The category of the subject entity subject_closure Field containing subject id and the ids of all of it's ancestors subject_closure_label Field containing subject name and the names of all of it's ancestors subject_id subject_information_content The IC of the subject subject_label The name of the subject entity subject_namespace The namespace/prefix of the subject entity subject_source the source for the first entity subject_taxon subject_taxon_label subject_termset subsumed_by_score subsumes_score super_classes symbol symmetric Whether the association type is symmetric, i synonym text text without tokens tokens A collection of entities or concepts total total number of items matching a query union_count uri The URI of the entity url version xref"},{"location":"Data-Model/#enumerations","title":"Enumerations","text":"Enumeration Description AssociationDirectionEnum The directionality of an association as it relates to a specified entity, wit..."},{"location":"Data-Model/#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer ItemCount Jsonpath A string encoding a JSON Path Jsonpointer A string encoding a JSON Pointer Ncname Prefix part of CURIE NegativeLogValue Nodeidentifier A URI, CURIE or BNODE that represents a node in a model NonNegativeFloat Objectidentifier A URI or CURIE that represents an object in the model Sparqlpath A string encoding a SPARQL Property Path String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE ZeroToOne"},{"location":"Data-Model/#subsets","title":"Subsets","text":"Subset Description"},{"location":"Data-Model/Association/","title":"Class: Association","text":"
    URI: https://w3id.org/monarch/monarch-py/:Association
     
     classDiagram\n    class Association\n    click Association href \"../Association\"\n      Association <|-- DirectionalAssociation\n        click DirectionalAssociation href \"../DirectionalAssociation\"\n\n      Association : agent_type\n\n      Association : aggregator_knowledge_source\n\n      Association : category\n\n      Association : disease_context_qualifier\n\n      Association : disease_context_qualifier_category\n\n      Association : disease_context_qualifier_closure\n\n      Association : disease_context_qualifier_closure_label\n\n      Association : disease_context_qualifier_label\n\n      Association : disease_context_qualifier_namespace\n\n      Association : evidence_count\n\n      Association : frequency_qualifier\n\n      Association : frequency_qualifier_category\n\n      Association : frequency_qualifier_closure\n\n      Association : frequency_qualifier_closure_label\n\n      Association : frequency_qualifier_label\n\n      Association : frequency_qualifier_namespace\n\n      Association : grouping_key\n\n      Association : has_count\n\n      Association : has_evidence\n\n      Association : has_evidence_links\n\n\n\n\n    Association --> \"*\" ExpandedCurie : has_evidence_links\n    click ExpandedCurie href \"../ExpandedCurie\"\n\n\n      Association : has_percentage\n\n      Association : has_quotient\n\n      Association : has_total\n\n      Association : id\n\n      Association : knowledge_level\n\n      Association : negated\n\n      Association : object\n\n      Association : object_category\n\n      Association : object_closure\n\n      Association : object_closure_label\n\n      Association : object_label\n\n      Association : object_namespace\n\n      Association : object_taxon\n\n      Association : object_taxon_label\n\n      Association : onset_qualifier\n\n      Association : onset_qualifier_category\n\n      Association : onset_qualifier_closure\n\n      Association : onset_qualifier_closure_label\n\n      Association : onset_qualifier_label\n\n      Association : onset_qualifier_namespace\n\n      Association : original_object\n\n      Association : original_subject\n\n      Association : pathway\n\n      Association : predicate\n\n      Association : primary_knowledge_source\n\n      Association : provided_by\n\n      Association : provided_by_link\n\n\n\n\n    Association --> \"0..1\" ExpandedCurie : provided_by_link\n    click ExpandedCurie href \"../ExpandedCurie\"\n\n\n      Association : publications\n\n      Association : publications_links\n\n\n\n\n    Association --> \"*\" ExpandedCurie : publications_links\n    click ExpandedCurie href \"../ExpandedCurie\"\n\n\n      Association : qualifier\n\n      Association : qualifier_category\n\n      Association : qualifier_closure\n\n      Association : qualifier_closure_label\n\n      Association : qualifier_label\n\n      Association : qualifier_namespace\n\n      Association : qualifiers\n\n      Association : qualifiers_category\n\n      Association : qualifiers_closure\n\n      Association : qualifiers_closure_label\n\n      Association : qualifiers_label\n\n      Association : qualifiers_namespace\n\n      Association : sex_qualifier\n\n      Association : sex_qualifier_category\n\n      Association : sex_qualifier_closure\n\n      Association : sex_qualifier_closure_label\n\n      Association : sex_qualifier_label\n\n      Association : sex_qualifier_namespace\n\n      Association : stage_qualifier\n\n      Association : stage_qualifier_category\n\n      Association : stage_qualifier_closure\n\n      Association : stage_qualifier_closure_label\n\n      Association : stage_qualifier_label\n\n      Association : stage_qualifier_namespace\n\n      Association : subject\n\n      Association : subject_category\n\n      Association : subject_closure\n\n      Association : subject_closure_label\n\n      Association : subject_label\n\n      Association : subject_namespace\n\n      Association : subject_taxon\n\n      Association : subject_taxon_label\n
    "},{"location":"Data-Model/Association/#inheritance","title":"Inheritance","text":"
       
    • Association
         
      • DirectionalAssociation
        •  
       
      •  
    "},{"location":"Data-Model/Association/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1  String direct category 0..1  String direct subject 1  String direct original_subject 0..1  String direct subject_namespace 0..1  String The namespace/prefix of the subject entity direct subject_category 0..1  String The category of the subject entity direct subject_closure *  String Field containing subject id and the ids of all of it's ancestors direct subject_label 0..1  String The name of the subject entity direct subject_closure_label *  String Field containing subject name and the names of all of it's ancestors direct subject_taxon 0..1  String direct subject_taxon_label 0..1  String direct predicate 1  String direct object 1  String direct original_object 0..1  String direct object_namespace 0..1  String The namespace/prefix of the object entity direct object_category 0..1  String The category of the object entity direct object_closure *  String Field containing object id and the ids of all of it's ancestors direct object_label 0..1  String The name of the object entity direct object_closure_label *  String Field containing object name and the names of all of it's ancestors direct object_taxon 0..1  String direct object_taxon_label 0..1  String direct primary_knowledge_source 0..1  String direct aggregator_knowledge_source *  String direct negated 0..1  Boolean direct pathway 0..1  String direct evidence_count 0..1  Integer count of supporting documents, evidence codes, and sources supplying evidence direct knowledge_level 1  String Describes the level of knowledge expressed in a statement, based on the reaso... direct agent_type 1  String Describes the high-level category of agent who originally generated a  statem... direct has_evidence *  String direct has_evidence_links *  ExpandedCurie List of ExpandedCuries with id and url for evidence direct has_count 0..1  Integer count of out of has_total representing a frequency direct has_total 0..1  Integer total, devided by has_count, representing a frequency direct has_percentage 0..1  Float percentage, which may be calculated from has_count and has_total, as 100 * qu... direct has_quotient 0..1  Float quotient, which should be 1/100 of has_percentage direct grouping_key 0..1  String A concatenation of fields used to group associations with the same essential/... direct provided_by 0..1  String direct provided_by_link 0..1  ExpandedCurie A link to the docs for the knowledge source that provided the node/edge direct publications *  String direct publications_links *  ExpandedCurie List of ExpandedCuries with id and url for publications direct frequency_qualifier 0..1  String direct onset_qualifier 0..1  String direct sex_qualifier 0..1  String direct stage_qualifier 0..1  String direct qualifiers *  String direct qualifiers_label 0..1  String The name of the frequency_qualifier entity direct qualifiers_namespace 0..1  String The namespace/prefix of the frequency_qualifier entity direct qualifiers_category 0..1  String The category of the frequency_qualifier entity direct qualifiers_closure *  String Field containing frequency_qualifier id and the ids of all of it's ancestors direct qualifiers_closure_label *  String Field containing frequency_qualifier name and the names of all of it's ancest... direct qualifier *  String direct qualifier_label 0..1  String The name of the frequency_qualifier entity direct qualifier_namespace 0..1  String The namespace/prefix of the frequency_qualifier entity direct qualifier_category 0..1  String The category of the frequency_qualifier entity direct qualifier_closure *  String Field containing frequency_qualifier id and the ids of all of it's ancestors direct qualifier_closure_label *  String Field containing frequency_qualifier name and the names of all of it's ancest... direct frequency_qualifier_label 0..1  String The name of the frequency_qualifier entity direct frequency_qualifier_namespace 0..1  String The namespace/prefix of the frequency_qualifier entity direct frequency_qualifier_category 0..1  String The category of the frequency_qualifier entity direct frequency_qualifier_closure *  String Field containing frequency_qualifier id and the ids of all of it's ancestors direct frequency_qualifier_closure_label *  String Field containing frequency_qualifier name and the names of all of it's ancest... direct onset_qualifier_label 0..1  String The name of the onset_qualifier entity direct onset_qualifier_namespace 0..1  String The namespace/prefix of the onset_qualifier entity direct onset_qualifier_category 0..1  String The category of the onset_qualifier entity direct onset_qualifier_closure *  String Field containing onset_qualifier id and the ids of all of it's ancestors direct onset_qualifier_closure_label *  String Field containing onset_qualifier name and the names of all of it's ancestors direct sex_qualifier_label 0..1  String The name of the sex_qualifier entity direct sex_qualifier_namespace 0..1  String The namespace/prefix of the sex_qualifier entity direct sex_qualifier_category 0..1  String The category of the sex_qualifier entity direct sex_qualifier_closure *  String Field containing sex_qualifier id and the ids of all of it's ancestors direct sex_qualifier_closure_label *  String Field containing sex_qualifier name and the names of all of it's ancestors direct stage_qualifier_label 0..1  String The name of the stage_qualifier entity direct stage_qualifier_namespace 0..1  String The namespace/prefix of the stage_qualifier entity direct stage_qualifier_category 0..1  String The category of the stage_qualifier entity direct stage_qualifier_closure *  String Field containing stage_qualifier id and the ids of all of it's ancestors direct stage_qualifier_closure_label *  String Field containing stage_qualifier name and the names of all of it's ancestors direct disease_context_qualifier 0..1  String A context qualifier representing a disease or condition in which a relationsh... direct disease_context_qualifier_label 0..1  String The name of the disease_context_qualifier entity direct disease_context_qualifier_namespace 0..1  String The namespace/prefix of the disease_context_qualifier entity direct disease_context_qualifier_category 0..1  String The category of the disease_context_qualifier entity direct disease_context_qualifier_closure *  String Field containing disease_context_qualifier id and the ids of all of it's ance... direct disease_context_qualifier_closure_label *  String Field containing disease_context_qualifier name and the names of all of it's ... direct"},{"location":"Data-Model/Association/#usages","title":"Usages","text":"used by used in type used AssociationResults items range Association CategoryGroupedAssociationResults items range Association"},{"location":"Data-Model/Association/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Association/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Association/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:Association native https://w3id.org/monarch/monarch-py/:Association"},{"location":"Data-Model/Association/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/Association/#direct","title":"Direct","text":"
    name: Association\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- id\n- category\n- subject\n- original_subject\n- subject_namespace\n- subject_category\n- subject_closure\n- subject_label\n- subject_closure_label\n- subject_taxon\n- subject_taxon_label\n- predicate\n- object\n- original_object\n- object_namespace\n- object_category\n- object_closure\n- object_label\n- object_closure_label\n- object_taxon\n- object_taxon_label\n- primary_knowledge_source\n- aggregator_knowledge_source\n- negated\n- pathway\n- evidence_count\n- knowledge_level\n- agent_type\n- has_evidence\n- has_evidence_links\n- has_count\n- has_total\n- has_percentage\n- has_quotient\n- grouping_key\n- provided_by\n- provided_by_link\n- publications\n- publications_links\n- frequency_qualifier\n- onset_qualifier\n- sex_qualifier\n- stage_qualifier\n- qualifiers\n- qualifiers_label\n- qualifiers_namespace\n- qualifiers_category\n- qualifiers_closure\n- qualifiers_closure_label\n- qualifier\n- qualifier_label\n- qualifier_namespace\n- qualifier_category\n- qualifier_closure\n- qualifier_closure_label\n- frequency_qualifier_label\n- frequency_qualifier_namespace\n- frequency_qualifier_category\n- frequency_qualifier_closure\n- frequency_qualifier_closure_label\n- onset_qualifier_label\n- onset_qualifier_namespace\n- onset_qualifier_category\n- onset_qualifier_closure\n- onset_qualifier_closure_label\n- sex_qualifier_label\n- sex_qualifier_namespace\n- sex_qualifier_category\n- sex_qualifier_closure\n- sex_qualifier_closure_label\n- stage_qualifier_label\n- stage_qualifier_namespace\n- stage_qualifier_category\n- stage_qualifier_closure\n- stage_qualifier_closure_label\n- disease_context_qualifier\n- disease_context_qualifier_label\n- disease_context_qualifier_namespace\n- disease_context_qualifier_category\n- disease_context_qualifier_closure\n- disease_context_qualifier_closure_label\n
    "},{"location":"Data-Model/Association/#induced","title":"Induced","text":"
    name: Association\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  id:\n    name: id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Association\n    domain_of:\n    - Association\n    - ExpandedCurie\n    - Entity\n    - HistoPheno\n    - HistoBin\n    - Mapping\n    - MultiEntityAssociationResults\n    - TermInfo\n    range: string\n    required: true\n  category:\n    name: category\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: category\n    owner: Association\n    domain_of:\n    - Association\n    - AssociationCount\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Entity\n    range: string\n    multivalued: false\n  subject:\n    name: subject\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: subject\n    owner: Association\n    domain_of:\n    - Association\n    - CompactAssociation\n    - SemsimSearchResult\n    range: string\n    required: true\n  original_subject:\n    name: original_subject\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: original_subject\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  subject_namespace:\n    name: subject_namespace\n    description: The namespace/prefix of the subject entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: subject_namespace\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  subject_category:\n    name: subject_category\n    description: The category of the subject entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: subject_category\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  subject_closure:\n    name: subject_closure\n    description: Field containing subject id and the ids of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: subject_closure\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  subject_label:\n    name: subject_label\n    description: The name of the subject entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: subject_label\n    owner: Association\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n  subject_closure_label:\n    name: subject_closure_label\n    description: Field containing subject name and the names of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: subject_closure_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  subject_taxon:\n    name: subject_taxon\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: in_taxon\n    alias: subject_taxon\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  subject_taxon_label:\n    name: subject_taxon_label\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: in_taxon_label\n    alias: subject_taxon_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: predicate\n    owner: Association\n    domain_of:\n    - Association\n    - CompactAssociation\n    range: string\n    required: true\n    multivalued: false\n  object:\n    name: object\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: object\n    owner: Association\n    domain_of:\n    - Association\n    - CompactAssociation\n    range: string\n    required: true\n  original_object:\n    name: original_object\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: original_object\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  object_namespace:\n    name: object_namespace\n    description: The namespace/prefix of the object entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: object_namespace\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  object_category:\n    name: object_category\n    description: The category of the object entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: object_category\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  object_closure:\n    name: object_closure\n    description: Field containing object id and the ids of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: object_closure\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  object_label:\n    name: object_label\n    description: The name of the object entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: object_label\n    owner: Association\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n  object_closure_label:\n    name: object_closure_label\n    description: Field containing object name and the names of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: object_closure_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  object_taxon:\n    name: object_taxon\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: in_taxon\n    alias: object_taxon\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  object_taxon_label:\n    name: object_taxon_label\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: in_taxon_label\n    alias: object_taxon_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  primary_knowledge_source:\n    name: primary_knowledge_source\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: primary_knowledge_source\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  aggregator_knowledge_source:\n    name: aggregator_knowledge_source\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: aggregator_knowledge_source\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  negated:\n    name: negated\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: negated\n    owner: Association\n    domain_of:\n    - Association\n    - CompactAssociation\n    range: boolean\n  pathway:\n    name: pathway\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: pathway\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  evidence_count:\n    name: evidence_count\n    description: count of supporting documents, evidence codes, and sources supplying\n      evidence\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: evidence_count\n    owner: Association\n    domain_of:\n    - Association\n    range: integer\n  knowledge_level:\n    name: knowledge_level\n    description: Describes the level of knowledge expressed in a statement, based\n      on the reasoning or analysis methods used to generate the statement, or the\n      scope or specificity of what the statement expresses to be true.\n    notes:\n    - The range in this schema is represented as a string, but is constrained  to\n      values from biolink:KnowledgeLevelEnum at ingest time\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    slot_uri: biolink:knowledge_level\n    alias: knowledge_level\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n    required: true\n    multivalued: false\n  agent_type:\n    name: agent_type\n    description: Describes the high-level category of agent who originally generated\n      a  statement of knowledge or other type of information.\n    notes:\n    - The range in this schema is represented as a string, but is constrained  to\n      values from biolink:AgentTypeEnum at ingest time\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    slot_uri: biolink:agent_type\n    alias: agent_type\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n    required: true\n    multivalued: false\n  has_evidence:\n    name: has_evidence\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_evidence\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  has_evidence_links:\n    name: has_evidence_links\n    description: List of ExpandedCuries with id and url for evidence\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_evidence_links\n    owner: Association\n    domain_of:\n    - Association\n    range: ExpandedCurie\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  has_count:\n    name: has_count\n    description: count of out of has_total representing a frequency\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_count\n    owner: Association\n    domain_of:\n    - Association\n    range: integer\n  has_total:\n    name: has_total\n    description: total, devided by has_count, representing a frequency\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_total\n    owner: Association\n    domain_of:\n    - Association\n    range: integer\n  has_percentage:\n    name: has_percentage\n    description: percentage, which may be calculated from has_count and has_total,\n      as 100 * quotient or provided directly, rounded to the integer level\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_percentage\n    owner: Association\n    domain_of:\n    - Association\n    range: float\n  has_quotient:\n    name: has_quotient\n    description: quotient, which should be 1/100 of has_percentage\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_quotient\n    owner: Association\n    domain_of:\n    - Association\n    range: float\n  grouping_key:\n    name: grouping_key\n    description: A concatenation of fields used to group associations with the same\n      essential/defining properties\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: grouping_key\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  provided_by:\n    name: provided_by\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: provided_by\n    owner: Association\n    domain_of:\n    - Association\n    - Entity\n    range: string\n  provided_by_link:\n    name: provided_by_link\n    description: A link to the docs for the knowledge source that provided the node/edge.\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: provided_by_link\n    owner: Association\n    domain_of:\n    - Association\n    - Node\n    range: ExpandedCurie\n    inlined: true\n  publications:\n    name: publications\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: publications\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  publications_links:\n    name: publications_links\n    description: List of ExpandedCuries with id and url for publications\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: publications_links\n    owner: Association\n    domain_of:\n    - Association\n    range: ExpandedCurie\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  frequency_qualifier:\n    name: frequency_qualifier\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: frequency_qualifier\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  onset_qualifier:\n    name: onset_qualifier\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: onset_qualifier\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  sex_qualifier:\n    name: sex_qualifier\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: sex_qualifier\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  stage_qualifier:\n    name: stage_qualifier\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: stage_qualifier\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  qualifiers:\n    name: qualifiers\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: qualifiers\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  qualifiers_label:\n    name: qualifiers_label\n    description: The name of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: qualifiers_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  qualifiers_namespace:\n    name: qualifiers_namespace\n    description: The namespace/prefix of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: qualifiers_namespace\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  qualifiers_category:\n    name: qualifiers_category\n    description: The category of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: qualifiers_category\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  qualifiers_closure:\n    name: qualifiers_closure\n    description: Field containing frequency_qualifier id and the ids of all of it's\n      ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: qualifiers_closure\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  qualifiers_closure_label:\n    name: qualifiers_closure_label\n    description: Field containing frequency_qualifier name and the names of all of\n      it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: qualifiers_closure_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  qualifier:\n    name: qualifier\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: qualifier\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  qualifier_label:\n    name: qualifier_label\n    description: The name of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: qualifier_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  qualifier_namespace:\n    name: qualifier_namespace\n    description: The namespace/prefix of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: qualifier_namespace\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  qualifier_category:\n    name: qualifier_category\n    description: The category of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: qualifier_category\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  qualifier_closure:\n    name: qualifier_closure\n    description: Field containing frequency_qualifier id and the ids of all of it's\n      ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: qualifier_closure\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  qualifier_closure_label:\n    name: qualifier_closure_label\n    description: Field containing frequency_qualifier name and the names of all of\n      it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: qualifier_closure_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  frequency_qualifier_label:\n    name: frequency_qualifier_label\n    description: The name of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: frequency_qualifier_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  frequency_qualifier_namespace:\n    name: frequency_qualifier_namespace\n    description: The namespace/prefix of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: frequency_qualifier_namespace\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  frequency_qualifier_category:\n    name: frequency_qualifier_category\n    description: The category of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: frequency_qualifier_category\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  frequency_qualifier_closure:\n    name: frequency_qualifier_closure\n    description: Field containing frequency_qualifier id and the ids of all of it's\n      ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: frequency_qualifier_closure\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  frequency_qualifier_closure_label:\n    name: frequency_qualifier_closure_label\n    description: Field containing frequency_qualifier name and the names of all of\n      it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: frequency_qualifier_closure_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  onset_qualifier_label:\n    name: onset_qualifier_label\n    description: The name of the onset_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: onset_qualifier_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  onset_qualifier_namespace:\n    name: onset_qualifier_namespace\n    description: The namespace/prefix of the onset_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: onset_qualifier_namespace\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  onset_qualifier_category:\n    name: onset_qualifier_category\n    description: The category of the onset_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: onset_qualifier_category\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  onset_qualifier_closure:\n    name: onset_qualifier_closure\n    description: Field containing onset_qualifier id and the ids of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: onset_qualifier_closure\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  onset_qualifier_closure_label:\n    name: onset_qualifier_closure_label\n    description: Field containing onset_qualifier name and the names of all of it's\n      ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: onset_qualifier_closure_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  sex_qualifier_label:\n    name: sex_qualifier_label\n    description: The name of the sex_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: sex_qualifier_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  sex_qualifier_namespace:\n    name: sex_qualifier_namespace\n    description: The namespace/prefix of the sex_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: sex_qualifier_namespace\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  sex_qualifier_category:\n    name: sex_qualifier_category\n    description: The category of the sex_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: sex_qualifier_category\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  sex_qualifier_closure:\n    name: sex_qualifier_closure\n    description: Field containing sex_qualifier id and the ids of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: sex_qualifier_closure\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  sex_qualifier_closure_label:\n    name: sex_qualifier_closure_label\n    description: Field containing sex_qualifier name and the names of all of it's\n      ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: sex_qualifier_closure_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  stage_qualifier_label:\n    name: stage_qualifier_label\n    description: The name of the stage_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: stage_qualifier_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  stage_qualifier_namespace:\n    name: stage_qualifier_namespace\n    description: The namespace/prefix of the stage_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: stage_qualifier_namespace\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  stage_qualifier_category:\n    name: stage_qualifier_category\n    description: The category of the stage_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: stage_qualifier_category\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  stage_qualifier_closure:\n    name: stage_qualifier_closure\n    description: Field containing stage_qualifier id and the ids of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: stage_qualifier_closure\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  stage_qualifier_closure_label:\n    name: stage_qualifier_closure_label\n    description: Field containing stage_qualifier name and the names of all of it's\n      ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: stage_qualifier_closure_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  disease_context_qualifier:\n    name: disease_context_qualifier\n    description: A context qualifier representing a disease or condition in which\n      a relationship expressed in an association took place.\n    examples:\n    - value: MONDO:0004979\n    - value: MONDO:0005148\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: disease_context_qualifier\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  disease_context_qualifier_label:\n    name: disease_context_qualifier_label\n    description: The name of the disease_context_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: disease_context_qualifier_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  disease_context_qualifier_namespace:\n    name: disease_context_qualifier_namespace\n    description: The namespace/prefix of the disease_context_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: disease_context_qualifier_namespace\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  disease_context_qualifier_category:\n    name: disease_context_qualifier_category\n    description: The category of the disease_context_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: disease_context_qualifier_category\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n  disease_context_qualifier_closure:\n    name: disease_context_qualifier_closure\n    description: Field containing disease_context_qualifier id and the ids of all\n      of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: disease_context_qualifier_closure\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  disease_context_qualifier_closure_label:\n    name: disease_context_qualifier_closure_label\n    description: Field containing disease_context_qualifier name and the names of\n      all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: disease_context_qualifier_closure_label\n    owner: Association\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n
    "},{"location":"Data-Model/AssociationCount/","title":"Class: AssociationCount","text":"
    URI: https://w3id.org/monarch/monarch-py/:AssociationCount
     
     classDiagram\n    class AssociationCount\n    click AssociationCount href \"../AssociationCount\"\n      FacetValue <|-- AssociationCount\n        click FacetValue href \"../FacetValue\"\n\n      AssociationCount : category\n\n      AssociationCount : count\n\n      AssociationCount : label\n
    "},{"location":"Data-Model/AssociationCount/#inheritance","title":"Inheritance","text":"
       
    • FacetValue
         
      • AssociationCount
        •  
       
      •  
    "},{"location":"Data-Model/AssociationCount/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance category 0..1  String direct label 1  String FacetValue count 0..1  Integer count of documents FacetValue"},{"location":"Data-Model/AssociationCount/#usages","title":"Usages","text":"used by used in type used AssociationCountList items range AssociationCount Node association_counts range AssociationCount"},{"location":"Data-Model/AssociationCount/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/AssociationCount/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/AssociationCount/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:AssociationCount native https://w3id.org/monarch/monarch-py/:AssociationCount"},{"location":"Data-Model/AssociationCount/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/AssociationCount/#direct","title":"Direct","text":"
    name: AssociationCount\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: FacetValue\nslots:\n- category\nslot_usage:\n  category:\n    name: category\n    multivalued: false\n
    "},{"location":"Data-Model/AssociationCount/#induced","title":"Induced","text":"
    name: AssociationCount\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: FacetValue\nslot_usage:\n  category:\n    name: category\n    multivalued: false\nattributes:\n  category:\n    name: category\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: category\n    owner: AssociationCount\n    domain_of:\n    - Association\n    - AssociationCount\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Entity\n    range: string\n    multivalued: false\n  label:\n    name: label\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: label\n    owner: AssociationCount\n    domain_of:\n    - FacetValue\n    - FacetField\n    - TermInfo\n    range: string\n    required: true\n  count:\n    name: count\n    description: count of documents\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: count\n    owner: AssociationCount\n    domain_of:\n    - FacetValue\n    range: integer\n
    "},{"location":"Data-Model/AssociationCountList/","title":"Class: AssociationCountList","text":"
    Container class for a list of association counts
     
    URI: https://w3id.org/monarch/monarch-py/:AssociationCountList
     
     classDiagram\n    class AssociationCountList\n    click AssociationCountList href \"../AssociationCountList\"\n      AssociationCountList : items\n\n\n\n\n    AssociationCountList --> \"1..*\" AssociationCount : items\n    click AssociationCount href \"../AssociationCount\"\n
    "},{"location":"Data-Model/AssociationCountList/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance items 1..*  AssociationCount A collection of items, with the type to be overriden by slot_usage direct"},{"location":"Data-Model/AssociationCountList/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/AssociationCountList/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/AssociationCountList/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:AssociationCountList native https://w3id.org/monarch/monarch-py/:AssociationCountList"},{"location":"Data-Model/AssociationCountList/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/AssociationCountList/#direct","title":"Direct","text":"
    name: AssociationCountList\ndescription: Container class for a list of association counts\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- items\nslot_usage:\n  items:\n    name: items\n    range: AssociationCount\n
    "},{"location":"Data-Model/AssociationCountList/#induced","title":"Induced","text":"
    name: AssociationCountList\ndescription: Container class for a list of association counts\nfrom_schema: https://w3id.org/monarch/monarch-py\nslot_usage:\n  items:\n    name: items\n    range: AssociationCount\nattributes:\n  items:\n    name: items\n    description: A collection of items, with the type to be overriden by slot_usage\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: items\n    owner: AssociationCountList\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: AssociationCount\n    required: true\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n
    "},{"location":"Data-Model/AssociationDirectionEnum/","title":"Enum: AssociationDirectionEnum","text":"
    The directionality of an association as it relates to a specified entity, with edges being categorized as incoming or outgoing
     
    URI: AssociationDirectionEnum
    "},{"location":"Data-Model/AssociationDirectionEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description incoming None An association for which a specified entity is the object or part of the obje... outgoing None An association for which a specified entity is the subject or part of the sub..."},{"location":"Data-Model/AssociationDirectionEnum/#slots","title":"Slots","text":"Name Description direction The directionality of the association relative to a given entity for an assoc..."},{"location":"Data-Model/AssociationDirectionEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/AssociationDirectionEnum/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/AssociationDirectionEnum/#linkml-source","title":"LinkML Source","text":"
    name: AssociationDirectionEnum\ndescription: The directionality of an association as it relates to a specified entity,\n  with edges being categorized as incoming or outgoing\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\npermissible_values:\n  incoming:\n    text: incoming\n    description: An association for which a specified entity is the object or part\n      of the object closure\n  outgoing:\n    text: outgoing\n    description: An association for which a specified entity is the subject or part\n      of the subject closure\n
    "},{"location":"Data-Model/AssociationResults/","title":"Class: AssociationResults","text":"
    URI: https://w3id.org/monarch/monarch-py/:AssociationResults
     
     classDiagram\n    class AssociationResults\n    click AssociationResults href \"../AssociationResults\"\n      Results <|-- AssociationResults\n        click Results href \"../Results\"\n\n      AssociationResults : items\n\n\n\n\n    AssociationResults --> \"1..*\" Association : items\n    click Association href \"../Association\"\n\n\n      AssociationResults : limit\n\n      AssociationResults : offset\n\n      AssociationResults : total\n
    "},{"location":"Data-Model/AssociationResults/#inheritance","title":"Inheritance","text":"
       
    • Results
         
      • AssociationResults
        •  
       
      •  
    "},{"location":"Data-Model/AssociationResults/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance items 1..*  Association A collection of items, with the type to be overriden by slot_usage direct limit 1  Integer number of items to return in a response Results offset 1  Integer offset into the total number of items Results total 1  Integer total number of items matching a query Results"},{"location":"Data-Model/AssociationResults/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/AssociationResults/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/AssociationResults/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:AssociationResults native https://w3id.org/monarch/monarch-py/:AssociationResults"},{"location":"Data-Model/AssociationResults/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/AssociationResults/#direct","title":"Direct","text":"
    name: AssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- items\nslot_usage:\n  items:\n    name: items\n    range: Association\n
    "},{"location":"Data-Model/AssociationResults/#induced","title":"Induced","text":"
    name: AssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n  items:\n    name: items\n    range: Association\nattributes:\n  items:\n    name: items\n    description: A collection of items, with the type to be overriden by slot_usage\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: items\n    owner: AssociationResults\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: Association\n    required: true\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  limit:\n    name: limit\n    description: number of items to return in a response\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: limit\n    owner: AssociationResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  offset:\n    name: offset\n    description: offset into the total number of items\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: offset\n    owner: AssociationResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  total:\n    name: total\n    description: total number of items matching a query\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: total\n    owner: AssociationResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n
    "},{"location":"Data-Model/AssociationTableResults/","title":"Class: AssociationTableResults","text":"
    URI: https://w3id.org/monarch/monarch-py/:AssociationTableResults
     
     classDiagram\n    class AssociationTableResults\n    click AssociationTableResults href \"../AssociationTableResults\"\n      Results <|-- AssociationTableResults\n        click Results href \"../Results\"\n\n      AssociationTableResults : items\n\n\n\n\n    AssociationTableResults --> \"1..*\" DirectionalAssociation : items\n    click DirectionalAssociation href \"../DirectionalAssociation\"\n\n\n      AssociationTableResults : limit\n\n      AssociationTableResults : offset\n\n      AssociationTableResults : total\n
    "},{"location":"Data-Model/AssociationTableResults/#inheritance","title":"Inheritance","text":"
       
    • Results
         
      • AssociationTableResults
        •  
       
      •  
    "},{"location":"Data-Model/AssociationTableResults/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance items 1..*  DirectionalAssociation A collection of items, with the type to be overriden by slot_usage direct limit 1  Integer number of items to return in a response Results offset 1  Integer offset into the total number of items Results total 1  Integer total number of items matching a query Results"},{"location":"Data-Model/AssociationTableResults/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/AssociationTableResults/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/AssociationTableResults/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:AssociationTableResults native https://w3id.org/monarch/monarch-py/:AssociationTableResults"},{"location":"Data-Model/AssociationTableResults/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/AssociationTableResults/#direct","title":"Direct","text":"
    name: AssociationTableResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- items\nslot_usage:\n  items:\n    name: items\n    range: DirectionalAssociation\n
    "},{"location":"Data-Model/AssociationTableResults/#induced","title":"Induced","text":"
    name: AssociationTableResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n  items:\n    name: items\n    range: DirectionalAssociation\nattributes:\n  items:\n    name: items\n    description: A collection of items, with the type to be overriden by slot_usage\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: items\n    owner: AssociationTableResults\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: DirectionalAssociation\n    required: true\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  limit:\n    name: limit\n    description: number of items to return in a response\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: limit\n    owner: AssociationTableResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  offset:\n    name: offset\n    description: offset into the total number of items\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: offset\n    owner: AssociationTableResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  total:\n    name: total\n    description: total number of items matching a query\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: total\n    owner: AssociationTableResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n
    "},{"location":"Data-Model/AssociationTypeMapping/","title":"Class: AssociationTypeMapping","text":"
    A data class to hold the necessary information to produce association type counts for given  entities with appropriate directional labels
     
    URI: https://w3id.org/monarch/monarch-py/:AssociationTypeMapping
     
     classDiagram\n    class AssociationTypeMapping\n    click AssociationTypeMapping href \"../AssociationTypeMapping\"\n      AssociationTypeMapping : category\n\n      AssociationTypeMapping : object_label\n\n      AssociationTypeMapping : subject_label\n\n      AssociationTypeMapping : symmetric\n
    "},{"location":"Data-Model/AssociationTypeMapping/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_label 0..1  String A label to describe the subjects of the association type as a whole for use i... direct object_label 0..1  String A label to describe the objects of the association type as a whole for use in... direct symmetric 1  Boolean Whether the association type is symmetric, meaning that the subject and objec... direct category 1  String The biolink category to use in queries for this association type direct"},{"location":"Data-Model/AssociationTypeMapping/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/AssociationTypeMapping/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/AssociationTypeMapping/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:AssociationTypeMapping native https://w3id.org/monarch/monarch-py/:AssociationTypeMapping"},{"location":"Data-Model/AssociationTypeMapping/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/AssociationTypeMapping/#direct","title":"Direct","text":"
    name: AssociationTypeMapping\ndescription: A data class to hold the necessary information to produce association\n  type counts for given  entities with appropriate directional labels\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- subject_label\n- object_label\n- symmetric\n- category\nslot_usage:\n  subject_label:\n    name: subject_label\n    description: A label to describe the subjects of the association type as a whole\n      for use in the UI\n  object_label:\n    name: object_label\n    description: A label to describe the objects of the association type as a whole\n      for use in the UI\n  symmetric:\n    name: symmetric\n    description: Whether the association type is symmetric, meaning that the subject\n      and object labels should be interchangeable\n    ifabsent: 'False'\n    required: true\n  category:\n    name: category\n    description: The biolink category to use in queries for this association type\n    required: true\n    multivalued: false\n
    "},{"location":"Data-Model/AssociationTypeMapping/#induced","title":"Induced","text":"
    name: AssociationTypeMapping\ndescription: A data class to hold the necessary information to produce association\n  type counts for given  entities with appropriate directional labels\nfrom_schema: https://w3id.org/monarch/monarch-py\nslot_usage:\n  subject_label:\n    name: subject_label\n    description: A label to describe the subjects of the association type as a whole\n      for use in the UI\n  object_label:\n    name: object_label\n    description: A label to describe the objects of the association type as a whole\n      for use in the UI\n  symmetric:\n    name: symmetric\n    description: Whether the association type is symmetric, meaning that the subject\n      and object labels should be interchangeable\n    ifabsent: 'False'\n    required: true\n  category:\n    name: category\n    description: The biolink category to use in queries for this association type\n    required: true\n    multivalued: false\nattributes:\n  subject_label:\n    name: subject_label\n    description: A label to describe the subjects of the association type as a whole\n      for use in the UI\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: subject_label\n    owner: AssociationTypeMapping\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n  object_label:\n    name: object_label\n    description: A label to describe the objects of the association type as a whole\n      for use in the UI\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: object_label\n    owner: AssociationTypeMapping\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n  symmetric:\n    name: symmetric\n    description: Whether the association type is symmetric, meaning that the subject\n      and object labels should be interchangeable\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    ifabsent: 'False'\n    alias: symmetric\n    owner: AssociationTypeMapping\n    domain_of:\n    - AssociationTypeMapping\n    range: boolean\n    required: true\n  category:\n    name: category\n    description: The biolink category to use in queries for this association type\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: category\n    owner: AssociationTypeMapping\n    domain_of:\n    - Association\n    - AssociationCount\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Entity\n    range: string\n    required: true\n    multivalued: false\n
    "},{"location":"Data-Model/BestMatch/","title":"Class: BestMatch","text":"
    URI: https://w3id.org/monarch/monarch-py/:BestMatch
     
     classDiagram\n    class BestMatch\n    click BestMatch href \"../BestMatch\"\n      BestMatch : match_source\n\n      BestMatch : match_source_label\n\n      BestMatch : match_subsumer\n\n      BestMatch : match_subsumer_label\n\n      BestMatch : match_target\n\n      BestMatch : match_target_label\n\n      BestMatch : score\n\n      BestMatch : similarity\n\n\n\n\n    BestMatch --> \"1\" TermPairwiseSimilarity : similarity\n    click TermPairwiseSimilarity href \"../TermPairwiseSimilarity\"\n
    "},{"location":"Data-Model/BestMatch/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance match_source 1  String direct match_source_label 0..1  String direct match_target 0..1  String the entity matches direct match_target_label 0..1  String direct score 1  Float direct match_subsumer 0..1  Uriorcurie direct match_subsumer_label 0..1  String direct similarity 1  TermPairwiseSimilarity direct"},{"location":"Data-Model/BestMatch/#usages","title":"Usages","text":"used by used in type used TermSetPairwiseSimilarity subject_best_matches range BestMatch TermSetPairwiseSimilarity object_best_matches range BestMatch"},{"location":"Data-Model/BestMatch/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/BestMatch/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/BestMatch/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:BestMatch native https://w3id.org/monarch/monarch-py/:BestMatch"},{"location":"Data-Model/BestMatch/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/BestMatch/#direct","title":"Direct","text":"
    name: BestMatch\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  match_source:\n    name: match_source\n    comments:\n    - note that the match_source is either the subject or the object\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    rank: 1000\n    identifier: true\n    domain_of:\n    - BestMatch\n    required: true\n  match_source_label:\n    name: match_source_label\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    rank: 1000\n    domain_of:\n    - BestMatch\n  match_target:\n    name: match_target\n    description: the entity matches\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    rank: 1000\n    domain_of:\n    - BestMatch\n  match_target_label:\n    name: match_target_label\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    rank: 1000\n    domain_of:\n    - BestMatch\n  score:\n    name: score\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    domain_of:\n    - SearchResult\n    - BestMatch\n    - SemsimSearchResult\n    range: float\n    required: true\n  match_subsumer:\n    name: match_subsumer\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    rank: 1000\n    domain_of:\n    - BestMatch\n    range: uriorcurie\n  match_subsumer_label:\n    name: match_subsumer_label\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    rank: 1000\n    domain_of:\n    - BestMatch\n  similarity:\n    name: similarity\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    domain_of:\n    - BestMatch\n    - SemsimSearchResult\n    range: TermPairwiseSimilarity\n    required: true\n
    "},{"location":"Data-Model/BestMatch/#induced","title":"Induced","text":"
    name: BestMatch\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  match_source:\n    name: match_source\n    comments:\n    - note that the match_source is either the subject or the object\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    rank: 1000\n    identifier: true\n    alias: match_source\n    owner: BestMatch\n    domain_of:\n    - BestMatch\n    range: string\n    required: true\n  match_source_label:\n    name: match_source_label\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    rank: 1000\n    alias: match_source_label\n    owner: BestMatch\n    domain_of:\n    - BestMatch\n    range: string\n  match_target:\n    name: match_target\n    description: the entity matches\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    rank: 1000\n    alias: match_target\n    owner: BestMatch\n    domain_of:\n    - BestMatch\n    range: string\n  match_target_label:\n    name: match_target_label\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    rank: 1000\n    alias: match_target_label\n    owner: BestMatch\n    domain_of:\n    - BestMatch\n    range: string\n  score:\n    name: score\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    alias: score\n    owner: BestMatch\n    domain_of:\n    - SearchResult\n    - BestMatch\n    - SemsimSearchResult\n    range: float\n    required: true\n  match_subsumer:\n    name: match_subsumer\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    rank: 1000\n    alias: match_subsumer\n    owner: BestMatch\n    domain_of:\n    - BestMatch\n    range: uriorcurie\n  match_subsumer_label:\n    name: match_subsumer_label\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    rank: 1000\n    alias: match_subsumer_label\n    owner: BestMatch\n    domain_of:\n    - BestMatch\n    range: string\n  similarity:\n    name: similarity\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    alias: similarity\n    owner: BestMatch\n    domain_of:\n    - BestMatch\n    - SemsimSearchResult\n    range: TermPairwiseSimilarity\n    required: true\n
    "},{"location":"Data-Model/Boolean/","title":"Type: Boolean","text":"
    A binary (true or false) value
     
