WormBase-Caltech Weekly Calls

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GoToMeeting link: https://www.gotomeet.me/wormbase1

2020 Meetings



March 5, 2020

WormBase curation

  • Tim Schedl: WB needs to do more curation for phenotype and variation
  • Doing community curation, but not fast enough
  • Would like to work on more automation; e.g. having Textpresso return all sentences mentioning an allele in papers that are predicted to have phenotype data


  • Joesph may be able to meet with Raymond
  • How can the tool be maintained? If it can't it needs to be pulled

Single cell expression tool

  • Tool is here: http://de.wormcells.com/
  • What do we need to consider for pulling into WormBase?
  • Where does the data sit and how does the tool access it? Can we integrate the data more into WormBase (e.g. local curation databases)?
    • Would want it to be in sync with WormBase releases
    • May not need to reprocess with every release with current (small-ish) data set
  • Fully integrated tool versus an embedded tool?

Name service updates

  • For now we will stick to the CGIs that Juancarlos has built for variations and strains
  • Juancarlos can discuss with Matt R. and Sibyl the possibility of integrating API requests to the Name service into a CGI form for the OA

March 12, 2020

Storing invalid/avoided WBPersons and email addresses in Postgres

  • Currently Chris has been maintaining (on Google sheets) a list of papers, people, and email addresses to omit from future WormBase outreach requests
  • Valerio would like to add these to Postgres to keep a more central repository of them
  • Chris would still like to be able to readily update/edit the content of those lists

Updates on Alaska

Noctua GO-CAM updates

  • Noctua is a production tool available for annotations
  • Create as many interconnected models and make available for curators is the ongoing goal
  • React models are in the process of being imported
  • Real time validation messages as curation is being done is being worked on
  • Kimberly will send out the details for logging into Noctua