Clinical Genomic APIs for Oracle Healthcare Foundation

Retrieve Genome Assembly Reference Versions for an Assembly Name

get

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

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

Request

Supported Media Types

application/json
application/xml

Path Parameters

name: string

Assembly/Alignment Name

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

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 parameter supplied

404 Response

genomeAssembly ensemblVersions not found

Examples

The following example submits a GET request.

API URL

http://localhost:7010/ohfapi/cg/v3.3/genomeAssemblyRefVersions/byName/grch37

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/byName/grch37"
    }
  ]
}