Ontology meeting 2013-11-20
Attendees: Jane, Becky, Paola, DavidOS, DavidH, Harold, Heiko, Chris, Judy
- 1 viral cross-products
- 2 Follow-up: TG TEMPLATE FOR ORGANELLE PART (LUMEN, MEMBRANE)
- 3 Stemming from question of adding 'luteinizing hormone' in GO (push to next meeting)
- 4 Review of template requests in Jira (push to next meeting)
- 5 New TG template for 'cell migration'? (push to next meeting)
- 6 Review proposed fixes to terms for extracellular & extra-organismal region terms - including status of 'other organism'
- 7 Moving logical defs into the editors obo file
- 8 Taxon constraints
- 9 Action potential
SET UP SEPARATE CALL - use next Wed (Nov. 27) SF call time for this
- 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)
See latest discussion:
Do we have action items/time-frames for this?
DavidOS has slides and suggestions. Keep in mind potential applicability of relations used for other ontologies. Compatibility with BFO? Ex. 'lumen' in GO and 'lumen' in BFO. DavidOS is on the job. Will sort out.
Stemming from question of adding 'luteinizing hormone' in GO (push to next meeting)
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 (push to next meeting)
- https://www.ebi.ac.uk/panda/jira/browse/GO-58 homeostasis xps
- https://www.ebi.ac.uk/panda/jira/browse/GO-168 TermGenie templates with UBERON
- https://www.ebi.ac.uk/panda/jira/browse/GO-177 assembly/disassembly of CC
- https://www.ebi.ac.uk/panda/jira/browse/GO-181 cell differentiation
- https://www.ebi.ac.uk/panda/jira/browse/GO-185 organelle part (lumen, membrane)
- https://www.ebi.ac.uk/panda/jira/browse/GO-204 Protein Complex by activity
New TG template for 'cell migration'? (push to next meeting)
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.."
Review proposed fixes to terms for extracellular & extra-organismal region terms - including status of 'other organism'
Moving logical defs into the editors obo file
There's a plan. Editing shouldn't be very different from xp generation within GO. Try making xps using external ontologies.
Testing of OE catalogs
Can all editors test the OE beta?
People have tested normal editing, no real test of adding xps to external ontologies yet. Also making regular relationships to external ontologies - example: axon part_of neuron, process has_participant xxx
- Day-to-day editing. OK? Should be unaffected
- Loading combined file: go_write_test.obo (file with production xps added) in editors directory
Make sure you click allow dangling references or it won't load. MAKE SURE YOU SAVE INTO THE SAME DIRECTORY THAT YOU LOADED FILE FROM - because zombie apocalypse otherwise.
Downstream changes (push to next meeting)
- Reconfigure TG to write all-in-one
- Change pipeline, at first just emulate existing pipeline
Taxon constraints will be easier to edit when the mega file exists, logical defs go in first, then tax constraints. Figure out a way to track publications (PMIDs) for taxon constraints. OE can't do this right now. Can add after by hand to OBO file. Could move the PMID to the gloss of the def and then add the PMID to the def dbxref.
Planning to generate GO process term for action potential if no objections. See: https://www.ebi.ac.uk/panda/jira/browse/GO-215
DavidH: 'generation of action potential'? action potential is something you measure DavidOS: No. Action potential = series of changes in potential across a membrane Paola: specific lots of stuff in comment, agrees with DavidOS' proposal All: Go ahead.