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| | = AGENDA= |
| | ==<em>[https://docs.google.com/document/d/1Px8AgghIABKaGP174Av2XYXQ8NfUrkMRT1yJ8kwCgx4/edit?usp=sharing Live version now here in Google Drive]</em>== |
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| = Suggestions for topics= | | ==Call-in information== |
| | Zoom: https://stanford.zoom.us/j/976175422 |
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| == Intro/Overview ==
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| Paul T
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| * Mention Alliance
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| * Beginning new fiscal year
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| == Infrastructure Projects ==
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| * Release pipeline/new release cycle [https://github.com/orgs/geneontology/projects/11] (Seth, Eric)
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| ** Documentation https://github.com/geneontology/go-site/issues/555
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| ** UPDATE: Injection of PAINT annotations at GO Central (Huaiyu)
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| ** Discussion: Injection of GPADs derived from production GO-CAMs (Chris)
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| ** Automated QC (Eric, Kimberley)
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| * public API (Nathan, Deepak)
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| ** Example of use: Ribbon (Nathan)
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| == GO-CAM and Noctua Project ==
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| * Noctua status reports
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| ** 1.0 Release [https://github.com/orgs/geneontology/projects/6] Seth, Chris
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| ** Tour of the SAE: Tremayne, Paul
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| ** Importing Reactome into Noctua: Ben, David
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| ** Seeding models from GAFs: Dustin, Eric
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| ** Roll-out plan/discussion: Kimberley
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| * Community usage of GO-CAMs
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| ** GO-CAM landing page [https://github.com/geneontology/go-site/issues/558] (Laurent-Phillippe)
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| ** Export to other formats and import into other databases (Laurent-Phillippe)
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| ** Loading GO-CAM annotations into MODS- The MGI Experience (David H)
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| == SAE hands-on session ==
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| (Paul's suggestion) - 1.5h
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| All curators should come with a paper or pathway that they would like to curation
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| Suggestion: curate signaling pathways ?
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| == Documentation and Outreach ==
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| * Presentation of update website/Report on Documentation jamboree
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| * Outreach plans (Suzi A)
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| ** SOPs for groups that want to submit annotations to the GOC
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| * 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.
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| == Projects ==
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| === Signaling Workshop Project ===
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| Paul/Pascale: Can we give an overview/lessons learned summary ?
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| * Canonical Wnt Signaling (Kimberly VA and Helen) (https://github.com/geneontology/go-annotation/issues/1595)
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| ** Report on Ontology Changes
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| ** Report on Annotation Review
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| *** Reviews Completed
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| *** Reviews Outstanding
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| *** New Annotation Practice Guidelines
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| * MAPK Cascade (DavidH and SabrinaT) (https://github.com/geneontology/go-annotation/issues/1592)
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| ** Report on ontology changes
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| ** Report on Annotation Review
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| *** Reviews Completed
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| *** Reviews Outstanding
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| *** New Annotation Practice Guidelines
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| * GPCR signaling (Pascale or Petra)(https://github.com/geneontology/go-annotation/issues/1591)
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| ** Report on ontology changes
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| ** Report on Annotation Review
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| *** Reviews Completed
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| *** Reviews Outstanding
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| *** New Annotation Practice Guidelines
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| * JAK/STAT cascade (Ruth Lovering) (https://github.com/geneontology/go-annotation/issues/1628)
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| ** Report on ontology changes
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| ** Report on Annotation Review
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| *** Reviews Completed
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| *** Reviews Outstanding
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| *** New Annotation Practice Guidelines
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| === Other projects ===
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| * HTP annotations : present annotation guidelines
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| * Complex working group report
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| ** Various tickets about complexes
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| *** https://github.com/geneontology/go-ontology/issues/15211
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| *** https://github.com/geneontology/go-ontology/issues/11094
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| *** https://github.com/geneontology/go-ontology/issues/11382
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| *** https://github.com/geneontology/go-ontology/issues/14375
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| * Update MF refactor (Pascale)
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| * Update: Tx refactor (Pascale)
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| == Quality Control Projects ==
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| * Report: QC group: annotation review stats
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| * Cancer signaling pathways review (note: I also have this under GP2Term relations below; Chris)
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| ** Case study: Xena and cancer signaling project (Suzi L)
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| * GP2Term Relations [https://github.com/orgs/geneontology/projects/13] (Suzi L, Kimberly)
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| ** See [[:Category:Gene_Product_to_Term_Relations]]
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| ** UPDATE: GP2Term Relations coming from Noctua (Chris)
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| ** UPDATE/discussion: Enabling usage by users and bioinformaticians (Deepak, Laurent-Phillippe)
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| ** UPDATE: Display in AmiGO (Suzi L, Seth)
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| * GP annotations to terms that refer to 'drugs'
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| ** https://github.com/geneontology/go-ontology/issues/15379
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| * Estimating literature coverage in curation*
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| **(Requested by SAB and all the time)
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| ***Get stats for
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| **** # genes with some annotation (IBA | EXP - separately - exclude HTP and probably ‘protein binding')
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| **** # annotations per gene -> group by: >100 annotations, 50-100 annotations, 10-50 annotations, <10 annotations
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| **** # papers per gene -> group by: >100 papers, 50-100 papers, 10-50 papers, <10 papers
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| * Redundant annotations: <BR>
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| ** https://github.com/geneontology/go-annotation/issues/1879
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| * Main GAF file: providing a high confidence GAF file
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| ** https://github.com/geneontology/go-ontology/issues/15498
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| * GOC-OWL inference pipeline concerns
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| **https://github.com/geneontology/go-annotation/issues/1487
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| =Will we be talking about those??=
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| == Future New Projects ==
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| * 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?)
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| *Evolutionary taxon relations (Paul, Chris)
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| *Enrichment in the cloud
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| ** Update (USC/LBL)
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| ==Other potential topics==
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| * Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928
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| * 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
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| == Suggestions for topics Fall 2018==
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| *'Response to' workshop (similar to the signaling WS)
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| [[Category: GO Consortium Meetings]] | | [[Category: GO Consortium Meetings]] |