WormBase-Caltech Weekly Calls

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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

Raymond

• 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

Gary

• 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

WB WBook chapters

Main outline here

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

Picture curation

• for topic curation
  • want to annotate figures with genes
  • want dynamic display with slide show, different highlighted figures, crowdsourcing

• for mutant phenotype