2018 NYU GOC Meeting Agenda: Difference between revisions
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** SOPs for groups that want to submit annotations to the GOC | ** SOPs for groups that want to submit annotations to the GOC | ||
* Licensing and community annotation (Seth?) <br / > 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agreements from re-used upstream resources (the http://reusabledata.org evaluation of Reactome, while possibly out of date, can be illustrative in the context of bulk model import), as well as the legal nature of the GOC. | * Licensing and community annotation (Seth?) <br / > 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agreements from re-used upstream resources (the http://reusabledata.org evaluation of Reactome, while possibly out of date, can be illustrative in the context of bulk model import), as well as the legal nature of the GOC. | ||
* Impact of GO qualifiers on Alliance gene descriptions (Mary D) | |||
== Projects == | == Projects == |
Revision as of 11:15, 19 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)
- 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 [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. - Impact of GO qualifiers on Alliance gene descriptions (Mary D)
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)
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 [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)
- 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
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
- 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)