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 -
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
Response
Supported Media Types
- application/json
- application/xml
200 Response
successful operation
Root Schema : PageableCollectionClinicalSpecimen
Type:
object
Model for paginated collections of data.
Show Source
-
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
Nested Schema : items
Type:
array
A collection of paged items.
Show Source
-
Array of:
object ClinicalSpecimen
Model for a Clinical Specimen object in CDM.
Nested Schema : links
Type:
array
A collection of links containing hrefs to the current, next, and previous pages as applicable.
Show Source
Example:
{rel: 'next',href: '/patientapi/patients?limit=100&offset=300'}
Nested Schema : ClinicalSpecimen
Type:
object
Model for a Clinical Specimen object in CDM.
Show Source
-
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.
Nested Schema : Collection
Type:
object
Model for a Clinical Specimen Collection details object in CDM.
Show Source
-
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.
Nested Schema : Coding
Type:
object
Model for a reference to a code defined by a terminology system.
Show Source
-
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.
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
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.
Show Source
-
coding(optional):
array coding
Read Only:
true
Code(s) defined by a terminology system. -
text(optional):
string
Plain text representation of the concept.
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.
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.
400 Response
Invalid parameters supplied
404 Response
Clinical specimen or clinical specimen metadata not found
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" } ] }