# HealthLake integrated NLP example requests **Example 1: `Patient` record ingested into a HealthLake data store** Following is an example of a clinical note based on of a `Patient` encounter with a health care professional. **Synthetic data** The text in the following example is synthetic content and does not contain protected health information (PHI). ``` 1991-08-31 # Chief Complaint - Headache - Sinus Pain - Nasal Congestion - Sore Throat - Pain with Bright Lights - Nasal Discharge - Cough # History of Present Illness Jerónimo599 is a 4 month-old non-hispanic white male. # Social History Patient has never smoked. Patient comes from a middle socioeconomic background. Patient currently has Aetna. # Allergies No Known Allergies. # Medications No Active Medications. # Assessment and Plan Patient is presenting with bee venom (substance), mold (organism), house dust mite (organism), animal dander (substance), grass pollen (substance), tree pollen (substance), lisinopril, sulfamethoxazole / trimethoprim, fish (substance). ## Plan The patient was prescribed the following medications: - astemizole 10 mg oral tablet - nda020800 0.3 ml epinephrine 1 mg/ml auto-injector The patient was placed on a careplan: - self-care interventions (procedure) ``` As a reminder, this information is encoded in base64 format in the `DocumentReference` resource. When this document is ingested into HealthLake and the Amazon Comprehend Medical API operations are complete, to see the results, you can start with the `GET`request on the `DocumentReference` resource type. ``` GET https://https://healthlake.{{region}}.amazonaws.com/datastore/{{datastoreId}}/r4/eeb8005725ae22b35b4edbdc68cf2dfd/r4/DocumentReference ``` When the Amazon Comprehend Medical API operations are successful, look for these key-value pairs inside the `extension` linked to the following `"url": "http://healthlake.amazonaws.com/aws-cm/"` ``` { "url": "http://healthlake.amazonaws.com/aws-cm/status/", "valueString": "SUCCESS" }, { "url": "http://healthlake.amazonaws.com/aws-cm/message/", "valueString": "The AWS HealthLake integrated medical NLP operation was successful." } ``` The following tabs show you how the ingested medical record is reported in your HealthLake data store based on the resource type. ------ #### [ DocumentReference ] To the see the results for a single `DocumentReference` resource type, make a `GET` request where the `id` of a specific resource is provided. ``` GET https://https://healthlake.{{region}}.amazonaws.com/datastore/{{datastoreId}}/r4/eeb8005725ae22b35b4edbdc68cf2dfd/r4/DocumentReference/0e938f03-da7f-4178-acd8-eea9586c46ed ``` When successful, you get a `200` HTTP response code, and the following JSON response (that has been truncated for clarity). Here is the `http://healthlake.amazonaws.com/system-generated-resources/` portion. You can see that a new `Linkage/{{e366d29f-2c22-4c19-866e-09603937935a}}` has been added. You can also see where HealthLake has added inference-based findings to specific `Observation` and `Condition` resource types. To see how these resource types have been amended, choose the related tabs. ``` { "extension": [ { "url": "http://healthlake.amazonaws.com/linkage", "valueReference": { "reference": "Linkage/e366d29f-2c22-4c19-866e-09603937935a" } }, { "url": "http://healthlake.amazonaws.com/nlp-entity", "valueReference": { "reference": "Observation/c6e0a3ff-7a17-4d8b-bfd0-d02d7da090c5" } }, { "url": "http://healthlake.amazonaws.com/nlp-entity", "valueReference": { "reference": "Condition/0854e1f3-894d-448e-a8d9-3af5b9902baf" } } ], "url": "http://healthlake.amazonaws.com/system-generated-resources/" } ``` ------ #### [ Linkage ] To the see the results for a single `Linkage` resource type, make a `GET` request where the `ID` of a specific resource is provided. ``` GET https://https://healthlake.