Ontology meeting 2014-11-06

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Minutes: David OS

Follow-up: Relationships

Follows up to GOC meeting discussion with Ruth on Annotation extension relationships. The action item was:

"Ontology group will dedicate a meeting to looking through the list of all relations used in annotation extensions. They will document those that are used in the ontology and will indicate whether the remainder should be dropped or kept and therefore documented. They will also note any new relations that need to be added e.g. adjacent_to.

Ontology group will make sure all the relationships are modeled correctly in LEGO."

Also see email thread 'Annotation extension relations'.

Chris writes: "The first task will be to migrate the editors version of the annotators extensions to RO to OWL so we can better manage these."

See email thread 'AE relationships from last meeting'.

       - reviewed all except 'over' relations  and marked whether in RO, should be obsoleted, or throw back to editors for more work 
           (see http://wiki.geneontology.org/images/2/28/AE_relations_GO_EDs_review.txt)
       - Paul T has made LEGO models in noctua based on existing AE wiki doc - he will link to these from the appropriate AE wiki pages.
  TODO: Work through relations in RO to check whether RO defs are clear enough and consistent with usage guidance from annotators (WHO, WHEN?)
  TODO: schedule meeting to discuss has_input  :DOS:
     When: Week of Nov 17th if poss (Chris away next week)
     invite: DH, Ruth. Val, Chris, DOS, Jane, Paul T. - anyone else?
     We MUST have prep of the various uses and suggested names for the variants
  TODO:  Discuss better formalising local domain and range (currently stored as ID strings - target should be actual ontology classes  (perhaps unions) :David:Chris:Tony:
  TODO:  Further restrict local domains in order to help protein2GO help annotators appropriately restrict term choice.   
       This is particularly important for specific relations rqd for dev branch.

Downloads page on GO website

Chris would like to discuss updating/fixing stuff.

   Chris has no idea what this is about.  If anyone remembers, please yell.

TermGenie and removal of all relationships

A couple of weeks ago, a TG commit resulted in the loss of ALL relationships from the obo file. This appears to be a one time glitch. We need to keep an eye on this, in case it reoccurs. We were made aware of this by Tony when the UniProt load of the GO failed.

A related issue: in the long run, we may want to consider moving away from term merges (as they may cause confusion in other ontologies) and just stick to 'obsolete + replaced by = merge; obsolete + consider = really obsolete'.

   AI: OBO2OWL round-tripping alt_id -> obsolete + replaced_by in OWL only.
       We gradually move towards using obsoletion + replaced_by as part of our Ed policy.   
       Need to trail this to MODs (who will then gnash teeth)

What's in the cell and what's out

Chris to report - he set up a Google doc to discuss this some time ago. Is this resolved now?

  Not discussed yet.  Move to next meeting.

Transcription factor activity

We had a request from the GOC meeting to add a union term for DNA-binding sequence-specific etc TF and protein-binding sequence-specific etc TF. What do we call this term? Should 'transcription factor activity' be reserved for DNA-binding only?

  Not discussed yet.  Move to next meeting.

Other action items for the whole team from GOC meeting?

Minutes here: https://docs.google.com/document/d/1NonH97s8xEpDdx6DfonKPKI_RdHbbG-yft85UZtUmF0/edit#

  Not discussed yet.  Move to next meeting.

Follow-up: cell migration

Action items from last call here: http://wiki.geneontology.org/index.php/Ontology_meeting_2014-10-09#TG_template_for_.27cell_migration.27

Heiko to change relationship type in TermGenie for this template. For the ontology bit, I made a SF ticket and assigned it to myself with priority 7 and am nearly done.

  Not discussed yet.  Move to next meeting (?)

Monthly review of Jira tickets

  Not discussed yet.  Move to next meeting.

Ontology term for protein family / protein domain (family)

Tony S is redoing imports for QuickGO and trying to be as ontology compliant as possible in how things are typed for import (JIRA ticket here: https://www.ebi.ac.uk/panda/jira/browse/GO-322)

I've pursuaded him that in most cases, he should be able to use an existing foundry ontology class. But there are still a few cases where we don't have an obvious term. In particular, what do Panther IDs and InterPro IDs refer to?

It is not particularly useful to have them refer to proteins and protein domains respectively - as Tony wants to distinguish from a protein in a specific species. If we say that Panther IDs refer to classes of protein, then we would type using an ID for protein. But perhaps it is better to treat protein family as some kind of information artefact - or in OWL terms as a individual with members rather than a class?

  Not discussed yet.  Move to next meeting.

Links to documentation

Following old discussion and recent email thread, in search of a more robust and logic-oriented approach than the one currently adopted in QuickGO.

See email thread 'Rough notes for OG from PAINT call'. Summary:

"The goal is to have a procedure that runs as part of the release process that propagates the URLs (or any annotation property) down the hierarchy based on a structured query (OPPL, SPARQL etc)

DavidOS - do you think this is possible based on your axiomatization for membrane proteins

Others - can we axiomatize the production terms to avoid dependence on regexs?"

      - Propagation rules will go in an OWL file - using DL or SPARQL or some combination (rather than hacking something with xref_abbs)
         - We should investigate using OWL image annotation system developed at VFB for OWL formalisation
         - *could* use super-relations in order to do 'unions' (e.g. IPR)
         - Chris notes - may also be an option for linking to LEGO exemplars for some terms.
      - Propagation would then happen at build time so the public would see propagated in dbxrefs.

Membrane proteins

David OS to report.

  Not discussed yet.  Move to next meeting.