WormBase-Caltech Weekly Calls

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 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

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