WormBase-Caltech Weekly Calls

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April 2015

April 2, 2015

Adding Species information to nightly geneace dumps

WormBase Ontology Browser WS248 online on Dev

  • Caveat: the rest of the WormBase data on the Dev site is WS247 (one release behind)
    • Would explain some discrepancies

Micropublication form

  • Daniela waiting for feedback from Paul's lab
  • Will send to Alison Frand and Elissa Hallem at UCLA to get input

Mary Ann's IWM abstract for community annotation

  • People can send comment over next day or two
  • Will make revisions and send around next week

April 9, 2015


  • Had some glitches with secondary hard drive this week, not sure what the problem is
  • /home2 directory is not intended as a primary storage; curators need to back data up
  • Paper PDFs stored on /home2 as the primary storage location
  • Papers are backed up on Athena (Wen's computer)
  • TIF files are stored on CDs
  • Main Tazendra hard drive backed up (RAIDed/mirrored), backed up nightly up to ~1 month (or 0.5 month), monthly for a year, but no older versions

Citace data upload

  • April 28th, 10am

Community Annotation Forms

  • Mary Ann's IWM (poster) abstract includes community annotation forms
  • Community annotation form list:
    • Micropublication
    • Gene Expression form (made 15 years ago); mostly not used; micropublication form could be co-opted
    • Gene description form (primarily for the community to edit the automated concise descriptions)
    • "Submit Data" list on WormBase (http://www.wormbase.org/about/userguide/submit_data#0--10)
  • Would be good to have a community annotation portal/landing page
  • Mary Ann will send around a summary of discussions about community annotation, along with prioritization of forms for curators and Juancarlos
  • Relevant curators should consider reviewing existing forms for updates


  • http://seek.princeton.edu/modSeek/
  • Princeton 6th year grad student developed it (leaving within 6 months)
  • "Seek" developed for human on microarray and RNAseq data
  • 5 model organisms in "modSeek": yeast, worm, fly, mouse, zebrafish
  • Pulls in data from Gene Expression Omnibus (GEO)
  • Analysis computed from raw data
  • Data from SPELL should be reasonably transferred to modSeek
  • We need to determine if WormBase data can be updated per release
  • Has text mining
  • Cross-species comparisons available