Reasoned and remove any disjoint

.gitignore

@@ -0,0 +1,7 @@
+src/ontology/mirror/*
+src/ontology/sources/*
+.DS_Store
+src/.DS_Store
+src/ontology/.DS_Store
+src/ontology/tmp.owl
+src/ontology/tmp.json

requirements.txt

@@ -1,2 +1,4 @@
 pandas
-openpyxl
+openpyxl
+linkml-owl
+ruamel.yaml

src/linkml/structure_graph_schema.yaml

@@ -0,0 +1,44 @@
+id: http://purl.obolibrary.org/obo/ABA_Uberon
+name: structure_graph
+prefixes:
+  UBERON: 'http://purl.obolibrary.org/obo/UBERON_'
+
+default_curi_maps:
+- semweb_context
+- obo_context
+
+types:
+  string:
+    base: str
+    uri: xsd:string
+
+classes:
+  Class:
+    slots:
+      - id
+      - name
+      - acronym
+      - parent_structure_id
+      - subclass_of
+    class_uri: owl:Class
+
+slots:
+  id:
+    identifier: true
+#    range: uriorcurie
+  name:
+    slot_uri: rdfs:label
+    annotations:
+      owl: AnnotationAssertion
+  acronym:
+    slot_uri: oboInOwl:hasExactSynonym
+    annotations:
+      owl: AnnotationAssertion
+  parent_structure_id:
+    slot_uri: BFO:0000050
+    annotations:
+      owl: SubClassOf, ObjectSomeValuesFrom
+  subclass_of:
+    slot_uri: rdfs:subclass_of
+    annotations:
+      owl: SubClassOf

src/ontology/Makefile

@@ -1,7 +1,22 @@
+### This makefile requires python3 & pip3 mapped as such
+
+JOBS = 1 17 10 16 8
+
 ROBOT = robot
+LINKML = linkml-data2owl
+
 URIBASE = http://purl.obolibrary.org/obo
 
-all: aba_uberon.owl report.xlsx
+STRUCTURE_GRAPHS = $(patsubst %, sources/%.json, $(JOBS))
+ALL_GRAPH_ONTOLOGIES = $(patsubst sources/%.json,sources/%.ofn,$(STRUCTURE_GRAPHS))
+
+
+all: dependencies $(ALL_GRAPH_ONTOLOGIES) aba_uberon.owl report.xlsx
+
+# Installing depedencies so it can run in ODK container
+.PHONY: dependencies
+dependencies:
+	pip3 install -r ../../requirements.txt
 
 IMP=true # Global parameter to bypass import generation
 MIR=true # Global parameter to bypass mirror generation
@@ -12,26 +27,65 @@ mirror/uberon.owl:
 
