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Retrieve Clinical Specimens having Omics Data for Specimen Identifiers

get

/ohfapi/cg/v3.3/{apiContext}/clinicalspecimens/hasOmicsData

This endpoint supports the retrieval of the Patient/Subject Clinical Specimens, which have at least one corresponding Omics Specimen, for the multiple Clinical Specimen Row IDs. It returns Paginated list of the Patient/Subject Clinical Specimens information like Identifier and Reference Link to the Patient/Subject details. If none of submitted Specimens has Omics Data, API returns 'Not Found' exception.

Request

Supported Media Types

• application/json
• application/xml

Path Parameters

• apiContext: string
  Pattern: subjectapi|patientapi

  Patient/Subject API context

Query Parameters

• id: array
  Collection Format: multi

  Minimum Number of Items: 1

  Maximum Number of Items: 2147483647

  Patient/Subject Clinical Specimen Row IDs List

  • [0]: integer(int64)

  {
      "name":"id",
      "in":"query",
      "description":"Patient/Subject Clinical Specimen Row IDs List",
      "required":true,
      "type":"array",
      "items":{
          "type":"integer",
          "format":"int64"
      },
      "collectionFormat":"multi",
      "maxItems":2147483647,
      "minItems":1
  }

• limit(optional): integer(int32)
  Pagination query params: ?limit=2&offset=0
• offset(optional): integer(int32)
  Pagination query params: ?limit=2&offset=0

Security

• basicAuth: basic
  Type: basic

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Response

Supported Media Types

• application/json
• application/xml

200 Response

successful operation

Body ()

Root Schema : PageableCollectionClinicalSpecimen

Type: object

Model for paginated collections of data.

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• count(optional): integer(int64)
  Number of objects in the 'items' collection.
• hasMore(optional): boolean
  A boolean indicating if more pages are available.
• 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/ClinicalSpecimen"
            }
        },
        "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"
            }
        }
    },
    "description":"Model for paginated collections of data."
}

Nested Schema : items

Type: array

A collection of paged items.

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• Array of: object ClinicalSpecimen
  Model for a Clinical Specimen object in CDM.

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

Nested Schema : links

Type: array

A collection of links containing hrefs to the current, next, and previous pages as applicable.

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• 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 : ClinicalSpecimen

Type: object

Model for a Clinical Specimen object in CDM.

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• accessionIdentifier(optional): string
  The Clinical Specimen identifier.
• biospecimenIdentifier(optional): string
  Biospecimen Identifier.
• collection(optional): object Collection
  Model for a Clinical Specimen Collection details object in CDM.
• cutThicknessUnitOfMeasure(optional): object Coding
  Model for a reference to a code defined by a terminology system.
• expirationDate(optional): string(date-time)
  The Clinical Specimen expiration date and time.
• identifier(optional): object Identifier
  Identifier assigned by a given system
• maximumCutThickness(optional): string
  The Clinical Specimen maximum Cut Thickness.
• mininumCutThickness(optional): string
  The Clinical Specimen mininum Cut Thickness.
• obtainedQuantityUnitOfMeasure(optional): object Coding
  Model for a reference to a code defined by a terminology system.
• patient(optional): object LinkedReference
• patientconditions(optional): object LinkedReference
• patientprocedure(optional): string
  Reference link to the procedure
• patientprocedures(optional): object LinkedReference
• receivedDate(optional): string(date-time)
  The Clinical Specimen received date and time.
• resourceType(optional): string
  API resource type. it's included if Response is not paginated.
• sentDate(optional): string(date-time)
  The Clinical Specimen sent date and time.
• sizeUnitOfMeasure(optional): object Coding
  Model for a reference to a code defined by a terminology system.
• specCollectionProcId(optional): string
  Clinical Specimen Collection Procedure Identifier.
• specimenFinalWeight(optional): string
  The Clinical Specimen Final Weight.
• specimenHeight(optional): string
  The Clinical Specimen Height.
• specimenInitialWeight(optional): string
  The Clinical Specimen Initial Weight.
• specimenIntermediateWeight(optional): string
  The Clinical Specimen Intermediate Weight.
• specimenLength(optional): string
  The Clinical Specimen Length.
• specimenObtainedQuantity(optional): string
  The Clinical Specimen Obtained Quantity.
• specimenPrepType(optional): object CodeableConcept
  Model that represents a value as a reference to one or more terminologies or ontologies or defined by the provision of text.
• specimenReportIdentifier(optional): string
  Clinical Specimen Report Identifier.
• specimenStorageStatus(optional): object CodeableConcept
  Model that represents a value as a reference to one or more terminologies or ontologies or defined by the provision of text.
• specimenVendorNumber(optional): string
  The Clinical Specimen Vendor identifier.
• specimenWidth(optional): string
  The Clinical Specimen Width.
• status(optional): object Coding
  Model for a reference to a code defined by a terminology system.
• subject(optional): object LinkedReference
• subtype(optional): object CodeableConcept
  Model that represents a value as a reference to one or more terminologies or ontologies or defined by the provision of text.
• type(optional): object CodeableConcept
  Model that represents a value as a reference to one or more terminologies or ontologies or defined by the provision of text.
• weightUnitOfMeasure(optional): object Coding
  Model for a reference to a code defined by a terminology system.

