2018 Montreal GOC Meeting Agenda

AGENDA

Milestones to be met for the Montreal meeting

GO rules update, pipeline and error reports

Eric & Pascale

• Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928
• Current rules status & future priorities
• For MODs: where to find reports

Pipeline documentation

Kimberly, Pascale, Chris, Seth, etc Must be completed (as much as possible) and announced http://wiki.geneontology.org/index.php/Release_Pipeline

Ontology and Annotation documentation update

David, Kimberly and Pascale (random thoughts:

• Ontology: mention the creation of 'projects' in GH where we moved old projects, so that its' easier t find old discussions

GO website migration

Laurent-Philippe, SuziA, etc

Noctua 1.1

Kimberly Seth, etc

PAINT

PAINT GAF file generation QC

Huaiyu and Pascale

PAINT tickets

Marc & Pascale https://github.com/geneontology/go-annotation/labels/PAINT%20annotation

Annotation

Suggestions:

• Signaling 2017 update
• Transcription reviews
• ECM reviews

Ontology

Suggestions:

• MF refactor update, including transcription
• ECM update

GO subsets update

Pascale:

• Deprecated a number of unused/unmaintained subsets
• Show subset yaml files and how they are used
• Each subset needs a maintainer

Suggestions for topics Fall 2018

Carried over from May 2018

• 'Response to' workshop (similar to the signaling WS)
• 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

New topics

Representing complete proteomes (added by Val)

• =====Datasets (obtaining/maintaining complete datasets with unique identifiers)=====

• https://github.com/geneontology/go-site/issues/756
• https://github.com/geneontology/amigo/issues/475
• What does reference proteome mean, why we have duplicates for pufferfish, and why it includes unreviewed proteins? See https://docs.google.com/document/d/1l4hZw_ZTor8RoTjYTNS4FtGAba4HZrewmjccrSXJ9Hs/edit
• https://github.com/pantherdb/Helpdesk/issues/1

Annotation

• Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation?

 Establish the difference  between: 
 * (1) "not in the GO database (not found); 
 * (2)  "unknown" (ND),  
 * (3) "unannotated" (no ND, and no annotation in Aspect of interest) 

(difference can be established using the complete known protein ID set for your organism and GO term mapper https://go.princeton.edu/cgi-bin/GOTermMapper)