{{region}}.amazonaws.com/datastore/{{datastoreId}}/r4/eeb8005725ae22b35b4edbdc68cf2dfd/r4/Linkage/e366d29f-2c22-4c19-866e-09603937935a ``` When successful, you get a `200` HTTP response code, and the following truncated JSON response. The response contains the `item` element. In it, the key-value pair `"type": "source"` indicates the specific `DocumentReference` entry used to modify the `Condition` and `Observations` listed under the `"type": "alternate"` key-value pair. *You also see the `meta` element, and a corresponding key-value pair, `"tag": [{"display": "SYSTEM_GENERATED"}]`, indicating these resources were created by HealthLake.* ``` { "resourceType": "Linkage", "id": "e366d29f-2c22-4c19-866e-09603937935a", "active": true, "item": [ { "type": "alternate", "resource": { "reference": "Observation/c6e0a3ff-7a17-4d8b-bfd0-d02d7da090c5", "type": "Observation" } }, { "type": "alternate", "resource": { "reference": "Condition/9d5c1ef6-f822-4faf-b55f-7c70f2a4aa8d", "type": "Condition" } }, { "type": "source", "resource": { "reference": "DocumentReference/0e938f03-da7f-4178-acd8-eea9586c46ed", "type": "DocumentReference" } } ], "meta": { "lastUpdated": "2022-10-21T19:38:31.327Z", "tag": [{ "display": "SYSTEM_GENERATED" }] } } ``` ------ #### [ Resource type: Observation ] To the see the results for a single `Observation` resource type, make a `GET` request where the `ID` of a specific resource is provided. ``` GET https://https://healthlake.{{region}}.amazonaws.com/datastore/{{datastoreId}}/r4/eeb8005725ae22b35b4edbdc68cf2dfd/r4/Observation/e366d29f-2c22-4c19-866e-09603937935a ``` The results of the Amazon Comprehend Medical API operations are amended to the following elements: `code`, `meta`, and `modifierExtension`. **`code`** An element of type `CodeableConcept`. To learn more, see [https://hl7.org/fhir/R4/datatypes.html#CodeableConcept](https://hl7.org/fhir/R4/datatypes.html#CodeableConcept) in the **FHIR R4 documentation**. HealthLake appends the following three key-value pairs. + `"system": "http://healthlake.amazonaws.com/aws-cm/infer-icd10/"`: Where the URL refers to a specific Amazon Comprehend Medical API operation. In this case, InferICD10CM. + `"code": "A52.06"`: Where `A52.06` is the ICD-10-CM code that identifies the concept found in the knowledge base from the Centers for Disease Control. + `"display": "Other syphilitic heart involvement"`: Where `"Other syphilitic heart involvement"` is the long description of the ICD-10-CM code in the ontology. The following truncated JSON response contains only the `code` element. ``` "code": { "coding": [ { "system": "http://healthlake.amazonaws.com/aws-cm/infer-icd10/", "code": "A52.06", "display": "Other syphilitic heart involvement" } ], "text": "Other syphilitic heart involvement" } ``` To understand the model's confidence that the assigned ICD-10-CM code is correct, use the `modifierExtension` element. **`meta`** The `meta` element contains metadata that indicates whether the `code` element contains details that have been added by the Amazon Comprehend Medical API operations. The following truncated JSON response contains only the `meta` element. ``` "meta": { "lastUpdated": "2022-10-21T19:38:30.879Z", "tag": [{ "display": "SYSTEM_GENERATED" }] } ``` **`modifierExtension`** The `modifierExtension` element contains more details about the level of confidence of the assigned codes found in the `code` element. It also has key-value pairs that provide a link back to the original DocumentReference used to generate the results and the related Linkage resource type. For each `coding` element added, you will see an `entity-score` and an `entity-Concept-Score` added to the modifierExtension. For each value in the key-value pair, you see a score. For `entity-score`, this score is the level of confidence that Amazon Comprehend Medical has in the accuracy of the detection. For `entity-Concept-Score`, this score is the level of confidence that Amazon Comprehend Medical has that the entity is accurately linked to an ICD-10-CM concept. The following truncated JSON response contains only the `modifierExtension` element. ``` "modifierExtension": [{ "url": "http://healthlake.amazonaws.com/aws-cm/infer-icd10/aws-cm-icd10-entity-score", "valueDecimal": 0.45005733 }, { "url": "http://healthlake.amazonaws.com/aws-cm/infer-icd10/aws-cm-icd10-entity-Concept-Score", "valueDecimal": 0.1111792 }, { "url": "http://healthlake.amazonaws.com/system-generated-linkage", "valueReference": { "reference": "Linkage/e366d29f-2c22-4c19-866e-09603937935a" } }, { "url": "http://healthlake.amazonaws.com/source-document-reference", "valueReference": { "reference": "DocumentReference/0e938f03-da7f-4178-acd8-eea9586c46ed" } } ] ``` **Full JSON Response** ``` { "subject": { "reference": "Patient/0679b7b7-937d-488a-b48d-6315b8e7003b" }, "resourceType": "Observation", "status": "unknown", "code": { "coding": [{ "system": "http://healthlake.amazonaws.com/aws-cm/infer-icd10/", "code": "A52.06", "display": "Other syphilitic heart involvement" }], "text": "Other syphilitic heart involvement" }, "meta": { "lastUpdated": "2022-10-21T19:38:30.879Z", "tag": [{ "display": "SYSTEM_GENERATED" }] }, "modifierExtension": [{ "url": "http://healthlake.amazonaws.com/aws-cm/infer-icd10/aws-cm-icd10-entity-score", "valueDecimal": 0.45005733 }, { "url": "http://healthlake.amazonaws.com/aws-cm/infer-icd10/aws-cm-icd10-entity-Concept-Score", "valueDecimal": 0.1111792 }, { "url": "http://healthlake.amazonaws.com/system-generated-linkage", "valueReference": { "reference": "Linkage/e366d29f-2c22-4c19-866e-09603937935a" } }, { "url": "http://healthlake.amazonaws.com/source-document-reference", "valueReference": { "reference": "DocumentReference/0e938f03-da7f-4178-acd8-eea9586c46ed" } } ], "id": "7e88c7c5-21a5-4dd7-8fc2-a02474fba583" } ``` ------ #### [ Condition ] To the see the results for a single `Condition` resource type, make a `GET` request where the `ID` of a specific resource is provided. ``` GET https://https://healthlake.{{region}}.amazonaws.com/datastore/{{datastoreId}}/r4/eeb8005725ae22b35b4edbdc68cf2dfd/r4/Condition/b06d343d-ddb8-4f36-82cb-853fcd434dfd ``` The results of the Amazon Comprehend Medical API operations are amended to the following elements: `code`, `meta`, and `modifierExtension`. **`code`** An element of type `CodeableConcept`. To learn more, see [https://hl7.org/fhir/R4/datatypes.html#CodeableConcept](https://hl7.org/fhir/R4/datatypes.html#CodeableConcept) in the **FHIR R4 documentation**. HealthLake appends the following three key-value pairs. + `"system": "http://healthlake.amazonaws.com/aws-cm/infer-icd10/"`: Where the URL refers to a specific Amazon Comprehend Medical API operation. In this case, InferICD10CM. + `"code": "I70.0"`: Where `A52.06` is the ICD-10-CM code that identifies the concept found in the knowledge base from the Centers for Disease Control. + `"display": "Atherosclerosis of aorta"`: Where `"Other syphilitic heart involvement"` is the long description of the ICD-10-CM code in the ontology. The following truncated JSON response contains only the `code` element. ``` "code": { "coding": [ { "system": "http://healthlake.amazonaws.com/aws-cm/infer-icd10/", "code": "I70.0", "display": "Atherosclerosis of aorta" } ], "text": "Atherosclerosis of aorta" } ``` To understand the model's confidence that the assigned ICD-10-CM code is correct, use the `modifierExtension` element. **`meta`** The `meta` element contains metadata that indicates whether the `code` element contains details that have been added by the Amazon Comprehend Medical API operations. The following truncated JSON response contains only the `meta` element. ``` "meta": { "lastUpdated": "2022-10-21T19:38:30.877Z", "tag": [{ "display": "SYSTEM_GENERATED" }] } ``` **`modifierExtension`** The `modifierExtension` element contains more details about the level of confidence of the assigned codes found in the `code` element. It also has key-value pairs that provide a link back to the original DocumentReference used to generate the results and the related Linkage resource type. For each `coding` element added, you will see an `entity-score` and an `entity-Concept-Score` added to the modifierExtension. For each value in the key-value pair, you see a score. For `entity-score`, this score is the level of confidence that Amazon Comprehend Medical has in the accuracy of the detection. For `entity-Concept-Score`, this score is the level of confidence that Amazon Comprehend Medical has that the entity is accurately linked to an ICD-10-CM concept. The following truncated JSON response