Ontology meeting 2013-12-05: Difference between revisions
No edit summary |
|||
Line 1: | Line 1: | ||
=== | ===Protein complex involved in bp terms?=== | ||
Stemming from this ticket of Birgit's [https://sourceforge.net/p/geneontology/ontology-requests/10543/] | Stemming from this ticket of Birgit's [https://sourceforge.net/p/geneontology/ontology-requests/10543/] |
Revision as of 09:07, 26 November 2013
Protein complex involved in bp terms?
Stemming from this ticket of Birgit's [1]
She's basically asking whether she should add 'x mf complex involved_in bp' as child terms to 'x mf complex' terms, or whether synonyms for the specific subtypes are sufficient on the 'x mf complex'.
Stemming from question of adding 'luteinizing hormone' in GO
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'?
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.."
Review proposed fixes to terms for extracellular & extra-organismal region terms - including status of 'other organism'
See: https://www.ebi.ac.uk/panda/jira/browse/GO-216
Patterns for defining maintenance of location.
Should maintenance of location be a subclass of localization rather than a part? This appears to be consistent with the current textual definition of localiation and would also allow complete automation of new term classification in this branch. Details here: https://www.ebi.ac.uk/panda/jira/browse/GO-232