Ontology meeting 2015-05-07: Difference between revisions

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   >  'cellular process' that 'results in assembly of' some 'dendritic spine')
   >  'cellular process' that 'results in assembly of' some 'dendritic spine')
     => automated classification under appropriate assembly/organisation terms.
     => automated classification under appropriate assembly/organisation terms.
  Note - possibly problematic that various tract morphogenesis terms are under axonogenesis, which is under 'neuron projection morphogenesis'
   AI: DOS will implement.
   AI: DOS will implement.
  Note - possibly problematic that various tract morphogenesis terms are under axonogenesis,  which is under 'neuron projection morphogenesis'.  Should we just make a new 'tract morphogenesis' term to put all of these under?  Should we retain some relationship with the cellular component organisation terms?  Could make parallel 'involved in' terms for each.


=== GO-SO issues ===
=== GO-SO issues ===

Revision as of 07:18, 7 May 2015

Attendees:

Minutes: Tanya


release GO job fail

See recent emails e.g. "release-go - Build # 1037 - Still Failing!"

The reason for the failure are redundant is_a/part_of links. David OS an David H were talking about this a few days ago. We need to fix this. Note that this error is preventing an ontology release, including a number of downstream processes (such as not getting the daily go-watchers email).

Follow-up: cellular component is_a anatomical structure?

Looking at http://wiki.geneontology.org/index.php/Ontology_meeting_2015-04-30#cellular_component_is_a_anatomical_structure.3F, could we please specify action items and point person(s).

 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.  
 e.g.: Dendritic spine morphogenesis -> dendritic spine assembly. 
  'anatomical structure morphogenesis'  and ('results in morphogenesis of' some 'dendritic spine')
  >  'cellular process' that 'results in assembly of' some 'dendritic spine')
   => automated classification under appropriate assembly/organisation terms.
  AI: DOS will implement.
 Note - possibly problematic that various tract morphogenesis terms are under axonogenesis,  which is under 'neuron projection morphogenesis'.  Should we just make a new 'tract morphogenesis' term to put all of these under?  Should we retain some relationship with the cellular component organisation terms?  Could make parallel 'involved in' terms for each.

GO-SO issues

Copying from last week:

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.

part_of vs has_part in export from nucleus

dph-All of the named RNAs that are exported from the nucleus are exported as part of RNP complexes. In the ontology we had asserted that the RNA export has_part RNP export. This seemed backwards to me since the RNA is part of the RNP. I reversed these relations to make the RNA transport part_of the RNP transport.