Ontology meeting 2013-04-25
Minutes: Jane
Attendees:
Project Management in JIRA
Follow-up: cell-type templates
See http://wiki.geneontology.org/index.php/Ontology_meeting_2013-04-18#Cell_type_templates
All children of GO:0097285 cell-type specific apoptotic process now map to a CL ID.
Chris/Heiko to report on feasibility/timeframe for TG template.
Follow-up on SF upgrade
See http://wiki.geneontology.org/index.php/Ontology_meeting_2013-04-18#SF_upgrade
Website
This discussion is about content of the ontology-related pages. Can we somehow link to some of the Drupal pages that are finished like the ontology download page? It seems that the whole website is going to take some time.
Subset metadata
Tony is adding the 'do not annotate' anti-slims to the DB so they can be used by in QuickGO and protein2go. They'd prefer to have the subset comments at the level of the subset itself rather than as a comment added to each individual term that belongs to that subset. Is there any way we had do this in OBO format, in the header or something?
Cell cycle issues
starts_with ends_with
Is there any reason we can't start using these in xps in gene_ontology_write.obo? I need them for the cell cycle logical defs.
happens_during
For between phases and transitions. I need this before I can progress editing. Is this the correct relation? What's the process for adding a new relation to gene_ontology_write.obo?
InTact xrefs
Birgit from InTact has been adding lots of complexes to cc via TG FF. They would like to have reciprocal links back to GO for InTact complexes. These will be the species-specific entities, one for each species so a max of about 8 per GO term. Updates to the xrefs could be handled manually at this stage. Two questions for us: are we happy to have the xrefs? Would we consider adding a general dbxref field in TG FF so Birgit could add the xrefs as she goes along?
Pending obsoletion subset?
I've been thinking it might be a good idea to have a 'pending obsoletion' subset for marking terms we intend to obsolete. This would allow us to easily identify terms we'd slated for obsoletion, and also would allow browsers to display this info to users.