Updating API code query from OTG to OpenTargets Platform

Data Access
21

We are not able to exposing full summary statistics via the API, however, we do allow users to find all known GWAS or QTL signals where the queried variant is part of the credible sets. Essentially reproducing the GWAS and QTL tables you can find on the variant page.

The API query examples show how to pull credible sets. This example also pulls study level information (studyId, disease, traitName) + corresponding disease and disease categories (diseaseName and therapeuticAreas). If these annotations are not enough you can add more study annotation eg. publicationFirstAuthor, pubmedId, cohorts etc

query GWASCredibleSetsQuery($variantId: String!, $size: Int!, $index: Int!) {
  variant(variantId: $variantId) {
    id
    referenceAllele
    alternateAllele
    gwasCredibleSets: credibleSets(studyTypes: [gwas], page: { size: $size, index: $index }) {
      count
      rows {
        studyLocusId
        pValueMantissa
        pValueExponent
        beta
        finemappingMethod
        confidence
        variant {
          id
          chromosome
          position
          referenceAllele
          alternateAllele
        }
        study {
          traitFromSource
          id
          diseases {
            name
            id
            therapeuticAreas {
              name
              id
            }
          }
        }
        locus(variantIds: [$variantId]) {
          rows {
            posteriorProbability
          }
        }
        locusSize: locus {
          count
        }
        l2GPredictions(page: { size: 1, index: 0 }) {
          rows {
            target {
              id
              approvedSymbol
            }
            score
          }
        }
      }
    }
  }
}

Given the following query parameters:

{
  "variantId": "1_154453788_C_T",
  "size": 500,
  "index": 0
}

This is one of the returned credible set:

{
  "studyLocusId": "00c812e382a81bd696d654936e960be3",
  "pValueMantissa": 1.0130000114440918,
  "pValueExponent": -10,
  "beta": -0.0751,
  "finemappingMethod": "PICS",
  "confidence": "PICS fine-mapped credible set extracted from summary statistics",
  "variant": {
    "id": "1_154452980_G_A",
    "chromosome": "1",
    "position": 154452980,
    "referenceAllele": "G",
    "alternateAllele": "A"
  },
  "study": {
    "traitFromSource": "Rheumatoid arthritis",
    "id": "GCST90013534",
    "diseases": [
      {
        "name": "rheumatoid arthritis",
        "id": "EFO_0000685",
        "therapeuticAreas": [
          {
            "name": "immune system disease",
            "id": "EFO_0000540"
          },
          {
            "name": "musculoskeletal or connective tissue disease",
            "id": "OTAR_0000006"
          },
          {
            "name": "phenotype",
            "id": "EFO_0000651"
          }
        ]
      }
    ]
  },
  "locus": {
    "rows": [
      {
        "posteriorProbability": 0.054693652754671196
      }
    ]
  },
  "locusSize": {
    "count": 31
  },
  "l2GPredictions": {
    "rows": [
      {
        "target": {
          "id": "ENSG00000160712",
          "approvedSymbol": "IL6R"
        },
        "score": 0.8838409781455994
      }
    ]
  }
}

Not exactly sure if anything else is missing for you?