Using the Healthcare Natural Language API

This page explains how to enable the Healthcare Natural Language API, configure permissions, and call the analyzeEntities method to extract medical insights from medical text.

Overview

The Healthcare Natural Language API provides machine learning solutions for deriving insights from medical text. The Healthcare Natural Language API is part of the Cloud Healthcare API. For an overview of the Healthcare Natural Language API, see the Healthcare Natural Language API conceptual documentation.

The Healthcare Natural Language API parses unstructured medical text such as medical records or insurance claims. It then generates a structured data representation of the medical knowledge entities stored in these data sources for downstream analysis and automation. For example, you can:

• Extract information about medical concepts like diseases, medications, medical devices, procedures, and their clinically relevant attributes
• Map medical concepts to standard medical vocabularies such as RxNorm, ICD-10, MeSH, and SNOMED CT (US users only)
• Derive medical insights from text and integrate them with data analytics products in Google Cloud

Note: You do not need to create a dataset in the Cloud Healthcare API to use the Healthcare Natural Language API.

Available locations

The Healthcare Natural Language API is available in the following locations:

Location name	Location description
asia-south1	Mumbai, India
australia-southeast1	Sydney, Australia
europe-west2	London, UK
europe-west4	Netherlands
northamerica-northeast1	Montréal, Canada
us-central1	Iowa, USA

Enabling the Healthcare Natural Language API

Before you begin using the Healthcare Natural Language API, you must enable the API for your Google Cloud project. You can use the Healthcare Natural Language API without enabling or using features of the Cloud Healthcare API.

To enable the API, complete the following steps:

1. Sign in to your Google Cloud account. If you're new to Google Cloud, create an account to evaluate how our products perform in real-world scenarios. New customers also get $300 in free credits to run, test, and deploy workloads.

2. In the Google Cloud console, on the project selector page, select or create a Google Cloud project.

   Note: If you don't plan to keep the resources that you create in this procedure, create a project instead of selecting an existing project. After you finish these steps, you can delete the project, removing all resources associated with the project.

   Go to project selector

3. Make sure that billing is enabled for your Cloud project. Learn how to check if billing is enabled on a project.

4. Create a service account:

   1. In the Google Cloud console, go to the Create service account page.

      Go to Create service account
   2. Select your project.

   3. In the Service account name field, enter a name. The Google Cloud console fills in the Service account ID field based on this name.

      In the Service account description field, enter a description. For example, Service account for quickstart.

   4. Click Create and continue.

   5. To provide access to your project, grant the Project > Owner role to your service account.

      To grant the role, find the Select a role list, then select Project > Owner.

      Note: The Role field affects which resources your service account can access in your project. You can revoke these roles or grant additional roles later. In production environments, do not grant the Owner, Editor, or Viewer roles. Instead, grant a predefined role or custom role that meets your needs.
   6. Click Continue.

   7. Click Done to finish creating the service account.

      Do not close your browser window. You will use it in the next step.

5. Create a service account key:

   1. In the Google Cloud console, click the email address for the service account that you created.
   2. Click Keys.
   3. Click Add key, and then click Create new key.
   4. Click Create. A JSON key file is downloaded to your computer.
   5. Click Close.

6. Set the environment variable GOOGLE_APPLICATION_CREDENTIALS to the path of the JSON file that contains your service account key. This variable only applies to your current shell session, so if you open a new session, set the variable again.

   Example: Linux or macOS

   export GOOGLE_APPLICATION_CREDENTIALS="KEY_PATH"

   Replace KEY_PATH with the path of the JSON file that contains your service account key.

   For example:

   export GOOGLE_APPLICATION_CREDENTIALS="/home/user/Downloads/service-account-file.json"

   Example: Windows

   For PowerShell:

   $env:GOOGLE_APPLICATION_CREDENTIALS="KEY_PATH"

   Replace KEY_PATH with the path of the JSON file that contains your service account key.

   For example:

   $env:GOOGLE_APPLICATION_CREDENTIALS="C:\Users\username\Downloads\service-account-file.json"

   For command prompt:

   set GOOGLE_APPLICATION_CREDENTIALS=KEY_PATH

   Replace KEY_PATH with the path of the JSON file that contains your service account key.

7. In the Google Cloud console, on the project selector page, select or create a Google Cloud project.

   Note: If you don't plan to keep the resources that you create in this procedure, create a project instead of selecting an existing project. After you finish these steps, you can delete the project, removing all resources associated with the project.

   Go to project selector

8. Make sure that billing is enabled for your Cloud project. Learn how to check if billing is enabled on a project.

9. Create a service account:

   1. In the Google Cloud console, go to the Create service account page.

      Go to Create service account
   2. Select your project.

   3. In the Service account name field, enter a name. The Google Cloud console fills in the Service account ID field based on this name.

      In the Service account description field, enter a description. For example, Service account for quickstart.

