WormBase-Caltech Weekly Calls
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- 1 Previous Years
- 2 2015 Meetings
- 2.1 December 3, 2015
- 2.2 December 10, 2105
- 2.3 December 17, 2105
December 3, 2015
- 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
- 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)
- Has anyone been working with Anita Bandrowski on this?
- It seems to have the same aims as our GSA markup pipeline.
- examples http://www.biomedcentral.com/1471-2202/16/25/ & https://scicrunch.org/resolver/RRID:CGC_N2
- Mins: WormBase supports this project and will work with Anita and Aric to enable them to get the info they need from WB.
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 "firstname.lastname@example.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
- 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
- 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)
- 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