Issue 6464 taxonspecific (#6477)

* add cross-species analog AP from axioms

closes #6464

@matentzn could you please review this PR?
In addition, I have specific questions:

* Finalise the cross species exact match injection

* updated sparql to include logical definition in taxon

---------

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

src/ontology/Makefile

@@ -204,6 +204,7 @@ filtered.obo: $(SRC)
 	if [ $(GITHUB_ACTION) = false ]; then $(ROBOT) query -i $@ --use-graphs false \
 		--update ../sparql/update/delete-axiom-annotations.ru \
 		--update ../sparql/update/delete-axiom-annotations-by-prefix.ru \
+		--update ../sparql/update/inject-cross-species-analog.ru \
 		remove --term-file config/remove-annotations-before-release.txt \
 		convert -f obo --check false -o $@.obo && mv $@.obo $@; fi
 #egrep -v 'MONDO:(subClassOf|superClassOf|relatedTo)' $< > $@

src/sparql/update/inject-cross-species-analog.ru

@@ -0,0 +1,54 @@
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+prefix IAO: <http://purl.obolibrary.org/obo/IAO_>
+prefix MONDO: <http://purl.obolibrary.org/obo/MONDO_>
+prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+prefix oio: <http://www.geneontology.org/formats/oboInOwl#>
+prefix def: <http://purl.obolibrary.org/obo/IAO_0000115>
+prefix owl: <http://www.w3.org/2002/07/owl#>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+
+INSERT {
+  <https://w3id.org/semapv/vocab/crossSpeciesExactMatch> a owl:AnnotationProperty .
+  ?cls <https://w3id.org/semapv/vocab/crossSpeciesExactMatch> ?mondohuman.
+}
+
+WHERE
+{
+  ?cls a owl:Class .
+  {
+    {
+      ?cls rdfs:subClassOf [
+        owl:onProperty MONDO:0700097 ;
+        owl:someValuesFrom ?mondohuman
+      ] .
+    }
+  } UNION {
+    ?cls owl:equivalentClass [
+      owl:intersectionOf (
+        MONDO:0005583
+        [ rdf:type owl:Restriction ;
+          owl:onProperty MONDO:0700097 ;
+          owl:someValuesFrom ?mondohuman
+        ]
+      )
+    ] .
+  }
+
+  UNION {
+    ?cls owl:equivalentClass [
+      owl:intersectionOf (
+        MONDO:0005583
+        [ rdf:type owl:Restriction ;
+          owl:onProperty MONDO:0700097 ;
+          owl:someValuesFrom ?mondohuman
+        ]
+        [ rdf:type owl:Restriction ;
+          owl:onProperty <http://purl.obolibrary.org/obo/RO_0002162> ;
+          owl:someValuesFrom ?ncbiTaxon
+        ]
+      )
+    ] .
+  }
+
+ FILTER( !isBlank(?cls) && STRSTARTS(str(?cls), "http://purl.obolibrary.org/obo/MONDO_"))
+}