Customize OBO artefacts.

Use a new command in the Uberon ROBOT plugin to produce "customized" OBO
artefacts in which:

* all "untranslatable" OWL axioms (owl-axioms tag) are stripped (they
  were already stripped before, this just changes the way we do it);
* all GCI axioms are stripped (#2856);
* when a class has several rdfs:comment annotations (which is not
  allowed in OBO), they are merged into a single annotation (#2847).

src/ontology/cl-odk.yaml

@@ -34,7 +34,7 @@ robot_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
+      mirror_from: https://github.com/gouttegd/uberon-robot-plugin/releases/download/uberon-robot-plugin-0.3.3/uberon.jar
 subset_group:
   products:
     - id: BDS_subset

src/ontology/cl.Makefile

@@ -175,10 +175,10 @@ test: $(REPORTDIR)/taxon-constraint-check.txt
 # ----------------------------------------
 
 .PHONY: obocheck
-obocheck: $(SRC)
+obocheck: $(SRC) | all_robot_plugins
 	$(ROBOT) merge -i $(SRC) \
 		 remove --base-iri $(URIBASE)/CL_ --axioms external --trim false \
-		 convert -f obo --check false -o $(TMPDIR)/cl-check.obo
+		 uberon:obo-export --merge-comments --obo-output $(TMPDIR)/cl-check.obo
 	fastobo-validator $(TMPDIR)/cl-check.obo
 
 test_obsolete: $(ONT).obo
@@ -258,6 +258,36 @@ pattern_docs: $(ALL_PATTERN_FILES)
 		       -o ../../docs/patterns/
 
 
+# ----------------------------------------
+# CUSTOM OBO OUTPUT
+# ----------------------------------------
+OBO_EXPORT_OPTIONS = --merge-comments --strip-gci-axioms --strip-owl-axioms
+
+$(SUBSETDIR)/%.obo: $(SUBSETDIR)/%.owl | all_robot_plugins
+	$(ROBOT) uberon:obo-export --input $< $(OBO_EXPORT_OPTIONS) --obo-output $@
+
+$(ONT).obo: $(ONT).owl | all_robot_plugins
+	$(ROBOT) uberon:obo-export --input $< $(OBO_EXPORT_OPTIONS) --obo-output $@
+
+$(ONT)-base.obo: $(ONT)-base.owl | all_robot_plugins
+	$(ROBOT) uberon:obo-export --input $< $(OBO_EXPORT_OPTIONS) --obo-output $@
+
+$(ONT)-full.obo: $(ONT)-full.owl | all_robot_plugins
+	$(ROBOT) uberon:obo-export --input $< $(OBO_EXPORT_OPTIONS) --obo-output $@
+
+$(ONT)-simple.obo: $(ONT)-simple.owl | all_robot_plugins
+	$(ROBOT) uberon:obo-export --input $< $(OBO_EXPORT_OPTIONS) --obo-output $@
+
+$(ONT)-basic.obo: $(ONT)-basic.owl | all_robot_plugins
+	$(ROBOT) uberon:obo-export --input $< $(OBO_EXPORT_OPTIONS) --obo-output $@
+
+$(ONT)-non-classified.obo: $(ONT)-non-classified.owl | all_robot_plugins
+	$(ROBOT) uberon:obo-export --input $< $(OBO_EXPORT_OPTIONS) --obo-output $@
+
+cl-plus.obo: cl-plus.owl | all_robot_plugins
+	$(ROBOT) uberon:obo-export --input $< $(OBO_EXPORT_OPTIONS) --obo-output $@
+
+
 # ----------------------------------------
 # DIFFS/REPORTS
 # ----------------------------------------