Ontology meeting 2013-01-17
MINUTES: Paola
ATTENDEES: Paola, Jane, David, Tanya, Judy, Heiko, Chris, Harold
ChEBI paper
Where are we?
AI: David will send pre-submission enquiry by the end of next week.
AI: Chris will work on the missing figure and incorporate it into the final version of the paper.
AI: Then we should all re-read through.
Merge behaviour
This arose from this SF item [1]. When terms are merged in OE, the subsets from the merged term are lost. Ideally we'd want them retained - is it possible to make this fix in OE? Or too time-consuming?
AI: Next time we see a failed merge with definitions, we should save a version of the file.
AI: Jane will add a ticket on the OE SF tracker. Chris will look into it.
Single-step processes
Rama and Paul have voiced concerns about processes that have some overlap with functions e.g. phosphorylation/kinase. See email thread. We should discuss this.
AI: Editors will suggest changes to definition. Tanya will discuss this on a future annotation call.
Follow-up on TermGenie free form
Judy agrees with strategy of granting access to only one representative per database/group.
AI: Jane will prepare list of suggested representatives and circulate it.
Protein/glycoprotein/lipoprotein terms in ChEBI
Chris: Anything new since http://wiki.geneontology.org/index.php/Ontology_meeting_2012-12-20#Follow-up:_Protein.2Fglycoprotein.2Flipoprotein_terms_in_ChEBI ?
AI: Chris will follow-up with them. DONE: upped priority of SF ticket https://sourceforge.net/tracker/?func=detail&atid=703818&aid=3592472&group_id=125463, and emailed Darren.
Daily digest emails for new/edited/obsoleted terms (obo-diff.html)
Is this working now?
Yes, in Jenkins, but emails are not ready yet and that's what curators want.
AI: Heiko will check if that's easily feasible.
Soft check for annotation to 'part' terms (nuclear_part, etc)
Is this in place now?
Yes, this is now as part of the Jenkins GAF validation. Before it only checked a small list of terms. Now all terms in the subset are checked. Unfortunately, there seems to be quite a bit of annotations. For example: TAIR 426, MGI 1687
AI: David will email Rama and Rachael to let them know about this. Each contributing annotation group should look into their own annotations and fix them.
Cell cycle meeting
Feb. 28th + March 1st (dates are confirmed), in Hinxton. Jane and Paola are taking care of logistics.
Wikis: http://wiki.geneontology.org/index.php/Cell_Cycle_Content_Meeting_Feb_2013 and http://wiki.geneontology.org/index.php/Cell_Cycle
Participants:
Jane
Paola
2 Reactome people?
Val
Midori
Jackie Hayles
David
Tanya
Mary Dolan?
Lisa Matthews (Reactome)?
Agenda?
Other comments:
1) Ask Val to ask David Morgan if Tanya can visit him and discuss before the meeting. Tanya is in contact w/Val about this and is exploring Stanford cell cycle labs for opportunities as well.
2) Mary would like to attend remotely. Lisa might also not make it in person to the meeting, but is interested in attending remotely.
AI: Adjust schedule considering that Mary and Lisa are on the US East Coast.
Monthly update: Project Management in JIRA
Missing xps:
AI: David and Tanya will work on the involved_in (not straightforward as some terms are missing in GO).
AI: Jane and Paola are working on metabolism (then we'll ask Heiko to do the roundtrip thing, to put the file back in the proper order).