contains only the `modifierExtension` element. ``` "modifierExtension": [{ "url": "http://healthlake.amazonaws.com/aws-cm/infer-icd10/aws-cm-icd10-entity-score", "valueDecimal": 0.94417894 }, { "url": "http://healthlake.amazonaws.com/aws-cm/infer-icd10/aws-cm-icd10-entity-Concept-Score", "valueDecimal": 0.8458298 }, { "url": "http://healthlake.amazonaws.com/system-generated-linkage", "valueReference": { "reference": "Linkage/e366d29f-2c22-4c19-866e-09603937935a" } }, { "url": "http://healthlake.amazonaws.com/source-document-reference", "valueReference": { "reference": "DocumentReference/0e938f03-da7f-4178-acd8-eea9586c46ed" } } ] ``` **Full JSON Response** ``` { "subject": { "reference": "Patient/0679b7b7-937d-488a-b48d-6315b8e7003b" }, "resourceType": "Condition", "code": { "coding": [{ "system": "http://healthlake.amazonaws.com/aws-cm/infer-icd10/", "code": "I70.0", "display": "Atherosclerosis of aorta" }], "text": "Atherosclerosis of aorta" }, "meta": { "lastUpdated": "2022-10-21T19:38:30.877Z", "tag": [{ "display": "SYSTEM_GENERATED" }] }, "modifierExtension": [{ "url": "http://healthlake.amazonaws.com/aws-cm/infer-icd10/aws-cm-icd10-entity-score", "valueDecimal": 0.94417894 }, { "url": "http://healthlake.amazonaws.com/aws-cm/infer-icd10/aws-cm-icd10-entity-Concept-Score", "valueDecimal": 0.8458298 }, { "url": "http://healthlake.amazonaws.com/system-generated-linkage", "valueReference": { "reference": "Linkage/e366d29f-2c22-4c19-866e-09603937935a" } }, { "url": "http://healthlake.amazonaws.com/source-document-reference", "valueReference": { "reference": "DocumentReference/0e938f03-da7f-4178-acd8-eea9586c46ed" } } ], "id": "b06d343d-ddb8-4f36-82cb-853fcd434dfd" } ``` ------ **Example 2: A `DocumentReference` that contains `MedicationStatement` resource type ** Here is an example of a clinical note based off of a patient's encounter with a medical professional. **Synthetic data** The text in this example is synthetic content and does not contain protected health information (PHI). ``` Tom is not prescribed Advil ``` The following tabs show how the ingested medical record is reported in your HealthLake data store based on the resource type. ------ #### [ DocumentReference ] To the see the results for a single `DocumentReference` resource type, make a `GET` request where the `ID` of a specific resource is provided. ``` GET https://https://healthlake.{{region}}.amazonaws.com/datastore/{{datastoreId}}/r4/eeb8005725ae22b35b4edbdc68cf2dfd/r4/DocumentReference/c549125d-a218-421f-b8bf-23614c5e796c ``` When successful, you get a `200` HTTP response code and the following truncated JSON response. The key-value pair, `"url": "http://healthlake.amazonaws.com/system-generated-resources/"`, indicates that the resource types inside this `extension` have been added by Amazon Comprehend Medical API operations. You can see the new `Linkage` resource type, and multiple `MedicationStatement` resources. ``` "extension": [{ "extension": [{ "url": "http://healthlake.amazonaws.com/linkage", "valueReference": { "reference": "Linkage/394bb244-177b-4409-8657-26b20ed56dd7" } }, { "url": "http://healthlake.amazonaws.com/nlp-entity", "valueReference": { "reference": "MedicationStatement/cbf6af10-b0b9-451c-bdde-99611e3498a8" } }, { "url": "http://healthlake.amazonaws.com/nlp-entity", "valueReference": { "reference": "MedicationStatement/9a89b0d3-6681-45ca-9926-27951edce5c7" } }, { "url": "http://healthlake.amazonaws.com/nlp-entity", "valueReference": { "reference": "MedicationStatement/4a01f6c8-5f3a-4122-80ab-405312f96aa2" } }, { "url": "http://healthlake.amazonaws.com/nlp-entity", "valueReference": { "reference": "MedicationStatement/fbfb77d8-70cf-4579-b4c0-d6fe3c01656b" } }, { "url": "http://healthlake.amazonaws.com/nlp-entity", "valueReference": { "reference": "MedicationStatement/1340c9ce-9c48-4bf9-9b2f-d0ab027f5e0b" } } ], "url": "http://healthlake.amazonaws.com/system-generated-resources/" } ``` ------ #### [ Linkage ] To the see the results for a single `Linkage` resource type, make a `GET` request where the `ID` of a specific resource is provided. ``` GET https://https://healthlake.