Clinical Genomic APIs for Oracle Healthcare Foundation

Retrieve Pathways

get

/ohfapi/cg/v3.3/pathways

This endpoint supports the retrieval of Pathways. It returns Pathway information like Pathway Identifier, Name, Source, Pathway Version, Species, Member Count and other Pathway associated information.

Request

Supported Media Types

application/json
application/xml

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 : PageableCollectionPathway

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/Pathway"
            }
        },
        "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 Pathway

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

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 : Pathway

Type: object

Show Source

geneReference(optional): object LinkedReference
identifier(optional): object Identifier

Identifier assigned by a given system
memberCount(optional): integer(int64)

Count of Gene symbols as per HUGO database
pathwayMember(optional): object LinkedReference
pathwayName(optional): string

Pathway Name for the Protien. For ex.,CCDC3
pathwaySource(optional): string

Reference to the Source where the Pathway was obtained. For ex.,Reactome
pathwayVersion(optional): string

Pathway Version Label. For ex.,SIFT_VER2_75
species(optional): string

Scientific Species Name

{
    "type":"object",
    "properties":{
        "identifier":{
            "description":"Pathway Identifier",
            "$ref":"#/definitions/Identifier"
        },
        "pathwayName":{
            "type":"string",
            "description":"Pathway Name for the Protien. For ex.,CCDC3"
        },
        "pathwaySource":{
            "type":"string",
            "description":"Reference to the Source where the Pathway was obtained. For ex.,Reactome"
        },
        "pathwayVersion":{
            "type":"string",
            "description":"Pathway Version Label. For ex.,SIFT_VER2_75"
        },
        "species":{
            "type":"string",
            "description":"Scientific Species Name"
        },
        "memberCount":{
            "type":"integer",
            "format":"int64",
            "description":"Count of Gene symbols as per HUGO database"
        },
        "pathwayMember":{
            "example":"{href: 'pathways/{pathwayId}'}",
            "description":"A link containing href to retrieve Pathway details",
            "$ref":"#/definitions/LinkedReference"
        },
        "geneReference":{
            "example":"{href: '/genes/{geneId}'}",
            "description":"A link containing href to retrieve Gene 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

pathways(s) not found

Examples

The following example submits a GET request.

API URL

http://localhost:7010/ohfapi/cg/v3.3/pathways

Example of Response Body

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

{
  "resourceType": "Pathways",
  "items": [
    {
      "identifier": {
        "system": "ODB",
        "value": "1"
      },
      "pathwayName": "The role of Nef in HIV-1 replication and disease pathogenesis",
      "pathwaySource": "REACTOME",
      "pathwayVersion": "GRCH37.75_PATHWAY",
      "species": "homo sapiens",
      "memberCount": 17,
      "pathwayMember": {
        "reference": "/ohfapi/cg/v3.3/pathways/1"
      }
    }],
  "count": 1,
  "hasMore": true,
  "links": [
    {
      "rel": "self",
      "href": "http://localhost:7010/ohfapi/cg/v3.3/pathways"
    }
  ]
}