Ontology meeting 2012-05-09

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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:


Also, Jane is looking into missing xps using OBO-Edit/Protege - WORK IN PROGRESS


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: Update on Cell Ontology (CL)

Is there any update on the Cell Ontology work, especially with regard to new cell-type term requests? Is there any paid editor working on this currently? If not, would it be an option to allow access to CL to the GO Editors, so we can put terms in ourselves when needed?

This stems from some open requests for neuronal and cardiac cell type terms - the former are long-standing and needed to create new GO terms, and the latter are needed for the cardiac conduction project.

See e.g.




Note from Alex: There is no paid editor for CL at this point. I am involved in several projects related to the CL, including some ontology editing work, but have not been good about getting back to the SF items. We are planning to apply for new funding for CL work through one or more grants.

Chris Mungall, Melissa Haendel, and Ceri van Slyke have all contributed edits to the CL in the past year for particular projects, and Chris has recently transitioned the CL to an svn repository. I will continue doing editing myself among other projects, but I would welcome any contributions from GOC editorial staff. If GOC editors wish to add new terms to the CL, please use the range CL:0009000-CL:0009999, and make comments to your SF entries as you complete them. Otherwise, I will make an effort to attend to these SF entries when I get a chance. Thanks --Alex

DISCUSSION ITEM II: 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 III (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