From 2a77940f175c5fb5f9ab22daefc439955a9126ae Mon Sep 17 00:00:00 2001 From: kevinschaper Date: Fri, 15 Nov 2024 22:38:14 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20monarch-?= =?UTF-8?q?initiative/monarch-app@ce0851b2193164f8c473c4515ed19e7bafbf1e5b?= =?UTF-8?q?=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- docs/API-Reference/index.html | 42 ++++++++++++ docs/Data-Model/AssociationResults/index.html | 65 +++++++++++++++++++ .../AssociationTableResults/index.html | 65 +++++++++++++++++++ .../CompactAssociationResults/index.html | 65 +++++++++++++++++++ docs/Data-Model/FacetField/index.html | 18 +++++ docs/Data-Model/FacetValue/index.html | 18 +++++ docs/Data-Model/SearchResults/index.html | 6 ++ docs/Data-Model/category/index.html | 36 +++++----- docs/Data-Model/count/index.html | 4 +- docs/Data-Model/deprecated/index.html | 10 +-- docs/Data-Model/description/index.html | 10 +-- docs/Data-Model/facet_fields/index.html | 18 +++++ docs/Data-Model/facet_queries/index.html | 18 +++++ docs/Data-Model/full_name/index.html | 10 +-- docs/Data-Model/has_phenotype/index.html | 10 +-- .../has_phenotype_closure/index.html | 10 +-- .../has_phenotype_closure_label/index.html | 10 +-- .../Data-Model/has_phenotype_count/index.html | 10 +-- .../Data-Model/has_phenotype_label/index.html | 10 +-- docs/Data-Model/id/index.html | 32 ++++----- docs/Data-Model/in_taxon/index.html | 10 +-- docs/Data-Model/in_taxon_label/index.html | 10 +-- docs/Data-Model/iri/index.html | 10 +-- docs/Data-Model/items/index.html | 26 ++++---- docs/Data-Model/label/index.html | 10 +-- docs/Data-Model/limit/index.html | 22 +++---- docs/Data-Model/name/index.html | 16 ++--- docs/Data-Model/namespace/index.html | 10 +-- docs/Data-Model/negated/index.html | 4 +- docs/Data-Model/object/index.html | 4 +- docs/Data-Model/object_id/index.html | 8 +-- docs/Data-Model/object_label/index.html | 26 ++++---- docs/Data-Model/offset/index.html | 22 +++---- docs/Data-Model/predicate/index.html | 4 +- docs/Data-Model/provided_by/index.html | 20 +++--- docs/Data-Model/score/index.html | 6 +- docs/Data-Model/subject/index.html | 14 ++-- docs/Data-Model/subject_id/index.html | 8 +-- docs/Data-Model/subject_label/index.html | 26 ++++---- docs/Data-Model/symbol/index.html | 10 +-- docs/Data-Model/synonym/index.html | 10 +-- docs/Data-Model/total/index.html | 22 +++---- docs/Data-Model/uri/index.html | 10 +-- docs/Data-Model/url/index.html | 8 +-- docs/Data-Model/xref/index.html | 10 +-- docs/Usage/Implementations/Solr/index.html | 42 ++++++++++++ docs/search/search_index.json | 2 +- 47 files changed, 597 insertions(+), 240 deletions(-) diff --git a/docs/API-Reference/index.html b/docs/API-Reference/index.html index 5da843276..04d080e81 100644 --- a/docs/API-Reference/index.html +++ b/docs/API-Reference/index.html @@ -2665,6 +2665,48 @@

+ facet_fields + + Optional[List[str]] + + +
+

List of fields to include facet counts for. Defaults to None.

+
+ + + None + + + + facet_queries + + Optional[List[str]] + + +
+

List of queries to include facet counts for. Defaults to None.

+
+ + + None + + + + filter_queries + + Optional[List[str]] + + +
+

List of queries to filter results by. Defaults to None.

+
+ + + None + + compact diff --git a/docs/Data-Model/AssociationResults/index.html b/docs/Data-Model/AssociationResults/index.html index f7f092aa7..ebd384d7b 100644 --- a/docs/Data-Model/AssociationResults/index.html +++ b/docs/Data-Model/AssociationResults/index.html @@ -1026,6 +1026,24 @@

Class: AssociationResults

Results <|-- AssociationResults click Results href "../Results" + AssociationResults : facet_fields + + + + + AssociationResults --> "*" FacetField : facet_fields + click FacetField href "../FacetField" + + + AssociationResults : facet_queries + + + + + AssociationResults --> "*" FacetValue : facet_queries + click FacetValue href "../FacetValue" + + AssociationResults : items @@ -1066,6 +1084,18 @@

Slots

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 @@ -1119,6 +1149,8 @@

Direct

is_a: Results slots: - items +- facet_fields +- facet_queries slot_usage: items: name: items @@ -1158,6 +1190,39 @@

Induced

multivalued: true inlined: true inlined_as_list: true + facet_fields: + name: facet_fields + description: Collection of facet field responses with the field values and counts + from_schema: https://w3id.org/monarch/monarch-py + rank: 1000 + alias: facet_fields + owner: AssociationResults + domain_of: + - AssociationResults + - CompactAssociationResults + - AssociationTableResults + - SearchResults + range: FacetField + multivalued: true + inlined: true + inlined_as_list: true + facet_queries: + name: facet_queries + description: Collection of facet query responses with the query string values + and counts + from_schema: https://w3id.org/monarch/monarch-py + rank: 1000 + alias: facet_queries + owner: AssociationResults + domain_of: + - AssociationResults + - CompactAssociationResults + - AssociationTableResults + - SearchResults + range: FacetValue + multivalued: true + inlined: true + inlined_as_list: true limit: name: limit description: number of items to return in a response diff --git a/docs/Data-Model/AssociationTableResults/index.html b/docs/Data-Model/AssociationTableResults/index.html index a6b5ff440..0e701e02a 100644 --- a/docs/Data-Model/AssociationTableResults/index.html +++ b/docs/Data-Model/AssociationTableResults/index.html @@ -1026,6 +1026,24 @@

Class: AssociationTableResults

Results <|-- AssociationTableResults click Results href "../Results" + AssociationTableResults : facet_fields + + + + + AssociationTableResults --> "*" FacetField : facet_fields + click FacetField href "../FacetField" + + + AssociationTableResults : facet_queries + + + + + AssociationTableResults --> "*" FacetValue : facet_queries + click FacetValue href "../FacetValue" + + AssociationTableResults : items @@ -1066,6 +1084,18 @@

Slots

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 @@ -1119,6 +1149,8 @@

Direct

is_a: Results slots: - items +- facet_fields +- facet_queries slot_usage: items: name: items @@ -1158,6 +1190,39 @@

Induced

multivalued: true inlined: true inlined_as_list: true + facet_fields: + name: facet_fields + description: Collection of facet field responses with the field values and counts + from_schema: https://w3id.org/monarch/monarch-py + rank: 1000 + alias: facet_fields + owner: AssociationTableResults + domain_of: + - AssociationResults + - CompactAssociationResults + - AssociationTableResults + - SearchResults + range: FacetField + multivalued: true + inlined: true + inlined_as_list: true + facet_queries: + name: facet_queries + description: Collection of facet query responses with the query string values + and counts + from_schema: https://w3id.org/monarch/monarch-py + rank: 1000 + alias: facet_queries + owner: AssociationTableResults + domain_of: + - AssociationResults + - CompactAssociationResults + - AssociationTableResults + - SearchResults + range: FacetValue + multivalued: true + inlined: true + inlined_as_list: true limit: name: limit description: number of items to return in a response diff --git a/docs/Data-Model/CompactAssociationResults/index.html b/docs/Data-Model/CompactAssociationResults/index.html index e9a83f138..e1ad62ec9 100644 --- a/docs/Data-Model/CompactAssociationResults/index.html +++ b/docs/Data-Model/CompactAssociationResults/index.html @@ -1026,6 +1026,24 @@

Class: CompactAssociationResults

Results <|-- CompactAssociationResults click Results href "../Results" + CompactAssociationResults : facet_fields + + + + + CompactAssociationResults --> "*" FacetField : facet_fields + click FacetField href "../FacetField" + + + CompactAssociationResults : facet_queries + + + + + CompactAssociationResults --> "*" FacetValue : facet_queries + click FacetValue href "../FacetValue" + + CompactAssociationResults : items @@ -1066,6 +1084,18 @@

Slots

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 @@ -1119,6 +1149,8 @@

Direct

is_a: Results slots: - items +- facet_fields +- facet_queries slot_usage: items: name: items @@ -1158,6 +1190,39 @@

