Difference between revisions of "WBConfCall 2021.10.07-Agenda and Minutes"
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** Do we have https downloads links available from the WormBase home page yet? | ** Do we have https downloads links available from the WormBase home page yet? | ||
** Should all WormBase downloads be available from the same site? | ** Should all WormBase downloads be available from the same site? | ||
| + | * Related to [https://github.com/WormBase/website/issues/8355 Add links to the https-driven downloads site] | ||
=== updating laboratory information === | === updating laboratory information === | ||
| Line 35: | Line 36: | ||
Additional C. briggsae operons | Additional C. briggsae operons | ||
| + | |||
Large batch of new strains and variants from KO consortium, CGC and NBRP | Large batch of new strains and variants from KO consortium, CGC and NBRP | ||
| + | == Any Other Business == | ||
| − | + | WormBase's All Species page (https://wormbase.org/species/all#0123--10-02) updated with new genomes from WB ParaSite release 16 | |
Todd and Magz set the 4 release dates for 2022. | Todd and Magz set the 4 release dates for 2022. | ||
| Line 44: | Line 47: | ||
Many thanks for being patient with the EBI FTP migration, which was very unfortunately timed. | Many thanks for being patient with the EBI FTP migration, which was very unfortunately timed. | ||
| + | == Minutes == | ||
| + | |||
| + | === Help Desk === | ||
| + | |||
| + | ==== Web of Science Data Citation Index ==== | ||
| + | * Having some FTP issues | ||
| + | * Also, was accessing a WS276 file; doesn't seem to be a current equivalent: | ||
| + | ** ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/species/c_elegans/PRJNA13758/annotation/c_elegans.PRJNA13758.WS276.reuters_citation_index.xml.gz | ||
| + | * Todd: These should be automatically updated; file name may have diverged and broken the link | ||
| + | |||
| + | ==== FTP issues; migration to HTTPS download site ==== | ||
| + | * Paul D added link from "Downloads" to User Guide with relevant links | ||
| + | * When WS282 is released, the live link will be added (today or tomorrow) | ||
| + | |||
| + | ==== Changing lab representative ==== | ||
| + | * Who curates this? Cecilia curates lab information, but not sure if she curates this | ||
| + | * Tim S sends monthly updates; may be a data update lag | ||
| + | * Paul D will check on update to data | ||
| + | * <b>Resolved</b> ticket as new assignment is in the October Update for Cecilia to process. | ||
| + | |||
| + | ==== Community Forum issues ==== | ||
| + | * User unable to make some comments; Todd will look into it and get back to user | ||
| + | * Unable to post links | ||
| + | |||
| + | ==== ePCR, GMap, and Tree Display issues ==== | ||
| + | * Adam looked into Tree Display issue; may be able to provide similar info from Datomic | ||
| + | * Adam would prefer we deprecate/retire Tree Display and remove one more dependency on ACEDB | ||
| + | * Todd: these are periodic, recurring issues about depending on ACEDB | ||
| + | ** Could possibly setup multiple redundancies providing ACEDB, but may not be worth it | ||
| + | * How important are these tools to WB and users? | ||
| + | * Curators really like the Tree Display | ||
| + | ** Are there current alternatives to Tree Display? | ||
| + | ** Adam can demo using REST endpoint for Datomic | ||
| + | ** Thomas Down had created a Datomic tree viewer; not sure what the state of that tool is | ||
| + | ** Maybe we can provide link to REST endpoint from Adam under the WB Tools menu | ||
| + | * We can add to Tree Display a REST endpoint link for that specific object in case Tree Display falls over | ||
| + | |||
| + | === Genetics Manuscript === | ||
| + | * Just about ready, Paul D finishing up for submission | ||
| + | |||
| + | === WS283 build === | ||
| + | * Hinxton received Caltech data and working on build | ||
| + | * Variation/Allele model changes | ||
| + | * New C. briggsae operons set | ||
| + | * Large batch of new strains from KO consortium, CGC, and NBP | ||
| + | * Can write up as a blog post | ||
| − | == | + | === All Species page Downloads widget === |
| + | * https://wormbase.org/species/all#0123--10-2 | ||
| + | * How do we edit? Todd will look into it and discuss with Hinxton (Dio and Magdalena) | ||
| + | * Could this be automatically updated? | ||
| + | * WB Parasite and WB have out of sync releases; maybe we can use an API endpoint to populate the data | ||
| + | |||
| + | === WB literature migration to Alliance === | ||
| + | * What identifiers of papers are useful at the Alliance? Should we port everything over? | ||
| + | * We have WBPaper IDs, PMIDs, DOIs | ||
| + | * We have legacy CGC IDs, meeting abstracts with our own custom format | ||
| + | ** Are these legacy IDs useful to port over or should they get tossed? | ||
| + | ** These would be imported as cross references, which requires entry in the resourceDescriptors.yaml | ||
| + | ** Could add a WB prefix | ||
| + | * We will keep meeting abstracts with WBPaper ID, but maybe we lose CGC; what about abstract custom title format? e.g. "wm2015ab797" | ||
| + | * If a list of papers is returned, can one tell if it is a, e.g., PubMed ID vs a meeting abstract | ||
| + | * Meeting abstracts still have a "Meeting abstract" type that would be stored at the Alliance | ||
| + | * Can the IDs be stored in some other text field (not officially as an ID) just to keep it? | ||
Latest revision as of 08:58, 8 October 2021
Contents
Agenda and Minutes
Helpdesk
ftp site questions
- Wormbase - Data Citation Index [Web of Science]
- Do we still have files that are agnostic wrt release name but always either current or current development?
