2018 NYU GOC Meeting Agenda: Difference between revisions
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= Suggestions for topics= | = Suggestions for topics= | ||
== Intro/Overview == | |||
Paul T | |||
* Mention Alliance | |||
* Beginning new fiscal year | |||
== Documentation and Outreach == | == Documentation and Outreach == | ||
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*Enrichment in the cloud | *Enrichment in the cloud | ||
** Update (USC/LBL) | ** Update (USC/LBL) | ||
==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== | == Suggestions for topics Fall 2018== |
Revision as of 16:20, 16 April 2018
Suggestions for topics
Intro/Overview
Paul T
- Mention Alliance
- Beginning new fiscal year
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agreements from re-used upstream resources (the http://reusabledata.org evaluation of Reactome, while possibly out of date, can be illustrative in the context of bulk model import), as well as the legal nature of the GOC.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
- 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)
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)
- GP2Term Relations [1] (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)
- GP annotations to terms that refer to 'drugs'
- 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)
- Redundant annotations:
- Main GAF file: providing a high confidence GAF file
- GOC-OWL inference pipeline concerns
Infrastructure Projects
- Release pipeline/new release cycle [2] (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 [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)
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)