Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
 
[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
 +
[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
  
== May 13, 2021 ==
+
[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
  
=== Textpresso supplement ===
 
* Due Monday
 
* Michael working with Paul S
 
  
=== AWS credits ===
+
== July 1, 2021 ==
* Michael and Valerio were awarded AWS credits, more than they can use
 
* Maybe they can be repurposed
 
* Valerio will play around with AWS to determine the best/cheapest configuration before migrating to the Alliance
 
  
=== Automated gene descriptions ===
+
=== Importing genes for tm alleles from GeneACE ===
* Will the Alliance ever accommodate non-elegans worm species? Can we port over the computed/derived descriptions for non-elegans species to the Alliance?
+
* https://github.com/WormBase/website/issues/8262
* Maybe have clade-specific descriptions based on the popular model (worms based on C. elegans); may be provided in MOD portal page(s)
+
* Nightly dump currently excludes tm allele genes
* May be the focus of an Alliance supplement
+
* Most tm (Mitani) alleles are not being manually connected to specific genes in GeneACE
* We want a flexible pipeline that can be configured depending on availability of data (e.g. protein domains)
+
* Should pull the data from WS release (into Postgres) after the build has mapped the alleles to genes
 +
* ~100,000 alleles in Postgres; ~70,000 don't have a gene connection
 +
* Would Hinxton be willing to take WS-mapped allele-to-gene associations and populate GeneACE with associations not already in there?
  
=== IWM 2021 WB Workshop ===
+
=== Citace upload ===
* Scheduled for June 22, 2021
+
* Curators upload files to Spica for citace upload on Tuesday (July 6)
* Session begins at 8:30am Pacific / 11:30am Eastern / 4:30pm UK
+
 
* Workshop runs for 90 minutes: 4 15-minute talks followed by 30 minute Q&A session
+
=== Chen B1 kitchen Usage Considerations ===
* Here is the submitted workshop schedule:
+
* Clean up after oneself.
11:30 am (EDT) Magdalena Zarowiecki, EMBL-EBI, A whistle-stop tour of all the types of data you can find in WormBase
+
* Mark food storage with name and date.
11:45 am (EDT) Chris Grove, California Institute of Technology, Researching transcriptional regulation using WormBase transcription factors, TF binding sites and the modENCODE data
+
* Mark storage drawers
12:00 pm (EDT) Ranjana Kishore, California Institute of Technology, Comparative genomics and disease research using Alliance of Genome Resources
+
* Consumables
12:15 pm (EDT) Daniela Raciti, California Institute of Technology, How can you contribute? Community curation and tools, and the author-first-pass (AFP) pipeline
+
 
12:30 pm (EDT) Chris Grove, California Institute of Technology, Open Discussion / Q & A
+
 
 +
== July 8, 2021 ==
 +
 
 +
=== Alliance work ===
 +
* Orange team presenting initial plans at Alliance PI meeting tomorrow
 +
* What working groups are still meeting? What are their responsibilities?
 +
** Expression
 +
** Variants
 +
** Disease & Phenotype
 +
** Technical working groups
 +
*** Technical call
 +
*** Data quartermasters
 +
*** DevOps
 +
* Expression working group working on LinkML model with Gil (FB)
 +
** Includes work on antibody class, image class, movie class
 +
** Are species-specific anatomy ontologies being utilized for expression annotations or still just Uberon?
 +
* Creating a curation interface/tool:
 +
** 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
 +
** 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
 +
** 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)
 +
** Micropublication curation forms have tackled a lot of issues of collecting lexica and entity names and IDs; should consider work already done with Micropubs
 +
 
 +
== July 15, 2021 ==
 +
 
 +
=== hlh-34 expression ===
 +
* Rebecca Mcwhirter (Miller lab) contacted WB saying that the annotations to AVJ for hlh-34 are incorrect. 4 evidences list AVJ -> the authors of the first paper that describes hlh-34 expression (Cunningham et al, 2012 : http://dx.doi.org/10.1016/j.cmet.2012.05.014) had to pick one neuron per reviewer's request. The neuron should instead be AVH.
 +
* Oliver is putting together a micropub to clarify the issue
 +
* How to deal with existing  annotations? Add a comment in the remarks that points to the microPub? remove AVJ from the anatomy association list?
 +
* Should we also add public comments to the relevant papers?
 +
 
 +
== July 22, 2021 ==
 +
 
 +
=== Copying data from textpresso-dev to tazendra ===
 +
* Michael has been asking curators to retrieve any data they might still want on textpresso-dev before the machine dies
 +
* Can we copy files to tazendra?
 +
* If so, do we need to have a more general approach/strategy other than creating new folders in the individual curator directories?
 +
* Are there any size considerations for what we copy over?  There are 1.1T free in /home2 which is not backed up
 +
 
 +
== July 29, 2021 ==
 +
 
 +
=== Textpresso Dev machine retiring ===
 +
* Need to work out when and how to move things off the machine before retiring for good
 +
 
