Difference between revisions of "WormBase-Caltech Weekly Calls"

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* Maybe move away from RESTful interface, so as not to deliver unnecessary data
 
* 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
 
* The plan is to rewrite portions of the website to accommodate Datomic and its capabilities
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 +
=== 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* Current user guide wiki is outdated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

Revision as of 17:25, 17 December 2015

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings


2015 Meetings

January

February

March

April

May

June

July

August

September

October

November


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