Ontology meeting 2015-04-09

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Attendees: Chris, DavidH, Harold, Heiko, Tanya, Judy

Minutes: Tanya

Discuss Request from NLM

http://jira.geneontology.org/browse/GO-792

 Trailing space issue has been resolved.  (was proximal issue)  Should we reach out to this NLM person?  Is there anything we can do to 
 facilitate better interaction between GO and NLM - alignment with UMLS?  Brings out issue of daily vs. monthly releases.  Shall we have 
 a pan-GO monthly release with cross-validation - ontology + annotations?
 For now, point him to the daily releases, well-documented set of files. Invite to further discussion. Chris will address JIRA issue.

Revise TG template for regulation_by?

Stemming from last week's discussion and implementation (see http://wiki.geneontology.org/index.php/Ontology_meeting_2015-04-02). Also, we may want to alert users of this change.

Update: Heiko disabled the template; Chris thinks it won't be straightforward to replace it, given the new nested structure (where we name the inner class).

 Update to update:  Chris thinks it won't be that hard after all but need a constraint that limits the genus to NOT a regulation term.
 'foo' regulates 'bar'  Chris and Heiko will redo the 'regulation by' template.

We may want to alert users that this template is no longer available, and indicate the procedure to request such terms from now on. Should they request via SF? They could use TG freeform, but I suspect that the likelihood of mistakes and/or having to approve and concatenate two terms one after the other is not negligible. What's simpler for both parts, submitters and approvers?

 There were two terms in the queue that were using this template.  DavidH fixed them to use the new pattern and not results_in.  There are still
 a few remaining ones in the ontology due to lack of axiomatization.
 [Term] id: GO:0010608 
 name: posttranscriptional regulation of gene expression 
 namespace: biological_process 
 def: "Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript." [GOC:dph, GOC:tb] 
 synonym: "mRNA localisation resulting in posttranscriptional regulation of gene expression" EXACT [] 
 synonym: "posttranscriptional regulation of gene expression by mRNA localisation" EXACT [GOC:mah] 
 synonym: "posttranscriptional regulation of gene expression by mRNA localization" EXACT [] 
 is_a: GO:0008298 {is_inferred="true"} ! intracellular mRNA localization 
 is_a: GO:0010608 ! posttranscriptional regulation of gene expression 
 intersection_of: GO:0008298 ! intracellular mRNA localization 
 intersection_of: results_in GO:0010608 ! posttranscriptional regulation of gene expression
 17 terms left using results_in that need to be cleaned up. Can see in Protege, click on results_in and usage.  DavidH will investigate
 and get back to Chris if necessary.

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

(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.

Monthly review of Jira tickets: TG-related issues

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. Here's a first pass at prioritization (Paola):

TG: is it possible to infer transmembrane transport parentage from location x to location y transport? https://www.ebi.ac.uk/panda/jira/browse/GO-200

 Tanya will take and close out, no global solution possible because 'transmembrane' could be taken to mean via vesicle or pore by a newbie, even 
 though we've cleared this up in GO to mean only "transport of a solute across a lipid bilayer."

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

 PUNTED

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

 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.

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

 PUNTED

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

 PUNTED

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


 PUNTED

There may be more, please add if I missed any long-pending/very important ones.