WBConfCall 2014.02.06-Agenda and Minutes

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Plans for WS243

  • Topic curation for WS243 & WS244: Repsonse to Pathogens, Signaling in Innate Immunity
    • Take papers and genes from two WormBook chapters:
  1. Interactions with microbial pathogens (2005) - Creg Darby
  2. Signaling in the immune response (2006) - Jonathan J. Ewbank

Upcoming Species

  • Necator americanus <= WS242
  • Gene set (finally) for Meloidogyne incognita (finally).
  • Pristionchus exspectatus
  • Pristionchus pacificus <= waiting for ENA submission

Models schedule

  • Decide on WS243 upload date (Proposed Friday 28th March)
  • Models Tagging -2 weeks (14th March)
  • Models proposal deadline -3 weeks (7th March)

Not tied to a call.

Generating gene association files that conform to the GAF 2.0 format (Ranjana, Raymond)

  • Gene association files (GAFs) are generated by Hinxton for GO, phenotype and anatomy data, but they currently don't conform to the GAF 2.0 format which is the industry standard, and required for the ontology browser that Raymond and Juancarlos are working on.
gene_association         all good
anatomy_association column 6  => "WB_REF:WBPaperDDDDDDDDD"
                    column 9  => leave empty, no aspect choice for our anatomy ontology.
                    column 12 => "gene"
                    column 13 => "taxon:DDDD"
phenotype_association    same as anatomy
  • We need to generate a GAF for gene-disease data (Ranjana and Paul D can talk offline about this)

Oustanding issues


I haven't found a satisfactory way to remap gene name changes across releases. If it's somewhere obvious I apologise in advance, but I've trawled through the ftp site plenty.




I have a list of a few hundred genes, and I want to retrieve all coding nucleotide sequences associated with each gene. This would be the equivalent of going to each gene's page in Wormbase, clicking on the link to go to the transcript page, and selecting "view spliced + UTR." 

This seems like it should be a straightforward thing to do via WormMine, but I can't seem to figure out how to do it. 

Thanks for your help!


  How do I export coordinates for start & end bp and exons for genes via WormMine? 

Can I get coordinates for the latest gene models but translate them so that they work on genome build WS220?

My C elegans resequencing has been aligned to the WS220 build, is there any way of using the most up to date gene models whilst using my current files, or do I need to realign to a more up to date genome build?