Induced

multivalued: true inlined: true inlined_as_list: true + facet_fields: + name: facet_fields + description: Collection of facet field responses with the field values and counts + from_schema: https://w3id.org/monarch/monarch-py + rank: 1000 + alias: facet_fields + owner: CompactAssociationResults + domain_of: + - AssociationResults + - CompactAssociationResults + - AssociationTableResults + - SearchResults + range: FacetField + multivalued: true + inlined: true + inlined_as_list: true + facet_queries: + name: facet_queries + description: Collection of facet query responses with the query string values + and counts + from_schema: https://w3id.org/monarch/monarch-py + rank: 1000 + alias: facet_queries + owner: CompactAssociationResults + domain_of: + - AssociationResults + - CompactAssociationResults + - AssociationTableResults + - SearchResults + range: FacetValue + multivalued: true + inlined: true + inlined_as_list: true limit: name: limit description: number of items to return in a response diff --git a/docs/Data-Model/FacetField/index.html b/docs/Data-Model/FacetField/index.html index 0740a5c18..14a2d9827 100644 --- a/docs/Data-Model/FacetField/index.html +++ b/docs/Data-Model/FacetField/index.html @@ -1073,6 +1073,24 @@

Usages

+AssociationResults +facet_fields +range +FacetField + + +CompactAssociationResults +facet_fields +range +FacetField + + +AssociationTableResults +facet_fields +range +FacetField + + SearchResults facet_fields range diff --git a/docs/Data-Model/FacetValue/index.html b/docs/Data-Model/FacetValue/index.html index 73b5a7d7c..444eb93e8 100644 --- a/docs/Data-Model/FacetValue/index.html +++ b/docs/Data-Model/FacetValue/index.html @@ -1086,6 +1086,24 @@

Usages

+AssociationResults +facet_queries +range +FacetValue + + +CompactAssociationResults +facet_queries +range +FacetValue + + +AssociationTableResults +facet_queries +range +FacetValue + + FacetField facet_values range diff --git a/docs/Data-Model/SearchResults/index.html b/docs/Data-Model/SearchResults/index.html index 52d98e98e..1625cc5d7 100644 --- a/docs/Data-Model/SearchResults/index.html +++ b/docs/Data-Model/SearchResults/index.html @@ -1198,6 +1198,9 @@

Induced

alias: facet_fields owner: SearchResults domain_of: + - AssociationResults + - CompactAssociationResults + - AssociationTableResults - SearchResults range: FacetField multivalued: true @@ -1212,6 +1215,9 @@

Induced

alias: facet_queries owner: SearchResults domain_of: + - AssociationResults + - CompactAssociationResults + - AssociationTableResults - SearchResults range: FacetValue multivalued: true diff --git a/docs/Data-Model/category/index.html b/docs/Data-Model/category/index.html index 9a5339954..3dd79f034 100644 --- a/docs/Data-Model/category/index.html +++ b/docs/Data-Model/category/index.html @@ -1031,17 +1031,7 @@

Applicable Classes

-DirectionalAssociation -An association that gives it's direction relative to a specified entity -no - - -CompactAssociation - -no - - -SearchResult +AssociationCount yes @@ -1051,25 +1041,35 @@

Applicable Classes

yes -Entity -Represents an Entity in the Monarch KG data model -no - - Association no -AssociationCount +CompactAssociation -yes +no Node UI container class extending Entity with additional information no + +DirectionalAssociation +An association that gives it's direction relative to a specified entity +no + + +Entity +Represents an Entity in the Monarch KG data model +no + + +SearchResult + +yes +

Properties

diff --git a/docs/Data-Model/count/index.html b/docs/Data-Model/count/index.html index 7e22064d4..178c7339d 100644 --- a/docs/Data-Model/count/index.html +++ b/docs/Data-Model/count/index.html @@ -1010,7 +1010,7 @@

Applicable Classes

-HistoBin +AssociationCount no @@ -1020,7 +1020,7 @@

Applicable Classes

no -AssociationCount +HistoBin no diff --git a/docs/Data-Model/deprecated/index.html b/docs/Data-Model/deprecated/index.html index c1abf6bd0..1b5aae8ea 100644 --- a/docs/Data-Model/deprecated/index.html +++ b/docs/Data-Model/deprecated/index.html @@ -1010,6 +1010,11 @@

Applicable Classes

+Entity +Represents an Entity in the Monarch KG data model +no + + SearchResult no @@ -1019,11 +1024,6 @@

Applicable Classes

UI container class extending Entity with additional information no - -Entity -Represents an Entity in the Monarch KG data model -no -

Properties

diff --git a/docs/Data-Model/description/index.html b/docs/Data-Model/description/index.html index 8a4acb531..60899a856 100644 --- a/docs/Data-Model/description/index.html +++ b/docs/Data-Model/description/index.html @@ -1009,6 +1009,11 @@

Applicable Classes

+Entity +Represents an Entity in the Monarch KG data model +no + + SearchResult no @@ -1018,11 +1023,6 @@

Applicable Classes

UI container class extending Entity with additional information no - -Entity -Represents an Entity in the Monarch KG data model -no -

Properties

diff --git a/docs/Data-Model/facet_fields/index.html b/docs/Data-Model/facet_fields/index.html index 4d1d44dd3..04aaf3bc6 100644 --- a/docs/Data-Model/facet_fields/index.html +++ b/docs/Data-Model/facet_fields/index.html @@ -1010,10 +1010,25 @@

Applicable Classes

+AssociationResults + +no + + SearchResults no + +AssociationTableResults + +no + + +CompactAssociationResults + +no +

Properties

@@ -1057,6 +1072,9 @@

LinkML Source

rank: 1000 alias: facet_fields domain_of: +- AssociationResults +- CompactAssociationResults +- AssociationTableResults - SearchResults range: FacetField multivalued: true diff --git a/docs/Data-Model/facet_queries/index.html b/docs/Data-Model/facet_queries/index.html index 85594a376..3c36ebbb2 100644 --- a/docs/Data-Model/facet_queries/index.html +++ b/docs/Data-Model/facet_queries/index.html @@ -1010,10 +1010,25 @@

Applicable Classes

+AssociationResults + +no + + SearchResults no + +AssociationTableResults + +no + + +CompactAssociationResults + +no +

Properties

@@ -1058,6 +1073,9 @@

LinkML Source

rank: 1000 alias: facet_queries domain_of: +- AssociationResults +- CompactAssociationResults +- AssociationTableResults - SearchResults range: FacetValue multivalued: true diff --git a/docs/Data-Model/full_name/index.html b/docs/Data-Model/full_name/index.html index 901d05268..60e53a070 100644 --- a/docs/Data-Model/full_name/index.html +++ b/docs/Data-Model/full_name/index.html @@ -1010,6 +1010,11 @@

Applicable Classes

+Entity +Represents an Entity in the Monarch KG data model +no + + SearchResult no @@ -1019,11 +1024,6 @@

Applicable Classes

UI container class extending Entity with additional information no - -Entity -Represents an Entity in the Monarch KG data model -no -

Properties

diff --git a/docs/Data-Model/has_phenotype/index.html b/docs/Data-Model/has_phenotype/index.html index 274a2088a..494c90c63 100644 --- a/docs/Data-Model/has_phenotype/index.html +++ b/docs/Data-Model/has_phenotype/index.html @@ -1010,6 +1010,11 @@

Applicable Classes

+Entity +Represents an Entity in the Monarch KG data model +no + + SearchResult no @@ -1019,11 +1024,6 @@

Applicable Classes

UI container class extending Entity with additional information no - -Entity -Represents an Entity in the Monarch KG data model -no -

Properties

diff --git a/docs/Data-Model/has_phenotype_closure/index.html b/docs/Data-Model/has_phenotype_closure/index.html index dd593c123..c9423dfb7 100644 --- a/docs/Data-Model/has_phenotype_closure/index.html +++ b/docs/Data-Model/has_phenotype_closure/index.html @@ -1010,6 +1010,11 @@

Applicable Classes

+Entity +Represents an Entity in the Monarch KG data model +no + + SearchResult no @@ -1019,11 +1024,6 @@

Applicable Classes

UI container class extending Entity with additional information no - -Entity -Represents an Entity in the Monarch KG data model -no -

Properties

diff --git a/docs/Data-Model/has_phenotype_closure_label/index.html b/docs/Data-Model/has_phenotype_closure_label/index.html index 92ccf7de1..0f86d8505 100644 --- a/docs/Data-Model/has_phenotype_closure_label/index.html +++ b/docs/Data-Model/has_phenotype_closure_label/index.html @@ -1010,6 +1010,11 @@

Applicable Classes

+Entity +Represents an Entity in the Monarch KG data model +no + + SearchResult no @@ -1019,11 +1024,6 @@

Applicable Classes

UI container class extending Entity with additional information no - -Entity -Represents an Entity in the Monarch KG data model -no -

Properties

diff --git a/docs/Data-Model/has_phenotype_count/index.html b/docs/Data-Model/has_phenotype_count/index.html index b848c4817..7ecf51261 100644 --- a/docs/Data-Model/has_phenotype_count/index.html +++ b/docs/Data-Model/has_phenotype_count/index.html @@ -1010,6 +1010,11 @@

Applicable Classes

+Entity +Represents an Entity in the Monarch KG data model +no + + SearchResult no @@ -1019,11 +1024,6 @@

Applicable Classes

UI container class extending Entity with additional information no - -Entity -Represents an Entity in the Monarch KG data model -no -

Properties

diff --git a/docs/Data-Model/has_phenotype_label/index.html b/docs/Data-Model/has_phenotype_label/index.html index b3cb690e8..996ed096e 100644 --- a/docs/Data-Model/has_phenotype_label/index.html +++ b/docs/Data-Model/has_phenotype_label/index.html @@ -1010,6 +1010,11 @@

