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 has looked into missing xps using OBO-Edit/Protege. She's come up with a list of ~300 missing xps, that we've split among EBI editors. We're currently working on adding these in, focusing on the ones that already have CHEBI IDs, and making notes about the others.

The binding ones and transport ones still need to go in. There are about a hundred of those. What do we do with the via terms? We could chain together two separate terms or we could have has_intermediate. Salvage and cycle terms are the other ones that are a bit problematic. What about the ones like aerobic, anaerobic and de novo. They are all basically different pathways where for example the starting material is different. Could we define these in terms of their inputs, intermediates and outputs. Karen says this might work. It would be problematic if we had to define them with a negation statement. Jane will look into them and see if this will work. Should we make a new genus term aerobic/anaerobic process. What about the protein terms that are not in ChEBI? Roles will become important.

What about dependecies such as "anaphase-promoting complex-dependent..." We should include the dependencies in the process. How will we do this? Does PRO do this? Could we say something like ubiquitin-dependent catabolic process starts with protein ubiquitination.

What about the ones that contain components? The process doesn't always occur in that component.

amino acid families----just keep them without cross-products

What about binding terms that have specific sequences. Should we use SO? For now, keep those as a separate set. We need to get the separate ontologies talking to each other, PRO, SO ChEBI.

Fermentation--is it an anaerobic catabolic process? Karen suggests that this is the case. Tanya it is not uniform. In some cases, it looks like it is not catabolism. Handle them when we can.


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

Chris..... he promises today!

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?

Just keep carrying on with this.

TermGenie and ChEBI

The first pattern using ChEBI is ready to be deployed. The local tests are working. The only requirement is an empty review queue, as there is a minor change in the database back-end.

  • As of ~6am California time today (Wed.), there are no terms left in the review queue. (However, I'd suggest emailing the GO list to temporarily halt new requests via TG.) Should there still be any request in the queue when you're ready to test, please email me a copy of any stanzas left in the TG commit page. You may then obsolete any pending request, and I'll reinstate them myself once you let us all know that TG is good to use again. -- Paola

TermGenie should be up today or tomorrow morning with ChEBI templates. Ready for testing of the SF items. Still need to fix up some chemical cross-products.

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

GO editors will be given write access. Paola will add the terms that she needs.

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

No discussion.

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

No Discussion