WormBase-Caltech Weekly Calls

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May 5, 2015

Tissue enrichment tool

  • Some slight modifications have been made
  • Raymond/Juancarlos request testing
  • Made adjustments to gene name handling
  • Tool could go live for the next release
  • Data will remain frozen at WS252

Gene summaries

  • Paul asked Norbert about gene descriptions
  • FB has been getting good community response for contributing gene descriptions
  • Automation still sounds like the right way to go
  • Ranjana will look at summaries at other MOD sites

Phenotype display

  • MGI/MGD had a graph display of phenotype ontology (Paul S.)
  • Made phenotype ontology slim for the summary heatmaps
  • How do all of the MODs display phenotypes?

Progress reports

  • Curators can write a paragraph on innovation
    • Community curation (report numbers)
    • WOBr
    • SObA
    • Automated descriptions
    • Micropublications

Curation pipeline comparisons

  • Would be nice to compare how MODs prioritize curation, triage papers, etc.
  • How many MODs curate paper-by-paper (for all datatypes at once) vs. our method, by datatype?
    • WB & MGI curate by datatype, most others by paper (for all datatypes)
  • How are all MODs doing in terms of paper coverage?
    • Do we need more manual effort, more automation? How much, given cost of each?


  • SGD uses SPELL but does not develop

May 12, 2016

Communication tools for umod teams

Human Disease working group meeting

  • Next Monday and Tuesday, in Kerckhoff 024
  • Curators will review data models for human disease at each site
  • Brainstorming session for future plans
  • Possibility of molecule-disease interactions ("exacerbated by", "ameliorated by")


  • Wen came across metabolic profiling papers while looking for proteomics papers
  • Wen will send to Karen, who is managing metabolites as part of molecule class
  • BIGG database, a new metabolite database (http://bigg.ucsd.edu/)

Progress Report

  • Send Paul progress report blurbs in next week (by Thursday)

Cross MOD call

  • Reviewed FlyBase and Rat Genome Database this week
  • Will review SGD and MGI next week
  • Suzi Lewis asking about Intermine instances; what can Mine do that the Base cannot, and vice versa?
  • Other MODs have more fully functional and fully populated InterMine instances



BioCADDIE developers are currently working on indexing datasets requested by the NIH for inclusion in a June 30 Prototype test. After then they will reach out to us to look into the WormData (micropublication) indexing.