{{region}}.amazonaws.com/datastore/{{datastoreId}}/r4/eeb8005725ae22b35b4edbdc68cf2dfd/r4/Linkage/394bb244-177b-4409-8657-26b20ed56dd7 ``` When successful, you get a `200` HTTP response code and the following JSON response. The response contains the `item` element. In it, the key-value pair `"type": "source"` indicates the specific `DocumentReference` entry used to modify the `MedicationStatement` resource types. You can also see the `meta` element and a corresponding key-value pair, `"tag": [{"display": "SYSTEM_GENERATED"}]`, indicating that these resources were created by HealthLake. ``` { "resourceType": "Linkage", "id": "394bb244-177b-4409-8657-26b20ed56dd7", "active": true, "item": [{ "type": "alternate", "resource": { "reference": "MedicationStatement/cbf6af10-b0b9-451c-bdde-99611e3498a8", "type": "MedicationStatement" } }, { "type": "alternate", "resource": { "reference": "MedicationStatement/9a89b0d3-6681-45ca-9926-27951edce5c7", "type": "MedicationStatement" } }, { "type": "alternate", "resource": { "reference": "MedicationStatement/4a01f6c8-5f3a-4122-80ab-405312f96aa2", "type": "MedicationStatement" } }, { "type": "alternate", "resource": { "reference": "MedicationStatement/fbfb77d8-70cf-4579-b4c0-d6fe3c01656b", "type": "MedicationStatement" } }, { "type": "alternate", "resource": { "reference": "MedicationStatement/1340c9ce-9c48-4bf9-9b2f-d0ab027f5e0b", "type": "MedicationStatement" } }, { "type": "source", "resource": { "reference": "DocumentReference/c549125d-a218-421f-b8bf-23614c5e796c", "type": "DocumentReference" } } ], "meta": { "lastUpdated": "2022-10-24T20:05:03.501Z", "tag": [{ "display": "SYSTEM_GENERATED" }] } } ``` ------ #### [ MedicationStatement ] To the see the results for a single `MedicationStatement` resource type, make a `GET` request where the `ID` of a specific resource is provided. ``` GET https://https://healthlake.{{region}}.amazonaws.com/datastore/{{datastoreId}}/r4/eeb8005725ae22b35b4edbdc68cf2dfd/r4/MedicationStatement/9a89b0d3-6681-45ca-9926-27951edce5c7 ``` The `MedicationStatement` resource type is where the results of the Amazon Comprehend Medical InferRxNorm API operation are found. The results are amended to the following elements: `medicationCodeableConcept`, `meta`, and `modifierExtension`. **medicationCodeableConcept** An element of type `CodeableConcept`. To learn more, see [https://hl7.org/fhir/R4/datatypes.html#CodeableConcept](https://hl7.org/fhir/R4/datatypes.html#CodeableConcept) in the **FHIR R4 documentation**. HealthLake appends the following three key-value pairs. + `"system": ""http://healthlake.amazonaws.com/aws-cm/infer-rxnorm/`: Where the URL refers to a specific Amazon Comprehend Medical API operation. In this case, InferRxNorm. + `"code": "731533"`: Where `731533` is an RxNorm concept ID, also known as the RxCUI. + `"display": "ibuprofen 200 MG Oral Capsule [Advil]"`: Where `ibuprofen 200 MG Oral Capsule [Advil]` is the description of the RxNorm concept. The following truncated JSON response contains only the `MedicationStatement` element. ``` "medicationCodeableConcept": { "coding": [ { "system": "http://healthlake.amazonaws.com/aws-cm/infer-rxnorm/", "code": "731533", "display": "ibuprofen 200 MG Oral Capsule [Advil]" } ] } ``` **`meta`** The `meta` element contains metadata that indicates whether the `code` element contains details that have been added by the Amazon Comprehend Medical API operations. The following truncated JSON response contains only the `meta` element. ``` "meta": { "lastUpdated": "2022-10-24T20:05:02.800Z", "tag": [ { "display": "SYSTEM_GENERATED" } ] } ``` **`modifierExtension`** The `modifierExtension` element contains key-value pairs that provide a link back to the original `DocumentReference` used to generate the results and the related Linkage resource type. ``` "modifierExtension": [ { "url": "http://healthlake.amazonaws.com/system-generated-linkage", "valueReference": { "reference": "Linkage/394bb244-177b-4409-8657-26b20ed56dd7" } }, { "url": "http://healthlake.amazonaws.com/source-document-reference", "valueReference": { "reference": "DocumentReference/c549125d-a218-421f-b8bf-23614c5e796c" } } ] ``` ------