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

https://github.com/WormBase/website/issues/2361 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. Thanks