Difference between revisions of "WormBase-Caltech Weekly Calls"

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*Ruihua will process 56 missing papers retroactively
 
*Ruihua will process 56 missing papers retroactively
 
*Still working on how to avoid this in the future
 
*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

Revision as of 17:38, 21 April 2011

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:
  • 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