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Retrieve Genomic Assembly Details for Assembly Identifiers

get

/ohfapi/cg/v3.3/genomeAssemblyDetails

This endpoint supports the retrieval of Genomic Assembly Details for multiple Assembly Idnetifiers passed. It returns Genomic Assembly Detail information like Assembly Identifier, Assembly Alias, Species, Name, PAR, Ensembl Version, Chromosome, Start Position, End Position, Date Of Loading, Version Identifier, Is Prefered Version and other Genomic Assembly assciated information.

Request

Supported Media Types

• application/json
• application/xml

Query Parameters

• id(optional): array
  Collection Format: multi

  ODB one or more alignmentwid value

  • [0]: integer(int64)

  {
      "name":"id",
      "in":"query",
      "description":"ODB one or more alignmentwid value",
      "required":false,
      "type":"array",
      "items":{
          "type":"integer",
          "format":"int64"
      },
      "collectionFormat":"multi"
  }

• limit(optional): integer(int32)
  Number of rows to return
• offset(optional): integer(int32)
  Row number to start from

Security

• basicAuth: basic
  Type: basic

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Response

Supported Media Types

• application/json
• application/xml

200 Response

successful operation

Body ()

Root Schema : PageableCollectionGenomicAssembly

Type: object

Model for paginated collections of data.

Show Source

• count(optional): integer(int64)
  Number of objects in the 'items' collection.
• hasMore(optional): boolean
  A boolean indicating if more pages are available.
• items(optional): array items
  A collection of paged items.
• links(optional): array links
  A collection of links containing hrefs to the current, next, and previous pages as applicable.
• resourceType(optional): string
  Identify the resource type

{
    "type":"object",
    "properties":{
        "resourceType":{
            "type":"string",
            "description":"Identify the resource type"
        },
        "items":{
            "type":"array",
            "xml":{
                "wrapped":true
            },
            "description":"A collection of paged items.",
            "items":{
                "$ref":"#/definitions/GenomicAssembly"
            }
        },
        "count":{
            "type":"integer",
            "format":"int64",
            "description":"Number of objects in the 'items' collection."
        },
        "hasMore":{
            "type":"boolean",
            "description":"A boolean indicating if more pages are available."
        },
        "links":{
            "type":"array",
            "example":"{rel: 'next',href: '/patientapi/patients?limit=100&offset=300'}",
            "xml":{
                "wrapped":true
            },
            "description":"A collection of links containing hrefs to the current, next, and previous pages as applicable.",
            "items":{
                "type":"string"
            }
        }
    },
    "description":"Model for paginated collections of data."
}

Nested Schema : items

Type: array

A collection of paged items.

Show Source

• Array of: object GenomicAssembly

{
    "type":"array",
    "xml":{
        "wrapped":true
    },
    "description":"A collection of paged items.",
    "items":{
        "$ref":"#/definitions/GenomicAssembly"
    }
}

Nested Schema : links

Type: array

A collection of links containing hrefs to the current, next, and previous pages as applicable.

Show Source

• Array of: string

{
    "type":"array",
    "example":"{rel: 'next',href: '/patientapi/patients?limit=100&offset=300'}",
    "xml":{
        "wrapped":true
    },
    "description":"A collection of links containing hrefs to the current, next, and previous pages as applicable.",
    "items":{
        "type":"string"
    }
}

Example:

{rel: 'next',href: '/patientapi/patients?limit=100&offset=300'}

Nested Schema : GenomicAssembly

Type: object

Show Source

• assembly(optional): string
  Assembly/Alignment Name. For ex.,GRCh38
• assemblyAlias(optional): string
  Alias Name
• ensemblVersion(optional): array ensemblVersion
  List of Ensembl Versions
• identifier(optional): object Identifier
  Identifier assigned by a given system
• PAR(optional): array PAR
  List of Chromosome Details
• species(optional): string
  Scientific Species Name

