Add support for extension slots (#375)

This commit updates the SSSOM model to allow for _defined extensions_ as
proposed in #328.

It also updates the description of the data model to describe the use of
both defined and undefined extension, and the specification of the
SSSOM/TSV format to explain how SSSOM/TSV parsers and writers should
deal with such extensions.

Overall, this is exactly what was proposed in [this
comment](#328 (comment))
in #328, except that here we need to split the specification in two
parts (one about extensions in general, independently of the
serialisation format, and one about the SSSOM/TSV serialisation of
extensions), while the initial proposition was in a single block.

Co-authored-by: Nico Matentzoglu <[email protected]>

Author: Damien Goutte-Gattat

CHANGELOG.md

@@ -3,6 +3,7 @@
 ## Next
 
 - Add the concept of "propagatable slots".
+- 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))
 

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

project/excel/sssom_schema.xlsx

@@ -1,3 +1,51 @@
+type ExtensionDefinition
+  {
+    slotName: Ncname!
+    property: Uriorcurie
+    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!
@@ -88,6 +136,7 @@ type MappingSet
     issueTracker: Uri
     other: String
     comment: String
+    extensionDefinitions: [ExtensionDefinition]
   }
 
 type MappingSetReference
@@ -100,3 +149,8 @@ type MappingSetReference
     localName: String
   }
 
+type Propagatable
+  {
+    propagated: Boolean
+  }
+