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 | ||
== | == Projects == | ||
* Report | === Signaling Workshop Project === | ||
** | |||
* Report: | * 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) (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, | * 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]] | ||
** 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) | ||
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** Example of use: Ribbon (Nathan) | ** Example of use: Ribbon (Nathan) | ||
== GO-CAM and Noctua Project == | |||
== GO- | |||
* Noctua status reports | * Noctua status reports | ||
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** Loading GO-CAM annotations into MODS- The MGI Experience (David H) | ** 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 [https://github.com/geneontology/go-ontology/issues/14984] (Jim, Ben?) | |||
*Evolutionary taxon relations (Paul, Chris) | |||
* | *Enrichment in the cloud | ||
** Update | ** Update (USC/LBL) | ||
== 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) | ||
[[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
- 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) (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)
Suggestions for topics Fall 2018
- 'Response to' workshop (similar to the signaling WS)