    URI: xsd:boolean
     
       
    •  
      base: Bool
       
      •  
    •  
      uri: xsd:boolean
       
      •  
    •  
      repr: bool
       
      •  
    "},{"location":"Data-Model/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Boolean/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Boolean/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:boolean native https://w3id.org/monarch/monarch-py/:boolean exact schema:Boolean"},{"location":"Data-Model/CategoryGroupedAssociationResults/","title":"Class: CategoryGroupedAssociationResults","text":"
    URI: https://w3id.org/monarch/monarch-py/:CategoryGroupedAssociationResults
     
     classDiagram\n    class CategoryGroupedAssociationResults\n    click CategoryGroupedAssociationResults href \"../CategoryGroupedAssociationResults\"\n      Results <|-- CategoryGroupedAssociationResults\n        click Results href \"../Results\"\n\n      CategoryGroupedAssociationResults : counterpart_category\n\n      CategoryGroupedAssociationResults : items\n\n\n\n\n    CategoryGroupedAssociationResults --> \"1..*\" Association : items\n    click Association href \"../Association\"\n\n\n      CategoryGroupedAssociationResults : limit\n\n      CategoryGroupedAssociationResults : offset\n\n      CategoryGroupedAssociationResults : total\n
    "},{"location":"Data-Model/CategoryGroupedAssociationResults/#inheritance","title":"Inheritance","text":"
       
    • Results
         
      • CategoryGroupedAssociationResults
        •  
       
      •  
    "},{"location":"Data-Model/CategoryGroupedAssociationResults/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance counterpart_category 0..1  String The category of the counterpart entity in a given association,  eg direct items 1..*  Association A collection of items, with the type to be overriden by slot_usage direct limit 1  Integer number of items to return in a response Results offset 1  Integer offset into the total number of items Results total 1  Integer total number of items matching a query Results"},{"location":"Data-Model/CategoryGroupedAssociationResults/#usages","title":"Usages","text":"used by used in type used MultiEntityAssociationResults associated_categories range CategoryGroupedAssociationResults"},{"location":"Data-Model/CategoryGroupedAssociationResults/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/CategoryGroupedAssociationResults/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/CategoryGroupedAssociationResults/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:CategoryGroupedAssociationResults native https://w3id.org/monarch/monarch-py/:CategoryGroupedAssociationResults"},{"location":"Data-Model/CategoryGroupedAssociationResults/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/CategoryGroupedAssociationResults/#direct","title":"Direct","text":"
    name: CategoryGroupedAssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- counterpart_category\n- items\nslot_usage:\n  items:\n    name: items\n    range: Association\n
    "},{"location":"Data-Model/CategoryGroupedAssociationResults/#induced","title":"Induced","text":"
    name: CategoryGroupedAssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n  items:\n    name: items\n    range: Association\nattributes:\n  counterpart_category:\n    name: counterpart_category\n    description: The category of the counterpart entity in a given association,  eg.\n      the category of the entity that is not the subject\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: counterpart_category\n    owner: CategoryGroupedAssociationResults\n    domain_of:\n    - CategoryGroupedAssociationResults\n    range: string\n  items:\n    name: items\n    description: A collection of items, with the type to be overriden by slot_usage\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: items\n    owner: CategoryGroupedAssociationResults\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: Association\n    required: true\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  limit:\n    name: limit\n    description: number of items to return in a response\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: limit\n    owner: CategoryGroupedAssociationResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  offset:\n    name: offset\n    description: offset into the total number of items\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: offset\n    owner: CategoryGroupedAssociationResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  total:\n    name: total\n    description: total number of items matching a query\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: total\n    owner: CategoryGroupedAssociationResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n
    "},{"location":"Data-Model/CompactAssociation/","title":"Class: CompactAssociation","text":"
    URI: https://w3id.org/monarch/monarch-py/:CompactAssociation
     
     classDiagram\n    class CompactAssociation\n    click CompactAssociation href \"../CompactAssociation\"\n      CompactAssociation : category\n\n      CompactAssociation : negated\n\n      CompactAssociation : object\n\n      CompactAssociation : object_label\n\n      CompactAssociation : predicate\n\n      CompactAssociation : subject\n\n      CompactAssociation : subject_label\n
    "},{"location":"Data-Model/CompactAssociation/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance category 0..1  String direct subject 1  String direct subject_label 0..1  String The name of the subject entity direct predicate 1  String direct object 1  String direct object_label 0..1  String The name of the object entity direct negated 0..1  Boolean direct"},{"location":"Data-Model/CompactAssociation/#usages","title":"Usages","text":"used by used in type used CompactAssociationResults items range CompactAssociation"},{"location":"Data-Model/CompactAssociation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/CompactAssociation/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/CompactAssociation/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:CompactAssociation native https://w3id.org/monarch/monarch-py/:CompactAssociation"},{"location":"Data-Model/CompactAssociation/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/CompactAssociation/#direct","title":"Direct","text":"
    name: CompactAssociation\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- category\n- subject\n- subject_label\n- predicate\n- object\n- object_label\n- negated\n
    "},{"location":"Data-Model/CompactAssociation/#induced","title":"Induced","text":"
    name: CompactAssociation\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  category:\n    name: category\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: category\n    owner: CompactAssociation\n    domain_of:\n    - Association\n    - AssociationCount\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Entity\n    range: string\n    multivalued: false\n  subject:\n    name: subject\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: subject\n    owner: CompactAssociation\n    domain_of:\n    - Association\n    - CompactAssociation\n    - SemsimSearchResult\n    range: string\n    required: true\n  subject_label:\n    name: subject_label\n    description: The name of the subject entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: subject_label\n    owner: CompactAssociation\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: predicate\n    owner: CompactAssociation\n    domain_of:\n    - Association\n    - CompactAssociation\n    range: string\n    required: true\n    multivalued: false\n  object:\n    name: object\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: object\n    owner: CompactAssociation\n    domain_of:\n    - Association\n    - CompactAssociation\n    range: string\n    required: true\n  object_label:\n    name: object_label\n    description: The name of the object entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: object_label\n    owner: CompactAssociation\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n  negated:\n    name: negated\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: negated\n    owner: CompactAssociation\n    domain_of:\n    - Association\n    - CompactAssociation\n    range: boolean\n
    "},{"location":"Data-Model/CompactAssociationResults/","title":"Class: CompactAssociationResults","text":"
    URI: https://w3id.org/monarch/monarch-py/:CompactAssociationResults
     
     classDiagram\n    class CompactAssociationResults\n    click CompactAssociationResults href \"../CompactAssociationResults\"\n      Results <|-- CompactAssociationResults\n        click Results href \"../Results\"\n\n      CompactAssociationResults : items\n\n\n\n\n    CompactAssociationResults --> \"1..*\" CompactAssociation : items\n    click CompactAssociation href \"../CompactAssociation\"\n\n\n      CompactAssociationResults : limit\n\n      CompactAssociationResults : offset\n\n      CompactAssociationResults : total\n
    "},{"location":"Data-Model/CompactAssociationResults/#inheritance","title":"Inheritance","text":"
       
    • Results
         
      • CompactAssociationResults
        •  
       
      •  
    "},{"location":"Data-Model/CompactAssociationResults/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance items 1..*  CompactAssociation A collection of items, with the type to be overriden by slot_usage direct limit 1  Integer number of items to return in a response Results offset 1  Integer offset into the total number of items Results total 1  Integer total number of items matching a query Results"},{"location":"Data-Model/CompactAssociationResults/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/CompactAssociationResults/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/CompactAssociationResults/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:CompactAssociationResults native https://w3id.org/monarch/monarch-py/:CompactAssociationResults"},{"location":"Data-Model/CompactAssociationResults/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/CompactAssociationResults/#direct","title":"Direct","text":"
    name: CompactAssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- items\nslot_usage:\n  items:\n    name: items\n    range: CompactAssociation\n
    "},{"location":"Data-Model/CompactAssociationResults/#induced","title":"Induced","text":"
    name: CompactAssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n  items:\n    name: items\n    range: CompactAssociation\nattributes:\n  items:\n    name: items\n    description: A collection of items, with the type to be overriden by slot_usage\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: items\n    owner: CompactAssociationResults\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: CompactAssociation\n    required: true\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  limit:\n    name: limit\n    description: number of items to return in a response\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: limit\n    owner: CompactAssociationResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  offset:\n    name: offset\n    description: offset into the total number of items\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: offset\n    owner: CompactAssociationResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  total:\n    name: total\n    description: total number of items matching a query\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: total\n    owner: CompactAssociationResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n
    "},{"location":"Data-Model/Curie/","title":"Type: Curie","text":"
    a compact URI
     
    URI: xsd:string
     
       
    •  
      base: Curie
       
      •  
    •  
      uri: xsd:string
       
      •  
    •  
      repr: str
       
      •  
    "},{"location":"Data-Model/Curie/#comments","title":"Comments","text":"
       
    • in RDF serializations this MUST be expanded to a URI
      •  
    • in non-RDF serializations MAY be serialized as the compact representation
      •  
    "},{"location":"Data-Model/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Curie/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Curie/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:string native https://w3id.org/monarch/monarch-py/:curie"},{"location":"Data-Model/Date/","title":"Type: Date","text":"
    a date (year, month and day) in an idealized calendar
     
    URI: xsd:date
     
       
    •  
      base: XSDDate
       
      •  
    •  
      uri: xsd:date
       
      •  
    •  
      repr: str
       
      •  
    "},{"location":"Data-Model/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Date/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Date/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:date native https://w3id.org/monarch/monarch-py/:date exact schema:Date"},{"location":"Data-Model/DateOrDatetime/","title":"Type: DateOrDatetime","text":"
    Either a date or a datetime
     
    URI: linkml:DateOrDatetime
     
       
    •  
      base: str
       
      •  
    •  
      uri: linkml:DateOrDatetime
       
      •  
    •  
      repr: str
       
      •  
    "},{"location":"Data-Model/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/DateOrDatetime/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/DateOrDatetime/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self linkml:DateOrDatetime native https://w3id.org/monarch/monarch-py/:date_or_datetime"},{"location":"Data-Model/Datetime/","title":"Type: Datetime","text":"
    The combination of a date and time
     
    URI: xsd:dateTime
     
       
    •  
      base: XSDDateTime
       
      •  
    •  
      uri: xsd:dateTime
       
      •  
    •  
      repr: str
       
      •  
    "},{"location":"Data-Model/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Datetime/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Datetime/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:dateTime native https://w3id.org/monarch/monarch-py/:datetime exact schema:DateTime"},{"location":"Data-Model/Decimal/","title":"Type: Decimal","text":"
    A real number with arbitrary precision that conforms to the xsd:decimal specification
     
    URI: xsd:decimal
     
       
    •  
      base: Decimal
       
      •  
    •  
      uri: xsd:decimal
       
      •  
    "},{"location":"Data-Model/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Decimal/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Decimal/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:decimal native https://w3id.org/monarch/monarch-py/:decimal broad schema:Number"},{"location":"Data-Model/DirectionalAssociation/","title":"Class: DirectionalAssociation","text":"
    An association that gives it's direction relative to a specified entity
     
    URI: https://w3id.org/monarch/monarch-py/:DirectionalAssociation
     
     classDiagram\n    class DirectionalAssociation\n    click DirectionalAssociation href \"../DirectionalAssociation\"\n      Association <|-- DirectionalAssociation\n        click Association href \"../Association\"\n\n      DirectionalAssociation : agent_type\n\n      DirectionalAssociation : aggregator_knowledge_source\n\n      DirectionalAssociation : category\n\n      DirectionalAssociation : direction\n\n\n\n\n    DirectionalAssociation --> \"1\" AssociationDirectionEnum : direction\n    click AssociationDirectionEnum href \"../AssociationDirectionEnum\"\n\n\n      DirectionalAssociation : disease_context_qualifier\n\n      DirectionalAssociation : disease_context_qualifier_category\n\n      DirectionalAssociation : disease_context_qualifier_closure\n\n      DirectionalAssociation : disease_context_qualifier_closure_label\n\n      DirectionalAssociation : disease_context_qualifier_label\n\n      DirectionalAssociation : disease_context_qualifier_namespace\n\n      DirectionalAssociation : evidence_count\n\n      DirectionalAssociation : frequency_qualifier\n\n      DirectionalAssociation : frequency_qualifier_category\n\n      DirectionalAssociation : frequency_qualifier_closure\n\n      DirectionalAssociation : frequency_qualifier_closure_label\n\n      DirectionalAssociation : frequency_qualifier_label\n\n      DirectionalAssociation : frequency_qualifier_namespace\n\n      DirectionalAssociation : grouping_key\n\n      DirectionalAssociation : has_count\n\n      DirectionalAssociation : has_evidence\n\n      DirectionalAssociation : has_evidence_links\n\n\n\n\n    DirectionalAssociation --> \"*\" ExpandedCurie : has_evidence_links\n    click ExpandedCurie href \"../ExpandedCurie\"\n\n\n      DirectionalAssociation : has_percentage\n\n      DirectionalAssociation : has_quotient\n\n      DirectionalAssociation : has_total\n\n      DirectionalAssociation : id\n\n      DirectionalAssociation : knowledge_level\n\n      DirectionalAssociation : negated\n\n      DirectionalAssociation : object\n\n      DirectionalAssociation : object_category\n\n      DirectionalAssociation : object_closure\n\n      DirectionalAssociation : object_closure_label\n\n      DirectionalAssociation : object_label\n\n      DirectionalAssociation : object_namespace\n\n      DirectionalAssociation : object_taxon\n\n      DirectionalAssociation : object_taxon_label\n\n      DirectionalAssociation : onset_qualifier\n\n      DirectionalAssociation : onset_qualifier_category\n\n      DirectionalAssociation : onset_qualifier_closure\n\n      DirectionalAssociation : onset_qualifier_closure_label\n\n      DirectionalAssociation : onset_qualifier_label\n\n      DirectionalAssociation : onset_qualifier_namespace\n\n      DirectionalAssociation : original_object\n\n      DirectionalAssociation : original_subject\n\n      DirectionalAssociation : pathway\n\n      DirectionalAssociation : predicate\n\n      DirectionalAssociation : primary_knowledge_source\n\n      DirectionalAssociation : provided_by\n\n      DirectionalAssociation : provided_by_link\n\n\n\n\n    DirectionalAssociation --> \"0..1\" ExpandedCurie : provided_by_link\n    click ExpandedCurie href \"../ExpandedCurie\"\n\n\n      DirectionalAssociation : publications\n\n      DirectionalAssociation : publications_links\n\n\n\n\n    DirectionalAssociation --> \"*\" ExpandedCurie : publications_links\n    click ExpandedCurie href \"../ExpandedCurie\"\n\n\n      DirectionalAssociation : qualifier\n\n      DirectionalAssociation : qualifier_category\n\n      DirectionalAssociation : qualifier_closure\n\n      DirectionalAssociation : qualifier_closure_label\n\n      DirectionalAssociation : qualifier_label\n\n      DirectionalAssociation : qualifier_namespace\n\n      DirectionalAssociation : qualifiers\n\n      DirectionalAssociation : qualifiers_category\n\n      DirectionalAssociation : qualifiers_closure\n\n      DirectionalAssociation : qualifiers_closure_label\n\n      DirectionalAssociation : qualifiers_label\n\n      DirectionalAssociation : qualifiers_namespace\n\n      DirectionalAssociation : sex_qualifier\n\n      DirectionalAssociation : sex_qualifier_category\n\n      DirectionalAssociation : sex_qualifier_closure\n\n      DirectionalAssociation : sex_qualifier_closure_label\n\n      DirectionalAssociation : sex_qualifier_label\n\n      DirectionalAssociation : sex_qualifier_namespace\n\n      DirectionalAssociation : stage_qualifier\n\n      DirectionalAssociation : stage_qualifier_category\n\n      DirectionalAssociation : stage_qualifier_closure\n\n      DirectionalAssociation : stage_qualifier_closure_label\n\n      DirectionalAssociation : stage_qualifier_label\n\n      DirectionalAssociation : stage_qualifier_namespace\n\n      DirectionalAssociation : subject\n\n      DirectionalAssociation : subject_category\n\n      DirectionalAssociation : subject_closure\n\n      DirectionalAssociation : subject_closure_label\n\n      DirectionalAssociation : subject_label\n\n      DirectionalAssociation : subject_namespace\n\n      DirectionalAssociation : subject_taxon\n\n      DirectionalAssociation : subject_taxon_label\n
    "},{"location":"Data-Model/DirectionalAssociation/#inheritance","title":"Inheritance","text":"
       
    • Association
         
      • DirectionalAssociation
        •  
       
      •  
    "},{"location":"Data-Model/DirectionalAssociation/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance direction 1  AssociationDirectionEnum The directionality of the association relative to a given entity for an assoc... direct id 1  String Association category 0..1  String Association subject 1  String Association original_subject 0..1  String Association subject_namespace 0..1  String The namespace/prefix of the subject entity Association subject_category 0..1  String The category of the subject entity Association subject_closure *  String Field containing subject id and the ids of all of it's ancestors Association subject_label 0..1  String The name of the subject entity Association subject_closure_label *  String Field containing subject name and the names of all of it's ancestors Association subject_taxon 0..1  String Association subject_taxon_label 0..1  String Association predicate 1  String Association object 1  String Association original_object 0..1  String Association object_namespace 0..1  String The namespace/prefix of the object entity Association object_category 0..1  String The category of the object entity Association object_closure *  String Field containing object id and the ids of all of it's ancestors Association object_label 0..1  String The name of the object entity Association object_closure_label *  String Field containing object name and the names of all of it's ancestors Association object_taxon 0..1  String Association object_taxon_label 0..1  String Association primary_knowledge_source 0..1  String Association aggregator_knowledge_source *  String Association negated 0..1  Boolean Association pathway 0..1  String Association evidence_count 0..1  Integer count of supporting documents, evidence codes, and sources supplying evidence Association knowledge_level 1  String Describes the level of knowledge expressed in a statement, based on the reaso... Association agent_type 1  String Describes the high-level category of agent who originally generated a  statem... Association has_evidence *  String Association has_evidence_links *  ExpandedCurie List of ExpandedCuries with id and url for evidence Association has_count 0..1  Integer count of out of has_total representing a frequency Association has_total 0..1  Integer total, devided by has_count, representing a frequency Association has_percentage 0..1  Float percentage, which may be calculated from has_count and has_total, as 100 * qu... Association has_quotient 0..1  Float quotient, which should be 1/100 of has_percentage Association grouping_key 0..1  String A concatenation of fields used to group associations with the same essential/... Association provided_by 0..1  String Association provided_by_link 0..1  ExpandedCurie A link to the docs for the knowledge source that provided the node/edge Association publications *  String Association publications_links *  ExpandedCurie List of ExpandedCuries with id and url for publications Association frequency_qualifier 0..1  String Association onset_qualifier 0..1  String Association sex_qualifier 0..1  String Association stage_qualifier 0..1  String Association qualifiers *  String Association qualifiers_label 0..1  String The name of the frequency_qualifier entity Association qualifiers_namespace 0..1  String The namespace/prefix of the frequency_qualifier entity Association qualifiers_category 0..1  String The category of the frequency_qualifier entity Association qualifiers_closure *  String Field containing frequency_qualifier id and the ids of all of it's ancestors Association qualifiers_closure_label *  String Field containing frequency_qualifier name and the names of all of it's ancest... Association qualifier *  String Association qualifier_label 0..1  String The name of the frequency_qualifier entity Association qualifier_namespace 0..1  String The namespace/prefix of the frequency_qualifier entity Association qualifier_category 0..1  String The category of the frequency_qualifier entity Association qualifier_closure *  String Field containing frequency_qualifier id and the ids of all of it's ancestors Association qualifier_closure_label *  String Field containing frequency_qualifier name and the names of all of it's ancest... Association frequency_qualifier_label 0..1  String The name of the frequency_qualifier entity Association frequency_qualifier_namespace 0..1  String The namespace/prefix of the frequency_qualifier entity Association frequency_qualifier_category 0..1  String The category of the frequency_qualifier entity Association frequency_qualifier_closure *  String Field containing frequency_qualifier id and the ids of all of it's ancestors Association frequency_qualifier_closure_label *  String Field containing frequency_qualifier name and the names of all of it's ancest... Association onset_qualifier_label 0..1  String The name of the onset_qualifier entity Association onset_qualifier_namespace 0..1  String The namespace/prefix of the onset_qualifier entity Association onset_qualifier_category 0..1  String The category of the onset_qualifier entity Association onset_qualifier_closure *  String Field containing onset_qualifier id and the ids of all of it's ancestors Association onset_qualifier_closure_label *  String Field containing onset_qualifier name and the names of all of it's ancestors Association sex_qualifier_label 0..1  String The name of the sex_qualifier entity Association sex_qualifier_namespace 0..1  String The namespace/prefix of the sex_qualifier entity Association sex_qualifier_category 0..1  String The category of the sex_qualifier entity Association sex_qualifier_closure *  String Field containing sex_qualifier id and the ids of all of it's ancestors Association sex_qualifier_closure_label *  String Field containing sex_qualifier name and the names of all of it's ancestors Association stage_qualifier_label 0..1  String The name of the stage_qualifier entity Association stage_qualifier_namespace 0..1  String The namespace/prefix of the stage_qualifier entity Association stage_qualifier_category 0..1  String The category of the stage_qualifier entity Association stage_qualifier_closure *  String Field containing stage_qualifier id and the ids of all of it's ancestors Association stage_qualifier_closure_label *  String Field containing stage_qualifier name and the names of all of it's ancestors Association disease_context_qualifier 0..1  String A context qualifier representing a disease or condition in which a relationsh... Association disease_context_qualifier_label 0..1  String The name of the disease_context_qualifier entity Association disease_context_qualifier_namespace 0..1  String The namespace/prefix of the disease_context_qualifier entity Association disease_context_qualifier_category 0..1  String The category of the disease_context_qualifier entity Association disease_context_qualifier_closure *  String Field containing disease_context_qualifier id and the ids of all of it's ance... Association disease_context_qualifier_closure_label *  String Field containing disease_context_qualifier name and the names of all of it's ... Association"},{"location":"Data-Model/DirectionalAssociation/#usages","title":"Usages","text":"used by used in type used AssociationTableResults items range DirectionalAssociation"},{"location":"Data-Model/DirectionalAssociation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/DirectionalAssociation/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/DirectionalAssociation/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:DirectionalAssociation native https://w3id.org/monarch/monarch-py/:DirectionalAssociation"},{"location":"Data-Model/DirectionalAssociation/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/DirectionalAssociation/#direct","title":"Direct","text":"
    name: DirectionalAssociation\ndescription: An association that gives it's direction relative to a specified entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Association\nslots:\n- direction\n
    "},{"location":"Data-Model/DirectionalAssociation/#induced","title":"Induced","text":"
    name: DirectionalAssociation\ndescription: An association that gives it's direction relative to a specified entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Association\nattributes:\n  direction:\n    name: direction\n    description: The directionality of the association relative to a given entity\n      for an association_count. If the entity is the subject or in the subject closure,\n      the direction is forwards, if it is the object or in the object closure, the\n      direction is backwards.\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: direction\n    owner: DirectionalAssociation\n    domain_of:\n    - DirectionalAssociation\n    range: AssociationDirectionEnum\n    required: true\n  id:\n    name: id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    - ExpandedCurie\n    - Entity\n    - HistoPheno\n    - HistoBin\n    - Mapping\n    - MultiEntityAssociationResults\n    - TermInfo\n    range: string\n    required: true\n  category:\n    name: category\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: category\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    - AssociationCount\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Entity\n    range: string\n    multivalued: false\n  subject:\n    name: subject\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: subject\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    - CompactAssociation\n    - SemsimSearchResult\n    range: string\n    required: true\n  original_subject:\n    name: original_subject\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: original_subject\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  subject_namespace:\n    name: subject_namespace\n    description: The namespace/prefix of the subject entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: subject_namespace\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  subject_category:\n    name: subject_category\n    description: The category of the subject entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: subject_category\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  subject_closure:\n    name: subject_closure\n    description: Field containing subject id and the ids of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: subject_closure\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  subject_label:\n    name: subject_label\n    description: The name of the subject entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: subject_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n  subject_closure_label:\n    name: subject_closure_label\n    description: Field containing subject name and the names of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: subject_closure_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  subject_taxon:\n    name: subject_taxon\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: in_taxon\n    alias: subject_taxon\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  subject_taxon_label:\n    name: subject_taxon_label\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: in_taxon_label\n    alias: subject_taxon_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  predicate:\n    name: predicate\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: predicate\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    - CompactAssociation\n    range: string\n    required: true\n    multivalued: false\n  object:\n    name: object\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: object\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    - CompactAssociation\n    range: string\n    required: true\n  original_object:\n    name: original_object\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: original_object\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  object_namespace:\n    name: object_namespace\n    description: The namespace/prefix of the object entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: object_namespace\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  object_category:\n    name: object_category\n    description: The category of the object entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: object_category\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  object_closure:\n    name: object_closure\n    description: Field containing object id and the ids of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: object_closure\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  object_label:\n    name: object_label\n    description: The name of the object entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: object_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n  object_closure_label:\n    name: object_closure_label\n    description: Field containing object name and the names of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: object_closure_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  object_taxon:\n    name: object_taxon\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: in_taxon\n    alias: object_taxon\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  object_taxon_label:\n    name: object_taxon_label\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: in_taxon_label\n    alias: object_taxon_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  primary_knowledge_source:\n    name: primary_knowledge_source\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: primary_knowledge_source\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  aggregator_knowledge_source:\n    name: aggregator_knowledge_source\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: aggregator_knowledge_source\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  negated:\n    name: negated\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: negated\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    - CompactAssociation\n    range: boolean\n  pathway:\n    name: pathway\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: pathway\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  evidence_count:\n    name: evidence_count\n    description: count of supporting documents, evidence codes, and sources supplying\n      evidence\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: evidence_count\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: integer\n  knowledge_level:\n    name: knowledge_level\n    description: Describes the level of knowledge expressed in a statement, based\n      on the reasoning or analysis methods used to generate the statement, or the\n      scope or specificity of what the statement expresses to be true.\n    notes:\n    - The range in this schema is represented as a string, but is constrained  to\n      values from biolink:KnowledgeLevelEnum at ingest time\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    slot_uri: biolink:knowledge_level\n    alias: knowledge_level\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n    required: true\n    multivalued: false\n  agent_type:\n    name: agent_type\n    description: Describes the high-level category of agent who originally generated\n      a  statement of knowledge or other type of information.\n    notes:\n    - The range in this schema is represented as a string, but is constrained  to\n      values from biolink:AgentTypeEnum at ingest time\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    slot_uri: biolink:agent_type\n    alias: agent_type\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n    required: true\n    multivalued: false\n  has_evidence:\n    name: has_evidence\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_evidence\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  has_evidence_links:\n    name: has_evidence_links\n    description: List of ExpandedCuries with id and url for evidence\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_evidence_links\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: ExpandedCurie\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  has_count:\n    name: has_count\n    description: count of out of has_total representing a frequency\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_count\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: integer\n  has_total:\n    name: has_total\n    description: total, devided by has_count, representing a frequency\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_total\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: integer\n  has_percentage:\n    name: has_percentage\n    description: percentage, which may be calculated from has_count and has_total,\n      as 100 * quotient or provided directly, rounded to the integer level\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_percentage\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: float\n  has_quotient:\n    name: has_quotient\n    description: quotient, which should be 1/100 of has_percentage\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_quotient\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: float\n  grouping_key:\n    name: grouping_key\n    description: A concatenation of fields used to group associations with the same\n      essential/defining properties\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: grouping_key\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  provided_by:\n    name: provided_by\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: provided_by\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    - Entity\n    range: string\n  provided_by_link:\n    name: provided_by_link\n    description: A link to the docs for the knowledge source that provided the node/edge.\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: provided_by_link\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    - Node\n    range: ExpandedCurie\n    inlined: true\n  publications:\n    name: publications\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: publications\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  publications_links:\n    name: publications_links\n    description: List of ExpandedCuries with id and url for publications\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: publications_links\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: ExpandedCurie\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  frequency_qualifier:\n    name: frequency_qualifier\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: frequency_qualifier\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  onset_qualifier:\n    name: onset_qualifier\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: onset_qualifier\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  sex_qualifier:\n    name: sex_qualifier\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: sex_qualifier\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  stage_qualifier:\n    name: stage_qualifier\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: stage_qualifier\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  qualifiers:\n    name: qualifiers\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: qualifiers\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  qualifiers_label:\n    name: qualifiers_label\n    description: The name of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: qualifiers_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  qualifiers_namespace:\n    name: qualifiers_namespace\n    description: The namespace/prefix of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: qualifiers_namespace\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  qualifiers_category:\n    name: qualifiers_category\n    description: The category of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: qualifiers_category\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  qualifiers_closure:\n    name: qualifiers_closure\n    description: Field containing frequency_qualifier id and the ids of all of it's\n      ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: qualifiers_closure\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  qualifiers_closure_label:\n    name: qualifiers_closure_label\n    description: Field containing frequency_qualifier name and the names of all of\n      it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: qualifiers_closure_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  qualifier:\n    name: qualifier\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: qualifier\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  qualifier_label:\n    name: qualifier_label\n    description: The name of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: qualifier_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  qualifier_namespace:\n    name: qualifier_namespace\n    description: The namespace/prefix of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: qualifier_namespace\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  qualifier_category:\n    name: qualifier_category\n    description: The category of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: qualifier_category\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  qualifier_closure:\n    name: qualifier_closure\n    description: Field containing frequency_qualifier id and the ids of all of it's\n      ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: qualifier_closure\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  qualifier_closure_label:\n    name: qualifier_closure_label\n    description: Field containing frequency_qualifier name and the names of all of\n      it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: qualifier_closure_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  frequency_qualifier_label:\n    name: frequency_qualifier_label\n    description: The name of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: frequency_qualifier_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  frequency_qualifier_namespace:\n    name: frequency_qualifier_namespace\n    description: The namespace/prefix of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: frequency_qualifier_namespace\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  frequency_qualifier_category:\n    name: frequency_qualifier_category\n    description: The category of the frequency_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: frequency_qualifier_category\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  frequency_qualifier_closure:\n    name: frequency_qualifier_closure\n    description: Field containing frequency_qualifier id and the ids of all of it's\n      ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: frequency_qualifier_closure\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  frequency_qualifier_closure_label:\n    name: frequency_qualifier_closure_label\n    description: Field containing frequency_qualifier name and the names of all of\n      it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: frequency_qualifier_closure_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  onset_qualifier_label:\n    name: onset_qualifier_label\n    description: The name of the onset_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: onset_qualifier_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  onset_qualifier_namespace:\n    name: onset_qualifier_namespace\n    description: The namespace/prefix of the onset_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: onset_qualifier_namespace\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  onset_qualifier_category:\n    name: onset_qualifier_category\n    description: The category of the onset_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: onset_qualifier_category\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  onset_qualifier_closure:\n    name: onset_qualifier_closure\n    description: Field containing onset_qualifier id and the ids of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: onset_qualifier_closure\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  onset_qualifier_closure_label:\n    name: onset_qualifier_closure_label\n    description: Field containing onset_qualifier name and the names of all of it's\n      ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: onset_qualifier_closure_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  sex_qualifier_label:\n    name: sex_qualifier_label\n    description: The name of the sex_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: sex_qualifier_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  sex_qualifier_namespace:\n    name: sex_qualifier_namespace\n    description: The namespace/prefix of the sex_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: sex_qualifier_namespace\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  sex_qualifier_category:\n    name: sex_qualifier_category\n    description: The category of the sex_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: sex_qualifier_category\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  sex_qualifier_closure:\n    name: sex_qualifier_closure\n    description: Field containing sex_qualifier id and the ids of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: sex_qualifier_closure\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  sex_qualifier_closure_label:\n    name: sex_qualifier_closure_label\n    description: Field containing sex_qualifier name and the names of all of it's\n      ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: sex_qualifier_closure_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  stage_qualifier_label:\n    name: stage_qualifier_label\n    description: The name of the stage_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: stage_qualifier_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  stage_qualifier_namespace:\n    name: stage_qualifier_namespace\n    description: The namespace/prefix of the stage_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: stage_qualifier_namespace\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  stage_qualifier_category:\n    name: stage_qualifier_category\n    description: The category of the stage_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: stage_qualifier_category\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  stage_qualifier_closure:\n    name: stage_qualifier_closure\n    description: Field containing stage_qualifier id and the ids of all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: stage_qualifier_closure\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  stage_qualifier_closure_label:\n    name: stage_qualifier_closure_label\n    description: Field containing stage_qualifier name and the names of all of it's\n      ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: stage_qualifier_closure_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  disease_context_qualifier:\n    name: disease_context_qualifier\n    description: A context qualifier representing a disease or condition in which\n      a relationship expressed in an association took place.\n    examples:\n    - value: MONDO:0004979\n    - value: MONDO:0005148\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: disease_context_qualifier\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  disease_context_qualifier_label:\n    name: disease_context_qualifier_label\n    description: The name of the disease_context_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: disease_context_qualifier_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  disease_context_qualifier_namespace:\n    name: disease_context_qualifier_namespace\n    description: The namespace/prefix of the disease_context_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: disease_context_qualifier_namespace\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  disease_context_qualifier_category:\n    name: disease_context_qualifier_category\n    description: The category of the disease_context_qualifier entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: category\n    alias: disease_context_qualifier_category\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n  disease_context_qualifier_closure:\n    name: disease_context_qualifier_closure\n    description: Field containing disease_context_qualifier id and the ids of all\n      of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: disease_context_qualifier_closure\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n  disease_context_qualifier_closure_label:\n    name: disease_context_qualifier_closure_label\n    description: Field containing disease_context_qualifier name and the names of\n      all of it's ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: disease_context_qualifier_closure_label\n    owner: DirectionalAssociation\n    domain_of:\n    - Association\n    range: string\n    multivalued: true\n
    "},{"location":"Data-Model/Double/","title":"Type: Double","text":"
    A real number that conforms to the xsd:double specification
     
    URI: xsd:double
     
       
    •  
      base: float
       
      •  
    •  
      uri: xsd:double
       
      •  
    "},{"location":"Data-Model/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Double/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Double/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:double native https://w3id.org/monarch/monarch-py/:double close schema:Float"},{"location":"Data-Model/Entity/","title":"Class: Entity","text":"
    Represents an Entity in the Monarch KG data model
     
    URI: https://w3id.org/monarch/monarch-py/:Entity
     
     classDiagram\n    class Entity\n    click Entity href \"../Entity\"\n      Entity <|-- Node\n        click Node href \"../Node\"\n      Entity <|-- SearchResult\n        click SearchResult href \"../SearchResult\"\n\n      Entity : category\n\n      Entity : deprecated\n\n      Entity : description\n\n      Entity : full_name\n\n      Entity : has_phenotype\n\n      Entity : has_phenotype_closure\n\n      Entity : has_phenotype_closure_label\n\n      Entity : has_phenotype_count\n\n      Entity : has_phenotype_label\n\n      Entity : id\n\n      Entity : in_taxon\n\n      Entity : in_taxon_label\n\n      Entity : iri\n\n      Entity : name\n\n      Entity : namespace\n\n      Entity : provided_by\n\n      Entity : symbol\n\n      Entity : synonym\n\n      Entity : uri\n\n      Entity : xref\n
    "},{"location":"Data-Model/Entity/#inheritance","title":"Inheritance","text":"
       
    • Entity
         
      • Node
        •  
      • SearchResult
        •  
       
      •  
    "},{"location":"Data-Model/Entity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1  String direct category 0..1  String direct name 0..1  String direct full_name 0..1  String The long form name of an entity direct deprecated 0..1  Boolean A boolean flag indicating that an entity is no longer considered current or v... direct description 0..1  String direct xref *  String direct provided_by 0..1  String direct in_taxon 0..1  String The biolink taxon that the entity is in the closure of direct in_taxon_label 0..1  String The label of the biolink taxon that the entity is in the closure of direct symbol 0..1  String direct synonym *  String direct uri 0..1  String The URI of the entity direct iri 0..1  String direct namespace 0..1  String The namespace/prefix portion of this entity's identifier direct has_phenotype *  String A list of phenotype identifiers that are known to be associated with this ent... direct has_phenotype_label *  String A list of phenotype labels that are known to be associated with this entity direct has_phenotype_closure *  String A list of phenotype identifiers that are known to be associated with this ent... direct has_phenotype_closure_label *  String A list of phenotype labels that are known to be associated with this entity e... direct has_phenotype_count 0..1  Integer A count of the number of phenotypes that are known to be associated with this... direct"},{"location":"Data-Model/Entity/#usages","title":"Usages","text":"used by used in type used EntityResults items range Entity Node inheritance range Entity Node causal_gene range Entity Node causes_disease range Entity NodeHierarchy super_classes range Entity NodeHierarchy sub_classes range Entity TextAnnotationResult tokens range Entity SemsimSearchResult subject range Entity"},{"location":"Data-Model/Entity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Entity/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Entity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:Entity native https://w3id.org/monarch/monarch-py/:Entity"},{"location":"Data-Model/Entity/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/Entity/#direct","title":"Direct","text":"
    name: Entity\ndescription: Represents an Entity in the Monarch KG data model\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- id\n- category\n- name\n- full_name\n- deprecated\n- description\n- xref\n- provided_by\n- in_taxon\n- in_taxon_label\n- symbol\n- synonym\n- uri\n- iri\n- namespace\n- has_phenotype\n- has_phenotype_label\n- has_phenotype_closure\n- has_phenotype_closure_label\n- has_phenotype_count\n
    "},{"location":"Data-Model/Entity/#induced","title":"Induced","text":"
    name: Entity\ndescription: Represents an Entity in the Monarch KG data model\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  id:\n    name: id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Entity\n    domain_of:\n    - Association\n    - ExpandedCurie\n    - Entity\n    - HistoPheno\n    - HistoBin\n    - Mapping\n    - MultiEntityAssociationResults\n    - TermInfo\n    range: string\n    required: true\n  category:\n    name: category\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: category\n    owner: Entity\n    domain_of:\n    - Association\n    - AssociationCount\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Entity\n    range: string\n    multivalued: false\n  name:\n    name: name\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: name\n    owner: Entity\n    domain_of:\n    - Entity\n    - MultiEntityAssociationResults\n    range: string\n  full_name:\n    name: full_name\n    description: The long form name of an entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: full_name\n    owner: Entity\n    domain_of:\n    - Entity\n    range: string\n  deprecated:\n    name: deprecated\n    description: A boolean flag indicating that an entity is no longer considered\n      current or valid.\n    from_schema: https://w3id.org/monarch/monarch-py\n    exact_mappings:\n    - oboInOwl:ObsoleteClass\n    rank: 1000\n    alias: deprecated\n    owner: Entity\n    domain_of:\n    - Entity\n    range: boolean\n  description:\n    name: description\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: description\n    owner: Entity\n    domain_of:\n    - Entity\n    range: string\n  xref:\n    name: xref\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: xref\n    owner: Entity\n    domain_of:\n    - Entity\n    range: string\n    multivalued: true\n  provided_by:\n    name: provided_by\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: provided_by\n    owner: Entity\n    domain_of:\n    - Association\n    - Entity\n    range: string\n  in_taxon:\n    name: in_taxon\n    description: The biolink taxon that the entity is in the closure of.\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: in_taxon\n    owner: Entity\n    domain_of:\n    - Entity\n    - Node\n    range: string\n  in_taxon_label:\n    name: in_taxon_label\n    description: The label of the biolink taxon that the entity is in the closure\n      of.\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: in_taxon_label\n    owner: Entity\n    domain_of:\n    - Entity\n    - Node\n    range: string\n  symbol:\n    name: symbol\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: symbol\n    owner: Entity\n    domain_of:\n    - Entity\n    range: string\n  synonym:\n    name: synonym\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: synonym\n    owner: Entity\n    domain_of:\n    - Entity\n    range: string\n    multivalued: true\n  uri:\n    name: uri\n    description: The URI of the entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: uri\n    owner: Entity\n    domain_of:\n    - Entity\n    range: string\n  iri:\n    name: iri\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: iri\n    owner: Entity\n    domain_of:\n    - Entity\n    range: string\n  namespace:\n    name: namespace\n    description: The namespace/prefix portion of this entity's identifier\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: namespace\n    owner: Entity\n    domain_of:\n    - Entity\n    range: string\n  has_phenotype:\n    name: has_phenotype\n    description: A list of phenotype identifiers that are known to be associated with\n      this entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_phenotype\n    owner: Entity\n    domain_of:\n    - Entity\n    range: string\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  has_phenotype_label:\n    name: has_phenotype_label\n    description: A list of phenotype labels that are known to be associated with this\n      entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_phenotype_label\n    owner: Entity\n    domain_of:\n    - Entity\n    range: string\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  has_phenotype_closure:\n    name: has_phenotype_closure\n    description: A list of phenotype identifiers that are known to be associated with\n      this entity expanded to include all ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_phenotype_closure\n    owner: Entity\n    domain_of:\n    - Entity\n    range: string\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  has_phenotype_closure_label:\n    name: has_phenotype_closure_label\n    description: A list of phenotype labels that are known to be associated with this\n      entity expanded to include all ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_phenotype_closure_label\n    owner: Entity\n    domain_of:\n    - Entity\n    range: string\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  has_phenotype_count:\n    name: has_phenotype_count\n    description: A count of the number of phenotypes that are known to be associated\n      with this entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_phenotype_count\n    owner: Entity\n    domain_of:\n    - Entity\n    range: integer\n
    "},{"location":"Data-Model/EntityResults/","title":"Class: EntityResults","text":"
    URI: https://w3id.org/monarch/monarch-py/:EntityResults
     
     classDiagram\n    class EntityResults\n    click EntityResults href \"../EntityResults\"\n      Results <|-- EntityResults\n        click Results href \"../Results\"\n\n      EntityResults : items\n\n\n\n\n    EntityResults --> \"1..*\" Entity : items\n    click Entity href \"../Entity\"\n\n\n      EntityResults : limit\n\n      EntityResults : offset\n\n      EntityResults : total\n
    "},{"location":"Data-Model/EntityResults/#inheritance","title":"Inheritance","text":"
       
