Difference between revisions of "WBConfCall 2020.03.19-Agenda and Minutes"
From WormBaseWiki
Jump to navigationJump to search(8 intermediate revisions by 4 users not shown) | |||
Line 1: | Line 1: | ||
= Agenda and Minutes = | = Agenda and Minutes = | ||
+ | |||
+ | == Looking for new ways to allocate students working remotely == | ||
+ | * Train students to do curation on phenotype and GO. | ||
+ | ** Kimberly will send out the GO micropub. | ||
== Proposed New File Format for GO == | == Proposed New File Format for GO == | ||
Line 6: | Line 10: | ||
** github ticket for comments: https://github.com/geneontology/go-annotation/issues/2864 | ** github ticket for comments: https://github.com/geneontology/go-annotation/issues/2864 | ||
*** Comments or questions accepted through the end of March | *** Comments or questions accepted through the end of March | ||
+ | |||
+ | * GAF files will still be supported in the future for current tools. | ||
+ | * RO is already used in WB, but not for annotation extension. | ||
Line 11: | Line 18: | ||
Jae would like to receive these digest emails with higher frequency (currently once a month). Need to discuss this with other curators and Hinxton | Jae would like to receive these digest emails with higher frequency (currently once a month). Need to discuss this with other curators and Hinxton | ||
+ | |||
+ | * Everybody agreed on weekly alerts. They will be set up for the next AFP release | ||
==WS277 upload== | ==WS277 upload== | ||
Line 17: | Line 26: | ||
*The new code reflects the change for orthology that now selects only those human orthologs for elegans genes that have been called by 3 or more methods. | *The new code reflects the change for orthology that now selects only those human orthologs for elegans genes that have been called by 3 or more methods. | ||
*We will alert Users to this change for WS276 descriptions via release notes, blog etc. | *We will alert Users to this change for WS276 descriptions via release notes, blog etc. | ||
+ | |||
+ | * We decided to wait for the previous release files. Wen is already generating her files from the staging ftp site. | ||
+ | |||
+ | == Human gene IDs from HGNC == | ||
+ | * Human genes should be referenced as HGNC ID objects in WB curation database. | ||
+ | * We are currently using Ensembl IDs. | ||
+ | * We decided that Hinxton will take care of generating a new file that will be imported into the OA. | ||
+ | |||
+ | == Mailing list issues == | ||
+ | * Caltech accounts are being blocked by Google. Everybody should subscribe to the lists with their google accounts (WB.org or other) | ||
+ | |||
+ | == WB f2f meeting == | ||
+ | * Topic specific calls could be easier to manage. | ||
+ | |||
+ | == Github tickets == | ||
+ | |||
+ | - https://github.com/WormBase/website/issues/7627 | ||
+ | Seems to be a gene descriptions issue. We are not including references atm. | ||
+ | |||
+ | - https://github.com/WormBase/website/issues/7626 - Paul D. Responded | ||
+ | |||
+ | - https://github.com/WormBase/website/issues/7623 - Paul D. Responded | ||
+ | |||
+ | - https://github.com/WormBase/website/issues/7621 - Non Help-Desk, Human disease widget | ||
+ | |||
+ | - https://github.com/WormBase/website/issues/7619 - Sibyl resolved and responded | ||
+ | |||
+ | - https://github.com/WormBase/website/issues/7609 - Closed | ||
+ | Changed gene descriptions code to pick orthologs only if they have number of methods >= 3 |
Latest revision as of 18:23, 24 March 2020
Contents
Agenda and Minutes
Looking for new ways to allocate students working remotely
- Train students to do curation on phenotype and GO.
- Kimberly will send out the GO micropub.
Proposed New File Format for GO
- GO has put a draft of the GPAD/GPI 2.0 file specifications on github for comment
- https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md
- github ticket for comments: https://github.com/geneontology/go-annotation/issues/2864
- Comments or questions accepted through the end of March
- GAF files will still be supported in the future for current tools.
- RO is already used in WB, but not for annotation extension.
AFP alerts for new positive papers for datatypes
Jae would like to receive these digest emails with higher frequency (currently once a month). Need to discuss this with other curators and Hinxton
- Everybody agreed on weekly alerts. They will be set up for the next AFP release
WS277 upload
Gene descriptions:
- As of Wed. 03/18, 3pm PST, there are no WS276 files to run our pipeline on, so we have run the new code on WS275 files.
- The new code reflects the change for orthology that now selects only those human orthologs for elegans genes that have been called by 3 or more methods.
- We will alert Users to this change for WS276 descriptions via release notes, blog etc.
- We decided to wait for the previous release files. Wen is already generating her files from the staging ftp site.
Human gene IDs from HGNC
- Human genes should be referenced as HGNC ID objects in WB curation database.
- We are currently using Ensembl IDs.
- We decided that Hinxton will take care of generating a new file that will be imported into the OA.
Mailing list issues
- Caltech accounts are being blocked by Google. Everybody should subscribe to the lists with their google accounts (WB.org or other)
WB f2f meeting
- Topic specific calls could be easier to manage.
Github tickets
- https://github.com/WormBase/website/issues/7627
Seems to be a gene descriptions issue. We are not including references atm.
- https://github.com/WormBase/website/issues/7626 - Paul D. Responded
- https://github.com/WormBase/website/issues/7623 - Paul D. Responded
- https://github.com/WormBase/website/issues/7621 - Non Help-Desk, Human disease widget
- https://github.com/WormBase/website/issues/7619 - Sibyl resolved and responded
- https://github.com/WormBase/website/issues/7609 - Closed
Changed gene descriptions code to pick orthologs only if they have number of methods >= 3