 # TODO: move to making uberon slice.
 
+sources/%.json:
+	curl -o $@ $(subst %,$(subst sources/,,$@),"http://api.brain-map.org/api/v2/structure_graph_download/%")
+
+../linkml/data/template_%.tsv: sources/%.json
+	python3 ../scripts/structure_graph_template.py -i $< -o $@
+
+sources/%.ofn: ../linkml/data/template_%.tsv
+	$(LINKML) -C Class -s ../linkml/structure_graph_schema.yaml $< -o $@
+.PRECIOUS: sources/%.ofn
+
+# download bridges
+
+sources/uberon-bridge-to-aba.obo:
+	curl -o sources/uberon-bridge-to-aba.obo "https://raw.githubusercontent.com/obophenotype/uberon/master/src/ontology/bridge/uberon-bridge-to-aba.obo"
+
+sources/uberon-bridge-to-dhba.obo: 
+	curl -o sources/uberon-bridge-to-dhba.obo "https://raw.githubusercontent.com/obophenotype/uberon/master/src/ontology/bridge/uberon-bridge-to-dhba.obo"
+
+sources/uberon-bridge-to-dmba.obo:
+	curl -o sources/uberon-bridge-to-dmba.obo "https://raw.githubusercontent.com/obophenotype/uberon/master/src/ontology/bridge/uberon-bridge-to-dmba.obo"
+
+sources/uberon-bridge-to-hba.obo:
+	curl -o sources/uberon-bridge-to-hba.obo "https://raw.githubusercontent.com/obophenotype/uberon/master/src/ontology/bridge/uberon-bridge-to-hba.obo"
+
+sources/uberon-bridge-to-mba.obo:
+	curl -o sources/uberon-bridge-to-mba.obo "https://raw.githubusercontent.com/obophenotype/uberon/master/src/ontology/bridge/uberon-bridge-to-mba.obo"
+
+sources/uberon-bridge-to-pba.obo:
+	curl -o sources/uberon-bridge-to-pba.obo "https://raw.githubusercontent.com/obophenotype/uberon/master/src/ontology/bridge/uberon-bridge-to-pba.obo"
+
+all_bridges:
+	make sources/uberon-bridge-to-aba.obo sources/uberon-bridge-to-dhba.obo sources/uberon-bridge-to-dmba.obo sources/uberon-bridge-to-hba.obo sources/uberon-bridge-to-mba.obo sources/uberon-bridge-to-pba.obo -B
+
+
 # Merge sources. # crudely listing dependencies for now - but could switch to using pattern expansion
-sources_merged.owl:
-	robot merge --input sources/allen-dhba.obo --input sources/allen-dmba.obo --input sources/allen-hba.obo --input sources/allen-mba.obo --input sources/allen-pba.obo --input sources/uberon-bridge-to-aba.obo --input sources/uberon-bridge-to-dhba.obo --input sources/uberon-bridge-to-dmba.obo --input sources/uberon-bridge-to-hba.obo --input sources/uberon-bridge-to-mba.obo --input sources/uberon-bridge-to-pba.obo annotate --ontology-iri $(URIBASE)/$@ -o $@
+sources_merged.owl: all_bridges 
+	robot merge --input sources/1.ofn --input sources/17.ofn --input sources/10.ofn --input sources/16.ofn --input sources/8.ofn --input sources/uberon-bridge-to-aba.obo --input sources/uberon-bridge-to-dhba.obo --input sources/uberon-bridge-to-dmba.obo --input sources/uberon-bridge-to-hba.obo --input sources/uberon-bridge-to-mba.obo --input sources/uberon-bridge-to-pba.obo remove --axioms disjoint annotate --ontology-iri $(URIBASE)/$@ -o $@
 
 
 # Generate seed for pulling relevant subset of Uberon
 terms.txt: sources_merged.owl
-	$(ROBOT) query --use-graphs true -f tsv -i $< --query ../sparql/terms.sparql $@
+	$(ROBOT) query --use-graphs true -f csv -i $< --query ../sparql/terms.sparql $@
 
 # Generate slice of uberon, removing disjoints
 # Using BOT for now - but this could potentially be more minimal
 
 uberon_slice.owl: mirror/uberon.owl terms.txt
-	$(ROBOT) extract --method BOT -i mirror/uberon.owl -T terms.txt remove --axioms disjoint -o $@
+	$(ROBOT) extract --method BOT --input mirror/uberon.owl --term-file terms.txt --force true remove --axioms disjoint --output $@
 
 
 # merge uberon + sources, reason & relax (EC -> SC)
+# remove all owl:Nothing - this causes massive amounts of unsats 
 
 tmp.owl: uberon_slice.owl sources_merged.owl
-	robot merge --input uberon_slice.owl --input sources_merged.owl reason relax annotate --ontology-iri $(URIBASE)/$@ -o $@
+	$(ROBOT) merge --input uberon_slice.owl --input sources_merged.owl \
+  remove --term http://www.w3.org/2002/07/owl#Nothing --select equivalents \
+  reason --annotate-inferred-axioms true \
+  relax \
+  annotate --ontology-iri $(URIBASE)/$@ -o $@
 
 # Make a json file for use in geneating ROBOT template
 tmp.json: tmp.owl
@@ -40,7 +94,7 @@ tmp.json: tmp.owl
 # Build robot  template - with linkouts and prefLabels
 
 ../robot_templates/linkouts.tsv: tmp.json
-	python ../scripts/gen_linkout_template.py $<
+	python3 ../scripts/gen_linkout_template.py $<
 
 # generate OWL from template