WormBase-Caltech Weekly Calls

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December 7th, 2017

Next Citace upload

  • Submit files to Wen by Jan 16, 2018
  • There shouldn't be model changes (that affect Caltech) for this next upload
  • Juancarlos goes on vacation Dec 19th

WB Curator candidate

  • April, could join WB for 1-2 years
  • Could possibly interview next Thursday
  • Could curate sequence features, enhancers, alleles/mutations/variations?
  • Could start in January

Expression clusters

  • Wen and Raymond discussed; will add an "uncertain" tag or something similar
  • Tag can be used to filter out datasets that are complex (like mixed cell/tissue types)

Automated descriptions & expression clusters

  • Many expression clusters are associated with infection
  • Such data not currently incorporated into automated gene descriptions
  • Wen can talk with Ranjana to incorporate (particularly for info-sparse genes)
  • Can use GO terms, but need to be careful about how they are applied (what relationships they have) to genes

Author First Pass Form

Overall approach

  • AFP form would move from being just a flagging pipeline towards a validation and data entry pipeline
  • Also move from free text boxes towards autocompletes, controlled vocabularies
  • If this is a validation and a portal for data entry forms, should we display everything we can mine?
  • Idea is to eventually create data entry forms for as many data types as possible
  • Long term goal would include linking to TPC and evidence sentences for validation
  • Data types not curated by WB would need to be re-evaluated: continue to mine but share with other curation groups? no longer mine? new WB objects or pages?
  • Periodically review the form and add/remove data types and curation forms as needed
  • Would be good to ask authors if they had to omit data from the recently published paper and if they want to micropublish

Questions

  • Question for WB curators: Are we missing data types?
  • Question for WB curators: Are there data types that we don't curate (e.g. domain analysis) but for which we could share mining information with other groups, e.g. UniProt?
  • Question for WB curators: Are there data types we should no longer mine?
  • Question for Wen: Does it make sense to include an afp flag for expression cluster?
  • Question for Karen: What afp tables are populated from the Genetics/G3 pipeline?
Details here: http://wiki.wormbase.org/index.php/Genetics_Markup_by_Textpresso_and_First_Pass
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