WormBase-Caltech Weekly Calls

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2009 Meetings


2011 Meetings

February

March

April


May 5, 2011

Citace upload

  • Using current citace release (WS226) for Progress Report


Pictures

  • Daniela did not actually curate ~7000 pictures this month ;)
  • Script to fetch pictures automatically


Snehal starts next week

  • working on phenotype curation
    • 90 genes >= 10 publications
    • Of these 90, 54 with no annotated phenotype
    • 20,000 genes with RNAi data
  • Concise Descriptions? May be appropriate
    • Prioritize by genes that currently have no description but have new papers
  • Picture curation?
  • Learning an ontology may be difficult, but she can stick to familiar material


Aldrin

  • Karen, Raymond, Chris will talk to Todd
  • Lineage browser for ontologies?
  • Cell lineage browser? Capture multi-parentage issues


Ranjana - Preplanning WormBase side meetings at IWM?


Periodically sending someone to different sites

  • E.g. Someone from Caltech goes to Hinxton, etc.


Practice Talks before International Worm Meeting

  • on Monday before meeting


May 12, 2011

Example of Bandana for International Worm Meeting

  • Looks good!


GO Consortium meeting next week

  • Paul, Michael, Ranjana, and Kimberly going
  • Discussion about tools (Juancarlos?)
  • Section in meeting agenda to discuss curation
    • Textpresso-based curation
    • Ontology Annotator
    • Demo by Kimberly or Ranjana?
    • Relatively trivial (depending on situation) to setup new OA for a new site (Juancarlos)
    • Discuss what's been proposed in the grant
    • What does the consortium want? Brainstorming/Fantasizing
    • People are likely partial to their own tools
    • Make use of the best parts of everyone's tools
    • Are others using flat/text files or web-based/java-based tools? Mostly web-based
    • Phenote? Funding? Bio-Portal e-mail?
    • PAINT tool (Phylogenetic Annotation and INference Tool) (http://wiki.geneontology.org/index.php/PAINT)


Progress Report

  • Paul has received some reports, but not all, yet


Picture curation

  • Started receiving permission from Elsevier!!
  • Blanket-permission for 11 journals
  • Publicly display list of cooperating journals online


Talks at the Int Worm Meeting

  • Paul S listed for a Plenary talk during Workshop
  • Two Wormbase Plenary talks


Snehal

  • Concise descriptions
  • Kimberly helping
  • Will get into phenotypes soon


Juancarlos waiting to hear back from some people about OA

  • People need more time to test
  • Karen has encountered some issues; needs to reproduce
  • Ranjana - loads slowly?
  • Mangolassi issues?


Genetic Interactions

  • Group met on Tuesday
  • Made headway on genetic interaction organization
  • Add "Additive" type term and "No Apparent Interaction", etc.


Paper pipeline

  • Kimberly & Juancarlos working on
  • Documented on Wiki
  • CGI's still being used?
  • Remove outdated or unused CGI's?


Rewriting script from Jack Chen

  • Neuron connection search
  • Inroad to working on more web-interface topics


Adding interaction datasets into WormMart (Xiaodong and Ruihua)


Gene interaction dumping script (Raymond/Todd)


Strain Display

  • Karen doing queries at CGC
  • How many genes represented in CGC strain list?
  • Protein-coding genes with alleles in strains?
  • 12,000 genes that are NOT represented in CGC
  • Discrepancy wrt alleles; negative in AQL query, but present on site
  • Strains with LOTS of alleles; how to handle?
  • Polymorphisms vs. alleles


Aldrin Montana working over the summer

  • We invited him to visit
  • We'll come up with projects
  • Web team fully involved in web site
  • Help with minor GO issues (Ranjana)
    • Requires knowledge of Perl
    • Non-C.elegans species
    • InterPro-to-GO mapping
    • Export pipelines for other species?
    • Maybe small project; requires more communication than coding?
  • Raymond could help provide projects
  • Would be nice to use PAINT across the nematodes for annotation


New Web site (Todd)

  • Web team wrapping up various projects
  • Polishing user interface
  • Abby working on user interface
  • Todd working on production environment
  • Norie working on code that interfaces with database
  • Release beta version at International Worm Meeting
  • Working with Kevin Howe to standardize formats of files used during build
  • Can now host new data for new species