 +
=== Proxies for Caltech-hosted tools broken ===
 +
* Several Caltech CGI tools using a proxy on WormBase site are broken (throwing 504 Gateway Time-out or Server Error)
 +
* Affected tools:
 +
** https://wormbase.org/tools/soba/soba.cgi?action=Gene+Pair+to+SObA+Graph
 +
** https://wormbase.org/tools/soba/soba.cgi?action=Terms+to+SObA+Graph
 +
** https://wormbase.org/tools/rnaseq/expression_dataset_locator.cgi
 +
** https://wormbase.org/tools/rnaseq/fpkmmine.cgi
 +
** https://wormbase.org/tools/ontology_browser
 +
 
 +
=== 2021 Genetics paper ===
 +
* Paul D has asked for contributions (~200 words each)
 +
* Paul's preliminary suggested sections:
 +
** CeNGen (CalTech)
 +
** Expression & Transcription (Wen)
 +
*** Spell (Wen)
 +
** SimpleMine (CalTech Wen)
 +
** WormiCloud - (Jae/Valerio Caltech)
 +
** Vennter (Jae/Caltech)
 +
** Gene Name Sanitizer (Wen/Raymond/Caltech?)
 +
** VFP (Valerio)
 +
** Author first pass (Daniela)
 +
** Human disease (Ranjana)
 +
** Molecular and genetic interactions (You/Chris)
 +
** Pathways and Processes (Karen)
 +
** Anatomy and Cell (Raymond)
 +
* Now have 'Community Curation' for AFP and other community curation
 +
* Also, gene descriptions section

Latest revision as of 18:30, 29 July 2021

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings

2021 Meetings

January

February

March

April

May

June


July 1, 2021

Importing genes for tm alleles from GeneACE

  • https://github.com/WormBase/website/issues/8262
  • Nightly dump currently excludes tm allele genes
  • Most tm (Mitani) alleles are not being manually connected to specific genes in GeneACE
  • Should pull the data from WS release (into Postgres) after the build has mapped the alleles to genes
  • ~100,000 alleles in Postgres; ~70,000 don't have a gene connection
  • Would Hinxton be willing to take WS-mapped allele-to-gene associations and populate GeneACE with associations not already in there?

Citace upload

  • Curators upload files to Spica for citace upload on Tuesday (July 6)

Chen B1 kitchen Usage Considerations

  • Clean up after oneself.
  • Mark food storage with name and date.
  • Mark storage drawers
  • Consumables


July 8, 2021

Alliance work

  • Orange team presenting initial plans at Alliance PI meeting tomorrow
  • What working groups are still meeting? What are their responsibilities?
    • Expression
    • Variants
    • Disease & Phenotype
    • Technical working groups
      • Technical call
      • Data quartermasters
      • DevOps
  • Expression working group working on LinkML model with Gil (FB)
    • Includes work on antibody class, image class, movie class
    • Are species-specific anatomy ontologies being utilized for expression annotations or still just Uberon?
  • Creating a curation interface/tool:
    • 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
    • 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
    • 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)
    • Micropublication curation forms have tackled a lot of issues of collecting lexica and entity names and IDs; should consider work already done with Micropubs

July 15, 2021

hlh-34 expression

  • Rebecca Mcwhirter (Miller lab) contacted WB saying that the annotations to AVJ for hlh-34 are incorrect. 4 evidences list AVJ -> the authors of the first paper that describes hlh-34 expression (Cunningham et al, 2012 : http://dx.doi.org/10.1016/j.cmet.2012.05.014) had to pick one neuron per reviewer's request. The neuron should instead be AVH.
  • Oliver is putting together a micropub to clarify the issue
  • How to deal with existing annotations? Add a comment in the remarks that points to the microPub? remove AVJ from the anatomy association list?
  • Should we also add public comments to the relevant papers?

July 22, 2021

Copying data from textpresso-dev to tazendra

  • Michael has been asking curators to retrieve any data they might still want on textpresso-dev before the machine dies
  • Can we copy files to tazendra?
  • If so, do we need to have a more general approach/strategy other than creating new folders in the individual curator directories?
  • Are there any size considerations for what we copy over? There are 1.1T free in /home2 which is not backed up

July 29, 2021

Textpresso Dev machine retiring

  • Need to work out when and how to move things off the machine before retiring for good

Proxies for Caltech-hosted tools broken

2021 Genetics paper

  • Paul D has asked for contributions (~200 words each)
  • Paul's preliminary suggested sections:
    • CeNGen (CalTech)
    • Expression & Transcription (Wen)
      • Spell (Wen)
    • SimpleMine (CalTech Wen)
    • WormiCloud - (Jae/Valerio Caltech)
    • Vennter (Jae/Caltech)
    • Gene Name Sanitizer (Wen/Raymond/Caltech?)
    • VFP (Valerio)
    • Author first pass (Daniela)
    • Human disease (Ranjana)
    • Molecular and genetic interactions (You/Chris)
    • Pathways and Processes (Karen)
    • Anatomy and Cell (Raymond)
  • Now have 'Community Curation' for AFP and other community curation
  • Also, gene descriptions section