Difference between revisions of "WBConfCall 2023.03.02-Agenda and Minutes"
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== Help Desk == | == Help Desk == | ||
| − | * #8959 Is it possible to get WS276 JBrowse again? Scott set it up. | + | * #8959 Is it possible to get WS276 JBrowse again? |
| − | * #8965 I have tried downloading gene data to CVS or any other format. It only shows html format. It seems to be the links for all buttons are broken. This is probably related to the Caltech power outage today. | + | ** Scott set it up on a dev site. |
| − | * #8966 C. inopinata ortholog info? | + | * #8965 I have tried downloading gene data to CVS or any other format. It only shows html format. It seems to be the links for all buttons are broken. |
| − | + | ** This is probably related to the Caltech power outage today. | |
| − | + | * #8966 C. inopinata ortholog info? | |
| − | * | + | ** Scott responded. |
| − | * | ||
== S. ratti community curation == | == S. ratti community curation == | ||
| Line 23: | Line 22: | ||
** Researchers can generate GFF and Scott can load it into WormBase asap | ** Researchers can generate GFF and Scott can load it into WormBase asap | ||
** No need to create gene pages for them | ** No need to create gene pages for them | ||
| + | |||
| + | == New elegans assemblies == | ||
| + | * VC2010 (CGC1) from Erich Schwarz (Cornell) | ||
| + | ** Is it time for us to switch over? | ||
| + | * 20 new assemblies from Cristian Riccio (Sanger) https://github.com/WormBase/website/issues/8958 | ||
| + | ** Need to discuss this at a future Advisory Board meeting | ||
== IWM 2023 == | == IWM 2023 == | ||
| − | * Parasite workshop | + | * Parasite workshop invites WormBase to participate in their discussion on how to establish gold standards on parasite community curation. |
| + | ** Hinxton people will be there | ||
| + | * WormBase workshop approved. We need to decide on speakers. | ||
== WormBase ParaSite == | == WormBase ParaSite == | ||
WBPS has just launched a newsletter: You can subscribe [https://forms.gle/JgFWTgNv8FtnRsbF7 here]. Please spread the word! | WBPS has just launched a newsletter: You can subscribe [https://forms.gle/JgFWTgNv8FtnRsbF7 here]. Please spread the word! | ||
*Posted on WB blog | *Posted on WB blog | ||
| + | |||
| + | == REST API Broken == | ||
| + | * It was caused by tazendra down caused by the Caltech power outage at the Chen building | ||
| + | * Juancarlos and Valerio are migrating tazendra to a dockerized server | ||
Latest revision as of 17:59, 2 March 2023
Contents
Help Desk
- #8959 Is it possible to get WS276 JBrowse again?
- Scott set it up on a dev site.
- #8965 I have tried downloading gene data to CVS or any other format. It only shows html format. It seems to be the links for all buttons are broken.
- This is probably related to the Caltech power outage today.
- #8966 C. inopinata ortholog info?
- Scott responded.
S. ratti community curation
- What is the current WormBase-preferred method of receiving community-driven manual curation data for S. ratti and what types of changes are sufficient?
- Researchers can keep a slim version of GFF and a CSV about gene info including gene history and information needed to update gene pages. These can be stored on github
- Wen and Hinxton will communicate with them about setting a standard of community curation.
- Gene pages at the Alliance
- Would minimally require a Basic Gene Information (BGI) JSON submission to the Alliance File Management System (FMS)
- BGI entries minimally require primary key (curie), taxon, symbol, and SO term
- agr_schema ingest JSON specifications: https://github.com/alliance-genome/agr_schemas/tree/master/ingest
- gene.json specification: https://github.com/alliance-genome/agr_schemas/blob/master/ingest/gene/gene.json
- basicGeneticEntity specification: https://github.com/alliance-genome/agr_schemas/blob/master/ingest/basicGeneticEntity.json
C. briggsae
- piRNAs from Wen Tang (Ohio State University College of Medicine) https://github.com/WormBase/website/issues/8962
- Researchers can generate GFF and Scott can load it into WormBase asap
- No need to create gene pages for them
New elegans assemblies
- VC2010 (CGC1) from Erich Schwarz (Cornell)
- Is it time for us to switch over?
- 20 new assemblies from Cristian Riccio (Sanger) https://github.com/WormBase/website/issues/8958
- Need to discuss this at a future Advisory Board meeting
IWM 2023
- Parasite workshop invites WormBase to participate in their discussion on how to establish gold standards on parasite community curation.
- Hinxton people will be there
- WormBase workshop approved. We need to decide on speakers.
WormBase ParaSite
WBPS has just launched a newsletter: You can subscribe here. Please spread the word!
- Posted on WB blog
REST API Broken
- It was caused by tazendra down caused by the Caltech power outage at the Chen building
- Juancarlos and Valerio are migrating tazendra to a dockerized server
