WormBase-Caltech Weekly Calls

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August 7, 2014

  • Topic Curation
    • Working out pipeline for curation
    • Collecting model/pathway diagrams from papers and reviews: should we make ?Picture objects for these?
      • Do we want to display these published diagrams on ?Paper pages and/or ?Topic pages
      • We need to determine copyrights/accessibility to images
    • Would be good to automate identification of Review articles (or "non-primary" in general) in the Topic OA
      • This could be done at the bulk import step
      • Would require a new (possibly read-only) field in the Topic OA to indicate "primary" or "non-primary"
    • Chris will look into whether "non-primary" articles are automatically excluded from the Curation Status Form
    • The "Curation Status Omit" toggle in the Topic OA may become obsolete once we have a field/column for primary/non-primary status
    • Current topic : Wnt signaling
    • We have a list of 282 papers from PubMed search using "Wnt" search term (not Mesh term) and C. elegans (Mesh term)
    • Finding all papers for a category/topic remains an ad hoc approach; different topics are harder or easier to find all papers for
    • We can create a Textpresso category for topics, like "Wnt signaling"

  • WormBase Ontology Browser
    • Needs documenting
    • Once everything is clarified, will be pushed to the live site

August 14, 2014

  • WormBase Ontology Browser (WOBr)
    • Should be ready but may need some additional testing before pushing to staging site
    • Juancarlos will push to staging during meeting
    • Curators should test this afternoon (on staging) and report any issues before 5pm
  • DataBase call this morning (and every Thursday that doesn't have a site-wide call)
    • Thomas Down testing Datomic (costs money) and Neo4J (very slow)
    • May look again at DynamoDB
    • No DB has been officially chosen
    • Will have an Amazon AWS for collaboration.
    • Expand smallace into bigger mediumace.
    • Demo off one database for advisory board meeting.
  • SAB
    • Paul Sternberg back next week; will settle travel plans then
    • What advisors are attending?
    • What feedback do we want to get from advisors?
    • How to show curation/DB progress? What stats/numbers to show?
    • We want big picture feedback from biologist advisors; what's useful to the community? What should we prioritize?
    • Karen: Perhaps a question to ask is "what are the main questions they are trying to answer when they go to the website?". When they explore a gene or protein function, what is it that they would want to see, and how? I don't think we are missing information so much as a lack of integration of the information at the model level, for example, variation phenotype affects linked to altered protein domain function
  • Belated apologies from Mary Ann - clash of evening events.

August 21, 2014

  • Topic 1
  • Topic 2

August 28, 2014

  • Topic 1
  • Topic 2