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: [http://xena.ucsc.edu/ Xena] and cancer signaling project (Suzi L) | ** Case study: [http://xena.ucsc.edu/ Xena] and cancer signaling project, [http://xenademo.berkeleybop.io/xena/ demo] (Suzi L) | ||
===Ideas for QC approaches=== | ===Ideas for QC approaches=== |
Revision as of 16:46, 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)
- 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, Kimberly)
- 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agreements from re-used upstream resources (the http://reusabledata.org evaluation of Reactome, while possibly out of date, can be illustrative in the context of bulk model import), as well as the legal nature of the GOC.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
- Canonical Wnt Signaling (Kimberly VA and Helen) (https://github.com/geneontology/go-annotation/issues/1595)
- Report on Ontology Changes
- Report on Annotation Review
- Reviews Completed
- Reviews Outstanding
- New Annotation Practice Guidelines
- MAPK Cascade (DavidH and SabrinaT) (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
- 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)
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
- Get stats for
- (Requested by SAB and all the time)
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
- GP annotations to terms that refer to 'drugs'
- Redundant annotations:
- Main GAF file: providing a high confidence GAF file
- GOC-OWL inference pipeline concerns
Other potential topics
- 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
Suggestions for topics Fall 2018
- 'Response to' workshop (similar to the signaling WS)