2018 NYU GOC Meeting Agenda: Difference between revisions

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= AGENDA=
==<em>[https://docs.google.com/document/d/1Px8AgghIABKaGP174Av2XYXQ8NfUrkMRT1yJ8kwCgx4/edit?usp=sharing Live version now here in Google Drive]</em>==


= Suggestions for topics=
==Call-in information==
Zoom: https://stanford.zoom.us/j/976175422


== Intro/Overview ==
Paul T
* Mention Alliance
* Beginning new fiscal year
== Infrastructure Projects ==
* Release pipeline/new release cycle [https://github.com/orgs/geneontology/projects/11] (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 [https://github.com/orgs/geneontology/projects/6] 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 [https://github.com/geneontology/go-site/issues/558] (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?) <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agreements from re-used upstream resources (the http://reusabledata.org evaluation of Reactome, while possibly out of date, can be illustrative in the context of bulk model import), as well as the legal nature of the GOC.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 ==
=== 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
** 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 ==
* 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]]
** 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'
** 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
=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 [https://github.com/geneontology/go-ontology/issues/14984] (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)


[[Category: GO Consortium Meetings]]
[[Category: GO Consortium Meetings]]

Latest revision as of 11:29, 25 June 2018