Ontology meeting 2013-03-14

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ATTENDEES: David, Tanya, Jane, Chris, Paola, Heiko, HJD, Judy

Testing new OBO-Edit release

  • Transition seems to have been okay, except for version number. Some old config files might need removing. We need to test obo/OWL round-trip. Jane will do this test next week.

Web Presence

  • Should we have a regular outreach / web presence part of this call?
  • New download site in progress: http://beta.geneontology.org/page/download-ontology
    • Everyone likes the new download page
    • Chris hoping to have at least a fully active beta by GOC meeting
    • Mechanism for generating the new ontology pages: David will make a shared doc with proposed new upper structure for a/ Main web documentation b/ Internal documentation in the Drupal book style. We can then all edit and migrate existing web content across.

Cell cycle

Any follow-up on this from last week? http://wiki.geneontology.org/index.php/Ontology_meeting_2013-03-7#Cell_cycle_arrest

What's our plan of action wrt to phases? Shall we just go ahead and do it as we're keeping them in BP? Need to decide on relationship between processes and phases - did we settle on happens_during?

  • Tanya to send out a short email to GOC warning people that we had a cell cycle meeting and to expect lots of changes to these terms.
  • Tangential item: lots of annotation errors coming from interpro2go and spkw2go. Do these get checked for automatically? Whose pipeline should this be in? Jane to check with Rachael and Tony.
  • Cell cycle phases: we're going to bring Chris up to speed on this call next week and make a decision.

SF upgrade

Follow-up from last week, see http://wiki.geneontology.org/index.php/Ontology_meeting_2013-03-7#SF_upgrade

  • Bumped to next week, Jane still to look into migration of categories

Definition of 'cellular' in GO terms

Any follow-up on this from last week? http://wiki.geneontology.org/index.php/Ontology_meeting_2013-03-7#Definition_of_.27cellular.27_in_GO_terms

  • We decided to make xps for exisiting 'cellular' terms using cellular terms as genus, bump the discussion of how to actually define 'cellular' to another day.

Protein complexes

Harold to follow up (see http://wiki.geneontology.org/index.php/Ontology_meeting_2013-03-7#Follow-up:_Protein_complexes)

  • Harold in the process of checking the protein complex xps before we incorporate.
  • Discussion of when to make 'capable_of' relations between cc and bp. We need to be conservative when we make these because the function is inherited by all species, even when the activity hasn't been proven experimentally.

Envenomation and multi-organism regulation

Monthly update: Project Management in JIRA