WormBase-Caltech Weekly Calls
From WormBaseWiki
January 10, 2013
Site-of-action pages
- No cell function pages exist
- Tried to display cell function info on anatomy pages
- Trying to display site-of-action data on relevant gene pages
Process pages
- Rudimentary process page up
- Has overview widget with all relevant entities
- Should be something by SAB
Intermine
- JD is working on; should have something ready by SAB
- Will replace WormMart entirely
- We should make an announcement on the main WormBase page that WormMart will remain at WS220 and Intermine will replace it
- We can perform queries for users in the meantime, if necessary
- Intermine interface isn't very intuitive; maybe we can improve it in time
- Can build queries with a query builder and perform complex queries
- Precanned queries could be made and proposed to users
- Curators can try YeastMine or FlyMine to try it out
Species expression data from Itai Yanai
- Importing pictures; potentially flagging each to a particular species
- Pictures typically linked to Expr_pattern objects
- Can images be linked to sequences, rather than gene objects?
Documentation for Protein-2-GO tool
Brugia database
- Mark Blaxter offered to donate his Brugia database into WormBase
- Papers from 1600s!!!
Nematode Textpresso
- ~10,000 new papers available (open access?)
Concise description form
Species in Phenotype curation
- Species tag in phenotype
- Default dumping with species as C. elegans; some data was removed during the dump
- Do phenotypes need a species tag? Not necessarily
- Do we create a separate Citace for each species (potentially 100s)?
- Dump all data for all species in one file for testing, and individual files for upload?
- Should discuss with Kevin Howe
