Clinical Genomic APIs for Oracle Healthcare Foundation

Retrieve Genes for Chromosome

get

/ohfapi/cg/v3.3/genes/byChromosome/{name}/{id}

This endpoint supports the retrieval of Genes for Chromosome Name, Start Position, End Position and Assembly/Alignment Identifier passed. It returns Gene information like Gene Name, HUGO Name, Assembly/Alignment, Chromosome and other Gene related information.

Request

Supported Media Types

application/json
application/xml

Path Parameters

id: integer(int64)

AlignmentWid
name: string

chromosomeName

Query Parameters

end_pos(optional): integer(int64)

end_position
limit(optional): integer(int32)

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

Row number to start from
start_pos(optional): integer(int64)

start_position

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 : PageableCollectionGene

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/Gene"
            }
        },
        "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 Gene

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

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 : Gene

Type: object

Show Source

assembly(optional): string

Assembly/Alignment Name. For ex.,GRCh38
cancerGenes(optional): object LinkedReference
chromosome(optional): string

Chromosome Name. For ex.,'Y'
chromosomeReference(optional): object LinkedReference
description(optional): string

Gene Description
diseaseGenes(optional): object LinkedReference
drugGenes(optional): object LinkedReference
geneName(optional): string

Gene Name. For ex.,RN5S300
geneReference(optional): object LinkedReference
geneXref(optional): object LinkedReference
genomicPositions(optional): object LinkedReference
hugoName(optional): string

Approved HUGO symbol for species loci, including protein coding genes, RNA genes and pseudogenes, e.g. 'SRY', 'DMRT1', 'FOXL2', etc.
identifier(optional): object Identifier

Identifier assigned by a given system
pathways(optional): object LinkedReference
resourceType(optional): string
transcripts(optional): object LinkedReference

{
    "type":"object",
    "properties":{
        "resourceType":{
            "type":"string"
        },
        "identifier":{
            "description":"Gene Identifier",
            "$ref":"#/definitions/Identifier"
        },
        "geneName":{
            "type":"string",
            "description":"Gene Name. For ex.,RN5S300"
        },
        "hugoName":{
            "type":"string",
            "description":"Approved HUGO symbol for species loci, including protein coding genes, RNA genes and pseudogenes, e.g. 'SRY', 'DMRT1', 'FOXL2', etc. "
        },
        "assembly":{
            "type":"string",
            "description":"Assembly/Alignment Name. For ex.,GRCh38"
        },
        "chromosomeReference":{
            "$ref":"#/definitions/LinkedReference"
        },
        "chromosome":{
            "type":"string",
            "description":"Chromosome Name. For ex.,'Y'"
        },
        "geneReference":{
            "example":"{href: '/genes/{geneId}'}",
            "description":"A link containing href to retrieve Gene details",
            "$ref":"#/definitions/LinkedReference"
        },
        "description":{
            "type":"string",
            "description":"Gene Description"
        },
        "genomicPositions":{
            "example":"{href: '/genes/{geneId}/genomicPositions'}",
            "description":"A link containing href to retrieve Gene Genomic Position details",
            "$ref":"#/definitions/LinkedReference"
        },
        "transcripts":{
            "example":"{href: '/genes/{geneId}/transcripts'}",
            "description":"A link containing href to retrieve Gene Transcipt details",
            "$ref":"#/definitions/LinkedReference"
        },
        "pathways":{
            "example":"{href: '/genes/{geneId}/pathways'}",
            "description":"A link containing href to retrieve Gene Pathway details",
            "$ref":"#/definitions/LinkedReference"
        },
        "diseaseGenes":{
            "example":"{href: '/genes/{geneId}/diseases'}",
            "description":"A link containing href to retrieve Gene Disease details",
            "$ref":"#/definitions/LinkedReference"
        },
        "drugGenes":{
            "example":"{href: '/genes/{geneId}/drugs'}",
            "description":"A link containing href to retrieve Gene Drug details",
            "$ref":"#/definitions/LinkedReference"
        },
        "cancerGenes":{
            "example":"{href: '/genes/{geneId}/cancer'}",
            "description":"A link containing href to retrieve Gene Cancer details",
            "$ref":"#/definitions/LinkedReference"
        },
        "geneXref":{
            "example":"{href: '/genes/{geneId}/geneXref'}",
            "description":"A link containing href to retrieve Gene Xref details",
            "$ref":"#/definitions/LinkedReference"
        }
    }
}

Nested Schema : LinkedReference

Type: object

Show Source

display(optional): string
reference(optional): string

{
    "type":"object",
    "properties":{
        "reference":{
            "type":"string"
        },
        "display":{
            "type":"string"
        }
    }
}

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"
}

400 Response

Invalid parameters supplied

404 Response

Genes(s) not found

Examples

The following example submits a GET request.

API URL

http://localhost:7010/ohfapi/cg/v3.3/genes/byChromosome/1/1?start_pos=1000&end_pos=3000&limit=10&offset=0

Example of Response Body

The following example shows the contents of the response body in JSON format:

{
 "resourceType": "Genes",
  "items": [
    {
      "identifier": {
        "system": "ODB",
        "value": "33687"
      },
      "geneName": "ENSG00000211459",
      "hugoName": "MT-RNR1",
      "assembly": "GRCh37",
      "chromosome": "MT",
      "geneReference": {
        "reference": "/ohfapi/cg/v3.3/genes/33687"
      }
    },
    {
      "identifier": {
        "system": "ODB",
        "value": "33688"
      },
      "geneName": "ENSG00000210077",
      "hugoName": "MT-TV",
      "assembly": "GRCh37",
      "chromosome": "MT",
      "geneReference": {
        "reference": "/ohfapi/cg/v3.3/genes/33688"
      }
    }
  ],
  "count": 2,
  "hasMore": true,
  "links": [
    {
      "rel": "self",
      "href": "http://localhost:7010/ohfapi/cg/v3.3/genes/byChromosome/1/1?start_pos=1000&end_pos=3000&limit=2&offset=0"
    },
    {
      "rel": "next",
      "href": "http://localhost:7010/ohfapi/cg/v3.3/genes/byChromosome/1/1?offset=2&end_pos=3000&limit=2&start_pos=1000"
    }
  ]}