Ontology meeting 2014-09-18

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Attendees:

Minutes: Harold

Molecular Function refactoring

Following up on http://wiki.geneontology.org/index.php/Ontology_meeting_2014-09-04#Trello_Items

 Paul: anyone added comments on web protege ; Jane: no, we need to review the comments and proposal. 
 (Paul's latest document is here: https://docs.google.com/document/d/1y-6to0vwEJHc3i3wdPnJoCAq910auPQp5jBvafpJvL0/edit)
Paola: new need something clearer about what are the aims; Is there a white paper? 
Paul/Chris: see files here: http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/experimental/lego/docs/
 We need to be clear in light of the recent discussions of GO changing. 
      Compound fuctions, like "cell adhesion mediator" ??
     See:  http://purl.obolibrary.org/obo/GO_0098631 protein binding involved in cell adhesion"
     How is this different from 'cell-adhesion mediator' 
      Is cell-adhesion mediator a compound?

Removing 'unknown' synonyms from the GO root terms (MF, BP, CC)

 Tanya thinks it does no harm. But we agreed to remove the synonyms.

From Chris, see https://sourceforge.net/p/geneontology/ontology-requests/11167/

Property chains for regulates/part_of

Do these property chains always make sense?

For SF11164 and SF11166

regulates o part_of = regulates

negatively regulates o part_of = negatively regulates

positively regulates o part_of = positively regulates

 So if you regulate a part of a process are you regulating the whole process? 
     http://sourceforge.net/p/geneontology/ontology-requests/11164/
     http://sourceforge.net/p/geneontology/ontology-requests/11166/
     Chris thinks we should add them.

SF items

Modified amino acids in ChEBI are is_a amino acid. This is causing weird parentage in the metabolism part of the graph.

 Will discuss with CHEBI on site

Please have a look at SF#11108, discussion about protein complexes.

         Macromolecular assembly? for actin, chromatin. Supermolecular (or supramolecular) structure?

'intracellular transport' does not apply to 'plasma membrane'

Should we relax the logical def. to point to 'cell' rather than 'intracellular', or do we need new terms?

See https://sourceforge.net/p/geneontology/ontology-requests/11158/

Following email discussion, we may need a new cc that is intracellular + plasma membrane only. Is there one already? If not, what should we call it?

Discussion moved to email thread.

TG template for 'cell migration'

It's out there in TG, does it need testing? Any necessary AIs?

Chris will test. Discussion moved to email thread about most appropriate relation to use.

Monthly review of Jira tickets

No time, so bump to next week.

GO into NCIt

https://docs.google.com/document/d/1ozliyTh-QPyyUdYjk8P1mhygWCWtCnZKX9FNGvU-XlM/edit#