Ontology meeting 2014-03-20

Attendees: Paola, Jane, David OS, Heiko, Tanya, David H, Harold

Minutes: Paola

Follow-up: New release of OBO-Edit

See http://wiki.geneontology.org/index.php?title=Ontology_meeting_2014-03-13

Test and report ASAP. Release will be done right after GOC meeting.

[Paola] Based on the log since the last call, looks like a couple of us have done simple edits (text changes) without problems. Have we tried more complex edits? I just added is_a and part_of links and a cross-product and it worked fine.

 Heiko will go ahead and release, it was just a small change from the previous version and we don't expect issues.

 AI for all: download the newest version from here:

 http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%202.3.1/

Do annotations propagate over 'capable_of'?

Stemming from a SF request from Birgit. She asked that 'ripoptosome' be made is_a 'catalytic complex'; where 'catalytic complex' is_a 'protein complex' capable_of 'catalytic activity'. I agree that the ripoptosome as a whole can perform a catalytic function, but this complex often contains non-enzymatic proteins that act as adaptors (FADD, CFLAR, TRIF/TICAM1). These adaptor proteins are indeed annotated to 'ripoptosome'. If I added the link 'ripoptosome' is_a 'catalytic complex', would the adaptor proteins become hard-linked to 'catalytic activity'? That would be incorrect.

This is somewhat similar to the previous issue of 'transmembrane' complexes where some of the components do not span the membrane. See discussion in SF ticket here: https://sourceforge.net/p/geneontology/ontology-requests/10711/

 David OS says that No, annotations do not propagate over 'capable_of', or any other relationship other than is_a, part_of and, possibly, regulates, but we need to make sure. 
 (For 'regulates' Chris said he'd provide documentation/details on exceptions but we couldn't find anything - Chris, did we miss it?) 
 We need documentation and we also need to make sure that this is not tool-dependent (does AmiGO2 do the right thing?). 
 Chris, please comment.

 (Following this discussion, Paola added the link 'ripoptosome' is_a 'catalytic complex'.)

Follow-up: 'colocalizes with' nuclear chromatin

See http://wiki.geneontology.org/index.php?title=Ontology_meeting_2014-03-13

Where are we with the planned action items?

 Carry over to next week so Chris can discuss too. David OS made a start on this. Transitive?

Follow-ups and action items from GOC and SAB meetings

Might also be a good time to do a critical assessment/review/update of our Jira tickets in view of the above.

 Carry over to next week

Some pending SF tickets

([Paola] Mentioning here rather than at a SF call because of broadness of topics involved. If you had time to read this and comment before the call please, that'd be great.)

1) There are a few open SF tickets labeled as 'recombination'. These were left pending because none of us editors has enough specific expertise in this area. (Some time ago we asked Eurie, but she said she's been away from the ontology for too long). The tickets are:

https://sourceforge.net/p/geneontology/ontology-requests/3598/ (creator=Varsha; owner=Eurie; status=open)

https://sourceforge.net/p/geneontology/ontology-requests/4689/ (creator=Val; owner=nobody; status=open)

https://sourceforge.net/p/geneontology/ontology-requests/5776/ (creator=Val; owner=nobody; status=open)

At the GOC meeting, Moni mentioned that she has an interest in recombination. Perhaps we could ask her to take a look at these tickets and at the current ontology, and see if she has any suggestions. I'll do that unless anyone has different advice. We also have a few recent tickets that come up when searching SF for 'recombination'. People may still be working on them, but just in case, I could ask Moni to look at these too:

https://sourceforge.net/p/geneontology/ontology-requests/10685/ (creator=Val; owner=Jane; status=open)

https://sourceforge.net/p/geneontology/ontology-requests/10702/ (creator=Val; owner=David OS; status=open)

 OK to ask Moni. Paola will do.

2) There is an old open SF tickets labeled as 'transcription' but actually dealing with translation terms. Harold commented recently:

"There are so many annotations using these terms that this is a major project. This might also need a content meeting to get some experts involved (I have some in mind), pending funding, etc.".

Looks like we may not have funding for big content meetings anytime soon, but maybe we could look into organizing a virtual meeting (say a couple of conference calls or a half-day remote meeting) with experts. The chat with the biochemists at College Station showed that we can get precious feedback in a short time if only we have the right people at hand. Should we go ahead with this, or at least plan it for the upcoming future? What nodes of the ontology need looking at for this - is it the whole node under GO:0006412 'translation'?

This is the SF ticket:

https://sourceforge.net/p/geneontology/ontology-requests/1438/ (creator=Amelia; owner=Harold; status=open-later)

Note that this other ticket also comes up when searching SF for 'translation', though it's mostly about 'production' terms where we don't know if an observed increase in protein levels is brought about by regulating transcription, translation or secretion:

https://sourceforge.net/p/geneontology/ontology-requests/10600/

Could translation experts be useful to dissect which, if any, of the terms in this ticket should be descendants of 'translation' or regulation thereof?

 Harold to survey and report back in 2-3 weeks.

Protege

To discuss with Chris:

Are we really ready for Protege?

David OS will write down something on the wiki. Chris has started asking people about the plug-in. The plan is to have a meeting to figure out what kind of progress we can have on that in a reasonable time-frame. We need a write-up of the sort of things that are currently hard for editors to do/render in Protege; things that you can do in OE but can't currently do (or easily do) in Protege. E.g. new terms, searches... rendering in tree views is virtually impossible now. We could have a period where we do things using both tools, but one worry is that some of us may not be able to work with both tools open on a machine that doesn't have loads of memory.

AI for all: For the time being, we can all try using Protege in our normal work flow and report on the difficulties we encounter. Jane made a wiki page and we can all add to it: http://wiki.geneontology.org/index.php/Protege_Feature_Requirements.

AI: DOS to add link to the specs document.