Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
 
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
 +
[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
== April 1, 2021 ==
+
[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
  
=== Antibodies ===
+
[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
* Alignment of the antibody class to Alliance:
 
** Propose to move possible_pseudonym (192) and Other_animal (37) to remarks. Those tags are not currently used for curation.
 
*** Other animal is sometimes used for older annotations, e.g. authors say that the antibodies were raised both  in rats and rabbits. Standard practice would create 2 records, one for the rat antibody and one for the rabbit.
 
*** Possible pseudonym was used when  a curator was not able to unambiguously assign a previous antibody to a record. (we have a Other name -synonym- tag to capture unambiguous ones). When moving to remarks we can keep a controlled vocabulary for easy future parsing, e.g. “possible_pseudonym:”
 
** Antigen field: currently separated into Protein, peptide, and other_antigen (e.g.: homogenate of early C.elegans embryos, sperm). Propose to use just one antigen field to capture antigen info.
 
  
All changes proposed above were approved by the group
 
  
=== textpress-dev clean up ===
+
== July 1, 2021 ==
* Michael has asked curators to assess what they have on textpresso-dev as it will not be around forever :-(
 
* is it okay to transfer data and files we want to keep to tazendra? and then to our own individual machines?
 
* Direct access may be possible via Caltech VPN
 
* Do we want to move content to AWS? May be complicated; it is still easy and cheap to maintain local file systems/machines
 
  
=== Braun servers ===
+
=== Importing genes for tm alleles from GeneACE ===
* 3 servers stored in Braun server room; is there a new contact person for accessing these servers?
+
* https://github.com/WormBase/website/issues/8262
* Mike Miranda replacement just getting settled; Paul will find out who is managing the server room and let Raymond know
+
* 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 ===
 
=== Citace upload ===
* Next Friday, April 9th, by end of the day
+
* Curators upload files to Spica for citace upload on Tuesday (July 6)
* Wen will contact Paul Davis for the frozen WS280 models file
+
 
 +
=== 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 ===
 +
* 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