WormBase-Caltech Weekly Calls

2009 Meetings

2011 Meetings

February

March

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:
  • http://wiki.wormbase.org/index.php/Expression_Pattern
• 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? (probably write a whole new interface depending on goal -- Juancarlos)
• 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

April 14, 2011

-Gene Class Descriptions-

• Concerns about maintenance and redundancy
• Uma here for ~ 3 months
• How many gene classes have alleles?
• How many are named by phenotype rather than just molecular data?
• How is this different from gene concise descriptions?
• Should it be a summary of all gene concise descriptions of the class?
• Things currently focused on:
  • using WormMart to look at genes in a class
  • pulls out all concise descriptions
  • look at similarities
  • interesting things to highlight
• Gene concise descriptions vs class descriptions
  • Gene-centric vs Class-centric
  • Consolidating/pooling all concise descriptions from individual genes?
• Going for maintenance-free statements
• Potentially building an interface
• Richard Durbin: development vs behavior?
• Prioritization?
• Focus on phenotype-based classes like UNC?
• Factors for prioritization:
  • Numbers of genes curated
  • molecular vs phenotype-based
  • Amount of info currently available?
  • Historical points
  • Most actively worked currently? (most mentioned in last year's publications?)
• Uma and Karen could communicate with Kimberly and Ranjana about
• What is most efficient for Uma to focus on?
• Uma can look at gene class description makes sense
• Skip gene classes for which only one gene exists
• GO term stats on each class?

-Papers missing from Textpresso-

• Issue: Genetics papers for GSA markup are missing from SVM analysis
• Juancarlos' file on caprica
• Discrepancy between papers on Textpresso and those gone through SVM
• SVM doesn't pick up GSA papers
• Generate a filtering to detect which ones have been missed by SVM
• Michael looking into reasons why the pipeline isn't working
• Tazendra vs Textpresso discrepancies?
• Ruihua will process 56 missing papers retroactively
• Still working on how to avoid this in the future