Ontology meeting 2015-04-16

Attendees:

Minutes: DavidH

Follow-up: qualifier for (regulation of process or process)

Copying from last week - we need to discuss more today, and Rama will join us:

(For background, see http://wiki.geneontology.org/index.php/Ontology_meeting_2015-04-02)

It was suggested to discuss this at a managers' call first, and then at an annotation call. Also, the issue was raised that there needs to be complete alignment from all parts (curators + editors) on what we mean by direct vs indirect regulation.

 If DNA replication doesn't happen, cell division doesn't happen.  However one doesn't want to say that DNA replication regulates cell division.
 Val enumerated three cases where the new qualifier could be used.  New qualifier was supposed to be very clear semantically = (BP + RofBP). Not
 cover the fuzzy, I don't know approach - I don't know if it's part of the process or regulates the process or is not involved!  May need to drop
 this qualifier.
 
 Problem annotations: embryo development IMP because of embryo lethality - are those gps really involved in embryogenesis?

 'implicated in' meant to be a hedge for process + indirectly/directly regulation of process NOT ("affected by"  but not necessarily 
 via a regulatory mechanism) but doesn't seem to map to the hedge that people want to make (where they don't know)

 Need broader discussion with annotation group, can't solve only in ontology group. Pretend that we made this qualifier and record when we would 
 use it, discuss in annotation call?  Collect information and bring to GOC meeting?  How about something more top down?  Maybe one can enumerate
 the possibilities in greater detail.  Push to discussion again next week.

Axiomatizing Regulation of Biological Quality

Any objections to Chris' suggestion of going ahead and adding?

Details on email thread with same title on ontology list:

David H and I have gone through the proposed logical defs for RoBQs

http://wiki.geneontology.org/index.php/Extensions/x-attribute

(the wiki is v out of date, but these extension pages can soon disappear once is everything is part of the normal edit cycle)

These make use of OBA, which you can find out more about here:

https://github.com/obophenotype/bio-attribute-ontology/

including links to the OBA TG etc

I think they are now all valid (completeness can wait). I propose just going ahead and adding, raise any objections on thursday call

(Transmembrane) transport templates in TG

See email thread "Transmembrane transport again..." started by Paola on April 10th. Please comment.

TermGenie access for students

Jim Hu (a few weeks ago) and Ruth both have students who wish to create a new class with TermGenie. From a technical perspective giving access to them is easy.

But so far every submitter has also been assigned a GOC reference. I do not know if it would be a good policy to introduce this for students too.

Ideas:

• Use the GOC ref of their supervisor to have a permanent record.
• Create a common GOC for the students of on institution (one for UT A&M students, one for UCL students)
• Other ideas?

New TG templates

Punted from last week:

The job of editors on SF and TG duties would benefit considerably if we could implement some TG functionalities we've already sort of agreed upon. We may want to revisit the related requests, prioritize, see what's missing.

1) TG: create MF-BP links when appropriate https://www.ebi.ac.uk/panda/jira/browse/GO-199

2) Create TermGenie templates with UBERON https://www.ebi.ac.uk/panda/jira/browse/GO-168 - follow-up

Last week we wrote:

 May be done already. Chris and Heiko will look into this.  Something is still missing. There was a problem with propagation over 'part_of' in
 the anatomy ontology and that extending into the GO ontology, development -- morphogenesis.  May be not urgent at this time.  Wait for requests
 to come in and then roll out the template.  Code is mostly in place but not switched on. Need to deal with the part_of thing before rolling out. 

A non-development request to add a part_of link that could have been inferred automatically: https://sourceforge.net/p/geneontology/ontology-requests/11635/

3) TG template for 'cellular component organization' https://www.ebi.ac.uk/panda/jira/browse/GO-327

4) TG template for 'cellular component binding' https://www.ebi.ac.uk/panda/jira/browse/GO-326

5) Create term genie template for response to organism https://www.ebi.ac.uk/panda/jira/browse/GO-212