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Variant information available via the REST API but not via the web search interface #82

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ramiromagno opened this issue Oct 15, 2018 · 2 comments
Open

Variant information available via the REST API but not via the web search interface #82

ramiromagno opened this issue Oct 15, 2018 · 2 comments
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@ramiromagno
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For SNP rs6431996:

Retrieving variant information via the REST API works:

curl 'https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs6431996' -i -H 'Accept: application/json'
HTTP/2 200 
server: Apache-Coyote/1.1
cache-control: no-cache, no-store, max-age=0, must-revalidate
content-type: application/json;charset=UTF-8
strict-transport-security: max-age=0
date: Mon, 15 Oct 2018 17:02:15 GMT
x-application-context: application
expires: 0
x-xss-protection: 1; mode=block
pragma: no-cache
x-content-type-options: nosniff
x-frame-options: DENY

{
  "rsId" : "rs6431996",
  "merged" : 0,
  "functionalClass" : "intron_variant",
  "lastUpdateDate" : "2018-07-23T02:31:12.565+0000",
  "locations" : [ {
    "chromosomeName" : "2",
    "chromosomePosition" : 9278145,
    "region" : {
      "name" : "2p25.1"
    },
    "_links" : {
      "snps" : {
        "href" : "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs6431996"
      }
    }
  } ],
  "genomicContexts" : [ {
    "isIntergenic" : true,
    "isUpstream" : true,
    "isDownstream" : false,
    "distance" : 6517,
    "gene" : {
      "geneName" : "EIF1P7",
      "entrezGeneIds" : [ {
        "entrezGeneId" : "106481691"
      } ],
      "ensemblGeneIds" : [ {
        "ensemblGeneId" : "ENSG00000213772"
      } ]
    },
    "location" : {
      "chromosomeName" : "2",
      "chromosomePosition" : 9278145,
      "region" : {
        "name" : "2p25.1"
      },
      "_links" : {
        "snps" : {
          "href" : "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs6431996"
        }
      }
    },
    "source" : "Ensembl",
    "mappingMethod" : "Ensembl_pipeline",
    "isClosestGene" : true,
    "_links" : {
      "snp" : {
        "href" : "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs6431996"
      }
    }
  }, {
    "isIntergenic" : true,
    "isUpstream" : true,
    "isDownstream" : false,
    "distance" : 71666,
    "gene" : {
      "geneName" : "LOC100506317",
      "entrezGeneIds" : [ {
        "entrezGeneId" : "100506317"
      } ],
      "ensemblGeneIds" : [ ]
    },
    "location" : {
      "chromosomeName" : "2",
      "chromosomePosition" : 9278145,
      "region" : {
        "name" : "2p25.1"
      },
      "_links" : {
        "snps" : {
          "href" : "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs6431996"
        }
      }
    },
    "source" : "NCBI",
    "mappingMethod" : "Ensembl_pipeline",
    "isClosestGene" : false,
    "_links" : {
      "snp" : {
        "href" : "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs6431996"
      }
    }
  }, {
    "isIntergenic" : false,
    "isUpstream" : false,
    "isDownstream" : false,
    "distance" : 0,
    "gene" : {
      "geneName" : "ASAP2",
      "entrezGeneIds" : [ {
        "entrezGeneId" : "8853"
      } ],
      "ensemblGeneIds" : [ {
        "ensemblGeneId" : "ENSG00000151693"
      } ]
    },
    "location" : {
      "chromosomeName" : "2",
      "chromosomePosition" : 9278145,
      "region" : {
        "name" : "2p25.1"
      },
      "_links" : {
        "snps" : {
          "href" : "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs6431996"
        }
      }
    },
    "source" : "Ensembl",
    "mappingMethod" : "Ensembl_pipeline",
    "isClosestGene" : false,
    "_links" : {
      "snp" : {
        "href" : "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs6431996"
      }
    }
  }, {
    "isIntergenic" : true,
    "isUpstream" : true,
    "isDownstream" : false,
    "distance" : 6517,
    "gene" : {
      "geneName" : "EIF1P7",
      "entrezGeneIds" : [ {
        "entrezGeneId" : "106481691"
      } ],
      "ensemblGeneIds" : [ {
        "ensemblGeneId" : "ENSG00000213772"
      } ]
    },
    "location" : {
      "chromosomeName" : "2",
      "chromosomePosition" : 9278145,
      "region" : {
        "name" : "2p25.1"
      },
      "_links" : {
        "snps" : {
          "href" : "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs6431996"
        }
      }
    },
    "source" : "NCBI",
    "mappingMethod" : "Ensembl_pipeline",
    "isClosestGene" : true,
    "_links" : {
      "snp" : {
        "href" : "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs6431996"
      }
    }
  }, {
    "isIntergenic" : false,
