Ontology meeting 2013-12-05: Difference between revisions

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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'.
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'.
There's also an additional question from Birgit about whether to create a class to group complexes where there is no obvious function. The example is a complex involved in the innate immune response. It's known to be nucleotide binding, but that's not really sufficient for a grouping class. Use the process? Or no grouping?


===Stemming from question of adding 'luteinizing hormone' in GO  ===
===Stemming from question of adding 'luteinizing hormone' in GO  ===

Revision as of 09:25, 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'.

There's also an additional question from Birgit about whether to create a class to group complexes where there is no obvious function. The example is a complex involved in the innate immune response. It's known to be nucleotide binding, but that's not really sufficient for a grouping class. Use the process? Or no grouping?

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)

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

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