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? | + | * #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. | + | ** 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 == | == 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? | * 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 == | == C. briggsae == | ||
* piRNAs from Wen Tang (Ohio State University College of Medicine) https://github.com/WormBase/website/issues/8962 | * 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 == | == 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 == | ||
| + | WBPS has just launched a newsletter: You can subscribe [https://forms.gle/JgFWTgNv8FtnRsbF7 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 | ||
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
