Difference between revisions of "Manager Call 2020-07-29"

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BCC2020 was organized with a new tool with virtual representation of a conference: https://remo.co/ Could ease breakout and functionality for interactive posters but each breakout limited to 8 people and the solution is not free.
 
BCC2020 was organized with a new tool with virtual representation of a conference: https://remo.co/ Could ease breakout and functionality for interactive posters but each breakout limited to 8 people and the solution is not free.
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==GO-CAM Jamboree==
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*Proposal to have a GO-CAM curation jamboree sometime this fall
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*How critical will it be to have Noctua on a more secure production footing by this time?
  
 
==GPAD/GPI==
 
==GPAD/GPI==
*There is a discussion about possibly duplicating effort by asking groups to submit a GPI file to GO and a BGI file to the Alliance.   
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*There is a discussion about possibly duplicating effort by asking groups to submit a GPI file to GO and a [https://github.com/alliance-genome/agr_schemas/blob/master/ingest/basicGeneticEntity.json BGI file] to the Alliance.   
**Stacia raised the issue of possiblly overlapping goals here on a GO annotation call some time ago.
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**Stacia raised the issue of possibly overlapping goals here on a GO annotation call some time ago.
**Should we re-visit this and discuss aligning these files more closely?
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**Should we re-visit this and discuss aligning these files more closely? Could one file be derived from the other?
**What would the development costs be for everyone?
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**Should these types of files be moving towards a more ontological representation of entities? We'd ultimately like to do that with annotatable entities in GO.
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**What would the development costs be for everyone to make changes?
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**Need to communicate our thoughts/decision on this to the Alliance PIs
 
*Would like to formalize groups’ review of the specifications and ask groups to sign off their review on a github ticket.
 
*Would like to formalize groups’ review of the specifications and ask groups to sign off their review on a github ticket.
 
*Would give groups until September 1st, but after that no changes would be allowed for 2.0.
 
*Would give groups until September 1st, but after that no changes would be allowed for 2.0.

Revision as of 07:47, 29 July 2020

Agenda

  • Agenda: Pascale
  • Minutes: Laurent-Philippe
  • Present:

GO Baltimore

Where are we ? There is no page for it at the moment on http://wiki.geneontology.org/index.php/Consortium_Meetings_and_Workshops Do we organize a go user meeting ?

BCC2020 was organized with a new tool with virtual representation of a conference: https://remo.co/ Could ease breakout and functionality for interactive posters but each breakout limited to 8 people and the solution is not free.

GO-CAM Jamboree

  • Proposal to have a GO-CAM curation jamboree sometime this fall
  • How critical will it be to have Noctua on a more secure production footing by this time?

GPAD/GPI

  • There is a discussion about possibly duplicating effort by asking groups to submit a GPI file to GO and a BGI file to the Alliance.
    • Stacia raised the issue of possibly overlapping goals here on a GO annotation call some time ago.
    • Should we re-visit this and discuss aligning these files more closely? Could one file be derived from the other?
    • Should these types of files be moving towards a more ontological representation of entities? We'd ultimately like to do that with annotatable entities in GO.
    • What would the development costs be for everyone to make changes?
    • Need to communicate our thoughts/decision on this to the Alliance PIs
  • Would like to formalize groups’ review of the specifications and ask groups to sign off their review on a github ticket.
  • Would give groups until September 1st, but after that no changes would be allowed for 2.0.

Data Visualization Workshop at ECCB

Are we interested in trying to register as a group?

GO Wiki Mediawiki installation

Last week, a hiccup on the go wiki machine again brought up considerations for long-term maintenance. When we get to finally taking this over from Stanford, we'll need to do one of 1) migrate to a hosted mediawiki service; 2) allocate standing resources for instance and software maintenance, updates, backups, and recoveries; 3) migrate away from mediawiki (e.g. RTDs, GH wiki).

Projects update

https://docs.google.com/document/d/1URLkEQBewlzD-NVAjbPLWD5Gu-5xq0RysTrm1GMbuiM/edit#


Legacy data

Laurent-Philippe Will try to use the SVN archive

Moving groups to Noctua (#3)

Kimberly has a GPAD file with full history and looking into loading this David is working on GPAD/GPI 2.0 files

GO pipeline solidified / Infrastructure / DevOps (#4)

Discussion: Seth: nothing to report Had no time to work on the pipeline Pascale asked if we could pay for any services to make the pipeline more efficient. Seth: Nothing on the main pipeline, but the Travis checks (go-ontology) perhaps. We need to check

GO-CAM content

i. List of BP to annotate ii. Annotation jamboree(s)

-> Do we want to schedule that ? Or are there Noctua features required first ? - Kimberly generated a list of pathways for C elegans - Kimberly: We *could* schedule a jamboree for the fall, but she is concerned that we have many questions about how to model certain things (namely, activity-regulating processes) - Kimberly will ask at the next annotation call to see who would be interested in attending, and will schedule a date


GO-CAMs from existing pathway resources

Ben is writing the paper


Creating GMT files

https://github.com/geneontology/go-site/issues/1536 Does this needs to be added in the priorities ?