Clinical Genomic APIs for Oracle Healthcare Foundation

Retrieve Genomic Assembly Reference Versions for Assembly Identifiers

get

/ohfapi/cg/v3.3/genomeAssemblyRefVersions

This endpoint supports the retrieval of Genomic Assembly Reference Versions for multiple Assembly/Alignment Identifiers. It returns Genomic Assembly Reference Version information like Version Identifiers, Version Name and other associated information.

Request

Supported Media Types

application/json
application/xml

Query Parameters

id: array

Collection Format: multi

Minimum Number of Items: 0

Maximum Number of Items: 2147483647

List of Assembly/Alignment Identifier

[0]: integer(int64)

{
    "name":"id",
    "in":"query",
    "description":"List of Assembly/Alignment Identifier",
    "required":true,
    "type":"array",
    "items":{
        "type":"integer",
        "format":"int64"
    },
    "collectionFormat":"multi",
    "maxItems":2147483647,
    "minItems":0
}

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

Model for paginated collections of data.

Root Schema : PageableCollectionDNARefVersion

Type: object

Model for paginated collections of data.

Show Source

count(optional): integer(int64)

Number of objects in the 'items' collection.
hasMore(optional): boolean

Default Value: false

A boolean indicating if more pages are available.
items(optional): array items

A collection of paged items.
links(optional): array link

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":{
                "name":"items",
                "wrapped":true
            },
            "description":"A collection of paged items.",
            "items":{
                "$ref":"#/definitions/DNARefVersion"
            }
        },
        "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.",
            "default":false
        },
        "links":{
            "type":"array",
            "example":"{rel: 'next',href: '/patientapi/patients?limit=100&offset=300'}",
            "xml":{
                "name":"link",
                "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 DNARefVersion

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

Nested Schema : link

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":{
        "name":"link",
        "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 : 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 : Identifier

Type: object

Identifier assigned by a given system

Show Source

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 : 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"
        }
    }
}

400 Response

Invalid parameters supplied

404 Response

genomeAssembly ensemblVersions not found

Examples

The following example shows how to view the genomic assembly reference versions for multiple assembly or alignment identifiers by submitting a GET request.

API URL

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

Example of Response Body

The following example shows the response returned in JSON format.

{
  "resourceType": "EnsemblVersions",
  "items": [
    {
      "identifier": {
        "system": "ODB",
        "value": "2"
      },
      "ensemblVersion": "GRCH37.75"
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "21"
      },
      "ensemblVersion": "GRCH37.70"
    }
  ],
  "count": 2,
  "hasMore": false,
  "links": [
    {
      "rel": "self",
      "href": "http://localhost:7010/ohfapi/cg/v3.3/genomeAssemblyRefVersions?id=1&id=2&limit=10&offset=0"
    }
  ]
}