extract: erroneous "Ontology does not contain" warnings

[turbomam]

I created Ontology/ontologies/animals_robot_transition/ro_denied_term_list.txt with

http://purl.obolibrary.org/obo/RO_0000086 # has quality... OBI?
http://purl.obolibrary.org/obo/RO_0000087 # has role... OBI?
http://purl.obolibrary.org/obo/RO_0000092 # disposition of
http://purl.obolibrary.org/obo/RO_0001000 # derives from... OBI?

And curled myself a fresh copy or ro.owl. Then I ran

-jar /C/robot/robot.jar  extract --individuals include --method BOT --force true \
--verbose --intermediates all --annotate-with-source true \
--input Box\ Sync/obo_owl/ro.owl \
--term-file Turbo-Ontology/ontologies/animals_robot_transition/ro_denied_term_list.txt \
--output Turbo-Ontology/ontologies/animals_robot_transition/ro_denied_term_list.txt.ttl

and was told

2020-01-31 14:57:34,429 WARN  org.obolibrary.robot.OntologyHelper - Ontology does not contain <http://purl.obolibrary.org/obo/RO_0000092>
2020-01-31 14:57:34,430 WARN  org.obolibrary.robot.OntologyHelper - Ontology does not contain <http://purl.obolibrary.org/obo/RO_0000086>
2020-01-31 14:57:34,430 WARN  org.obolibrary.robot.OntologyHelper - Ontology does not contain <http://purl.obolibrary.org/obo/RO_0001000>
2020-01-31 14:57:34,430 WARN  org.obolibrary.robot.OntologyHelper - Ontology does not contain <http://purl.obolibrary.org/obo/RO_0000087>
2020-01-31 14:57:34,715 WARN  org.obolibrary.robot.CommandManager - Subcommand Timing: extract took 3.756 seconds

But I don't think that's true. Not only are the terms present in the input ontology, they were successfully extracted:

$ grep -C 3 '<http://purl.obolibrary.org/obo/RO_0000092>' Turbo-Ontology/ontologies/animals_robot_transition/ro_denied_term_list.txt.ttl
###  http://purl.obolibrary.org/obo/RO_0000091
<http://purl.obolibrary.org/obo/RO_0000091> rdf:type owl:ObjectProperty ;
                                            rdfs:subPropertyOf <http://purl.obolibrary.org/obo/RO_0000053> ;
                                            owl:inverseOf <http://purl.obolibrary.org/obo/RO_0000092> ;
                                            rdfs:domain <http://purl.obolibrary.org/obo/BFO_0000004> ;
                                            rdfs:range <http://purl.obolibrary.org/obo/BFO_0000016> ;
                                            <http://purl.obolibrary.org/obo/IAO_0000115> "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence"@en ;
--


###  http://purl.obolibrary.org/obo/RO_0000092
<http://purl.obolibrary.org/obo/RO_0000092> rdf:type owl:ObjectProperty ;
                                            rdfs:subPropertyOf <http://purl.obolibrary.org/obo/RO_0000052> ;
                                            <http://purl.obolibrary.org/obo/IAO_0000115> "inverse of has disposition" ;
                                            <http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/RO_0002259> ;

[jamesaoverton]

Did we resolve this on the OBI call today, or is it still an open issue?

[turbomam]

No, your team resolved a lot of my ROBOT issues yesterday and last week, but I don't think this has been addressed yet. Since the warnings are erroneous and the requested terms actually are extracted, I guess it's not critical.

[beckyjackson]

Sorry for the delay on resolving this.

It looks like this is because these terms are part of an import, not actually declared in the RO file. As long as you don't specify --imports exclude, these should still be extracted, so this should not spit out a warning. I'm making a fix for this now, thanks for the catch!

[jamesaoverton]

This should be fixed by #625