    • Results
         
      • EntityResults
        •  
       
      •  
    "},{"location":"Data-Model/EntityResults/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance items 1..*  Entity A collection of items, with the type to be overriden by slot_usage direct limit 1  Integer number of items to return in a response Results offset 1  Integer offset into the total number of items Results total 1  Integer total number of items matching a query Results"},{"location":"Data-Model/EntityResults/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/EntityResults/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/EntityResults/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:EntityResults native https://w3id.org/monarch/monarch-py/:EntityResults"},{"location":"Data-Model/EntityResults/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/EntityResults/#direct","title":"Direct","text":"
    name: EntityResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- items\nslot_usage:\n  items:\n    name: items\n    range: Entity\n
    "},{"location":"Data-Model/EntityResults/#induced","title":"Induced","text":"
    name: EntityResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n  items:\n    name: items\n    range: Entity\nattributes:\n  items:\n    name: items\n    description: A collection of items, with the type to be overriden by slot_usage\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: items\n    owner: EntityResults\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: Entity\n    required: true\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  limit:\n    name: limit\n    description: number of items to return in a response\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: limit\n    owner: EntityResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  offset:\n    name: offset\n    description: offset into the total number of items\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: offset\n    owner: EntityResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  total:\n    name: total\n    description: total number of items matching a query\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: total\n    owner: EntityResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n
    "},{"location":"Data-Model/ExpandedCurie/","title":"Class: ExpandedCurie","text":"
    A curie bundled along with its expanded url
     
    URI: https://w3id.org/monarch/monarch-py/:ExpandedCurie
     
     classDiagram\n    class ExpandedCurie\n    click ExpandedCurie href \"../ExpandedCurie\"\n      ExpandedCurie : id\n\n      ExpandedCurie : url\n
    "},{"location":"Data-Model/ExpandedCurie/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1  String direct url 0..1  String direct"},{"location":"Data-Model/ExpandedCurie/#usages","title":"Usages","text":"used by used in type used Association has_evidence_links range ExpandedCurie Association provided_by_link range ExpandedCurie Association publications_links range ExpandedCurie DirectionalAssociation has_evidence_links range ExpandedCurie DirectionalAssociation provided_by_link range ExpandedCurie DirectionalAssociation publications_links range ExpandedCurie Node mappings range ExpandedCurie Node external_links range ExpandedCurie Node provided_by_link range ExpandedCurie"},{"location":"Data-Model/ExpandedCurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/ExpandedCurie/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/ExpandedCurie/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:ExpandedCurie native https://w3id.org/monarch/monarch-py/:ExpandedCurie"},{"location":"Data-Model/ExpandedCurie/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/ExpandedCurie/#direct","title":"Direct","text":"
    name: ExpandedCurie\ndescription: A curie bundled along with its expanded url\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- id\n- url\n
    "},{"location":"Data-Model/ExpandedCurie/#induced","title":"Induced","text":"
    name: ExpandedCurie\ndescription: A curie bundled along with its expanded url\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  id:\n    name: id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: ExpandedCurie\n    domain_of:\n    - Association\n    - ExpandedCurie\n    - Entity\n    - HistoPheno\n    - HistoBin\n    - Mapping\n    - MultiEntityAssociationResults\n    - TermInfo\n    range: string\n    required: true\n  url:\n    name: url\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: url\n    owner: ExpandedCurie\n    domain_of:\n    - ExpandedCurie\n    - Release\n    range: string\n
    "},{"location":"Data-Model/FacetField/","title":"Class: FacetField","text":"
    URI: https://w3id.org/monarch/monarch-py/:FacetField
     
     classDiagram\n    class FacetField\n    click FacetField href \"../FacetField\"\n      FacetField : facet_values\n\n\n\n\n    FacetField --> \"*\" FacetValue : facet_values\n    click FacetValue href \"../FacetValue\"\n\n\n      FacetField : label\n
    "},{"location":"Data-Model/FacetField/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance label 1  String direct facet_values *  FacetValue Collection of FacetValue label/value instances belonging to a FacetField direct"},{"location":"Data-Model/FacetField/#usages","title":"Usages","text":"used by used in type used SearchResults facet_fields range FacetField"},{"location":"Data-Model/FacetField/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/FacetField/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/FacetField/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:FacetField native https://w3id.org/monarch/monarch-py/:FacetField"},{"location":"Data-Model/FacetField/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/FacetField/#direct","title":"Direct","text":"
    name: FacetField\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- label\n- facet_values\n
    "},{"location":"Data-Model/FacetField/#induced","title":"Induced","text":"
    name: FacetField\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  label:\n    name: label\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: label\n    owner: FacetField\n    domain_of:\n    - FacetValue\n    - FacetField\n    - TermInfo\n    range: string\n    required: true\n  facet_values:\n    name: facet_values\n    description: Collection of FacetValue label/value instances belonging to a FacetField\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: facet_values\n    owner: FacetField\n    domain_of:\n    - FacetField\n    range: FacetValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n
    "},{"location":"Data-Model/FacetValue/","title":"Class: FacetValue","text":"
    URI: https://w3id.org/monarch/monarch-py/:FacetValue
     
     classDiagram\n    class FacetValue\n    click FacetValue href \"../FacetValue\"\n      FacetValue <|-- AssociationCount\n        click AssociationCount href \"../AssociationCount\"\n      FacetValue <|-- HistoBin\n        click HistoBin href \"../HistoBin\"\n\n      FacetValue : count\n\n      FacetValue : label\n
    "},{"location":"Data-Model/FacetValue/#inheritance","title":"Inheritance","text":"
       
    • FacetValue
         
      • AssociationCount
        •  
      • HistoBin
        •  
       
      •  
    "},{"location":"Data-Model/FacetValue/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance label 1  String direct count 0..1  Integer count of documents direct"},{"location":"Data-Model/FacetValue/#usages","title":"Usages","text":"used by used in type used FacetField facet_values range FacetValue SearchResults facet_queries range FacetValue"},{"location":"Data-Model/FacetValue/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/FacetValue/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/FacetValue/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:FacetValue native https://w3id.org/monarch/monarch-py/:FacetValue"},{"location":"Data-Model/FacetValue/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/FacetValue/#direct","title":"Direct","text":"
    name: FacetValue\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- label\n- count\n
    "},{"location":"Data-Model/FacetValue/#induced","title":"Induced","text":"
    name: FacetValue\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  label:\n    name: label\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: label\n    owner: FacetValue\n    domain_of:\n    - FacetValue\n    - FacetField\n    - TermInfo\n    range: string\n    required: true\n  count:\n    name: count\n    description: count of documents\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: count\n    owner: FacetValue\n    domain_of:\n    - FacetValue\n    range: integer\n
    "},{"location":"Data-Model/Float/","title":"Type: Float","text":"
    A real number that conforms to the xsd:float specification
     
    URI: xsd:float
     
       
    •  
      base: float
       
      •  
    •  
      uri: xsd:float
       
      •  
    "},{"location":"Data-Model/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Float/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Float/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:float native https://w3id.org/monarch/monarch-py/:float exact schema:Float"},{"location":"Data-Model/HistoBin/","title":"Class: HistoBin","text":"
    URI: https://w3id.org/monarch/monarch-py/:HistoBin
     
     classDiagram\n    class HistoBin\n    click HistoBin href \"../HistoBin\"\n      FacetValue <|-- HistoBin\n        click FacetValue href \"../FacetValue\"\n\n      HistoBin : count\n\n      HistoBin : id\n\n      HistoBin : label\n
    "},{"location":"Data-Model/HistoBin/#inheritance","title":"Inheritance","text":"
       
    • FacetValue
         
      • HistoBin
        •  
       
      •  
    "},{"location":"Data-Model/HistoBin/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1  String direct label 1  String FacetValue count 0..1  Integer count of documents FacetValue"},{"location":"Data-Model/HistoBin/#usages","title":"Usages","text":"used by used in type used HistoPheno items range HistoBin"},{"location":"Data-Model/HistoBin/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/HistoBin/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/HistoBin/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:HistoBin native https://w3id.org/monarch/monarch-py/:HistoBin"},{"location":"Data-Model/HistoBin/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/HistoBin/#direct","title":"Direct","text":"
    name: HistoBin\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: FacetValue\nslots:\n- id\n
    "},{"location":"Data-Model/HistoBin/#induced","title":"Induced","text":"
    name: HistoBin\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: FacetValue\nattributes:\n  id:\n    name: id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: HistoBin\n    domain_of:\n    - Association\n    - ExpandedCurie\n    - Entity\n    - HistoPheno\n    - HistoBin\n    - Mapping\n    - MultiEntityAssociationResults\n    - TermInfo\n    range: string\n    required: true\n  label:\n    name: label\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: label\n    owner: HistoBin\n    domain_of:\n    - FacetValue\n    - FacetField\n    - TermInfo\n    range: string\n    required: true\n  count:\n    name: count\n    description: count of documents\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: count\n    owner: HistoBin\n    domain_of:\n    - FacetValue\n    range: integer\n
    "},{"location":"Data-Model/HistoPheno/","title":"Class: HistoPheno","text":"
    URI: https://w3id.org/monarch/monarch-py/:HistoPheno
     
     classDiagram\n    class HistoPheno\n    click HistoPheno href \"../HistoPheno\"\n      HistoPheno : id\n\n      HistoPheno : items\n\n\n\n\n    HistoPheno --> \"1..*\" HistoBin : items\n    click HistoBin href \"../HistoBin\"\n
    "},{"location":"Data-Model/HistoPheno/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1  String direct items 1..*  HistoBin A collection of items, with the type to be overriden by slot_usage direct"},{"location":"Data-Model/HistoPheno/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/HistoPheno/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/HistoPheno/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:HistoPheno native https://w3id.org/monarch/monarch-py/:HistoPheno"},{"location":"Data-Model/HistoPheno/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/HistoPheno/#direct","title":"Direct","text":"
    name: HistoPheno\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- id\n- items\nslot_usage:\n  items:\n    name: items\n    range: HistoBin\n
    "},{"location":"Data-Model/HistoPheno/#induced","title":"Induced","text":"
    name: HistoPheno\nfrom_schema: https://w3id.org/monarch/monarch-py\nslot_usage:\n  items:\n    name: items\n    range: HistoBin\nattributes:\n  id:\n    name: id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: HistoPheno\n    domain_of:\n    - Association\n    - ExpandedCurie\n    - Entity\n    - HistoPheno\n    - HistoBin\n    - Mapping\n    - MultiEntityAssociationResults\n    - TermInfo\n    range: string\n    required: true\n  items:\n    name: items\n    description: A collection of items, with the type to be overriden by slot_usage\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: items\n    owner: HistoPheno\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: HistoBin\n    required: true\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n
    "},{"location":"Data-Model/Integer/","title":"Type: Integer","text":"
    An integer
     
    URI: xsd:integer
     
       
    •  
      base: int
       
      •  
    •  
      uri: xsd:integer
       
      •  
    "},{"location":"Data-Model/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Integer/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Integer/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:integer native https://w3id.org/monarch/monarch-py/:integer exact schema:Integer"},{"location":"Data-Model/ItemCount/","title":"Type: ItemCount","text":"
    URI: xsd:integer
     
       
    •  
      base: int
       
      •  
    •  
      uri: xsd:integer
       
      •  
    •  
      typeof: integer
       
      •  
    "},{"location":"Data-Model/ItemCount/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/ItemCount/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/ItemCount/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:ItemCount native https://w3id.org/monarch/monarch-py/:ItemCount"},{"location":"Data-Model/Jsonpath/","title":"Type: Jsonpath","text":"
    A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.
     
    URI: xsd:string
     
       
    •  
      base: str
       
      •  
    •  
      uri: xsd:string
       
      •  
    •  
      repr: str
       
      •  
    "},{"location":"Data-Model/Jsonpath/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Jsonpath/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Jsonpath/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:string native https://w3id.org/monarch/monarch-py/:jsonpath"},{"location":"Data-Model/Jsonpointer/","title":"Type: Jsonpointer","text":"
    A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.
     
    URI: xsd:string
     
       
    •  
      base: str
       
      •  
    •  
      uri: xsd:string
       
      •  
    •  
      repr: str
       
      •  
    "},{"location":"Data-Model/Jsonpointer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Jsonpointer/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Jsonpointer/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:string native https://w3id.org/monarch/monarch-py/:jsonpointer"},{"location":"Data-Model/Mapping/","title":"Class: Mapping","text":"
    A minimal class to hold a SSSOM mapping
     
    URI: https://w3id.org/monarch/monarch-py/:Mapping
     
     classDiagram\n    class Mapping\n    click Mapping href \"../Mapping\"\n      Mapping : id\n\n      Mapping : mapping_justification\n\n      Mapping : object_id\n\n      Mapping : object_label\n\n      Mapping : predicate_id\n\n      Mapping : subject_id\n\n      Mapping : subject_label\n
    "},{"location":"Data-Model/Mapping/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_id 1  String direct subject_label 0..1  String The name of the subject entity direct predicate_id 1  String direct object_id 1  String direct object_label 0..1  String The name of the object entity direct mapping_justification 0..1  String direct id 1  String direct"},{"location":"Data-Model/Mapping/#usages","title":"Usages","text":"used by used in type used MappingResults items range Mapping"},{"location":"Data-Model/Mapping/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Mapping/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Mapping/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:Mapping native https://w3id.org/monarch/monarch-py/:Mapping"},{"location":"Data-Model/Mapping/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/Mapping/#direct","title":"Direct","text":"
    name: Mapping\ndescription: A minimal class to hold a SSSOM mapping\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- subject_id\n- subject_label\n- predicate_id\n- object_id\n- object_label\n- mapping_justification\n- id\n
    "},{"location":"Data-Model/Mapping/#induced","title":"Induced","text":"
    name: Mapping\ndescription: A minimal class to hold a SSSOM mapping\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  subject_id:\n    name: subject_id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: subject_id\n    owner: Mapping\n    domain_of:\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n    required: true\n  subject_label:\n    name: subject_label\n    description: The name of the subject entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: subject_label\n    owner: Mapping\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n  predicate_id:\n    name: predicate_id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: predicate_id\n    owner: Mapping\n    domain_of:\n    - Mapping\n    range: string\n    required: true\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: object_id\n    owner: Mapping\n    domain_of:\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n    required: true\n  object_label:\n    name: object_label\n    description: The name of the object entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: object_label\n    owner: Mapping\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n  mapping_justification:\n    name: mapping_justification\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: mapping_justification\n    owner: Mapping\n    domain_of:\n    - Mapping\n    range: string\n  id:\n    name: id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Mapping\n    domain_of:\n    - Association\n    - ExpandedCurie\n    - Entity\n    - HistoPheno\n    - HistoBin\n    - Mapping\n    - MultiEntityAssociationResults\n    - TermInfo\n    range: string\n    required: true\n
    "},{"location":"Data-Model/MappingResults/","title":"Class: MappingResults","text":"
    SSSOM Mappings returned as a results collection
     
    URI: https://w3id.org/monarch/monarch-py/:MappingResults
     
     classDiagram\n    class MappingResults\n    click MappingResults href \"../MappingResults\"\n      Results <|-- MappingResults\n        click Results href \"../Results\"\n\n      MappingResults : items\n\n\n\n\n    MappingResults --> \"1..*\" Mapping : items\n    click Mapping href \"../Mapping\"\n\n\n      MappingResults : limit\n\n      MappingResults : offset\n\n      MappingResults : total\n
    "},{"location":"Data-Model/MappingResults/#inheritance","title":"Inheritance","text":"
       
    • Results
         
      • MappingResults
        •  
       
      •  
    "},{"location":"Data-Model/MappingResults/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance items 1..*  Mapping A collection of items, with the type to be overriden by slot_usage direct limit 1  Integer number of items to return in a response Results offset 1  Integer offset into the total number of items Results total 1  Integer total number of items matching a query Results"},{"location":"Data-Model/MappingResults/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/MappingResults/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/MappingResults/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:MappingResults native https://w3id.org/monarch/monarch-py/:MappingResults"},{"location":"Data-Model/MappingResults/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/MappingResults/#direct","title":"Direct","text":"
    name: MappingResults\ndescription: SSSOM Mappings returned as a results collection\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- items\nslot_usage:\n  items:\n    name: items\n    range: Mapping\n
    "},{"location":"Data-Model/MappingResults/#induced","title":"Induced","text":"
    name: MappingResults\ndescription: SSSOM Mappings returned as a results collection\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n  items:\n    name: items\n    range: Mapping\nattributes:\n  items:\n    name: items\n    description: A collection of items, with the type to be overriden by slot_usage\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: items\n    owner: MappingResults\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: Mapping\n    required: true\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  limit:\n    name: limit\n    description: number of items to return in a response\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: limit\n    owner: MappingResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  offset:\n    name: offset\n    description: offset into the total number of items\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: offset\n    owner: MappingResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  total:\n    name: total\n    description: total number of items matching a query\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: total\n    owner: MappingResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n
    "},{"location":"Data-Model/MultiEntityAssociationResults/","title":"Class: MultiEntityAssociationResults","text":"
    URI: https://w3id.org/monarch/monarch-py/:MultiEntityAssociationResults
     
     classDiagram\n    class MultiEntityAssociationResults\n    click MultiEntityAssociationResults href \"../MultiEntityAssociationResults\"\n      Results <|-- MultiEntityAssociationResults\n        click Results href \"../Results\"\n\n      MultiEntityAssociationResults : associated_categories\n\n\n\n\n    MultiEntityAssociationResults --> \"1..*\" CategoryGroupedAssociationResults : associated_categories\n    click CategoryGroupedAssociationResults href \"../CategoryGroupedAssociationResults\"\n\n\n      MultiEntityAssociationResults : id\n\n      MultiEntityAssociationResults : limit\n\n      MultiEntityAssociationResults : name\n\n      MultiEntityAssociationResults : offset\n\n      MultiEntityAssociationResults : total\n
    "},{"location":"Data-Model/MultiEntityAssociationResults/#inheritance","title":"Inheritance","text":"
       
    • Results
         
      • MultiEntityAssociationResults
        •  
       
      •  
    "},{"location":"Data-Model/MultiEntityAssociationResults/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1  String direct name 0..1  String direct associated_categories 1..*  CategoryGroupedAssociationResults direct limit 1  Integer number of items to return in a response Results offset 1  Integer offset into the total number of items Results total 1  Integer total number of items matching a query Results"},{"location":"Data-Model/MultiEntityAssociationResults/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/MultiEntityAssociationResults/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/MultiEntityAssociationResults/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:MultiEntityAssociationResults native https://w3id.org/monarch/monarch-py/:MultiEntityAssociationResults"},{"location":"Data-Model/MultiEntityAssociationResults/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/MultiEntityAssociationResults/#direct","title":"Direct","text":"
    name: MultiEntityAssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- id\n- name\n- associated_categories\n
    "},{"location":"Data-Model/MultiEntityAssociationResults/#induced","title":"Induced","text":"
    name: MultiEntityAssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nattributes:\n  id:\n    name: id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: MultiEntityAssociationResults\n    domain_of:\n    - Association\n    - ExpandedCurie\n    - Entity\n    - HistoPheno\n    - HistoBin\n    - Mapping\n    - MultiEntityAssociationResults\n    - TermInfo\n    range: string\n    required: true\n  name:\n    name: name\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: name\n    owner: MultiEntityAssociationResults\n    domain_of:\n    - Entity\n    - MultiEntityAssociationResults\n    range: string\n  associated_categories:\n    name: associated_categories\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: associated_categories\n    owner: MultiEntityAssociationResults\n    domain_of:\n    - MultiEntityAssociationResults\n    range: CategoryGroupedAssociationResults\n    required: true\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  limit:\n    name: limit\n    description: number of items to return in a response\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: limit\n    owner: MultiEntityAssociationResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  offset:\n    name: offset\n    description: offset into the total number of items\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: offset\n    owner: MultiEntityAssociationResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  total:\n    name: total\n    description: total number of items matching a query\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: total\n    owner: MultiEntityAssociationResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n
    "},{"location":"Data-Model/Ncname/","title":"Type: Ncname","text":"
    Prefix part of CURIE
     
    URI: xsd:string
     
       
    •  
      base: NCName
       
      •  
    •  
      uri: xsd:string
       
      •  
    •  
      repr: str
       
      •  
    "},{"location":"Data-Model/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Ncname/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Ncname/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:string native https://w3id.org/monarch/monarch-py/:ncname"},{"location":"Data-Model/NegativeLogValue/","title":"Type: NegativeLogValue","text":"
    URI: xsd:float
     
       
    •  
      base: float
       
      •  
    •  
      uri: xsd:float
       
      •  
    •  
      typeof: float
       
      •  
    "},{"location":"Data-Model/NegativeLogValue/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/NegativeLogValue/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/NegativeLogValue/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:NegativeLogValue native https://w3id.org/monarch/monarch-py/:NegativeLogValue"},{"location":"Data-Model/Node/","title":"Class: Node","text":"
    UI container class extending Entity with additional information
     
    URI: https://w3id.org/monarch/monarch-py/:Node
     
     classDiagram\n    class Node\n    click Node href \"../Node\"\n      Entity <|-- Node\n        click Entity href \"../Entity\"\n\n      Node : association_counts\n\n\n\n\n    Node --> \"1..*\" AssociationCount : association_counts\n    click AssociationCount href \"../AssociationCount\"\n\n\n      Node : category\n\n      Node : causal_gene\n\n\n\n\n    Node --> \"*\" Entity : causal_gene\n    click Entity href \"../Entity\"\n\n\n      Node : causes_disease\n\n\n\n\n    Node --> \"*\" Entity : causes_disease\n    click Entity href \"../Entity\"\n\n\n      Node : deprecated\n\n      Node : description\n\n      Node : external_links\n\n\n\n\n    Node --> \"*\" ExpandedCurie : external_links\n    click ExpandedCurie href \"../ExpandedCurie\"\n\n\n      Node : full_name\n\n      Node : has_phenotype\n\n      Node : has_phenotype_closure\n\n      Node : has_phenotype_closure_label\n\n      Node : has_phenotype_count\n\n      Node : has_phenotype_label\n\n      Node : id\n\n      Node : in_taxon\n\n      Node : in_taxon_label\n\n      Node : inheritance\n\n\n\n\n    Node --> \"0..1\" Entity : inheritance\n    click Entity href \"../Entity\"\n\n\n      Node : iri\n\n      Node : mappings\n\n\n\n\n    Node --> \"*\" ExpandedCurie : mappings\n    click ExpandedCurie href \"../ExpandedCurie\"\n\n\n      Node : name\n\n      Node : namespace\n\n      Node : node_hierarchy\n\n\n\n\n    Node --> \"0..1\" NodeHierarchy : node_hierarchy\n    click NodeHierarchy href \"../NodeHierarchy\"\n\n\n      Node : provided_by\n\n      Node : provided_by_link\n\n\n\n\n    Node --> \"0..1\" ExpandedCurie : provided_by_link\n    click ExpandedCurie href \"../ExpandedCurie\"\n\n\n      Node : symbol\n\n      Node : synonym\n\n      Node : uri\n\n      Node : xref\n
    "},{"location":"Data-Model/Node/#inheritance","title":"Inheritance","text":"
       
    • Entity
         
      • Node
        •  
       
      •  
    "},{"location":"Data-Model/Node/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance in_taxon 0..1  String The biolink taxon that the entity is in the closure of direct in_taxon_label 0..1  String The label of the biolink taxon that the entity is in the closure of direct inheritance 0..1  Entity direct causal_gene *  Entity A list of genes that are known to be causally associated with a disease direct causes_disease *  Entity A list of diseases that are known to be causally associated with a gene direct mappings *  ExpandedCurie List of ExpandedCuries with id and url for mapped entities direct external_links *  ExpandedCurie ExpandedCurie with id and url for xrefs direct provided_by_link 0..1  ExpandedCurie A link to the docs for the knowledge source that provided the node/edge direct association_counts 1..*  AssociationCount direct node_hierarchy 0..1  NodeHierarchy direct id 1  String Entity category 0..1  String Entity name 0..1  String Entity full_name 0..1  String The long form name of an entity Entity deprecated 0..1  Boolean A boolean flag indicating that an entity is no longer considered current or v... Entity description 0..1  String Entity xref *  String Entity provided_by 0..1  String Entity symbol 0..1  String Entity synonym *  String Entity uri 0..1  String The URI of the entity Entity iri 0..1  String Entity namespace 0..1  String The namespace/prefix portion of this entity's identifier Entity has_phenotype *  String A list of phenotype identifiers that are known to be associated with this ent... Entity has_phenotype_label *  String A list of phenotype labels that are known to be associated with this entity Entity has_phenotype_closure *  String A list of phenotype identifiers that are known to be associated with this ent... Entity has_phenotype_closure_label *  String A list of phenotype labels that are known to be associated with this entity e... Entity has_phenotype_count 0..1  Integer A count of the number of phenotypes that are known to be associated with this... Entity"},{"location":"Data-Model/Node/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Node/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Node/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:Node native https://w3id.org/monarch/monarch-py/:Node"},{"location":"Data-Model/Node/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/Node/#direct","title":"Direct","text":"
    name: Node\ndescription: UI container class extending Entity with additional information\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Entity\nslots:\n- in_taxon\n- in_taxon_label\n- inheritance\n- causal_gene\n- causes_disease\n- mappings\n- external_links\n- provided_by_link\n- association_counts\n- node_hierarchy\n
    "},{"location":"Data-Model/Node/#induced","title":"Induced","text":"
    name: Node\ndescription: UI container class extending Entity with additional information\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Entity\nattributes:\n  in_taxon:\n    name: in_taxon\n    description: The biolink taxon that the entity is in the closure of.\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: in_taxon\n    owner: Node\n    domain_of:\n    - Entity\n    - Node\n    range: string\n  in_taxon_label:\n    name: in_taxon_label\n    description: The label of the biolink taxon that the entity is in the closure\n      of.\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: in_taxon_label\n    owner: Node\n    domain_of:\n    - Entity\n    - Node\n    range: string\n  inheritance:\n    name: inheritance\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: inheritance\n    owner: Node\n    domain_of:\n    - Node\n    range: Entity\n    inlined: true\n  causal_gene:\n    name: causal_gene\n    description: A list of genes that are known to be causally associated with a disease\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: causal_gene\n    owner: Node\n    domain_of:\n    - Node\n    range: Entity\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  causes_disease:\n    name: causes_disease\n    description: A list of diseases that are known to be causally associated with\n      a gene\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: causes_disease\n    owner: Node\n    domain_of:\n    - Node\n    range: Entity\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  mappings:\n    name: mappings\n    description: List of ExpandedCuries with id and url for mapped entities\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: mappings\n    owner: Node\n    domain_of:\n    - Node\n    range: ExpandedCurie\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  external_links:\n    name: external_links\n    description: ExpandedCurie with id and url for xrefs\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: external_links\n    owner: Node\n    domain_of:\n    - Node\n    range: ExpandedCurie\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  provided_by_link:\n    name: provided_by_link\n    description: A link to the docs for the knowledge source that provided the node/edge.\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: provided_by_link\n    owner: Node\n    domain_of:\n    - Association\n    - Node\n    range: ExpandedCurie\n    inlined: true\n  association_counts:\n    name: association_counts\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: association_counts\n    owner: Node\n    domain_of:\n    - Node\n    range: AssociationCount\n    required: true\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  node_hierarchy:\n    name: node_hierarchy\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: node_hierarchy\n    owner: Node\n    domain_of:\n    - Node\n    range: NodeHierarchy\n    inlined: true\n  id:\n    name: id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: Node\n    domain_of:\n    - Association\n    - ExpandedCurie\n    - Entity\n    - HistoPheno\n    - HistoBin\n    - Mapping\n    - MultiEntityAssociationResults\n    - TermInfo\n    range: string\n    required: true\n  category:\n    name: category\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: category\n    owner: Node\n    domain_of:\n    - Association\n    - AssociationCount\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Entity\n    range: string\n    multivalued: false\n  name:\n    name: name\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: name\n    owner: Node\n    domain_of:\n    - Entity\n    - MultiEntityAssociationResults\n    range: string\n  full_name:\n    name: full_name\n    description: The long form name of an entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: full_name\n    owner: Node\n    domain_of:\n    - Entity\n    range: string\n  deprecated:\n    name: deprecated\n    description: A boolean flag indicating that an entity is no longer considered\n      current or valid.\n    from_schema: https://w3id.org/monarch/monarch-py\n    exact_mappings:\n    - oboInOwl:ObsoleteClass\n    rank: 1000\n    alias: deprecated\n    owner: Node\n    domain_of:\n    - Entity\n    range: boolean\n  description:\n    name: description\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: description\n    owner: Node\n    domain_of:\n    - Entity\n    range: string\n  xref:\n    name: xref\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: xref\n    owner: Node\n    domain_of:\n    - Entity\n    range: string\n    multivalued: true\n  provided_by:\n    name: provided_by\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: provided_by\n    owner: Node\n    domain_of:\n    - Association\n    - Entity\n    range: string\n  symbol:\n    name: symbol\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: symbol\n    owner: Node\n    domain_of:\n    - Entity\n    range: string\n  synonym:\n    name: synonym\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: synonym\n    owner: Node\n    domain_of:\n    - Entity\n    range: string\n    multivalued: true\n  uri:\n    name: uri\n    description: The URI of the entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: uri\n    owner: Node\n    domain_of:\n    - Entity\n    range: string\n  iri:\n    name: iri\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: iri\n    owner: Node\n    domain_of:\n    - Entity\n    range: string\n  namespace:\n    name: namespace\n    description: The namespace/prefix portion of this entity's identifier\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: namespace\n    owner: Node\n    domain_of:\n    - Entity\n    range: string\n  has_phenotype:\n    name: has_phenotype\n    description: A list of phenotype identifiers that are known to be associated with\n      this entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_phenotype\n    owner: Node\n    domain_of:\n    - Entity\n    range: string\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  has_phenotype_label:\n    name: has_phenotype_label\n    description: A list of phenotype labels that are known to be associated with this\n      entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_phenotype_label\n    owner: Node\n    domain_of:\n    - Entity\n    range: string\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  has_phenotype_closure:\n    name: has_phenotype_closure\n    description: A list of phenotype identifiers that are known to be associated with\n      this entity expanded to include all ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_phenotype_closure\n    owner: Node\n    domain_of:\n    - Entity\n    range: string\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  has_phenotype_closure_label:\n    name: has_phenotype_closure_label\n    description: A list of phenotype labels that are known to be associated with this\n      entity expanded to include all ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_phenotype_closure_label\n    owner: Node\n    domain_of:\n    - Entity\n    range: string\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  has_phenotype_count:\n    name: has_phenotype_count\n    description: A count of the number of phenotypes that are known to be associated\n      with this entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_phenotype_count\n    owner: Node\n    domain_of:\n    - Entity\n    range: integer\n
    "},{"location":"Data-Model/NodeHierarchy/","title":"Class: NodeHierarchy","text":"
    URI: https://w3id.org/monarch/monarch-py/:NodeHierarchy
     
     classDiagram\n    class NodeHierarchy\n    click NodeHierarchy href \"../NodeHierarchy\"\n      NodeHierarchy : sub_classes\n\n\n\n\n    NodeHierarchy --> \"1..*\" Entity : sub_classes\n    click Entity href \"../Entity\"\n\n\n      NodeHierarchy : super_classes\n\n\n\n\n    NodeHierarchy --> \"1..*\" Entity : super_classes\n    click Entity href \"../Entity\"\n
    "},{"location":"Data-Model/NodeHierarchy/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance super_classes 1..*  Entity direct sub_classes 1..*  Entity direct"},{"location":"Data-Model/NodeHierarchy/#usages","title":"Usages","text":"used by used in type used Node node_hierarchy range NodeHierarchy"},{"location":"Data-Model/NodeHierarchy/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/NodeHierarchy/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/NodeHierarchy/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:NodeHierarchy native https://w3id.org/monarch/monarch-py/:NodeHierarchy"},{"location":"Data-Model/NodeHierarchy/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/NodeHierarchy/#direct","title":"Direct","text":"
    name: NodeHierarchy\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- super_classes\n- sub_classes\n
    "},{"location":"Data-Model/NodeHierarchy/#induced","title":"Induced","text":"
    name: NodeHierarchy\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  super_classes:\n    name: super_classes\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: super_classes\n    owner: NodeHierarchy\n    domain_of:\n    - NodeHierarchy\n    range: Entity\n    required: true\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  sub_classes:\n    name: sub_classes\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: sub_classes\n    owner: NodeHierarchy\n    domain_of:\n    - NodeHierarchy\n    range: Entity\n    required: true\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n
    "},{"location":"Data-Model/Nodeidentifier/","title":"Type: Nodeidentifier","text":"
    A URI, CURIE or BNODE that represents a node in a model.
     
    URI: shex:nonLiteral
     
       
    •  
      base: NodeIdentifier
       
      •  
    •  
      uri: shex:nonLiteral
       
      •  
    •  
      repr: str
       
      •  
    "},{"location":"Data-Model/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Nodeidentifier/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Nodeidentifier/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self shex:nonLiteral native https://w3id.org/monarch/monarch-py/:nodeidentifier"},{"location":"Data-Model/NonNegativeFloat/","title":"Type: NonNegativeFloat","text":"
    URI: xsd:float
     
       
    •  
      base: float
       
      •  
    •  
      uri: xsd:float
       
      •  
    •  
      typeof: float
       
      •  
    "},{"location":"Data-Model/NonNegativeFloat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/NonNegativeFloat/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/NonNegativeFloat/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:NonNegativeFloat native https://w3id.org/monarch/monarch-py/:NonNegativeFloat"},{"location":"Data-Model/Objectidentifier/","title":"Type: Objectidentifier","text":"
    A URI or CURIE that represents an object in the model.
     
    URI: shex:iri
     
       
    •  
      base: ElementIdentifier
       
      •  
    •  
      uri: shex:iri
       
      •  
    •  
      repr: str
       
      •  
    "},{"location":"Data-Model/Objectidentifier/#comments","title":"Comments","text":"
       
    • Used for inheritance and type checking
      •  
    "},{"location":"Data-Model/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Objectidentifier/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Objectidentifier/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self shex:iri native https://w3id.org/monarch/monarch-py/:objectidentifier"},{"location":"Data-Model/PairwiseSimilarity/","title":"Class: PairwiseSimilarity","text":"
    Abstract grouping for representing individual pairwise similarities
     
       
    • NOTE: this is an abstract class and should not be instantiated directly
      •  
     
    URI: https://w3id.org/monarch/monarch-py/:PairwiseSimilarity
     
     classDiagram\n    class PairwiseSimilarity\n    click PairwiseSimilarity href \"../PairwiseSimilarity\"\n      PairwiseSimilarity <|-- TermPairwiseSimilarity\n        click TermPairwiseSimilarity href \"../TermPairwiseSimilarity\"\n      PairwiseSimilarity <|-- TermSetPairwiseSimilarity\n        click TermSetPairwiseSimilarity href \"../TermSetPairwiseSimilarity\"\n
    "},{"location":"Data-Model/PairwiseSimilarity/#inheritance","title":"Inheritance","text":"
       
    • PairwiseSimilarity
         
      • TermPairwiseSimilarity
        •  
      • TermSetPairwiseSimilarity
        •  
       
      •  
    "},{"location":"Data-Model/PairwiseSimilarity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance"},{"location":"Data-Model/PairwiseSimilarity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/PairwiseSimilarity/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/PairwiseSimilarity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:PairwiseSimilarity native https://w3id.org/monarch/monarch-py/:PairwiseSimilarity"},{"location":"Data-Model/PairwiseSimilarity/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/PairwiseSimilarity/#direct","title":"Direct","text":"
    name: PairwiseSimilarity\ndescription: Abstract grouping for representing individual pairwise similarities\nfrom_schema: https://w3id.org/monarch/monarch-py\nabstract: true\n
    "},{"location":"Data-Model/PairwiseSimilarity/#induced","title":"Induced","text":"
    name: PairwiseSimilarity\ndescription: Abstract grouping for representing individual pairwise similarities\nfrom_schema: https://w3id.org/monarch/monarch-py\nabstract: true\n
    "},{"location":"Data-Model/Release/","title":"Class: Release","text":"
    A class to hold information about a release of the Monarch KG
     
    URI: https://w3id.org/monarch/monarch-py/:Release
     
     classDiagram\n    class Release\n    click Release href \"../Release\"\n      Release : graph_stats\n\n      Release : kg\n\n      Release : metadata\n\n      Release : neo4j\n\n      Release : qc_report\n\n      Release : solr\n\n      Release : sqlite\n\n      Release : url\n\n      Release : version\n
    "},{"location":"Data-Model/Release/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance version 0..1  String direct url 0..1  String direct kg 0..1  String direct sqlite 0..1  String direct solr 0..1  String direct neo4j 0..1  String direct metadata 0..1  String direct graph_stats 0..1  String direct qc_report 0..1  String direct"},{"location":"Data-Model/Release/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Release/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Release/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:Release native https://w3id.org/monarch/monarch-py/:Release"},{"location":"Data-Model/Release/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/Release/#direct","title":"Direct","text":"
    name: Release\ndescription: A class to hold information about a release of the Monarch KG\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- version\n- url\n- kg\n- sqlite\n- solr\n- neo4j\n- metadata\n- graph_stats\n- qc_report\n
    "},{"location":"Data-Model/Release/#induced","title":"Induced","text":"
    name: Release\ndescription: A class to hold information about a release of the Monarch KG\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  version:\n    name: version\n    id_prefixes:\n    - string\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: version\n    owner: Release\n    domain_of:\n    - Release\n    range: string\n  url:\n    name: url\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: url\n    owner: Release\n    domain_of:\n    - ExpandedCurie\n    - Release\n    range: string\n  kg:\n    name: kg\n    id_prefixes:\n    - string\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: kg\n    owner: Release\n    domain_of:\n    - Release\n    range: string\n  sqlite:\n    name: sqlite\n    id_prefixes:\n    - string\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: sqlite\n    owner: Release\n    domain_of:\n    - Release\n    range: string\n  solr:\n    name: solr\n    id_prefixes:\n    - string\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: solr\n    owner: Release\n    domain_of:\n    - Release\n    range: string\n  neo4j:\n    name: neo4j\n    id_prefixes:\n    - string\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: neo4j\n    owner: Release\n    domain_of:\n    - Release\n    range: string\n  metadata:\n    name: metadata\n    id_prefixes:\n    - string\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: metadata\n    owner: Release\n    domain_of:\n    - Release\n    range: string\n  graph_stats:\n    name: graph_stats\n    id_prefixes:\n    - string\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: graph_stats\n    owner: Release\n    domain_of:\n    - Release\n    range: string\n  qc_report:\n    name: qc_report\n    id_prefixes:\n    - string\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: qc_report\n    owner: Release\n    domain_of:\n    - Release\n    range: string\n
    "},{"location":"Data-Model/Results/","title":"Class: Results","text":"
       
    • NOTE: this is an abstract class and should not be instantiated directly
      •  
     
    URI: https://w3id.org/monarch/monarch-py/:Results
     
     classDiagram\n    class Results\n    click Results href \"../Results\"\n      Results <|-- AssociationResults\n        click AssociationResults href \"../AssociationResults\"\n      Results <|-- CompactAssociationResults\n        click CompactAssociationResults href \"../CompactAssociationResults\"\n      Results <|-- AssociationTableResults\n        click AssociationTableResults href \"../AssociationTableResults\"\n      Results <|-- CategoryGroupedAssociationResults\n        click CategoryGroupedAssociationResults href \"../CategoryGroupedAssociationResults\"\n      Results <|-- EntityResults\n        click EntityResults href \"../EntityResults\"\n      Results <|-- MappingResults\n        click MappingResults href \"../MappingResults\"\n      Results <|-- MultiEntityAssociationResults\n        click MultiEntityAssociationResults href \"../MultiEntityAssociationResults\"\n      Results <|-- SearchResults\n        click SearchResults href \"../SearchResults\"\n\n      Results : limit\n\n      Results : offset\n\n      Results : total\n
    "},{"location":"Data-Model/Results/#inheritance","title":"Inheritance","text":"
       
    • Results
         
      • AssociationResults
        •  
      • CompactAssociationResults
        •  
      • AssociationTableResults
        •  
      • CategoryGroupedAssociationResults
        •  
      • EntityResults
        •  
      • MappingResults
        •  
      • MultiEntityAssociationResults
        •  
      • SearchResults
        •  
       
