Merge branch 'master' into add-curie-map-2

CHANGELOG.md

@@ -4,6 +4,9 @@
 
 - Add the concept of "propagatable slots".
 - Add the `curie_map` to the model (instead of it being a specificity of the SSSOM/TSV format).
+- Add the concept of "extension slots".
+- Add the entity reference `sssom:NoTermFound` to express the concept of an "unmapped entity" ([issue](https://github.com/mapping-commons/sssom/issues/28))
+- Replace `semantic_similarity_score` with `similarity_score` and `semantic_similarity_measure` with `similarity_measure` in the data model ([issue](https://github.com/mapping-commons/sssom/issues/385))
 
 ## SSSOM version 0.15.1
 

examples/schema/extension-slots.sssom.tsv

@@ -0,0 +1,23 @@
+#curie_map:
+#  COMENT: https://example.com/entities/
+#  EXPROP: https://example.org/properties/
+#  ORGENT: https://example.org/entities/
+#mapping_set_id: https://example.org/sets/exo2c-with-extensions
+#mapping_set_title: Sample set EXO2C with extension slots
+#license: https://creativecommons.org/licenses/by/4.0/
+#extension_definitions:
+#  - slot_name: ext_bar
+#    property: EXPROP:barProperty
+#    type_hint: xsd:integer
+#  - slot_name: ext_baz
+#    property: EXPROP:bazProperty
+#    type_hint: linkml:Uriorcurie
+#  - slot_name: ext_foo
+#    property: EXPROP:fooProperty
+#ext_foo: Foo A
+#ext_undeclared_foo: Foo B
+subject_id	subject_label	predicate_id	object_id	object_label	mapping_justification	ext_bar	ext_baz	ext_undeclared_baz
+ORGENT:0001	alice	skos:closeMatch	COMENT:0011	alpha	semapv:ManualMappingCuration	111	ORGENT:BAZ_0001	BAZ A
+ORGENT:0002	bob	skos:closeMatch	COMENT:0012	beta	semapv:ManualMappingCuration	112	ORGENT:BAZ_0002	
+ORGENT:0004	daphne	skos:closeMatch	COMENT:0014	delta	semapv:ManualMappingCuration	114		Baz C
+ORGENT:0005	eve	skos:closeMatch	COMENT:0015	epsilon	semapv:ManualMappingCuration	115	ORGENT:BAZ_0005	Baz E

examples/schema/no_term_found.sssom.tsv

@@ -0,0 +1,16 @@
+#curie_map:
+#  HP: http://purl.obolibrary.org/obo/HP_
+#  MP: http://purl.obolibrary.org/obo/MP_
+#  obo: http://purl.obolibrary.org/obo/
+#  orcid: https://orcid.org/
+#mapping_set_id: https://w3id.org/sssom/commons/examples/no_term_found.sssom.tsv
+#creator_id:
+#  - orcid:0000-0002-7356-1779
+#subject_source: obo:hp
+#object_source: obo:mp
+#license: "https://creativecommons.org/publicdomain/zero/1.0/"
+#mapping_provider: "https://w3id.org/sssom/core_team"
+#comment: This is an example file for the SSSOM for illustration only. Its contents are entirely fabricated.
+subject_id	predicate_id	object_id	mapping_justification
+HP:0009124	skos:exactMatch	MP:0000003	semapv:ManualMappingCuration
+HP:0000411	skos:exactMatch	sssom:NoTermFound	semapv:ManualMappingCuration

examples/schema/similarity_score.sssom.tsv

@@ -0,0 +1,15 @@
+#curie_map:
+#  HP: http://purl.obolibrary.org/obo/HP_
+#  MP: http://purl.obolibrary.org/obo/MP_
+#  orcid: https://orcid.org/
+#  wikidata: https://www.wikidata.org/entity/
+#mapping_set_id: https://w3id.org/sssom/commons/examples/similarity_score.sssom.tsv
+#license: "https://creativecommons.org/publicdomain/zero/1.0/"
+#creator_id:
+#  - orcid:0000-0002-7356-1779
+#mapping_provider: "https://w3id.org/sssom/core_team"
+#comment: This is an example file for the SSSOM for illustration only. Its contents are entirely fabricated.
+subject_id	predicate_id	object_id	mapping_justification	similarity_score	similarity_measure
+HP:0009124	skos:exactMatch	MP:0000003	semapv:LexicalSimilarityThresholdMatching	0.8	wikidata:Q865360
+HP:0008551	skos:exactMatch	MP:0000018	semapv:LexicalSimilarityThresholdMatching	0.4	wikidata:Q865360
+HP:0000411	skos:exactMatch	MP:0000021	semapv:SemanticSimilarityThresholdMatching	1.0	wikidata:Q1784941

project/graphql/sssom_schema.graphql

@@ -1,42 +1,8 @@
-type LiteralMapping
+type ExtensionDefinition
   {
-    literal: String!
-    literalDatatype: Uri
-    predicateId: EntityReference!
-    predicateLabel: String
-    predicateModifier: PredicateModifierEnum
-    objectId: EntityReference!
-    objectLabel: String
-    objectCategory: String
-    mappingJustification: EntityReference!
-    authorId: [EntityReference]
-    authorLabel: [String]
-    reviewerId: [EntityReference]
-    reviewerLabel: [String]
-    creatorId: [EntityReference]
-    creatorLabel: [String]
-    license: Uri
-    literalSource: EntityReference
-    literalSourceVersion: String
-    objectType: EntityTypeEnum
-    objectSource: EntityReference
-    objectSourceVersion: String
-    mappingProvider: Uri
-    mappingSource: EntityReference
-    mappingCardinality: MappingCardinalityEnum
-    mappingTool: String
-    mappingToolVersion: String
-    mappingDate: Date
-    confidence: Double
-    objectMatchField: [EntityReference]
-    matchString: [String]
-    literalPreprocessing: [EntityReference]
-    objectPreprocessing: [EntityReference]
-    similarityScore: Double
-    similarityMeasure: String
-    seeAlso: [String]
-    other: String
-    comment: String
+    slotName: Ncname!
+    property: Uriorcurie
+    typeHint: Uriorcurie
   }
 
 type Mapping
@@ -79,8 +45,8 @@ type Mapping
     matchString: [String]
     subjectPreprocessing: [EntityReference]
     objectPreprocessing: [EntityReference]
-    semanticSimilarityScore: Double
-    semanticSimilarityMeasure: String
+    similarityScore: Double
+    similarityMeasure: String
     seeAlso: [String]
     issueTrackerItem: EntityReference
     other: String
@@ -130,6 +96,7 @@ type MappingSet
     issueTracker: Uri
     other: String
     comment: String
+    extensionDefinitions: [ExtensionDefinition]
   }
 
 type MappingSetReference
@@ -142,6 +109,10 @@ type MappingSetReference
     localName: String
   }
 
+type NoTermFound
+  {
+  }
+
 type Prefix
   {
     prefixName: Ncname!

project/jsonld/sssom_schema.context.jsonld

@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2024-08-05T10:23:03",
+      "generation_date": "2024-08-06T18:58:48",
       "source": "sssom_schema.yaml"
    },
    "@context": {
@@ -54,6 +54,21 @@
          "@type": "@id",
          "@id": "documentation"
       },
+      "extension_definitions": {
+         "@type": "@id",
+         "@id": "extension_definitions"
+      },
+      "property": {
+         "@type": "@id",
+         "@id": "property"
+      },
+      "slot_name": {
+         "@id": "slot_name"
+      },
+      "type_hint": {
+         "@type": "@id",
+         "@id": "type_hint"
+      },
       "homepage": {
          "@type": "@id",
          "@id": "homepage"
@@ -78,24 +93,6 @@
          "@type": "@id",
          "@id": "dcterms:license"
       },
-      "literal": {
-         "@id": "owl:annotatedTarget"
-      },
-      "literal_datatype": {
-         "@type": "@id",
-         "@id": "rdf:datatype"
-      },
-      "literal_preprocessing": {
-         "@type": "rdfs:Resource",
-         "@id": "literal_preprocessing"
-      },
-      "literal_source": {
-         "@type": "rdfs:Resource",
-         "@id": "literal_source"
-      },
-      "literal_source_version": {
-         "@id": "literal_source_version"
-      },
       "local_name": {
          "@id": "local_name"
       },
@@ -266,13 +263,6 @@
       "see_also": {
          "@id": "rdfs:seeAlso"
       },
-      "semantic_similarity_measure": {
-         "@id": "semantic_similarity_measure"
-      },
-      "semantic_similarity_score": {
-         "@type": "xsd:double",
-         "@id": "semantic_similarity_score"
-      },
       "similarity_measure": {
          "@id": "similarity_measure"
       },
@@ -314,8 +304,8 @@
          },
          "@id": "subject_type"
       },
-      "LiteralMapping": {
-         "@id": "owl:Axiom"
+      "ExtensionDefinition": {
+         "@id": "ExtensionDefinition"
       },
       "Mapping": {
          "@id": "owl:Axiom"
@@ -329,6 +319,9 @@
       "MappingSetReference": {
          "@id": "MappingSetReference"
       },
+      "NoTermFound": {
+         "@id": "NoTermFound"
+      },
       "Prefix": {
          "@id": "Prefix"
       },