Genomics API v1
The Cerner variant model represents genomic variants acquired by sequencing the DNA, RNA, or amino acid chains of a sample and defines the framework necessary to support future genomic information in a health care environment. The Variant API is based on the Genetic Observation Fast Healthcare Interoperability Resources (FHIR) resource, and variant data is gathered from multiple sources using FHIR.
Note: You must have a HealtheIntent population ID and data partition ID for your tenant before you can use this API. To get started, log a service record (SR) in eService to the solution of Lab Sequence or contact your Cerner representative.
URL: https://cernerdemo.api.us-1.healtheintent.com/genomics/v1
Variants
Variants are alterations in the most common DNA nucleotide sequence. The term variant can be used to describe an alteration that can be benign, pathogenic, or of unknown significance. The term variant is frequently used in place of the term mutation.
Retrieve a List of Variants
Example Request:
require 'httparty' # Using HTTParty 0.16.2
require 'json'
headers = {
'Authorization' => '<auth_header>',
'Accept' => 'application/json'
}
result = HTTParty.get('https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/variants', headers: headers)
print JSON.pretty_generate(result)
# You can also use wget
curl -X GET https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/variants \
-H 'Authorization: {auth_header}' \
-H 'Accept: application/json'
Example response
{
"items": [
{
"sourcePersonId": "d4sad40b-fa0e-4f13-bc5d-645cea7ed1ds",
"orderId": "a2dad45b-fa0e-4f13-bc5d-645cea7ed3fd",
"id": "f1dad40b-fa0e-4f13-bc5d-645cea7ed1eb",
"text": {
"status": "generated",
"div": "<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">text</div>"
},
"secondaryFinding": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"identifiers": [
{
"use": "official",
"type": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"system": "http://www.example.com/patients",
"value": "44552",
"period": {
"start": "2019-08-29T06:25:13Z",
"end": "2019-10-29T06:12:21Z"
},
"assigner": "registry"
}
],
"status": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"bodySite": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"categories": [
{
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
}
],
"issued": "2018-06-29T06:25:13Z",
"effectiveDateTime": "2019-03-19T06:15:23Z",
"value": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"genes": [
{
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
}
],
"cytogeneticLocations": [
{
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
}
],
"refSequenceAssemblies": [
{
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
}
],
"dnaChg": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"dnaChgType": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"functionalAnnotations": [
{
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
}
],
"variationCode": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"genomicDnaChg": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"genomicSourceClass": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"aminoAcidChg": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"aminoAcidChgType": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"transcriptRefSeq": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"genomicRefSeq": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"sampleAllelicFrequency": {
"value": "25",
"comparator": ">",
"unit": "mcg/L",
"system": "http://unitsofmeasure.org",
"code": "ug"
},
"allelicReadDepths": [
{
"value": "25",
"comparator": ">",
"unit": "mcg/L",
"system": "http://unitsofmeasure.org",
"code": "ug"
}
],
"allelicState": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"copyNumber": "1",
"refAllele": "normal",
"altAllele": "test",
"coordinateSystem": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"exactStartEnd": {
"low": "1.6",
"high": "1.9"
},
"outerStartEnd": {
"low": "1.6",
"high": "1.9"
},
"innerStartEnd": {
"low": "1.6",
"high": "1.9"
},
"cytogenomicNomenclature": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"variantInheritance": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"tags": [
{
"key": "result",
"value": "+ve"
}
],
"comments": [
{
"authorType": "RelatedPerson",
"author": "Labseq Admin",
"time": "2020-11-05T08:15:30+05:30",
"text": "Modified"
}
]
}
],
"totalResults": 1,
"firstLink": "https://cernerdemo.api.us-1.healtheintent.com/example/v1/examples?offset=0&limit=20",
"lastLink": "https://cernerdemo.api.us-1.healtheintent.com/example/v1/examples?offset=0&limit=20"
}
GET /variants
Retrieves a list of all active variants that meet the specified parameters.
Parameters
Parameter | In | Type | Required | Default | Description | Accepted Values |
---|---|---|---|---|---|---|
sourcePersonId | query | string | false | N/A | The unique ID of the person. | - |
orderId | query | string | false | N/A | The unique ID of the order. | - |
geneName | query | string | false | N/A | The gene name of the variant. | - |
offset | query | integer(int32) | false | 0 | The number of results to skip from the beginning of the list of results (typically for the purpose of paging). The minimum offset is 0. There is no maximum offset. | - |
limit | query | integer(int32) | false | 20 | The maximum number of results to display per page. The minimum limit is 1. The maximum limit is 100. | - |
Response Statuses
Status | Meaning | Description | Schema |
---|---|---|---|
200 | OK | OK | VariantValues |
400 | Bad Request | Bad Request | Error |
401 | Unauthorized | Unauthorized | Error |
403 | Forbidden | Forbidden | Error |
404 | Not Found | Not Found | Error |
Create a Variant or Variants
Example Request:
require 'httparty' # Using HTTParty 0.16.2
require 'json'
headers = {
'Authorization' => '<auth_header>',
'Content-Type' => 'application/json',
'Accept' => 'application/json'
}
result = HTTParty.post('https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/variants', headers: headers, body: {"sourcePersonId":"3040865","partitionId":"99f31909-5b3b-4560-8c83-627828b2c97d","populationId":"ab9176be-4303-4e6c-aa8d-219d31e29d76","orderId":"57","variants":[{"text":{"status":"generated","div":"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">text</div>"},"secondaryFinding":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"identifiers":[{"use":"official","type":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"system":"http://www.example.com/patients","value":"44552","period":{"start":"2019-08-29T06:25:13Z","end":"2019-10-29T06:12:21Z"},"assigner":"registry"}],"status":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"bodySite":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"categories":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"issued":"2018-06-29T06:25:13Z","effectiveDateTime":"2019-03-19T06:15:23Z","value":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genes":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"cytogeneticLocations":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"refSequenceAssemblies":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"dnaChg":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"dnaChgType":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"functionalAnnotations":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"variationCode":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genomicDnaChg":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genomicSourceClass":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"aminoAcidChg":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"aminoAcidChgType":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"transcriptRefSeq":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genomicRefSeq":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"sampleAllelicFrequency":{"value":"25","comparator":">","unit":"mcg/L","system":"http://unitsofmeasure.org","code":"ug"},"allelicReadDepths":[{"value":"25","comparator":">","unit":"mcg/L","system":"http://unitsofmeasure.org","code":"ug"}],"allelicState":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"copyNumber":"1","refAllele":"normal","altAllele":"test","coordinateSystem":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"exactStartEnd":{"low":"1.6","high":"1.9"},"outerStartEnd":{"low":"1.6","high":"1.9"},"innerStartEnd":{"low":"1.6","high":"1.9"},"cytogenomicNomenclature":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"variantInheritance":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"tags":[{"key":"result","value":"+ve"}],"comments":[{"authorType":"RelatedPerson","author":"Labseq Admin","time":"2020-11-05T08:15:30+05:30","text":"Modified"}]}]}.to_json )
