Ontology meeting 2012-05-09

MINUTES: DAVID

45-minute call

FOLLOW-UP: chemical xps

For background, see discussion here: http://wiki.geneontology.org/index.php/Ontology_meeting_2012-05-02#DISCUSSION_ITEM_I:_Follow_up_on_chemical_xps

The google docs version of the compounds to sort out is here:

https://docs.google.com/spreadsheet/ccc?key=0AtGZO7sNc8MkdGlyYXlvOVhmMmNIUFVYTnk1SUtJS1E&pli=1#gid=0

FOLLOW-UP: EC numbers in GO

For background, see: http://wiki.geneontology.org/index.php/Ontology_meeting_2012-05-02#DISCUSSION_ITEM_II:_EC_numbers_in_GO

Jane, could you please report if there's any update on this?

FOLLOW-UP: ChEBI paper

Chris, not sure if you've had a chance to work on this, see http://wiki.geneontology.org/index.php/Ontology_meeting_2012-05-02#DISCUSSION_ITEM_III:_Follow-up_on_papers:_ChEBI_and_TermGenie

FOLLOW-UP: TermGenie paper

Done since last call: half of all new term requests (51.8% to be precise) between Jan. and June 2010 could have been dealt with, at least in part, using TG templates. See http://gocwiki.geneontology.org/index.php/Template-able_Requests_Prior_To_TG

The google doc has been update with this info. What do we need to do next?

DISCUSSION ITEM I: Follow up on "Moving biological_process_xp_cellular_component into live GO"

See previous discussion here: http://wiki.geneontology.org/index.php?title=Ontology_meeting_2012-03-07

• I'm ready for all the transport ones - one hold up has been thinking of a family of relation names that generalizes over both transport and localization that encompasses the different roles (cargo, source, destination, conduit). If we decide on these we can just move this lot in straight away. There was a thread on the list about this w/ Midori a month or two ago -- cjm

DISCUSSION ITEM II (related): Are we going to retrofit logical definitions for cell-type-specific cellular component terms?

Some of these (e.g. neuron projection) are in the scratch directory as cellular_component_xp_cell.obo.

Stems from this SF item: https://sourceforge.net/tracker/?func=detail&aid=3518879&group_id=36855&atid=440764

Also see this other SF item: https://sourceforge.net/tracker/?func=detail&aid=3410166&group_id=36855&atid=440764