Ontology meeting 2013-12-19

Attendees: Heiko, Chris, Harold, Paola, Becky, Jane, David H, David OS

Minutes: David

Next call

At least 3 of us will be on leave on Thursday Jan. 2nd. Resume calls on Jan. 9th?

Yes, resume calls on Jan 9th.

Multi-organism process proposal

Becky, Jane and David have come up with a proposal for annotating multi-org processes which requires an additional column in GPAD for dual taxon information. See this JIRA ticket at the end [1]. Let's discuss the implications.

(See this table for examples)[2]

There are a few groups who will do a lot of these annotations. In GPAD we will not need a new column. We can use GPAD column 8 along with a relation. The relation will be mandatory. Do all the groups that want to do this have the capability? UniProt does. Protein2GO can handle this. If groups use Protein2GO, then they will have access to these features.

Lego update

Chris

Very keen to push ahead an editing tool. At the end of the day is is just the instantiation of OWL classes. We would like to start with a starting graph in place based on the axioms in the ontology. We will need a very integrated procedure between the annotation and the ontology group. If a group wants to annotate say DNA replication, they will need to work with the ontology group first.

Holiday Shutdown for Jenkins services

During the holiday we will stop the the following Jenkins jobs

• build-go-assert-inferences (next run will be on Tuesday 2014-01-07)
• release-go (shutdown on 2013-12-20 until 2014-01-02 or 2014-01-06?)

Question: Should we also stop the SourceForge e-mail of the new and updated tickets?

TermGenie will be up all the time. There is a cron job that restarts it everyday. Also because the release-go job is not running it does not matter that the terms accumulate in the queue.

New TG template for 'cell migration'?

Note that 'cell chemotaxis' is_a 'cell migration', which is fine based on their definitions. However, both 'cell chemotaxis' and 'cell migration' terms have logical defs based on alters_location_of, e.g.

[Term]

id: GO:0072676 ! lymphocyte migration

intersection_of: GO:0016477 ! cell migration

intersection_of: alters_location_of CL:0000542 ! lymphocyte

Chris says: "It would be good to use a more generic relation, but this depends on the hierarchy being disjoint with other classes using the same relation with a different genus.."

What we need here is a further intersection tag to show that chemotaxis is responding to a chemical. This would further differentiate the migration term.

Drupal documentation for ontology pages

Tanya doing basic formatting, need others to review content. (Tanya could you add link here please?)

GO and vesicle nomenclature

Stemming from email thread

Patterns for defining maintenance of location.

Should maintenance of location be a subclass of localization rather than a part? This appears to be consistent with the current textual definition of localiation and would also allow complete automation of new term classification in this branch. Details here: https://www.ebi.ac.uk/panda/jira/browse/GO-232

protein-DNA complexes revisited

We decided some time ago that this was not a useful grouping because it's unclear what constitutes a protein-DNA complex (any protein complex that binds DNA?) making for very tricky manual classification under this term, and we didn't feel it was a useful grouping as this information can be arrived at in other ways. However when I cam eot make the change it became clear that this complex term is referenced in many other process terms e.g. protein-DNA complex assembly, protein-DNA complex remodeling, protein-DNA complex transport, protein-DNA-RNA complex remodeling some of which may be useful, esp the remodeling terms.

Test Megafile with OBO-Edit 2.3 release

Available at http://sourceforge.net/projects/geneontology/

Please install, test and comment. Paola has used it for everyday commits and it works fine.

Also see http://wiki.geneontology.org/index.php/Ontology_meeting_2013-11-20#Moving_logical_defs_into_the_editors_obo_file (Testing of OE catalogs, Downstream changes)