print JSON.pretty_generate(result)
# You can also use wget
curl -X POST https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/variants \
-H 'Authorization: {auth_header}' \
-H 'Content-Type: application/json' \ \
-H 'Accept: application/json' \
-d {"sourcePersonId":"3040865","partitionId":"99f31909-5b3b-4560-8c83-627828b2c97d","populationId":"ab9176be-4303-4e6c-aa8d-219d31e29d76","orderId":"57","variants":[{"text":{"status":"generated","div":"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">text</div>"},"secondaryFinding":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"identifiers":[{"use":"official","type":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"system":"http://www.example.com/patients","value":"44552","period":{"start":"2019-08-29T06:25:13Z","end":"2019-10-29T06:12:21Z"},"assigner":"registry"}],"status":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"bodySite":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"categories":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"issued":"2018-06-29T06:25:13Z","effectiveDateTime":"2019-03-19T06:15:23Z","value":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genes":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"cytogeneticLocations":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"refSequenceAssemblies":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"dnaChg":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"dnaChgType":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"functionalAnnotations":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"variationCode":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genomicDnaChg":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genomicSourceClass":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"aminoAcidChg":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"aminoAcidChgType":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"transcriptRefSeq":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genomicRefSeq":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"sampleAllelicFrequency":{"value":"25","comparator":">","unit":"mcg/L","system":"http://unitsofmeasure.org","code":"ug"},"allelicReadDepths":[{"value":"25","comparator":">","unit":"mcg/L","system":"http://unitsofmeasure.org","code":"ug"}],"allelicState":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"copyNumber":"1","refAllele":"normal","altAllele":"test","coordinateSystem":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"exactStartEnd":{"low":"1.6","high":"1.9"},"outerStartEnd":{"low":"1.6","high":"1.9"},"innerStartEnd":{"low":"1.6","high":"1.9"},"cytogenomicNomenclature":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"variantInheritance":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"tags":[{"key":"result","value":"+ve"}],"comments":[{"authorType":"RelatedPerson","author":"Labseq Admin","time":"2020-11-05T08:15:30+05:30","text":"Modified"}]}]}
Example response
{
"items": [
{
"variantId": "6313678f-7be1-4a54-a175-98749ab00664"
}
]
}
POST /variants
Creates or adds a variant or variants and saves them to the repository retrieved from FHIR. The variants are saved in the Variants service. The API treats the created or added variant information as the new, complete set of data for the variant.
Parameters
Parameter | In | Type | Required | Default | Description | Accepted Values |
---|---|---|---|---|---|---|
body | body | postVariants | true | N/A | No description | - |
Response Statuses
Status | Meaning | Description | Schema |
---|---|---|---|
201 | Created | Created | VariantIdList |
400 | Bad Request | Bad Request | Error |
401 | Unauthorized | Unauthorized | Error |
403 | Forbidden | Forbidden | Error |
Delete a Single Variant
Example Request:
require 'httparty' # Using HTTParty 0.16.2
require 'json'
headers = {
'Authorization' => '<auth_header>',
'Accept' => 'application/json'
}
result = HTTParty.delete('https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/variants/e92ca89f-8524-451a-9346-666d6ff39329', headers: headers)
print JSON.pretty_generate(result)
# You can also use wget
curl -X DELETE https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/variants/e92ca89f-8524-451a-9346-666d6ff39329 \
-H 'Authorization: {auth_header}' \
-H 'Accept: application/json'
DELETE /variants/{variantId}
Deletes a variant specific to the variant ID provided. The existing variant record is deleted. The implication record must be deleted if there are any associated implications with a single variant.
Parameters
Parameter | In | Type | Required | Default | Description | Accepted Values |
---|---|---|---|---|---|---|
variantId | path | string | true | N/A | The unique ID of the variant. | - |
Response Statuses
Status | Meaning | Description | Schema |
---|---|---|---|
204 | No Content | No content | None |
400 | Bad Request | Bad Request | Error |
401 | Unauthorized | Unauthorized | Error |
403 | Forbidden | Forbidden | Error |
404 | Not Found | Not Found | Error |
Update a Variant
Example Request:
require 'httparty' # Using HTTParty 0.16.2
require 'json'
headers = {
'Authorization' => '<auth_header>',
'Content-Type' => 'application/json',
'Accept' => 'application/json'
}
result = HTTParty.put('https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/variants/65752b39-78ed-496d-983e-64b361ad7890', headers: headers, body: {"sourcePersonId":"3040865","partitionId":"99f31909-5b3b-4560-8c83-627828b2c97d","populationId":"ab9176be-4303-4e6c-aa8d-219d31e29d76","orderId":"57","variant":{"text":{"status":"generated","div":"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">text</div>"},"secondaryFinding":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"identifiers":[{"use":"official","type":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"system":"http://www.example.com/patients","value":"44552","period":{"start":"2019-08-29T06:25:13Z","end":"2019-10-29T06:12:21Z"},"assigner":"registry"}],"status":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"bodySite":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"categories":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"issued":"2018-06-29T06:25:13Z","effectiveDateTime":"2019-03-19T06:15:23Z","value":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genes":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"cytogeneticLocations":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"refSequenceAssemblies":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"dnaChg":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"dnaChgType":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"functionalAnnotations":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"variationCode":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genomicDnaChg":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genomicSourceClass":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"aminoAcidChg":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"aminoAcidChgType":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"transcriptRefSeq":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genomicRefSeq":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"sampleAllelicFrequency":{"value":"25","comparator":">","unit":"mcg/L","system":"http://unitsofmeasure.org","code":"ug"},"allelicReadDepths":[{"value":"25","comparator":">","unit":"mcg/L","system":"http://unitsofmeasure.org","code":"ug"}],"allelicState":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"copyNumber":"1","refAllele":"normal","altAllele":"test","coordinateSystem":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"exactStartEnd":{"low":"1.6","high":"1.9"},"outerStartEnd":{"low":"1.6","high":"1.9"},"innerStartEnd":{"low":"1.6","high":"1.9"},"cytogenomicNomenclature":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"variantInheritance":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"tags":[{"key":"result","value":"+ve"}],"comments":[{"authorType":"RelatedPerson","author":"Labseq Admin","time":"2020-11-05T08:15:30+05:30","text":"Modified"}]}}.to_json )
