WIP: Measurement rewrite

src/ontology/Makefile

@@ -228,3 +228,31 @@ qc/uberon_diff.txt: qc/uberon_consider_terms.txt qc/uberon_current_terms.txt
 	diff -u $^ | grep '^-[^-]' | sed 's/^-//'
 
 all_diffs: $(ENTITY_DIFF_FILES) $(DIFF_REPORTS_FILES)
+
+	# ----------------------------------------
+	# Custom SPARQL queries
+	# ----------------------------------------
+
+#$(BUILDDIR)/$(ONT).owl:
+#	echo "Skipped."
+
+$(BUILDDIR)/$(ONT)-mod.owl: $(BUILDDIR)/$(ONT).owl
+	$(ROBOT) remove -i $(BUILDDIR)/$(ONT).owl --term http://purl.obolibrary.org/obo/IAO_0000136 --term http://purl.obolibrary.org/obo/RO_0002314 -o $@
+
+measurement_anatomy: $(BUILDDIR)/$(ONT).owl $(SPARQLDIR)/measurementisaboutanatomy.sparql
+	$(ROBOT) materialize -i $< -r ELK --term IAO:0000136 query --use-graphs true -q $(SPARQLDIR)/measurementisaboutanatomy.sparql [email protected]
+
+measurement_grouping: $(BUILDDIR)/$(ONT).owl $(SPARQLDIR)/measurementgroupingclasses.sparql
+	$(ROBOT) materialize -i $< -r ELK --term IAO:0000136 query --use-graphs true -q $(SPARQLDIR)/measurementgroupingclasses.sparql [email protected]
+
+$(BUILDDIR)/define_measurements.owl: $(BUILDDIR)/$(ONT).owl ../templates/definemeasurements.tsv
+	$(ROBOT) template -i $< --template ../templates/definemeasurements.tsv --prefix "EFO: http://www.ebi.ac.uk/efo/EFO_" --prefix "RO: http://purl.obolibrary.org/obo/RO_" --prefix "UBERON: http://purl.obolibrary.org/obo/UBERON_" -o $@
+
+$(BUILDDIR)/$(ONT)-iipo.owl: $(BUILDDIR)/$(ONT).owl
+	$(ROBOT) materialize -i $< -r ELK --term IAO:0000136 query --use-graphs true --update $(SPARQLDIR)/updatemeasurementisaboutanatomytoinheresin.ru remove --term http://purl.obolibrary.org/obo/IAO_0000136 --output $@
+
+$(BUILDDIR)/$(ONT)-iipo-def.owl: $(BUILDDIR)/$(ONT)-iipo.owl $(BUILDDIR)/define_measurements.owl
+	$(ROBOT) merge -i $< -i $(BUILDDIR)/define_measurements.owl reason -r HERMIT remove --term http://purl.obolibrary.org/obo/RO_0002314 -o $@
+
+iipo_exp.txt: $(BUILDDIR)/$(ONT)-mod.owl $(BUILDDIR)/$(ONT)-iipo-def.owl
+	$(ROBOT) diff --left $(BUILDDIR)/$(ONT)-mod.owl --right $(BUILDDIR)/$(ONT)-iipo-def.owl -o $@

src/ontology/run.sh

@@ -0,0 +1,12 @@
+#!/bin/sh
+# Wrapper script for docker.
+#
+# This is used primarily for wrapping the GNU Make workflow.
+# Instead of typing "make TARGET", type "./run.sh make TARGET".
+# This will run the make workflow within a docker container.
+#
+# The assumption is that you are working in the src/ontology folder;
+# we therefore map the whole repo (../..) to a docker volume.
+#
+# See README-editors.md for more details.
+docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx8G' --rm -ti obolibrary/odkfull "$@"

src/sparql/measurementgroupingclasses.sparql

@@ -0,0 +1,18 @@
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+
+SELECT ?measurement ?measurementlabel ?anatomy ?anatomylabel
+
+WHERE {
+  ?measurement rdfs:subClassOf ?x .
+  ?x rdf:type owl:Restriction ;
+    owl:onProperty <http://purl.obolibrary.org/obo/IAO_0000136>;
+    owl:someValuesFrom ?anatomy .
+  ?measurement rdfs:subClassOf* <http://www.ebi.ac.uk/efo/EFO_0001444> .
+  ?anatomy rdfs:subClassOf* <http://purl.obolibrary.org/obo/UBERON_0001062> .
+  ?measurement rdfs:label ?measurementlabel .
+  ?anatomy rdfs:label ?anatomylabel .
+  FILTER(isIRI(?anatomy) && isIRI(?measurement)) .
+  FILTER(regex(str(?label)," measurement$"))
+}

src/sparql/measurementisaboutanatomy.sparql

@@ -0,0 +1,17 @@
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+
+SELECT ?measurement ?measurementlabel ?anatomy ?anatomylabel
+
+WHERE {
+  ?measurement rdfs:subClassOf ?x .
+  ?x rdf:type owl:Restriction ;
+    owl:onProperty <http://purl.obolibrary.org/obo/IAO_0000136>;
+    owl:someValuesFrom ?anatomy .
+  ?measurement rdfs:subClassOf* <http://www.ebi.ac.uk/efo/EFO_0001444> .
+  ?anatomy rdfs:subClassOf* <http://purl.obolibrary.org/obo/UBERON_0001062> .
+  ?measurement rdfs:label ?measurementlabel .
+  ?anatomy rdfs:label ?anatomylabel .
+  FILTER(isIRI(?anatomy) && isIRI(?measurement))
+}

src/sparql/updatemeasurementisaboutanatomytoinheresin.ru

@@ -0,0 +1,29 @@
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+
+
+DELETE {
+?measurement rdfs:subClassOf ?x .
+?x rdf:type owl:Restriction ;
+  owl:onProperty <http://purl.obolibrary.org/obo/IAO_0000136>;
+  owl:someValuesFrom ?anatomy .
+}
+INSERT {
+?measurement rdfs:subClassOf ?x .
+?x rdf:type owl:Restriction ;
+  owl:onProperty <http://purl.obolibrary.org/obo/RO_0002314>;
+  owl:someValuesFrom ?anatomy .
+}
+
+WHERE {
+?measurement rdfs:subClassOf ?x .
+?x rdf:type owl:Restriction ;
+  owl:onProperty <http://purl.obolibrary.org/obo/IAO_0000136>;
+  owl:someValuesFrom ?anatomy .
+?measurement rdfs:subClassOf* <http://www.ebi.ac.uk/efo/EFO_0001444> .
+?anatomy rdfs:subClassOf* <http://purl.obolibrary.org/obo/UBERON_0001062> .
+?measurement rdfs:label ?measurementlabel .
+?anatomy rdfs:label ?anatomylabel .
+FILTER(isIRI(?anatomy) && isIRI(?measurement))
+}

src/templates/definemeasurements.tsv

@@ -0,0 +1,5 @@
+ID	Measurement definition
+ID	EC EFO:0001444 and ('inheres in part of' some %)
+EFO:0004515	UBERON:0001015
+EFO:0004464	UBERON:0000955
+EFO:0004742 UBERON:0001008