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ontodev / robot

ROBOT is an OBO Tool
http://robot.obolibrary.org
BSD 3-Clause "New" or "Revised" License
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Error in missing_superclass query #598

Closed ddooley closed 4 years ago

ddooley commented 4 years ago

First to say Robot report is a great QC addition to OBOFoundry, it will really help set the bar, so thanks. Now, the screenshot below shows that a class "antimicrobial resistance test platform" that is claimed not to have a parent actually does. Seems to be happening when a certain kind of reference to the class exists, like "term replaced by".

image

beckyjackson commented 4 years ago

Thanks for bringing this up. Could you provide a link to the ontology so I can check out what's going on?

ddooley commented 4 years ago

It is happening in the http://obo-dashboard-test.ontodev.com/ live GenEpiO report. I presume that one is looking at the OBOFoundry link which points to https://raw.githubusercontent.com/GenEpiO/genepio/master/genepio.owl

beckyjackson commented 4 years ago

When making the dashboard, we try to create a "base" product of the ontology to exclude any imported terms. This means that we keep all axioms that have a subject in the GENEPIO namespace. That said, any "nary" axioms (equivalent, disjoint) that use a GENEPIO term and another term are kept so you may end up with a disjoint axiom with an ARO subject. Hopefully this short explanation makes sense.

We updated the report queries to exclude terms that are only used in these nary axioms here - https://github.com/ontodev/robot/pull/570/commits/6694d6eddbc48dd4dd2416a15fde3bbb1e4b7714

Last time we ran the reports over the ontologies, it looks like we used an older version of ROBOT. I just ran report on GENEPIO with the current release of ROBOT and these INFO messages are gone. I will start another run of the dashboard with this update.

ddooley commented 4 years ago

ok, great!