{
    "type":"object",
    "properties":{
        "resourceType":{
            "type":"string",
            "description":"API resource type. it's included if Response is not paginated."
        },
        "identifier":{
            "description":"Clinical Specimen Row ID.",
            "$ref":"#/definitions/Identifier"
        },
        "status":{
            "description":"The Clinical Specimen status details, i.e. status code, name, description etc.",
            "$ref":"#/definitions/Coding"
        },
        "type":{
            "description":"The Clinical Specimen type details, i.e. type code, name, description etc.",
            "$ref":"#/definitions/CodeableConcept"
        },
        "subtype":{
            "description":"The Clinical Specimen subtype details, i.e. subtype code, name, description etc.",
            "$ref":"#/definitions/CodeableConcept"
        },
        "accessionIdentifier":{
            "type":"string",
            "description":"The Clinical Specimen identifier."
        },
        "specimenVendorNumber":{
            "type":"string",
            "description":"The Clinical Specimen Vendor identifier."
        },
        "sentDate":{
            "type":"string",
            "format":"date-time",
            "description":"The Clinical Specimen sent date and time."
        },
        "receivedDate":{
            "type":"string",
            "format":"date-time",
            "description":"The Clinical Specimen received date and time."
        },
        "expirationDate":{
            "type":"string",
            "format":"date-time",
            "description":"The Clinical Specimen expiration date and time."
        },
        "collection":{
            "description":"The Clinical Specimen Collection details, i.e. collection date and time, method, body site, and quantity.",
            "$ref":"#/definitions/Collection"
        },
        "specimenLength":{
            "type":"string",
            "description":"The Clinical Specimen Length."
        },
        "specimenWidth":{
            "type":"string",
            "description":"The Clinical Specimen Width."
        },
        "specimenHeight":{
            "type":"string",
            "description":"The Clinical Specimen Height."
        },
        "sizeUnitOfMeasure":{
            "description":"The Clinical Specimen Size unit of measure (UOM) details, i.e. UOM code, name, description etc.",
            "$ref":"#/definitions/Coding"
        },
        "mininumCutThickness":{
            "type":"string",
            "description":"The Clinical Specimen mininum Cut Thickness."
        },
        "maximumCutThickness":{
            "type":"string",
            "description":"The Clinical Specimen maximum Cut Thickness."
        },
        "cutThicknessUnitOfMeasure":{
            "description":"The Clinical Specimen Cut Thickness unit of measure (UOM) details, i.e. UOM code, name, description etc.",
            "$ref":"#/definitions/Coding"
        },
        "specimenInitialWeight":{
            "type":"string",
            "description":"The Clinical Specimen Initial Weight."
        },
        "specimenIntermediateWeight":{
            "type":"string",
            "description":"The Clinical Specimen Intermediate Weight."
        },
        "specimenFinalWeight":{
            "type":"string",
            "description":"The Clinical Specimen Final Weight."
        },
        "weightUnitOfMeasure":{
            "description":"The Clinical Specimen Weight unit of measure (UOM) details, i.e. UOM code, name, description etc.",
            "$ref":"#/definitions/Coding"
        },
        "specimenObtainedQuantity":{
            "type":"string",
            "description":"The Clinical Specimen Obtained Quantity."
        },
        "obtainedQuantityUnitOfMeasure":{
            "description":"The Clinical Specimen Obtained Quantity unit of measure (UOM) details, i.e. UOM code, name, description etc..",
            "$ref":"#/definitions/Coding"
        },
        "biospecimenIdentifier":{
            "type":"string",
            "description":"Biospecimen Identifier."
        },
        "specimenReportIdentifier":{
            "type":"string",
            "description":"Clinical Specimen Report Identifier."
        },
        "specCollectionProcId":{
            "type":"string",
            "description":"Clinical Specimen Collection Procedure Identifier."
        },
        "specimenPrepType":{
            "description":"Clinical Specimen Preparation Type.",
            "$ref":"#/definitions/CodeableConcept"
        },
        "specimenStorageStatus":{
            "description":"Clinical Specimen Storage Status.",
            "$ref":"#/definitions/CodeableConcept"
        },
        "patientprocedure":{
            "type":"string",
            "description":"Reference link to the procedure"
        },
        "subject":{
            "description":"Reference link to the subject",
            "$ref":"#/definitions/LinkedReference"
        },
        "patient":{
            "description":"Reference link to the patient",
            "$ref":"#/definitions/LinkedReference"
        },
        "patientconditions":{
            "description":"Reference link to the conditions",
            "$ref":"#/definitions/LinkedReference"
        },
        "patientprocedures":{
            "description":"Reference link to the procedures",
            "$ref":"#/definitions/LinkedReference"
        }
    },
    "description":"Model for a Clinical Specimen object in CDM."
}

