Manager Call 2018-03-15

Call in info

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

Agenda

NYC Meeting Agenda

• Need to remind people to register & book rooms
• Start working on the agenda in more detail
  • https://github.com/geneontology/go-ontology/milestone/5
  • https://github.com/geneontology/go-annotation/milestone/2
• SAB agenda, plans

Working Groups/Projects

GO Curation Survey

• Draft Survey

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?

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.

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

• What plans do we have for implementing consumption and display of GO-CAM models?
• How does the AGR GO working group fit into this task?
• https://github.com/geneontology/noctua/issues/519

Minutes

• On call: