Difference between revisions of "Manager Call 2020-04-15"

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* Agenda: Pascale
 
* Agenda: Pascale
* Minutes: Laurent-Philippe
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* Minutes: Pascale
* Present:  
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* Present: Pascale, Paul, Judy, David, Kimberly, Seth, Huaiyu, Suzi
* Regrets:
+
* Regrets:  
 +
 
 +
==May Consortium Meetings==
 +
'''Notes from meeting are in bold'''
  
 
==May Consortium Meetings==
 
==May Consortium Meetings==
 
*We are within a month of the May consortium meetings
 
*We are within a month of the May consortium meetings
 
*Need to start firming up [https://docs.google.com/document/d/1DTBCxib8aRwyw5IWLbYRHtPLCnmcbjUNAV1gwj_2hlo the agenda] so people can start planning their schedules and working on presentations
 
*Need to start firming up [https://docs.google.com/document/d/1DTBCxib8aRwyw5IWLbYRHtPLCnmcbjUNAV1gwj_2hlo the agenda] so people can start planning their schedules and working on presentations
 +
 +
'''ACTION: Finalize and discuss on next week's managers call'''
  
 
==Update on actions from last call==
 
==Update on actions from last call==
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* Time line: 4 months?  
 
* Time line: 4 months?  
 
* '''Actions:'''
 
* '''Actions:'''
# Pascale/Seth: Write formal specs documentation
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# Pascale/Seth: Write formal specs documentation - '''ONGOING - some small fixes needed'''
# Kimberly, David, Laurent-Phlippe: Write usage notes: aim in 2 weeks:  [https://docs.google.com/document/d/1Jbpm1l5xjSabywE6ulIflujcESkdkQvlVI7bECgLbtw Draft of announcement and usage notes]
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# Kimberly, David, Laurent-Phlippe: Write usage notes: aim in 2 weeks:  [https://docs.google.com/document/d/1Jbpm1l5xjSabywE6ulIflujcESkdkQvlVI7bECgLbtw Draft of announcement and usage notes] - '''ONGOING - feedback invited'''
 
# Kimberly, David, Laurent-Phlippe: Write some FAQs: what is the impact; why are we doing this ? Clarify the way a gene is related to a GO term
 
# Kimberly, David, Laurent-Phlippe: Write some FAQs: what is the impact; why are we doing this ? Clarify the way a gene is related to a GO term
 
# Send notice
 
# Send notice
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* Kimberly and David will continue training XenBase curators, they will join the call
 
* Kimberly and David will continue training XenBase curators, they will join the call
 
* Jim is adding the Xenopus anatomy to the imports
 
* Jim is adding the Xenopus anatomy to the imports
 +
 +
 +
'''Seth: no news from Malcom. Will follow up.'''
  
 
==Discussion topics==
 
==Discussion topics==
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=== GOLr search ===
 
=== GOLr search ===
 
Collect current issues (eg genes that can not be found) to start improving it
 
Collect current issues (eg genes that can not be found) to start improving it
 +
'''We dont know in which context this was added -> no discussion'''
  
 
=== Component for GO annotations in journals ===
 
=== Component for GO annotations in journals ===
 
Considering 1) easy to integrate web component and 2) current covid situation where submerged by literature difficult to mine retrospectively, try again to propose a very lightweight tool, probably optional, but that would allow an author to provide (gene, function) associations while submitting. Best journals to try ? biorxiv ?
 
Considering 1) easy to integrate web component and 2) current covid situation where submerged by literature difficult to mine retrospectively, try again to propose a very lightweight tool, probably optional, but that would allow an author to provide (gene, function) associations while submitting. Best journals to try ? biorxiv ?
 
+
'''Judy - been asking for this to publishing houses for many years. -- Alliance Literature discussion is also looking into this'''
  
 
===Pathway Genome Databases and the Alliance===
 
===Pathway Genome Databases and the Alliance===
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* https://github.com/evidenceontology/evidenceontology/issues/251
 
* https://github.com/evidenceontology/evidenceontology/issues/251
  
===Users versus group-contacts.yaml===
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* '''Many Evidence codes do not match to the 3-letter evidence codes that we would map to'''
 +
* '''ACTION: Pascale to contact Michelle to set up some virtual meeting to discuss some issues we'd like to see fixed'''
 +
 
 +
===users.yaml versus group-contacts.tsv===
 
https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv
 
https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv
https://github.com/geneontology/go-site/blob/master/metadata/groups.yaml
+
https://github.com/geneontology/go-site/blob/master/metadata/users.yaml
  
 
See discussion in https://github.com/geneontology/go-site/pull/1447
 
See discussion in https://github.com/geneontology/go-site/pull/1447
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* 'Expertise' should like people's expertise or role (developer/curator)
 
* 'Expertise' should like people's expertise or role (developer/curator)
 
-> How do we want to use those two files moving forward ? Do we need two files ?
 
