Ontology meeting 2013-09-12

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Attendees: Paola, DavidOS, DavidH, Judy, Chris, Tanya

Minutes: Tanya

GOC MEETING

David H to report.


Draft agenda is up. Please review. See if there are missing bits. Jane has to leave on Sat pm. Pls.
make ontology devt. early in meeting. Bulk of meeting will be Fri/Sat. 

GO GALAXY

How best to quote it and acknowledge it in the apoptosis paper?

Chris will send reference to Paola to use. Chris will look at paper today and is available for consult tomorrow.


DOCUMENTATION FOR NEW WEBSITE

  • Who is dividing up the old pages to distribute to people to rewrite?
  • Who is rewriting what?


Changes to external ontologies

At present (I think) we don't have any mechanism for reporting when an external ontology has changed and affected a GO axiom e.g. when CHEBI does a merge. Can we start generating a report of these?

V. important! Need to figure out a way to fit this into our workflow.  How do we handle alt_ids?

PROJECT MANAGEMENT IN JIRA

Please everyone review all the issues assigned to you.

FOLLOW-UP: happens_during

 David OS waiting for Jane to dig up original discussion and use cases (time expressions in PomBase)
 that led to wanting to use these in the first place. Needs these to proceed with evaluation. cell cycle 
 terms have dual usage: timing events and processes.  Yes: phases are timing events, others are processes.
 part_of vs. happens_during. Currently, column 16 data is a combination of usage, using either relationship
to link to process terms. 
 Also, GO EBI curators had meeting with IntAct curators yesterday. Suggested using 'happens_during' to capture 
timing of interaction.  There may be some issues with this application.  What are they capturing?  Complex formation 
or complex existence? Perhaps 'exists_during' would be a better relation. 

FOLLOW-UP: Equivalent classes for Acid/Base transport and transport activity

HJD on vacation. Report next week.

Template for 'protein localization to xxx' ?

Template is released. Look for cases where protein localization to xxx is part of 
some larger assembly process and manually make links in these cases. Ex. protein 
localization to T-cell secretory granule.  Consult Midori.