2018 NYU GOC Meeting Agenda

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Suggestions for topics

Intro/Overview

Paul T

  • Mention Alliance
  • Beginning new fiscal year

Infrastructure Projects

  • Release pipeline/new release cycle [1] (Seth, Eric)
  • public API (Nathan, Deepak)
    • Example of use: Ribbon (Nathan)
  • Interaction with data commons (Paul/Chris)
  • Enrichment analysis in the cloud (Paul/Chris)

GO-CAM and Noctua Project

  • Noctua status reports
    • 1.0 Release [2] Seth, Chris
    • Tour of the Noctua Form: Tremayne, Paul
    • Importing Reactome into Noctua: Ben, David
    • Seeding models from GAFs: Dustin, Eric
    • Roll-out plan: Kimberley
  • Community usage of GO-CAMs
    • GO-CAM landing page [3] (Laurent-Phillippe)
    • Export to other formats and import into other databases (Laurent-Phillippe)
    • Loading GO-CAM annotations into MODS- The MGI Experience (David H)

Noctua Form hands-on session

(Paul's suggestion) - 1.5h All curators should come with a paper or pathway that they would like to curate. Suggestion: curate signaling pathways?

Documentation and Outreach

  • Presentation of update website/Report on Documentation jamboree
    • New HTP annotations guidelines
  • Outreach plans (Suzi A)
    • SOPs for groups that want to submit annotations to the GOC
  • Licensing and community annotation (Seth?)
    With the possibility of a wider pool of annotation ingest, we should consider a copyright re-assignment policy to the GOC, getting pass-through agreements from re-used upstream resources (the http://reusabledata.org evaluation of Reactome, while possibly out of date, can be illustrative in the context of bulk model import), as well as the legal nature of the GOC.
  • Seth has included some copyright re-assignment text to the Noctua sign-up, especially as we are starting to take non-GOC annotations and users.

Projects

Signaling Workshop Project

Paul/Pascale: Can we give an overview/lessons learned summary ? General principles:

  • start and end of pathways
  • underannotation
  • overannotation
  • what does it mean to be part of a pathway/upstream/etc

Tickets to discuss

Protein Complex working group report


Update MF refactor

Pascale

Update: Tx refactor

Pascale

PAINT update

Huaiyu ~30-45 minutes

GP2Term Relations

GitHub Project: [4] (Suzi L, Kimberly)

    • See Category:Gene_Product_to_Term_Relations
    • UPDATE: GP2Term Relations coming from Noctua (Chris)
    • UPDATE/discussion: Enabling usage by users and bioinformaticians (Deepak, Laurent-Phillippe)
    • UPDATE: Display in AmiGO (Suzi L, Seth)

Quality Control Projects

  • Report: QC group: annotation review stats
  • Cancer signaling pathways review (note: I also have this under GP2Term relations below; Chris)
    • Case study: Xena and cancer signaling project, demo (Suzi L)

Ideas for QC approaches

  • Estimating literature coverage in curation*
    • (Requested by SAB and all the time)
      • Get stats for
        • # genes with some annotation (IBA | EXP - separately - exclude HTP and probably ‘protein binding')
        • # annotations per gene -> group by: >100 annotations, 50-100 annotations, 10-50 annotations, <10 annotations
        • # papers per gene -> group by: >100 papers, 50-100 papers, 10-50 papers, <10 papers

External Projects

  • Impact of GO qualifiers on Alliance gene descriptions (Mary D)

Sunday PM

Breakout sessions

Alignment of Rhea, Reactome, IntAct and GO

Alan B, Peter D, Sandra/Birgit, Jim, Ben? With their recommendations for moving forward. GH ticket is here [5]


QA and metrics

Suzi, Val, Kimberly, Pascale, Eric .. ?

Will we be talking about those??

Future New Projects

Evolutionary taxon relations

(Paul, Chris)

Tickets

Other potential topics

Suggestions for topics Fall 2018

  • 'Response to' workshop (similar to the signaling WS)