Merge pull request #1 from Cellular-Semantics/homba-initial-build-pipeline

Bootstrap HOMBA ODK pipeline and generated assets

Author: ubyndr

.gitignore

@@ -66,4 +66,12 @@ src/patterns/data/**/*.txt
 src/patterns/pattern_owl_seed.txt
 src/patterns/all_pattern_terms.txt
 
-# End of ODK-managed rules
+# End of ODK-managed rules
+
+__pycache__/
+*.pyc
+src/linkml/data/*.tsv
+src/ontology/components/linkouts.owl
+src/ontology/components/sources_merged.owl
+src/ontology/sources/HOMBA_v1.json
+src/ontology/sources/uberon-bridge-to-homba.owl

requirements.txt

@@ -0,0 +1,3 @@
+pandas
+ruamel.yaml
+linkml-owl

src/config/db_graph_atlas.yaml

@@ -0,0 +1,4 @@
+homba:
+  species: mammalian
+  prefix: https://purl.brain-bican.org/ontology/HOMBA_
+  atlases: []

src/linkml/structure_graph_schema.yaml

@@ -0,0 +1,51 @@
+id: http://purl.obolibrary.org/obo/ABA_Uberon
+name: structure_graph
+prefixes:
+  UBERON: 'http://purl.obolibrary.org/obo/UBERON_'
+  IAO: 'http://purl.obolibrary.org/obo/IAO_'
+
+default_curi_maps:
+- semweb_context
+- obo_context
+
+types:
+  string:
+    base: str
+    uri: xsd:string
+
+classes:
+  Class:
+    slots:
+      - id
+      - name
+      - acronym
+      - symbol
+      - parent_structure_id
+      - subclass_of
+    class_uri: owl:Class
+
+slots:
+  id:
+    identifier: true
+  name:
+    slot_uri: rdfs:label
+    annotations:
+      owl: AnnotationAssertion
+  acronym:
+    slot_uri: oboInOwl:hasExactSynonym
+    annotations:
+      owl: AnnotationAssertion
+  symbol:
+    slot_uri: IAO:0000028
+    annotations:
+      owl: AnnotationAssertion
+  parent_structure_id:
+    slot_uri: BFO:0000050
+    range: Class
+    annotations:
+      owl: SubClassOf, ObjectSomeValuesFrom
+  subclass_of:
+    slot_uri: rdfs:subclass_of
+    range: Class
+    annotations:
+      owl: SubClassOf

src/ontology/components/all_templates.owl

@@ -11,10 +11,11 @@ Prefix(dcterms:=<http://purl.org/dc/terms/>)
 Ontology(<https://purl.brain-bican.org/ontology/homba.owl>
 
 Import(<https://purl.brain-bican.org/ontology/homba/imports/merged_import.owl>)
+Import(<https://purl.brain-bican.org/ontology/homba/components/all_templates.owl>)
 
 
 Import(<https://purl.brain-bican.org/ontology/homba/patterns/definitions.owl>)
-Annotation(dcterms:description "None")
+Annotation(dcterms:description "An application ontology built by combining the HOMBA structure graph, curated Uberon mappings, generated linkouts, and standard ODK-managed releases.")
 Annotation(dcterms:license <https://creativecommons.org/licenses/unspecified>)
 Annotation(dcterms:title "Harmonized Ontology of Mammalian Brain Anatomy")
 

src/ontology/homba-edit.owl

@@ -22,6 +22,15 @@ primary_release: full
 import_group:
   use_base_merging: TRUE
   slme_individuals: exclude
+  exclude_iri_patterns:
+    - <http://www.informatics.jax.org/marker/MGI:*>
+    - <http://purl.obolibrary.org/obo/OBA_*>
+    - <http://purl.obolibrary.org/obo/ENVO_*>
+    - <http://purl.obolibrary.org/obo/OBI_*>
+    - <http://purl.obolibrary.org/obo/GOCHE_*>
+    - <http://purl.obolibrary.org/obo/CARO_*>
+    - <http://purl.obolibrary.org/obo/NCBITaxon_Union_*>
+    - <http://www.genenames.org/cgi-bin/gene_symbol_report*>
   products:
     - id: uberon
       use_base: TRUE

