WormBase-Caltech Weekly Calls
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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? (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
April 21, 2011
WormMart
- Stable for IWM?
- WormMart presentation for WormBase workshop
- Query examples
- Data content
- Features
- Plans for the next year; what data to be made available
- Discuss stability?
Igor's machine: elbrus
- Can have problems
- Input info has changed for WS225
- RNAi script stopped working
- Migration issues
- Decide on priorities
- Who will maintain what?
- Migrate things over to newer machines, locally
- On elbrus now:
- RNAi scripts (sequence mapping); Migrating to EBI
- Anatomy ontology browser (optional)
- Microarray tool (Wen will take over)
- Get-Sequence CGI (how many people use it?)
- Meet with Norie at IWM?
- We should write everything down first
BioGRID-WormBase data exchange:
- Questions about how to best do this
- How to handle/organize genetic interactions
- BioGRID meeting in May; will not be sufficient to solve the genetic interaction issues
- Chris still working on genetic interaction organization scheme
SPELL/Microarray
- Discuss at IWM?
- Patching changes into WS225
ModENCODE Meeting
- Gary Williams should go
Picture Page
- New developments
- Elsevier publishing; how to handle them? ($17.5 per figure!!!)
Informatics Resources Assessment
- Can we develop plan to determine informatics resources available
- Long-term plans for sustainable informatics resources