Specify how to express an unmapped entity using sssom:NoTermFound

CHANGELOG.md

@@ -3,6 +3,7 @@
 ## Next
 
 - Add the concept of "propagatable slots".
+- Add the entity reference `sssom:NoTermFound` of express the concept of an "unmapped entity" ([issue](https://github.com/mapping-commons/sssom/issues/28))
 
 ## SSSOM version 0.15.1
 

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

src/docs/spec-model.md

@@ -81,3 +81,17 @@ In addition, predicates from the following sources MAY also be encouraged:
 
 * any relation from the [Relation Ontology (RO)](https://obofoundry.org/ontology/ro.html);
 * any relation under [skos:mappingRelation](http://www.w3.org/2004/02/skos/core#mappingRelation) in the [Semantic Mapping Vocabulary](https://mapping-commons.github.io/semantic-mapping-vocabulary/).
+
+## Representing unmapped entities
+
+The special value `sssom:NoTermFound` MAY be used as the `object_id` of a mapping to explicitly state that the subject of said mapping cannot be mapped to any entity in the domain represented by the `object_source` slot.
+
+Likewise, the `sssom:NoTermFound` value MAY be used as the `subject_id` of a mapping to state that the object of said mapping cannot be mapped to any entity in the domain represented by the `subject_source` slot.
+
+When that special value is used as the `subject_id` (respectively `object_id`), the `subject_source` (respectively object_source) slot SHOULD be defined.
+
+The `sssom:NoTermFound` value MUST NOT be used in any other slot than subject_id or object_id.
+
+The meaning of the NOT predicate modifier in a mapping that refers to `sssom:NoTermFound` is unspecified.
+
+When computing cardinality values (to fill the mapping_cardinality slot), mappings that refer to `sssom:NoTermFound` MUST be ignored.

src/sssom_schema/schema/sssom_schema.yaml

@@ -781,3 +781,12 @@ classes:
         description: Indicates whether a slot can be propagated from a mapping
           down to individual mappings.
         range: boolean
+  NoTermFound:
+    class_uri: sssom:NoTermFound
+    description: sssom:NoTermFound can be used in place of a subject_id or object_id
+      when the corresponding entity could not be found. It SHOULD be used in conjuction with
+      a corresponding subject_source or object_source to signify where the term was not found.
+    see_also:
+      - https://github.com/mapping-commons/sssom/issues/28
+      - https://github.com/mapping-commons/sssom/blob/master/examples/schema/no_term_found.sssom.tsv
+