Ontology meeting 2013-11-14
Attendees:
Minutes: Paola
TG feature request
Can we add capable_of to the freeform template? Useful for all Birgit's complexes.
ChEBI roles again: 'acid'
See email thread and https://sourceforge.net/p/geneontology/ontology-requests/10492/
Stems from this SF request from Li (her request for 'steroid hormone binding'): https://sourceforge.net/p/geneontology/ontology-requests/10487/
Do people agree with Harold's comment and mine? Anything we need to do?
Dates for putative meeting in Jan-Feb 2014
Please fill in the doodle poll if you haven't already: http://doodle.com/qrdz2tzeze7bf43t
Paola to report if we have consensus dates.
Follow-up on 'response to x' vs. 'response to y stimulus'
We had an action item from last week: "As an aside, need to standardise terms since we have some 'response to x' and 'response to y stimulus'. Add or remove 'stimulus' from all these terms." Who is going to take care of this please?
Follow-up: TG TEMPLATE FOR ORGANELLE PART (LUMEN, MEMBRANE)
See latest discussion: http://wiki.geneontology.org/index.php/Ontology_meeting_2013-11-07#Follow-up:_TG_TEMPLATE_FOR_ORGANELLE_PART_.28LUMEN.2C_MEMBRANE.29
Do we have action items/time-frames for them?
New OE (bumped from last week)
Quick run through of new imports and visualization. Any tips to share?
Stemming from question of adding 'luteinizing hormone' in GO (bumped from last week)
See email thread. Chris says: "GO eds - we will want to switch IDs in the production logical definitions before this, to check the inferences. That's another external ontology imports file - not a big deal. Discuss on thursday?"
Review of template requests in Jira (carried over from last week)
- https://www.ebi.ac.uk/panda/jira/browse/GO-58
- https://www.ebi.ac.uk/panda/jira/browse/GO-168
- https://www.ebi.ac.uk/panda/jira/browse/GO-177
- https://www.ebi.ac.uk/panda/jira/browse/GO-181
- https://www.ebi.ac.uk/panda/jira/browse/GO-185
- https://www.ebi.ac.uk/panda/jira/browse/GO-204
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.."