Applicable Classes

+Entity +Represents an Entity in the Monarch KG data model +no + + SearchResult no @@ -1019,11 +1024,6 @@

Applicable Classes

UI container class extending Entity with additional information no - -Entity -Represents an Entity in the Monarch KG data model -no -

Properties

diff --git a/docs/Data-Model/id/index.html b/docs/Data-Model/id/index.html index a6fdd2fe1..0b4d80e22 100644 --- a/docs/Data-Model/id/index.html +++ b/docs/Data-Model/id/index.html @@ -1009,32 +1009,27 @@

Applicable Classes

-HistoPheno +Association no -DirectionalAssociation -An association that gives it's direction relative to a specified entity +ExpandedCurie +A curie bundled along with its expanded url no -SearchResult - +Node +UI container class extending Entity with additional information no -MultiEntityAssociationResults +HistoBin no -ExpandedCurie -A curie bundled along with its expanded url -no - - -TermInfo +HistoPheno no @@ -1044,23 +1039,28 @@

Applicable Classes

no +DirectionalAssociation +An association that gives it's direction relative to a specified entity +no + + Entity Represents an Entity in the Monarch KG data model no -HistoBin +MultiEntityAssociationResults no -Association +SearchResult no -Node -UI container class extending Entity with additional information +TermInfo + no diff --git a/docs/Data-Model/in_taxon/index.html b/docs/Data-Model/in_taxon/index.html index 75de821af..56a51fd65 100644 --- a/docs/Data-Model/in_taxon/index.html +++ b/docs/Data-Model/in_taxon/index.html @@ -1025,6 +1025,11 @@

Applicable Classes

+Entity +Represents an Entity in the Monarch KG data model +no + + SearchResult no @@ -1034,11 +1039,6 @@

Applicable Classes

UI container class extending Entity with additional information no - -Entity -Represents an Entity in the Monarch KG data model -no -

Properties

diff --git a/docs/Data-Model/in_taxon_label/index.html b/docs/Data-Model/in_taxon_label/index.html index 90d85e38a..8ec286986 100644 --- a/docs/Data-Model/in_taxon_label/index.html +++ b/docs/Data-Model/in_taxon_label/index.html @@ -1025,6 +1025,11 @@

Applicable Classes

+Entity +Represents an Entity in the Monarch KG data model +no + + SearchResult no @@ -1034,11 +1039,6 @@

Applicable Classes

UI container class extending Entity with additional information no - -Entity -Represents an Entity in the Monarch KG data model -no -

Properties

diff --git a/docs/Data-Model/iri/index.html b/docs/Data-Model/iri/index.html index 32140b547..000a357b9 100644 --- a/docs/Data-Model/iri/index.html +++ b/docs/Data-Model/iri/index.html @@ -1009,6 +1009,11 @@

Applicable Classes

+Entity +Represents an Entity in the Monarch KG data model +no + + SearchResult no @@ -1018,11 +1023,6 @@

Applicable Classes

UI container class extending Entity with additional information no - -Entity -Represents an Entity in the Monarch KG data model -no -

Properties

diff --git a/docs/Data-Model/items/index.html b/docs/Data-Model/items/index.html index 97823b033..440d50909 100644 --- a/docs/Data-Model/items/index.html +++ b/docs/Data-Model/items/index.html @@ -1010,48 +1010,48 @@

Applicable Classes

-HistoPheno +CategoryGroupedAssociationResults yes -SearchResults - +MappingResults +SSSOM Mappings returned as a results collection yes -AssociationResults - +AssociationCountList +Container class for a list of association counts yes -EntityResults +HistoPheno yes -AssociationCountList -Container class for a list of association counts +SearchResults + yes -CategoryGroupedAssociationResults +CompactAssociationResults yes -AssociationTableResults +AssociationResults yes -CompactAssociationResults +AssociationTableResults yes -MappingResults -SSSOM Mappings returned as a results collection +EntityResults + yes diff --git a/docs/Data-Model/label/index.html b/docs/Data-Model/label/index.html index b134fa359..e58b99a81 100644 --- a/docs/Data-Model/label/index.html +++ b/docs/Data-Model/label/index.html @@ -1009,27 +1009,27 @@

Applicable Classes

-FacetField +AssociationCount no -FacetValue +FacetField no -TermInfo +HistoBin no -HistoBin +FacetValue no -AssociationCount +TermInfo no diff --git a/docs/Data-Model/limit/index.html b/docs/Data-Model/limit/index.html index 0dbfaf715..e5f196e13 100644 --- a/docs/Data-Model/limit/index.html +++ b/docs/Data-Model/limit/index.html @@ -1010,48 +1010,48 @@

Applicable Classes

-SearchResults +CategoryGroupedAssociationResults no -AssociationResults +Results no -EntityResults - +MappingResults +SSSOM Mappings returned as a results collection no -MultiEntityAssociationResults +SearchResults no -CategoryGroupedAssociationResults +CompactAssociationResults no -Results +AssociationResults no -AssociationTableResults +MultiEntityAssociationResults no -CompactAssociationResults +AssociationTableResults no -MappingResults -SSSOM Mappings returned as a results collection +EntityResults + no diff --git a/docs/Data-Model/name/index.html b/docs/Data-Model/name/index.html index 97f05ecb9..957f442be 100644 --- a/docs/Data-Model/name/index.html +++ b/docs/Data-Model/name/index.html @@ -1031,23 +1031,23 @@

Applicable Classes

-Node -UI container class extending Entity with additional information +Entity +Represents an Entity in the Monarch KG data model no -SearchResult +MultiEntityAssociationResults -yes +no -MultiEntityAssociationResults +SearchResult -no +yes -Entity -Represents an Entity in the Monarch KG data model +Node +UI container class extending Entity with additional information no diff --git a/docs/Data-Model/namespace/index.html b/docs/Data-Model/namespace/index.html index 6dd99bd71..1574ad981 100644 --- a/docs/Data-Model/namespace/index.html +++ b/docs/Data-Model/namespace/index.html @@ -1010,6 +1010,11 @@

Applicable Classes

+Entity +Represents an Entity in the Monarch KG data model +no + + SearchResult no @@ -1019,11 +1024,6 @@

Applicable Classes

UI container class extending Entity with additional information no - -Entity -Represents an Entity in the Monarch KG data model -no -

Properties

diff --git a/docs/Data-Model/negated/index.html b/docs/Data-Model/negated/index.html index 0428658ed..f6f0a9412 100644 --- a/docs/Data-Model/negated/index.html +++ b/docs/Data-Model/negated/index.html @@ -1014,12 +1014,12 @@

Applicable Classes

no -Association +CompactAssociation no -CompactAssociation +Association no diff --git a/docs/Data-Model/object/index.html b/docs/Data-Model/object/index.html index bff6dca52..615cd1e75 100644 --- a/docs/Data-Model/object/index.html +++ b/docs/Data-Model/object/index.html @@ -1014,12 +1014,12 @@

Applicable Classes

no -Association +CompactAssociation no -CompactAssociation +Association no diff --git a/docs/Data-Model/object_id/index.html b/docs/Data-Model/object_id/index.html index 7d3678298..a55753c4d 100644 --- a/docs/Data-Model/object_id/index.html +++ b/docs/Data-Model/object_id/index.html @@ -1009,13 +1009,13 @@

Applicable Classes

-TermPairwiseSimilarity -A simple pairwise similarity between two atomic concepts/terms +Mapping +A minimal class to hold a SSSOM mapping no -Mapping -A minimal class to hold a SSSOM mapping +TermPairwiseSimilarity +A simple pairwise similarity between two atomic concepts/terms no diff --git a/docs/Data-Model/object_label/index.html b/docs/Data-Model/object_label/index.html index 3d260b897..53d892612 100644 --- a/docs/Data-Model/object_label/index.html +++ b/docs/Data-Model/object_label/index.html @@ -1024,19 +1024,24 @@

Applicable Classes

-DirectionalAssociation -An association that gives it's direction relative to a specified entity +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 -CompactAssociation +Association no -AssociationTypeMapping -A data class to hold the necessary information to produce association type co... -yes +CompactAssociation + +no Mapping @@ -1044,13 +1049,8 @@

Applicable Classes

no -TermPairwiseSimilarity -A simple pairwise similarity between two atomic concepts/terms -no - - -Association - +DirectionalAssociation +An association that gives it's direction relative to a specified entity no diff --git a/docs/Data-Model/offset/index.html b/docs/Data-Model/offset/index.html index 3b628b823..e5560e41e 100644 --- a/docs/Data-Model/offset/index.html +++ b/docs/Data-Model/offset/index.html @@ -1010,48 +1010,48 @@

Applicable Classes

-SearchResults +CategoryGroupedAssociationResults no -AssociationResults +Results no -EntityResults - +MappingResults +SSSOM Mappings returned as a results collection no -MultiEntityAssociationResults +SearchResults no -CategoryGroupedAssociationResults +CompactAssociationResults no -Results +AssociationResults no -AssociationTableResults +MultiEntityAssociationResults no -CompactAssociationResults +AssociationTableResults no -MappingResults -SSSOM Mappings returned as a results collection +EntityResults + no diff --git a/docs/Data-Model/predicate/index.html b/docs/Data-Model/predicate/index.html index 392d6b7d4..8e2322201 100644 --- a/docs/Data-Model/predicate/index.html +++ b/docs/Data-Model/predicate/index.html @@ -1014,12 +1014,12 @@