    "isUpstream" : false,
    "isDownstream" : false,
    "distance" : 0,
    "gene" : {
      "geneName" : "ASAP2",
      "entrezGeneIds" : [ {
        "entrezGeneId" : "8853"
      } ],
      "ensemblGeneIds" : [ {
        "ensemblGeneId" : "ENSG00000151693"
      } ]
    },
    "location" : {
      "chromosomeName" : "2",
      "chromosomePosition" : 9278145,
      "region" : {
        "name" : "2p25.1"
      },
      "_links" : {
        "snps" : {
          "href" : "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs6431996"
        }
      }
    },
    "source" : "NCBI",
    "mappingMethod" : "Ensembl_pipeline",
    "isClosestGene" : false,
    "_links" : {
      "snp" : {
        "href" : "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs6431996"
      }
    }
  }, {
    "isIntergenic" : true,
    "isUpstream" : false,
    "isDownstream" : true,
    "distance" : 127536,
    "gene" : {
      "geneName" : "ITGB1BP1",
      "entrezGeneIds" : [ {
        "entrezGeneId" : "9270"
      } ],
      "ensemblGeneIds" : [ {
        "ensemblGeneId" : "ENSG00000119185"
      } ]
    },
    "location" : {
      "chromosomeName" : "2",
      "chromosomePosition" : 9278145,
      "region" : {
        "name" : "2p25.1"
      },
      "_links" : {
        "snps" : {
          "href" : "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs6431996"
        }
      }
    },
    "source" : "NCBI",
    "mappingMethod" : "Ensembl_pipeline",
    "isClosestGene" : true,
    "_links" : {
      "snp" : {
        "href" : "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs6431996"
      }
    }
  }, {
    "isIntergenic" : true,
    "isUpstream" : true,
    "isDownstream" : false,
    "distance" : 63347,
    "gene" : {
      "geneName" : "LOC107985851",
      "entrezGeneIds" : [ {
        "entrezGeneId" : "107985851"
      } ],
      "ensemblGeneIds" : [ ]
    },
    "location" : {
      "chromosomeName" : "2",
      "chromosomePosition" : 9278145,
      "region" : {
        "name" : "2p25.1"
      },
      "_links" : {
        "snps" : {
          "href" : "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs6431996"
        }
      }
    },
    "source" : "NCBI",
    "mappingMethod" : "Ensembl_pipeline",
    "isClosestGene" : false,
    "_links" : {
      "snp" : {
        "href" : "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs6431996"
      }
    }
  }, {
    "isIntergenic" : true,
    "isUpstream" : false,
    "isDownstream" : true,
    "distance" : 125330,
    "gene" : {
      "geneName" : "ITGB1BP1",
      "entrezGeneIds" : [ {
        "entrezGeneId" : "9270"
      } ],
      "ensemblGeneIds" : [ {
        "ensemblGeneId" : "ENSG00000119185"
      } ]
    },
    "location" : {
      "chromosomeName" : "2",
      "chromosomePosition" : 9278145,
      "region" : {
        "name" : "2p25.1"
      },
      "_links" : {
        "snps" : {
          "href" : "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs6431996"
        }
      }
    },
    "source" : "Ensembl",
    "mappingMethod" : "Ensembl_pipeline",
    "isClosestGene" : true,
    "_links" : {
      "snp" : {
        "href" : "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs6431996"
      }
    }
  } ],
  "_links" : {
    "self" : {
      "href" : "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs6431996"
    },
    "singleNucleotidePolymorphism" : {
      "href" : "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs6431996"
    },
    "associationsBySnpSummary" : {
      "href" : "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs6431996/associations?projection=associationBySnp"
    },
    "associations" : {
      "href" : "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs6431996/associations"
    },
    "currentSnp" : {
      "href" : "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs6431996/currentSnp"
    },
    "studies" : {
      "href" : "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs6431996/studies"
    }
  }
}

But not via the web search interface:

https://www.ebi.ac.uk/gwas/variants/rs6431996

rs6431996_not_found
@cmalangone
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Contributor

cmalangone commented Oct 16, 2018 •
edited
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Hi Ramiro,
this is a bug. The study was not published and this variant should not be available.

HATEOAS gives the related endpoint
https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs6431996/studies

This endpoint gave an empty resultset.
The JIRA Task:
https://www.ebi.ac.uk/panda/jira/browse/GOCI-2447

@ramiromagno
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The same happens with variant rs7546498 .

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3 participants
@twhetzel @cmalangone @ramiromagno