-> How do we want to use those two files moving forward ? Do we need two files ?
 +
 +
* '''Judy, Paul, Kimberly: would be nice to have expertise file'''
 +
* '''Paul: would like to use a GO term - high level term if possible'''
 +
* '''Maybe an activity for the GO virtual meeting'''
  
 
===Publications===
 
===Publications===

Latest revision as of 09:08, 15 April 2020

Agenda

  • Agenda: Pascale
  • Minutes: Pascale
  • Present: Pascale, Paul, Judy, David, Kimberly, Seth, Huaiyu, Suzi
  • Regrets:

May Consortium Meetings

Notes from meeting are in bold

May Consortium Meetings

  • We are within a month of the May consortium meetings
  • Need to start firming up the agenda so people can start planning their schedules and working on presentations

ACTION: Finalize and discuss on next week's managers call

Update on actions from last call

GAF2.2

DECISIONS:

  • Time line: 4 months?
  • Actions:
  1. Pascale/Seth: Write formal specs documentation - ONGOING - some small fixes needed
  2. Kimberly, David, Laurent-Phlippe: Write usage notes: aim in 2 weeks: Draft of announcement and usage notes - ONGOING - feedback invited
  3. Kimberly, David, Laurent-Phlippe: Write some FAQs: what is the impact; why are we doing this ? Clarify the way a gene is related to a GO term
  4. Send notice
  5. Eric/Seth Adjust scripts
  6. Paul's group: Adjust enrichment tools

XenBase onboarding

ACTIONS

  • Seth will ask Malcom for his files, this will allow to test his pipeline
  • Kimberly and David will continue training XenBase curators, they will join the call
  • Jim is adding the Xenopus anatomy to the imports


Seth: no news from Malcom. Will follow up.

Discussion topics

Topics not discussed on last call

GO grant highlights and vision

Google doc with abridged grant with vision sections highlighted: https://docs.google.com/document/d/1t_Ube-ngprwBhyoKh5lDgtYYoQztl3yV1ETcfxrpquk

GOLr search

Collect current issues (eg genes that can not be found) to start improving it We dont know in which context this was added -> no discussion

Component for GO annotations in journals

Considering 1) easy to integrate web component and 2) current covid situation where submerged by literature difficult to mine retrospectively, try again to propose a very lightweight tool, probably optional, but that would allow an author to provide (gene, function) associations while submitting. Best journals to try ? biorxiv ? Judy - been asking for this to publishing houses for many years. -- Alliance Literature discussion is also looking into this

Pathway Genome Databases and the Alliance

See Chris' email

  • Explore bringing in other existing curated pathways in a similar way that we did for Reactome
  • Follow-up to Alliance call with Peter K. two weeks ago?

ECO and IEAs

In GPAD we mandate use of ECO over evidence codes. However, have we properly evaluated ECO for its use here? There is a massive mismatch in the GO meaning of IEA and the mapped term in ECO, see

  • Many Evidence codes do not match to the 3-letter evidence codes that we would map to
  • ACTION: Pascale to contact Michelle to set up some virtual meeting to discuss some issues we'd like to see fixed

users.yaml versus group-contacts.tsv

https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv https://github.com/geneontology/go-site/blob/master/metadata/users.yaml

See discussion in https://github.com/geneontology/go-site/pull/1447

  • users contain all users, including people not on the project anymore
  • Not sure where affiliations come from for eg Cath Brooksbank listed as GO_central).
  • users does not have GH handles
  • group-contacts includes only active members
  • 'Expertise' should like people's expertise or role (developer/curator)

-> How do we want to use those two files moving forward ? Do we need two files ?

  • Judy, Paul, Kimberly: would be nice to have expertise file
  • Paul: would like to use a GO term - high level term if possible
  • Maybe an activity for the GO virtual meeting

Publications

  • Val's matrix paper is available as a draft
  • Authors have reviewed and made comments
  • Do the GO PIs (besides Chris who is last author) also need to read?