Difference between revisions of "Annotation Conf. Call 2020-04-07"

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m (Agenda and Minutes)
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*github ticket for comments:  https://github.com/geneontology/go-annotation/issues/2864
 
*github ticket for comments:  https://github.com/geneontology/go-annotation/issues/2864
  
**Questions/Comments
+
*Questions/Comments
*** We need guidelines for how to represent proteins ids or accessions shared by multiple gene products, e.g. histones. [Stacia]
+
**We need guidelines for how to represent proteins ids or accessions shared by multiple gene products, e.g. histones. [Stacia]
 
 
**Response:
 
*** Groups should work with UniProt to disambiguate protein records that refer to multiple genes, i.e. generate gene-centric protein entries in UniProt
 
*** In the interim, we are working on specific guidelines for these types of entries in the gpi file (just a few relatively small decisions to make but we want entries to be consistent)
 
  
 +
*Response:
 +
**Groups should work with UniProt to disambiguate protein records that refer to multiple genes, i.e. generate gene-centric protein entries in UniProt
 +
**In the interim, we are working on specific guidelines for these types of entries in the gpi file (just a few relatively small decisions to make but we want entries to be consistent)
  
 
= Attendance =
 
= Attendance =

Revision as of 07:42, 6 April 2020

Agenda and Minutes

GOC Meeting - May 2020

  • Paris meeting scheduled for May 11 - 14th will be held virtually
  • Please keep the dates open
  • More details will be forthcoming, but note we are planning for shorter days to accommodate all time zones as best as possible
  • Agenda

File Formats

Proposed GAF Update, GAF 2.2

  • GAFs will continue to be produced and supported by the GOC into the foreseeable future
  • We are proposing an incremental update to the GAF, though, to allow for use of the full set of gp2term relations
  • Proposed set of allowed relations is in this github ticket: https://github.com/geneontology/go-annotation/issues/2917
    • This would be the same set of gp2term relations used in the GPAD, the main difference is that they are in the same column as negation and when both apply they are pipe-separted
    • Default gp2term relations:
      • Molecular Function: enables
      • Cellular Component: located_in
      • Biological Process: individual groups decide based on annotation practice
  • Why do this?
    • The expanded set of gp2term relations is available in annotation tools, e.g. Noctua and Protein2GO, but by not including them in the GAF, we don't give the GOC, or users, any mechanism to filter specific sets of annotations for GAFs and subsequent analyses. Making this change will allow GO and groups to do this.


GPAD/GPI 2.0 Specifications

  • Questions/Comments
    • We need guidelines for how to represent proteins ids or accessions shared by multiple gene products, e.g. histones. [Stacia]
  • Response:
    • Groups should work with UniProt to disambiguate protein records that refer to multiple genes, i.e. generate gene-centric protein entries in UniProt
    • In the interim, we are working on specific guidelines for these types of entries in the gpi file (just a few relatively small decisions to make but we want entries to be consistent)

Attendance

  • On call: