Clinical Genomic APIs for Oracle Healthcare Foundation

Retrieve Genomic Assembly Details for an Assembly Name

get

/ohfapi/cg/v3.3/genomeAssemblyDetails/byName/{name}

This endpoint supports the retrieval of Genomic Assembly Details by single Assembly/Alignment Name passed. It returns Genomic Assembly Detail information like Assembly/Alignment Identifier, Assembly/Alignment Alias, Species, Name, PAR, Ensembl Version, Chromosome, Start Position, End Position, Date Of Loading, Version Identifier, Is Prefered version and other Genomic Assembly associated information.

Request

Supported Media Types

application/json
application/xml

Path Parameters

name: string

Query Parameters

limit(optional): integer(int32)

Number of rows to return
offset(optional): integer(int32)

Row number to start from

Security

basicAuth: basic

Type: basic

Response

Supported Media Types

application/json
application/xml

200 Response

successful operation

Root Schema : PageableCollection

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/Serializable"
            }
        },
        "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 Serializable

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

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 : Serializable

Type: object

400 Response

Invalid parameter supplied

404 Response

genome assembly not found

Examples

The following example shows how to view the genomic assembly details for a single assembly or alignment name passed by submitting a GET request.

API URL

http://localhost:7010/ohfapi/cg/v3.3/genomeAssemblyDetails/byName/GRCh37

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/byName/GRCh37"
    }
  ]
}