      •  
    "},{"location":"Data-Model/Results/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance limit 1  Integer number of items to return in a response direct offset 1  Integer offset into the total number of items direct total 1  Integer total number of items matching a query direct"},{"location":"Data-Model/Results/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Results/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Results/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:Results native https://w3id.org/monarch/monarch-py/:Results"},{"location":"Data-Model/Results/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/Results/#direct","title":"Direct","text":"
    name: Results\nfrom_schema: https://w3id.org/monarch/monarch-py\nabstract: true\nslots:\n- limit\n- offset\n- total\n
    "},{"location":"Data-Model/Results/#induced","title":"Induced","text":"
    name: Results\nfrom_schema: https://w3id.org/monarch/monarch-py\nabstract: true\nattributes:\n  limit:\n    name: limit\n    description: number of items to return in a response\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: limit\n    owner: Results\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  offset:\n    name: offset\n    description: offset into the total number of items\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: offset\n    owner: Results\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  total:\n    name: total\n    description: total number of items matching a query\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: total\n    owner: Results\n    domain_of:\n    - Results\n    range: integer\n    required: true\n
    "},{"location":"Data-Model/SearchResult/","title":"Class: SearchResult","text":"
    URI: https://w3id.org/monarch/monarch-py/:SearchResult
     
     classDiagram\n    class SearchResult\n    click SearchResult href \"../SearchResult\"\n      Entity <|-- SearchResult\n        click Entity href \"../Entity\"\n\n      SearchResult : category\n\n      SearchResult : deprecated\n\n      SearchResult : description\n\n      SearchResult : full_name\n\n      SearchResult : has_phenotype\n\n      SearchResult : has_phenotype_closure\n\n      SearchResult : has_phenotype_closure_label\n\n      SearchResult : has_phenotype_count\n\n      SearchResult : has_phenotype_label\n\n      SearchResult : highlight\n\n      SearchResult : id\n\n      SearchResult : in_taxon\n\n      SearchResult : in_taxon_label\n\n      SearchResult : iri\n\n      SearchResult : name\n\n      SearchResult : namespace\n\n      SearchResult : provided_by\n\n      SearchResult : score\n\n      SearchResult : symbol\n\n      SearchResult : synonym\n\n      SearchResult : uri\n\n      SearchResult : xref\n
    "},{"location":"Data-Model/SearchResult/#inheritance","title":"Inheritance","text":"
       
    • Entity
         
      • SearchResult
        •  
       
      •  
    "},{"location":"Data-Model/SearchResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance highlight 0..1  String matching text snippet containing html tags direct score 0..1  Float direct id 1  String Entity category 1  String Entity name 1  String Entity full_name 0..1  String The long form name of an entity Entity deprecated 0..1  Boolean A boolean flag indicating that an entity is no longer considered current or v... Entity description 0..1  String Entity xref *  String Entity provided_by 0..1  String Entity in_taxon 0..1  String The biolink taxon that the entity is in the closure of Entity in_taxon_label 0..1  String The label of the biolink taxon that the entity is in the closure of Entity symbol 0..1  String Entity synonym *  String Entity uri 0..1  String The URI of the entity Entity iri 0..1  String Entity namespace 0..1  String The namespace/prefix portion of this entity's identifier Entity has_phenotype *  String A list of phenotype identifiers that are known to be associated with this ent... Entity has_phenotype_label *  String A list of phenotype labels that are known to be associated with this entity Entity has_phenotype_closure *  String A list of phenotype identifiers that are known to be associated with this ent... Entity has_phenotype_closure_label *  String A list of phenotype labels that are known to be associated with this entity e... Entity has_phenotype_count 0..1  Integer A count of the number of phenotypes that are known to be associated with this... Entity"},{"location":"Data-Model/SearchResult/#usages","title":"Usages","text":"used by used in type used SearchResults items range SearchResult"},{"location":"Data-Model/SearchResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/SearchResult/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/SearchResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:SearchResult native https://w3id.org/monarch/monarch-py/:SearchResult"},{"location":"Data-Model/SearchResult/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/SearchResult/#direct","title":"Direct","text":"
    name: SearchResult\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Entity\nslots:\n- highlight\n- score\nslot_usage:\n  category:\n    name: category\n    required: true\n  name:\n    name: name\n    required: true\n
    "},{"location":"Data-Model/SearchResult/#induced","title":"Induced","text":"
    name: SearchResult\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Entity\nslot_usage:\n  category:\n    name: category\n    required: true\n  name:\n    name: name\n    required: true\nattributes:\n  highlight:\n    name: highlight\n    description: matching text snippet containing html tags\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: highlight\n    owner: SearchResult\n    domain_of:\n    - SearchResult\n    range: string\n  score:\n    name: score\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: score\n    owner: SearchResult\n    domain_of:\n    - SearchResult\n    - BestMatch\n    - SemsimSearchResult\n    range: float\n  id:\n    name: id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    identifier: true\n    alias: id\n    owner: SearchResult\n    domain_of:\n    - Association\n    - ExpandedCurie\n    - Entity\n    - HistoPheno\n    - HistoBin\n    - Mapping\n    - MultiEntityAssociationResults\n    - TermInfo\n    range: string\n    required: true\n  category:\n    name: category\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: category\n    owner: SearchResult\n    domain_of:\n    - Association\n    - AssociationCount\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Entity\n    range: string\n    required: true\n    multivalued: false\n  name:\n    name: name\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: name\n    owner: SearchResult\n    domain_of:\n    - Entity\n    - MultiEntityAssociationResults\n    range: string\n    required: true\n  full_name:\n    name: full_name\n    description: The long form name of an entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: full_name\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: string\n  deprecated:\n    name: deprecated\n    description: A boolean flag indicating that an entity is no longer considered\n      current or valid.\n    from_schema: https://w3id.org/monarch/monarch-py\n    exact_mappings:\n    - oboInOwl:ObsoleteClass\n    rank: 1000\n    alias: deprecated\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: boolean\n  description:\n    name: description\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: description\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: string\n  xref:\n    name: xref\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: xref\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: string\n    multivalued: true\n  provided_by:\n    name: provided_by\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: provided_by\n    owner: SearchResult\n    domain_of:\n    - Association\n    - Entity\n    range: string\n  in_taxon:\n    name: in_taxon\n    description: The biolink taxon that the entity is in the closure of.\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: in_taxon\n    owner: SearchResult\n    domain_of:\n    - Entity\n    - Node\n    range: string\n  in_taxon_label:\n    name: in_taxon_label\n    description: The label of the biolink taxon that the entity is in the closure\n      of.\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: in_taxon_label\n    owner: SearchResult\n    domain_of:\n    - Entity\n    - Node\n    range: string\n  symbol:\n    name: symbol\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: symbol\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: string\n  synonym:\n    name: synonym\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: synonym\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: string\n    multivalued: true\n  uri:\n    name: uri\n    description: The URI of the entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: uri\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: string\n  iri:\n    name: iri\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: iri\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: string\n  namespace:\n    name: namespace\n    description: The namespace/prefix portion of this entity's identifier\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: namespace\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: string\n  has_phenotype:\n    name: has_phenotype\n    description: A list of phenotype identifiers that are known to be associated with\n      this entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_phenotype\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: string\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  has_phenotype_label:\n    name: has_phenotype_label\n    description: A list of phenotype labels that are known to be associated with this\n      entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_phenotype_label\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: string\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  has_phenotype_closure:\n    name: has_phenotype_closure\n    description: A list of phenotype identifiers that are known to be associated with\n      this entity expanded to include all ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_phenotype_closure\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: string\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  has_phenotype_closure_label:\n    name: has_phenotype_closure_label\n    description: A list of phenotype labels that are known to be associated with this\n      entity expanded to include all ancestors\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_phenotype_closure_label\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: string\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  has_phenotype_count:\n    name: has_phenotype_count\n    description: A count of the number of phenotypes that are known to be associated\n      with this entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: has_phenotype_count\n    owner: SearchResult\n    domain_of:\n    - Entity\n    range: integer\n
    "},{"location":"Data-Model/SearchResults/","title":"Class: SearchResults","text":"
    URI: https://w3id.org/monarch/monarch-py/:SearchResults
     
     classDiagram\n    class SearchResults\n    click SearchResults href \"../SearchResults\"\n      Results <|-- SearchResults\n        click Results href \"../Results\"\n\n      SearchResults : facet_fields\n\n\n\n\n    SearchResults --> \"*\" FacetField : facet_fields\n    click FacetField href \"../FacetField\"\n\n\n      SearchResults : facet_queries\n\n\n\n\n    SearchResults --> \"*\" FacetValue : facet_queries\n    click FacetValue href \"../FacetValue\"\n\n\n      SearchResults : items\n\n\n\n\n    SearchResults --> \"1..*\" SearchResult : items\n    click SearchResult href \"../SearchResult\"\n\n\n      SearchResults : limit\n\n      SearchResults : offset\n\n      SearchResults : total\n
    "},{"location":"Data-Model/SearchResults/#inheritance","title":"Inheritance","text":"
       
    • Results
         
      • SearchResults
        •  
       
      •  
    "},{"location":"Data-Model/SearchResults/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance items 1..*  SearchResult A collection of items, with the type to be overriden by slot_usage direct facet_fields *  FacetField Collection of facet field responses with the field values and counts direct facet_queries *  FacetValue Collection of facet query responses with the query string values and counts direct limit 1  Integer number of items to return in a response Results offset 1  Integer offset into the total number of items Results total 1  Integer total number of items matching a query Results"},{"location":"Data-Model/SearchResults/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/SearchResults/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/SearchResults/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:SearchResults native https://w3id.org/monarch/monarch-py/:SearchResults"},{"location":"Data-Model/SearchResults/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/SearchResults/#direct","title":"Direct","text":"
    name: SearchResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- items\n- facet_fields\n- facet_queries\nslot_usage:\n  items:\n    name: items\n    range: SearchResult\n
    "},{"location":"Data-Model/SearchResults/#induced","title":"Induced","text":"
    name: SearchResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n  items:\n    name: items\n    range: SearchResult\nattributes:\n  items:\n    name: items\n    description: A collection of items, with the type to be overriden by slot_usage\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: items\n    owner: SearchResults\n    domain_of:\n    - AssociationCountList\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\n    - CategoryGroupedAssociationResults\n    - EntityResults\n    - HistoPheno\n    - MappingResults\n    - SearchResults\n    range: SearchResult\n    required: true\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  facet_fields:\n    name: facet_fields\n    description: Collection of facet field responses with the field values and counts\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: facet_fields\n    owner: SearchResults\n    domain_of:\n    - SearchResults\n    range: FacetField\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  facet_queries:\n    name: facet_queries\n    description: Collection of facet query responses with the query string values\n      and counts\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: facet_queries\n    owner: SearchResults\n    domain_of:\n    - SearchResults\n    range: FacetValue\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  limit:\n    name: limit\n    description: number of items to return in a response\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: limit\n    owner: SearchResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  offset:\n    name: offset\n    description: offset into the total number of items\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: offset\n    owner: SearchResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n  total:\n    name: total\n    description: total number of items matching a query\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: total\n    owner: SearchResults\n    domain_of:\n    - Results\n    range: integer\n    required: true\n
    "},{"location":"Data-Model/SemsimSearchResult/","title":"Class: SemsimSearchResult","text":"
    URI: https://w3id.org/monarch/monarch-py/:SemsimSearchResult
     
     classDiagram\n    class SemsimSearchResult\n    click SemsimSearchResult href \"../SemsimSearchResult\"\n      SemsimSearchResult : score\n\n      SemsimSearchResult : similarity\n\n\n\n\n    SemsimSearchResult --> \"0..1\" TermSetPairwiseSimilarity : similarity\n    click TermSetPairwiseSimilarity href \"../TermSetPairwiseSimilarity\"\n\n\n      SemsimSearchResult : subject\n\n\n\n\n    SemsimSearchResult --> \"1\" Entity : subject\n    click Entity href \"../Entity\"\n
    "},{"location":"Data-Model/SemsimSearchResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject 1  Entity direct score 0..1  Float direct similarity 0..1  TermSetPairwiseSimilarity direct"},{"location":"Data-Model/SemsimSearchResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/SemsimSearchResult/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/SemsimSearchResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:SemsimSearchResult native https://w3id.org/monarch/monarch-py/:SemsimSearchResult"},{"location":"Data-Model/SemsimSearchResult/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/SemsimSearchResult/#direct","title":"Direct","text":"
    name: SemsimSearchResult\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- subject\n- score\n- similarity\nslot_usage:\n  subject:\n    name: subject\n    range: Entity\n    inlined: true\n
    "},{"location":"Data-Model/SemsimSearchResult/#induced","title":"Induced","text":"
    name: SemsimSearchResult\nfrom_schema: https://w3id.org/monarch/monarch-py\nslot_usage:\n  subject:\n    name: subject\n    range: Entity\n    inlined: true\nattributes:\n  subject:\n    name: subject\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: subject\n    owner: SemsimSearchResult\n    domain_of:\n    - Association\n    - CompactAssociation\n    - SemsimSearchResult\n    range: Entity\n    required: true\n    inlined: true\n  score:\n    name: score\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: score\n    owner: SemsimSearchResult\n    domain_of:\n    - SearchResult\n    - BestMatch\n    - SemsimSearchResult\n    range: float\n  similarity:\n    name: similarity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: similarity\n    owner: SemsimSearchResult\n    domain_of:\n    - BestMatch\n    - SemsimSearchResult\n    range: TermSetPairwiseSimilarity\n
    "},{"location":"Data-Model/Sparqlpath/","title":"Type: Sparqlpath","text":"
    A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.
     
    URI: xsd:string
     
       
    •  
      base: str
       
      •  
    •  
      uri: xsd:string
       
      •  
    •  
      repr: str
       
      •  
    "},{"location":"Data-Model/Sparqlpath/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Sparqlpath/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Sparqlpath/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:string native https://w3id.org/monarch/monarch-py/:sparqlpath"},{"location":"Data-Model/String/","title":"Type: String","text":"
    A character string
     
    URI: xsd:string
     
       
    •  
      base: str
       
      •  
    •  
      uri: xsd:string
       
      •  
    "},{"location":"Data-Model/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/String/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/String/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:string native https://w3id.org/monarch/monarch-py/:string exact schema:Text"},{"location":"Data-Model/TermInfo/","title":"Class: TermInfo","text":"
    URI: https://w3id.org/monarch/monarch-py/:TermInfo
     
     classDiagram\n    class TermInfo\n    click TermInfo href \"../TermInfo\"\n      TermInfo : id\n\n      TermInfo : label\n
    "},{"location":"Data-Model/TermInfo/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance id 1  String direct label 0..1  String direct"},{"location":"Data-Model/TermInfo/#usages","title":"Usages","text":"used by used in type used TermSetPairwiseSimilarity subject_termset range TermInfo TermSetPairwiseSimilarity object_termset range TermInfo"},{"location":"Data-Model/TermInfo/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/TermInfo/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/TermInfo/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:TermInfo native https://w3id.org/monarch/monarch-py/:TermInfo"},{"location":"Data-Model/TermInfo/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/TermInfo/#direct","title":"Direct","text":"
    name: TermInfo\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  id:\n    name: id\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    identifier: true\n    domain_of:\n    - Association\n    - ExpandedCurie\n    - Entity\n    - HistoPheno\n    - HistoBin\n    - Mapping\n    - MultiEntityAssociationResults\n    - TermInfo\n    required: true\n  label:\n    name: label\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    slot_uri: rdfs:label\n    domain_of:\n    - FacetValue\n    - FacetField\n    - TermInfo\n
    "},{"location":"Data-Model/TermInfo/#induced","title":"Induced","text":"
    name: TermInfo\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  id:\n    name: id\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    identifier: true\n    alias: id\n    owner: TermInfo\n    domain_of:\n    - Association\n    - ExpandedCurie\n    - Entity\n    - HistoPheno\n    - HistoBin\n    - Mapping\n    - MultiEntityAssociationResults\n    - TermInfo\n    range: string\n    required: true\n  label:\n    name: label\n    from_schema: https://w3id.org/monarch/monarch-py-similarity\n    slot_uri: rdfs:label\n    alias: label\n    owner: TermInfo\n    domain_of:\n    - FacetValue\n    - FacetField\n    - TermInfo\n    range: string\n
    "},{"location":"Data-Model/TermPairwiseSimilarity/","title":"Class: TermPairwiseSimilarity","text":"
    A simple pairwise similarity between two atomic concepts/terms
     
    URI: https://w3id.org/monarch/monarch-py/:TermPairwiseSimilarity
     
     classDiagram\n    class TermPairwiseSimilarity\n    click TermPairwiseSimilarity href \"../TermPairwiseSimilarity\"\n      PairwiseSimilarity <|-- TermPairwiseSimilarity\n        click PairwiseSimilarity href \"../PairwiseSimilarity\"\n\n      TermPairwiseSimilarity : ancestor_id\n\n      TermPairwiseSimilarity : ancestor_information_content\n\n      TermPairwiseSimilarity : ancestor_label\n\n      TermPairwiseSimilarity : ancestor_source\n\n      TermPairwiseSimilarity : cosine_similarity\n\n      TermPairwiseSimilarity : dice_similarity\n\n      TermPairwiseSimilarity : jaccard_similarity\n\n      TermPairwiseSimilarity : object_id\n\n      TermPairwiseSimilarity : object_information_content\n\n      TermPairwiseSimilarity : object_label\n\n      TermPairwiseSimilarity : object_source\n\n      TermPairwiseSimilarity : phenodigm_score\n\n      TermPairwiseSimilarity : subject_id\n\n      TermPairwiseSimilarity : subject_information_content\n\n      TermPairwiseSimilarity : subject_label\n\n      TermPairwiseSimilarity : subject_source\n
    "},{"location":"Data-Model/TermPairwiseSimilarity/#inheritance","title":"Inheritance","text":"
       
    • PairwiseSimilarity
         
      • TermPairwiseSimilarity
        •  
       
      •  
    "},{"location":"Data-Model/TermPairwiseSimilarity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_id 1  String direct subject_label 0..1  String The name of the subject entity direct subject_source 0..1  String the source for the first entity direct object_id 1  String direct object_label 0..1  String The name of the object entity direct object_source 0..1  String the source for the second entity direct ancestor_id 0..1  Uriorcurie the most recent common ancestor of the two compared entities direct ancestor_label 0..1  String the name or label of the ancestor concept direct ancestor_source 0..1  String direct object_information_content 0..1  NegativeLogValue The IC of the object direct subject_information_content 0..1  NegativeLogValue The IC of the subject direct ancestor_information_content 0..1  NegativeLogValue The IC of the object direct jaccard_similarity 0..1  ZeroToOne The number of concepts in the intersection divided by the number in the union direct cosine_similarity 0..1  Float the dot product of two node embeddings divided by the product of their length... direct dice_similarity 0..1  ZeroToOne direct phenodigm_score 0..1  NonNegativeFloat the geometric mean of the jaccard similarity and the information content direct"},{"location":"Data-Model/TermPairwiseSimilarity/#usages","title":"Usages","text":"used by used in type used BestMatch similarity range TermPairwiseSimilarity"},{"location":"Data-Model/TermPairwiseSimilarity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/TermPairwiseSimilarity/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/TermPairwiseSimilarity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:TermPairwiseSimilarity native https://w3id.org/monarch/monarch-py/:TermPairwiseSimilarity"},{"location":"Data-Model/TermPairwiseSimilarity/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/TermPairwiseSimilarity/#direct","title":"Direct","text":"
    name: TermPairwiseSimilarity\ndescription: A simple pairwise similarity between two atomic concepts/terms\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: PairwiseSimilarity\nslots:\n- subject_id\n- subject_label\n- subject_source\n- object_id\n- object_label\n- object_source\n- ancestor_id\n- ancestor_label\n- ancestor_source\n- object_information_content\n- subject_information_content\n- ancestor_information_content\n- jaccard_similarity\n- cosine_similarity\n- dice_similarity\n- phenodigm_score\n
    "},{"location":"Data-Model/TermPairwiseSimilarity/#induced","title":"Induced","text":"
    name: TermPairwiseSimilarity\ndescription: A simple pairwise similarity between two atomic concepts/terms\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: PairwiseSimilarity\nattributes:\n  subject_id:\n    name: subject_id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: subject_id\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n    required: true\n  subject_label:\n    name: subject_label\n    description: The name of the subject entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: subject_label\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n  subject_source:\n    name: subject_source\n    description: the source for the first entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    slot_uri: sssom:subject_source\n    alias: subject_source\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - TermPairwiseSimilarity\n    range: string\n  object_id:\n    name: object_id\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: object_id\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n    required: true\n  object_label:\n    name: object_label\n    description: The name of the object entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: name\n    alias: object_label\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - Association\n    - CompactAssociation\n    - AssociationTypeMapping\n    - Mapping\n    - TermPairwiseSimilarity\n    range: string\n  object_source:\n    name: object_source\n    description: the source for the second entity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    slot_uri: sssom:object_source\n    alias: object_source\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - TermPairwiseSimilarity\n    range: string\n  ancestor_id:\n    name: ancestor_id\n    description: the most recent common ancestor of the two compared entities. If\n      there are multiple MRCAs then the most informative one is selected\n    todos:\n    - decide on what to do when there are multiple possible ancestos\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: ancestor_id\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - TermPairwiseSimilarity\n    range: uriorcurie\n  ancestor_label:\n    name: ancestor_label\n    description: the name or label of the ancestor concept\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: ancestor_label\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - TermPairwiseSimilarity\n    range: string\n  ancestor_source:\n    name: ancestor_source\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: ancestor_source\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - TermPairwiseSimilarity\n    range: string\n  object_information_content:\n    name: object_information_content\n    description: The IC of the object\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: information_content\n    alias: object_information_content\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - TermPairwiseSimilarity\n    range: NegativeLogValue\n  subject_information_content:\n    name: subject_information_content\n    description: The IC of the subject\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: information_content\n    alias: subject_information_content\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - TermPairwiseSimilarity\n    range: NegativeLogValue\n  ancestor_information_content:\n    name: ancestor_information_content\n    description: The IC of the object\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: information_content\n    alias: ancestor_information_content\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - TermPairwiseSimilarity\n    range: NegativeLogValue\n  jaccard_similarity:\n    name: jaccard_similarity\n    description: The number of concepts in the intersection divided by the number\n      in the union\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: score\n    alias: jaccard_similarity\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - TermPairwiseSimilarity\n    range: ZeroToOne\n  cosine_similarity:\n    name: cosine_similarity\n    description: the dot product of two node embeddings divided by the product of\n      their lengths\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: score\n    alias: cosine_similarity\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - TermPairwiseSimilarity\n    range: float\n  dice_similarity:\n    name: dice_similarity\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: score\n    alias: dice_similarity\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - TermPairwiseSimilarity\n    range: ZeroToOne\n  phenodigm_score:\n    name: phenodigm_score\n    description: the geometric mean of the jaccard similarity and the information\n      content\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    is_a: score\n    alias: phenodigm_score\n    owner: TermPairwiseSimilarity\n    domain_of:\n    - TermPairwiseSimilarity\n    range: NonNegativeFloat\n    equals_expression: sqrt({jaccard_similarity} * {information_content})\n
    "},{"location":"Data-Model/TermSetPairwiseSimilarity/","title":"Class: TermSetPairwiseSimilarity","text":"
    A simple pairwise similarity between two sets of concepts/terms
     
    URI: https://w3id.org/monarch/monarch-py/:TermSetPairwiseSimilarity
     
     classDiagram\n    class TermSetPairwiseSimilarity\n    click TermSetPairwiseSimilarity href \"../TermSetPairwiseSimilarity\"\n      PairwiseSimilarity <|-- TermSetPairwiseSimilarity\n        click PairwiseSimilarity href \"../PairwiseSimilarity\"\n\n      TermSetPairwiseSimilarity : average_score\n\n      TermSetPairwiseSimilarity : best_score\n\n      TermSetPairwiseSimilarity : metric\n\n      TermSetPairwiseSimilarity : object_best_matches\n\n\n\n\n    TermSetPairwiseSimilarity --> \"*\" BestMatch : object_best_matches\n    click BestMatch href \"../BestMatch\"\n\n\n      TermSetPairwiseSimilarity : object_termset\n\n\n\n\n    TermSetPairwiseSimilarity --> \"*\" TermInfo : object_termset\n    click TermInfo href \"../TermInfo\"\n\n\n      TermSetPairwiseSimilarity : subject_best_matches\n\n\n\n\n    TermSetPairwiseSimilarity --> \"*\" BestMatch : subject_best_matches\n    click BestMatch href \"../BestMatch\"\n\n\n      TermSetPairwiseSimilarity : subject_termset\n\n\n\n\n    TermSetPairwiseSimilarity --> \"*\" TermInfo : subject_termset\n    click TermInfo href \"../TermInfo\"\n
    "},{"location":"Data-Model/TermSetPairwiseSimilarity/#inheritance","title":"Inheritance","text":"
       
    • PairwiseSimilarity
         
      • TermSetPairwiseSimilarity
        •  
       
      •  
    "},{"location":"Data-Model/TermSetPairwiseSimilarity/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance subject_termset *  TermInfo direct object_termset *  TermInfo direct subject_best_matches *  BestMatch direct object_best_matches *  BestMatch direct average_score 0..1  Float direct best_score 0..1  Float direct metric 0..1  Uriorcurie direct"},{"location":"Data-Model/TermSetPairwiseSimilarity/#usages","title":"Usages","text":"used by used in type used SemsimSearchResult similarity range TermSetPairwiseSimilarity"},{"location":"Data-Model/TermSetPairwiseSimilarity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/TermSetPairwiseSimilarity/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/TermSetPairwiseSimilarity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:TermSetPairwiseSimilarity native https://w3id.org/monarch/monarch-py/:TermSetPairwiseSimilarity"},{"location":"Data-Model/TermSetPairwiseSimilarity/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/TermSetPairwiseSimilarity/#direct","title":"Direct","text":"
    name: TermSetPairwiseSimilarity\ndescription: A simple pairwise similarity between two sets of concepts/terms\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: PairwiseSimilarity\nslots:\n- subject_termset\n- object_termset\n- subject_best_matches\n- object_best_matches\n- average_score\n- best_score\n- metric\n
    "},{"location":"Data-Model/TermSetPairwiseSimilarity/#induced","title":"Induced","text":"
    name: TermSetPairwiseSimilarity\ndescription: A simple pairwise similarity between two sets of concepts/terms\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: PairwiseSimilarity\nattributes:\n  subject_termset:\n    name: subject_termset\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: subject_termset\n    owner: TermSetPairwiseSimilarity\n    domain_of:\n    - TermSetPairwiseSimilarity\n    range: TermInfo\n    multivalued: true\n    inlined: true\n  object_termset:\n    name: object_termset\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: object_termset\n    owner: TermSetPairwiseSimilarity\n    domain_of:\n    - TermSetPairwiseSimilarity\n    range: TermInfo\n    multivalued: true\n    inlined: true\n  subject_best_matches:\n    name: subject_best_matches\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: subject_best_matches\n    owner: TermSetPairwiseSimilarity\n    domain_of:\n    - TermSetPairwiseSimilarity\n    range: BestMatch\n    multivalued: true\n    inlined: true\n  object_best_matches:\n    name: object_best_matches\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: object_best_matches\n    owner: TermSetPairwiseSimilarity\n    domain_of:\n    - TermSetPairwiseSimilarity\n    range: BestMatch\n    multivalued: true\n    inlined: true\n  average_score:\n    name: average_score\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: average_score\n    owner: TermSetPairwiseSimilarity\n    domain_of:\n    - TermSetPairwiseSimilarity\n    range: float\n    required: false\n  best_score:\n    name: best_score\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: best_score\n    owner: TermSetPairwiseSimilarity\n    domain_of:\n    - TermSetPairwiseSimilarity\n    range: float\n    required: false\n  metric:\n    name: metric\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: metric\n    owner: TermSetPairwiseSimilarity\n    domain_of:\n    - TermSetPairwiseSimilarity\n    range: uriorcurie\n
    "},{"location":"Data-Model/TextAnnotationResult/","title":"Class: TextAnnotationResult","text":"
    URI: https://w3id.org/monarch/monarch-py/:TextAnnotationResult
     
     classDiagram\n    class TextAnnotationResult\n    click TextAnnotationResult href \"../TextAnnotationResult\"\n      TextAnnotationResult : end\n\n      TextAnnotationResult : start\n\n      TextAnnotationResult : text\n\n      TextAnnotationResult : tokens\n\n\n\n\n    TextAnnotationResult --> \"*\" Entity : tokens\n    click Entity href \"../Entity\"\n
    "},{"location":"Data-Model/TextAnnotationResult/#slots","title":"Slots","text":"Name Cardinality and Range Description Inheritance text 0..1  String text without tokens direct tokens *  Entity A collection of entities or concepts direct start 0..1  Integer start position of the annotation direct end 0..1  Integer end position of the annotation direct"},{"location":"Data-Model/TextAnnotationResult/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/TextAnnotationResult/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/TextAnnotationResult/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:TextAnnotationResult native https://w3id.org/monarch/monarch-py/:TextAnnotationResult"},{"location":"Data-Model/TextAnnotationResult/#linkml-source","title":"LinkML Source","text":""},{"location":"Data-Model/TextAnnotationResult/#direct","title":"Direct","text":"
    name: TextAnnotationResult\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- text\n- tokens\n- start\n- end\n
    "},{"location":"Data-Model/TextAnnotationResult/#induced","title":"Induced","text":"
    name: TextAnnotationResult\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n  text:\n    name: text\n    description: text without tokens\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: text\n    owner: TextAnnotationResult\n    domain_of:\n    - TextAnnotationResult\n    range: string\n    inlined: true\n  tokens:\n    name: tokens\n    description: A collection of entities or concepts\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: tokens\n    owner: TextAnnotationResult\n    domain_of:\n    - TextAnnotationResult\n    range: Entity\n    multivalued: true\n    inlined: true\n    inlined_as_list: true\n  start:\n    name: start\n    description: start position of the annotation\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: start\n    owner: TextAnnotationResult\n    domain_of:\n    - TextAnnotationResult\n    range: integer\n  end:\n    name: end\n    description: end position of the annotation\n    from_schema: https://w3id.org/monarch/monarch-py\n    rank: 1000\n    alias: end\n    owner: TextAnnotationResult\n    domain_of:\n    - TextAnnotationResult\n    range: integer\n
    "},{"location":"Data-Model/Time/","title":"Type: Time","text":"
    A time object represents a (local) time of day, independent of any particular day
     
    URI: xsd:time
     
       
    •  
      base: XSDTime
       
      •  
    •  
      uri: xsd:time
       
      •  
    •  
      repr: str
       
      •  
    "},{"location":"Data-Model/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Time/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Time/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:time native https://w3id.org/monarch/monarch-py/:time exact schema:Time"},{"location":"Data-Model/Uri/","title":"Type: Uri","text":"
    a complete URI
     
    URI: xsd:anyURI
     
       
    •  
      base: URI
       
      •  
    •  
      uri: xsd:anyURI
       
      •  
    •  
      repr: str
       
      •  
    "},{"location":"Data-Model/Uri/#comments","title":"Comments","text":"
       
    • in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node
      •  
    "},{"location":"Data-Model/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Uri/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Uri/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:uri native https://w3id.org/monarch/monarch-py/:uri"},{"location":"Data-Model/Uriorcurie/","title":"Type: Uriorcurie","text":"
    a URI or a CURIE
     
    URI: xsd:anyURI
     
       
    •  
      base: URIorCURIE
       
      •  
    •  
      uri: xsd:anyURI
       
      •  
    •  
      repr: str
       
      •  
    "},{"location":"Data-Model/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Uriorcurie/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/Uriorcurie/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self xsd:anyURI native https://w3id.org/monarch/monarch-py/:uriorcurie"},{"location":"Data-Model/ZeroToOne/","title":"Type: ZeroToOne","text":"
    URI: xsd:float
     
       
    •  
      base: float
       
      •  
    •  
      uri: xsd:float
       
      •  
    •  
      typeof: float
       
      •  
    "},{"location":"Data-Model/ZeroToOne/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/ZeroToOne/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/ZeroToOne/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:ZeroToOne native https://w3id.org/monarch/monarch-py/:ZeroToOne"},{"location":"Data-Model/agent_type/","title":"Slot: agent_type","text":"
    Describes the high-level category of agent who originally generated a  statement of knowledge or other type of information.
     
    URI: biolink:agent_type
    "},{"location":"Data-Model/agent_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/agent_type/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/agent_type/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/agent_type/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/agent_type/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self biolink:agent_type native https://w3id.org/monarch/monarch-py/:agent_type"},{"location":"Data-Model/agent_type/#linkml-source","title":"LinkML Source","text":"
    name: agent_type\ndescription: Describes the high-level category of agent who originally generated a  statement\n  of knowledge or other type of information.\nnotes:\n- The range in this schema is represented as a string, but is constrained  to values\n  from biolink:AgentTypeEnum at ingest time\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nslot_uri: biolink:agent_type\nalias: agent_type\ndomain_of:\n- Association\nrange: string\nrequired: true\nmultivalued: false\n
    "},{"location":"Data-Model/aggregator_knowledge_source/","title":"Slot: aggregator_knowledge_source","text":"
    URI: https://w3id.org/monarch/monarch-py/:aggregator_knowledge_source
    "},{"location":"Data-Model/aggregator_knowledge_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/aggregator_knowledge_source/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/aggregator_knowledge_source/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/aggregator_knowledge_source/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/aggregator_knowledge_source/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:aggregator_knowledge_source native https://w3id.org/monarch/monarch-py/:aggregator_knowledge_source"},{"location":"Data-Model/aggregator_knowledge_source/#linkml-source","title":"LinkML Source","text":"
    name: aggregator_knowledge_source\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: aggregator_knowledge_source\ndomain_of:\n- Association\nrange: string\nmultivalued: true\n
    "},{"location":"Data-Model/ancestor_id/","title":"Slot: ancestor_id","text":"
    the most recent common ancestor of the two compared entities. If there are multiple MRCAs then the most informative one is selected
     
    URI: https://w3id.org/monarch/monarch-py/:ancestor_id
    "},{"location":"Data-Model/ancestor_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/ancestor_id/#properties","title":"Properties","text":"
       
    • Range: Uriorcurie
      •  
    "},{"location":"Data-Model/ancestor_id/#todos","title":"TODOs","text":"
       
    • decide on what to do when there are multiple possible ancestos
      •  
    "},{"location":"Data-Model/ancestor_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/ancestor_id/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/ancestor_id/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:ancestor_id native https://w3id.org/monarch/monarch-py/:ancestor_id"},{"location":"Data-Model/ancestor_id/#linkml-source","title":"LinkML Source","text":"
    name: ancestor_id\ndescription: the most recent common ancestor of the two compared entities. If there\n  are multiple MRCAs then the most informative one is selected\ntodos:\n- decide on what to do when there are multiple possible ancestos\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: ancestor_id\ndomain_of:\n- TermPairwiseSimilarity\nrange: uriorcurie\n
    "},{"location":"Data-Model/ancestor_information_content/","title":"Slot: ancestor_information_content","text":"
    The IC of the object
     
    URI: https://w3id.org/monarch/monarch-py/:ancestor_information_content
    "},{"location":"Data-Model/ancestor_information_content/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • information_content
           
        • ancestor_information_content
          •  
         
        •  
       
      •  
    "},{"location":"Data-Model/ancestor_information_content/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/ancestor_information_content/#properties","title":"Properties","text":"
       
    • Range: NegativeLogValue
      •  
    "},{"location":"Data-Model/ancestor_information_content/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/ancestor_information_content/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/ancestor_information_content/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:ancestor_information_content native https://w3id.org/monarch/monarch-py/:ancestor_information_content"},{"location":"Data-Model/ancestor_information_content/#linkml-source","title":"LinkML Source","text":"
    name: ancestor_information_content\ndescription: The IC of the object\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: information_content\nalias: ancestor_information_content\ndomain_of:\n- TermPairwiseSimilarity\nrange: NegativeLogValue\n
    "},{"location":"Data-Model/ancestor_label/","title":"Slot: ancestor_label","text":"
    the name or label of the ancestor concept
     
    URI: https://w3id.org/monarch/monarch-py/:ancestor_label
    "},{"location":"Data-Model/ancestor_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/ancestor_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/ancestor_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/ancestor_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/ancestor_label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:ancestor_label native https://w3id.org/monarch/monarch-py/:ancestor_label"},{"location":"Data-Model/ancestor_label/#linkml-source","title":"LinkML Source","text":"
    name: ancestor_label\ndescription: the name or label of the ancestor concept\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: ancestor_label\ndomain_of:\n- TermPairwiseSimilarity\nrange: string\n
    "},{"location":"Data-Model/ancestor_source/","title":"Slot: ancestor_source","text":"
    URI: https://w3id.org/monarch/monarch-py/:ancestor_source
    "},{"location":"Data-Model/ancestor_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/ancestor_source/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/ancestor_source/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/ancestor_source/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/ancestor_source/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:ancestor_source native https://w3id.org/monarch/monarch-py/:ancestor_source"},{"location":"Data-Model/ancestor_source/#linkml-source","title":"LinkML Source","text":"
    name: ancestor_source\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: ancestor_source\ndomain_of:\n- TermPairwiseSimilarity\nrange: string\n
    "},{"location":"Data-Model/associated_categories/","title":"Slot: associated_categories","text":"
    URI: https://w3id.org/monarch/monarch-py/:associated_categories
    "},{"location":"Data-Model/associated_categories/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MultiEntityAssociationResults no"},{"location":"Data-Model/associated_categories/#properties","title":"Properties","text":"
       
    •  
      Range: CategoryGroupedAssociationResults
       
      •  
    •  
      Multivalued: True
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/associated_categories/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/associated_categories/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/associated_categories/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:associated_categories native https://w3id.org/monarch/monarch-py/:associated_categories"},{"location":"Data-Model/associated_categories/#linkml-source","title":"LinkML Source","text":"
    name: associated_categories\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: associated_categories\ndomain_of:\n- MultiEntityAssociationResults\nrange: CategoryGroupedAssociationResults\nrequired: true\nmultivalued: true\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/association_counts/","title":"Slot: association_counts","text":"
    URI: https://w3id.org/monarch/monarch-py/:association_counts
    "},{"location":"Data-Model/association_counts/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/association_counts/#properties","title":"Properties","text":"
       
    •  
      Range: AssociationCount
       
      •  
    •  
      Multivalued: True
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/association_counts/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/association_counts/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/association_counts/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:association_counts native https://w3id.org/monarch/monarch-py/:association_counts"},{"location":"Data-Model/association_counts/#linkml-source","title":"LinkML Source","text":"
    name: association_counts\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: association_counts\ndomain_of:\n- Node\nrange: AssociationCount\nrequired: true\nmultivalued: true\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/average_score/","title":"Slot: average_score","text":"
    URI: https://w3id.org/monarch/monarch-py/:average_score
    "},{"location":"Data-Model/average_score/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/average_score/#properties","title":"Properties","text":"
       
    • Range: Float
      •  
    "},{"location":"Data-Model/average_score/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/average_score/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/average_score/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:average_score native https://w3id.org/monarch/monarch-py/:average_score"},{"location":"Data-Model/average_score/#linkml-source","title":"LinkML Source","text":"
    name: average_score\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: average_score\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: float\nrequired: false\n
    "},{"location":"Data-Model/best_score/","title":"Slot: best_score","text":"
    URI: https://w3id.org/monarch/monarch-py/:best_score
    "},{"location":"Data-Model/best_score/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/best_score/#properties","title":"Properties","text":"
       
    • Range: Float
      •  
    "},{"location":"Data-Model/best_score/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/best_score/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/best_score/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:best_score native https://w3id.org/monarch/monarch-py/:best_score"},{"location":"Data-Model/best_score/#linkml-source","title":"LinkML Source","text":"
    name: best_score\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: best_score\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: float\nrequired: false\n
    "},{"location":"Data-Model/category/","title":"Slot: category","text":"
    URI: https://w3id.org/monarch/monarch-py/:category
    "},{"location":"Data-Model/category/#inheritance","title":"Inheritance","text":"
       
    • category
         
      • subject_category
        •  
      • object_category
        •  
      • qualifiers_category
        •  
      • qualifier_category
        •  
      • frequency_qualifier_category
        •  
      • onset_qualifier_category
        •  
      • sex_qualifier_category
        •  
      • stage_qualifier_category
        •  
      • disease_context_qualifier_category
        •  
       
      •  
    "},{"location":"Data-Model/category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no Entity Represents an Entity in the Monarch KG data model no Node UI container class extending Entity with additional information no AssociationCount yes AssociationTypeMapping A data class to hold the necessary information to produce association type co... yes SearchResult yes CompactAssociation no"},{"location":"Data-Model/category/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/category/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/category/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:category native https://w3id.org/monarch/monarch-py/:category"},{"location":"Data-Model/category/#linkml-source","title":"LinkML Source","text":"
    name: category\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: category\ndomain_of:\n- Association\n- AssociationCount\n- CompactAssociation\n- AssociationTypeMapping\n- Entity\nrange: string\nmultivalued: false\n
    "},{"location":"Data-Model/causal_gene/","title":"Slot: causal_gene","text":"
    A list of genes that are known to be causally associated with a disease
     
    URI: https://w3id.org/monarch/monarch-py/:causal_gene
    "},{"location":"Data-Model/causal_gene/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/causal_gene/#properties","title":"Properties","text":"
       
    •  
      Range: Entity
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/causal_gene/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/causal_gene/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/causal_gene/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:causal_gene native https://w3id.org/monarch/monarch-py/:causal_gene"},{"location":"Data-Model/causal_gene/#linkml-source","title":"LinkML Source","text":"
    name: causal_gene\ndescription: A list of genes that are known to be causally associated with a disease\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: causal_gene\ndomain_of:\n- Node\nrange: Entity\nmultivalued: true\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/causes_disease/","title":"Slot: causes_disease","text":"
    A list of diseases that are known to be causally associated with a gene
     
    URI: https://w3id.org/monarch/monarch-py/:causes_disease
    "},{"location":"Data-Model/causes_disease/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/causes_disease/#properties","title":"Properties","text":"
       
    •  
      Range: Entity
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/causes_disease/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/causes_disease/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/causes_disease/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:causes_disease native https://w3id.org/monarch/monarch-py/:causes_disease"},{"location":"Data-Model/causes_disease/#linkml-source","title":"LinkML Source","text":"
    name: causes_disease\ndescription: A list of diseases that are known to be causally associated with a gene\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: causes_disease\ndomain_of:\n- Node\nrange: Entity\nmultivalued: true\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/cosine_similarity/","title":"Slot: cosine_similarity","text":"
    the dot product of two node embeddings divided by the product of their lengths
     
    URI: https://w3id.org/monarch/monarch-py/:cosine_similarity
    "},{"location":"Data-Model/cosine_similarity/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • cosine_similarity
        •  
       
      •  
    "},{"location":"Data-Model/cosine_similarity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/cosine_similarity/#properties","title":"Properties","text":"
       
    • Range: Float
      •  
    "},{"location":"Data-Model/cosine_similarity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/cosine_similarity/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/cosine_similarity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:cosine_similarity native https://w3id.org/monarch/monarch-py/:cosine_similarity"},{"location":"Data-Model/cosine_similarity/#linkml-source","title":"LinkML Source","text":"
    name: cosine_similarity\ndescription: the dot product of two node embeddings divided by the product of their\n  lengths\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: cosine_similarity\ndomain_of:\n- TermPairwiseSimilarity\nrange: float\n
    "},{"location":"Data-Model/count/","title":"Slot: count","text":"
    count of documents
     
    URI: https://w3id.org/monarch/monarch-py/:count
    "},{"location":"Data-Model/count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot HistoBin no FacetValue no AssociationCount no"},{"location":"Data-Model/count/#properties","title":"Properties","text":"
       
    • Range: Integer
      •  
    "},{"location":"Data-Model/count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/count/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/count/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:count native https://w3id.org/monarch/monarch-py/:count"},{"location":"Data-Model/count/#linkml-source","title":"LinkML Source","text":"
    name: count\ndescription: count of documents\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: count\ndomain_of:\n- FacetValue\nrange: integer\n
    "},{"location":"Data-Model/counterpart_category/","title":"Slot: counterpart_category","text":"
    The category of the counterpart entity in a given association,  eg. the category of the entity that is not the subject
     
    URI: https://w3id.org/monarch/monarch-py/:counterpart_category
    "},{"location":"Data-Model/counterpart_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CategoryGroupedAssociationResults no"},{"location":"Data-Model/counterpart_category/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/counterpart_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/counterpart_category/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/counterpart_category/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:counterpart_category native https://w3id.org/monarch/monarch-py/:counterpart_category"},{"location":"Data-Model/counterpart_category/#linkml-source","title":"LinkML Source","text":"
    name: counterpart_category\ndescription: The category of the counterpart entity in a given association,  eg. the\n  category of the entity that is not the subject\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: counterpart_category\ndomain_of:\n- CategoryGroupedAssociationResults\nrange: string\n
    "},{"location":"Data-Model/deprecated/","title":"Slot: deprecated","text":"
    A boolean flag indicating that an entity is no longer considered current or valid.
     
