Ontology meeting 2015-04-30

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Minutes: David OS

cellular component is_a anatomical structure?

Summary: some of us are questioning the assumption we made some time ago, that cellular structures are anatomical structures, and that morphogenesis of cellular components is an instance of anatomical structure morphogenesis. In particular:

[Paola] I can see that in multicellular organisms a cellular component is usually ultimately part of an anatomical structure. But what about unicellular organisms? A ciliate cell (think Giardia and more) is an organism - but it doesn't have anatomical structures.

[David H] At some point way back when, we decided that cellular structures were also anatomical structures, that is the term anatomical structure is not limited to gross anatomy. If this needs to be revisited then I have no objection. I think the bigger issue here is the transitivity of the morphogenesis of parts of a structure with respect to the structure itself. The morphogeneis of an internal part of a structure does not necessarily contribute to the shape of the structure of which it is part.

(For full details, see email thread 'cellular component assembly & morphogenesis', started by Paola on April 24th.)

  Decision: We should no longer use morhogenesis/results_in_morphogenesis 
  to refer to assembly or generation of shape of a cellular component.  But OK to make that
  assembly part of some antaomical structure morphogenesis -including morphogenesis of cells.
  Make sure that definitions and comments indicate this.

Protein complexes

David OS and Paola met with Sandra and Birgit to discuss protein complexes. Participants were asked to update this page with relevant bits of the discussion: http://wiki.geneontology.org/index.php/Guidelines_on_%27protein_complex%27_terms

In detail, items that we'd like to go over with the wider OG today are:

- Creating broad, cellular-location-related, parent protein complex terms to aid in automated classification. E.g. if we created GO:NEW 'membrane protein complex' and defined it as a protein complex that is also a membrane part, hundreds of leaf-nodes complexes would find a more structured home in the GO;

   Everyone happy with this.

- Subunit composition issues;

   Editors more positive about formalising composition than we were after meeting with Intact.  
   In cases where complex differs a lot between yeast and vertebrates, may be possible to do this
   by specifying core subunits + function.

- (Optional) Families of complexes (see GO:0097136 Bcl-2 family protein complex and children).

If useful, we may want to invite Sandra and Birgit to a future ontology call.

  Seems reasonable to add protein family terms where complexes consist entirely of
  of homo/hetero oligomers from one family members:
  smad, integrin, rel, Immunoglobulins.  In these cases we may want to
  punt adding the various subclasses to Intact.
  Decision: Ask Intact for a reasonable list of family-based classes to add, using above criteria.

GitHub Latest

Discuss: https://docs.google.com/document/d/1iyVY8kDBJIEydoWFLG9j5BoO4VmdIXES95fVhIkFXfk/edit#

Notes from last week:

  Chris went over this briefly, and some of us already commented on the doc, 
    but we bumped discussion to next week when more people are on the call.
  DOS: Two potential issues we need to be careful of: 
    - file sizes are not yet a problem, but only because we still have an OBO master.  
    - Need to come up with a set of labels for priority, close status etc as GH doesn't have independent fields for these

Follow-up: Prefixing of obsolete to label of all obsoletes

Where are we with action items agreed on last week? No hurry, just so we keep track:

"For new (future) obsoletions: Protege will do this automatically, OE won’t. So, AI for all, a reminder to make sure that the prefix ‘obsolete’ is appended.

AI: For pre-existing terms, Chris will automate this, and use the form ‘obsolete’.

AI: Heiko will look into making things consistent in TG."

Note: we may forget to manually append the prefix 'obsolete', so we may want to schedule periodic checks or runs of the ad-hoc Chris' script above?

  No more to discuss.

New TG templates

Punted from two weeks ago:

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

  Can we generalise the pattern used in  https://www.ebi.ac.uk/panda/jira/browse/GO-199 for other MF-BP links?
  Note - will require more axiomatisation of MF. 
  AI: Chris and Heiko to investigate.  Report back.

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/

  AI: Chris to update Uberon and GO JIRA tickets.

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

GO-UBERON issues

Can we discuss Stan's hindgut issue and the issue of multi-species fuzziness in general?


 Potential solutions:
   1. Split into ectodermal (arthro) vs endodermal
   2. Redefine to ectodermal and re-annotate relatively small number of vertebtrate annotations - but to where?
 AI: punt decision to next week when we can get DH's input.

GO-SO issues

There are various problems with our use of SO, some of which requires co-ordination with SO dev:

  1. We need a bridge from SO transcript terms -> ChEBI:RNA. In the absence of this, lots of inference is mising. Will the long planned SO molecular save us, or do we need our own bridge axoims?
  2. We use the SO terms nRNA, ncRNA and its children as if they refer to both mature and immature states of transcripts. In fact, according to SO they refer to the mature state. To align with SO properly we would need to review usage and use alternative SO terms where available. SO has an additional set of terms for primary transcripts, but no terms for immature. Primary transcript refers only to before splicing so no terms for intermediate state after splcing and before other modifications involved in maturation such as capping and polyadenylation for mRNA. Need to discuss possibilities of adding these with SO.
  DOS organising meeting with Karen Elibeck.  Details of this issue punted to future meeting.

new dbxref

Should we make a new dbxref for the upcoming autophagy work?

  YEP. Now done: GOC:autophagy