WormBase-Caltech Weekly Calls
From WormBaseWiki
2011 Meetings
April 7, 2011
Transgene Model
- On Wiki
- Sent out to people
- Have a look; report any concerns
- Can follow on BitBucket; search for transgene; link to Wiki
- No objections at Caltech; Karen will send to Paul Davis
- Changes to ACE dumping script; Karen will talk to Juancarlos
- Changes needed in OA (softer deadline than dump)
Interactions
- Murky genetic interaction curation?
- Err on the side of generality/trusting author statements
- When in doubt, curate as "genetic interaction"
- Chris is working on decision tree/pipeline for curation
- Kimberly working on Physical Interaction model
BioGRID meeting at Princeton in May
- Call in
- What will Rose propose?
Expression Pattern Curation (Daniela/Wen)
- Daniela sent out picture page for review
- Expr Pattern OA wiki is in place:
- As soon as Juancarlos is done with the modularization will start working on the code.
- In the meanwhile Daniela will curate expression pattern writing .ace files
- Expr_pattern OA should be ready by the next upload (May26th). (I really doubt this, parsing in data, writing dumpers, and checking it take a long time. Picture and Interaction each probably took longer than 2 months, and we're not starting Expr until May at the earliest -- Juancarlos)
Patch file/Interbuild (Raymond)
- Developed good patch file
- Tested patch file to update WS224 to WS225 - seems OK
- Less than 5 minutes for upload
- Testing now should be done by Todd/OICR team
Uma started
- Working on concise descriptions of gene classes
- Karen has reviewed with Uma; Uma is reading papers
- Discussing details of descriptions
- Inconsistencies/discrepancies of gene class names
- >2400 gene classes
- Can work on generating formula for this curation
- Arun can help with automation
- May need to get Uma an interface to enter data into postgres
- Adapt concise description CGI for her?
- Gene class name and a text field
- Using Textpresso/WormMart output; sentence saver?
eggNOG data into citace?
- Who's going to handle the data? curate?
- Michael? OK