    URI: https://w3id.org/monarch/monarch-py/:deprecated
    "},{"location":"Data-Model/deprecated/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/deprecated/#properties","title":"Properties","text":"
       
    • Range: Boolean
      •  
    "},{"location":"Data-Model/deprecated/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/deprecated/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/deprecated/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:deprecated native https://w3id.org/monarch/monarch-py/:deprecated exact oboInOwl:ObsoleteClass"},{"location":"Data-Model/deprecated/#linkml-source","title":"LinkML Source","text":"
    name: deprecated\ndescription: A boolean flag indicating that an entity is no longer considered current\n  or valid.\nfrom_schema: https://w3id.org/monarch/monarch-py\nexact_mappings:\n- oboInOwl:ObsoleteClass\nrank: 1000\nalias: deprecated\ndomain_of:\n- Entity\nrange: boolean\n
    "},{"location":"Data-Model/description/","title":"Slot: description","text":"
    URI: https://w3id.org/monarch/monarch-py/:description
    "},{"location":"Data-Model/description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/description/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/description/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/description/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/description/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:description native https://w3id.org/monarch/monarch-py/:description"},{"location":"Data-Model/description/#linkml-source","title":"LinkML Source","text":"
    name: description\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: description\ndomain_of:\n- Entity\nrange: string\n
    "},{"location":"Data-Model/dice_similarity/","title":"Slot: dice_similarity","text":"
    URI: https://w3id.org/monarch/monarch-py/:dice_similarity
    "},{"location":"Data-Model/dice_similarity/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • dice_similarity
        •  
       
      •  
    "},{"location":"Data-Model/dice_similarity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/dice_similarity/#properties","title":"Properties","text":"
       
    • Range: ZeroToOne
      •  
    "},{"location":"Data-Model/dice_similarity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/dice_similarity/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/dice_similarity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:dice_similarity native https://w3id.org/monarch/monarch-py/:dice_similarity"},{"location":"Data-Model/dice_similarity/#linkml-source","title":"LinkML Source","text":"
    name: dice_similarity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: dice_similarity\ndomain_of:\n- TermPairwiseSimilarity\nrange: ZeroToOne\n
    "},{"location":"Data-Model/direction/","title":"Slot: direction","text":"
    The directionality of the association relative to a given entity for an association_count. If the entity is the subject or in the subject closure, the direction is forwards, if it is the object or in the object closure, the direction is backwards.
     
    URI: https://w3id.org/monarch/monarch-py/:direction
    "},{"location":"Data-Model/direction/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/direction/#properties","title":"Properties","text":"
       
    •  
      Range: AssociationDirectionEnum
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/direction/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/direction/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/direction/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:direction native https://w3id.org/monarch/monarch-py/:direction"},{"location":"Data-Model/direction/#linkml-source","title":"LinkML Source","text":"
    name: direction\ndescription: The directionality of the association relative to a given entity for\n  an association_count. If the entity is the subject or in the subject closure, the\n  direction is forwards, if it is the object or in the object closure, the direction\n  is backwards.\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: direction\ndomain_of:\n- DirectionalAssociation\nrange: AssociationDirectionEnum\nrequired: true\n
    "},{"location":"Data-Model/disease_context_qualifier/","title":"Slot: disease_context_qualifier","text":"
    A context qualifier representing a disease or condition in which a relationship expressed in an association took place.
     
    URI: https://w3id.org/monarch/monarch-py/:disease_context_qualifier
    "},{"location":"Data-Model/disease_context_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/disease_context_qualifier/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/disease_context_qualifier/#examples","title":"Examples","text":"Value MONDO:0004979 MONDO:0005148"},{"location":"Data-Model/disease_context_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/disease_context_qualifier/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/disease_context_qualifier/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:disease_context_qualifier native https://w3id.org/monarch/monarch-py/:disease_context_qualifier"},{"location":"Data-Model/disease_context_qualifier/#linkml-source","title":"LinkML Source","text":"
    name: disease_context_qualifier\ndescription: A context qualifier representing a disease or condition in which a relationship\n  expressed in an association took place.\nexamples:\n- value: MONDO:0004979\n- value: MONDO:0005148\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: disease_context_qualifier\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/disease_context_qualifier_category/","title":"Slot: disease_context_qualifier_category","text":"
    The category of the disease_context_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:disease_context_qualifier_category
    "},{"location":"Data-Model/disease_context_qualifier_category/#inheritance","title":"Inheritance","text":"
       
    • category
         
      • disease_context_qualifier_category
        •  
       
      •  
    "},{"location":"Data-Model/disease_context_qualifier_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/disease_context_qualifier_category/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/disease_context_qualifier_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/disease_context_qualifier_category/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/disease_context_qualifier_category/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:disease_context_qualifier_category native https://w3id.org/monarch/monarch-py/:disease_context_qualifier_category"},{"location":"Data-Model/disease_context_qualifier_category/#linkml-source","title":"LinkML Source","text":"
    name: disease_context_qualifier_category\ndescription: The category of the disease_context_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: disease_context_qualifier_category\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/disease_context_qualifier_closure/","title":"Slot: disease_context_qualifier_closure","text":"
    Field containing disease_context_qualifier id and the ids of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:disease_context_qualifier_closure
    "},{"location":"Data-Model/disease_context_qualifier_closure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/disease_context_qualifier_closure/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/disease_context_qualifier_closure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/disease_context_qualifier_closure/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/disease_context_qualifier_closure/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:disease_context_qualifier_closure native https://w3id.org/monarch/monarch-py/:disease_context_qualifier_closure"},{"location":"Data-Model/disease_context_qualifier_closure/#linkml-source","title":"LinkML Source","text":"
    name: disease_context_qualifier_closure\ndescription: Field containing disease_context_qualifier id and the ids of all of it's\n  ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: disease_context_qualifier_closure\ndomain_of:\n- Association\nrange: string\nmultivalued: true\n
    "},{"location":"Data-Model/disease_context_qualifier_closure_label/","title":"Slot: disease_context_qualifier_closure_label","text":"
    Field containing disease_context_qualifier name and the names of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:disease_context_qualifier_closure_label
    "},{"location":"Data-Model/disease_context_qualifier_closure_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/disease_context_qualifier_closure_label/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/disease_context_qualifier_closure_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/disease_context_qualifier_closure_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/disease_context_qualifier_closure_label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:disease_context_qualifier_closure_label native https://w3id.org/monarch/monarch-py/:disease_context_qualifier_closure_label"},{"location":"Data-Model/disease_context_qualifier_closure_label/#linkml-source","title":"LinkML Source","text":"
    name: disease_context_qualifier_closure_label\ndescription: Field containing disease_context_qualifier name and the names of all\n  of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: disease_context_qualifier_closure_label\ndomain_of:\n- Association\nrange: string\nmultivalued: true\n
    "},{"location":"Data-Model/disease_context_qualifier_label/","title":"Slot: disease_context_qualifier_label","text":"
    The name of the disease_context_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:disease_context_qualifier_label
    "},{"location":"Data-Model/disease_context_qualifier_label/#inheritance","title":"Inheritance","text":"
       
    • name
         
      • disease_context_qualifier_label
        •  
       
      •  
    "},{"location":"Data-Model/disease_context_qualifier_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/disease_context_qualifier_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/disease_context_qualifier_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/disease_context_qualifier_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/disease_context_qualifier_label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:disease_context_qualifier_label native https://w3id.org/monarch/monarch-py/:disease_context_qualifier_label"},{"location":"Data-Model/disease_context_qualifier_label/#linkml-source","title":"LinkML Source","text":"
    name: disease_context_qualifier_label\ndescription: The name of the disease_context_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: disease_context_qualifier_label\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/disease_context_qualifier_namespace/","title":"Slot: disease_context_qualifier_namespace","text":"
    The namespace/prefix of the disease_context_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:disease_context_qualifier_namespace
    "},{"location":"Data-Model/disease_context_qualifier_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/disease_context_qualifier_namespace/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/disease_context_qualifier_namespace/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/disease_context_qualifier_namespace/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/disease_context_qualifier_namespace/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:disease_context_qualifier_namespace native https://w3id.org/monarch/monarch-py/:disease_context_qualifier_namespace"},{"location":"Data-Model/disease_context_qualifier_namespace/#linkml-source","title":"LinkML Source","text":"
    name: disease_context_qualifier_namespace\ndescription: The namespace/prefix of the disease_context_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: disease_context_qualifier_namespace\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/end/","title":"Slot: end","text":"
    end position of the annotation
     
    URI: https://w3id.org/monarch/monarch-py/:end
    "},{"location":"Data-Model/end/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextAnnotationResult no"},{"location":"Data-Model/end/#properties","title":"Properties","text":"
       
    • Range: Integer
      •  
    "},{"location":"Data-Model/end/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/end/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/end/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:end native https://w3id.org/monarch/monarch-py/:end"},{"location":"Data-Model/end/#linkml-source","title":"LinkML Source","text":"
    name: end\ndescription: end position of the annotation\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: end\ndomain_of:\n- TextAnnotationResult\nrange: integer\n
    "},{"location":"Data-Model/evidence_count/","title":"Slot: evidence_count","text":"
    count of supporting documents, evidence codes, and sources supplying evidence
     
    URI: https://w3id.org/monarch/monarch-py/:evidence_count
    "},{"location":"Data-Model/evidence_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/evidence_count/#properties","title":"Properties","text":"
       
    • Range: Integer
      •  
    "},{"location":"Data-Model/evidence_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/evidence_count/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/evidence_count/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:evidence_count native https://w3id.org/monarch/monarch-py/:evidence_count"},{"location":"Data-Model/evidence_count/#linkml-source","title":"LinkML Source","text":"
    name: evidence_count\ndescription: count of supporting documents, evidence codes, and sources supplying\n  evidence\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: evidence_count\ndomain_of:\n- Association\nrange: integer\n
    "},{"location":"Data-Model/external_links/","title":"Slot: external_links","text":"
    ExpandedCurie with id and url for xrefs
     
    URI: https://w3id.org/monarch/monarch-py/:external_links
    "},{"location":"Data-Model/external_links/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/external_links/#properties","title":"Properties","text":"
       
    •  
      Range: ExpandedCurie
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/external_links/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/external_links/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/external_links/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:external_links native https://w3id.org/monarch/monarch-py/:external_links"},{"location":"Data-Model/external_links/#linkml-source","title":"LinkML Source","text":"
    name: external_links\ndescription: ExpandedCurie with id and url for xrefs\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: external_links\ndomain_of:\n- Node\nrange: ExpandedCurie\nmultivalued: true\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/facet_fields/","title":"Slot: facet_fields","text":"
    Collection of facet field responses with the field values and counts
     
    URI: https://w3id.org/monarch/monarch-py/:facet_fields
    "},{"location":"Data-Model/facet_fields/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResults no"},{"location":"Data-Model/facet_fields/#properties","title":"Properties","text":"
       
    •  
      Range: FacetField
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/facet_fields/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/facet_fields/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/facet_fields/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:facet_fields native https://w3id.org/monarch/monarch-py/:facet_fields"},{"location":"Data-Model/facet_fields/#linkml-source","title":"LinkML Source","text":"
    name: facet_fields\ndescription: Collection of facet field responses with the field values and counts\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: facet_fields\ndomain_of:\n- SearchResults\nrange: FacetField\nmultivalued: true\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/facet_queries/","title":"Slot: facet_queries","text":"
    Collection of facet query responses with the query string values and counts
     
    URI: https://w3id.org/monarch/monarch-py/:facet_queries
    "},{"location":"Data-Model/facet_queries/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResults no"},{"location":"Data-Model/facet_queries/#properties","title":"Properties","text":"
       
    •  
      Range: FacetValue
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/facet_queries/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/facet_queries/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/facet_queries/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:facet_queries native https://w3id.org/monarch/monarch-py/:facet_queries"},{"location":"Data-Model/facet_queries/#linkml-source","title":"LinkML Source","text":"
    name: facet_queries\ndescription: Collection of facet query responses with the query string values and\n  counts\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: facet_queries\ndomain_of:\n- SearchResults\nrange: FacetValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/facet_values/","title":"Slot: facet_values","text":"
    Collection of FacetValue label/value instances belonging to a FacetField
     
    URI: https://w3id.org/monarch/monarch-py/:facet_values
    "},{"location":"Data-Model/facet_values/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FacetField no"},{"location":"Data-Model/facet_values/#properties","title":"Properties","text":"
       
    •  
      Range: FacetValue
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/facet_values/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/facet_values/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/facet_values/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:facet_values native https://w3id.org/monarch/monarch-py/:facet_values"},{"location":"Data-Model/facet_values/#linkml-source","title":"LinkML Source","text":"
    name: facet_values\ndescription: Collection of FacetValue label/value instances belonging to a FacetField\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: facet_values\ndomain_of:\n- FacetField\nrange: FacetValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/frequency_qualifier/","title":"Slot: frequency_qualifier","text":"
    URI: https://w3id.org/monarch/monarch-py/:frequency_qualifier
    "},{"location":"Data-Model/frequency_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/frequency_qualifier/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/frequency_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/frequency_qualifier/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/frequency_qualifier/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:frequency_qualifier native https://w3id.org/monarch/monarch-py/:frequency_qualifier"},{"location":"Data-Model/frequency_qualifier/#linkml-source","title":"LinkML Source","text":"
    name: frequency_qualifier\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: frequency_qualifier\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/frequency_qualifier_category/","title":"Slot: frequency_qualifier_category","text":"
    The category of the frequency_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:frequency_qualifier_category
    "},{"location":"Data-Model/frequency_qualifier_category/#inheritance","title":"Inheritance","text":"
       
    • category
         
      • frequency_qualifier_category
        •  
       
      •  
    "},{"location":"Data-Model/frequency_qualifier_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/frequency_qualifier_category/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/frequency_qualifier_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/frequency_qualifier_category/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/frequency_qualifier_category/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:frequency_qualifier_category native https://w3id.org/monarch/monarch-py/:frequency_qualifier_category"},{"location":"Data-Model/frequency_qualifier_category/#linkml-source","title":"LinkML Source","text":"
    name: frequency_qualifier_category\ndescription: The category of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: frequency_qualifier_category\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/frequency_qualifier_closure/","title":"Slot: frequency_qualifier_closure","text":"
    Field containing frequency_qualifier id and the ids of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:frequency_qualifier_closure
    "},{"location":"Data-Model/frequency_qualifier_closure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/frequency_qualifier_closure/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/frequency_qualifier_closure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/frequency_qualifier_closure/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/frequency_qualifier_closure/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:frequency_qualifier_closure native https://w3id.org/monarch/monarch-py/:frequency_qualifier_closure"},{"location":"Data-Model/frequency_qualifier_closure/#linkml-source","title":"LinkML Source","text":"
    name: frequency_qualifier_closure\ndescription: Field containing frequency_qualifier id and the ids of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: frequency_qualifier_closure\ndomain_of:\n- Association\nrange: string\nmultivalued: true\n
    "},{"location":"Data-Model/frequency_qualifier_closure_label/","title":"Slot: frequency_qualifier_closure_label","text":"
    Field containing frequency_qualifier name and the names of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:frequency_qualifier_closure_label
    "},{"location":"Data-Model/frequency_qualifier_closure_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/frequency_qualifier_closure_label/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/frequency_qualifier_closure_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/frequency_qualifier_closure_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/frequency_qualifier_closure_label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:frequency_qualifier_closure_label native https://w3id.org/monarch/monarch-py/:frequency_qualifier_closure_label"},{"location":"Data-Model/frequency_qualifier_closure_label/#linkml-source","title":"LinkML Source","text":"
    name: frequency_qualifier_closure_label\ndescription: Field containing frequency_qualifier name and the names of all of it's\n  ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: frequency_qualifier_closure_label\ndomain_of:\n- Association\nrange: string\nmultivalued: true\n
    "},{"location":"Data-Model/frequency_qualifier_label/","title":"Slot: frequency_qualifier_label","text":"
    The name of the frequency_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:frequency_qualifier_label
    "},{"location":"Data-Model/frequency_qualifier_label/#inheritance","title":"Inheritance","text":"
       
    • name
         
      • frequency_qualifier_label
        •  
       
      •  
    "},{"location":"Data-Model/frequency_qualifier_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/frequency_qualifier_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/frequency_qualifier_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/frequency_qualifier_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/frequency_qualifier_label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:frequency_qualifier_label native https://w3id.org/monarch/monarch-py/:frequency_qualifier_label"},{"location":"Data-Model/frequency_qualifier_label/#linkml-source","title":"LinkML Source","text":"
    name: frequency_qualifier_label\ndescription: The name of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: frequency_qualifier_label\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/frequency_qualifier_namespace/","title":"Slot: frequency_qualifier_namespace","text":"
    The namespace/prefix of the frequency_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:frequency_qualifier_namespace
    "},{"location":"Data-Model/frequency_qualifier_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/frequency_qualifier_namespace/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/frequency_qualifier_namespace/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/frequency_qualifier_namespace/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/frequency_qualifier_namespace/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:frequency_qualifier_namespace native https://w3id.org/monarch/monarch-py/:frequency_qualifier_namespace"},{"location":"Data-Model/frequency_qualifier_namespace/#linkml-source","title":"LinkML Source","text":"
    name: frequency_qualifier_namespace\ndescription: The namespace/prefix of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: frequency_qualifier_namespace\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/full_name/","title":"Slot: full_name","text":"
    The long form name of an entity
     
    URI: https://w3id.org/monarch/monarch-py/:full_name
    "},{"location":"Data-Model/full_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/full_name/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/full_name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/full_name/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/full_name/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:full_name native https://w3id.org/monarch/monarch-py/:full_name"},{"location":"Data-Model/full_name/#linkml-source","title":"LinkML Source","text":"
    name: full_name\ndescription: The long form name of an entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: full_name\ndomain_of:\n- Entity\nrange: string\n
    "},{"location":"Data-Model/graph_stats/","title":"Slot: graph_stats","text":"
    URI: https://w3id.org/monarch/monarch-py/:graph_stats
    "},{"location":"Data-Model/graph_stats/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/graph_stats/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/graph_stats/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/graph_stats/#valid-id-prefixes","title":"Valid ID Prefixes","text":"
    Instances of this class should have identifiers with one of the following prefixes:
     
       
    • string
      •  
    "},{"location":"Data-Model/graph_stats/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/graph_stats/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:graph_stats native https://w3id.org/monarch/monarch-py/:graph_stats"},{"location":"Data-Model/graph_stats/#linkml-source","title":"LinkML Source","text":"
    name: graph_stats\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: graph_stats\ndomain_of:\n- Release\nrange: string\n
    "},{"location":"Data-Model/grouping_key/","title":"Slot: grouping_key","text":"
    A concatenation of fields used to group associations with the same essential/defining properties
     
    URI: https://w3id.org/monarch/monarch-py/:grouping_key
    "},{"location":"Data-Model/grouping_key/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/grouping_key/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/grouping_key/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/grouping_key/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/grouping_key/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:grouping_key native https://w3id.org/monarch/monarch-py/:grouping_key"},{"location":"Data-Model/grouping_key/#linkml-source","title":"LinkML Source","text":"
    name: grouping_key\ndescription: A concatenation of fields used to group associations with the same essential/defining\n  properties\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: grouping_key\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/has_count/","title":"Slot: has_count","text":"
    count of out of has_total representing a frequency
     
    URI: https://w3id.org/monarch/monarch-py/:has_count
    "},{"location":"Data-Model/has_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/has_count/#properties","title":"Properties","text":"
       
    • Range: Integer
      •  
    "},{"location":"Data-Model/has_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/has_count/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/has_count/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:has_count native https://w3id.org/monarch/monarch-py/:has_count"},{"location":"Data-Model/has_count/#linkml-source","title":"LinkML Source","text":"
    name: has_count\ndescription: count of out of has_total representing a frequency\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_count\ndomain_of:\n- Association\nrange: integer\n
    "},{"location":"Data-Model/has_evidence/","title":"Slot: has_evidence","text":"
    URI: https://w3id.org/monarch/monarch-py/:has_evidence
    "},{"location":"Data-Model/has_evidence/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/has_evidence/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/has_evidence/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/has_evidence/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/has_evidence/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:has_evidence native https://w3id.org/monarch/monarch-py/:has_evidence"},{"location":"Data-Model/has_evidence/#linkml-source","title":"LinkML Source","text":"
    name: has_evidence\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_evidence\ndomain_of:\n- Association\nrange: string\nmultivalued: true\n
    "},{"location":"Data-Model/has_evidence_links/","title":"Slot: has_evidence_links","text":"
    List of ExpandedCuries with id and url for evidence
     
    URI: https://w3id.org/monarch/monarch-py/:has_evidence_links
    "},{"location":"Data-Model/has_evidence_links/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/has_evidence_links/#properties","title":"Properties","text":"
       
    •  
      Range: ExpandedCurie
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/has_evidence_links/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/has_evidence_links/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/has_evidence_links/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:has_evidence_links native https://w3id.org/monarch/monarch-py/:has_evidence_links"},{"location":"Data-Model/has_evidence_links/#linkml-source","title":"LinkML Source","text":"
    name: has_evidence_links\ndescription: List of ExpandedCuries with id and url for evidence\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_evidence_links\ndomain_of:\n- Association\nrange: ExpandedCurie\nmultivalued: true\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/has_percentage/","title":"Slot: has_percentage","text":"
    percentage, which may be calculated from has_count and has_total, as 100 * quotient or provided directly, rounded to the integer level
     
    URI: https://w3id.org/monarch/monarch-py/:has_percentage
    "},{"location":"Data-Model/has_percentage/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/has_percentage/#properties","title":"Properties","text":"
       
    • Range: Float
      •  
    "},{"location":"Data-Model/has_percentage/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/has_percentage/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/has_percentage/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:has_percentage native https://w3id.org/monarch/monarch-py/:has_percentage"},{"location":"Data-Model/has_percentage/#linkml-source","title":"LinkML Source","text":"
    name: has_percentage\ndescription: percentage, which may be calculated from has_count and has_total, as\n  100 * quotient or provided directly, rounded to the integer level\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_percentage\ndomain_of:\n- Association\nrange: float\n
    "},{"location":"Data-Model/has_phenotype/","title":"Slot: has_phenotype","text":"
    A list of phenotype identifiers that are known to be associated with this entity
     
    URI: https://w3id.org/monarch/monarch-py/:has_phenotype
    "},{"location":"Data-Model/has_phenotype/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/has_phenotype/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/has_phenotype/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/has_phenotype/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/has_phenotype/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:has_phenotype native https://w3id.org/monarch/monarch-py/:has_phenotype"},{"location":"Data-Model/has_phenotype/#linkml-source","title":"LinkML Source","text":"
    name: has_phenotype\ndescription: A list of phenotype identifiers that are known to be associated with\n  this entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_phenotype\ndomain_of:\n- Entity\nrange: string\nmultivalued: true\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/has_phenotype_closure/","title":"Slot: has_phenotype_closure","text":"
    A list of phenotype identifiers that are known to be associated with this entity expanded to include all ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:has_phenotype_closure
    "},{"location":"Data-Model/has_phenotype_closure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/has_phenotype_closure/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/has_phenotype_closure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/has_phenotype_closure/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/has_phenotype_closure/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:has_phenotype_closure native https://w3id.org/monarch/monarch-py/:has_phenotype_closure"},{"location":"Data-Model/has_phenotype_closure/#linkml-source","title":"LinkML Source","text":"
    name: has_phenotype_closure\ndescription: A list of phenotype identifiers that are known to be associated with\n  this entity expanded to include all ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_phenotype_closure\ndomain_of:\n- Entity\nrange: string\nmultivalued: true\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/has_phenotype_closure_label/","title":"Slot: has_phenotype_closure_label","text":"
    A list of phenotype labels that are known to be associated with this entity expanded to include all ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:has_phenotype_closure_label
    "},{"location":"Data-Model/has_phenotype_closure_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/has_phenotype_closure_label/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/has_phenotype_closure_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/has_phenotype_closure_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/has_phenotype_closure_label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:has_phenotype_closure_label native https://w3id.org/monarch/monarch-py/:has_phenotype_closure_label"},{"location":"Data-Model/has_phenotype_closure_label/#linkml-source","title":"LinkML Source","text":"
    name: has_phenotype_closure_label\ndescription: A list of phenotype labels that are known to be associated with this\n  entity expanded to include all ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_phenotype_closure_label\ndomain_of:\n- Entity\nrange: string\nmultivalued: true\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/has_phenotype_count/","title":"Slot: has_phenotype_count","text":"
    A count of the number of phenotypes that are known to be associated with this entity
     
    URI: https://w3id.org/monarch/monarch-py/:has_phenotype_count
    "},{"location":"Data-Model/has_phenotype_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/has_phenotype_count/#properties","title":"Properties","text":"
       
    • Range: Integer
      •  
    "},{"location":"Data-Model/has_phenotype_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/has_phenotype_count/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/has_phenotype_count/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:has_phenotype_count native https://w3id.org/monarch/monarch-py/:has_phenotype_count"},{"location":"Data-Model/has_phenotype_count/#linkml-source","title":"LinkML Source","text":"
    name: has_phenotype_count\ndescription: A count of the number of phenotypes that are known to be associated with\n  this entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_phenotype_count\ndomain_of:\n- Entity\nrange: integer\n
    "},{"location":"Data-Model/has_phenotype_label/","title":"Slot: has_phenotype_label","text":"
    A list of phenotype labels that are known to be associated with this entity
     
    URI: https://w3id.org/monarch/monarch-py/:has_phenotype_label
    "},{"location":"Data-Model/has_phenotype_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/has_phenotype_label/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/has_phenotype_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/has_phenotype_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/has_phenotype_label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:has_phenotype_label native https://w3id.org/monarch/monarch-py/:has_phenotype_label"},{"location":"Data-Model/has_phenotype_label/#linkml-source","title":"LinkML Source","text":"
    name: has_phenotype_label\ndescription: A list of phenotype labels that are known to be associated with this\n  entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_phenotype_label\ndomain_of:\n- Entity\nrange: string\nmultivalued: true\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/has_quotient/","title":"Slot: has_quotient","text":"
    quotient, which should be 1/100 of has_percentage
     
    URI: https://w3id.org/monarch/monarch-py/:has_quotient
    "},{"location":"Data-Model/has_quotient/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/has_quotient/#properties","title":"Properties","text":"
       
    • Range: Float
      •  
    "},{"location":"Data-Model/has_quotient/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/has_quotient/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/has_quotient/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:has_quotient native https://w3id.org/monarch/monarch-py/:has_quotient"},{"location":"Data-Model/has_quotient/#linkml-source","title":"LinkML Source","text":"
    name: has_quotient\ndescription: quotient, which should be 1/100 of has_percentage\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_quotient\ndomain_of:\n- Association\nrange: float\n
    "},{"location":"Data-Model/has_total/","title":"Slot: has_total","text":"
    total, devided by has_count, representing a frequency
     
    URI: https://w3id.org/monarch/monarch-py/:has_total
    "},{"location":"Data-Model/has_total/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/has_total/#properties","title":"Properties","text":"
       
    • Range: Integer
      •  
    "},{"location":"Data-Model/has_total/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/has_total/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/has_total/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:has_total native https://w3id.org/monarch/monarch-py/:has_total"},{"location":"Data-Model/has_total/#linkml-source","title":"LinkML Source","text":"
    name: has_total\ndescription: total, devided by has_count, representing a frequency\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_total\ndomain_of:\n- Association\nrange: integer\n
    "},{"location":"Data-Model/highlight/","title":"Slot: highlight","text":"
    matching text snippet containing html tags
     
    URI: https://w3id.org/monarch/monarch-py/:highlight
    "},{"location":"Data-Model/highlight/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no"},{"location":"Data-Model/highlight/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/highlight/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/highlight/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/highlight/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:highlight native https://w3id.org/monarch/monarch-py/:highlight"},{"location":"Data-Model/highlight/#linkml-source","title":"LinkML Source","text":"
    name: highlight\ndescription: matching text snippet containing html tags\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: highlight\ndomain_of:\n- SearchResult\nrange: string\n
    "},{"location":"Data-Model/id/","title":"Slot: id","text":"
    URI: https://w3id.org/monarch/monarch-py/:id
    "},{"location":"Data-Model/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no HistoPheno no Association no Entity Represents an Entity in the Monarch KG data model no Node UI container class extending Entity with additional information no TermInfo no ExpandedCurie A curie bundled along with its expanded url no Mapping A minimal class to hold a SSSOM mapping no HistoBin no MultiEntityAssociationResults no SearchResult no"},{"location":"Data-Model/id/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/id/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/id/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:id native https://w3id.org/monarch/monarch-py/:id"},{"location":"Data-Model/id/#linkml-source","title":"LinkML Source","text":"
    name: id\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nidentifier: true\nalias: id\ndomain_of:\n- Association\n- ExpandedCurie\n- Entity\n- HistoPheno\n- HistoBin\n- Mapping\n- MultiEntityAssociationResults\n- TermInfo\nrange: string\nrequired: true\n
    "},{"location":"Data-Model/in_taxon/","title":"Slot: in_taxon","text":"
    The biolink taxon that the entity is in the closure of.
     
    URI: https://w3id.org/monarch/monarch-py/:in_taxon
    "},{"location":"Data-Model/in_taxon/#inheritance","title":"Inheritance","text":"
       
    • in_taxon
         
      • subject_taxon
        •  
      • object_taxon
        •  
       
      •  
    "},{"location":"Data-Model/in_taxon/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/in_taxon/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/in_taxon/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/in_taxon/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/in_taxon/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:in_taxon native https://w3id.org/monarch/monarch-py/:in_taxon"},{"location":"Data-Model/in_taxon/#linkml-source","title":"LinkML Source","text":"
    name: in_taxon\ndescription: The biolink taxon that the entity is in the closure of.\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: in_taxon\ndomain_of:\n- Entity\n- Node\nrange: string\n
    "},{"location":"Data-Model/in_taxon_label/","title":"Slot: in_taxon_label","text":"
    The label of the biolink taxon that the entity is in the closure of.
     
    URI: https://w3id.org/monarch/monarch-py/:in_taxon_label
    "},{"location":"Data-Model/in_taxon_label/#inheritance","title":"Inheritance","text":"
       
    • in_taxon_label
         
      • subject_taxon_label
        •  
      • object_taxon_label
        •  
       
      •  
    "},{"location":"Data-Model/in_taxon_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/in_taxon_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/in_taxon_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/in_taxon_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/in_taxon_label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:in_taxon_label native https://w3id.org/monarch/monarch-py/:in_taxon_label"},{"location":"Data-Model/in_taxon_label/#linkml-source","title":"LinkML Source","text":"
    name: in_taxon_label\ndescription: The label of the biolink taxon that the entity is in the closure of.\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: in_taxon_label\ndomain_of:\n- Entity\n- Node\nrange: string\n
    "},{"location":"Data-Model/information_content/","title":"Slot: information_content","text":"
    The IC is the negative log of the probability of the concept
     
       
    • NOTE: this is an abstract slot and should not be populated directly
      •  
     
    URI: https://w3id.org/monarch/monarch-py/:information_content
    "},{"location":"Data-Model/information_content/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • information_content
           
        • subject_information_content
          •  
        • object_information_content
          •  
        • ancestor_information_content
          •  
         
        •  
       
      •  
    "},{"location":"Data-Model/information_content/#properties","title":"Properties","text":"
       
    • Range: NegativeLogValue
      •  
    "},{"location":"Data-Model/information_content/#aliases","title":"Aliases","text":"
       
    • IC
      •  
    "},{"location":"Data-Model/information_content/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/information_content/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/information_content/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:information_content native https://w3id.org/monarch/monarch-py/:information_content"},{"location":"Data-Model/information_content/#linkml-source","title":"LinkML Source","text":"
    name: information_content\ndescription: The IC is the negative log of the probability of the concept\nfrom_schema: https://w3id.org/monarch/monarch-py\naliases:\n- IC\nrank: 1000\nis_a: score\nabstract: true\nalias: information_content\nrange: NegativeLogValue\n
    "},{"location":"Data-Model/inheritance/","title":"Slot: inheritance","text":"
    URI: https://w3id.org/monarch/monarch-py/:inheritance
    "},{"location":"Data-Model/inheritance/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/inheritance/#properties","title":"Properties","text":"
       
    • Range: Entity
      •  
    "},{"location":"Data-Model/inheritance/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/inheritance/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/inheritance/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:inheritance native https://w3id.org/monarch/monarch-py/:inheritance"},{"location":"Data-Model/inheritance/#linkml-source","title":"LinkML Source","text":"
    name: inheritance\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: inheritance\ndomain_of:\n- Node\nrange: Entity\ninlined: true\n
    "},{"location":"Data-Model/intersection_count/","title":"Slot: intersection_count","text":"
    URI: https://w3id.org/monarch/monarch-py/:intersection_count
    "},{"location":"Data-Model/intersection_count/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • intersection_count
        •  
       
      •  
    "},{"location":"Data-Model/intersection_count/#properties","title":"Properties","text":"
       
    • Range: ItemCount
      •  
    "},{"location":"Data-Model/intersection_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/intersection_count/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/intersection_count/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:intersection_count native https://w3id.org/monarch/monarch-py/:intersection_count"},{"location":"Data-Model/intersection_count/#linkml-source","title":"LinkML Source","text":"
    name: intersection_count\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: intersection_count\nrange: ItemCount\n
    "},{"location":"Data-Model/iri/","title":"Slot: iri","text":"
    URI: https://w3id.org/monarch/monarch-py/:iri
    "},{"location":"Data-Model/iri/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/iri/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/iri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/iri/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/iri/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:iri native https://w3id.org/monarch/monarch-py/:iri"},{"location":"Data-Model/iri/#linkml-source","title":"LinkML Source","text":"
    name: iri\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: iri\ndomain_of:\n- Entity\nrange: string\n
    "},{"location":"Data-Model/items/","title":"Slot: items","text":"
    A collection of items, with the type to be overriden by slot_usage
     
    URI: https://w3id.org/monarch/monarch-py/:items
    "},{"location":"Data-Model/items/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MappingResults SSSOM Mappings returned as a results collection yes CategoryGroupedAssociationResults yes HistoPheno yes EntityResults yes AssociationResults yes CompactAssociationResults yes AssociationCountList Container class for a list of association counts yes AssociationTableResults yes SearchResults yes"},{"location":"Data-Model/items/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/items/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/items/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/items/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:items native https://w3id.org/monarch/monarch-py/:items"},{"location":"Data-Model/items/#linkml-source","title":"LinkML Source","text":"
    name: items\ndescription: A collection of items, with the type to be overriden by slot_usage\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: items\ndomain_of:\n- AssociationCountList\n- AssociationResults\n- CompactAssociationResults\n- AssociationTableResults\n- CategoryGroupedAssociationResults\n- EntityResults\n- HistoPheno\n- MappingResults\n- SearchResults\nrange: string\nrequired: true\nmultivalued: true\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/jaccard_similarity/","title":"Slot: jaccard_similarity","text":"
    The number of concepts in the intersection divided by the number in the union
     
    URI: https://w3id.org/monarch/monarch-py/:jaccard_similarity
    "},{"location":"Data-Model/jaccard_similarity/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • jaccard_similarity
        •  
       
      •  
    "},{"location":"Data-Model/jaccard_similarity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/jaccard_similarity/#properties","title":"Properties","text":"
       
    • Range: ZeroToOne
      •  
    "},{"location":"Data-Model/jaccard_similarity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/jaccard_similarity/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/jaccard_similarity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:jaccard_similarity native https://w3id.org/monarch/monarch-py/:jaccard_similarity"},{"location":"Data-Model/jaccard_similarity/#linkml-source","title":"LinkML Source","text":"
    name: jaccard_similarity\ndescription: The number of concepts in the intersection divided by the number in the\n  union\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: jaccard_similarity\ndomain_of:\n- TermPairwiseSimilarity\nrange: ZeroToOne\n
    "},{"location":"Data-Model/kg/","title":"Slot: kg","text":"
    URI: https://w3id.org/monarch/monarch-py/:kg
    "},{"location":"Data-Model/kg/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/kg/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/kg/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/kg/#valid-id-prefixes","title":"Valid ID Prefixes","text":"
    Instances of this class should have identifiers with one of the following prefixes:
     
       
    • string
      •  
    "},{"location":"Data-Model/kg/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/kg/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:kg native https://w3id.org/monarch/monarch-py/:kg"},{"location":"Data-Model/kg/#linkml-source","title":"LinkML Source","text":"
    name: kg\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: kg\ndomain_of:\n- Release\nrange: string\n
    "},{"location":"Data-Model/knowledge_level/","title":"Slot: knowledge_level","text":"
    Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true.
     
