Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
 
[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
  
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[[WormBase-Caltech_Weekly_Calls_July_2021|July]]
  
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== July 1, 2021 ==
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[[WormBase-Caltech_Weekly_Calls_August_2021|August]]
  
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=== Importing genes for tm alleles from GeneACE ===
 
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* https://github.com/WormBase/website/issues/8262
 
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* Nightly dump currently excludes tm allele genes
 
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* Most tm (Mitani) alleles are not being manually connected to specific genes in GeneACE
 
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* Should pull the data from WS release (into Postgres) after the build has mapped the alleles to genes
 
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* ~100,000 alleles in Postgres; ~70,000 don't have a gene connection
 
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* Would Hinxton be willing to take WS-mapped allele-to-gene associations and populate GeneACE with associations not already in there?
 
  
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=== Citace upload ===
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== September 2, 2021 ==
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* Curators upload files to Spica for citace upload on Tuesday (July 6)
 
  
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=== Chen B1 kitchen Usage Considerations ===
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1. Moving forward with Alliance-friendly Person pages for community curation/authorship tracking<br>
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* Clean up after oneself.
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Needed for
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* Mark food storage with name and date.
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*AFP community curation
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* Mark storage drawers
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*microPublication author tracking for all species
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* Consumables
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*stub of person Alliance model already exists made by Adam http://dev.alliancegenome.org:11223/redoc#tag/Person
  
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Problems:
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*this is not an Alliance-wide interest for tracking their communities person; however, Alliance is not against person pages, just not supportive of developing this class into the many ways it will be useful for us and our communities
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*need to do this outside of Alliance
  
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== July 8, 2021 ==
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Action
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*Paul talks to zfin about interest in person pages
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*Juancarlos talks to Cecilia -need to know important elements to make author to person connection for biolink schema
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*Daniela and Karen invite PomBase to start harmonizing a person model, will send all Alliance an invite
  
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=== Alliance work ===
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Will do
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* Orange team presenting initial plans at Alliance PI meeting tomorrow
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*create biolink model based on current WB postgres/Caltech model
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* What working groups are still meeting? What are their responsibilities?
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*Adam will add tables when we have them
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** Expression
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** Variants
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2. Need to make sure CenGen stuff is included in this next release - need to request Todd to delay release until Adam returns from vacation to deal with it.
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** Disease & Phenotype
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** Technical working groups
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== September 16, 2021 ==
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*** Technical call
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*** Data quartermasters
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1. CeNGEN enriched genes per cell type data targeted for WS283.
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*** DevOps
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* Expression working group working on LinkML model with Gil (FB)
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2. some non-WB objects were present in the Strains and Variations lists coming from the nightly geneace dump.  Juancarlos changed the OA population script script to exclude those.
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** Includes work on antibody class, image class, movie class
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** Are species-specific anatomy ontologies being utilized for expression annotations or still just Uberon?
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== September 23, 2021 ==
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* Creating a curation interface/tool:
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** Will require loading auxiliary data types in addition to primary data types (e.g. if we are focused on disease annotation curation, we will need to load genes, alleles, strains, etc. in addition to the disease annotations themselves) to be available to make connections to
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1. Help desk ticket on citing the bar graph / FPKM expression data from selected modENCODE libraries - okay to just cite WormBase or should the user cite additional, or other, resources/publications?
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** One requirement already expressed by curators is the need to generate new entities, like alleles, and have them quickly (immediately?) available for use in curation
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* Okay to cite WormBase, but also ask user to cite the WormBase paper (for now NAR, but in the future, Genetics)
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** Maybe this could be handled by an Alliance central name server that mints new IDs (Alliance IDs and maybe also MOD IDs?) for the objects to make them available (also with a mechanism for these new objects/IDs to make their way back to the MODs as well)
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* Update the WB page on citing WormBase
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** Micropublication curation forms have tackled a lot of issues of collecting lexica and entity names and IDs; should consider work already done with Micropubs
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 +
2. CeNGEN data on Gene page for WS282. A short blog to highlight.
 +
 
 +
3. Server room in Braun power down for no apparent reason. Reset.

Revision as of 18:17, 23 September 2021

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March

April

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June

July

August


September 2, 2021

1. Moving forward with Alliance-friendly Person pages for community curation/authorship tracking
Needed for

Problems:

  • this is not an Alliance-wide interest for tracking their communities person; however, Alliance is not against person pages, just not supportive of developing this class into the many ways it will be useful for us and our communities
  • need to do this outside of Alliance

Action

  • Paul talks to zfin about interest in person pages
  • Juancarlos talks to Cecilia -need to know important elements to make author to person connection for biolink schema
  • Daniela and Karen invite PomBase to start harmonizing a person model, will send all Alliance an invite

Will do

  • create biolink model based on current WB postgres/Caltech model
  • Adam will add tables when we have them

2. Need to make sure CenGen stuff is included in this next release - need to request Todd to delay release until Adam returns from vacation to deal with it.

September 16, 2021

1. CeNGEN enriched genes per cell type data targeted for WS283.

2. some non-WB objects were present in the Strains and Variations lists coming from the nightly geneace dump. Juancarlos changed the OA population script script to exclude those.

September 23, 2021

1. Help desk ticket on citing the bar graph / FPKM expression data from selected modENCODE libraries - okay to just cite WormBase or should the user cite additional, or other, resources/publications?

  • Okay to cite WormBase, but also ask user to cite the WormBase paper (for now NAR, but in the future, Genetics)
  • Update the WB page on citing WormBase

2. CeNGEN data on Gene page for WS282. A short blog to highlight.

3. Server room in Braun power down for no apparent reason. Reset.

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