{
    "type":"object",
    "properties":{
        "identifier":{
            "description":"Assembly/Alignment Identifier",
            "$ref":"#/definitions/Identifier"
        },
        "assembly":{
            "type":"string",
            "description":"Assembly/Alignment Name. For ex.,GRCh38"
        },
        "assemblyAlias":{
            "type":"string",
            "description":"Alias Name"
        },
        "species":{
            "type":"string",
            "description":"Scientific Species Name"
        },
        "PAR":{
            "type":"array",
            "description":"List of Chromosome Details",
            "items":{
                "xml":{
                    "name":"PAR"
                },
                "$ref":"#/definitions/AssemblyPar"
            }
        },
        "ensemblVersion":{
            "type":"array",
            "description":"List of Ensembl Versions",
            "items":{
                "xml":{
                    "name":"ensemblVersion"
                },
                "$ref":"#/definitions/DNARefVersion"
            }
        }
    }
}

Nested Schema : ensemblVersion

Type: array

List of Ensembl Versions

Show Source

• Array of: object DNARefVersion

{
    "type":"array",
    "description":"List of Ensembl Versions",
    "items":{
        "xml":{
            "name":"ensemblVersion"
        },
        "$ref":"#/definitions/DNARefVersion"
    }
}

Nested Schema : Identifier

Type: object

Identifier assigned by a given system

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• system(optional): string
  System which assigned this identifier
• value(optional): string
  Identifier value

{
    "type":"object",
    "properties":{
        "system":{
            "type":"string",
            "description":"System which assigned this identifier"
        },
        "value":{
            "type":"string",
            "description":"Identifier value"
        }
    },
    "description":"Identifier assigned by a given system"
}

Nested Schema : PAR

Type: array

List of Chromosome Details

Show Source

• Array of: object AssemblyPar

{
    "type":"array",
    "description":"List of Chromosome Details",
    "items":{
        "xml":{
            "name":"PAR"
        },
        "$ref":"#/definitions/AssemblyPar"
    }
}

Nested Schema : DNARefVersion

Type: object

Show Source

• chromosome(optional): array chromosome
  List of Chromosome Genomic Positions
• ensemblVersion(optional): string
  Ensembl Version. For ex.,GRCH37.75
• identifier(optional): object Identifier
  Identifier assigned by a given system
• isPreferred(optional): string
• versionWID(optional): integer(int64)

{
    "type":"object",
    "properties":{
        "identifier":{
            "description":"Version Row ID",
            "$ref":"#/definitions/Identifier"
        },
        "versionWID":{
            "type":"integer",
            "format":"int64"
        },
        "ensemblVersion":{
            "type":"string",
            "description":"Ensembl Version. For ex.,GRCH37.75"
        },
        "chromosome":{
            "type":"array",
            "description":"List of Chromosome Genomic Positions",
            "items":{
                "$ref":"#/definitions/GenomicPosition"
            }
        },
        "isPreferred":{
            "type":"string"
        }
    }
}

Nested Schema : chromosome

Type: array

List of Chromosome Genomic Positions

Show Source

• Array of: object GenomicPosition

{
    "type":"array",
    "description":"List of Chromosome Genomic Positions",
    "items":{
        "$ref":"#/definitions/GenomicPosition"
    }
}

Nested Schema : GenomicPosition

Type: object

Show Source

• chromosome(optional): string
  Chromosome Name. For ex.,'Y'
• chromosomeId(optional): string
• chromosomeName(optional): string
  Chromosome Name. For ex.,'Y'
• dateOfLoading(optional): string(date-time)
  Insert Date
• dnaReferenceVersion(optional): string
  Version Label. For ex.,SIFT_VER2_75
• endPosition(optional): integer(int64)
  End location of sequence
• ensemblReleaseDate(optional): string(date-time)
  Date that this sequence source is released to be used to add versions of the same data
• numberInSequence(optional): integer(int64)
  Ordering of each Segment of the Component
• position(optional): integer(int64)
• startPosition(optional): integer(int64)
  Start location of sequence
• strand(optional): string
  Strand Value

{
    "type":"object",
    "properties":{
        "chromosomeId":{
            "type":"string"
        },
        "chromosomeName":{
            "type":"string",
            "description":"Chromosome Name. For ex.,'Y'"
        },
        "chromosome":{
            "type":"string",
            "description":"Chromosome Name. For ex.,'Y'"
        },
        "position":{
            "type":"integer",
            "format":"int64"
        },
        "startPosition":{
            "type":"integer",
            "format":"int64",
            "description":"Start location of sequence"
        },
        "endPosition":{
            "type":"integer",
            "format":"int64",
            "description":"End location of sequence"
        },
        "dateOfLoading":{
            "type":"string",
            "format":"date-time",
            "description":"Insert Date"
        },
        "strand":{
            "type":"string",
            "description":"Strand Value"
        },
        "dnaReferenceVersion":{
            "type":"string",
            "description":"Version Label. For ex.,SIFT_VER2_75"
        },
        "numberInSequence":{
            "type":"integer",
            "format":"int64",
            "description":"Ordering of each Segment of the Component"
        },
        "ensemblReleaseDate":{
            "type":"string",
            "format":"date-time",
            "description":"Date that this sequence source is released to be used to add versions of the same data"
        }
    }
}

Nested Schema : AssemblyPar

Type: object

Show Source

• chromosome(optional): string
  Chromosome Name. For ex.,'Y'
• endPosition(optional): integer(int64)
  End location of sequence
• startPosition(optional): integer(int64)
  Start location of sequence

{
    "type":"object",
    "properties":{
        "chromosome":{
            "type":"string",
            "description":"Chromosome Name. For ex.,'Y'"
        },
        "startPosition":{
            "type":"integer",
            "format":"int64",
            "description":"Start location of sequence"
        },
        "endPosition":{
            "type":"integer",
            "format":"int64",
            "description":"End location of sequence"
        }
    }
}

400 Response

Invalid parameters supplied

404 Response

genomeAssemblies not found

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Examples

The following example shows how to view the genomic assembly details for a multiple identifiers by submitting a GET request.

API URL

http://localhost:7010/ohfapi/cg/v3.3/genomeAssemblyDetails?id=1&id=2&id=3&limit=10&offset=0

Example of Response Body

The following example shows the response returned in JSON format.

{
  "resourceType": "GenomeDetails",
  "items": [
    {
      "identifier": {
        "system": "ODB",
        "value": "1"
      },
      "assembly": "GRCh37",
      "assemblyAlias": "GRCh37",
      "species": "homo sapiens",
      "PAR": [
        {
          "chromosome": "X",
          "startPosition": 60001,
          "endPosition": 2699520
        },
        {
          "chromosome": "Y",
          "startPosition": 10001,
          "endPosition": 2649520
        },
        {
          "chromosome": "X",
          "startPosition": 154931044,
          "endPosition": 155260560
        },
        {
          "chromosome": "Y",
          "startPosition": 59034050,
          "endPosition": 59363566
        }
      ],
      "ensemblVersion": [
        {
          "versionWID": 2,
          "ensemblVersion": "GRCH37.75",
          "chromosome": [
            {
              "chromosome": "1",
              "startPosition": 1,
              "endPosition": 249250621,
              "dateOfLoading": "01/25/2016",
              "ensemblReleaseDate": "02/08/2014"
            },
            {
              "chromosome": "2",
              "startPosition": 1,
              "endPosition": 243199373,
              "dateOfLoading": "01/25/2016",
              "ensemblReleaseDate": "02/08/2014"
            },
            {
              "chromosome": "3",
              "startPosition": 1,
              "endPosition": 198022430,
              "dateOfLoading": "01/25/2016",
              "ensemblReleaseDate": "02/08/2014"
            },
            {
              "chromosome": "4",
              "startPosition": 1,
              "endPosition": 191154276,
              "dateOfLoading": "01/25/2016",
              "ensemblReleaseDate": "02/08/2014"
            },
            {
              "chromosome": "5",
              "startPosition": 1,
              "endPosition": 180915260,
              "dateOfLoading": "01/25/2016",
              "ensemblReleaseDate": "02/08/2014"
            },
            {
              "chromosome": "6",
              "startPosition": 1,
              "endPosition": 171115067,
              "dateOfLoading": "01/25/2016",
              "ensemblReleaseDate": "02/08/2014"
            },
            {
              "chromosome": "7",
              "startPosition": 1,
              "endPosition": 159138663,
              "dateOfLoading": "01/25/2016",
              "ensemblReleaseDate": "02/08/2014"
            },
            {
              "chromosome": "8",
              "startPosition": 1,
              "endPosition": 146364022,
              "dateOfLoading": "01/25/2016",
              "ensemblReleaseDate": "02/08/2014"
            },
            {
              "chromosome": "9",
              "startPosition": 1,
              "endPosition": 141213431,
              "dateOfLoading": "01/25/2016",
              "ensemblReleaseDate": "02/08/2014"
            },
            {
              "chromosome": "10",
              "startPosition": 1,
              "endPosition": 135534747,
              "dateOfLoading": "01/25/2016",
              "ensemblReleaseDate": "02/08/2014"
            },
            {
              "chromosome": "11",
              "startPosition": 1,
              "endPosition": 135006516,
