From 9ae000688c40f7a4f4f7aa6dd7358c8c8ebeb580 Mon Sep 17 00:00:00 2001
From: Jim Balhoff <jim@balhoff.org>
Date: Sat, 28 Oct 2023 15:13:07 -0400
Subject: [PATCH] Improve redundancy check for computed never-in-taxon.

---
 ...n-constraints-never-in-taxon-annotation.rq | 36 ++++++++++++++-----
 1 file changed, 27 insertions(+), 9 deletions(-)

diff --git a/src/sparql/taxon-constraints-never-in-taxon-annotation.rq b/src/sparql/taxon-constraints-never-in-taxon-annotation.rq
index 7b489cbba4..b973c8f11d 100644
--- a/src/sparql/taxon-constraints-never-in-taxon-annotation.rq
+++ b/src/sparql/taxon-constraints-never-in-taxon-annotation.rq
@@ -42,16 +42,34 @@ WHERE {
   FILTER(STRENDS(STR(?taxon_complement), "#NOT"))
   BIND(IRI(STRBEFORE(STR(?taxon_complement), "#NOT")) AS ?taxon)
   FILTER (
-    EXISTS {
-      ?term rdfs:subClassOf+ [
-        a owl:Restriction ;
-        owl:onProperty in_taxon: ;
-        owl:someValuesFrom ?super_taxon
-      ] .
-      FILTER(!STRENDS(STR(?super_taxon), "#NOT"))
-      ?taxon rdfs:subClassOf+ ?super_taxon .
-    } 
+    # only include computed never-in-taxon if...
+    (
+      # there is a computed in-taxon that is a superclass of the never...
+      EXISTS {
+        ?term rdfs:subClassOf+ [
+          a owl:Restriction ;
+          owl:onProperty in_taxon: ;
+          owl:someValuesFrom ?super_taxon
+        ] .
+        FILTER(!STRENDS(STR(?super_taxon), "#NOT"))
+        ?taxon rdfs:subClassOf+ ?super_taxon .
+      }
+      &&
+      # and there is not another computed in-taxon that is not a superclass of the never...
+      NOT EXISTS {
+        ?term rdfs:subClassOf+ [
+          a owl:Restriction ;
+          owl:onProperty in_taxon: ;
+          owl:someValuesFrom ?super_taxon
+        ] .
+        FILTER(!STRENDS(STR(?super_taxon), "#NOT"))
+        FILTER NOT EXISTS {
+          ?taxon rdfs:subClassOf+ ?super_taxon .
+        }
+      }
+    )
     || 
+    # or else if there are no computed in-taxon
     NOT EXISTS {
       ?term rdfs:subClassOf+ [
         a owl:Restriction ;