Manager Call 2018-04-05: Difference between revisions

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===Software===
===Software===
* Release pipeline: informing users/curators of the releases, so we can know what data we are looking at (Pascale: For annotation reviews this has been problematic for me)
* Release pipeline: informing users/curators of the releases, so we can know what data we are looking at (Pascale: For annotation reviews this has been problematic for me)
* New qualifier: This changes the specs of the GAF file. Apparently some people parse the GAF file by stripping off lines containing a qualifier to remove the NOTs.  
* New qualifier: Adding a qualifier to every annotation in a GAF file changes the file dramatically. It would impact any user or tool that filters annotations by looking for a null value in the qualifier field.  
** Is it time to spec out a new file and stop supporting GAF?  
** Do we really want to make this large chnge to annotations in the gaf file, or do we want to encourage users who want the additional information to start consuming GPAD, where the qualifier is required?


== Working Groups/Projects ==
== Working Groups/Projects ==

Revision as of 10:08, 28 March 2018


Agenda

NYC Meeting Agenda

Working Groups/Projects

Software

  • Release pipeline: informing users/curators of the releases, so we can know what data we are looking at (Pascale: For annotation reviews this has been problematic for me)
  • New qualifier: Adding a qualifier to every annotation in a GAF file changes the file dramatically. It would impact any user or tool that filters annotations by looking for a null value in the qualifier field.
    • Do we really want to make this large chnge to annotations in the gaf file, or do we want to encourage users who want the additional information to start consuming GPAD, where the qualifier is required?

Working Groups/Projects

GO Curation Survey

  • Draft Survey
  • Action from last meeting: (Kimberly): Move to Survey monkey, make changes discussed, and send it around


Protein Complexes

HTP Codes

RCA Evidence Code

  • Need to work with several groups to review their annotations:
    • Gramene (35815 annotations)
    • As an example, 2929 RCA Molecular Function annotations
      • Date: 20060831
      • Reference: GR_REF:8030
      • Manual review of mappings; can we suggest ISM?
    • GeneDB
      • Some annotations from reviews, but some to papers that describe a systems analysis that is probably more in line with the original intent of RCA
      • RCA -> CCA (combined computational analysis)??
    • EcoCyc
    • AgBase
    • AspGD
    • PAMGO_MGG
  • If we decide to keep RCA, then we'd need to remove the one-year limit; it doesn't make sense.

Documentation

QA/QC

Working Group Meetings

  • Quarterly?
    • Rotate between ontology and annotation (small, focused groups)
    • Test virtual meetings, but still focused on the task

Noctua

1.0 Rollout

  • Merge Tremayne's fork with Noctua-dev for further testing
  • Some outstanding issues on SAE
  • Single source file for MODs to consume

Reactome Imports

  • David, Kimberly have looked at some imports/translations
  • Ben's work looks to be potentially very useful and promising for seeding templates, models
  • Will probably require significant manual input, refinement, testing

End User Tools

GO Helpdesk

Ontology

Announcing changes to the wider user community

  • This was brought up by Birgit in the protein complex merge ticket - she was suggesting we make an announcement. However we never made annoucements before (except for obsoletions); should we start? What would be the guidelines? For example when a merge affects more than 100, 1000 annotations ? EXP only ?
  • Pascale: changes to definitions of root terms: https://github.com/geneontology/go-ontology/issues/14899; isn't this a big change ? How should we notify people?
    • Should we create a label in GH 'Major change', so we can easily pull out the tickets and show them at Ontology and Annotation calls ? (perhaps in annual reports as well)
  • Pascale: suggestion: create a new label 'major change' and announce them either on twitter and/or on the website as user stories (or whatever it's called).


Minutes

  • On call:
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