Add curie_map to the model (#376)

This commit makes the `curie_map` a _bona fide_ slot of the `MappingSet` class, that exists independently of the serialisation format. --------- Co-authored-by: Nico Matentzoglu <[email protected]>
mapping-commons · Aug 6, 2024 · 81fe996 · 81fe996
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Showing 18 changed files with 956 additions and 1,939 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,7 @@
 ## Next
 
 - 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))

diff --git a/examples/schema/curie_map.sssom.tsv b/examples/schema/curie_map.sssom.tsv
@@ -0,0 +1,14 @@
+#curie_map:
+#  HP: http://purl.obolibrary.org/obo/HP_
+#  MP: http://purl.obolibrary.org/obo/MP_
+#  orcid: https://orcid.org/
+#mapping_set_id: https://w3id.org/sssom/commons/examples/curie_map.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
+HP:0009124	skos:exactMatch	MP:0000003	semapv:ManualMappingCuration
+HP:0008551	skos:exactMatch	MP:0000018	semapv:ManualMappingCuration
+HP:0000411	skos:exactMatch	MP:0000021	semapv:ManualMappingCuration
diff --git a/project/excel/sssom_schema.xlsx b/project/excel/sssom_schema.xlsx
diff --git a/project/graphql/sssom_schema.graphql b/project/graphql/sssom_schema.graphql
@@ -5,47 +5,6 @@ type ExtensionDefinition
     typeHint: Uriorcurie
   }
 
-type LiteralMapping
-  {
-    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
-  }
-
 type Mapping
   {
     subjectId: EntityReference!
@@ -86,8 +45,8 @@ type Mapping
     matchString: [String]
     subjectPreprocessing: [EntityReference]
     objectPreprocessing: [EntityReference]
-    semanticSimilarityScore: Double
-    semanticSimilarityMeasure: String
+    similarityScore: Double
+    similarityMeasure: String
     seeAlso: [String]
     issueTrackerItem: EntityReference
     other: String
@@ -108,6 +67,7 @@ type MappingRegistry
 
 type MappingSet
   {
+    curieMap: [Prefix]
     mappings: [Mapping]
     mappingSetId: Uri!
     mappingSetVersion: String
@@ -149,6 +109,16 @@ type MappingSetReference
     localName: String
   }
 
+type NoTermFound
+  {
+  }
+
+type Prefix
+  {
+    prefixName: Ncname!
+    prefixUrl: Uri
+  }
+
 type Propagatable
   {
     propagated: Boolean

diff --git a/project/jsonld/sssom_schema.context.jsonld b/project/jsonld/sssom_schema.context.jsonld
@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2024-08-05T10:18:22",
+      "generation_date": "2024-08-06T18:58:48",
       "source": "sssom_schema.yaml"
    },
    "@context": {
@@ -46,6 +46,10 @@
       "curation_rule_text": {
          "@id": "curation_rule_text"
       },
+      "curie_map": {
+         "@type": "@id",
+         "@id": "curie_map"
+      },
       "documentation": {
          "@type": "@id",
          "@id": "documentation"
@@ -89,24 +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"
       },
@@ -248,6 +234,13 @@
          },
          "@id": "predicate_type"
       },
+      "prefix_name": {
+         "@id": "prefix_name"
+      },
+      "prefix_url": {
+         "@type": "@id",
+         "@id": "prefix_url"
+      },
       "propagated": {
          "@type": "xsd:boolean",
          "@id": "propagated"
@@ -270,13 +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"
       },
@@ -321,9 +307,6 @@
       "ExtensionDefinition": {
          "@id": "ExtensionDefinition"
       },
-      "LiteralMapping": {
-         "@id": "owl:Axiom"
-      },
       "Mapping": {
          "@id": "owl:Axiom"
       },
@@ -336,6 +319,12 @@
       "MappingSetReference": {
          "@id": "MappingSetReference"
       },
+      "NoTermFound": {
+         "@id": "NoTermFound"
+      },
+      "Prefix": {
+         "@id": "Prefix"
+      },
       "Propagatable": {
          "@id": "Propagatable"
       }