Ontology meeting 2013-11-20
- 1 viral cross-products (bumped to next week)
- 2 Follow-up: TG TEMPLATE FOR ORGANELLE PART (LUMEN, MEMBRANE) (bumped to next week)
- 3 Stemming from question of adding 'luteinizing hormone' in GO (bumped to next week)
- 4 Review of template requests in Jira (bumped to next week)
- 5 New TG template for 'cell migration'? (bumped to next week)
- 6 Review proposed fixes to terms for extracellular & extra-organismal region terms - including status of 'other organism'
- We need a better way to represent viral modulation of cell activity. We've used has_particiapnt for now:
[Term] id: GO:0039671 ! evasion by virus of host natural killer cell activity intersection_of: GO:0030683 ! evasion or tolerance by virus of host immune response intersection_of: has_participant CL:0000623 ! natural killer cell
but what we really need to do is say e.g. natural killer cell activity = some biological process has_participant natural killer cell and this process is the regulation of that activity.
Also CL:0000451 ! dendritic cell term
- We've got lots of terms that reference a specific host protein, where the virus modulates one or more functions of that protein e.g.
id: GO:0039548 name: suppression by virus of host IRF3 activity
IRF3 has multiple activities so we wouldn't make an MF term 'IRF3 activity' but we need it somewhere to be able to say the virus modulates it.
- Processes where the differentia is that it involves a virus e.g.
id: GO:0039699 name: viral mRNA cap methylation
has_participant is wrong here...need to say has_participant some protein encoded_by virus
Follow-up: TG TEMPLATE FOR ORGANELLE PART (LUMEN, MEMBRANE) (bumped to next week)
Do we have action items/time-frames for them?
Stemming from question of adding 'luteinizing hormone' in GO (bumped to next 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 (bumped to next week)
New TG template for 'cell migration'? (bumped to next week)
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.
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.."