src/ontology/homba-odk.yaml

@@ -2,3 +2,141 @@
 ## 
 ## If you need to customize your Makefile, make
 ## changes here rather than in the main Makefile
+
+URIBASE = https://purl.brain-bican.org/ontology
+
+JOBS = HOMBA_v1
+BRIDGES = homba
+TARGETS = homba
+
+LINKML = linkml-data2owl
+
+STRUCTURE_GRAPHS = $(patsubst %, sources/%.json, $(JOBS))
+ALL_GRAPH_ONTOLOGIES = $(patsubst sources/%.json,sources/%.ofn,$(STRUCTURE_GRAPHS))
+ALL_BRIDGES = $(patsubst %, sources/uberon-bridge-to-%.owl, $(BRIDGES))
+# Keep the template-regenerated bridge workflow disabled until HOMBA has a
+# manually curated mapping table to compare against the legacy bridge.
+# SOURCE_TEMPLATES = $(patsubst %, ../templates/%_CCF_to_UBERON_source.tsv, $(TARGETS))
+# NEW_BRIDGES = $(patsubst %, new-bridges/new-uberon-bridge-to-%.owl, $(TARGETS))
+
+
+.PHONY: $(COMPONENTSDIR)/all_templates.owl
+$(COMPONENTSDIR)/all_templates.owl: clean_files dependencies $(COMPONENTSDIR)/linkouts.owl $(COMPONENTSDIR)/sources_merged.owl
+	$(ROBOT) merge -i $(COMPONENTSDIR)/linkouts.owl -i $(COMPONENTSDIR)/sources_merged.owl annotate --ontology-iri $(URIBASE)/$@ convert -f ofn -o $@
+.PRECIOUS: $(COMPONENTSDIR)/all_templates.owl
+
+.PHONY: dependencies
+dependencies:
+	python3 -m pip install --break-system-packages -r ../../requirements.txt
+
+
+LOCAL_CLEAN_FILES = $(ALL_GRAPH_ONTOLOGIES) $(ALL_BRIDGES) $(TMPDIR)/tmp.json $(TMPDIR)/tmp.owl $(COMPONENTSDIR)/sources_merged.owl $(COMPONENTSDIR)/linkouts.owl $(TEMPLATEDIR)/linkouts.tsv
+# Template-regenerated bridge artifacts to restore later if HOMBA gets a curated mapping workflow:
+# LOCAL_CLEAN_FILES += $(SOURCE_TEMPLATES) $(NEW_BRIDGES)
+
+.PHONY: clean_files
+clean_files:
+	rm -f $(LOCAL_CLEAN_FILES)
+
+sources/HOMBA_v1.json:
+	mkdir -p $(dir $@)
+	curl -L -o $@ "https://allen-hmba-releases.s3.us-west-2.amazonaws.com/terminology/HOMBA_v1.json"
+
+../linkml/data/template_%.tsv: sources/%.json
+	mkdir -p $(dir $@)
+	python3 $(SCRIPTSDIR)/structure_graph_template.py -i $< -o $@
+.PRECIOUS: ../linkml/data/template_%.tsv
+
+sources/%.ofn: ../linkml/data/template_%.tsv
+	$(LINKML) -C Class -s ../linkml/structure_graph_schema.yaml $< -o $@
+.PRECIOUS: sources/%.ofn
+
+sources/uberon-bridge-to-homba.owl:
+	mkdir -p $(dir $@)
+	curl -L -o $(TMPDIR)/uberon-bridge-to-homba.download.owl "https://raw.githubusercontent.com/obophenotype/uberon/refs/heads/add-homba-bridge/src/ontology/bridge/uberon-bridge-to-homba.owl"
+	python3 $(SCRIPTSDIR)/normalize_homba_bridge_xml.py $(TMPDIR)/uberon-bridge-to-homba.download.owl $@
+
+# Disabled for now: provenance/template regeneration workflow that compares the legacy bridge
+# against a manually curated HOMBA mapping table and rebuilds a fresh bridge.
+# $(TMPDIR)/%_old_mapping.tsv: sources/uberon-bridge-to-%.owl
+# 	$(ROBOT) query --input $< --query ../sparql/bridge_mappings.sparql $@
+#
+# ../templates/%_CCF_to_UBERON_source.tsv: $(TMPDIR)/%_old_mapping.tsv ../templates/%_CCF_to_UBERON.tsv
+# 	python3 ../scripts/mapping_source_template_generator.py -i1 $< -i2 $(word 2, $^) -o $@
+# .PRECIOUS: ../templates/%_CCF_to_UBERON_source.tsv
+#
+# new-bridges/new-uberon-bridge-to-%.owl: ../templates/%_CCF_to_UBERON.tsv ../templates/%_CCF_to_UBERON_source.tsv $(MIRRORDIR)/uberon.owl
+# 	mkdir -p $(dir $@)
+# 	$(ROBOT) template --input $(MIRRORDIR)/uberon.owl --template $< --output $(TMPDIR)/sourceless-new-uberon-bridge.owl