print JSON.pretty_generate(result)
# You can also use wget
curl -X PUT https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/variants/65752b39-78ed-496d-983e-64b361ad7890 \
-H 'Authorization: {auth_header}' \
-H 'Content-Type: application/json' \ \
-H 'Accept: application/json' \
-d {"sourcePersonId":"3040865","partitionId":"99f31909-5b3b-4560-8c83-627828b2c97d","populationId":"ab9176be-4303-4e6c-aa8d-219d31e29d76","orderId":"57","variant":{"text":{"status":"generated","div":"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">text</div>"},"secondaryFinding":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"identifiers":[{"use":"official","type":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"system":"http://www.example.com/patients","value":"44552","period":{"start":"2019-08-29T06:25:13Z","end":"2019-10-29T06:12:21Z"},"assigner":"registry"}],"status":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"bodySite":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"categories":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"issued":"2018-06-29T06:25:13Z","effectiveDateTime":"2019-03-19T06:15:23Z","value":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genes":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"cytogeneticLocations":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"refSequenceAssemblies":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"dnaChg":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"dnaChgType":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"functionalAnnotations":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"variationCode":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genomicDnaChg":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genomicSourceClass":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"aminoAcidChg":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"aminoAcidChgType":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"transcriptRefSeq":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"genomicRefSeq":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"sampleAllelicFrequency":{"value":"25","comparator":">","unit":"mcg/L","system":"http://unitsofmeasure.org","code":"ug"},"allelicReadDepths":[{"value":"25","comparator":">","unit":"mcg/L","system":"http://unitsofmeasure.org","code":"ug"}],"allelicState":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"copyNumber":"1","refAllele":"normal","altAllele":"test","coordinateSystem":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"exactStartEnd":{"low":"1.6","high":"1.9"},"outerStartEnd":{"low":"1.6","high":"1.9"},"innerStartEnd":{"low":"1.6","high":"1.9"},"cytogenomicNomenclature":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"variantInheritance":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"tags":[{"key":"result","value":"+ve"}],"comments":[{"authorType":"RelatedPerson","author":"Labseq Admin","time":"2020-11-05T08:15:30+05:30","text":"Modified"}]}}
PUT /variants/{variantId}
Updates the variant with the specified ID. The API does not support PATCH
requests to update only certain pieces of the variant data. This means that all known variant data must be specified in each request to update existing variants using all the information.
Parameters
Parameter | In | Type | Required | Default | Description | Accepted Values |
---|---|---|---|---|---|---|
variantId | path | string | true | N/A | The unique ID of the variant. | - |
body | body | putVariants | true | N/A | No description | - |
Response Statuses
Status | Meaning | Description | Schema |
---|---|---|---|
204 | No Content | No content | None |
400 | Bad Request | Bad Request | Error |
401 | Unauthorized | Unauthorized | Error |
403 | Forbidden | Forbidden | Error |
404 | Not Found | Not Found | Error |
Retrieve a Single Variant
Example Request:
require 'httparty' # Using HTTParty 0.16.2
require 'json'
headers = {
'Authorization' => '<auth_header>',
'Accept' => 'application/json'
}
result = HTTParty.get('https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/variants/e92ca89f-8524-451a-9346-666d6ff39329', headers: headers)
print JSON.pretty_generate(result)
# You can also use wget
curl -X GET https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/variants/e92ca89f-8524-451a-9346-666d6ff39329 \
-H 'Authorization: {auth_header}' \
-H 'Accept: application/json'
Example response
{
"sourcePersonId": "d4sad40b-fa0e-4f13-bc5d-645cea7ed1ds",
"orderId": "a2dad45b-fa0e-4f13-bc5d-645cea7ed3fd",
"id": "f1dad40b-fa0e-4f13-bc5d-645cea7ed1eb",
"text": {
"status": "generated",
"div": "<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">text</div>"
},
"secondaryFinding": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"identifiers": [
{
"use": "official",
"type": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"system": "http://www.example.com/patients",
"value": "44552",
"period": {
"start": "2019-08-29T06:25:13Z",
"end": "2019-10-29T06:12:21Z"
},
"assigner": "registry"
}
],
"status": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"bodySite": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"categories": [
{
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
}
],
"issued": "2018-06-29T06:25:13Z",
"effectiveDateTime": "2019-03-19T06:15:23Z",
"value": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"genes": [
{
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
}
],
"cytogeneticLocations": [
{
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
}
],
"refSequenceAssemblies": [
{
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
}
],
"dnaChg": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"dnaChgType": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"functionalAnnotations": [
{
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
}
],
"variationCode": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"genomicDnaChg": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"genomicSourceClass": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"aminoAcidChg": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"aminoAcidChgType": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"transcriptRefSeq": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"genomicRefSeq": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"sampleAllelicFrequency": {
"value": "25",
"comparator": ">",
"unit": "mcg/L",
"system": "http://unitsofmeasure.org",
"code": "ug"
},
"allelicReadDepths": [
{
"value": "25",
"comparator": ">",
"unit": "mcg/L",
"system": "http://unitsofmeasure.org",
"code": "ug"
}
],
"allelicState": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"copyNumber": "1",
"refAllele": "normal",
"altAllele": "test",
"coordinateSystem": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"exactStartEnd": {
"low": "1.6",
"high": "1.9"
},
"outerStartEnd": {
"low": "1.6",
"high": "1.9"
},
"innerStartEnd": {
"low": "1.6",
"high": "1.9"
},
"cytogenomicNomenclature": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"variantInheritance": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"tags": [
{
"key": "result",
"value": "+ve"
}
],
"comments": [
{
"authorType": "RelatedPerson",
"author": "Labseq Admin",
"time": "2020-11-05T08:15:30+05:30",
"text": "Modified"
}
]
}
GET /variants/{variantId}
Retrieves all data for a specified variant ID.