Nested Schema : Collection

Type: object

Model for a Clinical Specimen Collection details object in CDM.

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• bodySite(optional): object CodeableConcept
  Model that represents a value as a reference to one or more terminologies or ontologies or defined by the provision of text.
• collectedDateTime(optional): string(date-time)
  The Clinical Specimen collection date and time.
• method(optional): object Coding
  Model for a reference to a code defined by a terminology system.
• quantity(optional): object Quantity
  Model for a Quantity object in CDM.

{
    "type":"object",
    "properties":{
        "collectedDateTime":{
            "type":"string",
            "format":"date-time",
            "description":"The Clinical Specimen collection date and time."
        },
        "method":{
            "description":"Technique used to perform collection, i.e. collection method code, name , description, etc.",
            "$ref":"#/definitions/Coding"
        },
        "bodySite":{
            "description":"Anatomical collection site details, i.e. anatomical collection site code, name, description, etc.",
            "$ref":"#/definitions/CodeableConcept"
        },
        "quantity":{
            "description":"The quantity of specimen collected, i.e. collection quantity value, units name, code, description, etc.",
            "$ref":"#/definitions/Quantity"
        }
    },
    "description":"Model for a Clinical Specimen Collection details object in CDM."
}

Nested Schema : Coding

Type: object

Model for a reference to a code defined by a terminology system.

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• code(optional): string
  Symbol in syntax defined by the system.
• description(optional): string
  Description defined by the system.
• display(optional): string
  Representation defined by the system.
• srvcProviderId(optional): string
  Service Provider Id of Specimen Alias .
• srvcProviderName(optional): string
  Service Provider Name of Specimen Alias .
• sysId(optional): string
  Identity of the terminology system.
• sysName(optional): string
  Name of the terminology system.
• sysVersion(optional): string
  Version of the system - if relevant.

{
    "type":"object",
    "properties":{
        "code":{
            "type":"string",
            "description":"Symbol in syntax defined by the system."
        },
        "display":{
            "type":"string",
            "description":"Representation defined by the system."
        },
        "description":{
            "type":"string",
            "description":"Description defined by the system."
        },
        "sysId":{
            "type":"string",
            "description":"Identity of the terminology system."
        },
        "sysName":{
            "type":"string",
            "description":"Name of the terminology system."
        },
        "sysVersion":{
            "type":"string",
            "description":"Version of the system - if relevant."
        },
        "srvcProviderId":{
            "type":"string",
            "description":"Service Provider Id of Specimen Alias ."
        },
        "srvcProviderName":{
            "type":"string",
            "description":"Service Provider Name of Specimen Alias ."
        }
    },
    "description":"Model for a reference to a code defined by a terminology system."
}

Nested Schema : Identifier

Type: object

Identifier assigned by a given system

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• 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 : LinkedReference

Type: object

Show Source

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

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

Nested Schema : CodeableConcept

Type: object

Model that represents a value as a reference to one or more terminologies or ontologies or defined by the provision of text.

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• coding(optional): array coding
  Read Only: true

  Code(s) defined by a terminology system.
• text(optional): string
  Plain text representation of the concept.

