WormBase-Caltech Weekly Calls

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December 3, 2015

Datomic conversion

  • There are automated conversion systems being established to convert ACEDB data and models into Datomic
  • The Datomic data models and querying language may take some time to get used to
  • Curators will likely need to work with a models "master" to make model changes
  • Being able to perform complex queries is an important requirement
  • (Mary Ann) Datomic table maker (from Thomas) is reasonably intuitive and should be helpful to users

Wen's data viz proposal

  • Tool or graphic? We would like a tool
  • Question about sustainability: what happens after a tool is developed?
  • Proposal looks good, but need to specify requirements for maintenance and data updates
  • Is it possible to recreate SPELL with a new/different API and/or interface? Likely problematic

SObA phenotype graph

  • Juancarlos has been working on integrating into
  • http://juancarlos.wormbase.org , look at a gene page, open Phenotype Graph widget
  • Looks great, maybe need to tweak the legend position

Uberon linking to WormBase anatomy ontology

  • Chris Mungall had established connections between the two
  • We don't have a current plan to make these fully integrated

December 10, 2105

RRID (Mary Ann)

Lab head email list (Mary Ann)

  • Request from Ann (CGC) to have a single email address containing all lab heads.
  • Used sparingly to send the community important announcements etc.
  • Mins: Could ask Todd to create a "labheads@wormbase.org" or something like that
  • Ticket https://github.com/WormBase/website/issues/4424

SObA graph on staging

  • Sibyl helped Juancarlos get the phenotype SObA graph into it's own gene page widget "Phenotype Graph"
  • Raymond will write up a Wiki page for documentation
  • Would be good to link to the Wiki from the widget (should apply to all widgets)

Data Viz proposal

  • Wen's proposal: how much is the proposed feature a tool versus visually appealing display?
  • Modify language for a general audience (Paul S providing suggested changes)

Community curation of allele-phenotype

  • Stats:
    • 500 emails gone out for 500 papers
    • 88 out of 500 have some curation by community (~18%)
    • 601 community annotations in Phenotype OA by 121 distinct people
  • Want to expand the form to accommodate RNAi and transgene (priority)
    • separate forms or expanded single form? Chris will discuss with Juancarlos

SAB meeting

  • Feb 4, 5
  • Pre-meeting on Wednesday Feb 3, group meeting in afternoon
  • Focus of presentations?
    • Efficiency improvements
    • Community curation (allele-phenotype, concise descriptions, etc.)
    • Text mining
    • Database migration
    • SObA (Solr/Amigo/Cytoscape re-use)
    • Automated concise descriptions
    • Documentation plans (granular (per widget/object/feature) links from website to wiki)
    • Micropublications
    • Human disease / pathways