Manager Call 2020-04-15: Difference between revisions
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* Agenda: Pascale | * Agenda: Pascale | ||
* Minutes: | * Minutes: Pascale | ||
* Present: | * 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 | # Pascale/Seth: Write formal specs documentation - '''ONGOING - some small fixes needed''' | ||
# Kimberly, David, Laurent-Phlippe: Write usage notes: aim in 2 weeks | # 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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* Seth will ask Malcom for his files, this will allow to test his pipeline | * 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 | * 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== | ==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 | ||
=== | * '''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/ | 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 12:08, 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:
- Pascale/Seth: Write formal specs documentation - ONGOING - some small fixes needed
- Kimberly, David, Laurent-Phlippe: Write usage notes: aim in 2 weeks: 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
- Send notice
- Eric/Seth Adjust scripts
- 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 handlesgroup-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?