Ontology meeting 2014-04-03

Attendees: Harold, Jane, Tanya, Paola, David H, Chris

Minutes: David H

Abstract for Bio-Ontologies SIG at ISMB

As per Judy's email. Discuss & report back.

None of the people on the ontology development call are planning to go at this point. The group will work on an abstract for Judy to present. Paola will create a Google doc.

Google doc is here: https://docs.google.com/document/d/1KFCa7LDvz8bEBC_gFmzpt_xPM6KyZXh3cSiqSwT806U/edit

Reactome ontology mappings

Reactome maintain mappings between their processes, reaction etc and GO terms. We have mappings to Reactome in GO, but these are not in sync - one of Amelia's legacies I think. How do we want to handle this? The nuclear option would be just to remove the mappings from the ontology file, or alternatively we could set up a regular job to get the GO-Reactome mappings from their BioPax. Thoughts?

Heiko and Chris will set up a job to make these automatic. Jane will open a Jira ticket.

Adding taxon rules in the live ontology

Can we have a live demo of how to add them in OE?

Just drag and drop the taxon group into Parent Editor and select the right relation. What happens if it is a taxon rule that is not a large class?

Adding a new taxon:Open the file in the extensions directory called imports_requests. Add a new relation line to the generic stanza file and commit. In 24 hours, your term should be imported.

I [Paola] need to add several only_in_taxon links for Giardia-specific terms. The relevant taxonomy ID is not in ncbitaxon_import (nor the megafile) yet:

Taxonomy ID: 5740 (Giardia) (full lineage: cellular organisms; Eukaryota; Fornicata; Diplomonadida; Hexamitidae; Giardiinae) (none of these classes below 'Eukaryota' is represented in the editors file).

What's the procedure? Can I just add 'Giardia' as is_a Eukaryota in OE, rather than filling in all the intermediate classes. Or shall we add intermediate classes on an ad-hoc basis only (so in this case I'd add Fornicata; Diplomonadida; Hexamitidae; Giardiinae; Giardia). I presume we may want to avoid clogging the editors file with the entire Lynnaeus system.

Review of Jira tickets

Or we may want to do it 'in our own time' if we can't get to it at this meeting.

Jane reviewed the tickets. We got through 50 out of 63. Lots of the tickets are for missing logical defs. Perhaps it would be good to have a jamboree and just get these done.