WormBase-Caltech Weekly Calls November 2016

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November 3, 2016

Micropublication update

  • First Nemametrix micro in for WS257
  • Two lined up for WS258
  • Karen and Daniela in touch with e-publishing platforms (HighWire [1], Collaborative knowledge foundation[2]), to set up collaborations for the Micropublication: biology e-journal [3]
  • Discussing putting worm breeder's gazette articles into micropublications
  • Collaborative knowledge foundation is a non-profit publisher, some former member of Highwire
  • Would be good to have a faster way to display micropublications (standard WB pipeline needs at least 4 months)
    • Could use content management systems (CMSs)
  • Maybe will propose a workshop for the 2017 international C. elegans meeting

Intellectual (Person) Lineage

Tim Schedl visiting WB tomorrow

  • Will come to WB CIT around 11:30am

November 10, 2016

Update from AGR portal use case working group

  • Preparing document for the Dec. 6th leadership meeting
  • Need to address several questions about prototype development process
  • Communication has been insufficient, leading to a lag in use case implementation and possibly off-target expectations
  • Working group would like to know:
    • What are the boundaries of responsibility for the use case working group?
    • Will there be a data integration working group to collect data as required for a use case?
    • What group or groups does the use case working group need to hand off tasks to?
    • What overall decisions about technologies need to be made about AGR before implementing use cases?
  • Working on an idea to show comparisons between transcript and protein isoforms
  • Would be great to be able to have a common display of phenotypes, using a ribbon-style and a standard ontology slim

Person Lineage graph

  • current view Low complexity person, High complexity person
  • ~31,000 orphans in DB; ~14,000 orphans with an email address
  • Do we need to distinguish between "real" WB people and those simply created as a co-author?
  • Will email ~14,000 people to ask them to provide person connections

Micropublications

  • Karen and Daniela spoke to person at HighWire
  • Working on publication platform, getting cost estimates
  • Met with people at Collaborative Knowledge Foundation
  • Similar in scope to HighWire, but have more modern software
  • Will probably write a grant together with Collaborative Knowledge Foundation
  • Also planning to apply for a Big Data to Knowledge grant
  • Added two pubications from nemametrix, adding one more today
  • Need a window of time to handle submissions given the turn around time for reviewers
  • "Data not shown" references could be handled as micropublication
  • Tim Schedl suggested doing a workshop at the 2017 IWM for micropublications
    • The Future of Scholarly Communication
    • Who else would be involved? GSA (WormBook, G3)? JoVE?

Wild isolate library (Erik Anderson)

  • CeNDR (C. elegans Natural Diversity Resource)
  • https://elegansvariation.org/
  • Want to have links out to their database from WormBase
  • WormBase already has 250 strains; many more that are not in WB
  • Has 342 strains in total
  • They would like to have integrated views of their database in WB; may be too difficult to have an integrated view
  • WB will take in all of their strains
  • CGC has most but not all of their strains
  • Can discuss on next WB site-wide call

WormBase IWM Workshop

  • Ranjana will send in a workshop proposal

2017 IWM

  • What do we want to communicate/emphasize about WormBase at the 2017 IWM?
  • Maybe explain and discuss AGR; what it means to our users
  • What do we want to ask our user community for?


November 17, 2016

  • lineage tool good for featuring in AGR
  • AGR curator call - SGD simpler, fewer datatype, impressed with triaging and organization of paper curation prioritization, curation is paper-by-paper, author response form is minimal - no specific author comments captured, just check boxes
  • SGD moving spell to the cloud, and will give us an amazon image, into which we will be able to load WB data
  • Caltech has an amazon cloud already for use for SPELL, but not enough for all our data
  • SPELL built locally on textpresso, once built, data loaded up; users download a lot
  • Post GO meeting

Pascal, David Hill and Kimberly piloting a pathway annotation - looking at PAINT annotations to create templates for curation of the signaling pathway in NOCTUA and look for ontology and other issues that need to be addressed - using the TOR pathway, will be useful in the AGR

  • Strain requests will be sent from disease OA to Mary Ann
  • Strains included in nightly_genace.pl
  • Next Thursday = Thanksgiving
  • AGR meeting Dec 6, Paul S.
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