WormBase-Caltech Weekly Calls

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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