Parameters
Parameter | In | Type | Required | Default | Description | Accepted Values |
---|---|---|---|---|---|---|
variantId | path | string | true | N/A | The unique ID of the variant. | - |
Response Statuses
Status | Meaning | Description | Schema |
---|---|---|---|
200 | OK | OK | VariantValue |
400 | Bad Request | Bad Request | Error |
401 | Unauthorized | Unauthorized | Error |
403 | Forbidden | Forbidden | Error |
404 | Not Found | Not Found | Error |
Implications
Implication is a profile needed to extend understanding of the likely effects a variant may have on the patient, tumor or other subject. These observations can convey potential impact of characteristics, suggested medication or nonmedicinal therapy, and the strength of the evidence behind the assertion.
Retrieve a List of Implications
Example Request:
require 'httparty' # Using HTTParty 0.16.2
require 'json'
headers = {
'Authorization' => '<auth_header>',
'Accept' => 'application/json'
}
result = HTTParty.get('https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/implications', headers: headers)
print JSON.pretty_generate(result)
# You can also use wget
curl -X GET https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/implications \
-H 'Authorization: {auth_header}' \
-H 'Accept: application/json'
Example response
{
"items": [
{
"sourcePersonId": "d4sad40b-fa0e-4f13-bc5d-645cea7ed1ds",
"orderId": "a2dad45b-fa0e-4f13-bc5d-645cea7ed3fd",
"id": "f1dad40b-fa0e-4f13-bc5d-645cea7ed1eb",
"implicationType": "DIAGNOSTIC",
"categories": [
{
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
}
],
"status": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"associatedCancers": [
{
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
}
],
"associatedPhenotypes": [
{
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
}
],
"clinicalSignificance": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"comments": [
{
"authorType": "RelatedPerson",
"author": "Labseq Admin",
"time": "2020-11-05T08:15:30+05:30",
"text": "Modified"
}
],
"effectMedicationEfficacy": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"effectMedicationHighRisk": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"effectMedicationMetabolism": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"evidenceLevel": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"identifiers": [
{
"use": "official",
"type": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"system": "http://www.example.com/patients",
"value": "44552",
"period": {
"start": "2019-08-29T06:25:13Z",
"end": "2019-10-29T06:12:21Z"
},
"assigner": "registry"
}
],
"implicationVariants": [
{
"variantId": "cd3176be-4303-4e6c-aa8d-219d31e29d76"
}
],
"medicationAssessed": [
{
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
}
],
"method": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"modeOfInheritance": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"prognosis": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"secondaryFinding": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"text": {
"status": "generated",
"div": "<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">text</div>"
},
"therapyAssessed": [
{
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
}
]
}
],
"totalResults": 1,
"firstLink": "https://cernerdemo.api.us-1.healtheintent.com/example/v1/examples?offset=0&limit=20",
"lastLink": "https://cernerdemo.api.us-1.healtheintent.com/example/v1/examples?offset=0&limit=20"
}
GET /implications
Retrieves a list of all active implications that meet the specified parameters.
Parameters
Parameter | In | Type | Required | Default | Description | Accepted Values |
---|---|---|---|---|---|---|
sourcePersonId | query | string | false | N/A | The unique ID of the person. | - |
orderId | query | string | false | N/A | The unique ID of the order. | - |
offset | query | integer(int32) | false | 0 | The number of results to skip from the beginning of the list of results (typically for the purpose of paging). The minimum offset is 0. There is no maximum offset. | - |
limit | query | integer(int32) | false | 20 | The maximum number of results to display per page. The minimum limit is 1. The maximum limit is 100. | - |
Response Statuses
Status | Meaning | Description | Schema |
---|---|---|---|
200 | OK | OK | Implications |
400 | Bad Request | Bad Request | Error |
401 | Unauthorized | Unauthorized | Error |
403 | Forbidden | Forbidden | Error |
404 | Not Found | Not Found | Error |
Create an Implication or Implications
Example Request:
require 'httparty' # Using HTTParty 0.16.2
require 'json'
headers = {
'Authorization' => '<auth_header>',
'Content-Type' => 'application/json',
'Accept' => 'application/json'
}
result = HTTParty.post('https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/implications', headers: headers, body: {"sourcePersonId":"3040865","partitionId":"99f31909-5b3b-4560-8c83-627828b2c97d","populationId":"ab9176be-4303-4e6c-aa8d-219d31e29d76","orderId":"57","implications":[{"implicationType":"DIAGNOSTIC","categories":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"status":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"associatedCancers":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"associatedPhenotypes":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"clinicalSignificance":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"comments":[{"authorType":"RelatedPerson","author":"Labseq Admin","time":"2020-11-05T08:15:30+05:30","text":"Modified"}],"effectMedicationEfficacy":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"effectMedicationHighRisk":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"effectMedicationMetabolism":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"evidenceLevel":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"identifiers":[{"use":"official","type":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"system":"http://www.example.com/patients","value":"44552","period":{"start":"2019-08-29T06:25:13Z","end":"2019-10-29T06:12:21Z"},"assigner":"registry"}],"implicationVariants":[{"variantId":"cd3176be-4303-4e6c-aa8d-219d31e29d76"}],"medicationAssessed":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"method":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"modeOfInheritance":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"prognosis":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"secondaryFinding":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"text":{"status":"generated","div":"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">text</div>"},"therapyAssessed":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}]}]}.to_json )
print JSON.pretty_generate(result)
# You can also use wget
curl -X POST https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/implications \
-H 'Authorization: {auth_header}' \
-H 'Content-Type: application/json' \ \
-H 'Accept: application/json' \
-d {"sourcePersonId":"3040865","partitionId":"99f31909-5b3b-4560-8c83-627828b2c97d","populationId":"ab9176be-4303-4e6c-aa8d-219d31e29d76","orderId":"57","implications":[{"implicationType":"DIAGNOSTIC","categories":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"status":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"associatedCancers":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"associatedPhenotypes":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"clinicalSignificance":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"comments":[{"authorType":"RelatedPerson","author":"Labseq Admin","time":"2020-11-05T08:15:30+05:30","text":"Modified"}],"effectMedicationEfficacy":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"effectMedicationHighRisk":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"effectMedicationMetabolism":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"evidenceLevel":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"identifiers":[{"use":"official","type":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"system":"http://www.example.com/patients","value":"44552","period":{"start":"2019-08-29T06:25:13Z","end":"2019-10-29T06:12:21Z"},"assigner":"registry"}],"implicationVariants":[{"variantId":"cd3176be-4303-4e6c-aa8d-219d31e29d76"}],"medicationAssessed":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"method":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"modeOfInheritance":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"prognosis":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"secondaryFinding":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"text":{"status":"generated","div":"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">text</div>"},"therapyAssessed":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}]}]}
Example response
{
"items": [
{
"implicationId": "6313678f-7be1-4a54-a175-98749ab00664"
}
]
}
POST /implications
Creates or adds an implication or implications and saves them to the repository retrieved from Fast Healthcare Interoperability Resources (FHIR). The implications are saved in the variants service. The created or added implication information is treated as the new, complete set of data for the implication.
