Ontology meeting 2015-04-23

Attendees:

Minutes:

Please, Please, Please could we propagate from EC to subclass axioms on public release

We still need to redundantly repeat everything we say in Equivalent Class axioms in subclassing axioms in order to get things to appear in GO releases. While editing in Protege, it is almost inevitable that these are missed some times. This is a waste of everyone's time. e.g. see" https://sourceforge.net/p/geneontology/ontology-requests/11646/

If we need to keep some types of relationships out of the release file, can we please control this via a filtering mechanism at release. Relying on editors to police this via what goes in subclassing axioms is incompatible with sensible use of logic for autoclassification (sometimes subclassing axioms are needed for classification, but equivalent class axioms would be wrong).

Follow-up: Prefixing of obsolete to label of all obsoletes

Last week we discussed and resolved:

We should really do this for consistency. Or alternately remove from the release version since they are primarily there for the edit cycle. 

Consensus is we should be consistent and just prepend all the obsolete terms with obsolete-. The tag will still remain.

Are we going to retrofit and do this (automatically) for existing obsolete terms too? (We should, but can't remember.) Currently, obsolete term names come in 4 flavors, we need consistency:

- term name

- term name prefixed with 'obsolete' e.g. 'obsolete ATP catabolic process'

- term name prefixed with 'OBSOLETE' (only one example)

- term name prefixed with 'OBSOLETE:' (only one example)

ORE 2015

We should enter GO for this year's OWL reasoner evaluation competition. DOS: I'll enter go-plus.owl, but would also like to enter this combined with an annotation set expressed as OWL along with some queries across data. Can we get this ready for May 1st?