`subsets/life-stages-composite.obo` is incomplete

[anitacaron]

The life-stages-composite is generated using this owltools command:

subsets/life-stages-composite.owl: composite-metazoan.owl
	$(OWLTOOLS) $< --reasoner-query -r elk -l 'life cycle stage' 
          --make-ontology-from-results $(URIBASE)/uberon/$@ 
          --add-ontology-annotation $(DC)/description "Life cycle stage subset of uberon composite-vertebrate ontology (includes species stage ontologies)" -o $@ 
          --reasoner-dispose 2>&1 > [email protected]

For some unknown reason, it's not getting the life stage related terms for all species in composite-metazoan.owl Right now, if I run the command, it only returns the terms related to chicken, and in the last release, there're only terms related to human.

Note, the obo file is generated from the owl file.

[anitacaron]

To fix this issue, I propose injecting a subset 'life-stage' to the related terms using SPARQL and filtering them using the same command ODK uses for subsets.

$(OWLTOOLS) $< --extract-ontology-subset --fill-gaps --subset $* -o [email protected] && mv [email protected] $@ &&\
$(ROBOT) annotate --input $@ --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o [email protected] && mv [email protected] $@

Any other suggestions?

[anitacaron]

It is still not complete yet. Need to change the SPARQL query to tag all subclasses of the terms with 'life cycle stage'