Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
= 2021 Meetings =
  
= 2020 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
[[WormBase-Caltech_Weekly_Calls_January_2020|January]]
+
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
 +
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
== February 6, 2020 ==
+
[[WormBase-Caltech_Weekly_Calls_April_2021|April]]
  
=== Worcester Area Worm Meeting talk ===
+
[[WormBase-Caltech_Weekly_Calls_May_2021|May]]
* Confirmed for December 2020 or February 2021
 
  
=== Alaska software ===
+
[[WormBase-Caltech_Weekly_Calls_June_2021|June]]
* Code developed and maintained by Joseph, but not long term solution
 
* Raymond and Eduardo talked about taking it over
 
* Why have a web application vs. a command-line application?
 
** Wanted to make it easy, but also to capture meta data for WB
 
* Should/will find out from Joseph about how hard it is to maintain the software
 
* Maybe it could be taken over by Alliance, as RNA-Seq/Microarray meta data are getting harmonized
 
* Expression working group working with Brian Oliver to have GEO take in more structured meta data
 
* Array Express tried requiring more structured meta data, but authors stopped submitting
 
* May be possible to build a form that collects meta data while simultaneously submitting to GEO in parallel
 
  
  
== February 13, 2020 ==
+
== July 1, 2021 ==
  
=== Alliance Literature Group ===
+
=== Importing genes for tm alleles from GeneACE ===
* Held first meeting on Monday, February 10th
+
* https://github.com/WormBase/website/issues/8262
* Regular meetings will be on Tuesdays at 10am/1pm/6pm
+
* Nightly dump currently excludes tm allele genes
* Representatives from each group will give a brief overview of their literature pipelines before the group gets into details about deliverables
+
* Most tm (Mitani) alleles are not being manually connected to specific genes in GeneACE
* Question about centralized paper repository; group needs guidance from Alliance PIs on how to proceed
+
* 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?
  
=== ?Genotype class model ===
+
=== Citace upload ===
* [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq58NGp4eaXBT42Ch3gDE/edit?pli=1#bookmark=id.7r3e8pg19rd8 Proposal]
+
* Curators upload files to Spica for citace upload on Tuesday (July 6)
* Can aim to implement for WS277 but may have to wait until WS278
 
  
=== Genotype OA ===
+
=== Chen B1 kitchen Usage Considerations ===
* Will put documentation [[Genotype|here]]
+
* Clean up after oneself.
 +
* Mark food storage with name and date.
 +
* Mark storage drawers
 +
* Consumables
  
=== WB All-Hands Meeting ===
 
* [https://doodle.com/poll/7f65p4ba6d88ztzt Doodle poll]
 
* Any thoughts at this point?  Still need to discuss with Hinxton, Toronto.
 
  
 +
== July 8, 2021 ==
  
== February 20, 2020 ==
+
=== 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
  
=== Genotype ===
+
== July 15, 2021 ==
* We will equate superficially similar/identical genotypes for now
 
* What if labs sequence strains later and find out more?
 
* Labs will have to report strains and their sequence and we back-curate accordingly
 
  
=== VC2010 assembly genes ===
+
=== hlh-34 expression ===
* WormMine now returning double the gene count for C. elegans genes because of incorporation of newest VC2010 assembly
+
* 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.
* How to best handle these "extra" genes?
+
* Oliver is putting together a micropub to clarify the issue
* We could make different species entries that specify the assembly version
+
* 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 ==
  
== February 27, 2020 ==
+
=== 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
=== Genotype ===
+
* Can we copy files to tazendra?
* [[Genotype|Genotype Wiki page]] updated
+
* If so, do we need to have a more general approach/strategy other than creating new folders in the individual curator directories?
* Will start building Genotype OA
+
* Are there any size considerations for what we copy over?  There are 1.1T free in /home2 which is not backed up
 
 
=== Outreach inbox ===
 
* 65 unread messages pertaining to AFP, some dating back to June. Can we clean these up?
 
* Many are bounced emails messages
 
* Do we want a common place to track bad/bouncing email addresses? We need to distinguish addresses that bounce for policy/SPAM reasons versus those that are likely outdated or no longer in use.
 

Latest revision as of 18:00, 22 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