Applicable Classes

no -Association +CompactAssociation no -CompactAssociation +Association no diff --git a/docs/Data-Model/provided_by/index.html b/docs/Data-Model/provided_by/index.html index 2fb349c75..2abb5e41c 100644 --- a/docs/Data-Model/provided_by/index.html +++ b/docs/Data-Model/provided_by/index.html @@ -1009,28 +1009,28 @@

Applicable Classes

-DirectionalAssociation -An association that gives it's direction relative to a specified entity +Association + no -SearchResult - +Node +UI container class extending Entity with additional information no -Entity -Represents an Entity in the Monarch KG data model +DirectionalAssociation +An association that gives it's direction relative to a specified entity no -Association - +Entity +Represents an Entity in the Monarch KG data model no -Node -UI container class extending Entity with additional information +SearchResult + no diff --git a/docs/Data-Model/score/index.html b/docs/Data-Model/score/index.html index 880540c9f..50e984ef6 100644 --- a/docs/Data-Model/score/index.html +++ b/docs/Data-Model/score/index.html @@ -1032,17 +1032,17 @@

Applicable Classes

-SearchResult +SemsimSearchResult no -SemsimSearchResult +BestMatch no -BestMatch +SearchResult no diff --git a/docs/Data-Model/subject/index.html b/docs/Data-Model/subject/index.html index a07b18469..cf40fd4e4 100644 --- a/docs/Data-Model/subject/index.html +++ b/docs/Data-Model/subject/index.html @@ -1009,22 +1009,22 @@

Applicable Classes

+SemsimSearchResult + +yes + + DirectionalAssociation An association that gives it's direction relative to a specified entity no -Association +CompactAssociation no -SemsimSearchResult - -yes - - -CompactAssociation +Association no diff --git a/docs/Data-Model/subject_id/index.html b/docs/Data-Model/subject_id/index.html index e8ac15b96..4465006e7 100644 --- a/docs/Data-Model/subject_id/index.html +++ b/docs/Data-Model/subject_id/index.html @@ -1009,13 +1009,13 @@

Applicable Classes

-TermPairwiseSimilarity -A simple pairwise similarity between two atomic concepts/terms +Mapping +A minimal class to hold a SSSOM mapping no -Mapping -A minimal class to hold a SSSOM mapping +TermPairwiseSimilarity +A simple pairwise similarity between two atomic concepts/terms no diff --git a/docs/Data-Model/subject_label/index.html b/docs/Data-Model/subject_label/index.html index c5f5a9eec..a8ce91c44 100644 --- a/docs/Data-Model/subject_label/index.html +++ b/docs/Data-Model/subject_label/index.html @@ -1024,19 +1024,24 @@

Applicable Classes

-DirectionalAssociation -An association that gives it's direction relative to a specified entity +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 -CompactAssociation +Association no -AssociationTypeMapping -A data class to hold the necessary information to produce association type co... -yes +CompactAssociation + +no Mapping @@ -1044,13 +1049,8 @@

Applicable Classes

no -TermPairwiseSimilarity -A simple pairwise similarity between two atomic concepts/terms -no - - -Association - +DirectionalAssociation +An association that gives it's direction relative to a specified entity no diff --git a/docs/Data-Model/symbol/index.html b/docs/Data-Model/symbol/index.html index 83b78471e..84eb09dd8 100644 --- a/docs/Data-Model/symbol/index.html +++ b/docs/Data-Model/symbol/index.html @@ -1009,6 +1009,11 @@

Applicable Classes

+Entity +Represents an Entity in the Monarch KG data model +no + + SearchResult no @@ -1018,11 +1023,6 @@

Applicable Classes

UI container class extending Entity with additional information no - -Entity -Represents an Entity in the Monarch KG data model -no -

Properties

diff --git a/docs/Data-Model/synonym/index.html b/docs/Data-Model/synonym/index.html index 737bfef49..1d3ef4aa6 100644 --- a/docs/Data-Model/synonym/index.html +++ b/docs/Data-Model/synonym/index.html @@ -1009,6 +1009,11 @@

Applicable Classes

+Entity +Represents an Entity in the Monarch KG data model +no + + SearchResult no @@ -1018,11 +1023,6 @@

Applicable Classes

UI container class extending Entity with additional information no - -Entity -Represents an Entity in the Monarch KG data model -no -

Properties

diff --git a/docs/Data-Model/total/index.html b/docs/Data-Model/total/index.html index b5c2d98e9..d92407afe 100644 --- a/docs/Data-Model/total/index.html +++ b/docs/Data-Model/total/index.html @@ -1010,48 +1010,48 @@

Applicable Classes

-SearchResults +CategoryGroupedAssociationResults no -AssociationResults +Results no -EntityResults - +MappingResults +SSSOM Mappings returned as a results collection no -MultiEntityAssociationResults +SearchResults no -CategoryGroupedAssociationResults +CompactAssociationResults no -Results +AssociationResults no -AssociationTableResults +MultiEntityAssociationResults no -CompactAssociationResults +AssociationTableResults no -MappingResults -SSSOM Mappings returned as a results collection +EntityResults + no diff --git a/docs/Data-Model/uri/index.html b/docs/Data-Model/uri/index.html index 933517fc9..51d0977f4 100644 --- a/docs/Data-Model/uri/index.html +++ b/docs/Data-Model/uri/index.html @@ -1010,6 +1010,11 @@

Applicable Classes

+Entity +Represents an Entity in the Monarch KG data model +no + + SearchResult no @@ -1019,11 +1024,6 @@

Applicable Classes

UI container class extending Entity with additional information no - -Entity -Represents an Entity in the Monarch KG data model -no -

Properties

diff --git a/docs/Data-Model/url/index.html b/docs/Data-Model/url/index.html index ace691a2c..17b07bb5c 100644 --- a/docs/Data-Model/url/index.html +++ b/docs/Data-Model/url/index.html @@ -1009,13 +1009,13 @@

Applicable Classes

-ExpandedCurie -A curie bundled along with its expanded url +Release +A class to hold information about a release of the Monarch KG no -Release -A class to hold information about a release of the Monarch KG +ExpandedCurie +A curie bundled along with its expanded url no diff --git a/docs/Data-Model/xref/index.html b/docs/Data-Model/xref/index.html index 476acd4fe..499d37d86 100644 --- a/docs/Data-Model/xref/index.html +++ b/docs/Data-Model/xref/index.html @@ -1009,6 +1009,11 @@

Applicable Classes

+Entity +Represents an Entity in the Monarch KG data model +no + + SearchResult no @@ -1018,11 +1023,6 @@

Applicable Classes

UI container class extending Entity with additional information no - -Entity -Represents an Entity in the Monarch KG data model -no -

Properties

diff --git a/docs/Usage/Implementations/Solr/index.html b/docs/Usage/Implementations/Solr/index.html index 694906079..999166886 100644 --- a/docs/Usage/Implementations/Solr/index.html +++ b/docs/Usage/Implementations/Solr/index.html @@ -1377,6 +1377,48 @@

+ facet_fields + + Optional[List[str]] + + +
+

List of fields to include facet counts for. Defaults to None.

+
+ + + None + + + + facet_queries + + Optional[List[str]] + + +
+

List of queries to include facet counts for. Defaults to None.

+
+ + + None + + + + filter_queries + + Optional[List[str]] + + +
+

List of queries to filter results by. Defaults to None.

+
+ + + None + + compact diff --git a/docs/search/search_index.json b/docs/search/search_index.json index 2c16fcaf3..9716efd10 100644 --- a/docs/search/search_index.json +++ b/docs/search/search_index.json @@ -1 +1 @@ -{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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

"},{"location":"Data-Model/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Boolean/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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

"},{"location":"Data-Model/Curie/#comments","title":"Comments","text":""},{"location":"Data-Model/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Curie/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Date/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Datetime/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Decimal/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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

"},{"location":"Data-Model/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Double/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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

"},{"location":"Data-Model/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Float/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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

"},{"location":"Data-Model/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Integer/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/ItemCount/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/ItemCount/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/Jsonpath/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Jsonpath/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/Jsonpointer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Jsonpointer/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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

"},{"location":"Data-Model/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Ncname/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/NegativeLogValue/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/NegativeLogValue/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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

"},{"location":"Data-Model/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/NonNegativeFloat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/NonNegativeFloat/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/Objectidentifier/#comments","title":"Comments","text":""},{"location":"Data-Model/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"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

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":""},{"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":""},{"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":""},{"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":"

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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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

"},{"location":"Data-Model/Sparqlpath/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Sparqlpath/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/String/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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

