Ontology meeting 2012-04-25

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45 minutes call

DISCUSSION ITEM I: Follow up on chemical xps

See previous discussion here: http://wiki.geneontology.org/index.php/Ontology_meeting_2012-04-11

This was followed up by an email thread on the go-editors list. Could we please discuss Jane's questions on the latest message in the thread:

"I think we should definitely do that [i.e. in response to Chris' suggestion "just switch TG to point to UCHEBI and request further changes in CHEBI directly"]. So then new chemicals would only need to go into CHEBI, and we would add xps by hand to x-chemical-edit.obo?

And then we wait to see if Heiko can figure a way to write the xps from TG1.

  • We're making progress here, Heiko can give an update --cjm

The downside, I guess, is that we can't leverage the CHEBI structure to place new terms by using TG0 and cut/pasting?"

We keep having frequent requests for chemical terms in SF, so it would be helpful to know how to proceed as effectively as possible. Thanks!


The Enzyme Commission has been updating EC numbers at a very high rate lately.

If we wish to continue to maintain the EC xrefs, we need a strategy to make this viable, possibly by automating part of the work.

  • Can we formally collaborate with them? What is their development process? In a sane world we would have a single ontology that we both work on, and new reactions are added with logical defs to CHEBI. In fact, they should add EC numbers using TG. The hierarchical IDs would pose a challenge but this is doable. --cjm

DISCUSSION ITEM III: 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 IV (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

DISCUSSION ITEM V: Follow-up on papers: ChEBI and TermGenie

DISCUSSION ITEM VI: legacy terms without logical definition

There are still lots of terms with labels like

  • X involved in Y
  • X by Y

That lack a logical definition. Note that this means TG will give incomplete inferences for these templates, as the above terms are effectively invisible to it.

What's the plan here? Is everyone aware of the bold / not bold highlighting in OE - this makes it easy to search for strings that lack logical definitions. We need to stay on top of these. There was a tracker item about the involved in ones a while ago, but it just dropped off the radar. Maybe we need to have a person/role whose task is to stay on top of this. In theory it should just be a retrospective task if new terms come in via TG -- cjm

Tanya and I will find the orphans and fix them. -- dph