Manager Call 2018-03-15

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Call in info

https://stanford.zoom.us/j/754529609

Agenda

NYC Meeting Agenda

Alliance

  • How do the priorities of the Alliance GO working group align with the priorities of the GOC overall?
  • What are the most important things for GO to do in the next six months?

Discussion


Working Groups/Projects

GO Curation Survey

Discussion Action to Survey monkey, make changes discussed, and send it around

Expanded Set of Relations

  • Implementation requirements to meet our May goal of at least having acts_upstream_of_or_within
    • Guidelines/examples for use
      • acts upstream of: sperm motility, lipidation of ras, glycine transport -> heme biosynthesis
      • regulation: glycolysis, signaling
      • involved in: F-P links
      • make use of other F-P co-annotation
      • other ontology relations could be used to devise rules
      • PAINT annotations
    • Have a mechanism for groups to propose new rules
    • Review annotations to process and regulation of process
      • Can Mary D. generate lists for all groups, put on a webpage for review?
    • Other software support needed for this?

Discussion

  • David: should we make it clear that this is for existing annotations?
  • Chris: in the NYC agenda there is a more up to date version of these relations, see http://wiki.geneontology.org/index.php/Annotation_Relations
  • Wiki links to RO and RO links back to the wiki pages
  • LOTS of discussion - we need to schedule a few calls before the GOC meeting to sort this out. We're not ready to bring this to the group yet.

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 ?

Term Genie status

This keeps on coming up at the Ontology call. What's the status ?

Minutes

  • On call: