2018 NYU GOC Meeting Agenda: Difference between revisions

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* Report: QC group: annotation review stats
* Report: QC group: annotation review stats
* Cancer signaling pathways review (note: I also have this under GP2Term relations below; Chris)
* Cancer signaling pathways review (note: I also have this under GP2Term relations below; Chris)
** Case study: Xena and cancer signaling project (Suzi L)
** Case study: [http://xena.ucsc.edu/ Xena] and cancer signaling project (Suzi L)


===Ideas for QC approaches===
===Ideas for QC approaches===
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**** # annotations per gene -> group by: >100 annotations, 50-100 annotations, 10-50 annotations, <10 annotations
**** # 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
**** # papers per gene -> group by: >100 papers, 50-100 papers, 10-50 papers, <10 papers


== External Projects==
== External Projects==

Revision as of 16:43, 2 May 2018

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
  • 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.

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

Other projects

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 (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)


Breakout sessions

Alignment of Rhea, Reactome, IntAct and GO

With their recommendations for moving forward. GH ticket is here [5] (Jim, Ben?)


QA and metrics

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)