"},{"location":"Data-Model/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Time/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/Uri/#comments","title":"Comments","text":""},{"location":"Data-Model/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Uri/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/ZeroToOne/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/ZeroToOne/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"location":"Data-Model/ancestor_id/#todos","title":"TODOs","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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 CompactAssociation no SearchResult yes 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 Association no AssociationCount yes Node UI container class extending Entity with additional information no"},{"location":"Data-Model/category/#properties","title":"Properties","text":""},{"location":"Data-Model/category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/category/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"location":"Data-Model/count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/count/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"location":"Data-Model/deprecated/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/deprecated/#schema-source","title":"Schema Source","text":""},{"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":""},{"location":"Data-Model/description/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/description/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"location":"Data-Model/direction/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/direction/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"location":"Data-Model/end/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/end/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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:

"},{"location":"Data-Model/graph_stats/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"location":"Data-Model/highlight/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/highlight/#schema-source","title":"Schema Source","text":""},{"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 HistoPheno no DirectionalAssociation An association that gives it's direction relative to a specified entity no SearchResult no MultiEntityAssociationResults no ExpandedCurie A curie bundled along with its expanded url no TermInfo no Mapping A minimal class to hold a SSSOM mapping no Entity Represents an Entity in the Monarch KG data model no HistoBin no Association no Node UI container class extending Entity with additional information no"},{"location":"Data-Model/id/#properties","title":"Properties","text":""},{"location":"Data-Model/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/id/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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

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

"},{"location":"Data-Model/information_content/#inheritance","title":"Inheritance","text":""},{"location":"Data-Model/information_content/#properties","title":"Properties","text":""},{"location":"Data-Model/information_content/#aliases","title":"Aliases","text":""},{"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":""},{"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":""},{"location":"Data-Model/inheritance/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/inheritance/#schema-source","title":"Schema Source","text":""},{"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":""},{"location":"Data-Model/intersection_count/#properties","title":"Properties","text":""},{"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":""},{"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":""},{"location":"Data-Model/iri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/iri/#schema-source","title":"Schema Source","text":""},{"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 HistoPheno yes SearchResults yes AssociationResults yes EntityResults yes AssociationCountList Container class for a list of association counts yes CategoryGroupedAssociationResults yes AssociationTableResults yes CompactAssociationResults yes MappingResults SSSOM Mappings returned as a results collection yes"},{"location":"Data-Model/items/#properties","title":"Properties","text":""},{"location":"Data-Model/items/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/items/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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:

"},{"location":"Data-Model/kg/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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 FacetField no FacetValue no TermInfo no HistoBin no AssociationCount no"},{"location":"Data-Model/label/#properties","title":"Properties","text":""},{"location":"Data-Model/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/label/#schema-source","title":"Schema Source","text":""},{"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 SearchResults no AssociationResults no EntityResults no MultiEntityAssociationResults no CategoryGroupedAssociationResults no Results no AssociationTableResults no CompactAssociationResults no MappingResults SSSOM Mappings returned as a results collection no"},{"location":"Data-Model/limit/#properties","title":"Properties","text":""},{"location":"Data-Model/limit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/limit/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"location":"Data-Model/mappings/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/mappings/#schema-source","title":"Schema Source","text":""},{"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":""},{"location":"Data-Model/match_source/#comments","title":"Comments","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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:

"},{"location":"Data-Model/metadata/#schema-source","title":"Schema Source","text":""},{"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":""},{"location":"Data-Model/metric/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/metric/#schema-source","title":"Schema Source","text":""},{"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":""},{"location":"Data-Model/name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no SearchResult yes MultiEntityAssociationResults no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/name/#properties","title":"Properties","text":""},{"location":"Data-Model/name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/name/#schema-source","title":"Schema Source","text":""},{"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":""},{"location":"Data-Model/namespace/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/namespace/#schema-source","title":"Schema Source","text":""},{"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 Association no CompactAssociation no"},{"location":"Data-Model/negated/#properties","title":"Properties","text":""},{"location":"Data-Model/negated/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/negated/#schema-source","title":"Schema Source","text":""},{"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":""},{"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:

"},{"location":"Data-Model/neo4j/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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 Association no CompactAssociation no"},{"location":"Data-Model/object/#properties","title":"Properties","text":""},{"location":"Data-Model/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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 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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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 CompactAssociation no AssociationTypeMapping A data class to hold the necessary information to produce association type co... yes Mapping A minimal class to hold a SSSOM mapping no TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no Association no"},{"location":"Data-Model/object_label/#properties","title":"Properties","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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 SearchResults no AssociationResults no EntityResults no MultiEntityAssociationResults no CategoryGroupedAssociationResults no Results no AssociationTableResults no CompactAssociationResults no MappingResults SSSOM Mappings returned as a results collection no"},{"location":"Data-Model/offset/#properties","title":"Properties","text":""},{"location":"Data-Model/offset/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/offset/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"location":"Data-Model/overlap_coefficient/#properties","title":"Properties","text":""},{"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":""},{"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":""},{"location":"Data-Model/pathway/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/pathway/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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 Association no CompactAssociation no"},{"location":"Data-Model/predicate/#properties","title":"Properties","text":""},{"location":"Data-Model/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/predicate/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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 SearchResult no Entity Represents an Entity in the Monarch KG data model no Association no Node UI container class extending Entity with additional information no"},{"location":"Data-Model/provided_by/#properties","title":"Properties","text":""},{"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":""},{"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 DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no Node UI container class extending Entity with additional information no"},{"location":"Data-Model/provided_by_link/#properties","title":"Properties","text":""},{"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":""},{"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":""},{"location":"Data-Model/publications/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/publications/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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:

"},{"location":"Data-Model/qc_report/#schema-source","title":"Schema Source","text":""},{"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":""},{"location":"Data-Model/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifier/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"location":"Data-Model/qualifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifiers/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"location":"Data-Model/score/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no SemsimSearchResult no BestMatch no"},{"location":"Data-Model/score/#properties","title":"Properties","text":""},{"location":"Data-Model/score/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/score/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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 SemsimSearchResult no BestMatch no"},{"location":"Data-Model/similarity/#properties","title":"Properties","text":""},{"location":"Data-Model/similarity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/similarity/#schema-source","title":"Schema Source","text":""},{"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":""},{"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:

"},{"location":"Data-Model/solr/#schema-source","title":"Schema Source","text":""},{"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":""},{"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:

"},{"location":"Data-Model/sqlite/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"location":"Data-Model/start/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/start/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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 Association no SemsimSearchResult yes CompactAssociation no"},{"location":"Data-Model/subject/#properties","title":"Properties","text":""},{"location":"Data-Model/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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 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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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 CompactAssociation no AssociationTypeMapping A data class to hold the necessary information to produce association type co... yes Mapping A minimal class to hold a SSSOM mapping no TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no Association no"},{"location":"Data-Model/subject_label/#properties","title":"Properties","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"location":"Data-Model/subsumed_by_score/#properties","title":"Properties","text":""},{"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":""},{"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":""},{"location":"Data-Model/subsumes_score/#properties","title":"Properties","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"location":"Data-Model/symbol/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/symbol/#schema-source","title":"Schema Source","text":""},{"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":""},{"location":"Data-Model/symmetric/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/symmetric/#schema-source","title":"Schema Source","text":""},{"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":""},{"location":"Data-Model/synonym/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/synonym/#schema-source","title":"Schema Source","text":""},{"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":""},{"location":"Data-Model/text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/text/#schema-source","title":"Schema Source","text":""},{"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":""},{"location":"Data-Model/tokens/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/tokens/#schema-source","title":"Schema Source","text":""},{"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 SearchResults no AssociationResults no EntityResults no MultiEntityAssociationResults no CategoryGroupedAssociationResults no Results no AssociationTableResults no CompactAssociationResults no MappingResults SSSOM Mappings returned as a results collection no"},{"location":"Data-Model/total/#properties","title":"Properties","text":""},{"location":"Data-Model/total/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/total/#schema-source","title":"Schema Source","text":""},{"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":""},{"location":"Data-Model/union_count/#properties","title":"Properties","text":""},{"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":""},{"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":""},{"location":"Data-Model/uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/uri/#schema-source","title":"Schema Source","text":""},{"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":""},{"location":"Data-Model/url/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/url/#schema-source","title":"Schema Source","text":""},{"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":""},{"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:

"},{"location":"Data-Model/version/#schema-source","title":"Schema Source","text":""},{"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":""},{"location":"Data-Model/xref/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/xref/#schema-source","title":"Schema Source","text":""},{"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":""},{"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:

Commands:

"},{"location":"Usage/CLI/#monarch-association-counts","title":"monarch association-counts","text":"

Retrieve the association counts for a given entity

Usage:

$ monarch association-counts [OPTIONS] ENTITY\n

Arguments:

Options:

"},{"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:

Options:

"},{"location":"Usage/CLI/#monarch-associations","title":"monarch associations","text":"

Paginate through associations

Usage:

$ monarch associations [OPTIONS]\n

Options:

"},{"location":"Usage/CLI/#monarch-autocomplete","title":"monarch autocomplete","text":"

Return entity autcomplete matches for a query string

Usage:

$ monarch autocomplete [OPTIONS] Q\n

Arguments:

Options:

"},{"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:

Options:

"},{"location":"Usage/CLI/#monarch-entity","title":"monarch entity","text":"

Retrieve an entity by ID

Usage:

$ monarch entity [OPTIONS] ENTITY_ID\n

Arguments:

Options:

"},{"location":"Usage/CLI/#monarch-histopheno","title":"monarch histopheno","text":"

Retrieve the histopheno associations for a given subject

Usage:

$ monarch histopheno [OPTIONS] SUBJECT\n

Arguments:

Options:

"},{"location":"Usage/CLI/#monarch-mappings","title":"monarch mappings","text":"

Usage:

$ monarch mappings [OPTIONS]\n

Options:

"},{"location":"Usage/CLI/#monarch-multi-entity-associations","title":"monarch multi-entity-associations","text":"

Paginate through associations for multiple entities

Usage:

$ monarch multi-entity-associations [OPTIONS]\n

Options:

"},{"location":"Usage/CLI/#monarch-release","title":"monarch release","text":"

Retrieve metadata for a specific release

Usage:

$ monarch release [OPTIONS] RELEASE_VER\n

Arguments:

Options:

"},{"location":"Usage/CLI/#monarch-releases","title":"monarch releases","text":"

List all available releases of the Monarch Knowledge Graph

Usage:

$ monarch releases [OPTIONS]\n

Options:

"},{"location":"Usage/CLI/#monarch-schema","title":"monarch schema","text":"

Print the linkml schema for the data model

Usage:

$ monarch schema [OPTIONS]\n

Options:

"},{"location":"Usage/CLI/#monarch-search","title":"monarch search","text":"

Search for entities

Usage:

$ monarch search [OPTIONS]\n

Options:

"},{"location":"Usage/CLI/#monarch-solr","title":"monarch solr","text":"

Usage:

$ monarch solr [OPTIONS] COMMAND [ARGS]...\n

Options:

Commands:

"},{"location":"Usage/CLI/#monarch-solr-association-counts","title":"monarch solr association-counts","text":"

Retrieve the association counts for a given entity

Usage:

$ monarch solr association-counts [OPTIONS] ENTITY\n

Arguments:

Options:

"},{"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:

Options:

"},{"location":"Usage/CLI/#monarch-solr-associations","title":"monarch solr associations","text":"

Paginate through associations

Usage:

$ monarch solr associations [OPTIONS]\n

Options:

"},{"location":"Usage/CLI/#monarch-solr-autocomplete","title":"monarch solr autocomplete","text":"

Return entity autcomplete matches for a query string

Usage:

$ monarch solr autocomplete [OPTIONS] Q\n

Arguments:

Options:

"},{"location":"Usage/CLI/#monarch-solr-download","title":"monarch solr download","text":"

Download the Monarch Solr KG.

Usage:

$ monarch solr download [OPTIONS] [VERSION]\n

Arguments:

Options:

"},{"location":"Usage/CLI/#monarch-solr-entity","title":"monarch solr entity","text":"

Retrieve an entity by ID

Usage:

$ monarch solr entity [OPTIONS] ENTITY_ID\n

Arguments:

Options:

"},{"location":"Usage/CLI/#monarch-solr-histopheno","title":"monarch solr histopheno","text":"

Retrieve the histopheno associations for a given subject

Usage:

$ monarch solr histopheno [OPTIONS] SUBJECT\n

Arguments:

Options:

"},{"location":"Usage/CLI/#monarch-solr-mappings","title":"monarch solr mappings","text":"

Usage:

$ monarch solr mappings [OPTIONS]\n

Options:

"},{"location":"Usage/CLI/#monarch-solr-multi-entity-associations","title":"monarch solr multi-entity-associations","text":"

Paginate through associations for multiple entities

Usage:

$ monarch solr multi-entity-associations [OPTIONS]\n

Options:

"},{"location":"Usage/CLI/#monarch-solr-search","title":"monarch solr search","text":"

Search for entities

Usage:

$ monarch solr search [OPTIONS]\n

Options:

"},{"location":"Usage/CLI/#monarch-solr-start","title":"monarch solr start","text":"

Starts a local Solr container.

Usage:

$ monarch solr start [OPTIONS]\n

Options:

"},{"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:

"},{"location":"Usage/CLI/#monarch-solr-stop","title":"monarch solr stop","text":"

Stops the local Solr container.

Usage:

$ monarch solr stop [OPTIONS]\n

Options:

"},{"location":"Usage/CLI/#monarch-sql","title":"monarch sql","text":"

Usage:

$ monarch sql [OPTIONS] COMMAND [ARGS]...\n

Options:

Commands:

"},{"location":"Usage/CLI/#monarch-sql-associations","title":"monarch sql associations","text":"

Paginate through associations

Usage:

$ monarch sql associations [OPTIONS]\n

Options:

"},{"location":"Usage/CLI/#monarch-sql-entity","title":"monarch sql entity","text":"

Retrieve an entity by ID

Usage:

$ monarch sql entity [OPTIONS] ENTITY_ID\n

Arguments:

Options:

"},{"location":"Usage/CLI/#monarch-test","title":"monarch test","text":"

Test the CLI

Usage:

$ monarch test [OPTIONS]\n

Options:

"},{"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":""},{"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 facet_fields Optional[List[str]]

List of fields to include facet counts for. Defaults to None.

None facet_queries Optional[List[str]]

List of queries to include facet counts for. Defaults to None.

None filter_queries Optional[List[str]]

List of queries to filter results by. 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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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 : facet_fields\n\n\n\n\n    AssociationResults --> \"*\" FacetField : facet_fields\n    click FacetField href \"../FacetField\"\n\n\n      AssociationResults : facet_queries\n\n\n\n\n    AssociationResults --> \"*\" FacetValue : facet_queries\n    click FacetValue href \"../FacetValue\"\n\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":""},{"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 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/AssociationResults/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/AssociationResults/#schema-source","title":"Schema Source","text":""},{"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\n- facet_fields\n- facet_queries\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  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: AssociationResults\n    domain_of:\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\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: AssociationResults\n    domain_of:\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\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: 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 : facet_fields\n\n\n\n\n    AssociationTableResults --> \"*\" FacetField : facet_fields\n    click FacetField href \"../FacetField\"\n\n\n      AssociationTableResults : facet_queries\n\n\n\n\n    AssociationTableResults --> \"*\" FacetValue : facet_queries\n    click FacetValue href \"../FacetValue\"\n\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":""},{"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 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/AssociationTableResults/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/AssociationTableResults/#schema-source","title":"Schema Source","text":""},{"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\n- facet_fields\n- facet_queries\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  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: AssociationTableResults\n    domain_of:\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\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: AssociationTableResults\n    domain_of:\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\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: 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":""},{"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":""},{"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

"},{"location":"Data-Model/Boolean/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Boolean/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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 : facet_fields\n\n\n\n\n    CompactAssociationResults --> \"*\" FacetField : facet_fields\n    click FacetField href \"../FacetField\"\n\n\n      CompactAssociationResults : facet_queries\n\n\n\n\n    CompactAssociationResults --> \"*\" FacetValue : facet_queries\n    click FacetValue href \"../FacetValue\"\n\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":""},{"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 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/CompactAssociationResults/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/CompactAssociationResults/#schema-source","title":"Schema Source","text":""},{"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\n- facet_fields\n- facet_queries\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  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: CompactAssociationResults\n    domain_of:\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\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: CompactAssociationResults\n    domain_of:\n    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\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: 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

"},{"location":"Data-Model/Curie/#comments","title":"Comments","text":""},{"location":"Data-Model/Curie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Curie/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/Date/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Date/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/DateOrDatetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/DateOrDatetime/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/Datetime/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Datetime/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/Decimal/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Decimal/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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

"},{"location":"Data-Model/Double/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Double/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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 AssociationResults facet_fields range FacetField CompactAssociationResults facet_fields range FacetField AssociationTableResults facet_fields range FacetField 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":""},{"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":""},{"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 AssociationResults facet_queries range FacetValue CompactAssociationResults facet_queries range FacetValue AssociationTableResults facet_queries range FacetValue 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":""},{"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

"},{"location":"Data-Model/Float/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Float/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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

"},{"location":"Data-Model/Integer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Integer/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/ItemCount/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/ItemCount/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/Jsonpath/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Jsonpath/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/Jsonpointer/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Jsonpointer/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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

"},{"location":"Data-Model/Ncname/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Ncname/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/NegativeLogValue/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/NegativeLogValue/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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

"},{"location":"Data-Model/Nodeidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Nodeidentifier/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/NonNegativeFloat/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/NonNegativeFloat/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/Objectidentifier/#comments","title":"Comments","text":""},{"location":"Data-Model/Objectidentifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Objectidentifier/#schema-source","title":"Schema Source","text":""},{"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

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":""},{"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":""},{"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":""},{"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":"

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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\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    - AssociationResults\n    - CompactAssociationResults\n    - AssociationTableResults\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":""},{"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

"},{"location":"Data-Model/Sparqlpath/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Sparqlpath/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/String/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/String/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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

"},{"location":"Data-Model/Time/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Time/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/Uri/#comments","title":"Comments","text":""},{"location":"Data-Model/Uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Uri/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/Uriorcurie/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/Uriorcurie/#schema-source","title":"Schema Source","text":""},{"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

