WormBase-Caltech Weekly Calls

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Previous Years

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2013 Meetings

2014 Meetings

2015 Meetings

January 2015

January 8, 2015

Community annotation

  • author participation
    • Cecilia: still lots of work to process data, need to process data submitted by authors
    • old data kept for history and for comparison
    • people mess up institution names - is being changed to a controlled vocabulary
    • campus addresses also not standardized - organize/create address fields, e.g., street address, mail-code, etc.,
    • add example address
    • ~10 author submissions a week
    • most curation is extracting people information from papers (~800 week), as automated as possible right now - people and affiliation are extracted from xml, but still needs to be parsed
    • how to mine author data from other sources (institution, laboratory); important to get laboratory address for sending strains; two sets of data- easy to mine from laboratory, those not in a registered lab

Cross-product development


  • embarking on cross-product generation- ex., male tail, versus hermaphrodite tail - better to have one 'tail' and add modifiers
  • wants to move to OWL now; comment is that obo relationships not directly translatable into OWL
  • Uberon has elegans anatomy


  • starting to work with Chris and Karen on developing cross-products, still in exploration phase
  • not looking at OWL yet
  • will get relationships from Raymond

Sequence feature curation

Daniela, Gary, Xiaodong, Mary Ann are validating papers as positive/negative in curation status form. As soon as ready Mary Ann/Gary will start curating

Rose alleles

  • 150,000 new alleles, Mary Ann done just all bar 12 of them in time for WS247
  • phenotypes were only reported for a small fraction

CGC strains

Mary Ann received latest update, CGC very busy with new gene engineering technique

WB WBook chapters

Main outline here

  • Gene Function and Interaction google docs (Chris, Gary S., Karen, Kimberly)


  • Pathways and Processes (Karen) here
  • Expression (Daniela)


  • Hobert- micropublication for expression = small facts, data will never be published (Daniela)
  • Community annotation not linked to a publication
  • a couple models
    • WB captures submissions blind
    • WB reviews
  • need to establish microattributions to increase the value of submissions
  • involve semi-peer review through automated feed back to scientists who've worked on the gene, cell, entity, etc.
  • need to set up a pilot, to see how popular

Picture curation

  • for topic curation
    • want to annotate figures with genes
    • want dynamic display with slide show, different highlighted figures,
  • community voting - crowdsourcing
  • WB-blessed image represented through wikipathways


Continuing work on the new GO model


  • management of automated descriptions with Ranjana
  • phenotype requests through RNAi and allele phenotype

Automated descriptions

  • playing with pulling out useful data to add to description automation