    URI: biolink:knowledge_level
    "},{"location":"Data-Model/knowledge_level/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/knowledge_level/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/knowledge_level/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/knowledge_level/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/knowledge_level/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self biolink:knowledge_level native https://w3id.org/monarch/monarch-py/:knowledge_level"},{"location":"Data-Model/knowledge_level/#linkml-source","title":"LinkML Source","text":"
    name: knowledge_level\ndescription: Describes the level of knowledge expressed in a statement, based on the\n  reasoning or analysis methods used to generate the statement, or the scope or specificity\n  of what the statement expresses to be true.\nnotes:\n- The range in this schema is represented as a string, but is constrained  to values\n  from biolink:KnowledgeLevelEnum at ingest time\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nslot_uri: biolink:knowledge_level\nalias: knowledge_level\ndomain_of:\n- Association\nrange: string\nrequired: true\nmultivalued: false\n
    "},{"location":"Data-Model/knowledge_source/","title":"Slot: knowledge_source","text":"
    URI: https://w3id.org/monarch/monarch-py/:knowledge_source
    "},{"location":"Data-Model/knowledge_source/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/knowledge_source/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/knowledge_source/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/knowledge_source/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:knowledge_source native https://w3id.org/monarch/monarch-py/:knowledge_source"},{"location":"Data-Model/knowledge_source/#linkml-source","title":"LinkML Source","text":"
    name: knowledge_source\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: knowledge_source\nrange: string\nmultivalued: true\n
    "},{"location":"Data-Model/label/","title":"Slot: label","text":"
    URI: https://w3id.org/monarch/monarch-py/:label
    "},{"location":"Data-Model/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FacetValue no TermInfo no AssociationCount no FacetField no HistoBin no"},{"location":"Data-Model/label/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:label native https://w3id.org/monarch/monarch-py/:label"},{"location":"Data-Model/label/#linkml-source","title":"LinkML Source","text":"
    name: label\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: label\ndomain_of:\n- FacetValue\n- FacetField\n- TermInfo\nrange: string\nrequired: true\n
    "},{"location":"Data-Model/limit/","title":"Slot: limit","text":"
    number of items to return in a response
     
    URI: https://w3id.org/monarch/monarch-py/:limit
    "},{"location":"Data-Model/limit/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MappingResults SSSOM Mappings returned as a results collection no CategoryGroupedAssociationResults no Results no EntityResults no AssociationResults no CompactAssociationResults no AssociationTableResults no SearchResults no MultiEntityAssociationResults no"},{"location":"Data-Model/limit/#properties","title":"Properties","text":"
       
    •  
      Range: Integer
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/limit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/limit/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/limit/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:limit native https://w3id.org/monarch/monarch-py/:limit"},{"location":"Data-Model/limit/#linkml-source","title":"LinkML Source","text":"
    name: limit\ndescription: number of items to return in a response\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: limit\ndomain_of:\n- Results\nrange: integer\nrequired: true\n
    "},{"location":"Data-Model/mapping_justification/","title":"Slot: mapping_justification","text":"
    URI: https://w3id.org/monarch/monarch-py/:mapping_justification
    "},{"location":"Data-Model/mapping_justification/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Mapping A minimal class to hold a SSSOM mapping no"},{"location":"Data-Model/mapping_justification/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/mapping_justification/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/mapping_justification/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/mapping_justification/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:mapping_justification native https://w3id.org/monarch/monarch-py/:mapping_justification"},{"location":"Data-Model/mapping_justification/#linkml-source","title":"LinkML Source","text":"
    name: mapping_justification\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: mapping_justification\ndomain_of:\n- Mapping\nrange: string\n
    "},{"location":"Data-Model/mappings/","title":"Slot: mappings","text":"
    List of ExpandedCuries with id and url for mapped entities
     
    URI: https://w3id.org/monarch/monarch-py/:mappings
    "},{"location":"Data-Model/mappings/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/mappings/#properties","title":"Properties","text":"
       
    •  
      Range: ExpandedCurie
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/mappings/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/mappings/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/mappings/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:mappings native https://w3id.org/monarch/monarch-py/:mappings"},{"location":"Data-Model/mappings/#linkml-source","title":"LinkML Source","text":"
    name: mappings\ndescription: List of ExpandedCuries with id and url for mapped entities\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: mappings\ndomain_of:\n- Node\nrange: ExpandedCurie\nmultivalued: true\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/match_source/","title":"Slot: match_source","text":"
    URI: https://w3id.org/monarch/monarch-py/:match_source
    "},{"location":"Data-Model/match_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no"},{"location":"Data-Model/match_source/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/match_source/#comments","title":"Comments","text":"
       
    • note that the match_source is either the subject or the object
      •  
    "},{"location":"Data-Model/match_source/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/match_source/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/match_source/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:match_source native https://w3id.org/monarch/monarch-py/:match_source"},{"location":"Data-Model/match_source/#linkml-source","title":"LinkML Source","text":"
    name: match_source\ncomments:\n- note that the match_source is either the subject or the object\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nidentifier: true\nalias: match_source\nowner: BestMatch\ndomain_of:\n- BestMatch\nrange: string\nrequired: true\n
    "},{"location":"Data-Model/match_source_label/","title":"Slot: match_source_label","text":"
    URI: https://w3id.org/monarch/monarch-py/:match_source_label
    "},{"location":"Data-Model/match_source_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no"},{"location":"Data-Model/match_source_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/match_source_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/match_source_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/match_source_label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:match_source_label native https://w3id.org/monarch/monarch-py/:match_source_label"},{"location":"Data-Model/match_source_label/#linkml-source","title":"LinkML Source","text":"
    name: match_source_label\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: match_source_label\nowner: BestMatch\ndomain_of:\n- BestMatch\nrange: string\n
    "},{"location":"Data-Model/match_subsumer/","title":"Slot: match_subsumer","text":"
    URI: https://w3id.org/monarch/monarch-py/:match_subsumer
    "},{"location":"Data-Model/match_subsumer/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no"},{"location":"Data-Model/match_subsumer/#properties","title":"Properties","text":"
       
    • Range: Uriorcurie
      •  
    "},{"location":"Data-Model/match_subsumer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/match_subsumer/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/match_subsumer/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:match_subsumer native https://w3id.org/monarch/monarch-py/:match_subsumer"},{"location":"Data-Model/match_subsumer/#linkml-source","title":"LinkML Source","text":"
    name: match_subsumer\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: match_subsumer\nowner: BestMatch\ndomain_of:\n- BestMatch\nrange: uriorcurie\n
    "},{"location":"Data-Model/match_subsumer_label/","title":"Slot: match_subsumer_label","text":"
    URI: https://w3id.org/monarch/monarch-py/:match_subsumer_label
    "},{"location":"Data-Model/match_subsumer_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no"},{"location":"Data-Model/match_subsumer_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/match_subsumer_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/match_subsumer_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/match_subsumer_label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:match_subsumer_label native https://w3id.org/monarch/monarch-py/:match_subsumer_label"},{"location":"Data-Model/match_subsumer_label/#linkml-source","title":"LinkML Source","text":"
    name: match_subsumer_label\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: match_subsumer_label\nowner: BestMatch\ndomain_of:\n- BestMatch\nrange: string\n
    "},{"location":"Data-Model/match_target/","title":"Slot: match_target","text":"
    the entity matches
     
    URI: https://w3id.org/monarch/monarch-py/:match_target
    "},{"location":"Data-Model/match_target/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no"},{"location":"Data-Model/match_target/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/match_target/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/match_target/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/match_target/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:match_target native https://w3id.org/monarch/monarch-py/:match_target"},{"location":"Data-Model/match_target/#linkml-source","title":"LinkML Source","text":"
    name: match_target\ndescription: the entity matches\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: match_target\nowner: BestMatch\ndomain_of:\n- BestMatch\nrange: string\n
    "},{"location":"Data-Model/match_target_label/","title":"Slot: match_target_label","text":"
    URI: https://w3id.org/monarch/monarch-py/:match_target_label
    "},{"location":"Data-Model/match_target_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no"},{"location":"Data-Model/match_target_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/match_target_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/match_target_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/match_target_label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:match_target_label native https://w3id.org/monarch/monarch-py/:match_target_label"},{"location":"Data-Model/match_target_label/#linkml-source","title":"LinkML Source","text":"
    name: match_target_label\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: match_target_label\nowner: BestMatch\ndomain_of:\n- BestMatch\nrange: string\n
    "},{"location":"Data-Model/metadata/","title":"Slot: metadata","text":"
    URI: https://w3id.org/monarch/monarch-py/:metadata
    "},{"location":"Data-Model/metadata/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/metadata/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/metadata/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/metadata/#valid-id-prefixes","title":"Valid ID Prefixes","text":"
    Instances of this class should have identifiers with one of the following prefixes:
     
       
    • string
      •  
    "},{"location":"Data-Model/metadata/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/metadata/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:metadata native https://w3id.org/monarch/monarch-py/:metadata"},{"location":"Data-Model/metadata/#linkml-source","title":"LinkML Source","text":"
    name: metadata\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: metadata\ndomain_of:\n- Release\nrange: string\n
    "},{"location":"Data-Model/metric/","title":"Slot: metric","text":"
    URI: https://w3id.org/monarch/monarch-py/:metric
    "},{"location":"Data-Model/metric/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/metric/#properties","title":"Properties","text":"
       
    • Range: Uriorcurie
      •  
    "},{"location":"Data-Model/metric/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/metric/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/metric/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:metric native https://w3id.org/monarch/monarch-py/:metric"},{"location":"Data-Model/metric/#linkml-source","title":"LinkML Source","text":"
    name: metric\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: metric\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: uriorcurie\n
    "},{"location":"Data-Model/monarch-py/","title":"monarch-py","text":"
    Data models for the Monarch Initiative data access library
     
    URI: https://w3id.org/monarch/monarch-py
    "},{"location":"Data-Model/name/","title":"Slot: name","text":"
    URI: https://w3id.org/monarch/monarch-py/:name
    "},{"location":"Data-Model/name/#inheritance","title":"Inheritance","text":"
       
    • name
         
      • subject_label
        •  
      • object_label
        •  
      • qualifiers_label
        •  
      • qualifier_label
        •  
      • frequency_qualifier_label
        •  
      • onset_qualifier_label
        •  
      • sex_qualifier_label
        •  
      • stage_qualifier_label
        •  
      • disease_context_qualifier_label
        •  
       
      •  
    "},{"location":"Data-Model/name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MultiEntityAssociationResults no SearchResult yes Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/name/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/name/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/name/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:name native https://w3id.org/monarch/monarch-py/:name"},{"location":"Data-Model/name/#linkml-source","title":"LinkML Source","text":"
    name: name\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: name\ndomain_of:\n- Entity\n- MultiEntityAssociationResults\nrange: string\n
    "},{"location":"Data-Model/namespace/","title":"Slot: namespace","text":"
    The namespace/prefix portion of this entity's identifier
     
    URI: https://w3id.org/monarch/monarch-py/:namespace
    "},{"location":"Data-Model/namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/namespace/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/namespace/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/namespace/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/namespace/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:namespace native https://w3id.org/monarch/monarch-py/:namespace"},{"location":"Data-Model/namespace/#linkml-source","title":"LinkML Source","text":"
    name: namespace\ndescription: The namespace/prefix portion of this entity's identifier\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: namespace\ndomain_of:\n- Entity\nrange: string\n
    "},{"location":"Data-Model/negated/","title":"Slot: negated","text":"
    URI: https://w3id.org/monarch/monarch-py/:negated
    "},{"location":"Data-Model/negated/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no CompactAssociation no Association no"},{"location":"Data-Model/negated/#properties","title":"Properties","text":"
       
    • Range: Boolean
      •  
    "},{"location":"Data-Model/negated/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/negated/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/negated/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:negated native https://w3id.org/monarch/monarch-py/:negated"},{"location":"Data-Model/negated/#linkml-source","title":"LinkML Source","text":"
    name: negated\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: negated\ndomain_of:\n- Association\n- CompactAssociation\nrange: boolean\n
    "},{"location":"Data-Model/neo4j/","title":"Slot: neo4j","text":"
    URI: https://w3id.org/monarch/monarch-py/:neo4j
    "},{"location":"Data-Model/neo4j/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/neo4j/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/neo4j/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/neo4j/#valid-id-prefixes","title":"Valid ID Prefixes","text":"
    Instances of this class should have identifiers with one of the following prefixes:
     
       
    • string
      •  
    "},{"location":"Data-Model/neo4j/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/neo4j/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:neo4j native https://w3id.org/monarch/monarch-py/:neo4j"},{"location":"Data-Model/neo4j/#linkml-source","title":"LinkML Source","text":"
    name: neo4j\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: neo4j\ndomain_of:\n- Release\nrange: string\n
    "},{"location":"Data-Model/node_hierarchy/","title":"Slot: node_hierarchy","text":"
    URI: https://w3id.org/monarch/monarch-py/:node_hierarchy
    "},{"location":"Data-Model/node_hierarchy/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/node_hierarchy/#properties","title":"Properties","text":"
       
    • Range: NodeHierarchy
      •  
    "},{"location":"Data-Model/node_hierarchy/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/node_hierarchy/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/node_hierarchy/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:node_hierarchy native https://w3id.org/monarch/monarch-py/:node_hierarchy"},{"location":"Data-Model/node_hierarchy/#linkml-source","title":"LinkML Source","text":"
    name: node_hierarchy\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: node_hierarchy\ndomain_of:\n- Node\nrange: NodeHierarchy\ninlined: true\n
    "},{"location":"Data-Model/object/","title":"Slot: object","text":"
    URI: https://w3id.org/monarch/monarch-py/:object
    "},{"location":"Data-Model/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no CompactAssociation no Association no"},{"location":"Data-Model/object/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/object/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:object native https://w3id.org/monarch/monarch-py/:object"},{"location":"Data-Model/object/#linkml-source","title":"LinkML Source","text":"
    name: object\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: object\ndomain_of:\n- Association\n- CompactAssociation\nrange: string\nrequired: true\n
    "},{"location":"Data-Model/object_best_matches/","title":"Slot: object_best_matches","text":"
    URI: https://w3id.org/monarch/monarch-py/:object_best_matches
    "},{"location":"Data-Model/object_best_matches/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/object_best_matches/#properties","title":"Properties","text":"
       
    •  
      Range: BestMatch
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/object_best_matches/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object_best_matches/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/object_best_matches/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:object_best_matches native https://w3id.org/monarch/monarch-py/:object_best_matches"},{"location":"Data-Model/object_best_matches/#linkml-source","title":"LinkML Source","text":"
    name: object_best_matches\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: object_best_matches\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: BestMatch\nmultivalued: true\ninlined: true\n
    "},{"location":"Data-Model/object_category/","title":"Slot: object_category","text":"
    The category of the object entity
     
    URI: https://w3id.org/monarch/monarch-py/:object_category
    "},{"location":"Data-Model/object_category/#inheritance","title":"Inheritance","text":"
       
    • category
         
      • object_category
        •  
       
      •  
    "},{"location":"Data-Model/object_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/object_category/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/object_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object_category/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/object_category/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:object_category native https://w3id.org/monarch/monarch-py/:object_category"},{"location":"Data-Model/object_category/#linkml-source","title":"LinkML Source","text":"
    name: object_category\ndescription: The category of the object entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: object_category\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/object_closure/","title":"Slot: object_closure","text":"
    Field containing object id and the ids of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:object_closure
    "},{"location":"Data-Model/object_closure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/object_closure/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/object_closure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object_closure/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/object_closure/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:object_closure native https://w3id.org/monarch/monarch-py/:object_closure"},{"location":"Data-Model/object_closure/#linkml-source","title":"LinkML Source","text":"
    name: object_closure\ndescription: Field containing object id and the ids of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: object_closure\ndomain_of:\n- Association\nrange: string\nmultivalued: true\n
    "},{"location":"Data-Model/object_closure_label/","title":"Slot: object_closure_label","text":"
    Field containing object name and the names of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:object_closure_label
    "},{"location":"Data-Model/object_closure_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/object_closure_label/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/object_closure_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object_closure_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/object_closure_label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:object_closure_label native https://w3id.org/monarch/monarch-py/:object_closure_label"},{"location":"Data-Model/object_closure_label/#linkml-source","title":"LinkML Source","text":"
    name: object_closure_label\ndescription: Field containing object name and the names of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: object_closure_label\ndomain_of:\n- Association\nrange: string\nmultivalued: true\n
    "},{"location":"Data-Model/object_id/","title":"Slot: object_id","text":"
    URI: https://w3id.org/monarch/monarch-py/:object_id
    "},{"location":"Data-Model/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Mapping A minimal class to hold a SSSOM mapping no TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/object_id/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/object_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object_id/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/object_id/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:object_id native https://w3id.org/monarch/monarch-py/:object_id"},{"location":"Data-Model/object_id/#linkml-source","title":"LinkML Source","text":"
    name: object_id\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: object_id\ndomain_of:\n- Mapping\n- TermPairwiseSimilarity\nrange: string\nrequired: true\n
    "},{"location":"Data-Model/object_information_content/","title":"Slot: object_information_content","text":"
    The IC of the object
     
    URI: https://w3id.org/monarch/monarch-py/:object_information_content
    "},{"location":"Data-Model/object_information_content/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • information_content
           
        • object_information_content
          •  
         
        •  
       
      •  
    "},{"location":"Data-Model/object_information_content/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/object_information_content/#properties","title":"Properties","text":"
       
    • Range: NegativeLogValue
      •  
    "},{"location":"Data-Model/object_information_content/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object_information_content/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/object_information_content/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:object_information_content native https://w3id.org/monarch/monarch-py/:object_information_content"},{"location":"Data-Model/object_information_content/#linkml-source","title":"LinkML Source","text":"
    name: object_information_content\ndescription: The IC of the object\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: information_content\nalias: object_information_content\ndomain_of:\n- TermPairwiseSimilarity\nrange: NegativeLogValue\n
    "},{"location":"Data-Model/object_label/","title":"Slot: object_label","text":"
    The name of the object entity
     
    URI: https://w3id.org/monarch/monarch-py/:object_label
    "},{"location":"Data-Model/object_label/#inheritance","title":"Inheritance","text":"
       
    • name
         
      • object_label
        •  
       
      •  
    "},{"location":"Data-Model/object_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no Mapping A minimal class to hold a SSSOM mapping no AssociationTypeMapping A data class to hold the necessary information to produce association type co... yes CompactAssociation no"},{"location":"Data-Model/object_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/object_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/object_label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:object_label native https://w3id.org/monarch/monarch-py/:object_label"},{"location":"Data-Model/object_label/#linkml-source","title":"LinkML Source","text":"
    name: object_label\ndescription: The name of the object entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: object_label\ndomain_of:\n- Association\n- CompactAssociation\n- AssociationTypeMapping\n- Mapping\n- TermPairwiseSimilarity\nrange: string\n
    "},{"location":"Data-Model/object_namespace/","title":"Slot: object_namespace","text":"
    The namespace/prefix of the object entity
     
    URI: https://w3id.org/monarch/monarch-py/:object_namespace
    "},{"location":"Data-Model/object_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/object_namespace/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/object_namespace/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object_namespace/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/object_namespace/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:object_namespace native https://w3id.org/monarch/monarch-py/:object_namespace"},{"location":"Data-Model/object_namespace/#linkml-source","title":"LinkML Source","text":"
    name: object_namespace\ndescription: The namespace/prefix of the object entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: object_namespace\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/object_source/","title":"Slot: object_source","text":"
    the source for the second entity
     
    URI: sssom:object_source
    "},{"location":"Data-Model/object_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/object_source/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/object_source/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object_source/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/object_source/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sssom:object_source native https://w3id.org/monarch/monarch-py/:object_source"},{"location":"Data-Model/object_source/#linkml-source","title":"LinkML Source","text":"
    name: object_source\ndescription: the source for the second entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nslot_uri: sssom:object_source\nalias: object_source\ndomain_of:\n- TermPairwiseSimilarity\nrange: string\n
    "},{"location":"Data-Model/object_taxon/","title":"Slot: object_taxon","text":"
    URI: https://w3id.org/monarch/monarch-py/:object_taxon
    "},{"location":"Data-Model/object_taxon/#inheritance","title":"Inheritance","text":"
       
    • in_taxon
         
      • object_taxon
        •  
       
      •  
    "},{"location":"Data-Model/object_taxon/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/object_taxon/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/object_taxon/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object_taxon/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/object_taxon/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:object_taxon native https://w3id.org/monarch/monarch-py/:object_taxon"},{"location":"Data-Model/object_taxon/#linkml-source","title":"LinkML Source","text":"
    name: object_taxon\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: in_taxon\nalias: object_taxon\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/object_taxon_label/","title":"Slot: object_taxon_label","text":"
    URI: https://w3id.org/monarch/monarch-py/:object_taxon_label
    "},{"location":"Data-Model/object_taxon_label/#inheritance","title":"Inheritance","text":"
       
    • in_taxon_label
         
      • object_taxon_label
        •  
       
      •  
    "},{"location":"Data-Model/object_taxon_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/object_taxon_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/object_taxon_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object_taxon_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/object_taxon_label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:object_taxon_label native https://w3id.org/monarch/monarch-py/:object_taxon_label"},{"location":"Data-Model/object_taxon_label/#linkml-source","title":"LinkML Source","text":"
    name: object_taxon_label\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: in_taxon_label\nalias: object_taxon_label\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/object_termset/","title":"Slot: object_termset","text":"
    URI: https://w3id.org/monarch/monarch-py/:object_termset
    "},{"location":"Data-Model/object_termset/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/object_termset/#properties","title":"Properties","text":"
       
    •  
      Range: TermInfo
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/object_termset/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object_termset/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/object_termset/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:object_termset native https://w3id.org/monarch/monarch-py/:object_termset"},{"location":"Data-Model/object_termset/#linkml-source","title":"LinkML Source","text":"
    name: object_termset\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: object_termset\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: TermInfo\nmultivalued: true\ninlined: true\n
    "},{"location":"Data-Model/offset/","title":"Slot: offset","text":"
    offset into the total number of items
     
    URI: https://w3id.org/monarch/monarch-py/:offset
    "},{"location":"Data-Model/offset/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MappingResults SSSOM Mappings returned as a results collection no CategoryGroupedAssociationResults no Results no EntityResults no AssociationResults no CompactAssociationResults no AssociationTableResults no SearchResults no MultiEntityAssociationResults no"},{"location":"Data-Model/offset/#properties","title":"Properties","text":"
       
    •  
      Range: Integer
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/offset/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/offset/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/offset/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:offset native https://w3id.org/monarch/monarch-py/:offset"},{"location":"Data-Model/offset/#linkml-source","title":"LinkML Source","text":"
    name: offset\ndescription: offset into the total number of items\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: offset\ndomain_of:\n- Results\nrange: integer\nrequired: true\n
    "},{"location":"Data-Model/onset_qualifier/","title":"Slot: onset_qualifier","text":"
    URI: https://w3id.org/monarch/monarch-py/:onset_qualifier
    "},{"location":"Data-Model/onset_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/onset_qualifier/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/onset_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/onset_qualifier/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/onset_qualifier/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:onset_qualifier native https://w3id.org/monarch/monarch-py/:onset_qualifier"},{"location":"Data-Model/onset_qualifier/#linkml-source","title":"LinkML Source","text":"
    name: onset_qualifier\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: onset_qualifier\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/onset_qualifier_category/","title":"Slot: onset_qualifier_category","text":"
    The category of the onset_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:onset_qualifier_category
    "},{"location":"Data-Model/onset_qualifier_category/#inheritance","title":"Inheritance","text":"
       
    • category
         
      • onset_qualifier_category
        •  
       
      •  
    "},{"location":"Data-Model/onset_qualifier_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/onset_qualifier_category/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/onset_qualifier_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/onset_qualifier_category/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/onset_qualifier_category/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:onset_qualifier_category native https://w3id.org/monarch/monarch-py/:onset_qualifier_category"},{"location":"Data-Model/onset_qualifier_category/#linkml-source","title":"LinkML Source","text":"
    name: onset_qualifier_category\ndescription: The category of the onset_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: onset_qualifier_category\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/onset_qualifier_closure/","title":"Slot: onset_qualifier_closure","text":"
    Field containing onset_qualifier id and the ids of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:onset_qualifier_closure
    "},{"location":"Data-Model/onset_qualifier_closure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/onset_qualifier_closure/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/onset_qualifier_closure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/onset_qualifier_closure/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/onset_qualifier_closure/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:onset_qualifier_closure native https://w3id.org/monarch/monarch-py/:onset_qualifier_closure"},{"location":"Data-Model/onset_qualifier_closure/#linkml-source","title":"LinkML Source","text":"
    name: onset_qualifier_closure\ndescription: Field containing onset_qualifier id and the ids of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: onset_qualifier_closure\ndomain_of:\n- Association\nrange: string\nmultivalued: true\n
    "},{"location":"Data-Model/onset_qualifier_closure_label/","title":"Slot: onset_qualifier_closure_label","text":"
    Field containing onset_qualifier name and the names of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:onset_qualifier_closure_label
    "},{"location":"Data-Model/onset_qualifier_closure_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/onset_qualifier_closure_label/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/onset_qualifier_closure_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/onset_qualifier_closure_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/onset_qualifier_closure_label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:onset_qualifier_closure_label native https://w3id.org/monarch/monarch-py/:onset_qualifier_closure_label"},{"location":"Data-Model/onset_qualifier_closure_label/#linkml-source","title":"LinkML Source","text":"
    name: onset_qualifier_closure_label\ndescription: Field containing onset_qualifier name and the names of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: onset_qualifier_closure_label\ndomain_of:\n- Association\nrange: string\nmultivalued: true\n
    "},{"location":"Data-Model/onset_qualifier_label/","title":"Slot: onset_qualifier_label","text":"
    The name of the onset_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:onset_qualifier_label
    "},{"location":"Data-Model/onset_qualifier_label/#inheritance","title":"Inheritance","text":"
       
    • name
         
      • onset_qualifier_label
        •  
       
      •  
    "},{"location":"Data-Model/onset_qualifier_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/onset_qualifier_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/onset_qualifier_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/onset_qualifier_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/onset_qualifier_label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:onset_qualifier_label native https://w3id.org/monarch/monarch-py/:onset_qualifier_label"},{"location":"Data-Model/onset_qualifier_label/#linkml-source","title":"LinkML Source","text":"
    name: onset_qualifier_label\ndescription: The name of the onset_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: onset_qualifier_label\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/onset_qualifier_namespace/","title":"Slot: onset_qualifier_namespace","text":"
    The namespace/prefix of the onset_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:onset_qualifier_namespace
    "},{"location":"Data-Model/onset_qualifier_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/onset_qualifier_namespace/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/onset_qualifier_namespace/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/onset_qualifier_namespace/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/onset_qualifier_namespace/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:onset_qualifier_namespace native https://w3id.org/monarch/monarch-py/:onset_qualifier_namespace"},{"location":"Data-Model/onset_qualifier_namespace/#linkml-source","title":"LinkML Source","text":"
    name: onset_qualifier_namespace\ndescription: The namespace/prefix of the onset_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: onset_qualifier_namespace\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/original_object/","title":"Slot: original_object","text":"
    URI: https://w3id.org/monarch/monarch-py/:original_object
    "},{"location":"Data-Model/original_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/original_object/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/original_object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/original_object/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/original_object/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:original_object native https://w3id.org/monarch/monarch-py/:original_object"},{"location":"Data-Model/original_object/#linkml-source","title":"LinkML Source","text":"
    name: original_object\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: original_object\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/original_subject/","title":"Slot: original_subject","text":"
    URI: https://w3id.org/monarch/monarch-py/:original_subject
    "},{"location":"Data-Model/original_subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/original_subject/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/original_subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/original_subject/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/original_subject/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:original_subject native https://w3id.org/monarch/monarch-py/:original_subject"},{"location":"Data-Model/original_subject/#linkml-source","title":"LinkML Source","text":"
    name: original_subject\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: original_subject\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/overlap_coefficient/","title":"Slot: overlap_coefficient","text":"
    URI: https://w3id.org/monarch/monarch-py/:overlap_coefficient
    "},{"location":"Data-Model/overlap_coefficient/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • overlap_coefficient
        •  
       
      •  
    "},{"location":"Data-Model/overlap_coefficient/#properties","title":"Properties","text":"
       
    • Range: ZeroToOne
      •  
    "},{"location":"Data-Model/overlap_coefficient/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/overlap_coefficient/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/overlap_coefficient/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:overlap_coefficient native https://w3id.org/monarch/monarch-py/:overlap_coefficient"},{"location":"Data-Model/overlap_coefficient/#linkml-source","title":"LinkML Source","text":"
    name: overlap_coefficient\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: overlap_coefficient\nrange: ZeroToOne\n
    "},{"location":"Data-Model/pathway/","title":"Slot: pathway","text":"
    URI: https://w3id.org/monarch/monarch-py/:pathway
    "},{"location":"Data-Model/pathway/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/pathway/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/pathway/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/pathway/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/pathway/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:pathway native https://w3id.org/monarch/monarch-py/:pathway"},{"location":"Data-Model/pathway/#linkml-source","title":"LinkML Source","text":"
    name: pathway\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: pathway\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/phenodigm_score/","title":"Slot: phenodigm_score","text":"
    the geometric mean of the jaccard similarity and the information content
     
    URI: https://w3id.org/monarch/monarch-py/:phenodigm_score
    "},{"location":"Data-Model/phenodigm_score/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • phenodigm_score
        •  
       
      •  
    "},{"location":"Data-Model/phenodigm_score/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/phenodigm_score/#properties","title":"Properties","text":"
       
    • Range: NonNegativeFloat
      •  
    "},{"location":"Data-Model/phenodigm_score/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/phenodigm_score/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/phenodigm_score/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:phenodigm_score native https://w3id.org/monarch/monarch-py/:phenodigm_score"},{"location":"Data-Model/phenodigm_score/#linkml-source","title":"LinkML Source","text":"
    name: phenodigm_score\ndescription: the geometric mean of the jaccard similarity and the information content\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: phenodigm_score\ndomain_of:\n- TermPairwiseSimilarity\nrange: NonNegativeFloat\nequals_expression: sqrt({jaccard_similarity} * {information_content})\n
    "},{"location":"Data-Model/predicate/","title":"Slot: predicate","text":"
    URI: https://w3id.org/monarch/monarch-py/:predicate
    "},{"location":"Data-Model/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no CompactAssociation no Association no"},{"location":"Data-Model/predicate/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/predicate/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/predicate/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:predicate native https://w3id.org/monarch/monarch-py/:predicate"},{"location":"Data-Model/predicate/#linkml-source","title":"LinkML Source","text":"
    name: predicate\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: predicate\ndomain_of:\n- Association\n- CompactAssociation\nrange: string\nrequired: true\nmultivalued: false\n
    "},{"location":"Data-Model/predicate_id/","title":"Slot: predicate_id","text":"
    URI: https://w3id.org/monarch/monarch-py/:predicate_id
    "},{"location":"Data-Model/predicate_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Mapping A minimal class to hold a SSSOM mapping no"},{"location":"Data-Model/predicate_id/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/predicate_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/predicate_id/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/predicate_id/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:predicate_id native https://w3id.org/monarch/monarch-py/:predicate_id"},{"location":"Data-Model/predicate_id/#linkml-source","title":"LinkML Source","text":"
    name: predicate_id\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: predicate_id\ndomain_of:\n- Mapping\nrange: string\nrequired: true\n
    "},{"location":"Data-Model/primary_knowledge_source/","title":"Slot: primary_knowledge_source","text":"
    URI: https://w3id.org/monarch/monarch-py/:primary_knowledge_source
    "},{"location":"Data-Model/primary_knowledge_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/primary_knowledge_source/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/primary_knowledge_source/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/primary_knowledge_source/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/primary_knowledge_source/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:primary_knowledge_source native https://w3id.org/monarch/monarch-py/:primary_knowledge_source"},{"location":"Data-Model/primary_knowledge_source/#linkml-source","title":"LinkML Source","text":"
    name: primary_knowledge_source\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: primary_knowledge_source\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/provided_by/","title":"Slot: provided_by","text":"
    URI: https://w3id.org/monarch/monarch-py/:provided_by
    "},{"location":"Data-Model/provided_by/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Node UI container class extending Entity with additional information no Association no Entity Represents an Entity in the Monarch KG data model no SearchResult no"},{"location":"Data-Model/provided_by/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/provided_by/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/provided_by/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/provided_by/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:provided_by native https://w3id.org/monarch/monarch-py/:provided_by"},{"location":"Data-Model/provided_by/#linkml-source","title":"LinkML Source","text":"
    name: provided_by\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: provided_by\ndomain_of:\n- Association\n- Entity\nrange: string\n
    "},{"location":"Data-Model/provided_by_link/","title":"Slot: provided_by_link","text":"
    A link to the docs for the knowledge source that provided the node/edge.
     
    URI: https://w3id.org/monarch/monarch-py/:provided_by_link
    "},{"location":"Data-Model/provided_by_link/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/provided_by_link/#properties","title":"Properties","text":"
       
    • Range: ExpandedCurie
      •  
    "},{"location":"Data-Model/provided_by_link/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/provided_by_link/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/provided_by_link/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:provided_by_link native https://w3id.org/monarch/monarch-py/:provided_by_link"},{"location":"Data-Model/provided_by_link/#linkml-source","title":"LinkML Source","text":"
    name: provided_by_link\ndescription: A link to the docs for the knowledge source that provided the node/edge.\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: provided_by_link\ndomain_of:\n- Association\n- Node\nrange: ExpandedCurie\ninlined: true\n
    "},{"location":"Data-Model/publications/","title":"Slot: publications","text":"
    URI: https://w3id.org/monarch/monarch-py/:publications
    "},{"location":"Data-Model/publications/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/publications/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/publications/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/publications/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/publications/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:publications native https://w3id.org/monarch/monarch-py/:publications"},{"location":"Data-Model/publications/#linkml-source","title":"LinkML Source","text":"
    name: publications\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: publications\ndomain_of:\n- Association\nrange: string\nmultivalued: true\n
    "},{"location":"Data-Model/publications_links/","title":"Slot: publications_links","text":"
    List of ExpandedCuries with id and url for publications
     
    URI: https://w3id.org/monarch/monarch-py/:publications_links
    "},{"location":"Data-Model/publications_links/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/publications_links/#properties","title":"Properties","text":"
       
    •  
      Range: ExpandedCurie
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/publications_links/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/publications_links/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/publications_links/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:publications_links native https://w3id.org/monarch/monarch-py/:publications_links"},{"location":"Data-Model/publications_links/#linkml-source","title":"LinkML Source","text":"
    name: publications_links\ndescription: List of ExpandedCuries with id and url for publications\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: publications_links\ndomain_of:\n- Association\nrange: ExpandedCurie\nmultivalued: true\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/qc_report/","title":"Slot: qc_report","text":"
    URI: https://w3id.org/monarch/monarch-py/:qc_report
    "},{"location":"Data-Model/qc_report/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/qc_report/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/qc_report/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qc_report/#valid-id-prefixes","title":"Valid ID Prefixes","text":"
    Instances of this class should have identifiers with one of the following prefixes:
     
       
    • string
      •  
    "},{"location":"Data-Model/qc_report/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/qc_report/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:qc_report native https://w3id.org/monarch/monarch-py/:qc_report"},{"location":"Data-Model/qc_report/#linkml-source","title":"LinkML Source","text":"
    name: qc_report\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: qc_report\ndomain_of:\n- Release\nrange: string\n
    "},{"location":"Data-Model/qualifier/","title":"Slot: qualifier","text":"
    URI: https://w3id.org/monarch/monarch-py/:qualifier
    "},{"location":"Data-Model/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/qualifier/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifier/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/qualifier/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:qualifier native https://w3id.org/monarch/monarch-py/:qualifier"},{"location":"Data-Model/qualifier/#linkml-source","title":"LinkML Source","text":"
    name: qualifier\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: qualifier\ndomain_of:\n- Association\nrange: string\nmultivalued: true\n
    "},{"location":"Data-Model/qualifier_category/","title":"Slot: qualifier_category","text":"
    The category of the frequency_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:qualifier_category
    "},{"location":"Data-Model/qualifier_category/#inheritance","title":"Inheritance","text":"
       
    • category
         
      • qualifier_category
        •  
       
      •  
    "},{"location":"Data-Model/qualifier_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/qualifier_category/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/qualifier_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifier_category/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/qualifier_category/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:qualifier_category native https://w3id.org/monarch/monarch-py/:qualifier_category"},{"location":"Data-Model/qualifier_category/#linkml-source","title":"LinkML Source","text":"
    name: qualifier_category\ndescription: The category of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: qualifier_category\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/qualifier_closure/","title":"Slot: qualifier_closure","text":"
    Field containing frequency_qualifier id and the ids of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:qualifier_closure
    "},{"location":"Data-Model/qualifier_closure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/qualifier_closure/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/qualifier_closure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifier_closure/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/qualifier_closure/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:qualifier_closure native https://w3id.org/monarch/monarch-py/:qualifier_closure"},{"location":"Data-Model/qualifier_closure/#linkml-source","title":"LinkML Source","text":"
    name: qualifier_closure\ndescription: Field containing frequency_qualifier id and the ids of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: qualifier_closure\ndomain_of:\n- Association\nrange: string\nmultivalued: true\n
    "},{"location":"Data-Model/qualifier_closure_label/","title":"Slot: qualifier_closure_label","text":"
    Field containing frequency_qualifier name and the names of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:qualifier_closure_label
    "},{"location":"Data-Model/qualifier_closure_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/qualifier_closure_label/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/qualifier_closure_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifier_closure_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/qualifier_closure_label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:qualifier_closure_label native https://w3id.org/monarch/monarch-py/:qualifier_closure_label"},{"location":"Data-Model/qualifier_closure_label/#linkml-source","title":"LinkML Source","text":"
    name: qualifier_closure_label\ndescription: Field containing frequency_qualifier name and the names of all of it's\n  ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: qualifier_closure_label\ndomain_of:\n- Association\nrange: string\nmultivalued: true\n
    "},{"location":"Data-Model/qualifier_label/","title":"Slot: qualifier_label","text":"
    The name of the frequency_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:qualifier_label
    "},{"location":"Data-Model/qualifier_label/#inheritance","title":"Inheritance","text":"
       
    • name
         
      • qualifier_label
        •  
       
      •  
    "},{"location":"Data-Model/qualifier_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/qualifier_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/qualifier_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifier_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/qualifier_label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:qualifier_label native https://w3id.org/monarch/monarch-py/:qualifier_label"},{"location":"Data-Model/qualifier_label/#linkml-source","title":"LinkML Source","text":"
    name: qualifier_label\ndescription: The name of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: qualifier_label\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/qualifier_namespace/","title":"Slot: qualifier_namespace","text":"
    The namespace/prefix of the frequency_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:qualifier_namespace
    "},{"location":"Data-Model/qualifier_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/qualifier_namespace/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/qualifier_namespace/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifier_namespace/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/qualifier_namespace/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:qualifier_namespace native https://w3id.org/monarch/monarch-py/:qualifier_namespace"},{"location":"Data-Model/qualifier_namespace/#linkml-source","title":"LinkML Source","text":"
    name: qualifier_namespace\ndescription: The namespace/prefix of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: qualifier_namespace\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/qualifiers/","title":"Slot: qualifiers","text":"
    URI: https://w3id.org/monarch/monarch-py/:qualifiers
    "},{"location":"Data-Model/qualifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/qualifiers/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/qualifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifiers/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/qualifiers/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:qualifiers native https://w3id.org/monarch/monarch-py/:qualifiers"},{"location":"Data-Model/qualifiers/#linkml-source","title":"LinkML Source","text":"
    name: qualifiers\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: qualifiers\ndomain_of:\n- Association\nrange: string\nmultivalued: true\n
    "},{"location":"Data-Model/qualifiers_category/","title":"Slot: qualifiers_category","text":"
    The category of the frequency_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:qualifiers_category
    "},{"location":"Data-Model/qualifiers_category/#inheritance","title":"Inheritance","text":"
       
    • category
         
      • qualifiers_category
        •  
       
      •  
    "},{"location":"Data-Model/qualifiers_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/qualifiers_category/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/qualifiers_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifiers_category/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/qualifiers_category/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:qualifiers_category native https://w3id.org/monarch/monarch-py/:qualifiers_category"},{"location":"Data-Model/qualifiers_category/#linkml-source","title":"LinkML Source","text":"
    name: qualifiers_category\ndescription: The category of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: qualifiers_category\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/qualifiers_closure/","title":"Slot: qualifiers_closure","text":"
    Field containing frequency_qualifier id and the ids of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:qualifiers_closure
    "},{"location":"Data-Model/qualifiers_closure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/qualifiers_closure/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/qualifiers_closure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifiers_closure/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/qualifiers_closure/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:qualifiers_closure native https://w3id.org/monarch/monarch-py/:qualifiers_closure"},{"location":"Data-Model/qualifiers_closure/#linkml-source","title":"LinkML Source","text":"
    name: qualifiers_closure\ndescription: Field containing frequency_qualifier id and the ids of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: qualifiers_closure\ndomain_of:\n- Association\nrange: string\nmultivalued: true\n
    "},{"location":"Data-Model/qualifiers_closure_label/","title":"Slot: qualifiers_closure_label","text":"
    Field containing frequency_qualifier name and the names of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:qualifiers_closure_label
    "},{"location":"Data-Model/qualifiers_closure_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/qualifiers_closure_label/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/qualifiers_closure_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifiers_closure_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/qualifiers_closure_label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:qualifiers_closure_label native https://w3id.org/monarch/monarch-py/:qualifiers_closure_label"},{"location":"Data-Model/qualifiers_closure_label/#linkml-source","title":"LinkML Source","text":"
    name: qualifiers_closure_label\ndescription: Field containing frequency_qualifier name and the names of all of it's\n  ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: qualifiers_closure_label\ndomain_of:\n- Association\nrange: string\nmultivalued: true\n
    "},{"location":"Data-Model/qualifiers_label/","title":"Slot: qualifiers_label","text":"
    The name of the frequency_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:qualifiers_label
    "},{"location":"Data-Model/qualifiers_label/#inheritance","title":"Inheritance","text":"
       
