From d163c515ac634011084e9f67fe978f87e7303388 Mon Sep 17 00:00:00 2001
From: cmungall <cjm@berkeleybop.org>
Date: Tue, 9 Nov 2021 13:19:57 -0800
Subject: [PATCH] Steps to get taxon exclusions from relation graph

---
 src/ontology/uberon.Makefile                  | 30 +++++++++---
 .../taxon-violation-relation-graph.sparql     | 47 +++++++++++++++++++
 2 files changed, 71 insertions(+), 6 deletions(-)
 create mode 100644 src/sparql/taxon-violation-relation-graph.sparql

diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile
index 6fc46805c4..4def93b76e 100644
--- a/src/ontology/uberon.Makefile
+++ b/src/ontology/uberon.Makefile
@@ -111,7 +111,7 @@ core.owl: $(OWLSRC)
 # FIXED apparently our base does not contain phenoscape-ext!! (It does, through unreasoned)
 #$(TMPDIR)/phenoscape-ext-src.owl: $(SRC)
 #	wget --no-check-certificate https://raw.githubusercontent.com/obophenotype/uberon-phenoscape-ext/master/phenoscape-ext.owl -O $@ && touch $@
-	
+
 # including the imports would lead to circularity, so we remove these here
 #$(COMPONENTSDIR)/phenoscape-ext.owl: $(TMPDIR)/phenoscape-ext-src.owl core.owl
 #	owltools $(UCAT) $< --remove-imports-declarations -o -f functional $@
@@ -1702,8 +1702,8 @@ reports/robot_release_diff.md: $(TMPDIR)/$(ONT)-obo.obo $(TMPDIR)/$(ONT)-obo-mai
 
 .PHONY: feature_diff
 feature_diff: reports/robot_main_diff.md
-	
-	
+
+
 ########################
 #### Utility commands ##
 
@@ -1734,7 +1734,6 @@ clean:
 	rm -rf ./uberon-base.*
 	rm -f uberon.owl uberon.obo core.owl BUILDLOGUBERON.txt unsat_all_explanation.md
 	rm -f ext.owl
-	
 
 explain:
 	$(ROBOT) explain --input $(TMPDIR)/unreasoned-composite-metazoan.owl --reasoner ELK \
@@ -1745,13 +1744,13 @@ explain:
 #	echo "skipping $@"
 
 unsat: $(TMPDIR)/bundled-metazoan.owl_unsat.ofn $(TMPDIR)/cl_mondo_merged.owl_unsat.ofn
-	
+
 $(TMPDIR)/%_unsat.ofn: %
 	$(ROBOT) merge --input $< explain --reasoner ELK \
   -M unsatisfiability --unsatisfiable random:3 --explanation $@.md \
     annotate --ontology-iri "$(ONTBASE)/$@" \
     --output $@
-		
+
 cl_mondo_merged.owl:
 	$(ROBOT) merge -i uberon.owl -I $(URIBASE)/cl.owl -o $@
 
@@ -1861,3 +1860,22 @@ docs/releases.md: uberon-odk.yaml
 	# Amazing: only generate links to release artefacts if they truly exist:
 	# if http://purl.obolibrary.org/obo/mondo/releases/2021-01-01/mondo.owl exists, include it in overview.
 	# Use Github or obo purls (include switch that we can conficgue with ODK)
+
+
+# ----------------------------------------
+# TAXON CONSTRAINTS VIA RELATION GRAPH
+# ----------------------------------------
+# see https://github.com/obophenotype/uberon/issues/2137#issuecomment-963594082
+
+# make a relationgraph ttl file (assumes RG 2.0 - may not be in ODK yet)
+tmp/%.relationgraph.ttl: %.obo
+	relation-graph --ontology-file $< --equivalence-as-subclass true --output-subclasses true --reflexive-subclasses true --output-file $@
+.PRECIOUS: tmp/%.relationgraph.ttl
+
+tmp/%.rgmerged.ttl: tmp/%.relationgraph.ttl %.obo
+	robot merge -i $< -i $*.obo -o $@
+.PRECIOUS: tmp/%.rgmerged.ttl
+
+# This is currently hardcoded to a subset of species
+tmp/class-taxon-exclusions.tsv: tmp/uberon-edit.rgmerged.ttl
+	 robot query -i $< --tdb true --query ../sparql/taxon-violation-relation-graph.sparql $@
diff --git a/src/sparql/taxon-violation-relation-graph.sparql b/src/sparql/taxon-violation-relation-graph.sparql
new file mode 100644
index 0000000000..ee5d8905d9
--- /dev/null
+++ b/src/sparql/taxon-violation-relation-graph.sparql
@@ -0,0 +1,47 @@
+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#>
+
+PREFIX human: <http://purl.obolibrary.org/obo/NCBITaxon_9606>
+PREFIX mammal: <http://purl.obolibrary.org/obo/NCBITaxon_40674>
+PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161>
+PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162>
+
+SELECT  ?c ?cLabel ?p ?pLabel ?clsWithConstraint  ?clsWithConstraintLabel ?taxonWithConstraint ?taxonWithConstraintLabel ?queryTaxon
+WHERE {
+
+   ?c        ?p                    ?clsWithConstraint .
+
+      # NEVER IN
+      { 
+        ?clsWithConstraint       never_in_taxon:  ?taxonWithConstraint .
+        ?queryTaxon
+                  rdfs:subClassOf  ?taxonWithConstraint
+      }
+    UNION
+      # ONLY IN
+      {
+        ?clsWithConstraint  in_taxon:  ?taxonWithConstraint
+        FILTER NOT EXISTS { ?queryTaxon
+                                      rdfs:subClassOf  ?taxonWithConstraint
+                          }
+      }
+
+  # add to this as required
+  VALUES ?queryTaxon {
+    human: mammal:
+  }
+    OPTIONAL
+          { ?c  rdfs:label  ?cLabel }
+    OPTIONAL
+          { ?p  rdfs:label  ?pLabel }
+    OPTIONAL
+          { ?clsWithConstraint  rdfs:label  ?clsWithConstraintLabel }
+    OPTIONAL
+          { ?taxonWithConstraint  rdfs:label  ?taxonWithConstraintLabel }
+
+
+  FILTER isIRI(?c)
+ 
+
+  }