"},{"location":"Data-Model/ZeroToOne/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/ZeroToOne/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"location":"Data-Model/ancestor_id/#todos","title":"TODOs","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"location":"Data-Model/category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AssociationCount yes AssociationTypeMapping A data class to hold the necessary information to produce association type co... yes Association no CompactAssociation no Node UI container class extending Entity with additional information no DirectionalAssociation An association that gives it's direction relative to a specified entity no Entity Represents an Entity in the Monarch KG data model no SearchResult yes"},{"location":"Data-Model/category/#properties","title":"Properties","text":""},{"location":"Data-Model/category/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/category/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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 AssociationCount no FacetValue no HistoBin no"},{"location":"Data-Model/count/#properties","title":"Properties","text":""},{"location":"Data-Model/count/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/count/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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 Entity Represents an Entity in the Monarch KG data model no SearchResult no Node UI container class extending Entity with additional information no"},{"location":"Data-Model/deprecated/#properties","title":"Properties","text":""},{"location":"Data-Model/deprecated/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/deprecated/#schema-source","title":"Schema Source","text":""},{"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 Entity Represents an Entity in the Monarch KG data model no SearchResult no Node UI container class extending Entity with additional information no"},{"location":"Data-Model/description/#properties","title":"Properties","text":""},{"location":"Data-Model/description/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/description/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"location":"Data-Model/direction/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/direction/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"location":"Data-Model/end/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/end/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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 AssociationResults no SearchResults no AssociationTableResults no CompactAssociationResults no"},{"location":"Data-Model/facet_fields/#properties","title":"Properties","text":""},{"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":""},{"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- AssociationResults\n- CompactAssociationResults\n- AssociationTableResults\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 AssociationResults no SearchResults no AssociationTableResults no CompactAssociationResults no"},{"location":"Data-Model/facet_queries/#properties","title":"Properties","text":""},{"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":""},{"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- AssociationResults\n- CompactAssociationResults\n- AssociationTableResults\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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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 Entity Represents an Entity in the Monarch KG data model no SearchResult no Node UI container class extending Entity with additional information no"},{"location":"Data-Model/full_name/#properties","title":"Properties","text":""},{"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":""},{"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":""},{"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:

"},{"location":"Data-Model/graph_stats/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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 Entity Represents an Entity in the Monarch KG data model no SearchResult no Node UI container class extending Entity with additional information no"},{"location":"Data-Model/has_phenotype/#properties","title":"Properties","text":""},{"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":""},{"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 Entity Represents an Entity in the Monarch KG data model no SearchResult no Node UI container class extending Entity with additional information no"},{"location":"Data-Model/has_phenotype_closure/#properties","title":"Properties","text":""},{"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":""},{"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 Entity Represents an Entity in the Monarch KG data model no SearchResult no Node UI container class extending Entity with additional information no"},{"location":"Data-Model/has_phenotype_closure_label/#properties","title":"Properties","text":""},{"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":""},{"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 Entity Represents an Entity in the Monarch KG data model no SearchResult no Node UI container class extending Entity with additional information no"},{"location":"Data-Model/has_phenotype_count/#properties","title":"Properties","text":""},{"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":""},{"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 Entity Represents an Entity in the Monarch KG data model no SearchResult no Node UI container class extending Entity with additional information no"},{"location":"Data-Model/has_phenotype_label/#properties","title":"Properties","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"location":"Data-Model/highlight/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/highlight/#schema-source","title":"Schema Source","text":""},{"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 Association no ExpandedCurie A curie bundled along with its expanded url no Node UI container class extending Entity with additional information no HistoBin no HistoPheno no Mapping A minimal class to hold a SSSOM mapping no DirectionalAssociation An association that gives it's direction relative to a specified entity no Entity Represents an Entity in the Monarch KG data model no MultiEntityAssociationResults no SearchResult no TermInfo no"},{"location":"Data-Model/id/#properties","title":"Properties","text":""},{"location":"Data-Model/id/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/id/#schema-source","title":"Schema Source","text":""},{"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":""},{"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 SearchResult no Node UI container class extending Entity with additional information no"},{"location":"Data-Model/in_taxon/#properties","title":"Properties","text":""},{"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":""},{"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":""},{"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 SearchResult no Node UI container class extending Entity with additional information no"},{"location":"Data-Model/in_taxon_label/#properties","title":"Properties","text":""},{"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":""},{"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

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

"},{"location":"Data-Model/information_content/#inheritance","title":"Inheritance","text":""},{"location":"Data-Model/information_content/#properties","title":"Properties","text":""},{"location":"Data-Model/information_content/#aliases","title":"Aliases","text":""},{"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":""},{"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":""},{"location":"Data-Model/inheritance/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/inheritance/#schema-source","title":"Schema Source","text":""},{"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":""},{"location":"Data-Model/intersection_count/#properties","title":"Properties","text":""},{"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":""},{"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 Entity Represents an Entity in the Monarch KG data model no SearchResult no Node UI container class extending Entity with additional information no"},{"location":"Data-Model/iri/#properties","title":"Properties","text":""},{"location":"Data-Model/iri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/iri/#schema-source","title":"Schema Source","text":""},{"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 CategoryGroupedAssociationResults yes MappingResults SSSOM Mappings returned as a results collection yes AssociationCountList Container class for a list of association counts yes HistoPheno yes SearchResults yes CompactAssociationResults yes AssociationResults yes AssociationTableResults yes EntityResults yes"},{"location":"Data-Model/items/#properties","title":"Properties","text":""},{"location":"Data-Model/items/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/items/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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:

"},{"location":"Data-Model/kg/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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 AssociationCount no FacetField no HistoBin no FacetValue no TermInfo no"},{"location":"Data-Model/label/#properties","title":"Properties","text":""},{"location":"Data-Model/label/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/label/#schema-source","title":"Schema Source","text":""},{"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 CategoryGroupedAssociationResults no Results no MappingResults SSSOM Mappings returned as a results collection no SearchResults no CompactAssociationResults no AssociationResults no MultiEntityAssociationResults no AssociationTableResults no EntityResults no"},{"location":"Data-Model/limit/#properties","title":"Properties","text":""},{"location":"Data-Model/limit/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/limit/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"location":"Data-Model/mappings/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/mappings/#schema-source","title":"Schema Source","text":""},{"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":""},{"location":"Data-Model/match_source/#comments","title":"Comments","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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:

"},{"location":"Data-Model/metadata/#schema-source","title":"Schema Source","text":""},{"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":""},{"location":"Data-Model/metric/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/metric/#schema-source","title":"Schema Source","text":""},{"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":""},{"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 MultiEntityAssociationResults no SearchResult yes Node UI container class extending Entity with additional information no"},{"location":"Data-Model/name/#properties","title":"Properties","text":""},{"location":"Data-Model/name/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/name/#schema-source","title":"Schema Source","text":""},{"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 Entity Represents an Entity in the Monarch KG data model no SearchResult no Node UI container class extending Entity with additional information no"},{"location":"Data-Model/namespace/#properties","title":"Properties","text":""},{"location":"Data-Model/namespace/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/namespace/#schema-source","title":"Schema Source","text":""},{"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":""},{"location":"Data-Model/negated/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/negated/#schema-source","title":"Schema Source","text":""},{"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":""},{"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:

"},{"location":"Data-Model/neo4j/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"location":"Data-Model/object/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/object/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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 Association no CompactAssociation no Mapping A minimal class to hold a SSSOM mapping no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/object_label/#properties","title":"Properties","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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 CategoryGroupedAssociationResults no Results no MappingResults SSSOM Mappings returned as a results collection no SearchResults no CompactAssociationResults no AssociationResults no MultiEntityAssociationResults no AssociationTableResults no EntityResults no"},{"location":"Data-Model/offset/#properties","title":"Properties","text":""},{"location":"Data-Model/offset/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/offset/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"location":"Data-Model/overlap_coefficient/#properties","title":"Properties","text":""},{"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":""},{"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":""},{"location":"Data-Model/pathway/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/pathway/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"location":"Data-Model/predicate/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/predicate/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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 Association no Node UI container class extending Entity with additional information no DirectionalAssociation An association that gives it's direction relative to a specified entity no Entity Represents an Entity in the Monarch KG data model no SearchResult no"},{"location":"Data-Model/provided_by/#properties","title":"Properties","text":""},{"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":""},{"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 DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no Node UI container class extending Entity with additional information no"},{"location":"Data-Model/provided_by_link/#properties","title":"Properties","text":""},{"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":""},{"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":""},{"location":"Data-Model/publications/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/publications/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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:

"},{"location":"Data-Model/qc_report/#schema-source","title":"Schema Source","text":""},{"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":""},{"location":"Data-Model/qualifier/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifier/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"location":"Data-Model/qualifiers/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/qualifiers/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"location":"Data-Model/score/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SemsimSearchResult no BestMatch no SearchResult no"},{"location":"Data-Model/score/#properties","title":"Properties","text":""},{"location":"Data-Model/score/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/score/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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 SemsimSearchResult no BestMatch no"},{"location":"Data-Model/similarity/#properties","title":"Properties","text":""},{"location":"Data-Model/similarity/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/similarity/#schema-source","title":"Schema Source","text":""},{"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":""},{"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:

"},{"location":"Data-Model/solr/#schema-source","title":"Schema Source","text":""},{"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":""},{"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:

