Ontology meeting 2016-11-10

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Attendees:

Minutes: David OS?

Regrets:

GoToMeeting invite: https://global.gotomeeting.com/join/859015101

GitHub projects page (we'll try to follow this, as a test - see columns "Ontology meeting TBD" and "Ready to be worked on"): https://github.com/geneontology/go-ontology/projects/1

Agenda below is there as backup.

Debrief from GOC meeting: ontology group update and breakout session on ontology priorities

For reference, minutes are here: https://docs.google.com/document/d/1MAnnOfs-e2LY9MnqdCZscalbxbNUDSJ9pbMZ-f2WS9U/edit#


From ontology priorities discussion:

David H: 1. Some suggestions for how to automate finding area of ontology to work on based on annotations (see minutes) 2. SIB - Viralzone complained about their edits taking too long. DOS: There seemed to be agreement that we should prioritise this as a project. Need to work on splitting out discrete tasks from monster ticket.

AI: DOS to set up conf call on ViralZone terms with SIB eds + Jim Hu

General discussion of how to prioritize tickets:

Judy: Shouldn’t we be prioritizing closing tickets. Assigning some proportion of FTE to general ticket work. Do we have a page of priorities?

David H: We should redo the wiki page.

Judy: We should make a table with projects + who is on + priority.

Paola: We have labels: high_priority, lower_priority, mini_project, jamboree/editors_discussion

DOS: Can we clean up labels?

Paola: complexity of labels indicates complexity of project. We have labels for project, we have labels for submitting group, we have labels for subject matter, priority….

Judy: We need to work through priorities as a priority. Is there a plan we could implement in the next week or two to reorganize so we know what’s going on.

Paola: We only have 12 high priority tickets. We can review those ASAP. <-- all agreed with this.

Discussion of 'positive regulation' and 'maintenance' from last annotation call

See http://wiki.geneontology.org/index.php/Annotation_Conf._Call_2016-10-25#Discussion_of_Outstanding_github_Tickets_2

Tanya: Please make discussion of this a high priority for the next meeting.

Modified Proteins Proposal

The proposal was not well received by annotators at the GO meeting. The annotators thought that these terms were too important biologically for them not to be in the ontology. We need to come up with alternatives.


  1. Continue to add these terms by hand. Unsustainable?
  2. Figure out a way to add these terms automatically. Use PRO?, Chebi?, PsiMod?, will this lead to annotation inconsistency. Probably.
  3. Only add a few very high-level terms. What is the specificity cut off and what happens when annotators make a case that the very specific term that they want is important.
  4. Have do-not-annotate' terms that are generated automatically as in #1 below and categorize gene products by the entity that is captured in binding annotations.

We discussed three possible semantic interpretations of modified protein binding terms:

https://docs.google.com/document/d/1MAnnOfs-e2LY9MnqdCZscalbxbNUDSJ9pbMZ-f2WS9U/edit#heading=h.vzsyf1ss0k8h

  1. . Binds a protein that happens to have a modification, but not necessarily the modification site <- We previously agreed in an Eds meeting that this was too broad.
  2. . Binds to the modified part of a protein <- Sylvan wants this. Seems to be most broadly supported.
  3. . Binding to some specific protein partner is dependent on the modification state of the partner even if binding is not to the modified bit. <- More controversial Pascale likes this, some other seem to support. DOS objection: this seems like annotating a property of the bound protein. Also specific to one binding interaction (whereas 2 is likely to be a general function)

Number 2 in this list - binds to the modified part of a protein - had the most support. Example: SH2 domain confers binding to phospho-tryosine in the context of a specific peptide motif: https://en.wikipedia.org/wiki/SH2_domain

For terms like this, we could add a comment that it should only be used where there is high confidence that binding is to the modification + protein (simple dependency on phosphorylation of target is not sufficient but one that localizes the domain by deletion/mutagenesis analysis of the protein is). This still leaves the question of how detailed we should get in specifying the target (see histone binding).

Link to Judy's presentation on Post-Translational Modifications: http://wiki.geneontology.org/index.php/File:PROandModified_forms.pptx

Notes on discussion can be found on this ticket: https://github.com/geneontology/go-ontology/issues/12787#issuecomment-259692111

Follow-up: contacts for UniProt annotations

Background: http://wiki.geneontology.org/index.php/Ontology_meeting_2016-10-13#Update:_contacts_for_UniProt_annotations

AI from last call was "Sylvain will discuss with Chris and David H at the GOC meeting". Any news on this please?