Makefile doesn't find object properties when seeding import modules

[balhoff]

There are a few RO terms used in go-plus which aren't in ro_import (e.g. 'bearer of'). This is easily missed because some RO axioms are duplicated in go-edit.

The makefile creates a seed file for module extraction by dumping the term IRIs referenced in the ontology:

go-ontology/src/ontology/Makefile

Lines 245 to 246 in 7f5f14e

	seed.txt: enhanced.owl
	owltools --use-catalog $< --export-table $@.tmp && cut -f1 $@.tmp > $@

The owltools command used to extract the terms referenced in the ontology seems to leave out object properties:

https://github.com/owlcollab/owltools/blob/178e1f994aa4a5e9e4d43c7a5243145436c553a8/OWLTools-Core/src/main/java/owltools/io/TableRenderer.java#L44-L45

Either owltools should be fixed, or the makefile should use a robot SPARQL query (or both).

[cmungall]

+1 to robot sparql. I think this part of the Makefile predates that possibility

[balhoff]

I’ve got this done, will be submitting a PR.

…

On Dec 21, 2017, at 3:03 PM, Chris Mungall ***@***.***> wrote: +1 to robot sparql. I think this part of the Makefile predates that possibility — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub, or mute the thread.