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  1. NIF
  2. NIF-11854

DISCO: add new resource EuroPhenome

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    • NIF
    • Issues closed as MONARCH has transitioned from UCSD services

    Description

      NOT YET IN DISCO.
      Resource url: http://www.europhenome.org
      Description of use: This is Geno-Pheno data for various mouse strains, and has phenotype data resulting from the knockout consortium project. I don't think this data is in MGI. Phenotypes are both quantitative, and curated to an MP term. Alleles are recorded, if present, as well as zygosity. The "phenotype procedure" is listed (which is the assay performed), but I don't know where that vocabulary comes from. We can filter by statistical significance (which is what is in the query below, but perhaps we don't want to?)

      Data Format: CSV (via BioMart)
      Data is available via Biomart. Here's an example query:

      <?xml version="1.0" encoding="UTF-8"?>
      <!DOCTYPE Query>
      <Query virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" >

      <Dataset name = "europhenome" interface = "default" >
      <Filter name = "significance" value = "0.0001"/>
      <Attribute name = "europhenome_id" />
      <Attribute name = "line_name" />
      <Attribute name = "sex" />
      <Attribute name = "zygosity" />
      <Attribute name = "allele_id" />
      <Attribute name = "allele_name" />
      <Attribute name = "mgi_accession_id" />
      <Attribute name = "marker_name" />
      <Attribute name = "marker_symbol" />
      <Attribute name = "emma_id" />
      <Attribute name = "international_strain_name" />
      <Attribute name = "ensembl_gene_id" />
      <Attribute name = "stocklist_id" />
      <Attribute name = "escell_clone" />
      <Attribute name = "pipeline" />
      <Attribute name = "procedure_name" />
      <Attribute name = "procedure_eslim_id" />
      <Attribute name = "parameter_name" />
      <Attribute name = "parameter_eslim_id" />
      <Attribute name = "significance" />
      <Attribute name = "mp_term" />
      <Attribute name = "mp_term_name" />
      </Dataset>
      </Query>

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            bandrow Anita Bandrowski (use this one!)
            nlw Nicole Washington
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              Created:
              Updated:
              Resolved: