Ontology meeting 2015-03-12

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Attendees: Paola, David OS, David H, Harold, Tanya, Chris

Minutes: Paola

Review of Jira tickets

Time for our periodic review. Before the call, could we all please take a look at items assigned to us. Can any be closed as out-of-date, should any be made priorities, do any need discussion at (the next) editors call, etc. Feel free to add to next week's agenda http://wiki.geneontology.org/index.php?title=Ontology_meeting_2015-03-19. Thanks!

We looked at a few tickets, especially the few critical ones.

High level disjoints to request from ChEBI

David OS met with ChEBI curator Gareth today. Summary:

- ChEBI curators are now signed up to get email warnings when inconsistent classes come up.

- They’re happy to add more disjoints for us

- David OS will send round a list of disjoints he proposes so we can double-check them, and maybe add to them, e.g. by looking at the 'binding' branch.

- Janna will give a hand with this work in the next couple of months before she leaves

- Like us, ChEBI has a SF backlog, so if we need anything looked at urgently, we should email them, or just go to them in person.

- Deletion vs absolution (right... obsoletion. Thanks autocorrect) in ChEBI: see https://sourceforge.net/p/chebi/curator-requests/2429/

- There's potential for working with ChEBI on roles in the future.

Should more relations live under has_participant

Most of the results_in_... relations do not, but probably should. This has implications for work on Annotation extensions. Can we review?

We reviewed. Resolution: for now, David OS will only put in the non-controversial ones. Some are done already. Some could be moved directly from gorel to ro. David OS and Chris went over the procedure to do this: 1. Add a new RO rel. 2. Switch the URI of the existing rel in GOREL. Edit the resulting merged class so that there is only one label, def, comment etc & makes sure it has the GOREL shortFormID as an alt_id. 3. Switch the the URI of the existing rel to the new one while all of GO is loaded (but when in relation to 2?)

New Protege release (not covered today)

Please test and give feedback (or plan to do so by the next call if possible). For details, see Chris' email 'New Build of Protege 5.0.0 Beta available' dated March 11th.

Follow-up: Acids and bases in GO (not covered today)

Copying from last week - any action item left for this? Documentation?

Stemming from https://sourceforge.net/p/geneontology/ontology-requests/11524/

The solution we've adopted so far is proving unsatisfactory specifically with respect to NH4+, NH3 and NH2- conjugate-acid-base relations. We need to think of an alternative, with or without the direct involvement of ChEBI. 

Does NH2- exist in biology (azanide ion) (Harold: I can't find; it is really unstable; reacts with
water quickly to form NH3 + OH-; Azanides as a class: Chebi has; these aren't like natural metabilites
More like drugs, etc. 
Option: exception to the GCI generation rule (equivalence is transitive so we have to do this): 
for azanide; We should document this somewhere very well for all times we have to do this.

Update from Heiko (March 10th): "as discussed on the call, we have modified the generator for bio-chebi. It now supports exceptions for the generation of the GCI axioms, i.e. ammonia and it's conj base/acids. The current approach to define these exception is a new subset in the seed file for bio-chebi generation called no_conj_equiv. The bio-chebi.owl update file has been committed today. "

Follow-up: Rhea plans

Do we have any action items (and designated personnel) after last week's discussion?

http://wiki.geneontology.org/index.php/Ontology_meeting_2015-03-05#Rhea_plans

David H: Paul T discussed with Alan Bridge about this when he was in Switzerland. Just not sure what the plan is yet.

Chris: one final aim could be to get GO terms directly from Rhea. Chris proposes a hackaton, and showed his slides on this (Chris, could you link them here please?) Note: we might change has_substance_bag into reactants, or reactant set perhaps.

results_in strategy (not covered today)

See emails from Chris (threads on go-ontology 'results_in outliers' and 'results_jn refactor'). Chris asked for feedback on his proposal. Discuss, then reply to email thread.

results_jn refactor: Looks OK, but has many very indirect cases.

(Note that, since generation of Chris' list above, we've approved a couple of terms created with the old reg_by_reg TG template)

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