2018 NYU GOC Meeting Agenda: Difference between revisions

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** Update on various Signaling Projects
** Update on various Signaling Projects
*** Canonical Wnt Signaling (https://github.com/geneontology/go-annotation/issues/1595)
*** Canonical Wnt Signaling (https://github.com/geneontology/go-annotation/issues/1595)
*** MAPK Cascade (https://github.com/geneontology/go-annotation/issues/1592)
*** MAPK Cascade (DavidH) (https://github.com/geneontology/go-annotation/issues/1592)
*** GPCR signaling (https://github.com/geneontology/go-annotation/issues/1591)
*** GPCR signaling (https://github.com/geneontology/go-annotation/issues/1591)
*** JAK/STAT cascade (https://github.com/geneontology/go-annotation/issues/1628)
*** JAK/STAT cascade (Ruth Lovering) (https://github.com/geneontology/go-annotation/issues/1628)


* Report from ontology group on alignment of Rhea, Reactome, IntAct and GO with their recommendations for moving forward. GH ticket is here [https://github.com/geneontology/go-ontology/issues/14984] (Jim, Ben?)
* Report from ontology group on alignment of Rhea, Reactome, IntAct and GO with their recommendations for moving forward. GH ticket is here [https://github.com/geneontology/go-ontology/issues/14984] (Jim, Ben?)

Revision as of 11:42, 5 April 2018

Suggestions for topics

Documentation and Outreach

  • Presentation of update website/Report on Documentation jamboree
  • Outreach plans (Suzi A)

Annotation

  • Report: Annotation group (https://github.com/geneontology/go-annotation/milestone/2)
    • Status Signaling workshop tasks
  • Report: QC group: annotation review stats
    • Cancer signaling pathways review (note: I also have this under GP2Term relations below; chris)
  • HTP annotations : present annotation guidelines
  • Complex working group report


Infrastructure

  • Release pipeline/new release cycle [2] (Seth, Eric)
  • public API (Nathan, Deepak)
    • Example of use: Ribbon (Nathan)
  • Redundant annotations:

https://github.com/geneontology/go-annotation/issues/1879


GOC-OWL inference pipeline concerns

https://github.com/geneontology/go-annotation/issues/1487

GO-CAMs

  • Noctua status reports
    • 1.0 Release [3] Seth, Chris
    • Tour of the SAE: Tremayne, Paul
    • Importing Reactome into Noctua: Ben, David
    • Seeding models from GAFs: Dustin, Eric
    • Roll-out plan/discussion: Kimberley
  • Community usage of GO-CAMs
    • GO-CAM landing page [4] (Laurent-Phillippe)
    • Export to other formats and import into other databases (Laurent-Phillippe)
    • Loading GO-CAM annotations into MODS- The MGI Experience (David H)

Enrichment in the cloud

  • Update (USC/LBL)

Ontology Group (David H Moderator)

  • Report from ontology group on alignment of Rhea, Reactome, IntAct and GO with their recommendations for moving forward. GH ticket is here [5] (Jim, Ben?)
  • Evolutionary taxon relations (Paul, Chris)

Suggestions for topics Fall 2018

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


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

Main GAF file: providing a high confidence GAF file

https://github.com/geneontology/go-ontology/issues/15498