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

• Generating a Site-Map for WormBase
  • Use a crawler to generate? Output would need to be made human-readable
  • We could use the legacy site as a site map

August 28, 2014

• Topic 1
• Topic 2