Ontology meeting 2013-11-14

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Attendees: Paola, David OS, Harold, Heiko, Judy, Becky, Jane, Tanya, David H, Chris

Minutes: Paola

single/multi-organism template

Can we go ahead and make this template now that the PATO terms are in place? I will go ahead and make the xps. If we decide to use PCO instead, we can change retrospectively.


TG feature requests

  1. Can we add capable_of to the freeform template? Useful for all Birgit's complexes. (David is going to send an announcement that these will be going in the main file, at the moment we hide them in gene_ontology_xp_write.obo...what's our lead time for this?)

We don't need an announcement as we are already using capable_of in the TG template. We decided we would add the capable_of option in TG FF.

  1. Rama's request for a comment box.

This would appear as a definition comment. On top of the text box, we should indicate that the comment will be made public, and request that the comment is entered in the following format:

"An example of this is [*name* of gene product, such as LysZ] in [species name] [then add UniProt symbol here] in PMID:xxx. [add evidence code here]"

TG reviewers will simply have to strip off the evidence code. This is to avoid comments such as

"Note for self, IMP Q12345 (or other such UniProt symbol) in PMID:xxx".

and save TG reviewers from searching and emailing.

Made TG request ticket: http://code.google.com/p/termgenie/issues/detail?id=32

viral cross-products (bumped to next week)

  • We need a better way to represent viral modulation of cell activity. We've used has_particiapnt for now:
id: GO:0039671 ! evasion by virus of host natural killer cell activity
intersection_of: GO:0030683 ! evasion or tolerance by virus of host immune response
intersection_of: has_participant CL:0000623 ! natural killer cell

but what we really need to do is say e.g. natural killer cell activity = some biological process has_participant natural killer cell and this process is the regulation of that activity.

Also CL:0000451 ! dendritic cell term

  • We've got lots of terms that reference a specific host protein, where the virus modulates one or more functions of that protein e.g.
id: GO:0039548
name: suppression by virus of host IRF3 activity

IRF3 has multiple activities so we wouldn't make an MF term 'IRF3 activity' but we need it somewhere to be able to say the virus modulates it.

  • Processes where the differentia is that it involves a virus e.g.
id: GO:0039699
name: viral mRNA cap methylation

has_participant is wrong here...need to say has_participant some protein encoded_by virus

ChEBI roles again: 'acid'

See email thread and https://sourceforge.net/p/geneontology/ontology-requests/10492/

AI: MGI to look at their manual, direct annotations to 'response to acid' and see if they can be moved elsewhere. David/Harold to then comment on SF ticket above, and contact other databases if necessary so they also look at their annotations. Decide what changes we may want to make in the ontology. Paola to make changes where necessary.

(Also related to ChEBI roles) Hormone binding terms

Stems from this SF request from Li (her request for 'steroid hormone binding'): https://sourceforge.net/p/geneontology/ontology-requests/10487/

Do people agree with Harold's comment and mine? Anything we need to do?

AI: Paola to add a new term:

steroid hormone binding

Definition: Interacting selectively and non-covalently with a steroid hormone

add it as a child of both GO:0005496 steroid binding and GO:0042562 hormone binding


Dates for putative meeting in Jan-Feb 2014

Doodle poll: http://doodle.com/qrdz2tzeze7bf43t

Wed. Feb. 5th and Thu. Feb. 6th are two consecutive days that would work for the entire 'core' group. These dates would also give Chris and Heiko enough advance to inform DOE (4 to 6 weeks ahead).

Next step - Judy to inform us about roll-over funding if/when it becomes available. No news as of today yet.

Follow-up on 'response to x' vs. 'response to y stimulus'

We had an action item from last week: "As an aside, need to standardise terms since we have some 'response to x' and 'response to y stimulus'. Add or remove 'stimulus' from all these terms." Who is going to take care of this please?

AI: David OS to look into this. We've decided that 'stimulus' can stay where it's a helpful addition, so we will keep both formats, but with a rationale.

Follow-up: TG TEMPLATE FOR ORGANELLE PART (LUMEN, MEMBRANE) (bumped to next week)

See latest discussion: http://wiki.geneontology.org/index.php/Ontology_meeting_2013-11-07#Follow-up:_TG_TEMPLATE_FOR_ORGANELLE_PART_.28LUMEN.2C_MEMBRANE.29

Do we have action items/time-frames for them?

New OE

Quick run through of new imports and visualization. Any tips to share?

Those of us who tested it said it works fine.

Stemming from question of adding 'luteinizing hormone' in GO (bumped to next week)

See email thread. Chris says: "GO eds - we will want to switch IDs in the production logical definitions before this, to check the inferences. That's another external ontology imports file - not a big deal. Discuss on thursday?"

Review of template requests in Jira (bumped to next week)

New TG template for 'cell migration'? (bumped to next week)

Note that 'cell chemotaxis' is_a 'cell migration', which is fine based on their definitions. However, both 'cell chemotaxis' and 'cell migration' terms have logical defs based on alters_location_of, e.g.


id: GO:0072676 ! lymphocyte migration

intersection_of: GO:0016477 ! cell migration

intersection_of: alters_location_of CL:0000542 ! lymphocyte

Chris says: "It would be good to use a more generic relation, but this depends on the hierarchy being disjoint with other classes using the same relation with a different genus.."

Next week

EBIers have a group retreat next Thursday. The week after that it's Thanksgiving, so we decided that we're going to meet next Wed. 20th, from 4:30 onwards. This means that Jane, David and Chris will have to cut the Managers' call short if necessary.