Parameters
Parameter | In | Type | Required | Default | Description | Accepted Values |
---|---|---|---|---|---|---|
body | body | postImplications | true | N/A | No description | - |
Response Statuses
Status | Meaning | Description | Schema |
---|---|---|---|
201 | Created | Created | ImplicationIdList |
400 | Bad Request | Bad Request | Error |
401 | Unauthorized | Unauthorized | Error |
403 | Forbidden | Forbidden | Error |
Delete a Single Implication
Example Request:
require 'httparty' # Using HTTParty 0.16.2
require 'json'
headers = {
'Authorization' => '<auth_header>',
'Accept' => 'application/json'
}
result = HTTParty.delete('https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/implications/e92ca89f-8524-451a-9346-666d6ff39329', headers: headers)
print JSON.pretty_generate(result)
# You can also use wget
curl -X DELETE https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/implications/e92ca89f-8524-451a-9346-666d6ff39329 \
-H 'Authorization: {auth_header}' \
-H 'Accept: application/json'
DELETE /implications/{implicationId}
Deletes the implication specific to the implication ID provided. The existing implication record is deleted. Variants associated with the implication must not have any impacts.
Parameters
Parameter | In | Type | Required | Default | Description | Accepted Values |
---|---|---|---|---|---|---|
implicationId | path | string | true | N/A | The unique ID of the implication. | - |
Response Statuses
Status | Meaning | Description | Schema |
---|---|---|---|
204 | No Content | No content | None |
400 | Bad Request | Bad Request | Error |
401 | Unauthorized | Unauthorized | Error |
403 | Forbidden | Forbidden | Error |
404 | Not Found | Not Found | Error |
Update an Implication
Example Request:
require 'httparty' # Using HTTParty 0.16.2
require 'json'
headers = {
'Authorization' => '<auth_header>',
'Content-Type' => 'application/json',
'Accept' => 'application/json'
}
result = HTTParty.put('https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/implications/65752b39-78ed-496d-983e-64b361ad7890', headers: headers, body: {"sourcePersonId":"3040865","partitionId":"99f31909-5b3b-4560-8c83-627828b2c97d","populationId":"ab9176be-4303-4e6c-aa8d-219d31e29d76","orderId":"57","implication":{"implicationType":"DIAGNOSTIC","categories":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"status":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"associatedCancers":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"associatedPhenotypes":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"clinicalSignificance":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"comments":[{"authorType":"RelatedPerson","author":"Labseq Admin","time":"2020-11-05T08:15:30+05:30","text":"Modified"}],"effectMedicationEfficacy":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"effectMedicationHighRisk":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"effectMedicationMetabolism":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"evidenceLevel":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"identifiers":[{"use":"official","type":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"system":"http://www.example.com/patients","value":"44552","period":{"start":"2019-08-29T06:25:13Z","end":"2019-10-29T06:12:21Z"},"assigner":"registry"}],"implicationVariants":[{"variantId":"cd3176be-4303-4e6c-aa8d-219d31e29d76"}],"medicationAssessed":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"method":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"modeOfInheritance":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"prognosis":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"secondaryFinding":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"text":{"status":"generated","div":"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">text</div>"},"therapyAssessed":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}]}}.to_json )
print JSON.pretty_generate(result)
# You can also use wget
curl -X PUT https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/implications/65752b39-78ed-496d-983e-64b361ad7890 \
-H 'Authorization: {auth_header}' \
-H 'Content-Type: application/json' \ \
-H 'Accept: application/json' \
-d {"sourcePersonId":"3040865","partitionId":"99f31909-5b3b-4560-8c83-627828b2c97d","populationId":"ab9176be-4303-4e6c-aa8d-219d31e29d76","orderId":"57","implication":{"implicationType":"DIAGNOSTIC","categories":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"status":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"associatedCancers":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"associatedPhenotypes":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"clinicalSignificance":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"comments":[{"authorType":"RelatedPerson","author":"Labseq Admin","time":"2020-11-05T08:15:30+05:30","text":"Modified"}],"effectMedicationEfficacy":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"effectMedicationHighRisk":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"effectMedicationMetabolism":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"evidenceLevel":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"identifiers":[{"use":"official","type":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"system":"http://www.example.com/patients","value":"44552","period":{"start":"2019-08-29T06:25:13Z","end":"2019-10-29T06:12:21Z"},"assigner":"registry"}],"implicationVariants":[{"variantId":"cd3176be-4303-4e6c-aa8d-219d31e29d76"}],"medicationAssessed":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}],"method":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"modeOfInheritance":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"prognosis":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"secondaryFinding":{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]},"text":{"status":"generated","div":"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">text</div>"},"therapyAssessed":[{"text":"Cellulitis of the foot","codings":[{"system":"http://snomed.info/sct","version":"V1","code":"laboratory","display":"AR2"}]}]}}
PUT /implications/{implicationId}
Updates the implication with the specified ID. PATCH
requests to update only certain pieces of the implication data are not supported. This means that all known implication data must be specified in each request to update existing implications using all of the information.