              "dateOfLoading": "01/25/2016",
              "ensemblReleaseDate": "02/08/2014"
            },
            {
              "chromosome": "12",
              "startPosition": 1,
              "endPosition": 133851895,
              "dateOfLoading": "01/25/2016",
              "ensemblReleaseDate": "02/08/2014"
            },
            {
              "chromosome": "13",
              "startPosition": 1,
              "endPosition": 115169878,
              "dateOfLoading": "01/25/2016",
              "ensemblReleaseDate": "02/08/2014"
            },
            {
              "chromosome": "14",
              "startPosition": 1,
              "endPosition": 107349540,
              "dateOfLoading": "01/25/2016",
              "ensemblReleaseDate": "02/08/2014"
            },
            {
              "chromosome": "15",
              "startPosition": 1,
              "endPosition": 102531392,
              "dateOfLoading": "01/25/2016",
              "ensemblReleaseDate": "02/08/2014"
            },
            {
              "chromosome": "16",
              "startPosition": 1,
              "endPosition": 90354753,
              "dateOfLoading": "01/25/2016",
              "ensemblReleaseDate": "02/08/2014"
            },
            {
              "chromosome": "17",
              "startPosition": 1,
              "endPosition": 81195210,
              "dateOfLoading": "01/25/2016",
              "ensemblReleaseDate": "02/08/2014"
            },
            {
              "chromosome": "18",
              "startPosition": 1,
              "endPosition": 78077248,
              "dateOfLoading": "01/25/2016",
              "ensemblReleaseDate": "02/08/2014"
            },
            {
              "chromosome": "19",
              "startPosition": 1,
              "endPosition": 59128983,
              "dateOfLoading": "01/25/2016",
              "ensemblReleaseDate": "02/08/2014"
            },
            {
              "chromosome": "20",
              "startPosition": 1,
              "endPosition": 63025520,
              "dateOfLoading": "01/25/2016",
              "ensemblReleaseDate": "02/08/2014"
            },
            {
              "chromosome": "21",
              "startPosition": 1,
              "endPosition": 48129895,
              "dateOfLoading": "01/25/2016",
              "ensemblReleaseDate": "02/08/2014"
            },
            {
              "chromosome": "22",
              "startPosition": 1,
              "endPosition": 51304566,
              "dateOfLoading": "01/25/2016",
              "ensemblReleaseDate": "02/08/2014"
            },
            {
              "chromosome": "X",
              "startPosition": 1,
              "endPosition": 155270560,
              "dateOfLoading": "01/25/2016",
              "ensemblReleaseDate": "02/08/2014"
            },
            {
              "chromosome": "Y",
              "startPosition": 1,
              "endPosition": 10000,
              "dateOfLoading": "01/25/2016",
              "ensemblReleaseDate": "02/08/2014"
            },
            {
              "chromosome": "Y",
              "startPosition": 2649521,
              "endPosition": 59034049,
              "dateOfLoading": "01/25/2016",
              "ensemblReleaseDate": "02/08/2014"
            },
            {
              "chromosome": "MT",
              "startPosition": 1,
              "endPosition": 16569,
              "dateOfLoading": "01/25/2016",
              "ensemblReleaseDate": "02/08/2014"
            }
          ],
          "isPreferred": "Y"
        },
        {
          "versionWID": 21,
          "ensemblVersion": "GRCH37.70",
          "chromosome": [
            {
              "chromosome": "Y",
              "startPosition": 2649521,
              "endPosition": 59034049,
              "dateOfLoading": "12/13/2016",
              "ensemblReleaseDate": "12/12/2012"
            },
            {
              "chromosome": "Y",
              "startPosition": 1,
              "endPosition": 10000,
              "dateOfLoading": "12/13/2016",
              "ensemblReleaseDate": "12/12/2012"
            }
          ],
          "isPreferred": "N"
        }
      ]
    }
  ],
  "count": 1,
  "hasMore": false,
  "links": [
    {
      "rel": "self",
      "href": "http://localhost:7010/ohfapi/cg/v3.3/genomeAssemblyDetails?id=1&id=2&id=3&limit=10&offset=0"
    }
  ]
}

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