WormBase-Caltech Weekly Calls December 2015

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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

December 17, 2105

Lab heads email list

  • Mary Ann working with Todd to create mailing list with all worm lab PI's
  • Should the email info come from ACEDB or local Caltech postgres database?
  • Todd planning to use Google Groups to create a distribution list
  • Cecilia could update the Google Groups list when updating PI information
  • Juancarlos will send Todd the first list of email addresses

Database migration & website

  • OICR exploring new, modern web technologies
  • We would want a more client-side model, as opposed to a server-side model; more flexible
  • Maybe move away from RESTful interface, so as not to deliver unnecessary data
  • The plan is to rewrite portions of the website to accommodate Datomic and its capabilities

Help documentation

  • Current user guide wiki is outdated
  • Can we have links to relevant help wiki pages from within the website? Yes, but need to establish standard linking syntax
  • Raymond will pilot this with help docs for the new SObA phenotype graph

Phenotype Form for community curation

  • Chris and Juancarlos are working on adapting the existing Allele-Phenotype form
  • Goal is accommodate RNAi and transgene phenotypes
  • Interface updates are almost complete; now working on backend integration
  • Currently no link to a transgene form, but will link once such a form exists

Tissue enrichment tool (Raymond)

  • David Angeles' hypergeometric test incorporated into a tool
  • Tool will take a list of genes and look for tissue enrichment
  • Data coming from GAF for expression (not individual expression patterns)
  • Will eventually be incorporated as tool into WormBase
  • What to call tool: "Enrichment tool", maybe separate for each data type?
  • Could create labels for each data type: "Phenotype Enrichment Tool", "GO Enrichment Tool", "Tissue Enrichment Tool" and link to different pages or the same pages with radio buttons to specify data type
  • "Enrichment Analysis" single link is best

Micropublications

  • Keep with WormBook or create new journal?
  • DataMed portal could be used to discover micropublication data
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