Ontology meeting 2013-03-28

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MINUTES: Tanya

ATTENDEES: Chris, Heiko, Tanya, Jane, Harold, David

Stuff for GOC

Agenda is here: http://wiki.geneontology.org/index.php/2013_Cambridge_GOC_Meeting_Agenda

Let's check it over and see if there's anything we want to change or add. Check the right people are presenting.

DONE

Envenomation

There is a request for an envenomation template. There seem to be no or very few xp defined for any of the existing envenomation terms and their related modulation/neg or pos regulation of process in other organism terms.

Jane will address this. Heiko will pick up when Jane is done. Probably after GOC meeting. 

Dual taxon annotations

Transfer to c16? What about the role (host/symbiont) - also c16?

These (~300 where there are two taxon ids in the taxon col)  predate col. 16.  Chris proposes post-processing the file and moving the second taxon id into c16.   Would be nice to have a LEGO modeled example for this type of situation.

Beyond cell cycle: other phases in GO

menstrual cycle phase SF item (children: menarche, menopause, menstruation)

estrous cycle phase (children: diestrus, estrus, metestrus, proestrus)

 revisit definitions of the terms and make more process-y if necessary, also molting cycle and hair cycle 

Testing new OBO-Edit release

Jane to report on test obo/OWL round-trip.

D & T will test tomorrow @ Berkeley. 

SF upgrade

Follow-up from last week: (background is here: http://wiki.geneontology.org/index.php/Ontology_meeting_2013-03-7#SF_upgrade)

Jane to report on migration of categories; she put a ticket on SF asking them about the categories, and is still waiting to hear from them. Any news?

Other projects are switching to or using github because they don't like new SF. 
Ex. Uberon [http://github.com/cmungall/uberon/issues], can link ontology devt and commits, 
commit messages and issue tracker can be linked. We're probably not ready for this 
but it's a nice example.  Other possibilities are moving the ontology to googlecode 
but Stanford svn will do for now.  On hold for SF transition for now. 

How do we want to define 'cellular' in GO terms?

Stems from discussions here

http://wiki.geneontology.org/index.php/Ontology_meeting_2013-03-7#Definition_of_.27cellular.27_in_GO_terms

and here

http://wiki.geneontology.org/index.php/Ontology_meeting_2013-03-14#Definition_of_.27cellular.27_in_GO_terms

Additional transport template?

SF request [1]

We need Chemical X transport from cellular component 1 to cellular component 2.

 Fresh template to be created. Maybe with options to include either origin or 
destination. Need to check for base xps in existing ontology for this. 

Migration to Drupal

Chris has been adding some pages to the beta web page.

BETA SITE MAPPINGS

Subset name changes

  • No_direct_annotation_ever
  • No_direct_annotation_manual

Something like this but these are the sets we want to represent. Jane will let Heiko know and Heiko will implement in Jenkins.