Ontology meeting 2014-12-09

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Attendees:

Minutes: Paola


Progress Report

Ontology requests

Numbers are high again, but SF stats suggest that if we had a couple of week-long SF jamborees per year, we'd be able to keep the numbers stable. (We would still have a backlog, given current resources, but at least it wouldn't spin out of control). Shall we try and plan a jamboree around February - is there money for 1 or 2 people traveling? How about bimonthly SF calls: are we interested in having those regularly, or just ad-hoc? E.g. there's a slot available tomorrow.

Moving relations from RO to gorel

What's the process for this? I know gorel imports a subset of RO, how do we expand that subset? We need the has_symbiont etc relations in gorel.

Enzyme binding PUNTED

We agreed to obsolete 'DNA methyltransferase binding' from the TG queue a couple of weeks ago, we need to follow up with a plan for how to handle the existing terms in this branch, and guidance as to whether annotators request these terms. They've asked for us to report back on an annotation call.

Axiomatizing multi-organism processes PUNTED

We've agreed it's a good idea to try and axiomatize at least some of these terms before I leave. We need to agree which relationship I should use - can I go ahead and use regulates or do we need the more specific regulates_in_other_species?

Follow-ups from last call PUNTED

Everyone please take a look at AIs here: http://wiki.geneontology.org/index.php/Ontology_meeting_2014-11-20

Follow-up from last week as Chris and David OS were away: 'Response to' terms again

From this week's assert report:

ADD GO:0097044 'histone H3-K56 acetylation in response to DNA damage' GO:0043200 'response to amino acid'

This seems to come from GO:0097044 being descendant of 'response to stimulus' and having an amino acid as input... same as the logical def of 'response to amino acid'.

This is an interesting case. Is the inference too broad for our liking, or are we happy to keep it? If the former, how do we restrict the ancestor?

  Should not be 'response to amino acid.' Wrong genus is asserted for one of the terms between 'response to amino acid' and 'GO:0097044', fix that.
  The term 'peptidyl-amino acid modification' needs to be sorted out, has_input to 'amino acid residue.'  
  Action item:  Jane will consult with Gareth @ ChEBI about which 
  ChEBI term to use for the logical def. What is the difference between 'peptidyl-amino acid' and 'amino-acid residue'?  In common usage, these would
  be the same.  What was ChEBI's intention?  Ex. ubiquitinated proteins vs. 'normal' protein chain (alpha peptide chain)?  What about amino acid
  derivative vs. modified amino acid?  Sort out implications for GO.  
  Problem is broader.  Has_input as a relationship for 'response to x' results in the inability to specify 'what' is being responded to.  In this example,
  we'd expect 'damaged DNA' as the input.  ChEBI is not likely to have 'damaged DNA' as an entry.  Need a different relationship, 'responds to' perhaps.
  Action Item (not Amelia Ireland):  Chris and DOS to comment on 'responds to'
  Chris emails: 
  "Usual issue. Either: (1) make response and metabolic response disjoint (2) Make a distinct relation for every possible genus
  I favor (1)"

And again:

For response-to, regardless of the relation used, I think it would be better to treat the response as the entire process of response, making the relationship between metabolism etc and response to be part-of-some, not SubClassOf. Think in terms of lego, see the cellular response to UV here:
http://geneontology.org//experimental/lego/docs/PThomaslego-Whitepaper-2010-03.pdf

And from a standard ontology design pattern perspective, it's better to combine disjoint hierarchies rather than isa-overload.

UV-response.png

Follow-up: Protein oligomerization

See discussion from last week: http://wiki.geneontology.org/index.php/Ontology_meeting_2014-12-02#Protein_oligomerization

Any progress on the action items? [Paola]

Also, we couldn't complete this discussion: "New terms: 'protein heterodimer' and 'protein homodimer' not in GO but PRO? Pragmatically, this might be the best solution."

Protege 4 vs 5

Chris writes: "Protege 4 is stuck on an old version of the OWLAPI. This is not ideal - we have to do conversion separately and not natively. It's a bigger issue for ontologies like CL that are edited in OWL - lagging behind with the owlapi will cause even bigger diffs as TG edits alternate with Protege edits. From the perspective of software development, it would be hugely advantageous to switch to P5. We can build this from maven easily, and make versions that are in sync with TG. Also, P4 will presumably eventually rot. However, P5 is apparently currently unusable. Can we collect some of the requirements in a doc, place a request on the protege feedback list, and then evaluate our strategy based on the response? Has anyone else rather than DavidOS tried it out? "

Jane replies: "I was using P5 for a while, it was fine for me. It didn't cause any problems with the round-trip. The 'improved' search isn't perfect, but Matt gave us some tips on using it when he was here. I'd be happy to switch over."

Anyone else? Let's collect requirements.