{
    "type":"object",
    "properties":{
        "text":{
            "type":"string",
            "description":"Plain text representation of the concept."
        },
        "coding":{
            "type":"array",
            "description":"Code(s) defined by a terminology system.",
            "readOnly":true,
            "items":{
                "xml":{
                    "name":"coding"
                },
                "$ref":"#/definitions/Coding"
            }
        }
    },
    "description":"Model that represents a value as a reference to one or more terminologies or ontologies or defined by the provision of text."
}

Nested Schema : Quantity

Type: object

Model for a Quantity object in CDM.

Show Source

• code(optional): string
  The quantity units symbol in syntax defined by the system.
• description(optional): string
  The quantity units description.
• sysId(optional): string
  The quantity units terminology system identifier.
• sysName(optional): string
  The quantity units terminology system name.
• sysVersion(optional): string
  The quantity units terminology system version.
• units(optional): string
  The quantity units displayable name.
• value(optional): string
  The numerical value of the quantity.

{
    "type":"object",
    "properties":{
        "value":{
            "type":"string",
            "description":"The numerical value of the quantity."
        },
        "units":{
            "type":"string",
            "description":"The quantity units displayable name."
        },
        "code":{
            "type":"string",
            "description":"The quantity units symbol in syntax defined by the system."
        },
        "description":{
            "type":"string",
            "description":"The quantity units description."
        },
        "sysId":{
            "type":"string",
            "description":"The quantity units terminology system identifier."
        },
        "sysName":{
            "type":"string",
            "description":"The quantity units terminology system name."
        },
        "sysVersion":{
            "type":"string",
            "description":"The quantity units terminology system version."
        }
    },
    "description":"Model for a Quantity object in CDM."
}

Nested Schema : coding

Type: array

Read Only: true

Code(s) defined by a terminology system.

Show Source

• Array of: object Coding
  Model for a reference to a code defined by a terminology system.

{
    "type":"array",
    "description":"Code(s) defined by a terminology system.",
    "readOnly":true,
    "items":{
        "xml":{
            "name":"coding"
        },
        "$ref":"#/definitions/Coding"
    }
}

400 Response

Invalid parameters supplied

404 Response

Clinical specimen or clinical specimen metadata not found

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Examples

The following example submits a GET request.

API URL ??? Patient Context

http://localhost:7010/ohfapi/cg/v3.3/patientapi/clinicalspecimens/hasOmicsData?id=96&id=97&limit=20&offset=0

Example of Response Body

The following example shows the response returned in JSON format.

{
  "resourceType": "Specimen",
  "items": [
    {
      "identifier": {
        "system": "CDM",
        "value": "96"
      },
      "patient": {
        "reference": "/ohfapi/cg/v3.3/patientapi/clinicalspecimens/96"
      }
    },
    {
      "identifier": {
        "system": "CDM",
        "value": "97"
      },
      "patient": {
        "reference": "/ohfapi/cg/v3.3/patientapi/clinicalspecimens/97"
      }
    }
  ],
  "count": 2,
  "hasMore": false,
  "links": [
    {
      "rel": "self",
      "href": "http://localhost:7010/ohfapi/cg/v3.3/patientapi/clinicalspecimens/hasOmicsData?id=96&id=97&limit=20&offset=0"
    }
  ]
}

API URL ??? Subject Context

http://localhost:7010/ohfapi/cg/v3.3/subjectapi/clinicalspecimens/hasOmicsData?id=96&id=97&limit=20&offset=0

Example of Response Body

The following example shows the response returned in JSON format.

{
  "resourceType": "Specimen",
  "items": [
    {
      "identifier": {
        "system": "CDM",
        "value": "96"
      },
      "subject": {
        "reference": "/ohfapi/cg/v3.3/subjectapi/clinicalspecimens/96"
      }
    },
    {
      "identifier": {
        "system": "CDM",
        "value": "97"
      },
      "subject": {
        "reference": "/ohfapi/cg/v3.3/subjectapi/clinicalspecimens/97"
      }
    }
  ],
  "count": 2,
  "hasMore": false,
  "links": [
    {
      "rel": "self",
      "href": "http://localhost:7010/ohfapi/cg/v3.3/subjectapi/clinicalspecimens/hasOmicsData?id=96&id=97&limit=20&offset=0"
    }
  ]
}

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