WormBase-Caltech Weekly Calls January 2016

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January 7, 2016

SAB 2016

  • Schedule for Caltech talks:
    • SAB wiki: http://wiki.wormbase.org/index.php/2016_Advisory_Board_Meeting#Organisation_of_SAB_talks
    • Mary Ann, Chris, and Ranjana will discuss how to condense and streamline a presentation on community curation
    • We should have a talk about LEGO curation and pathways; Kimberly happy to present
      • LEGO adoption can be made cross-MOD and encourage collaboration
    • Maybe move micropublication talk to the end of the day; it will generate a lot of discussion; will try earlier in the day, 5 min talk, 5 min discussion before longer discussion
    • Maybe include discussion of expression summary description in Gary Williams talk about large scale expression data and visualization

Expression summaries

  • We want to consolidate large-scale expression data into a human-readable summary
  • Would be good to consolidate large-scale and small-scale expression data
  • We will adapt anatomical expression data for the SObA graph in future

Phenotype form

  • Now on sandbox, allows for RNAi transgene data
  • Will finish up, write documentation and make live
  • Will continue to send out e-mail requests

E-Merge Tech outsourcing

  • Company called Chris asking if we would want them to curate for us
  • Website: http://www.e-mergeglobal.com/
  • Will send them some phenotype curation for some papers and ask them to curate new papers, as a pilot
  • They will give us a cost estimate after a free pilot
  • Will see if it is cost-effective; good to know what they charge

January 14, 2016


  • Sent out slides for an overview talk of LEGO and the Noctua curation tool. (Kimberly)

Collecting info for SAB

January 21, 2016


  • Agenda items for literature curation overview
  • Todd will discuss outreach; Chris will talk to Todd about Caltech plans for outreach
  • Cataloging web usage on WB site, SPELL, etc.
  • We can discuss hosting all WB services and tools under the same web domain

Phenotype form

  • New phenotype form is live: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/allele_phenotype.cgi
  • We should point out response rate and paper coverage for community curation
  • How long can we expect to complete curation for phenotype with current pipelines
  • Can request PIs to check coverage of their allele phenotypes
  • We want this to lead to development of pathways

The Allied Genetics Conference, Orlando, July 2016

  • WB needs to decide who will go
  • Intermine project will have their own room
  • MODs will present together

January 28, 2016

SAB talks

  • Literature curation overview
    • General publication trends for C. elegans and data types
    • Our coverage, backlogs, outreach and curation efforts
  • Automated paper flagging and data identification (Karen)
    • SVM pipeline, keyword/string matching, data extraction
  • Automated gene descriptions (Ranjana)
    • Manual writing doesn't scale (currently ~5000 descriptions)
    • Amenable to automation (pulling together primary data for descriptions)
    • Mention gene description form
  • Community annnotation numbers (Mary Ann & Chris)
    • Other MODs efforts
    • WB submission forms and pilot response rates
  • Micropublications
    • Incentivizing community contributions
    • Micropublication form
    • How data is displayed on WormBase
  • LEGO
    • What it is, how it's different, why it's important
    • Priorities for LEGO models: signaling pathways, development, human disease biology (signal transduction, cilia pathology, etc.)
  • SObA
    • WB uses ontologies extensively, many annotations
    • Need an easy-to-consume data display
    • Have WOBr
    • Convention is to provide list format of data display, e.g. mouse expression summary
    • SObA: intuitive summary view of ontology annotations from gene perspective
    • Ontology trimmed to display only relevant ontology terms
  • What do we not have a talk about:
    • Human disease curation
    • SPELL/modSeek
    • Metabolite curation
  • Google Doc: https://docs.google.com/document/d/1uvSIIecWTmVjhUPA8f4FHIECSTJhloy8Z2ocujx96Uw/edit