+# 	$(ROBOT) template --input $(MIRRORDIR)/uberon.owl --template $(word 2, $^) --output $(TMPDIR)/CCF_to_UBERON_source.owl
+# 	$(ROBOT) merge --input $(TMPDIR)/sourceless-new-uberon-bridge.owl --output $(TMPDIR)/CCF_to_UBERON_source.owl --output $@
+
+$(COMPONENTSDIR)/sources_merged.owl: $(ALL_GRAPH_ONTOLOGIES) $(ALL_BRIDGES)
+	$(ROBOT) merge $(patsubst %, -i %, $^) relax annotate --ontology-iri $(URIBASE)/$@ -o $@
+
+$(TMPDIR)/tmp.owl: $(SRC) $(COMPONENTSDIR)/sources_merged.owl
+	$(ROBOT) merge $(patsubst %, -i %, $^) relax annotate --ontology-iri $(URIBASE)/$@ -o $@
+
+$(TMPDIR)/tmp.json: $(TMPDIR)/tmp.owl
+	$(ROBOT) convert --input $< -f json -o $@
+
+$(TEMPLATEDIR)/linkouts.tsv: $(TMPDIR)/tmp.json
+	python3 $(SCRIPTSDIR)/gen_linkout_template.py $<
+
+$(COMPONENTSDIR)/linkouts.owl: $(TMPDIR)/tmp.owl $(TEMPLATEDIR)/linkouts.tsv
+	$(ROBOT) template --template $(word 2, $^) --input $< --add-prefixes template_prefixes.json -o $@
+
+
+## ONTOLOGY: uberon (remove disjoint classes and properties to keep merged bridge reasoning tractable)
+.PHONY: mirror-uberon
+.PRECIOUS: $(MIRRORDIR)/uberon.owl
+mirror-uberon: | $(TMPDIR)
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/uberon-base.owl -o $(TMPDIR)/uberon-download.owl && \
+		$(ROBOT) remove -i $(TMPDIR)/uberon-download.owl --axioms disjoint -o $(TMPDIR)/$@.owl; fi
+
+
+## Disable '--equivalent-classes-allowed asserted-only' due to bridge-level equivalence patterns
+.PHONY: reason_test
+reason_test: $(EDIT_PREPROCESSED)
+	$(ROBOT) reason --input $< --reasoner ELK \
+		--exclude-tautologies structural --output test.owl && rm test.owl
+
+## Disable '--equivalent-classes-allowed asserted-only' for the base release
+## because HOMBA currently contains inferred equivalent classes.
+$(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES)
+	$(ROBOT_RELEASE_IMPORT_MODE) \
+	reason --reasoner $(REASONER) --exclude-tautologies structural --annotate-inferred-axioms false \
+	relax $(RELAX_OPTIONS) \
+	reduce -r $(REASONER) $(REDUCE_OPTIONS) \
+	remove --base-iri $(URIBASE)/HOMBA --axioms external --preserve-structure false --trim false \
+	$(SHARED_ROBOT_COMMANDS) \
+	annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \
+		--ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
+		--output $@.tmp.owl && mv $@.tmp.owl $@
+
+$(ONT)-full.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES)
+	$(ROBOT_RELEASE_IMPORT_MODE) \
+		reason --reasoner ELK --exclude-tautologies structural \
+		relax \
+		reduce -r ELK \
+		$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@
+
+$(ONT)-simple.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(IMPORT_FILES)
+	$(ROBOT_RELEASE_IMPORT_MODE) \
+		reason --reasoner ELK --exclude-tautologies structural \
+		relax \
+		remove --axioms equivalent \
+		relax \
+		filter --term-file $(SIMPLESEED) --select "annotations ontology anonymous self" --trim true --signature true \
+		reduce -r ELK \
+		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru \
+		$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@
+
+$(ONT).owl: $(ONT)-full.owl
+	$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
+		convert -o $@.tmp.owl && mv $@.tmp.owl $@
+
+$(ONT).json: $(ONT).owl
+	$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
+		convert --check false -f json -o $@.tmp.json && \
+		mv $@.tmp.json $@