Add taxon subsets

.gitignore

@@ -56,10 +56,14 @@ subsets/BDS_subset.tsv
 subsets/BDS_subset.owl
 subsets/BDS_subset.obo
 subsets/BDS_subset.json
+subsets/*-view.*
+subsets/*-tags.*
 src/ontology/subsets/BDS_subset.tsv
 src/ontology/subsets/BDS_subset.owl
 src/ontology/subsets/BDS_subset.obo
 src/ontology/subsets/BDS_subset.json
+src/ontology/subsets/*-view.*
+src/ontology/subsets/*-tags.*
 src/mappings/cl-local.sssom.tsv
 src/mappings/cl.sssom.tsv
 cl.json

src/ontology/Makefile

@@ -10,7 +10,7 @@
 # More information: https://github.com/INCATools/ontology-development-kit/
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                f7d9e8d156ea19124c47084171b68728b3f6cf2fddba07984f7985402bfc2b36
+CONFIG_HASH=                d4e868f8bbec3ce7b0d7656c824520ab0b96d8901a8c2b9cf400c27c3fb3dac2
 
 
 # ----------------------------------------
@@ -132,7 +132,7 @@ custom_robot_plugins:
 
 
 .PHONY: extra_robot_plugins
-extra_robot_plugins:  $(ROBOT_PLUGINS_DIRECTORY)/flybase.jar 
+extra_robot_plugins:  $(ROBOT_PLUGINS_DIRECTORY)/flybase.jar  $(ROBOT_PLUGINS_DIRECTORY)/uberon.jar 
 
 
 # Install all ROBOT plugins to the runtime plugins directory
@@ -155,6 +155,9 @@ $(ROBOT_PLUGINS_DIRECTORY)/%.jar:
 $(ROBOT_PLUGINS_DIRECTORY)/flybase.jar:
 	curl -L -o $@ https://github.com/FlyBase/flybase-robot-plugin/releases/download/flybase-robot-plugin-0.2.2/flybase.jar
 
+$(ROBOT_PLUGINS_DIRECTORY)/uberon.jar:
+	curl -L -o $@ https://github.com/gouttegd/uberon-robot-plugin/releases/download/uberon-robot-plugin-0.3.1/uberon.jar
+
 
 # ----------------------------------------
 # Release assets
@@ -188,7 +191,7 @@ all_imports: $(IMPORT_FILES)
 # ----------------------------------------
 
 
-SUBSETS =  BDS_subset blood_and_immune_upper_slim eye_upper_slim general_cell_types_upper_slim kidney_upper_slim
+SUBSETS =  BDS_subset blood_and_immune_upper_slim eye_upper_slim general_cell_types_upper_slim kidney_upper_slim human-view mouse-view
 
 SUBSET_ROOTS = $(patsubst %, $(SUBSETDIR)/%, $(SUBSETS))
 SUBSET_FILES = $(foreach n,$(SUBSET_ROOTS), $(foreach f,$(FORMATS_INCL_TSV), $(n).$(f)))

src/ontology/cl-odk.yaml

@@ -31,13 +31,17 @@ robot_plugins:
   plugins:
     - name: flybase
       mirror_from: https://github.com/FlyBase/flybase-robot-plugin/releases/download/flybase-robot-plugin-0.2.2/flybase.jar
+    - name: uberon
+      mirror_from: https://github.com/gouttegd/uberon-robot-plugin/releases/download/uberon-robot-plugin-0.3.1/uberon.jar
 subset_group:
   products:
     - id: BDS_subset
     - id: blood_and_immune_upper_slim
     - id: eye_upper_slim
     - id: general_cell_types_upper_slim
     - id: kidney_upper_slim
+    - id: human-view
+    - id: mouse-view
 sssom_mappingset_group:
   products:
     - id: cl-local

src/ontology/cl.Makefile

@@ -10,7 +10,7 @@
 # ----------------------------------------
 
 # Preprocessing: automatically generate text definitions from logical definitions
-$(EDIT_PREPROCESSED): $(SRC) all_robot_plugins
+$(EDIT_PREPROCESSED): $(SRC) | all_robot_plugins
 	$(ROBOT) flybase:rewrite-def -i $< --dot-definitions --null-definitions \
 		                     --no-ids --filter-prefix CL_ \
 		                     --add-annotation "oboInOwl:hasDbXref FBC:Autogenerated" \
@@ -34,6 +34,16 @@ cl-plus.owl: $(ONT)-full.owl
 		 annotate --ontology-iri $(ONTBASE)/$@ \
 		 $(ANNOTATE_ONTOLOGY_VERSION) --output $@
 
+# Main release artefact (cl.owl)
+# We override the standard ODK-generate rule so that we can merge in the
+# tags for the taxon subsets.
+POSTPROCESS_ADDITIONS = subsets/human-tags.ofn \
+                        subsets/mouse-tags.ofn
+$(ONT).owl: $(ONT)-full.owl $(POSTPROCESS_ADDITIONS)
+	$(ROBOT) merge -i $< $(foreach add,$(POSTPROCESS_ADDITIONS),-i $(add)) \
+		 annotate --ontology-iri $(URIBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
+		 convert -o $@
+
 
 # ----------------------------------------
 # SSSOM MAPPINGS
@@ -178,6 +188,41 @@ test: obocheck \
       test_obsolete
 
 
+# ----------------------------------------
+# TAXON SUBSETS
+# ----------------------------------------
+
+TAXON_ID_human = NCBITaxon:9606
+TAXON_ID_mouse = NCBITaxon:10090
+
+# Create a taxon-specific subset. This rule creates two distinct files:
+# (1) the subset proper (subsets/%-view.owl), which can be used on its
+#     own (and can be published as a release artifact if desired);
+# (2) a small containing oboInOwl:inSubset annotations to "tag" all
+#     terms that belong to the subset (subsets/%-tags.ofn); that file
+#     can then be combined with a CL release product.
+.PRECIOUS: subsets/%-view.owl
+subsets/%-view.owl subsets/%-tags.ofn: $(ONT)-full.owl | all_robot_plugins
+	$(ROBOT) expand --input $< --expand-term RO:0002161 \
+		 uberon:create-species-subset --taxon $(TAXON_ID_$*) \
+		                              --strategy precise \
+		                              --reasoner WHELK \
+		                              --root CL:0000000 \
+		                              --prefix 'cl: http://purl.obolibrary.org/cl#' \
+		                              --subset-name cl:$*_subset \
+		                              --only-tag-in CL: \
+		                              --write-tags-to subsets/$*-tags.ofn \
+		 reason --reasoner WHELK --equivalent-classes-allowed all \
+		        --exclude-tautologies structural \
+		 relax \
+		 remove --axioms equivalent \
+		 reduce --reasoner WHELK \
+		 annotate --ontology-iri $(ONTBASE)/subsets/$*-view.owl \
+		          --version-iri $(ONTBASE)/releases/$(VERSION)/subsets/$*-view.owl \
+		          --annotation owl:versionInfo $(VERSION) \
+		 convert --format ofn --output subsets/$*-view.owl
+
+
 # ----------------------------------------
 # DOSDP PATTERNS HACKS
 # ----------------------------------------