Merge pull request #299 from monarch-initiative/medicalspecialtybranch

Add medical examination terms and close #287

src/sparql/COUNTtotalnotobsolete.sparql

@@ -0,0 +1,21 @@
+prefix IAO: <http://purl.obolibrary.org/obo/IAO_>
+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#>
+
+# count how many non-obsolete classes are in MAXO
+
+SELECT (count(distinct ?cls) as ?count) 
+
+WHERE 
+{
+  ?cls a owl:Class .
+  ?cls rdfs:label ?cls_label .
+  FILTER NOT EXISTS {
+    ?cls owl:deprecated "true"^^xsd:boolean
+  }
+
+FILTER( !isBlank(?cls) && regex(str(?cls), "^http://purl.obolibrary.org/obo/MAXO_"))
+}

src/sparql/test2.sparql → src/sparql/basic-report-test.sparql

@@ -4,12 +4,9 @@ prefix owl: <http://www.w3.org/2002/07/owl#>
 
 SELECT ?cls ?def (group_concat(?xref) as ?xrefs) WHERE 
 {
-  ?cls a owl:Class ;
-  oio:hasDbXref ?xref ;
+  ?cls a owl:Class .
   OPTIONAL { ?cls oio:hasDbXref ?xref } .
   OPTIONAL { ?cls def: ?def } .
-  FILTER (!isBlank(?cls))
-  FILTER (!isBlank(?def))
-  FILTER (!isBlank(?xref))
+  FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/MAXO_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/MAXO_")))
 }
 GROUP BY ?cls ?def

src/sparql/labels_test.sparql

@@ -0,0 +1,11 @@
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+SELECT DISTINCT ?term (STR(?lab) AS ?label) WHERE {
+	?x rdf:type owl:Class .
+	OPTIONAL {?x rdfs:label ?lab}
+	FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/MAXO_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/MAXO_")))}
+ORDER BY ?x
+
+

src/sparql/test.sparql → src/sparql/maxo_classes_test.sparql

@@ -5,13 +5,10 @@ prefix def: <http://purl.obolibrary.org/obo/IAO_0000115>
 SELECT ?cls ?xref ?def WHERE 
 {
   ?cls a owl:Class ;
-  def: ?def .
-       #the 'optional' bracket makes everything option, and therefore prints out everything even if they ar missing a field 
-       OPTIONAL {
+ # def: ?def .
        ?ano a owl:Axiom ;
          owl:annotatedSource ?cls ;
          owl:annotatedProperty  def: ;
          owl:annotatedTarget ?def ;
          oio:hasDbXref ?xref . 
 }
-}