- Hello, I am trying to download all th...
- Do we have https downloads links available from the WormBase home page yet?
- Should all WormBase downloads be available from the same site?
- Related to Add links to the https-driven downloads site
updating laboratory information
user accounts at WB and the Alliance
e-PCR and gmap tools throwing errors
tree display
WB Genetics manuscript
Thank you so much to everyone for your contributions to content and edits! [Paul D]
Build WS283
Build WS283 has started in Hinxton
New and interesting things: Several model changes, eg to variants
Additional C. briggsae operons
Large batch of new strains and variants from KO consortium, CGC and NBRP
Any Other Business
WormBase's All Species page (https://wormbase.org/species/all#0123--10-02) updated with new genomes from WB ParaSite release 16
Todd and Magz set the 4 release dates for 2022.
Many thanks for being patient with the EBI FTP migration, which was very unfortunately timed.
Minutes
Help Desk
Web of Science Data Citation Index
- Having some FTP issues
- Also, was accessing a WS276 file; doesn't seem to be a current equivalent:
- Todd: These should be automatically updated; file name may have diverged and broken the link
FTP issues; migration to HTTPS download site
- Paul D added link from "Downloads" to User Guide with relevant links
- When WS282 is released, the live link will be added (today or tomorrow)
Changing lab representative
- Who curates this? Cecilia curates lab information, but not sure if she curates this
- Tim S sends monthly updates; may be a data update lag
- Paul D will check on update to data
- Resolved ticket as new assignment is in the October Update for Cecilia to process.
Community Forum issues
- User unable to make some comments; Todd will look into it and get back to user
- Unable to post links
ePCR, GMap, and Tree Display issues
- Adam looked into Tree Display issue; may be able to provide similar info from Datomic
- Adam would prefer we deprecate/retire Tree Display and remove one more dependency on ACEDB
- Todd: these are periodic, recurring issues about depending on ACEDB
- Could possibly setup multiple redundancies providing ACEDB, but may not be worth it
- How important are these tools to WB and users?
- Curators really like the Tree Display
- Are there current alternatives to Tree Display?
- Adam can demo using REST endpoint for Datomic
- Thomas Down had created a Datomic tree viewer; not sure what the state of that tool is
- Maybe we can provide link to REST endpoint from Adam under the WB Tools menu
- We can add to Tree Display a REST endpoint link for that specific object in case Tree Display falls over
Genetics Manuscript
- Just about ready, Paul D finishing up for submission
WS283 build
- Hinxton received Caltech data and working on build
- Variation/Allele model changes
- New C. briggsae operons set
- Large batch of new strains from KO consortium, CGC, and NBP
- Can write up as a blog post
All Species page Downloads widget
- https://wormbase.org/species/all#0123--10-2
- How do we edit? Todd will look into it and discuss with Hinxton (Dio and Magdalena)
- Could this be automatically updated?
- WB Parasite and WB have out of sync releases; maybe we can use an API endpoint to populate the data
WB literature migration to Alliance
- What identifiers of papers are useful at the Alliance? Should we port everything over?
- We have WBPaper IDs, PMIDs, DOIs
- We have legacy CGC IDs, meeting abstracts with our own custom format
- Are these legacy IDs useful to port over or should they get tossed?
- These would be imported as cross references, which requires entry in the resourceDescriptors.yaml
- Could add a WB prefix
- We will keep meeting abstracts with WBPaper ID, but maybe we lose CGC; what about abstract custom title format? e.g. "wm2015ab797"
- If a list of papers is returned, can one tell if it is a, e.g., PubMed ID vs a meeting abstract
- Meeting abstracts still have a "Meeting abstract" type that would be stored at the Alliance
- Can the IDs be stored in some other text field (not officially as an ID) just to keep it?