    • name
         
      • qualifiers_label
        •  
       
      •  
    "},{"location":"Data-Model/qualifiers_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/qualifiers_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/qualifiers_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifiers_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/qualifiers_label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:qualifiers_label native https://w3id.org/monarch/monarch-py/:qualifiers_label"},{"location":"Data-Model/qualifiers_label/#linkml-source","title":"LinkML Source","text":"
    name: qualifiers_label\ndescription: The name of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: qualifiers_label\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/qualifiers_namespace/","title":"Slot: qualifiers_namespace","text":"
    The namespace/prefix of the frequency_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:qualifiers_namespace
    "},{"location":"Data-Model/qualifiers_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/qualifiers_namespace/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/qualifiers_namespace/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifiers_namespace/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/qualifiers_namespace/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:qualifiers_namespace native https://w3id.org/monarch/monarch-py/:qualifiers_namespace"},{"location":"Data-Model/qualifiers_namespace/#linkml-source","title":"LinkML Source","text":"
    name: qualifiers_namespace\ndescription: The namespace/prefix of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: qualifiers_namespace\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/score/","title":"Slot: score","text":"
    URI: https://w3id.org/monarch/monarch-py/:score
    "},{"location":"Data-Model/score/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • information_content
        •  
      • jaccard_similarity
        •  
      • cosine_similarity
        •  
      • dice_similarity
        •  
      • phenodigm_score
        •  
      • overlap_coefficient
        •  
      • subsumes_score
        •  
      • subsumed_by_score
        •  
      • intersection_count
        •  
      • union_count
        •  
       
      •  
    "},{"location":"Data-Model/score/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no SearchResult no SemsimSearchResult no"},{"location":"Data-Model/score/#properties","title":"Properties","text":"
       
    • Range: Float
      •  
    "},{"location":"Data-Model/score/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/score/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/score/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:score native https://w3id.org/monarch/monarch-py/:score"},{"location":"Data-Model/score/#linkml-source","title":"LinkML Source","text":"
    name: score\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: score\ndomain_of:\n- SearchResult\n- BestMatch\n- SemsimSearchResult\nrange: float\n
    "},{"location":"Data-Model/sex_qualifier/","title":"Slot: sex_qualifier","text":"
    URI: https://w3id.org/monarch/monarch-py/:sex_qualifier
    "},{"location":"Data-Model/sex_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/sex_qualifier/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/sex_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/sex_qualifier/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/sex_qualifier/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:sex_qualifier native https://w3id.org/monarch/monarch-py/:sex_qualifier"},{"location":"Data-Model/sex_qualifier/#linkml-source","title":"LinkML Source","text":"
    name: sex_qualifier\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: sex_qualifier\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/sex_qualifier_category/","title":"Slot: sex_qualifier_category","text":"
    The category of the sex_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:sex_qualifier_category
    "},{"location":"Data-Model/sex_qualifier_category/#inheritance","title":"Inheritance","text":"
       
    • category
         
      • sex_qualifier_category
        •  
       
      •  
    "},{"location":"Data-Model/sex_qualifier_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/sex_qualifier_category/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/sex_qualifier_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/sex_qualifier_category/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/sex_qualifier_category/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:sex_qualifier_category native https://w3id.org/monarch/monarch-py/:sex_qualifier_category"},{"location":"Data-Model/sex_qualifier_category/#linkml-source","title":"LinkML Source","text":"
    name: sex_qualifier_category\ndescription: The category of the sex_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: sex_qualifier_category\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/sex_qualifier_closure/","title":"Slot: sex_qualifier_closure","text":"
    Field containing sex_qualifier id and the ids of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:sex_qualifier_closure
    "},{"location":"Data-Model/sex_qualifier_closure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/sex_qualifier_closure/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/sex_qualifier_closure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/sex_qualifier_closure/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/sex_qualifier_closure/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:sex_qualifier_closure native https://w3id.org/monarch/monarch-py/:sex_qualifier_closure"},{"location":"Data-Model/sex_qualifier_closure/#linkml-source","title":"LinkML Source","text":"
    name: sex_qualifier_closure\ndescription: Field containing sex_qualifier id and the ids of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: sex_qualifier_closure\ndomain_of:\n- Association\nrange: string\nmultivalued: true\n
    "},{"location":"Data-Model/sex_qualifier_closure_label/","title":"Slot: sex_qualifier_closure_label","text":"
    Field containing sex_qualifier name and the names of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:sex_qualifier_closure_label
    "},{"location":"Data-Model/sex_qualifier_closure_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/sex_qualifier_closure_label/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/sex_qualifier_closure_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/sex_qualifier_closure_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/sex_qualifier_closure_label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:sex_qualifier_closure_label native https://w3id.org/monarch/monarch-py/:sex_qualifier_closure_label"},{"location":"Data-Model/sex_qualifier_closure_label/#linkml-source","title":"LinkML Source","text":"
    name: sex_qualifier_closure_label\ndescription: Field containing sex_qualifier name and the names of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: sex_qualifier_closure_label\ndomain_of:\n- Association\nrange: string\nmultivalued: true\n
    "},{"location":"Data-Model/sex_qualifier_label/","title":"Slot: sex_qualifier_label","text":"
    The name of the sex_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:sex_qualifier_label
    "},{"location":"Data-Model/sex_qualifier_label/#inheritance","title":"Inheritance","text":"
       
    • name
         
      • sex_qualifier_label
        •  
       
      •  
    "},{"location":"Data-Model/sex_qualifier_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/sex_qualifier_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/sex_qualifier_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/sex_qualifier_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/sex_qualifier_label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:sex_qualifier_label native https://w3id.org/monarch/monarch-py/:sex_qualifier_label"},{"location":"Data-Model/sex_qualifier_label/#linkml-source","title":"LinkML Source","text":"
    name: sex_qualifier_label\ndescription: The name of the sex_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: sex_qualifier_label\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/sex_qualifier_namespace/","title":"Slot: sex_qualifier_namespace","text":"
    The namespace/prefix of the sex_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:sex_qualifier_namespace
    "},{"location":"Data-Model/sex_qualifier_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/sex_qualifier_namespace/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/sex_qualifier_namespace/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/sex_qualifier_namespace/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/sex_qualifier_namespace/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:sex_qualifier_namespace native https://w3id.org/monarch/monarch-py/:sex_qualifier_namespace"},{"location":"Data-Model/sex_qualifier_namespace/#linkml-source","title":"LinkML Source","text":"
    name: sex_qualifier_namespace\ndescription: The namespace/prefix of the sex_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: sex_qualifier_namespace\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/similarity/","title":"Slot: similarity","text":"
    URI: https://w3id.org/monarch/monarch-py/:similarity
    "},{"location":"Data-Model/similarity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no SemsimSearchResult no"},{"location":"Data-Model/similarity/#properties","title":"Properties","text":"
       
    • Range: TermSetPairwiseSimilarity
      •  
    "},{"location":"Data-Model/similarity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/similarity/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/similarity/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:similarity native https://w3id.org/monarch/monarch-py/:similarity"},{"location":"Data-Model/similarity/#linkml-source","title":"LinkML Source","text":"
    name: similarity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: similarity\ndomain_of:\n- BestMatch\n- SemsimSearchResult\nrange: TermSetPairwiseSimilarity\n
    "},{"location":"Data-Model/solr/","title":"Slot: solr","text":"
    URI: https://w3id.org/monarch/monarch-py/:solr
    "},{"location":"Data-Model/solr/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/solr/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/solr/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/solr/#valid-id-prefixes","title":"Valid ID Prefixes","text":"
    Instances of this class should have identifiers with one of the following prefixes:
     
       
    • string
      •  
    "},{"location":"Data-Model/solr/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/solr/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:solr native https://w3id.org/monarch/monarch-py/:solr"},{"location":"Data-Model/solr/#linkml-source","title":"LinkML Source","text":"
    name: solr\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: solr\ndomain_of:\n- Release\nrange: string\n
    "},{"location":"Data-Model/sqlite/","title":"Slot: sqlite","text":"
    URI: https://w3id.org/monarch/monarch-py/:sqlite
    "},{"location":"Data-Model/sqlite/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/sqlite/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/sqlite/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/sqlite/#valid-id-prefixes","title":"Valid ID Prefixes","text":"
    Instances of this class should have identifiers with one of the following prefixes:
     
       
    • string
      •  
    "},{"location":"Data-Model/sqlite/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/sqlite/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:sqlite native https://w3id.org/monarch/monarch-py/:sqlite"},{"location":"Data-Model/sqlite/#linkml-source","title":"LinkML Source","text":"
    name: sqlite\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: sqlite\ndomain_of:\n- Release\nrange: string\n
    "},{"location":"Data-Model/stage_qualifier/","title":"Slot: stage_qualifier","text":"
    URI: https://w3id.org/monarch/monarch-py/:stage_qualifier
    "},{"location":"Data-Model/stage_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/stage_qualifier/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/stage_qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/stage_qualifier/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/stage_qualifier/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:stage_qualifier native https://w3id.org/monarch/monarch-py/:stage_qualifier"},{"location":"Data-Model/stage_qualifier/#linkml-source","title":"LinkML Source","text":"
    name: stage_qualifier\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: stage_qualifier\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/stage_qualifier_category/","title":"Slot: stage_qualifier_category","text":"
    The category of the stage_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:stage_qualifier_category
    "},{"location":"Data-Model/stage_qualifier_category/#inheritance","title":"Inheritance","text":"
       
    • category
         
      • stage_qualifier_category
        •  
       
      •  
    "},{"location":"Data-Model/stage_qualifier_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/stage_qualifier_category/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/stage_qualifier_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/stage_qualifier_category/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/stage_qualifier_category/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:stage_qualifier_category native https://w3id.org/monarch/monarch-py/:stage_qualifier_category"},{"location":"Data-Model/stage_qualifier_category/#linkml-source","title":"LinkML Source","text":"
    name: stage_qualifier_category\ndescription: The category of the stage_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: stage_qualifier_category\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/stage_qualifier_closure/","title":"Slot: stage_qualifier_closure","text":"
    Field containing stage_qualifier id and the ids of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:stage_qualifier_closure
    "},{"location":"Data-Model/stage_qualifier_closure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/stage_qualifier_closure/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/stage_qualifier_closure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/stage_qualifier_closure/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/stage_qualifier_closure/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:stage_qualifier_closure native https://w3id.org/monarch/monarch-py/:stage_qualifier_closure"},{"location":"Data-Model/stage_qualifier_closure/#linkml-source","title":"LinkML Source","text":"
    name: stage_qualifier_closure\ndescription: Field containing stage_qualifier id and the ids of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: stage_qualifier_closure\ndomain_of:\n- Association\nrange: string\nmultivalued: true\n
    "},{"location":"Data-Model/stage_qualifier_closure_label/","title":"Slot: stage_qualifier_closure_label","text":"
    Field containing stage_qualifier name and the names of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:stage_qualifier_closure_label
    "},{"location":"Data-Model/stage_qualifier_closure_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/stage_qualifier_closure_label/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/stage_qualifier_closure_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/stage_qualifier_closure_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/stage_qualifier_closure_label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:stage_qualifier_closure_label native https://w3id.org/monarch/monarch-py/:stage_qualifier_closure_label"},{"location":"Data-Model/stage_qualifier_closure_label/#linkml-source","title":"LinkML Source","text":"
    name: stage_qualifier_closure_label\ndescription: Field containing stage_qualifier name and the names of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: stage_qualifier_closure_label\ndomain_of:\n- Association\nrange: string\nmultivalued: true\n
    "},{"location":"Data-Model/stage_qualifier_label/","title":"Slot: stage_qualifier_label","text":"
    The name of the stage_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:stage_qualifier_label
    "},{"location":"Data-Model/stage_qualifier_label/#inheritance","title":"Inheritance","text":"
       
    • name
         
      • stage_qualifier_label
        •  
       
      •  
    "},{"location":"Data-Model/stage_qualifier_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/stage_qualifier_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/stage_qualifier_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/stage_qualifier_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/stage_qualifier_label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:stage_qualifier_label native https://w3id.org/monarch/monarch-py/:stage_qualifier_label"},{"location":"Data-Model/stage_qualifier_label/#linkml-source","title":"LinkML Source","text":"
    name: stage_qualifier_label\ndescription: The name of the stage_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: stage_qualifier_label\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/stage_qualifier_namespace/","title":"Slot: stage_qualifier_namespace","text":"
    The namespace/prefix of the stage_qualifier entity
     
    URI: https://w3id.org/monarch/monarch-py/:stage_qualifier_namespace
    "},{"location":"Data-Model/stage_qualifier_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/stage_qualifier_namespace/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/stage_qualifier_namespace/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/stage_qualifier_namespace/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/stage_qualifier_namespace/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:stage_qualifier_namespace native https://w3id.org/monarch/monarch-py/:stage_qualifier_namespace"},{"location":"Data-Model/stage_qualifier_namespace/#linkml-source","title":"LinkML Source","text":"
    name: stage_qualifier_namespace\ndescription: The namespace/prefix of the stage_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: stage_qualifier_namespace\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/start/","title":"Slot: start","text":"
    start position of the annotation
     
    URI: https://w3id.org/monarch/monarch-py/:start
    "},{"location":"Data-Model/start/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextAnnotationResult no"},{"location":"Data-Model/start/#properties","title":"Properties","text":"
       
    • Range: Integer
      •  
    "},{"location":"Data-Model/start/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/start/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/start/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:start native https://w3id.org/monarch/monarch-py/:start"},{"location":"Data-Model/start/#linkml-source","title":"LinkML Source","text":"
    name: start\ndescription: start position of the annotation\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: start\ndomain_of:\n- TextAnnotationResult\nrange: integer\n
    "},{"location":"Data-Model/sub_classes/","title":"Slot: sub_classes","text":"
    URI: https://w3id.org/monarch/monarch-py/:sub_classes
    "},{"location":"Data-Model/sub_classes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NodeHierarchy no"},{"location":"Data-Model/sub_classes/#properties","title":"Properties","text":"
       
    •  
      Range: Entity
       
      •  
    •  
      Multivalued: True
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/sub_classes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/sub_classes/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/sub_classes/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:sub_classes native https://w3id.org/monarch/monarch-py/:sub_classes"},{"location":"Data-Model/sub_classes/#linkml-source","title":"LinkML Source","text":"
    name: sub_classes\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: sub_classes\ndomain_of:\n- NodeHierarchy\nrange: Entity\nrequired: true\nmultivalued: true\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/subject/","title":"Slot: subject","text":"
    URI: https://w3id.org/monarch/monarch-py/:subject
    "},{"location":"Data-Model/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no CompactAssociation no Association no SemsimSearchResult yes"},{"location":"Data-Model/subject/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subject/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:subject native https://w3id.org/monarch/monarch-py/:subject"},{"location":"Data-Model/subject/#linkml-source","title":"LinkML Source","text":"
    name: subject\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: subject\ndomain_of:\n- Association\n- CompactAssociation\n- SemsimSearchResult\nrange: string\nrequired: true\n
    "},{"location":"Data-Model/subject_best_matches/","title":"Slot: subject_best_matches","text":"
    URI: https://w3id.org/monarch/monarch-py/:subject_best_matches
    "},{"location":"Data-Model/subject_best_matches/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/subject_best_matches/#properties","title":"Properties","text":"
       
    •  
      Range: BestMatch
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/subject_best_matches/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject_best_matches/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subject_best_matches/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:subject_best_matches native https://w3id.org/monarch/monarch-py/:subject_best_matches"},{"location":"Data-Model/subject_best_matches/#linkml-source","title":"LinkML Source","text":"
    name: subject_best_matches\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: subject_best_matches\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: BestMatch\nmultivalued: true\ninlined: true\n
    "},{"location":"Data-Model/subject_category/","title":"Slot: subject_category","text":"
    The category of the subject entity
     
    URI: https://w3id.org/monarch/monarch-py/:subject_category
    "},{"location":"Data-Model/subject_category/#inheritance","title":"Inheritance","text":"
       
    • category
         
      • subject_category
        •  
       
      •  
    "},{"location":"Data-Model/subject_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/subject_category/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/subject_category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject_category/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subject_category/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:subject_category native https://w3id.org/monarch/monarch-py/:subject_category"},{"location":"Data-Model/subject_category/#linkml-source","title":"LinkML Source","text":"
    name: subject_category\ndescription: The category of the subject entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: subject_category\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/subject_closure/","title":"Slot: subject_closure","text":"
    Field containing subject id and the ids of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:subject_closure
    "},{"location":"Data-Model/subject_closure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/subject_closure/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/subject_closure/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject_closure/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subject_closure/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:subject_closure native https://w3id.org/monarch/monarch-py/:subject_closure"},{"location":"Data-Model/subject_closure/#linkml-source","title":"LinkML Source","text":"
    name: subject_closure\ndescription: Field containing subject id and the ids of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: subject_closure\ndomain_of:\n- Association\nrange: string\nmultivalued: true\n
    "},{"location":"Data-Model/subject_closure_label/","title":"Slot: subject_closure_label","text":"
    Field containing subject name and the names of all of it's ancestors
     
    URI: https://w3id.org/monarch/monarch-py/:subject_closure_label
    "},{"location":"Data-Model/subject_closure_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/subject_closure_label/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/subject_closure_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject_closure_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subject_closure_label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:subject_closure_label native https://w3id.org/monarch/monarch-py/:subject_closure_label"},{"location":"Data-Model/subject_closure_label/#linkml-source","title":"LinkML Source","text":"
    name: subject_closure_label\ndescription: Field containing subject name and the names of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: subject_closure_label\ndomain_of:\n- Association\nrange: string\nmultivalued: true\n
    "},{"location":"Data-Model/subject_id/","title":"Slot: subject_id","text":"
    URI: https://w3id.org/monarch/monarch-py/:subject_id
    "},{"location":"Data-Model/subject_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Mapping A minimal class to hold a SSSOM mapping no TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/subject_id/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/subject_id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject_id/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subject_id/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:subject_id native https://w3id.org/monarch/monarch-py/:subject_id"},{"location":"Data-Model/subject_id/#linkml-source","title":"LinkML Source","text":"
    name: subject_id\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: subject_id\ndomain_of:\n- Mapping\n- TermPairwiseSimilarity\nrange: string\nrequired: true\n
    "},{"location":"Data-Model/subject_information_content/","title":"Slot: subject_information_content","text":"
    The IC of the subject
     
    URI: https://w3id.org/monarch/monarch-py/:subject_information_content
    "},{"location":"Data-Model/subject_information_content/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • information_content
           
        • subject_information_content
          •  
         
        •  
       
      •  
    "},{"location":"Data-Model/subject_information_content/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/subject_information_content/#properties","title":"Properties","text":"
       
    • Range: NegativeLogValue
      •  
    "},{"location":"Data-Model/subject_information_content/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject_information_content/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subject_information_content/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:subject_information_content native https://w3id.org/monarch/monarch-py/:subject_information_content"},{"location":"Data-Model/subject_information_content/#linkml-source","title":"LinkML Source","text":"
    name: subject_information_content\ndescription: The IC of the subject\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: information_content\nalias: subject_information_content\ndomain_of:\n- TermPairwiseSimilarity\nrange: NegativeLogValue\n
    "},{"location":"Data-Model/subject_label/","title":"Slot: subject_label","text":"
    The name of the subject entity
     
    URI: https://w3id.org/monarch/monarch-py/:subject_label
    "},{"location":"Data-Model/subject_label/#inheritance","title":"Inheritance","text":"
       
    • name
         
      • subject_label
        •  
       
      •  
    "},{"location":"Data-Model/subject_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no Mapping A minimal class to hold a SSSOM mapping no AssociationTypeMapping A data class to hold the necessary information to produce association type co... yes CompactAssociation no"},{"location":"Data-Model/subject_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/subject_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subject_label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:subject_label native https://w3id.org/monarch/monarch-py/:subject_label"},{"location":"Data-Model/subject_label/#linkml-source","title":"LinkML Source","text":"
    name: subject_label\ndescription: The name of the subject entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: subject_label\ndomain_of:\n- Association\n- CompactAssociation\n- AssociationTypeMapping\n- Mapping\n- TermPairwiseSimilarity\nrange: string\n
    "},{"location":"Data-Model/subject_namespace/","title":"Slot: subject_namespace","text":"
    The namespace/prefix of the subject entity
     
    URI: https://w3id.org/monarch/monarch-py/:subject_namespace
    "},{"location":"Data-Model/subject_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/subject_namespace/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/subject_namespace/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject_namespace/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subject_namespace/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:subject_namespace native https://w3id.org/monarch/monarch-py/:subject_namespace"},{"location":"Data-Model/subject_namespace/#linkml-source","title":"LinkML Source","text":"
    name: subject_namespace\ndescription: The namespace/prefix of the subject entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: subject_namespace\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/subject_source/","title":"Slot: subject_source","text":"
    the source for the first entity
     
    URI: sssom:subject_source
    "},{"location":"Data-Model/subject_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/subject_source/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/subject_source/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject_source/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subject_source/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self sssom:subject_source native https://w3id.org/monarch/monarch-py/:subject_source"},{"location":"Data-Model/subject_source/#linkml-source","title":"LinkML Source","text":"
    name: subject_source\ndescription: the source for the first entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nslot_uri: sssom:subject_source\nalias: subject_source\ndomain_of:\n- TermPairwiseSimilarity\nrange: string\n
    "},{"location":"Data-Model/subject_taxon/","title":"Slot: subject_taxon","text":"
    URI: https://w3id.org/monarch/monarch-py/:subject_taxon
    "},{"location":"Data-Model/subject_taxon/#inheritance","title":"Inheritance","text":"
       
    • in_taxon
         
      • subject_taxon
        •  
       
      •  
    "},{"location":"Data-Model/subject_taxon/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/subject_taxon/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/subject_taxon/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject_taxon/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subject_taxon/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:subject_taxon native https://w3id.org/monarch/monarch-py/:subject_taxon"},{"location":"Data-Model/subject_taxon/#linkml-source","title":"LinkML Source","text":"
    name: subject_taxon\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: in_taxon\nalias: subject_taxon\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/subject_taxon_label/","title":"Slot: subject_taxon_label","text":"
    URI: https://w3id.org/monarch/monarch-py/:subject_taxon_label
    "},{"location":"Data-Model/subject_taxon_label/#inheritance","title":"Inheritance","text":"
       
    • in_taxon_label
         
      • subject_taxon_label
        •  
       
      •  
    "},{"location":"Data-Model/subject_taxon_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no"},{"location":"Data-Model/subject_taxon_label/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/subject_taxon_label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject_taxon_label/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subject_taxon_label/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:subject_taxon_label native https://w3id.org/monarch/monarch-py/:subject_taxon_label"},{"location":"Data-Model/subject_taxon_label/#linkml-source","title":"LinkML Source","text":"
    name: subject_taxon_label\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: in_taxon_label\nalias: subject_taxon_label\ndomain_of:\n- Association\nrange: string\n
    "},{"location":"Data-Model/subject_termset/","title":"Slot: subject_termset","text":"
    URI: https://w3id.org/monarch/monarch-py/:subject_termset
    "},{"location":"Data-Model/subject_termset/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/subject_termset/#properties","title":"Properties","text":"
       
    •  
      Range: TermInfo
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/subject_termset/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject_termset/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subject_termset/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:subject_termset native https://w3id.org/monarch/monarch-py/:subject_termset"},{"location":"Data-Model/subject_termset/#linkml-source","title":"LinkML Source","text":"
    name: subject_termset\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: subject_termset\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: TermInfo\nmultivalued: true\ninlined: true\n
    "},{"location":"Data-Model/subsumed_by_score/","title":"Slot: subsumed_by_score","text":"
    URI: https://w3id.org/monarch/monarch-py/:subsumed_by_score
    "},{"location":"Data-Model/subsumed_by_score/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • subsumed_by_score
        •  
       
      •  
    "},{"location":"Data-Model/subsumed_by_score/#properties","title":"Properties","text":"
       
    • Range: ZeroToOne
      •  
    "},{"location":"Data-Model/subsumed_by_score/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subsumed_by_score/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subsumed_by_score/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:subsumed_by_score native https://w3id.org/monarch/monarch-py/:subsumed_by_score"},{"location":"Data-Model/subsumed_by_score/#linkml-source","title":"LinkML Source","text":"
    name: subsumed_by_score\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: subsumed_by_score\nrange: ZeroToOne\n
    "},{"location":"Data-Model/subsumes_score/","title":"Slot: subsumes_score","text":"
    URI: https://w3id.org/monarch/monarch-py/:subsumes_score
    "},{"location":"Data-Model/subsumes_score/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • subsumes_score
        •  
       
      •  
    "},{"location":"Data-Model/subsumes_score/#properties","title":"Properties","text":"
       
    • Range: ZeroToOne
      •  
    "},{"location":"Data-Model/subsumes_score/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subsumes_score/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/subsumes_score/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:subsumes_score native https://w3id.org/monarch/monarch-py/:subsumes_score"},{"location":"Data-Model/subsumes_score/#linkml-source","title":"LinkML Source","text":"
    name: subsumes_score\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: subsumes_score\nrange: ZeroToOne\n
    "},{"location":"Data-Model/super_classes/","title":"Slot: super_classes","text":"
    URI: https://w3id.org/monarch/monarch-py/:super_classes
    "},{"location":"Data-Model/super_classes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NodeHierarchy no"},{"location":"Data-Model/super_classes/#properties","title":"Properties","text":"
       
    •  
      Range: Entity
       
      •  
    •  
      Multivalued: True
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/super_classes/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/super_classes/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/super_classes/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:super_classes native https://w3id.org/monarch/monarch-py/:super_classes"},{"location":"Data-Model/super_classes/#linkml-source","title":"LinkML Source","text":"
    name: super_classes\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: super_classes\ndomain_of:\n- NodeHierarchy\nrange: Entity\nrequired: true\nmultivalued: true\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/symbol/","title":"Slot: symbol","text":"
    URI: https://w3id.org/monarch/monarch-py/:symbol
    "},{"location":"Data-Model/symbol/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/symbol/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/symbol/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/symbol/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/symbol/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:symbol native https://w3id.org/monarch/monarch-py/:symbol"},{"location":"Data-Model/symbol/#linkml-source","title":"LinkML Source","text":"
    name: symbol\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: symbol\ndomain_of:\n- Entity\nrange: string\n
    "},{"location":"Data-Model/symmetric/","title":"Slot: symmetric","text":"
    Whether the association type is symmetric, i.e. the subject and object labels are interchangeable.
     
    URI: https://w3id.org/monarch/monarch-py/:symmetric
    "},{"location":"Data-Model/symmetric/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AssociationTypeMapping A data class to hold the necessary information to produce association type co... yes"},{"location":"Data-Model/symmetric/#properties","title":"Properties","text":"
       
    • Range: Boolean
      •  
    "},{"location":"Data-Model/symmetric/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/symmetric/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/symmetric/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:symmetric native https://w3id.org/monarch/monarch-py/:symmetric"},{"location":"Data-Model/symmetric/#linkml-source","title":"LinkML Source","text":"
    name: symmetric\ndescription: Whether the association type is symmetric, i.e. the subject and object\n  labels are interchangeable.\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: symmetric\ndomain_of:\n- AssociationTypeMapping\nrange: boolean\n
    "},{"location":"Data-Model/synonym/","title":"Slot: synonym","text":"
    URI: https://w3id.org/monarch/monarch-py/:synonym
    "},{"location":"Data-Model/synonym/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/synonym/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/synonym/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/synonym/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/synonym/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:synonym native https://w3id.org/monarch/monarch-py/:synonym"},{"location":"Data-Model/synonym/#linkml-source","title":"LinkML Source","text":"
    name: synonym\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: synonym\ndomain_of:\n- Entity\nrange: string\nmultivalued: true\n
    "},{"location":"Data-Model/text/","title":"Slot: text","text":"
    text without tokens
     
    URI: https://w3id.org/monarch/monarch-py/:text
    "},{"location":"Data-Model/text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextAnnotationResult no"},{"location":"Data-Model/text/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/text/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/text/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:text native https://w3id.org/monarch/monarch-py/:text"},{"location":"Data-Model/text/#linkml-source","title":"LinkML Source","text":"
    name: text\ndescription: text without tokens\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: text\ndomain_of:\n- TextAnnotationResult\nrange: string\ninlined: true\n
    "},{"location":"Data-Model/tokens/","title":"Slot: tokens","text":"
    A collection of entities or concepts
     
    URI: https://w3id.org/monarch/monarch-py/:tokens
    "},{"location":"Data-Model/tokens/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextAnnotationResult no"},{"location":"Data-Model/tokens/#properties","title":"Properties","text":"
       
    •  
      Range: Entity
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/tokens/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/tokens/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/tokens/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:tokens native https://w3id.org/monarch/monarch-py/:tokens"},{"location":"Data-Model/tokens/#linkml-source","title":"LinkML Source","text":"
    name: tokens\ndescription: A collection of entities or concepts\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: tokens\ndomain_of:\n- TextAnnotationResult\nrange: Entity\nmultivalued: true\ninlined: true\ninlined_as_list: true\n
    "},{"location":"Data-Model/total/","title":"Slot: total","text":"
    total number of items matching a query
     
    URI: https://w3id.org/monarch/monarch-py/:total
    "},{"location":"Data-Model/total/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MappingResults SSSOM Mappings returned as a results collection no CategoryGroupedAssociationResults no Results no EntityResults no AssociationResults no CompactAssociationResults no AssociationTableResults no SearchResults no MultiEntityAssociationResults no"},{"location":"Data-Model/total/#properties","title":"Properties","text":"
       
    •  
      Range: Integer
       
      •  
    •  
      Required: True
       
      •  
    "},{"location":"Data-Model/total/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/total/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/total/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:total native https://w3id.org/monarch/monarch-py/:total"},{"location":"Data-Model/total/#linkml-source","title":"LinkML Source","text":"
    name: total\ndescription: total number of items matching a query\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: total\ndomain_of:\n- Results\nrange: integer\nrequired: true\n
    "},{"location":"Data-Model/union_count/","title":"Slot: union_count","text":"
    URI: https://w3id.org/monarch/monarch-py/:union_count
    "},{"location":"Data-Model/union_count/#inheritance","title":"Inheritance","text":"
       
    • score
         
      • union_count
        •  
       
      •  
    "},{"location":"Data-Model/union_count/#properties","title":"Properties","text":"
       
    • Range: ItemCount
      •  
    "},{"location":"Data-Model/union_count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/union_count/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/union_count/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:union_count native https://w3id.org/monarch/monarch-py/:union_count"},{"location":"Data-Model/union_count/#linkml-source","title":"LinkML Source","text":"
    name: union_count\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: union_count\nrange: ItemCount\n
    "},{"location":"Data-Model/uri/","title":"Slot: uri","text":"
    The URI of the entity
     
    URI: https://w3id.org/monarch/monarch-py/:uri
    "},{"location":"Data-Model/uri/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/uri/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/uri/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/uri/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:uri native https://w3id.org/monarch/monarch-py/:uri"},{"location":"Data-Model/uri/#linkml-source","title":"LinkML Source","text":"
    name: uri\ndescription: The URI of the entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: uri\ndomain_of:\n- Entity\nrange: string\n
    "},{"location":"Data-Model/url/","title":"Slot: url","text":"
    URI: https://w3id.org/monarch/monarch-py/:url
    "},{"location":"Data-Model/url/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ExpandedCurie A curie bundled along with its expanded url no Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/url/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/url/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/url/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/url/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:url native https://w3id.org/monarch/monarch-py/:url"},{"location":"Data-Model/url/#linkml-source","title":"LinkML Source","text":"
    name: url\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: url\ndomain_of:\n- ExpandedCurie\n- Release\nrange: string\n
    "},{"location":"Data-Model/version/","title":"Slot: version","text":"
    URI: https://w3id.org/monarch/monarch-py/:version
    "},{"location":"Data-Model/version/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/version/#properties","title":"Properties","text":"
       
    • Range: String
      •  
    "},{"location":"Data-Model/version/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/version/#valid-id-prefixes","title":"Valid ID Prefixes","text":"
    Instances of this class should have identifiers with one of the following prefixes:
     
       
    • string
      •  
    "},{"location":"Data-Model/version/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/version/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:version native https://w3id.org/monarch/monarch-py/:version"},{"location":"Data-Model/version/#linkml-source","title":"LinkML Source","text":"
    name: version\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: version\ndomain_of:\n- Release\nrange: string\n
    "},{"location":"Data-Model/xref/","title":"Slot: xref","text":"
    URI: https://w3id.org/monarch/monarch-py/:xref
    "},{"location":"Data-Model/xref/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/xref/#properties","title":"Properties","text":"
       
    •  
      Range: String
       
      •  
    •  
      Multivalued: True
       
      •  
    "},{"location":"Data-Model/xref/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/xref/#schema-source","title":"Schema Source","text":"
       
    • from schema: https://w3id.org/monarch/monarch-py
      •  
    "},{"location":"Data-Model/xref/#mappings","title":"Mappings","text":"Mapping Type Mapped Value self https://w3id.org/monarch/monarch-py/:xref native https://w3id.org/monarch/monarch-py/:xref"},{"location":"Data-Model/xref/#linkml-source","title":"LinkML Source","text":"
    name: xref\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: xref\ndomain_of:\n- Entity\nrange: string\nmultivalued: true\n
    "},{"location":"FastAPI/","title":"Monarch-Py FastAPI","text":"
    A FastAPI is also available for browsing the knowledge graph produced by the Monarch Initiative, which wraps the monarch-py library.
     
    It is included automatically as part of monarch-py when installed via pip or pipx.
    "},{"location":"FastAPI/#running-the-api-server","title":"Running the API Server","text":"
    A local development server can be started with the command:
     
    monarch-api\n
     
    or using uvicorn:
     
    # Using uvicorn directly:\npoetry run uvicorn src.monarch_py.api.main:app --reload\n\n# Using the Makefile shortcut:\ncd <path-to>/monarch-app\nmake dev-api\n
     
    The API is then available at http://127.0.0.1:8000/v3/api.
     
    Swagger documentation is available at http://127.0.0.1:8000/v3/docs, and a ReDoc interface at http://127.0.0.1:8000/v3/redoc.
    "},{"location":"FastAPI/#documentation","title":"Documentation","text":"
    API Reference
     
    Data Response Model
    "},{"location":"FastAPI/Endpoints/","title":"Monarch API Endpoints","text":"
    This section contains API reference for the various endpoints provided by monarch-api.
    "},{"location":"FastAPI/Endpoints/#endpoints","title":"Endpoints:","text":"
       
    • Association 
      •  
    • Entity 
      •  
    • SemSim (Semantic Similarity)
      •  
    "},{"location":"FastAPI/Endpoints/association/","title":"Association Endpoints","text":""},{"location":"FastAPI/Endpoints/entity/","title":"Entity Endpoints","text":""},{"location":"FastAPI/Endpoints/semsim/","title":"SemSim Endpoints","text":""},{"location":"FastAPI/Endpoints/semsim/#src.monarch_py.api.semsim.autocomplete","title":"autocomplete","text":"
    Autocomplete for semantic similarity lookups, prioritizes entities which have direct phenotype associations. Note: This API endpoint is experimental and may evolve or disappear over time.
     
    Parameters:
     Name Type Description Default q str 
    Query string to autocomplete against
     Query(default='*:*', title='Query string to autocomplete against', examples=['fanc', 'ehler']) 
    Returns:
     Type Description SearchResults 
    SearchResults
    "},{"location":"Usage/","title":"Usage","text":"
    monarch-py can be used via command line, or as a Python module.
    "},{"location":"Usage/#cli","title":"CLI","text":""},{"location":"Usage/#overview","title":"Overview","text":"
    monarch-py can be used to query various implementations of the Monarch knowledge graph. The default, and more feature-rich, implementation is Solr, and is the default.
     
    Subcommands are available to specify the backend.
     