Parameters
Parameter | In | Type | Required | Default | Description | Accepted Values |
---|---|---|---|---|---|---|
implicationId | path | string | true | N/A | The unique ID of the implication. | - |
body | body | putImplications | true | N/A | No description | - |
Response Statuses
Status | Meaning | Description | Schema |
---|---|---|---|
204 | No Content | No content | None |
400 | Bad Request | Bad Request | Error |
401 | Unauthorized | Unauthorized | Error |
403 | Forbidden | Forbidden | Error |
404 | Not Found | Not Found | Error |
Retrieve a Single Implication
Example Request:
require 'httparty' # Using HTTParty 0.16.2
require 'json'
headers = {
'Authorization' => '<auth_header>',
'Accept' => 'application/json'
}
result = HTTParty.get('https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/implications/e92ca89f-8524-451a-9346-666d6ff39329', headers: headers)
print JSON.pretty_generate(result)
# You can also use wget
curl -X GET https://cernerdemo.api.us-1.healtheintent.com/genomics/v1/implications/e92ca89f-8524-451a-9346-666d6ff39329 \
-H 'Authorization: {auth_header}' \
-H 'Accept: application/json'
Example response
{
"sourcePersonId": "d4sad40b-fa0e-4f13-bc5d-645cea7ed1ds",
"orderId": "a2dad45b-fa0e-4f13-bc5d-645cea7ed3fd",
"id": "f1dad40b-fa0e-4f13-bc5d-645cea7ed1eb",
"implicationType": "DIAGNOSTIC",
"categories": [
{
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
}
],
"status": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"associatedCancers": [
{
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
}
],
"associatedPhenotypes": [
{
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
}
],
"clinicalSignificance": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"comments": [
{
"authorType": "RelatedPerson",
"author": "Labseq Admin",
"time": "2020-11-05T08:15:30+05:30",
"text": "Modified"
}
],
"effectMedicationEfficacy": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"effectMedicationHighRisk": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"effectMedicationMetabolism": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"evidenceLevel": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"identifiers": [
{
"use": "official",
"type": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"system": "http://www.example.com/patients",
"value": "44552",
"period": {
"start": "2019-08-29T06:25:13Z",
"end": "2019-10-29T06:12:21Z"
},
"assigner": "registry"
}
],
"implicationVariants": [
{
"variantId": "cd3176be-4303-4e6c-aa8d-219d31e29d76"
}
],
"medicationAssessed": [
{
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
}
],
"method": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"modeOfInheritance": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"prognosis": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"secondaryFinding": {
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
},
"text": {
"status": "generated",
"div": "<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">text</div>"
},
"therapyAssessed": [
{
"text": "Cellulitis of the foot",
"codings": [
{
"system": "http://snomed.info/sct",
"version": "V1",
"code": "laboratory",
"display": "AR2"
}
]
}
]
}
GET /implications/{implicationId}
Retrieves all data for a specified implication ID.
Parameters
Parameter | In | Type | Required | Default | Description | Accepted Values |
---|---|---|---|---|---|---|
implicationId | path | string | true | N/A | The unique ID of the implication. | - |
Response Statuses
Status | Meaning | Description | Schema |
---|---|---|---|
200 | OK | OK | Implication |
400 | Bad Request | Bad Request | Error |
401 | Unauthorized | Unauthorized | Error |
403 | Forbidden | Forbidden | Error |
404 | Not Found | Not Found | Error |
Schema Definitions
VariantValues
Name | Type | Required | Description | Accepted Values |
---|---|---|---|---|
items | [VariantValue] | true | An array containing the current page of results. | - |
totalResults | integer(int32) | false | The total number of results for the specified parameters. | - |
firstLink | string | true | The first page of results. | - |
lastLink | string | false | The last page of results. | - |
prevLink | string | false | The previous page of results. | - |
nextLink | string | false | The next page of results. | - |
VariantValue
Name | Type | Required | Description | Accepted Values |
---|---|---|---|---|
sourcePersonId | string | false | The unique ID of the person. | - |
orderId | string | false | The unique ID of the order. | - |
id | string | false | The unique ID of the variant. | - |
text | Narrative | false | A human-readable narrative that contains a summary of the content in a resource. The narrative must contain enough detail to make it clinically safe for a human to read only the narrative, but it is not required to encode all the structured data. Resource definitions can define what content should be represented in the narrative to ensure clinical safety. | - |
secondaryFinding | CodeableConcept | false | Enables flagging variants that should be considered secondary findings. | - |
identifiers | [Identifier] | false | A unique ID assigned to the observation. | - |
status | CodeableConcept | false | The status of the variant observation or result. | - |
bodySite | CodeableConcept | false | Indicates the site on the patient’s body where the observation was made (the target site). | - |
categories | [CodeableConcept] | false | A code that classifies the general type of the observation. | - |
issued | string(date-time) | false | The date and time on which this version of the observation was made available to providers. This is typically after the results have been reviewed and verified. | - |
effectiveDateTime | string(date-time) | false | The time or time period during which the value was observed. For biological subjects (human patients), this is usually called the physiologically relevant time and is usually the time of either the procedure or specimen collection. The source of the date and time is not usually known, only the date and time itself. | - |
value | CodeableConcept | false | Indicates whether the specified variation was found. | - |
genes | [CodeableConcept] | false | The HUGO Gene Nomenclature Committee (HGNC) ID for a gene. List the gene or genes that were examined in full or in part by the study. If the study addresses multiple genes, they can be recorded in multiple gene-studied components. The required coding uses the HGNC gene symbol as the display text and the HGNC gene ID as the code. | - |
cytogeneticLocations | [CodeableConcept] | false | The cytogenetic (chromosome) location. Some observations contain multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes; for example, systolic and diastolic component observations for blood pressure measurements and multiple component observations for genetics observations. | - |
refSequenceAssemblies | [CodeableConcept] | false | The human reference sequence assembly version. Some observations contain multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes; for example, systolic and diastolic component observations for blood pressure measurements and multiple component observations for genetics observations. | - |
dnaChg | CodeableConcept | false | The DNA change transcript (cHGVS), which is the Human Genome Variation Society (HGVS) nomenclature for a single DNA marker. | - |
dnaChgType | CodeableConcept | false | The codified type for the associated DNA marker. DNA markers use the HGVS notation to imply the DNA marker type, but this code allows you to use a standard and explicit type for technical and display convenience. | - |
functionalAnnotations | [CodeableConcept] | false | Annotated changes that this variant made to sequence features. | - |
variationCode | CodeableConcept | false | The unique ID of the simple variant found in this study. | - |
genomicDnaChg | CodeableConcept | false | The DNA change genomic (gHGVS), which is the HGVS nomenclature for the name of a structural variant. | - |
genomicSourceClass | CodeableConcept | false | The genomic class of the specimen being analyzed. You can use germline for inherited genome, somatic for cancer genome, and prenatal for fetal genome. | - |
