2018 NYU GOC Meeting Agenda: Difference between revisions
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** Update on various Signaling Projects | ** Update on various Signaling Projects | ||
*** Canonical Wnt Signaling (https://github.com/geneontology/go-annotation/issues/1595) | *** Canonical Wnt Signaling (https://github.com/geneontology/go-annotation/issues/1595) | ||
*** MAPK Cascade (https://github.com/geneontology/go-annotation/issues/1592) | *** MAPK Cascade (DavidH) (https://github.com/geneontology/go-annotation/issues/1592) | ||
*** GPCR signaling (https://github.com/geneontology/go-annotation/issues/1591) | *** GPCR signaling (https://github.com/geneontology/go-annotation/issues/1591) | ||
*** JAK/STAT cascade (https://github.com/geneontology/go-annotation/issues/1628) | *** 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?) | * 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?) |
Revision as of 11:42, 5 April 2018
Suggestions for topics
Documentation and Outreach
- Presentation of update website/Report on Documentation jamboree
- Outreach plans (Suzi A)
Annotation
- Report: Annotation group (https://github.com/geneontology/go-annotation/milestone/2)
- Status Signaling workshop tasks
- Report: QC group: annotation review stats
- Cancer signaling pathways review (note: I also have this under GP2Term relations below; chris)
- HTP annotations : present annotation guidelines
- Complex working group report
- GP2Term Relations [1] (Suzi L, Kimberley)
- See Category:Gene_Product_to_Term_Relations
- Case study: Xena and cancer signaling project (Suzi L)
- 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'
Infrastructure
- 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)
- Redundant annotations:
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
- 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)
Enrichment in the cloud
- Update (USC/LBL)
Ontology Group (David H Moderator)
- Report on ontology development group
- Update MF refactor (Pascale)
- Update: Tx refactor (Pascale)
- Various tickets about complexes
- 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 [5] (Jim, Ben?)
- Evolutionary taxon relations (Paul, Chris)
Suggestions for topics Fall 2018
- '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