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? If anyone is interested, there is a very quick/easy way to establish the difference between: (1) "not in the GO database (not found); (2) "unknown" (ND), and (3) "unannotated" (no ND, and no annotation in Aspect of interest) for your organisms proteins using the complete known protein ID set for your organism and the GO term mapper tool https://go.princeton.edu/cgi-bin/GOTermMapper (GOTermMapper provides these numbers as part of the output so that the slim set results can be interpreted correctly).