aminoAcidChg | CodeableConcept | false | The HGVS nomenclature for an amino acid sequence. You can derive this value from the DNA marker value if it is available. This value is provided for convenience. The use of the nomenclature must be extended to describe nonvariations (wild types). | - |
aminoAcidChgType | CodeableConcept | false | The codified type for the associated amino acid marker. Amino acid markers use the HGVS notation to imply the amino acid marker type, but the concurrent use of this code enables you to use a standard and explicit type for technical and display convenience. | - |
transcriptRefSeq | CodeableConcept | false | The ID for the transcribed reference sequence. This value is the portion of the genomic reference sequence that is converted to messenger RNA after the introns are removed. | - |
genomicRefSeq | CodeableConcept | false | The ID for the genomic reference sequence. The genomic reference sequence is a contiguous stretch of chromosome DNA that spans all of the exons of the gene and includes transcribed and nontranscribed stretches. You can use either the National Center for Biotechnology Information (NCBI) genomic nucleotide RefSeq IDs with their version number (see the RefSeq page on the NCBI Reference Sequence Database website for more information) or the Locus Reference Genomic (LRG) IDs without transcript (t or p) extensions when they become available (see the Locus Reference Genomic website for more information. The NCBI RefSeq genomic IDs are distinguished by a prefix of NG for genes from the nuclear chromosomes and a prefix of NC for genes from mitochondria. The LRG IDs use a prefix of LRG_ . Mitochondrial genes are not in the scope of LRG. |
- |
sampleAllelicFrequency | Quantity | false | The sample allelic frequency. Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes; for example, the systolic and diastolic component observations for blood pressure measurements and multiple component observations for genetics observations. | - |
allelicReadDepths | [Quantity] | false | The allelic read depth specifies the number of reads that identified the allele, whether it consists of one nucleotide or a small sequence of contiguous nucleotides. Different methods and purposes require different numbers of reads, usually more than 400 but possibly as few as 2 to 4. | - |
allelicState | CodeableConcept | false | The allelic state is the level of occurrence of a single DNA marker in a set of chromosomes. Heterozygous indicates that the DNA marker is present in only one of the two genes contained in homologous chromosomes. Homozygous indicates that the DNA marker is present in both genes contained in homologous chromosomes. Hemizygous indicates that the DNA marker exists in the only single copy of a gene in a nonhomologous chromosome; for example, the male X and Y chromosomes are nonhomologous. Hemiplasmic indicates that the DNA marker is present in some but not all of the copies of mitochondrial DNA. Homoplasmic indicates that the DNA marker is present in all of the copies of mitochondrial DNA. |
- |
copyNumber | string | false | The genomic structural variant copy number is the copy number of the large variant. In HGVS, this is the numeric value following the X . It is a unitless value. A copy number of 1 implies a deletion. The copy number can usually be inferred from the HGVS or International System for Human Cytogenetic Nomenclature (ISCN) fields. |
- |
refAllele | string | false | The genomic reference allele contains reference values (for example, normal ) examined in the reference sequence. |
- |
altAllele | string | false | The genomic alternative allele is the contiguous segment of DNA in the test sample that differs from the reference allele at the same location and thus defines a variant. | - |
coordinateSystem | CodeableConcept | false | The base number of the coordinate system. This can be 0-based, with an inclusive start and exclusive end (interval), or 1-based, with an inclusive start and end. Two versions of 1-based are in common use: HGVS 1-based (variant method) and VCF 1-based (alignment method). In general, HGVS recommends right justification and Variant Call Format (VCF) recommends left justification. These systems address questions such as insertion placement relative to the nucleotide and after the end of the sequence. Additionally, the systems handle the boundary effects of numbers between features. For more information, see the HGVS and VCF guides. | - |
exactStartEnd | Range | false | The location of the first genomic position in the reference allele that contains a change from the reference allele. For example, for the simple variant NM_014049.4(ACAD9):c.1249C>T (p.Arg417Cys), the location is Chr3: 128906220 on Assembly GRCh38. | - |
outerStartEnd | Range | false | The genomic coordinates of the widest genomic range in which the variant may reside. | - |
innerStartEnd | Range | false | The genomic coordinates of the narrowest genomic range in which the structural variant may reside. | - |
cytogenomicNomenclature | CodeableConcept | false | The cytogenomic nomenclature fully describes a variant with a single code. This is typically a large variant, such as a mosaic, or abnormal chromosome numbers. | - |
variantInheritance | CodeableConcept | false | The variant inheritance. Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes; for example, systolic and diastolic component observations for blood pressure measurements and multiple component observations for genetics observations. | - |
tags | [Tags] | false | No description | - |
comments | [Comments] | false | No description | - |
Narrative
Name | Type | Required | Description | Accepted Values |
---|---|---|---|---|
status | string | true | The status of the narrative. See the Valueset-narrative-status page in the FHIR standard on the Health Level Seven (HL7) website for more information about the accepted values. | generated, extensions, additional, empty |
div | string | true | The XHTML content of the narrative, which is limited to basic HTML formatting elements and attributes. | - |
CodeableConcept
Name | Type | Required | Description | Accepted Values |
---|---|---|---|---|
text | string | false | A codeable concept is a value that is usually supplied by providing a reference to one or more terminologies or ontologies, but it can also be defined by the provision of text. | - |
codings | [Coding] | false | A coding is a concept defined using a symbol from a specific code system. | - |
Coding
Name | Type | Required | Description | Accepted Values |
---|---|---|---|---|
system | string | false | A URI that identifies the system. | - |
version | string | false | The version of the system. | - |
code | string | false | A concept defined in the code system. | - |
display | string | false | A description of the concept as defined in the code system. | - |
Identifier
Name | Type | Required | Description | Accepted Values |
---|---|---|---|---|
use | string | false | No description | - |
type | CodeableConcept | false | The type of the ID. | - |
system | string | false | The namespace of the ID. | - |
value | string | false | The unique value of the ID. | - |
period | Period | false | The time period during which the ID is or was valid for use. | - |
assigner | string | false | The organization that issued the ID. This can be only text. | - |
Period
Name | Type | Required | Description | Accepted Values |
---|---|---|---|---|
start | string(date-time) | false | The start date and time with an inclusive boundary. | - |
end | string(date-time) | false | The end date and time with an inclusive boundary if the period is not ongoing. | - |
Quantity
Name | Type | Required | Description | Accepted Values |
---|---|---|---|---|
value | number(double) | false | A numeric value with implicit precision. | - |
comparator | string | false | How the quantity should be understood and represented. | - |
unit | string | false | The unit of the quantity. | - |
system | string | false | The system that defines the coded form of the unit. | - |
