change definition pattern to population only

src/ontology/afpo.Makefile

@@ -4,8 +4,8 @@
 ## changes here rather than in the main Makefile
 
 .PHONY: update_def_table
-update_def_table: $(PATTERNDIR)/data/default/create_definition.tsv
+update_def_table: $(PATTERNDIR)/data/default/create_population_definition.tsv
 
-$(PATTERNDIR)/data/default/create_definition.tsv: $(SPARQLDIR)/annotation_definition.sparql $(SRC)
+$(PATTERNDIR)/data/default/create_population_definition.tsv: $(SPARQLDIR)/population_annotation_definition.sparql $(SRC)
 	$(ROBOT) query --input $(SRC) --query $< $@.tmp.tsv
 	sed -e 's/?//g' -e 's/"//g' -e 's/http:\/\/purl.obolibrary.org\/obo\/AfPO_/AfPO:/g' < $@.tmp.tsv >$@ && rm $@.tmp.tsv

src/patterns/dosdp-patterns/create_population_definition.yaml

@@ -0,0 +1,23 @@
+pattern_name: create_population_definition
+pattern_iri:  http://purl.obolibrary.org/obo/afpo/patterns/create_population_definition.yaml
+
+description: "This pattern creates population class definition using annotations from the classes."
+
+annotationProperties:
+  xref: oio:hasDbXref
+
+data_vars:
+  parent_class_label: "xsd:string"
+  population_size: "xsd:string"
+
+data_list_vars:
+  wiki: "'xref'"
+
+def:
+  text: "A %s population with a population size of %s"
+  vars:
+    - parent_class_label
+    - population_size
+  annotations:
+    - annotationProperty: xref
+      value: wiki

src/patterns/pattern.owl

@@ -10,8 +10,9 @@ Ontology(<urn:unnamed:ontology#ont1>
 
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))
 Declaration(AnnotationProperty(<http://purl.org/dc/terms/title>))
+Declaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasDbXref>))
 
 
-AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/afpo/patterns/create_definition.yaml> "A country in xsd:string with a population size of xsd:string"^^xsd:string)
-AnnotationAssertion(<http://purl.org/dc/terms/title> <http://purl.obolibrary.org/obo/afpo/patterns/create_definition.yaml> "create_definition"^^xsd:string)
+AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "'xref'"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/afpo/patterns/create_population_definition.yaml> "A xsd:string population with a population size of xsd:string"^^xsd:string)
+AnnotationAssertion(<http://purl.org/dc/terms/title> <http://purl.obolibrary.org/obo/afpo/patterns/create_population_definition.yaml> "create_population_definition"^^xsd:string)
 )

src/sparql/annotation_definition.sparql → src/sparql/population_annotation_definition.sparql

@@ -1,17 +1,20 @@
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 PREFIX owl: <http://www.w3.org/2002/07/owl#>
 PREFIX population_size: <http://purl.obolibrary.org/obo/AfPO_0000459>
+PREFIX Population: <http://purl.obolibrary.org/obo/AfPO_0000146>
 PREFIX wiki_ref: <http://purl.obolibrary.org/obo/AfPO_0000235>
+PREFIX wiki: <https://en.wikipedia.org/wiki/>
 
-SELECT ?defined_class ?defined_class_label ?parent_class_label ?population_size ?xref
+SELECT ?defined_class ?defined_class_label ?parent_class_label ?population_size ?wiki
 WHERE {
     ?dc a owl:Class .
     ?dc rdfs:label ?defined_class_label .
     ?dc rdfs:subClassOf ?pc .
-    ?dc population_size: ?population_size .
+    OPTIONAL { ?dc population_size: ?population_size . }
     OPTIONAL { ?dc wiki_ref: ?x . }
     ?pc a owl:Class .
+    ?pc rdfs:subClassOf* Population: .
     ?pc rdfs:label ?parent_class_label .
     BIND(STR(?dc) AS ?defined_class)
-    BIND(STR(?x) AS ?xref)
+    BIND(STR(?x) AS ?wiki)
 }