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?

Axiomatizing Regulation of Biological Quality

Any objections to Chris' suggestion of going ahead and adding?

   DOS: Mostly looks good.  Not sure about location pattern though.
   occurs_in definition has domain process (although this is not formalised).

Details on email thread with same title on ontology list:

David H and I have gone through the proposed logical defs for RoBQs

http://wiki.geneontology.org/index.php/Extensions/x-attribute

(the wiki is v out of date, but these extension pages can soon disappear once is everything is part of the normal edit cycle)

These make use of OBA, which you can find out more about here:

https://github.com/obophenotype/bio-attribute-ontology/

including links to the OBA TG etc

I think they are now all valid (completeness can wait). I propose just going ahead and adding, raise any objections on thursday call