"},{"location":"Data-Model/sqlite/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"location":"Data-Model/start/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/start/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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 SemsimSearchResult yes DirectionalAssociation An association that gives it's direction relative to a specified entity no CompactAssociation no Association no"},{"location":"Data-Model/subject/#properties","title":"Properties","text":""},{"location":"Data-Model/subject/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/subject/#schema-source","title":"Schema Source","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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 Association no CompactAssociation no Mapping A minimal class to hold a SSSOM mapping no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/subject_label/#properties","title":"Properties","text":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"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":""},{"location":"Data-Model/subsumed_by_score/#properties","title":"Properties","text":""},{"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":""},{"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":""},{"location":"Data-Model/subsumes_score/#properties","title":"Properties","text":""},{"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":""},{"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":""},{"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":""},{"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 Entity Represents an Entity in the Monarch KG data model no SearchResult no Node UI container class extending Entity with additional information no"},{"location":"Data-Model/symbol/#properties","title":"Properties","text":""},{"location":"Data-Model/symbol/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/symbol/#schema-source","title":"Schema Source","text":""},{"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":""},{"location":"Data-Model/symmetric/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/symmetric/#schema-source","title":"Schema Source","text":""},{"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 Entity Represents an Entity in the Monarch KG data model no SearchResult no Node UI container class extending Entity with additional information no"},{"location":"Data-Model/synonym/#properties","title":"Properties","text":""},{"location":"Data-Model/synonym/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/synonym/#schema-source","title":"Schema Source","text":""},{"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":""},{"location":"Data-Model/text/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/text/#schema-source","title":"Schema Source","text":""},{"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":""},{"location":"Data-Model/tokens/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/tokens/#schema-source","title":"Schema Source","text":""},{"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 CategoryGroupedAssociationResults no Results no MappingResults SSSOM Mappings returned as a results collection no SearchResults no CompactAssociationResults no AssociationResults no MultiEntityAssociationResults no AssociationTableResults no EntityResults no"},{"location":"Data-Model/total/#properties","title":"Properties","text":""},{"location":"Data-Model/total/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/total/#schema-source","title":"Schema Source","text":""},{"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":""},{"location":"Data-Model/union_count/#properties","title":"Properties","text":""},{"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":""},{"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 Entity Represents an Entity in the Monarch KG data model no SearchResult no Node UI container class extending Entity with additional information no"},{"location":"Data-Model/uri/#properties","title":"Properties","text":""},{"location":"Data-Model/uri/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/uri/#schema-source","title":"Schema Source","text":""},{"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 Release A class to hold information about a release of the Monarch KG no ExpandedCurie A curie bundled along with its expanded url no"},{"location":"Data-Model/url/#properties","title":"Properties","text":""},{"location":"Data-Model/url/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/url/#schema-source","title":"Schema Source","text":""},{"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":""},{"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:

"},{"location":"Data-Model/version/#schema-source","title":"Schema Source","text":""},{"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 Entity Represents an Entity in the Monarch KG data model no SearchResult no Node UI container class extending Entity with additional information no"},{"location":"Data-Model/xref/#properties","title":"Properties","text":""},{"location":"Data-Model/xref/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/xref/#schema-source","title":"Schema Source","text":""},{"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":""},{"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:

Commands:

"},{"location":"Usage/CLI/#monarch-association-counts","title":"monarch association-counts","text":"

Retrieve the association counts for a given entity

Usage:

$ monarch association-counts [OPTIONS] ENTITY\n

Arguments:

Options:

"},{"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:

Options:

"},{"location":"Usage/CLI/#monarch-associations","title":"monarch associations","text":"

Paginate through associations

Usage:

$ monarch associations [OPTIONS]\n

Options:

"},{"location":"Usage/CLI/#monarch-autocomplete","title":"monarch autocomplete","text":"

Return entity autcomplete matches for a query string

Usage:

$ monarch autocomplete [OPTIONS] Q\n

Arguments:

Options:

"},{"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:

Options:

"},{"location":"Usage/CLI/#monarch-entity","title":"monarch entity","text":"

Retrieve an entity by ID

Usage:

$ monarch entity [OPTIONS] ENTITY_ID\n

Arguments:

Options:

"},{"location":"Usage/CLI/#monarch-histopheno","title":"monarch histopheno","text":"

Retrieve the histopheno associations for a given subject

Usage:

$ monarch histopheno [OPTIONS] SUBJECT\n

Arguments:

Options:

"},{"location":"Usage/CLI/#monarch-mappings","title":"monarch mappings","text":"

Usage:

$ monarch mappings [OPTIONS]\n

Options:

"},{"location":"Usage/CLI/#monarch-multi-entity-associations","title":"monarch multi-entity-associations","text":"

Paginate through associations for multiple entities

Usage:

$ monarch multi-entity-associations [OPTIONS]\n

Options:

"},{"location":"Usage/CLI/#monarch-release","title":"monarch release","text":"

Retrieve metadata for a specific release

Usage:

$ monarch release [OPTIONS] RELEASE_VER\n

Arguments:

Options:

"},{"location":"Usage/CLI/#monarch-releases","title":"monarch releases","text":"

List all available releases of the Monarch Knowledge Graph

Usage:

$ monarch releases [OPTIONS]\n

Options:

"},{"location":"Usage/CLI/#monarch-schema","title":"monarch schema","text":"

Print the linkml schema for the data model

Usage:

$ monarch schema [OPTIONS]\n

Options:

"},{"location":"Usage/CLI/#monarch-search","title":"monarch search","text":"

Search for entities

Usage:

$ monarch search [OPTIONS]\n

Options:

"},{"location":"Usage/CLI/#monarch-solr","title":"monarch solr","text":"

Usage:

$ monarch solr [OPTIONS] COMMAND [ARGS]...\n

Options:

Commands:

"},{"location":"Usage/CLI/#monarch-solr-association-counts","title":"monarch solr association-counts","text":"

Retrieve the association counts for a given entity

Usage:

$ monarch solr association-counts [OPTIONS] ENTITY\n

Arguments:

Options:

"},{"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:

Options:

"},{"location":"Usage/CLI/#monarch-solr-associations","title":"monarch solr associations","text":"

Paginate through associations

Usage:

$ monarch solr associations [OPTIONS]\n

Options:

"},{"location":"Usage/CLI/#monarch-solr-autocomplete","title":"monarch solr autocomplete","text":"

Return entity autcomplete matches for a query string

Usage:

$ monarch solr autocomplete [OPTIONS] Q\n

Arguments:

Options:

"},{"location":"Usage/CLI/#monarch-solr-download","title":"monarch solr download","text":"

Download the Monarch Solr KG.

Usage:

$ monarch solr download [OPTIONS] [VERSION]\n

Arguments:

Options:

"},{"location":"Usage/CLI/#monarch-solr-entity","title":"monarch solr entity","text":"

Retrieve an entity by ID

Usage:

$ monarch solr entity [OPTIONS] ENTITY_ID\n

Arguments:

Options:

"},{"location":"Usage/CLI/#monarch-solr-histopheno","title":"monarch solr histopheno","text":"

Retrieve the histopheno associations for a given subject

Usage:

$ monarch solr histopheno [OPTIONS] SUBJECT\n

Arguments:

Options:

"},{"location":"Usage/CLI/#monarch-solr-mappings","title":"monarch solr mappings","text":"

Usage:

$ monarch solr mappings [OPTIONS]\n

Options:

"},{"location":"Usage/CLI/#monarch-solr-multi-entity-associations","title":"monarch solr multi-entity-associations","text":"

Paginate through associations for multiple entities

Usage:

$ monarch solr multi-entity-associations [OPTIONS]\n

Options:

"},{"location":"Usage/CLI/#monarch-solr-search","title":"monarch solr search","text":"

Search for entities

Usage:

$ monarch solr search [OPTIONS]\n

Options:

"},{"location":"Usage/CLI/#monarch-solr-start","title":"monarch solr start","text":"

Starts a local Solr container.

Usage:

$ monarch solr start [OPTIONS]\n

Options:

"},{"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:

"},{"location":"Usage/CLI/#monarch-solr-stop","title":"monarch solr stop","text":"

Stops the local Solr container.

Usage:

$ monarch solr stop [OPTIONS]\n

Options:

"},{"location":"Usage/CLI/#monarch-sql","title":"monarch sql","text":"

Usage:

$ monarch sql [OPTIONS] COMMAND [ARGS]...\n

Options:

Commands:

"},{"location":"Usage/CLI/#monarch-sql-associations","title":"monarch sql associations","text":"

Paginate through associations

Usage:

$ monarch sql associations [OPTIONS]\n

Options:

"},{"location":"Usage/CLI/#monarch-sql-entity","title":"monarch sql entity","text":"

Retrieve an entity by ID

Usage:

$ monarch sql entity [OPTIONS] ENTITY_ID\n

Arguments:

Options:

"},{"location":"Usage/CLI/#monarch-test","title":"monarch test","text":"

Test the CLI

Usage:

$ monarch test [OPTIONS]\n

Options:

"},{"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 facet_fields Optional[List[str]]

List of fields to include facet counts for. Defaults to None.

None facet_queries Optional[List[str]]

List of queries to include facet counts for. Defaults to None.

None filter_queries Optional[List[str]]

List of queries to filter results by. 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":""},{"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