Difference between revisions of "Manager Call 2016-06-1"

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(Identifier Space in GAF and GPAD)
(Identifier Space in GAF and GPAD)
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**GAF:
 
**GAF:
 
***Column 2 - would stay as is using identifiers for genes, gene-centric protein set, ncRNAs, and protein complexes
 
***Column 2 - would stay as is using identifiers for genes, gene-centric protein set, ncRNAs, and protein complexes
***With/From and Annotation Extensions: curators could use whatever identifiers they want, but their annotation group must provide a Gene Product Information (GPI) file that would allow users to map those identifiers to the canonical, or parent, ID in Column 2
+
***With/From and Annotation Extensions: curators could use whatever identifiers they want, but their annotation group must provide a Gene Product Information (GPI) file that would allow users to map those identifiers to a canonical, or parent, ID as for Column 2
 +
**GPAD:
 +
***Column 2 - would stay as is with most granular identifier
 +
***With/From and Annotation Extensions: same as above
 +
*Question 1: Should GO provide the digested GAF that contains only the canonical IDs in all columns (except Column 17 of GAF)?
 +
*Question 2: How should mapping of protein complex members be handled?  We probably do want to have a mechanism for mapping between gene or gene-centric protein IDs and protein complexes and then automatically unfold annotations to each member of a complex using the contributes_to qualifier for MF?  Need to check with Sandra Orchard about how mappings are currently handled.
 
*'''AI:'''Determine if there currently are uses cases for the more granular gene or gene product information in AEs and With/From.  Consult with Val and Ruth on this.
 
*'''AI:'''Determine if there currently are uses cases for the more granular gene or gene product information in AEs and With/From.  Consult with Val and Ruth on this.
 
*'''AI:'''More generally, look for examples of AE usage in literature.   
 
*'''AI:'''More generally, look for examples of AE usage in literature.   

Revision as of 07:36, 2 June 2016

Agenda

Identifier Space in GO Annotations

  • In response to the May 18th call's discussion on gene and gene product identifier space (see minutes), I've put together a spreadsheet that documents our current practice wrt for GAF and GPAD:
    • Annotated Entity IDs
    • With/From Entity IDs (note only for gene and gene product)
    • Annotation Extension Entity IDs (note only for gene and gene product)
    • Annotation Isoform Entity IDs
  • Then, for the purposes of discussion, I also added two other possible approaches:
    • Gene IDs only
    • Broad range of gene, transcript, protein, protein complex entity IDs
  • At the top of the spreadsheet are three general questions that we need to consider - there may be more; please add if needed
  • The plan was to review the different approaches, debate the pros and cons and then either get more feedback or finalize the proposal for presentation on an annotation or all-hands call

Review action items from Geneva meeting, and add items to Trello if necessary

Periodic review of the Trello board

https://trello.com/b/IdtTLGEt/go-priorities

Minutes

Attendees: Chris, David H, Kimberly, Moni, Paola, Paul T.

Regrets: Moni Munoz-Torres (Teaching 9th & 10th graders about research and the scientific method from 7:00AM - 9:30AM PDT).

Agenda: Paola; Minutes: Kimberly

Identifier Space in GAF and GPAD

  • We discussed different options for what to use as gene and gene product identifiers in GAF and GPAD.
  • Much of the discussion was centered around cost/benefit for curators and users of using gene or gene-centric protein identifiers vs using more specific or granular identifiers, such as UniProtKB protein isoform IDs or PRO IDs for modified forms of proteins, for annotations.
  • There is currently an important distinction between GAF and GPAD in that GPAD specs indicate that Column 2 can use the more granular identifier, e.g. P34187-1, while in GAF Column 2 uses canonical identifiers for gene, protein, ncRNA, or protein complex.
  • Curators may want to capture the most granular information possible, but what use cases do we have for use of that more granular info?
  • Enrichment analysis still seems to be the more common use case of GO annotations and for that, most users still just use gene or gene-centric annotations
  • Possible proposal:
    • GAF:
      • Column 2 - would stay as is using identifiers for genes, gene-centric protein set, ncRNAs, and protein complexes
      • With/From and Annotation Extensions: curators could use whatever identifiers they want, but their annotation group must provide a Gene Product Information (GPI) file that would allow users to map those identifiers to a canonical, or parent, ID as for Column 2
    • GPAD:
      • Column 2 - would stay as is with most granular identifier
      • With/From and Annotation Extensions: same as above
  • Question 1: Should GO provide the digested GAF that contains only the canonical IDs in all columns (except Column 17 of GAF)?
  • Question 2: How should mapping of protein complex members be handled? We probably do want to have a mechanism for mapping between gene or gene-centric protein IDs and protein complexes and then automatically unfold annotations to each member of a complex using the contributes_to qualifier for MF? Need to check with Sandra Orchard about how mappings are currently handled.
  • AI:Determine if there currently are uses cases for the more granular gene or gene product information in AEs and With/From. Consult with Val and Ruth on this.
  • AI:More generally, look for examples of AE usage in literature.