code | string | false | The coded form of the unit. | - |
Range
Name | Type | Required | Description | Accepted Values |
---|---|---|---|---|
low | string | false | The lowest boundary of the reference range. | - |
high | string | false | The highest boundary of the reference range. | - |
Tags
Name | Type | Required | Description | Accepted Values |
---|---|---|---|---|
key | string | false | The variant tag key. | - |
value | string | false | Indicates whether the variation value of the variant tag is found. | - |
Comments
Name | Type | Required | Description | Accepted Values |
---|---|---|---|---|
authorType | string | false | The type of user who made the annotation. | - |
author | string | false | The user who made the annotation. | - |
time | string(date-time) | false | The date and time at which a specific annotation was created. | - |
text | string | true | The text of the annotation in markdown format. | - |
Error
Name | Type | Required | Description | Accepted Values |
---|---|---|---|---|
code | integer(int32) | true | The HTTP response status code that represents the error. | - |
message | string | true | A human-readable description of the error. | - |
errorDetails | [ErrorDetail] | false | A list of additional error details. | - |
ErrorDetail
Name | Type | Required | Description | Accepted Values |
---|---|---|---|---|
domain | string | false | A subsystem or context where an error occurred. | - |
reason | string | false | A codified value that represents the specific error that caused the current error status. | - |
message | string | false | A human-readable description of an error. | - |
locationType | string | false | The location or type of the field that caused an error. | query, header, path, formData, body |
location | string | false | The name of the field that caused an error. | - |
postVariants
Name | Type | Required | Description | Accepted Values |
---|---|---|---|---|
sourcePersonId | string | true | The unique ID of the person. | - |
partitionId | string | true | The unique ID of the partition associated with the HealtheIntent population for a specified client. | - |
populationId | string | true | The unique ID of the HealtheIntent population for a specified client. | - |
orderId | string | true | The unique ID of the order. | - |
variants | [VariantValue] | true | The collection of variant data. | - |
VariantIdList
Name | Type | Required | Description | Accepted Values |
---|---|---|---|---|
VariantId | string | false | The unique ID of the variant. | - |
putVariants
Name | Type | Required | Description | Accepted Values |
---|---|---|---|---|
sourcePersonId | string | true | The unique ID of the person. | - |
partitionId | string | true | The unique ID of the partition associated with the HealtheIntent population for a specified client. | - |
populationId | string | true | The unique ID of the HealtheIntent population for a specified client. | - |
orderId | string | true | The unique ID of the order. | - |
variant | VariantValue | true | The collection of variant data. | - |
Implications
Name | Type | Required | Description | Accepted Values |
---|---|---|---|---|
items | [Implication] | true | An array containing the current page of results. | - |
totalResults | integer(int32) | false | The total number of results for the specified parameters. | - |
firstLink | string | true | The first page of results. | - |
lastLink | string | false | The last page of results. | - |
prevLink | string | false | The previous page of results. | - |
nextLink | string | false | The next page of results. | - |
Implication
Name | Type | Required | Description | Accepted Values |
---|---|---|---|---|
sourcePersonId | string | false | The unique ID of the person. | - |
orderId | string | false | The unique ID of the order. | - |
id | string | false | The unique ID of the implication. | - |
implicationType | string | false | The type of the implication. | DIAGNOSTIC, THERAPEUTIC |
categories | [CodeableConcept] | false | A code that classifies the general type of the observation. | - |
status | CodeableConcept | false | The status of the variant observation or result. | - |
associatedCancers | [CodeableConcept] | false | Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations. | - |
associatedPhenotypes | [CodeableConcept] | false | The possible phenotype associated with the genetic variant found in this study. | - |
clinicalSignificance | CodeableConcept | false | Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations. | - |
comments | [Comments] | false | No description | - |
effectMedicationEfficacy | CodeableConcept | false | The genomic variations effect on drug efficacy. | - |
effectMedicationHighRisk | CodeableConcept | false | Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations. | - |
effectMedicationMetabolism | CodeableConcept | false | The genomic variations effect on drug metabolism. | - |
evidenceLevel | CodeableConcept | false | Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations. | - |
identifiers | [Identifier] | false | A unique ID assigned to the observation. | - |
implicationVariants | object | false | The list of variants associated with the given implication. | - |
medicationAssessed | [CodeableConcept] | false | The medication whose implication is being described. | - |
method | CodeableConcept | false | Indicates the mechanism used to perform the observation. | - |
modeOfInheritance | CodeableConcept | false | Some observations have multiple component observations. These component observations are expressed as separate code value pairs that share the same attributes. Examples include systolic and diastolic component observations for blood pressure measurement and multiple component observations for genetics observations. | - |
prognosis | CodeableConcept | false | Component observations share the same attributes in the Observation resource as the primary observation and are always treated as part of a single observation. However, the reference range for the primary observation value is not inherited by the component values and is required when appropriate for each component observation. | - |
secondaryFinding | CodeableConcept | false | Enables flagging variants that should be considered secondary findings. | - |
text | Narrative | false | A human-readable narrative that contains a summary of the content in a resource. The narrative must contain enough detail to make it clinically safe for a human to read only the narrative, but it is not required to encode all the structured data. Resource definitions can define what content should be represented in the narrative to ensure clinical safety. | - |
therapyAssessed | [CodeableConcept] | false | The nonmedication therapy whose implication on the cancer outcome is being predicted. For example, altered diet, radiation therapy, surgery, and so on. | - |
postImplications
Name | Type | Required | Description | Accepted Values |
---|---|---|---|---|
sourcePersonId | string | true | The unique ID of the person. | - |
partitionId | string | true | The unique ID of the partition associated with the HealtheIntent population for a specified client. | - |
populationId | string | true | The unique ID of the HealtheIntent population for a specified client. | - |
orderId | string | true | The unique ID of the order. | - |
implications | [Implication] | true | The collection of implication data. | - |
ImplicationIdList
Name | Type | Required | Description | Accepted Values |
---|---|---|---|---|
implicationId | string | false | The unique ID of the implication. | - |
putImplications
Name | Type | Required | Description | Accepted Values |
---|---|---|---|---|
sourcePersonId | string | true | The unique ID of the person. | - |
partitionId | string | true | The unique ID of the partition associated with the HealtheIntent population for a specified client. | - |
populationId | string | true | The unique ID of the HealtheIntent population for a specified client. | - |
orderId | string | true | The unique ID of the order. | - |
implication | Implication | true | The collection of implication data. | - |