2018 NYU GOC Meeting Agenda: Difference between revisions

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* Mention Alliance  
* Mention Alliance  
* Beginning new fiscal year
* Beginning new fiscal year
== Infrastructure Projects ==
* Release pipeline/new release cycle [https://github.com/orgs/geneontology/projects/11] (Seth, Eric)
** Documentation https://github.com/geneontology/go-site/issues/555
** UPDATE: Injection of PAINT annotations at GO Central (Huaiyu)
** Discussion: Injection of GPADs derived from production GO-CAMs (Chris)
** Automated QC (Eric, Kimberley)
* 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 [https://github.com/orgs/geneontology/projects/6] 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 [https://github.com/geneontology/go-site/issues/558] (Laurent-Phillippe)
** Export to other formats and import into other databases (Laurent-Phillippe)
** Loading GO-CAM annotations into MODS- The MGI Experience (David H)
== SAE hands-on session ==
(Paul's suggestion) - 1.5h
All curators should come with a paper or pathway that they would like to curation
Suggestion: curate signaling pathways ?


== Documentation and Outreach ==
== Documentation and Outreach ==
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=== Signaling Workshop Project ===
=== 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


* Canonical Wnt Signaling (Kimberly VA and Helen) (https://github.com/geneontology/go-annotation/issues/1595)
* Canonical Wnt Signaling (Kimberly VA and Helen) (https://github.com/geneontology/go-annotation/issues/1595)
Line 82: Line 119:
* GOC-OWL inference pipeline concerns  
* GOC-OWL inference pipeline concerns  
**https://github.com/geneontology/go-annotation/issues/1487
**https://github.com/geneontology/go-annotation/issues/1487
== Infrastructure Projects ==
* Release pipeline/new release cycle [https://github.com/orgs/geneontology/projects/11] (Seth, Eric)
** Documentation https://github.com/geneontology/go-site/issues/555
** UPDATE: Injection of PAINT annotations at GO Central (Huaiyu)
** Discussion: Injection of GPADs derived from production GO-CAMs (Chris)
** Automated QC (Eric, Kimberley)
* public API (Nathan, Deepak)
** Example of use: Ribbon (Nathan)
== GO-CAM and Noctua Project ==
* Noctua status reports
** 1.0 Release [https://github.com/orgs/geneontology/projects/6] 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 [https://github.com/geneontology/go-site/issues/558] (Laurent-Phillippe)
** Export to other formats and import into other databases (Laurent-Phillippe)
** Loading GO-CAM annotations into MODS- The MGI Experience (David H)




=Will we be talking about those??=
== Future New Projects ==
== Future New Projects ==
* 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?)
* 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?)


*Evolutionary taxon relations (Paul, Chris)
*Evolutionary taxon relations (Paul, Chris)
*Enrichment in the cloud
** Update (USC/LBL)


==Other potential topics==
==Other potential topics==
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928
* Use cases:  Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit
* Use cases:  Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit



Revision as of 15:59, 18 April 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 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 [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)

SAE hands-on session

(Paul's suggestion) - 1.5h All curators should come with a paper or pathway that they would like to curation 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

Quality Control Projects


Will we be talking about those??

Future New Projects

  • 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)

Other potential topics

Suggestions for topics Fall 2018

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