2018 NYU GOC Meeting Agenda: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
No edit summary
Line 8: Line 8:
** SOPs for groups that want to submit annotations to the GOC
** SOPs for groups that want to submit annotations to the GOC


== Annotation ==
== Projects ==


* Report: Annotation group (https://github.com/geneontology/go-annotation/milestone/2)
=== Signaling Workshop Project ===
** Status Signaling workshop tasks
 
* Report: QC group: annotation review stats
* Canonical Wnt Signaling (Kimberly VA and Helen) (https://github.com/geneontology/go-annotation/issues/1595)
** Cancer signaling pathways review (note: I also have this under GP2Term relations below; chris)
** Report on Ontology Changes
** Report on Annotation Review
*** Reviews Completed
*** Reviews Outstanding
*** New Annotation Practice Guidelines
 
* MAPK Cascade (DavidH) (https://github.com/geneontology/go-annotation/issues/1592)
** Report on ontology changes
** Report on Annotation Review
*** Reviews Completed
*** Reviews Outstanding
*** New Annotation Practice Guidelines
 
* GPCR signaling (Pascale or Petra)(https://github.com/geneontology/go-annotation/issues/1591)
** Report on ontology changes
** Report on Annotation Review
*** Reviews Completed
*** Reviews Outstanding
*** New Annotation Practice Guidelines
 
* JAK/STAT cascade (Ruth Lovering) (https://github.com/geneontology/go-annotation/issues/1628)
** Report on ontology changes
** Report on Annotation Review
*** Reviews Completed
*** Reviews Outstanding
*** New Annotation Practice Guidelines
 
=== Other projects ===
* HTP annotations : present annotation guidelines
* HTP annotations : present annotation guidelines
* Complex working group report  
* Complex working group report
** Various tickets about complexes
*** https://github.com/geneontology/go-ontology/issues/15211
*** https://github.com/geneontology/go-ontology/issues/11094
*** https://github.com/geneontology/go-ontology/issues/11382
*** https://github.com/geneontology/go-ontology/issues/14375
* Update MF refactor (Pascale)
* Update: Tx refactor (Pascale)
 
== Quality Control Projects ==


* GP2Term Relations [https://github.com/orgs/geneontology/projects/13] (Suzi L, Kimberley)
* 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)
* GP2Term Relations [https://github.com/orgs/geneontology/projects/13] (Suzi L, Kimberly)
** See [[:Category:Gene_Product_to_Term_Relations]]
** See [[:Category:Gene_Product_to_Term_Relations]]
** Case study: Xena and cancer signaling project (Suzi L)
** UPDATE: GP2Term Relations coming from Noctua (Chris)
** UPDATE: GP2Term Relations coming from Noctua (Chris)
** UPDATE/discussion: Enabling usage by users and bioinformaticians (Deepak, Laurent-Phillippe)
** UPDATE/discussion: Enabling usage by users and bioinformaticians (Deepak, Laurent-Phillippe)
** UPDATE: Display in AmiGO (Suzi L, Seth)
** UPDATE: Display in AmiGO (Suzi L, Seth)
* GP annotations to terms that refer to 'drugs'
* GP annotations to terms that refer to 'drugs'
**https://github.com/geneontology/go-ontology/issues/15379
** https://github.com/geneontology/go-ontology/issues/15379
* 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
* Redundant annotations: <BR>
** https://github.com/geneontology/go-annotation/issues/1879
* Main GAF file: providing a high confidence GAF file
** https://github.com/geneontology/go-ontology/issues/15498
* GOC-OWL inference pipeline concerns
**https://github.com/geneontology/go-annotation/issues/1487


 
== Infrastructure Projects ==
== Infrastructure ==


* Release pipeline/new release cycle [https://github.com/orgs/geneontology/projects/11] (Seth, Eric)
* Release pipeline/new release cycle [https://github.com/orgs/geneontology/projects/11] (Seth, Eric)
Line 37: Line 87:
** Example of use: Ribbon (Nathan)
** Example of use: Ribbon (Nathan)


* Redundant annotations:
== GO-CAM and Noctua Project ==  
 
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
* Noctua status reports
Line 58: Line 100:
** Loading GO-CAM annotations into MODS- The MGI Experience (David H)
** Loading GO-CAM annotations into MODS- The MGI Experience (David H)


== Enrichment in the cloud ==


* Update (USC/LBL)
== 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?)


== Ontology Group (David H Moderator) ==
*Evolutionary taxon relations (Paul, Chris)


* Report on ontology development group
*Enrichment in the cloud
** Update MF refactor (Pascale)
** Update (USC/LBL)
** Update: Tx refactor (Pascale)
** Various tickets about complexes
*** https://github.com/geneontology/go-ontology/issues/15211
*** https://github.com/geneontology/go-ontology/issues/11094
*** https://github.com/geneontology/go-ontology/issues/11382
*** https://github.com/geneontology/go-ontology/issues/14375
** Update on various Signaling Projects
*** Canonical Wnt Signaling (https://github.com/geneontology/go-annotation/issues/1595)
*** MAPK Cascade (DavidH) (https://github.com/geneontology/go-annotation/issues/1592)
*** GPCR signaling (https://github.com/geneontology/go-annotation/issues/1591)
*** 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?)
 
*Evolutionary taxon relations (Paul, Chris)


== Suggestions for topics Fall 2018==
== Suggestions for topics Fall 2018==
*'Response to' workshop (similar to the signaling WS)
*'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


[[Category: GO Consortium Meetings]]
[[Category: GO Consortium Meetings]]

Revision as of 16:04, 11 April 2018

Suggestions for topics

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

Projects

Signaling Workshop Project

Other projects

Quality Control Projects

Infrastructure Projects

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

GO-CAM and Noctua Project

  • 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)


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)
  • Enrichment in the cloud
    • Update (USC/LBL)

Suggestions for topics Fall 2018

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