Difference between revisions of "Annotation Conf. Call 2020-03-24"

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m (Status of GAFs)
m (Status of GAFs)
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== Status of GAFs ==
 
== Status of GAFs ==
 
* GAFs will continue to be produced and supported by the GOC into the foreseeable future
 
* GAFs will continue to be produced and supported by the GOC into the foreseeable future
* We would like to propose an incremental update to the GAF, though, to allow for use of the full set of gp2term relations
+
* We would like to '''propose''' an incremental update to the GAF, though, to allow for use of the full set of gp2term relations
 
** This would be the same set of gp2term relations used in the GPAD, the main difference would be that they are in the same column as negation and where both occur they would be pipe-separted
 
** This would be the same set of gp2term relations used in the GPAD, the main difference would be that they are in the same column as negation and where both occur they would be pipe-separted
 
*** acts_upstream_of_or_within
 
*** acts_upstream_of_or_within
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**** acts_upstream_of_or_within
 
**** acts_upstream_of_or_within
 
**** involved_in
 
**** involved_in
 +
*Why do this?
 +
** The expanded set of gp2term relations is available in annotation tools, e.g. Noctua and Protein2GO, but by not including the full set of gp2term relations 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.
  
 
= Attendance =
 
= Attendance =

Revision as of 11:34, 23 March 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

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)

Status of GAFs

  • GAFs will continue to be produced and supported by the GOC into the foreseeable future
  • We would like to propose an incremental update to the GAF, though, to allow for use of the full set of gp2term relations
    • This would be the same set of gp2term relations used in the GPAD, the main difference would be that they are in the same column as negation and where both occur they would be pipe-separted
      • acts_upstream_of_or_within
      • NOT|acts_upstream_of_or_within
    • Default gp2term relations:
      • Molecular Function: enables
      • Cellular Component: located_in
      • Biological Process: individual groups decide based on annotation practice
        • acts_upstream_of_or_within
        • involved_in
  • Why do this?
    • The expanded set of gp2term relations is available in annotation tools, e.g. Noctua and Protein2GO, but by not including the full set of gp2term relations 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.

Attendance

  • On call: