Clinical Genomic APIs for Oracle Healthcare Foundation

Retrieve Genomic Assembly Details for Assembly Names

get

/ohfapi/cg/v3.3/genomeAssemblyDetails/byName

This endpoint supports the retrieval of Genomic Assembly Details by multiple Assembly/Alignment Names 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

Query Parameters

limit(optional): integer(int32)

Number of rows to return

name(optional): array

Collection Format: multi

ODB one or more alignmentName value

[0]: string

{
    "name":"name",
    "in":"query",
    "description":"ODB one or more alignmentName value",
    "required":false,
    "type":"array",
    "items":{
        "type":"string"
    },
    "collectionFormat":"multi"
}

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 : PageableDetailedCollection

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.
invalidAssemblies(optional): array invalidAssemblies

List of Invalid Assemblies in request.
invalidGeneNames(optional): array invalidGeneNames

List of Invalid Genenames in request.
invalidHugoNames(optional): array invalidHugoNames

List of Invalid Hugonames in request.
invalidReferenceIds(optional): array invalidReferenceIds

List of Invalid Reference IDs in request.
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"
            }
        },
        "invalidReferenceIds":{
            "type":"array",
            "description":"List of Invalid Reference IDs in request.",
            "items":{
                "type":"string"
            }
        },
        "invalidHugoNames":{
            "type":"array",
            "description":"List of Invalid Hugonames in request.",
            "items":{
                "type":"string"
            }
        },
        "invalidGeneNames":{
            "type":"array",
            "description":"List of Invalid Genenames in request.",
            "items":{
                "type":"string"
            }
        },
        "invalidAssemblies":{
            "type":"array",
            "description":"List of Invalid Assemblies in request.",
            "items":{
                "type":"string"
            }
        }
    },
    "description":"Model for paginated collections of data."
}

Nested Schema : invalidAssemblies

Type: array

List of Invalid Assemblies in request.

Show Source

Array of: string

{
    "type":"array",
    "description":"List of Invalid Assemblies in request.",
    "items":{
        "type":"string"
    }
}

Nested Schema : invalidGeneNames

Type: array

List of Invalid Genenames in request.

Show Source

Array of: string

{
    "type":"array",
    "description":"List of Invalid Genenames in request.",
    "items":{
        "type":"string"
    }
}

Nested Schema : invalidHugoNames

Type: array

List of Invalid Hugonames in request.

Show Source

Array of: string

{
    "type":"array",
    "description":"List of Invalid Hugonames in request.",
    "items":{
        "type":"string"
    }
}

Nested Schema : invalidReferenceIds

Type: array

List of Invalid Reference IDs in request.

Show Source

Array of: string

{
    "type":"array",
    "description":"List of Invalid Reference IDs in request.",
    "items":{
        "type":"string"
    }
}

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 assemblies not found

Examples

The following example submits a GET request.

API URL

http://localhost:7010/ohfapi/cg/v3.3/genomeAssemblyDetails/byName?name=grch37&name=grch38&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/byName?name=grch37&name=grch38&limit=10&offset=0"
    }
  ],
  "invalidAssemblies": [
    "grch38"
  ]
}