    For example: 
    # The following two commands are equivalent,\n# as both query the Solr KG\n$ monarch entity MONDO:0012933 \n$ monarch solr entity MONDO:0012933\n\n# Whereas the following specifies the SQL implementation\n$ monarch sql entity MONDO:0012933\n
     
    You can also use an environment variable to specify a Solr URL to query a different Solr instance. monarch-py checks for the MONARCH_SOLR_URL environment variable, and uses it if it exists. If not, it uses the default Solr URL of http://localhost:8983/solr.
    "},{"location":"Usage/#commands","title":"Commands","text":"
    CLI commands are listed here, or can be found by running monarch --help.
    "},{"location":"Usage/#module","title":"Module","text":"
    TBD
    "},{"location":"Usage/CLI/","title":"monarch","text":"
    Usage:
     
    $ monarch [OPTIONS] COMMAND [ARGS]...\n
     
    Options:
     
       
    • --version / --no-version
      •  
    • --quiet / --no-quiet: [default: no-quiet]
      •  
    • --debug / --no-debug: [default: no-debug]
      •  
    • --install-completion: Install completion for the current shell.
      •  
    • --show-completion: Show completion for the current shell, to copy it or customize the installation.
      •  
    • --help: Show this message and exit.
      •  
     
    Commands:
     
       
    • association-counts: Retrieve association counts for an entity...
      •  
    • association-table
      •  
    • associations: Paginate through associations
      •  
    • autocomplete: Return entity autcomplete matches for a...
      •  
    • compare: Compare two sets of phenotypes using...
      •  
    • entity: Retrieve an entity by ID
      •  
    • histopheno: Retrieve the histopheno data for an entity...
      •  
    • mappings
      •  
    • multi-entity-associations: Paginate through associations for multiple...
      •  
    • release: Retrieve metadata for a specific release
      •  
    • releases: List all available releases of the Monarch...
      •  
    • schema: Print the linkml schema for the data model
      •  
    • search: Search for entities
      •  
    • solr
      •  
    • sql
      •  
    • test: Test the CLI
      •  
    "},{"location":"Usage/CLI/#monarch-association-counts","title":"monarch association-counts","text":"
    Retrieve association counts for an entity by ID
     
    Args:     entity: The entity to get association counts for     fmt: The format of the output (json, yaml, tsv, table). Default JSON     output: The path to the output file. Default stdout
     
    Returns:     A list of association counts for the given entity containing association type, label and count
     
    Usage:
     
    $ monarch association-counts [OPTIONS] [ENTITY]\n
     
    Arguments:
     
       
    • [ENTITY]: The entity to get association counts for
      •  
     
    Options:
     
       
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-association-table","title":"monarch association-table","text":"
    Usage:
     
    $ monarch association-table [OPTIONS] ENTITY CATEGORY:{biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation}\n
     
    Arguments:
     
       
    • ENTITY: The entity to get associations for  [required]
      •  
    • CATEGORY:{biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation}: The association category to get associations for, ex. biolink:GeneToPhenotypicFeatureAssociation  [required]
      •  
     
    Options:
     
       
    • -q, --query TEXT
      •  
    • -t, --traverse-orthologs: Whether to traverse orthologs when getting associations
      •  
    • -s, --sort TEXT
      •  
    • -l, --limit INTEGER: [default: 5]
      •  
    • --offset INTEGER: [default: 0]
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-associations","title":"monarch associations","text":"
    Paginate through associations
     
    Args:     category: A comma-separated list of categories     subject: A comma-separated list of subjects     predicate: A comma-separated list of predicates     object: A comma-separated list of objects     entity: A comma-separated list of entities     limit: The number of associations to return     direct: Whether to exclude associations with subject/object as ancestors     offset: The offset of the first association to be retrieved     fmt: The format of the output (json, yaml, tsv, table)     output: The path to the output file (stdout if not specified)
     
    Usage:
     
    $ monarch associations [OPTIONS]\n
     
    Options:
     
       
    • -c, --category [biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation]: Category to get associations for
      •  
    • -s, --subject TEXT: Subject ID to get associations for
      •  
    • -p, --predicate [biolink:interacts_with|biolink:expressed_in|biolink:has_phenotype|biolink:is_sequence_variant_of|biolink:enables|biolink:actively_involved_in|biolink:orthologous_to|biolink:located_in|biolink:subclass_of|biolink:related_to|biolink:participates_in|biolink:acts_upstream_of_or_within|biolink:active_in|biolink:part_of|biolink:model_of|biolink:causes|biolink:acts_upstream_of|biolink:has_mode_of_inheritance|biolink:contributes_to|biolink:gene_associated_with_condition|biolink:treats_or_applied_or_studied_to_treat|biolink:colocalizes_with|biolink:acts_upstream_of_positive_effect|biolink:acts_upstream_of_or_within_positive_effect|biolink:acts_upstream_of_negative_effect|biolink:acts_upstream_of_or_within_negative_effect]: Predicate ID to get associations for
      •  
    • -o, --object TEXT: Object ID to get associations for
      •  
    • -e, --entity TEXT: Entity (subject or object) ID to get associations for
      •  
    • -d, --direct: Whether to exclude associations with subject/object as ancestors
      •  
    • -C, --compact: Whether to return a compact representation of the associations
      •  
    • -l, --limit INTEGER: The number of associations to return  [default: 20]
      •  
    • --offset INTEGER: The offset of the first association to be retrieved  [default: 0]
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-autocomplete","title":"monarch autocomplete","text":"
    Return entity autcomplete matches for a query string
     
    Args:     q: The query string to autocomplete against     fmt: The format of the output (json, yaml, tsv, table)     output: The path to the output file (stdout if not specified)
     
    Usage:
     
    $ monarch autocomplete [OPTIONS] [Q]\n
     
    Arguments:
     
       
    • [Q]: Query string to autocomplete against
      •  
     
    Options:
     
       
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-compare","title":"monarch compare","text":"
    Compare two sets of phenotypes using semantic similarity via SemSimian
     
    Usage:
     
    $ monarch compare [OPTIONS] SUBJECTS OBJECTS\n
     
    Arguments:
     
       
    • SUBJECTS: Comma separated list of subjects to compare  [required]
      •  
    • OBJECTS: Comma separated list of objects to compare  [required]
      •  
     
    Options:
     
       
    • -m, --metric [ancestor_information_content|jaccard_similarity|phenodigm_score]: The metric to use for comparison  [default: ancestor_information_content]
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-entity","title":"monarch entity","text":"
    Retrieve an entity by ID
     
    Args:     id: The identifier of the entity to be retrieved     fmt: The format of the output (json, yaml, tsv, table)     output: The path to the output file (stdout if not specified)
     
    Usage:
     
    $ monarch entity [OPTIONS] [ID]\n
     
    Arguments:
     
       
    • [ID]: The identifier of the entity to be retrieved
      •  
     
    Options:
     
       
    • -e, --extra: Include extra fields in the output (association_counts and node_hierarchy)
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-histopheno","title":"monarch histopheno","text":"
    Retrieve the histopheno data for an entity by ID
     
    Args:     subject: The subject of the association
     
    Optional Args:     fmt (str): The format of the output (json, yaml, tsv, table). Default JSON     output (str): The path to the output file. Default stdout
     
    Usage:
     
    $ monarch histopheno [OPTIONS] [SUBJECT]\n
     
    Arguments:
     
       
    • [SUBJECT]: The subject of the association
      •  
     
    Options:
     
       
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-mappings","title":"monarch mappings","text":"
    Usage:
     
    $ monarch mappings [OPTIONS]\n
     
    Options:
     
       
    • -e, --entity-id TEXT: entity ID to get mappings for
      •  
    • -s, --subject-id TEXT: subject ID to get mappings for
      •  
    • -p, --predicate-id [skos:exactMatch|skos:broadMatch]: predicate ID to get mappings for
      •  
    • -o, --object-id TEXT: object ID to get mappings for
      •  
    • -m, --mapping-justification TEXT: mapping justification to get mappings for
      •  
    • --offset INTEGER: The offset of the first mapping to be retrieved  [default: 0]
      •  
    • -l, --limit INTEGER: The number of mappings to return  [default: 20]
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-multi-entity-associations","title":"monarch multi-entity-associations","text":"
    Paginate through associations for multiple entities
     
    Args:     entity: A comma-separated list of entities     counterpart_category: A comma-separated list of counterpart categories     limit: The number of associations to return     offset: The offset of the first association to be retrieved     fmt: The format of the output (json, yaml, tsv, table)     output: The path to the output file (stdout if not specified)
     
    Usage:
     
    $ monarch multi-entity-associations [OPTIONS]\n
     
    Options:
     
       
    • -e, --entity TEXT: Comma-separated list of entities
      •  
    • -c, --counterpart-category TEXT
      •  
    • -l, --limit INTEGER: [default: 20]
      •  
    • --offset INTEGER: [default: 0]
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -o, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-release","title":"monarch release","text":"
    Retrieve metadata for a specific release
     
    Args:     release_ver: The release version to get metadata for     fmt: The format of the output (json, yaml, tsv, table)     output: The path to the output file (stdout if not specified)
     
    Usage:
     
    $ monarch release [OPTIONS] [RELEASE_VER]\n
     
    Arguments:
     
       
    • [RELEASE_VER]: The release version to get metadata for
      •  
     
    Options:
     
       
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-releases","title":"monarch releases","text":"
    List all available releases of the Monarch Knowledge Graph
     
    Usage:
     
    $ monarch releases [OPTIONS]\n
     
    Options:
     
       
    • --dev: Get dev releases of the KG (default is False)
      •  
    • -l, --limit INTEGER: The number of releases to return  [default: 0]
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-schema","title":"monarch schema","text":"
    Print the linkml schema for the data model
     
    Usage:
     
    $ monarch schema [OPTIONS]\n
     
    Options:
     
       
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-search","title":"monarch search","text":"
    Search for entities
     
    Args:     q: The query string to search for     category: The category of the entity     in_taxon_label: The taxon label to filter by     limit: The number of entities to return     offset: The offset of the first entity to be retrieved     fmt: The format of the output (json, yaml, tsv, table)     output: The path to the output file (stdout if not specified)
     
    Usage:
     
    $ monarch search [OPTIONS]\n
     
    Options:
     
       
    • -q, --query TEXT
      •  
    • -c, --category [biolink:SequenceVariant|biolink:Gene|biolink:Genotype|biolink:PhenotypicFeature|biolink:BiologicalProcessOrActivity|biolink:Disease|biolink:GrossAnatomicalStructure|biolink:Cell|biolink:Pathway|biolink:NamedThing|biolink:AnatomicalEntity|biolink:CellularComponent|biolink:MolecularEntity|biolink:BiologicalProcess|biolink:MacromolecularComplex|biolink:MolecularActivity|biolink:Protein|biolink:CellularOrganism|biolink:Vertebrate|biolink:Virus|biolink:BehavioralFeature|biolink:ChemicalEntity|biolink:LifeStage|biolink:PathologicalProcess|biolink:Drug|biolink:SmallMolecule|biolink:OrganismTaxon|biolink:InformationContentEntity|biolink:NucleicAcidEntity|biolink:EvidenceType|biolink:RNAProduct|biolink:Transcript|biolink:Fungus|biolink:Plant|biolink:ProcessedMaterial|biolink:Activity|biolink:Agent|biolink:ConfidenceLevel|biolink:Dataset|biolink:EnvironmentalFeature|biolink:GeneticInheritance|biolink:Haplotype|biolink:Invertebrate|biolink:Mammal|biolink:PopulationOfIndividualOrganisms|biolink:ProteinFamily|biolink:Publication|biolink:AccessibleDnaRegion|biolink:Bacterium|biolink:BiologicalSex|biolink:CellLine|biolink:ChemicalExposure|biolink:ChemicalMixture|biolink:DatasetDistribution|biolink:DiagnosticAid|biolink:DrugExposure|biolink:EnvironmentalProcess|biolink:Event|biolink:Exon|biolink:Genome|biolink:GenotypicSex|biolink:Human|biolink:IndividualOrganism|biolink:MaterialSample|biolink:MicroRNA|biolink:OrganismalEntity|biolink:Patent|biolink:PhenotypicSex|biolink:Polypeptide|biolink:ProteinDomain|biolink:ReagentTargetedGene|biolink:RegulatoryRegion|biolink:SiRNA|biolink:Snv|biolink:Study|biolink:StudyVariable|biolink:TranscriptionFactorBindingSite|biolink:Treatment|biolink:WebPage|biolink:Zygosity]
      •  
    • -t, --in-taxon-label TEXT
      •  
    • -ff, --facet-fields TEXT
      •  
    • --facet-queries TEXT
      •  
    • -l, --limit INTEGER: [default: 20]
      •  
    • --offset INTEGER: [default: 0]
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-solr","title":"monarch solr","text":"
    Usage:
     
    $ monarch solr [OPTIONS] COMMAND [ARGS]...\n
     
    Options:
     
       
    • --quiet / --no-quiet: [default: no-quiet]
      •  
    • --debug / --no-debug: [default: no-debug]
      •  
    • --help: Show this message and exit.
      •  
     
    Commands:
     
       
    • association-counts: Retrieve the association counts for a...
      •  
    • association-table
      •  
    • associations: Paginate through associations
      •  
    • autocomplete: Return entity autcomplete matches for a...
      •  
    • download: Download the Monarch Solr KG.
      •  
    • entity: Retrieve an entity by ID
      •  
    • histopheno: Retrieve the histopheno associations for a...
      •  
    • mappings
      •  
    • multi-entity-associations: Paginate through associations for multiple...
      •  
    • search: Search for entities
      •  
    • start: Starts a local Solr container.
      •  
    • status: Checks the status of the local Solr...
      •  
    • stop: Stops the local Solr container.
      •  
    "},{"location":"Usage/CLI/#monarch-solr-association-counts","title":"monarch solr association-counts","text":"
    Retrieve the association counts for a given entity
     
    Args:     entity (str): The entity to get association counts for
     
    Optional Args:     fmt (str): The format of the output (json, yaml, tsv, table). Default JSON     output (str): The path to the output file. Default stdout
     
    Usage:
     
    $ monarch solr association-counts [OPTIONS] [ENTITY]\n
     
    Arguments:
     
       
    • [ENTITY]: The entity to get association counts for
      •  
     
    Options:
     
       
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-solr-association-table","title":"monarch solr association-table","text":"
    Usage:
     
    $ monarch solr association-table [OPTIONS] ENTITY [CATEGORY]:[biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation]\n
     
    Arguments:
     
       
    • ENTITY: The entity to get associations for  [required]
      •  
    • [CATEGORY]:[biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation]: The association category to get associations for, ex. biolink:GeneToPhenotypicFeatureAssociation
      •  
     
    Options:
     
       
    • -t, --traverse-orthologs: Whether to traverse orthologs when getting associations
      •  
    • -q, --query TEXT
      •  
    • -s, --sort TEXT
      •  
    • -l, --limit INTEGER: [default: 5]
      •  
    • --offset INTEGER: [default: 0]
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-solr-associations","title":"monarch solr associations","text":"
    Paginate through associations
     
    Args:     category: The category of the association (multi-valued)     subject: The subject of the association (multi-valued)     predicate: The predicate of the association (multi-valued)     object: The object of the association (multi-valued)     entity: The entity (subject or object) of the association (multi-valued)     limit: The number of associations to return (default 20)     direct: Whether to exclude associations with subject/object as ancestors (default False)     offset: The offset of the first association to be retrieved     fmt: The format of the output (json, yaml, tsv, table) (default json)     output: The path to the output file (stdout if not specified) (default None)
     
    Usage:
     
    $ monarch solr associations [OPTIONS]\n
     
    Options:
     
       
    • -c, --category [biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation]: Category to get associations for
      •  
    • -s, --subject TEXT: Subject ID to get associations for
      •  
    • -p, --predicate [biolink:interacts_with|biolink:expressed_in|biolink:has_phenotype|biolink:is_sequence_variant_of|biolink:enables|biolink:actively_involved_in|biolink:orthologous_to|biolink:located_in|biolink:subclass_of|biolink:related_to|biolink:participates_in|biolink:acts_upstream_of_or_within|biolink:active_in|biolink:part_of|biolink:model_of|biolink:causes|biolink:acts_upstream_of|biolink:has_mode_of_inheritance|biolink:contributes_to|biolink:gene_associated_with_condition|biolink:treats_or_applied_or_studied_to_treat|biolink:colocalizes_with|biolink:acts_upstream_of_positive_effect|biolink:acts_upstream_of_or_within_positive_effect|biolink:acts_upstream_of_negative_effect|biolink:acts_upstream_of_or_within_negative_effect]: Predicate ID to get associations for
      •  
    • -o, --object TEXT: Object ID to get associations for
      •  
    • -e, --entity TEXT: Entity (subject or object) ID to get associations for
      •  
    • -d, --direct: Whether to exclude associations with subject/object as ancestors
      •  
    • -C, --compact: Whether to return a compact representation of the associations
      •  
    • -l, --limit INTEGER: The number of associations to return  [default: 20]
      •  
    • --offset INTEGER: The offset of the first association to be retrieved  [default: 0]
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-solr-autocomplete","title":"monarch solr autocomplete","text":"
    Return entity autcomplete matches for a query string
     
    Args:     q: The query string to autocomplete against     fmt: The format of the output (json, yaml, tsv, table)     output: The path to the output file (stdout if not specified)
     
    Usage:
     
    $ monarch solr autocomplete [OPTIONS] [Q]\n
     
    Arguments:
     
       
    • [Q]: Query string to autocomplete against
      •  
     
    Options:
     
       
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-solr-download","title":"monarch solr download","text":"
    Download the Monarch Solr KG.
     
    Usage:
     
    $ monarch solr download [OPTIONS]\n
     
    Options:
     
       
    • --version TEXT: [default: latest]
      •  
    • --overwrite / --no-overwrite: [default: no-overwrite]
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-solr-entity","title":"monarch solr entity","text":"
    Retrieve an entity by ID
     
    Args:     id (str): The identifier of the entity to be retrieved
     
    Optional Args:     fmt (str): The format of the output (json, yaml, tsv, table). Default JSON     output (str): The path to the output file. Default stdout
     
    Usage:
     
    $ monarch solr entity [OPTIONS] [ID]\n
     
    Arguments:
     
       
    • [ID]: The identifier of the entity to be retrieved
      •  
     
    Options:
     
       
    • -e, --extra: Include extra fields in the output (association_counts and node_hierarchy)
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-solr-histopheno","title":"monarch solr histopheno","text":"
    Retrieve the histopheno associations for a given subject
     
    Args:     subject (str): The subject of the association
     
    Optional Args:     fmt (str): The format of the output (json, yaml, tsv, table). Default JSON     output (str): The path to the output file. Default stdout
     
    Usage:
     
    $ monarch solr histopheno [OPTIONS] [SUBJECT]\n
     
    Arguments:
     
       
    • [SUBJECT]: The subject of the association
      •  
     
    Options:
     
       
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: JSON]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-solr-mappings","title":"monarch solr mappings","text":"
    Usage:
     
    $ monarch solr mappings [OPTIONS]\n
     
    Options:
     
       
    • -e, --entity-id TEXT: entity ID to get mappings for
      •  
    • -s, --subject-id TEXT: subject ID to get mappings for
      •  
    • -p, --predicate-id [skos:exactMatch|skos:broadMatch]: predicate ID to get mappings for
      •  
    • -o, --object-id TEXT: object ID to get mappings for
      •  
    • -m, --mapping-justification TEXT: mapping justification to get mappings for
      •  
    • --offset INTEGER: The offset of the first mapping to be retrieved  [default: 0]
      •  
    • -l, --limit INTEGER: The number of mappings to return  [default: 20]
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-solr-multi-entity-associations","title":"monarch solr multi-entity-associations","text":"
    Paginate through associations for multiple entities
     
    Args:     entity: A comma-separated list of entities     counterpart_category: A comma-separated list of counterpart categories     limit: The number of associations to return     offset: The offset of the first association to be retrieved     fmt: The format of the output (json, yaml, tsv, table)     output: The path to the output file (stdout if not specified)
     
    Usage:
     
    $ monarch solr multi-entity-associations [OPTIONS]\n
     
    Options:
     
       
    • -e, --entity TEXT: Entity ID to get associations for
      •  
    • -c, --counterpart-category TEXT: Counterpart category to get associations for
      •  
    • -l, --limit INTEGER: [default: 20]
      •  
    • --offset INTEGER: [default: 0]
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-solr-search","title":"monarch solr search","text":"
    Search for entities
     
    Optional Args:     q: The query string to search for     category: The category of the entity     in_taxon_label: The taxon label to filter on     facet_fields: The fields to facet on     facet_queries: The queries to facet on     limit: The number of entities to return     offset: The offset of the first entity to be retrieved     fmt (str): The format of the output (json, yaml, tsv, table). Default JSON     output (str): The path to the output file. Default stdout
     
    Usage:
     
    $ monarch solr search [OPTIONS]\n
     
    Options:
     
       
    • -q, --query TEXT: [default: :]
      •  
    • -c, --category [biolink:SequenceVariant|biolink:Gene|biolink:Genotype|biolink:PhenotypicFeature|biolink:BiologicalProcessOrActivity|biolink:Disease|biolink:GrossAnatomicalStructure|biolink:Cell|biolink:Pathway|biolink:NamedThing|biolink:AnatomicalEntity|biolink:CellularComponent|biolink:MolecularEntity|biolink:BiologicalProcess|biolink:MacromolecularComplex|biolink:MolecularActivity|biolink:Protein|biolink:CellularOrganism|biolink:Vertebrate|biolink:Virus|biolink:BehavioralFeature|biolink:ChemicalEntity|biolink:LifeStage|biolink:PathologicalProcess|biolink:Drug|biolink:SmallMolecule|biolink:OrganismTaxon|biolink:InformationContentEntity|biolink:NucleicAcidEntity|biolink:EvidenceType|biolink:RNAProduct|biolink:Transcript|biolink:Fungus|biolink:Plant|biolink:ProcessedMaterial|biolink:Activity|biolink:Agent|biolink:ConfidenceLevel|biolink:Dataset|biolink:EnvironmentalFeature|biolink:GeneticInheritance|biolink:Haplotype|biolink:Invertebrate|biolink:Mammal|biolink:PopulationOfIndividualOrganisms|biolink:ProteinFamily|biolink:Publication|biolink:AccessibleDnaRegion|biolink:Bacterium|biolink:BiologicalSex|biolink:CellLine|biolink:ChemicalExposure|biolink:ChemicalMixture|biolink:DatasetDistribution|biolink:DiagnosticAid|biolink:DrugExposure|biolink:EnvironmentalProcess|biolink:Event|biolink:Exon|biolink:Genome|biolink:GenotypicSex|biolink:Human|biolink:IndividualOrganism|biolink:MaterialSample|biolink:MicroRNA|biolink:OrganismalEntity|biolink:Patent|biolink:PhenotypicSex|biolink:Polypeptide|biolink:ProteinDomain|biolink:ReagentTargetedGene|biolink:RegulatoryRegion|biolink:SiRNA|biolink:Snv|biolink:Study|biolink:StudyVariable|biolink:TranscriptionFactorBindingSite|biolink:Treatment|biolink:WebPage|biolink:Zygosity]
      •  
    • -t, --in-taxon-label TEXT
      •  
    • -ff, --facet-fields TEXT
      •  
    • --facet-queries TEXT
      •  
    • -l, --limit INTEGER: [default: 20]
      •  
    • --offset INTEGER: [default: 0]
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -O, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-solr-start","title":"monarch solr start","text":"
    Starts a local Solr container.
     
    Usage:
     
    $ monarch solr start [OPTIONS]\n
     
    Options:
     
       
    • --update / --no-update: [default: no-update]
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-solr-status","title":"monarch solr status","text":"
    Checks the status of the local Solr container.
     
    Usage:
     
    $ monarch solr status [OPTIONS]\n
     
    Options:
     
       
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-solr-stop","title":"monarch solr stop","text":"
    Stops the local Solr container.
     
    Usage:
     
    $ monarch solr stop [OPTIONS]\n
     
    Options:
     
       
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-sql","title":"monarch sql","text":"
    Usage:
     
    $ monarch sql [OPTIONS] COMMAND [ARGS]...\n
     
    Options:
     
       
    • --quiet / --no-quiet: [default: no-quiet]
      •  
    • --debug / --no-debug: [default: no-debug]
      •  
    • --help: Show this message and exit.
      •  
     
    Commands:
     
       
    • associations: Paginate through associations
      •  
    • entity: Retrieve an entity by ID
      •  
    "},{"location":"Usage/CLI/#monarch-sql-associations","title":"monarch sql associations","text":"
    Paginate through associations
     
    Args:     category: A comma-separated list of categories     subject: A comma-separated list of subjects     predicate: A comma-separated list of predicates     object: A comma-separated list of objects     entity: A comma-separated list of entities     direct: Whether to exclude associations with subject/object as ancestors     compact: Whether to return a compact representation of the associations     limit: The number of associations to return     offset: The offset of the first association to be retrieved     fmt: The format of the output (json, yaml, tsv, table)     output: The path to the output file (stdout if not specified)
     
    Usage:
     
    $ monarch sql associations [OPTIONS]\n
     
    Options:
     
       
    • -c, --category [biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation]: Category to get associations for
      •  
    • -s, --subject TEXT: Subject ID to get associations for
      •  
    • -p, --predicate [biolink:interacts_with|biolink:expressed_in|biolink:has_phenotype|biolink:is_sequence_variant_of|biolink:enables|biolink:actively_involved_in|biolink:orthologous_to|biolink:located_in|biolink:subclass_of|biolink:related_to|biolink:participates_in|biolink:acts_upstream_of_or_within|biolink:active_in|biolink:part_of|biolink:model_of|biolink:causes|biolink:acts_upstream_of|biolink:has_mode_of_inheritance|biolink:contributes_to|biolink:gene_associated_with_condition|biolink:treats_or_applied_or_studied_to_treat|biolink:colocalizes_with|biolink:acts_upstream_of_positive_effect|biolink:acts_upstream_of_or_within_positive_effect|biolink:acts_upstream_of_negative_effect|biolink:acts_upstream_of_or_within_negative_effect]: Predicate ID to get associations for
      •  
    • -o, --object TEXT: Object ID to get associations for
      •  
    • -e, --entity TEXT: Entity (subject or object) ID to get associations for
      •  
    • -d, --direct: Whether to exclude associations with subject/object as ancestors
      •  
    • -C, --compact: Whether to return a compact representation of the associations
      •  
    • -l, --limit INTEGER: The number of associations to return  [default: 20]
      •  
    • --offset INTEGER: The offset of the first association to be retrieved  [default: 0]
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -o, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-sql-entity","title":"monarch sql entity","text":"
    Retrieve an entity by ID
     
    Args:     id (str): The identifier of the entity to be retrieved     update (bool): = Whether to re-download the Monarch KG. Default False     fmt (str): The format of the output (json, yaml, tsv, table). Default JSON     output (str): The path to the output file. Default stdout
     
    Usage:
     
    $ monarch sql entity [OPTIONS] [ID]\n
     
    Arguments:
     
       
    • [ID]: The identifier of the entity to be retrieved
      •  
     
    Options:
     
       
    • -e, --extra: Include extra fields in the output (association_counts and node_hierarchy)
      •  
    • -u, --update: Whether to re-download the Monarch KG
      •  
    • -f, --format TEXT: The format of the output (json, yaml, tsv, table)  [default: json]
      •  
    • -o, --output TEXT: The path to the output file
      •  
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/CLI/#monarch-test","title":"monarch test","text":"
    Test the CLI
     
    Usage:
     
    $ monarch test [OPTIONS]\n
     
    Options:
     
       
    • --help: Show this message and exit.
      •  
    "},{"location":"Usage/Implementations/","title":"Implementations","text":"
    monarch-py provides implementations of the abstract Interfaces for different Monarch KG endpoints/backends.
    "},{"location":"Usage/Implementations/#implementations_1","title":"Implementations:","text":""},{"location":"Usage/Implementations/#solr","title":"Solr","text":""},{"location":"Usage/Implementations/#sqlite","title":"SQLite","text":""},{"location":"Usage/Implementations/SQL/","title":"SQL","text":""},{"location":"Usage/Implementations/SQL/#src.monarch_py.implementations.sql.sql_implementation.SQLImplementation","title":"SQLImplementation  dataclass","text":"
                   Bases: EntityInterface, AssociationInterface
     
    Implementation of Monarch Interfaces for SQL endpoint
    "},{"location":"Usage/Implementations/SQL/#src.monarch_py.implementations.sql.sql_implementation.SQLImplementation.get_associations","title":"get_associations","text":"
    Retrieve paginated association records, with filter options
     
    Parameters:
     Name Type Description Default category str 
    Filter to only associations matching the specified category. Defaults to None.
     None predicate str 
    Filter to only associations matching the specified predicate. Defaults to None.
     None subject str 
    Filter to only associations matching the specified subject. Defaults to None.
     None object str 
    Filter to only associations matching the specified object. Defaults to None.
     None subject_closure str 
    Filter to only associations with the specified term ID as an ancestor of the subject. Defaults to None.
     None object_closure str 
    Filter to only associations the specified term ID as an ancestor of the object. Defaults to None.
     None entity str 
    Filter to only associations where the specified entity is the subject or the object. Defaults to None.
     None association_type str 
    Filter to only associations matching the specified association label. Defaults to None.
     required compact bool 
    Whether to return compact or full association records. Defaults to False.
     False offset int 
    Result offset, for pagination. Defaults to 0.
     0 limit int 
    Limit results to specified number. Defaults to 20.
     20 
    Returns:
     Name Type Description AssociationResults Union[AssociationResults, CompactAssociationResults] 
    Dataclass representing results of an association search.
    "},{"location":"Usage/Implementations/SQL/#src.monarch_py.implementations.sql.sql_implementation.SQLImplementation.get_entity","title":"get_entity","text":"
    Retrieve a specific entity by exact ID match, writh optional extras
     
    Parameters:
     Name Type Description Default id str 
    id of the entity to search for.
     required get_association_counts bool 
    Whether to get association counts. Defaults to False.
     required get_hierarchy bool 
    Whether to get the entity hierarchy. Defaults to False.
     required 
    Returns:
     Name Type Description Entity Entity 
    Dataclass representing results of an entity search.
    "},{"location":"Usage/Implementations/Solr/","title":"Solr","text":""},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation","title":"SolrImplementation  dataclass","text":"
                   Bases: EntityInterface, AssociationInterface, SearchInterface, GroundingInterface
     
    Implementation of Monarch Interfaces for Solr endpoint
    "},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_association_counts","title":"get_association_counts","text":"
    Get list of association counts for a given entity
    "},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_associations","title":"get_associations","text":"
    Retrieve paginated association records, with filter options
     
    Parameters:
     Name Type Description Default category List[AssociationCategory] 
    Filter to only associations matching the specified categories. Defaults to None.
     None predicate List[AssociationPredicate] 
    Filter to only associations matching the specified predicates. Defaults to None.
     None subject Optional[List[str]] 
    Filter to only associations matching the specified subjects. Defaults to None.
     None object Optional[List[str]] 
    Filter to only associations matching the specified objects. Defaults to None.
     None subject_closure Optional[str] 
    Filter to only associations with the specified term ID as an ancestor of the subject. Defaults to None
     None object_closure Optional[str] 
    Filter to only associations with the specified term ID as an ancestor of the object. Defaults to None
     None entity Optional[List[str]] 
    Filter to only associations where the specified entities are the subject or the object. Defaults to None.
     None q Optional[str] 
    Query string to search within matches. Defaults to None.
     None compact bool 
    Return compact results with fewer fields. Defaults to False.
     False offset int 
    Result offset, for pagination. Defaults to 0.
     0 limit int 
    Limit results to specified number. Defaults to 20.
     20 
    Returns:
     Name Type Description AssociationResults Union[AssociationResults, CompactAssociation] 
    Dataclass representing results of an association search.
    "},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_counterpart_entities","title":"get_counterpart_entities","text":"
    Get a list of entities directly associated with this_entity fetched from associations in the Solr index
     
    Parameters:
     Name Type Description Default this_entity Entity 
    The entity to get associations for
     required entity str 
    an entity ID occurring in either the subject or object. Defaults to None.
     None subject str 
    an entity ID occurring in the subject. Defaults to None.
     None predicate str 
    a predicate value. Defaults to None.
     None object str 
    an entity ID occurring in the object. Defaults to None.
     None"},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_entity","title":"get_entity","text":"
    Retrieve a specific entity by exact ID match, with optional extras
     
    Parameters:
     Name Type Description Default id str 
    id of the entity to search for.
     required extra bool 
    Whether to include association counts and hierarchy in the response.
     required 
    Returns:
     Name Type Description Entity Optional[Union[Node, Entity]] 
    Dataclass representing results of an entity search.
     Node Optional[Union[Node, Entity]] 
    Dataclass representing results of an entity search with extra=True.
    "},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_histopheno","title":"get_histopheno","text":"
    Get histopheno counts for a given subject_closure
    "},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_multi_entity_associations","title":"get_multi_entity_associations","text":"
    Get associations between multiple entities and counterparts of a given category
     
    Parameters:
     Name Type Description Default entity List[str] 
    List of entity IDs to get associations for
     required counterpart_category List[str] 
    List of categories of counterpart entity to get associations for. Defaults to None.
     None offset int 
    Result offset, for pagination. Defaults to 0.
     0 limit int 
    Limit results to specified number. Defaults to 20.
     required limit_per_group int 
    Limit results to specified number per group. Defaults to 20.
     20"},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.ground_entity","title":"ground_entity","text":"
    Grounds a single entity
     
    Parameters:
     Name Type Description Default text str 
    Text to ground
     required 
    Returns:
     Name Type Description Entity List[Entity] 
    Dataclass representing a single entity
    "},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.search","title":"search","text":"
    Search for entities by label, with optional filters
     
    Parameters:
     Name Type Description Default q str 
    Query string. Defaults to \":\".
     '*:*' offset int 
    Result offset, for pagination. Defaults to 0.
     0 limit int 
    Limit results to specified number. Defaults to 20.
     20 category List[str] 
    Filter to only entities matching the specified categories. Defaults to None.
     None in_taxon_label List[str] 
    Filter to only entities matching the specified taxon label. Defaults to None.
     None facet_fields List[str] 
    List of fields to include facet counts for. Defaults to None.
     None facet_queries List[str] 
    List of queries to include facet counts for. Defaults to None.
     None filter_queries List[str] 
    List of queries to filter results by. Defaults to None.
     None sort str 
    Sort results by the specified field. Defaults to None.
     None 
    Returns:
     Name Type Description SearchResults SearchResults 
    Dataclass representing results of a search.
    "},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.solr_is_available","title":"solr_is_available","text":"
    Check if the Solr instance is available
    "},{"location":"Usage/Interfaces/","title":"Interfaces","text":"
    monarch-py provides a collection of interfaces that abstractify implementation details, and provide a coherent set of graph operations.  
     
    Developers can code according to the interface, mostly ignoring whether the implementation is a relational database, a local file, etc. 
    "},{"location":"Usage/Interfaces/#interface","title":"Interface","text":"
       
    • Entity
      •  
    • Association
      •  
    • Query
      •  
    • Search
      •  
    "},{"location":"Usage/Interfaces/Association/","title":"Association","text":""},{"location":"Usage/Interfaces/Association/#src.monarch_py.interfaces.association_interface.AssociationInterface","title":"AssociationInterface","text":"
                   Bases: ABC
     
    Abstract interface for associations in the Monarch KG
    "},{"location":"Usage/Interfaces/Association/#src.monarch_py.interfaces.association_interface.AssociationInterface.get_associations","title":"get_associations  abstractmethod","text":"
    Retrieve paginated association records, with filter options
     
    Parameters:
     Name Type Description Default category str 
    Filter to only associations matching the specified category. Defaults to None.
     None predicate str 
    Filter to only associations matching the specified predicate. Defaults to None.
     None subject str 
    Filter to only associations matching the specified subject. Defaults to None.
     None subject_closure str 
    Filter to only associations with the specified term ID as an ancestor of the subject. Defaults to None
     None object str 
    Filter to only associations matching the specified object. Defaults to None.
     None object_closure str 
    Filter to only associations with the specified term ID as an ancestor of the object. Defaults to None
     None entity str 
    Filter to only associations where the specified entity is the subject or the object. Defaults to None.
     None offset int 
    Result offset, for pagination. Defaults to 0.
     0 limit int 
    Limit results to specified number. Defaults to 20.
     20 
    Raises:
     Type Description NotImplementedError 
    Use a specific implementation (see the documentation for a list of implementations)
     
    Returns:
     Type Description AssociationResults 
    AssociationResults: Dataclass representing results of an association search.
    "},{"location":"Usage/Interfaces/Entity/","title":"Entity","text":""},{"location":"Usage/Interfaces/Entity/#src.monarch_py.interfaces.entity_interface.EntityInterface","title":"EntityInterface","text":"
                   Bases: ABC
     
    Abstract interface for entities in the Monarch KG
    "},{"location":"Usage/Interfaces/Entity/#src.monarch_py.interfaces.entity_interface.EntityInterface.get_entity","title":"get_entity  abstractmethod","text":"
    Retrieve a specific entity by exact ID match, with optional extras
     
    Parameters:
     Name Type Description Default id str 
    id of the entity to search for.
     required get_association_counts bool 
    Whether to get a count of associations for the entity. Defaults to False.
     False get_hierarchy bool 
    Whether to get the entity's heirarchy in the data model. Defaults to False.
     False 
    Raises:
     Type Description NotImplementedError 
    Use a specific implementation (see the documentation for a list of implementations)
     
    Returns:
     Name Type Description Entity Entity 
    Dataclass representing results of an entity search.
    "},{"location":"Usage/Interfaces/Query/","title":"Query","text":""},{"location":"Usage/Interfaces/Query/#src.monarch_py.interfaces.query_interface.QueryInterface","title":"QueryInterface","text":"
                   Bases: ABC
     
    Abstract interface for querying the Monarch KG in a SQL way
    "},{"location":"Usage/Interfaces/Query/#src.monarch_py.interfaces.query_interface.QueryInterface.query","title":"query  abstractmethod","text":"
    Parameters:
     Name Type Description Default q str 
    Query string to match against
     required category str 
    Limit results to only this category
     required taxon str 
    Limit results to only this taxon
     required offset int 
    Offset of the first result to return, defaults to 0
     required limit int 
    Limit the number of results to return, defaults to 20
     required 
    Raises:
     Type Description NotImplementedError 
    Use a specific implementation (see the documentation for a list of implementations)
     
    Returns:
     Name Type Description EntityResults EntityResults 
    Dataclass representing results of a generic entity search.
    "},{"location":"Usage/Interfaces/Search/","title":"Search","text":""},{"location":"Usage/Interfaces/Search/#src.monarch_py.interfaces.search_interface.SearchInterface","title":"SearchInterface","text":"
                   Bases: ABC
     
    Abstract interface for searching the Monarch KG in a Lucene way
    "},{"location":"Usage/Interfaces/Search/#src.monarch_py.interfaces.search_interface.SearchInterface.autocomplete","title":"autocomplete","text":"
    Parameters:
     Name Type Description Default q str 
    Query string to match against
     required 
    Raises:
     Type Description NotImplementedError 
    Use a specific implementation (see the documentation for a list of implementations)
     
    Returns:
     Name Type Description SearchResults SearchResults 
    Dataclass representing results of a generic entity search.
    "},{"location":"Usage/Interfaces/Search/#src.monarch_py.interfaces.search_interface.SearchInterface.get_association_counts","title":"get_association_counts","text":"
    Get counts of associations for a given entity Args:     entity (str): Entity to get association counts for Returns:     List[FacetValue]: List of FacetValue objects representing the counts of associations for the given entity
    "},{"location":"Usage/Interfaces/Search/#src.monarch_py.interfaces.search_interface.SearchInterface.get_association_facets","title":"get_association_facets","text":"
    Get facet counts and facet query counts for associations Args:     facet_fields (List[str]): Facet fields to return counts for     facet_queries (List[str]): Facet queries to return counts for     category (str): Filter to only associations matching the specified category     predicate (str): Filter to only associations matching the specified predicate     subject (str): Filter to only associations matching the specified subject     subject_closure (str): Filter to only associations with the specified term ID as an ancestor of the subject     object (str): Filter to only associations matching the specified object     object_closure (str): Filter to only associations with the specified term ID as an ancestor of the object     entity (str): Filter to only associations where the specified entity is the subject or the object Returns:     SearchResults: Dataclass representing results of a search, with zero rows returned but total count     and faceting information populated
    "},{"location":"Usage/Interfaces/Search/#src.monarch_py.interfaces.search_interface.SearchInterface.get_association_table","title":"get_association_table","text":"
    Get associations for an entity matching a specified type, with optional search and sort parameters
     
    Parameters:
     Name Type Description Default entity str 
    Entity to get associations for
     required category str 
    Category of associations to return
     required query str 
    Query string to match against
     None sort str 
    Sort order, defaults to None
     None offset int 
    Offset of the first result to return, defaults to 0
     0 limit int 
    Limit the number of results to return, defaults to 20
     5 
    Returns:
     Name Type Description AssociationResults AssociationTableResults 
    Dataclass representing results of an association search.
    "},{"location":"Usage/Interfaces/Search/#src.monarch_py.interfaces.search_interface.SearchInterface.search","title":"search  abstractmethod","text":"
    Parameters:
     Name Type Description Default q str 
    Query string to match against
     required category str 
    Limit results to only this category
     None taxon str 
    Limit results to only this taxon
     required offset int 
    Offset of the first result to return, defaults to 0
     0 limit int 
    Limit the number of results to return, defaults to 20
     20 
    Raises:
     Type Description NotImplementedError 
    Use a specific implementation (see the documentation for a list of implementations)
     
    Returns:
     Name Type Description EntityResults SearchResults 
    Dataclass representing results of a generic entity search.
    "}]}
\ No newline at end of file
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index 161a83636..707dea0aa 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -2,1217 +2,1247 @@
 
     
          https://monarch-app.monarchinitiative.org/docs/
-         2024-10-04
+         2024-10-17
          daily
     
     
          https://monarch-app.monarchinitiative.org/docs/API-Reference/
-         2024-10-04
+         2024-10-17
          daily
     
     
          https://monarch-app.monarchinitiative.org/docs/Data-Model/
-         2024-10-04
+         2024-10-17
          daily
     
     
          https://monarch-app.monarchinitiative.org/docs/Data-Model/Association/
-         2024-10-04
+         2024-10-17
          daily
     
     
          https://monarch-app.monarchinitiative.org/docs/Data-Model/AssociationCount/
-         2024-10-04
+         2024-10-17
          daily
     
     
          https://monarch-app.monarchinitiative.org/docs/Data-Model/AssociationCountList/
-         2024-10-04
+         2024-10-17
          daily
     
     
          https://monarch-app.monarchinitiative.org/docs/Data-Model/AssociationDirectionEnum/
-         2024-10-04
+         2024-10-17
          daily
     
     
          https://monarch-app.monarchinitiative.org/docs/Data-Model/AssociationResults/
-         2024-10-04
+         2024-10-17
          daily
     
     
          https://monarch-app.monarchinitiative.org/docs/Data-Model/AssociationTableResults/
-         2024-10-04
+         2024-10-17
          daily
     
     
          https://monarch-app.monarchinitiative.org/docs/Data-Model/AssociationTypeMapping/
-         2024-10-04
+         2024-10-17
          daily
     
     
          https://monarch-app.monarchinitiative.org/docs/Data-Model/BestMatch/
-         2024-10-04
+         2024-10-17
          daily
     
     
          https://monarch-app.monarchinitiative.org/docs/Data-Model/Boolean/
-         2024-10-04
+         2024-10-17
          daily
     
     
          https://monarch-app.monarchinitiative.org/docs/Data-Model/CategoryGroupedAssociationResults/
-         2024-10-04
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/onset_qualifier_closure_label/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/original_subject/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/primary_knowledge_source/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/provided_by/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/provided_by_link/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/publications/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/publications_links/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/qc_report/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/qualifier_category/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/qualifier_closure/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/qualifier_closure_label/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/qualifier_namespace/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/qualifiers_category/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/qualifiers_closure/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/qualifiers_label/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/qualifiers_namespace/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/score/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/sex_qualifier/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/sex_qualifier_category/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/sex_qualifier_closure/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/sex_qualifier_closure_label/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/sex_qualifier_label/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/sex_qualifier_namespace/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/similarity/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/solr/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/sqlite/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/stage_qualifier/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/stage_qualifier_category/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/stage_qualifier_closure/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/stage_qualifier_closure_label/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/stage_qualifier_label/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/stage_qualifier_namespace/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/start/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/subject/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/subject_best_matches/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/subject_category/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/subject_closure/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/subject_closure_label/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/subject_id/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/subject_information_content/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/subject_label/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/subject_namespace/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/subject_source/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/subject_taxon/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/subject_taxon_label/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/subject_termset/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/subsumed_by_score/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/subsumes_score/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/super_classes/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/symbol/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/symmetric/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/synonym/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/text/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/tokens/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/total/
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/union_count/
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          daily
     
     
          https://monarch-app.monarchinitiative.org/docs/Data-Model/uri/
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          daily
     
     
          https://monarch-app.monarchinitiative.org/docs/Data-Model/url/
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          daily
     
     
          https://monarch-app.monarchinitiative.org/docs/Data-Model/version/
-         2024-10-04
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          https://monarch-app.monarchinitiative.org/docs/Data-Model/xref/
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          https://monarch-app.monarchinitiative.org/docs/FastAPI/
-         2024-10-04
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          https://monarch-app.monarchinitiative.org/docs/FastAPI/Endpoints/
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          https://monarch-app.monarchinitiative.org/docs/FastAPI/Endpoints/association/
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          https://monarch-app.monarchinitiative.org/docs/FastAPI/Endpoints/entity/
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          https://monarch-app.monarchinitiative.org/docs/FastAPI/Endpoints/semsim/
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          daily
     
     
          https://monarch-app.monarchinitiative.org/docs/Usage/
-         2024-10-04
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          daily
     
     
          https://monarch-app.monarchinitiative.org/docs/Usage/CLI/
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          daily
     
     
          https://monarch-app.monarchinitiative.org/docs/Usage/Implementations/
-         2024-10-04
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          daily
     
     
          https://monarch-app.monarchinitiative.org/docs/Usage/Implementations/OAK/
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          daily
     
     
          https://monarch-app.monarchinitiative.org/docs/Usage/Implementations/SQL/
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          daily
     
     
          https://monarch-app.monarchinitiative.org/docs/Usage/Implementations/Solr/
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          daily
     
     
          https://monarch-app.monarchinitiative.org/docs/Usage/Interfaces/
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          daily
     
     
          https://monarch-app.monarchinitiative.org/docs/Usage/Interfaces/Association/
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          daily
     
     
          https://monarch-app.monarchinitiative.org/docs/Usage/Interfaces/Entity/
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          daily
     
     
          https://monarch-app.monarchinitiative.org/docs/Usage/Interfaces/Query/
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          https://monarch-app.monarchinitiative.org/docs/Usage/Interfaces/Search/
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