   4. Click Create and continue.

   5. To provide access to your project, grant the Project > Owner role to your service account.

      To grant the role, find the Select a role list, then select Project > Owner.

      Note: The Role field affects which resources your service account can access in your project. You can revoke these roles or grant additional roles later. In production environments, do not grant the Owner, Editor, or Viewer roles. Instead, grant a predefined role or custom role that meets your needs.
   6. Click Continue.

   7. Click Done to finish creating the service account.

      Do not close your browser window. You will use it in the next step.

10. Create a service account key:

    1. In the Google Cloud console, click the email address for the service account that you created.
    2. Click Keys.
    3. Click Add key, and then click Create new key.
    4. Click Create. A JSON key file is downloaded to your computer.
    5. Click Close.

11. Set the environment variable GOOGLE_APPLICATION_CREDENTIALS to the path of the JSON file that contains your service account key. This variable only applies to your current shell session, so if you open a new session, set the variable again.

    Example: Linux or macOS

    export GOOGLE_APPLICATION_CREDENTIALS="KEY_PATH"

    Replace KEY_PATH with the path of the JSON file that contains your service account key.

    For example:

    export GOOGLE_APPLICATION_CREDENTIALS="/home/user/Downloads/service-account-file.json"

    Example: Windows

    For PowerShell:

    $env:GOOGLE_APPLICATION_CREDENTIALS="KEY_PATH"

    Replace KEY_PATH with the path of the JSON file that contains your service account key.

    For example:

    $env:GOOGLE_APPLICATION_CREDENTIALS="C:\Users\username\Downloads\service-account-file.json"

    For command prompt:

    set GOOGLE_APPLICATION_CREDENTIALS=KEY_PATH

    Replace KEY_PATH with the path of the JSON file that contains your service account key.

12. Enable the Cloud Healthcare API.

    Enable the API

13. Install the Google Cloud CLI.

14. To initialize the gcloud CLI, run the following command:

    gcloud init

Set up permissions

To use the features in this guide, you must have the healthcare.nlpservice.analyzeEntities permission, which is included in the healthcare.nlpServiceViewer role.

To assign this role, run the gcloud projects add-iam-policy-binding command:

gcloud projects add-iam-policy-binding PROJECT_ID \
    --member serviceAccount:SERVICE_ACCOUNT_ID \
    --role roles/healthcare.nlpServiceViewer

Extracting entities, relations, and contextual attributes

The Healthcare Natural Language API uses context-aware models to extract medical entities, relations, and contextual attributes. Each text entity is extracted into a medical dictionary entry. To extract this level of medical insights from medical text, use the projects.locations.services.nlp.analyzeEntities method.

To include licensed vocabularies, such as International Classification of Diseases, Tenth Revision, Clinical Modification (ICD10CM) and SNOMED Clinical Terms, US Version (SNOMEDCT_US), in your request, see Including licensed vocabularies.

To extract medical insights from medical text using the Healthcare Natural Language API, make a POST request and specify the following information in the request:

• The name of the parent service, including the project ID and location
• The target text. The maximum size is 20,000 unicode characters.

curl

The following sample shows a POST request using curl:

curl -X POST \
   -H "Authorization: Bearer "$(gcloud auth application-default print-access-token) \
   -H "Content-Type:application/json" \
   --data "{
    'nlpService':'projects/PROJECT_ID/locations/LOCATION/services/nlp',
    'documentContent':'Insulin regimen human 5 units IV administered.'
   }" \
   "https://healthcare.googleapis.com/v1/projects/PROJECT_ID/locations/LOCATION/services/nlp:analyzeEntities"

PowerShell

The following sample shows a POST request using Windows PowerShell:

$cred = gcloud auth application-default print-access-token
$headers = @{ Authorization = "Bearer $cred" }

Invoke-WebRequest `
  -Method Post `
  -Headers $headers `
  -ContentType: "application/json; charset=utf-8" `
  -Body "{
    'nlpService':'projects/PROJECT_ID/locations/LOCATION/services/nlp',
    'documentContent':'Insulin regimen human 5 units IV administered.'
   }" `
   -Uri "https://healthcare.googleapis.com/v1/projects/PROJECT_ID/locations/LOCATION/services/nlp:analyzeEntities"  | Select-Object -Expand Content

If the request is successful, the response includes the following information:

• Recognized medical knowledge entities
• Functional features
• Relations between the recognized entities
• Contextual attributes
• Mappings of the medical knowledge entities into standard terminologies

For a list of supported entity, attribute, and relation types, see the Healthcare Natural Language API conceptual documentation.

The following response from the preceding samples identified Therapeutic Insulin, the entity with code C581 in the NCI terminology system, as the medication. The response also includes the confidence score assigned to the response. For more information about the response fields, see the analyzeEntities documentation.

{
  "entityMentions": [
    {
      "mentionId": "1",
      "type": "MEDICINE",
      "text": {
        "content": "Insulin regimen human"
      },
      "linkedEntities": [
        {
          "entityId": "UMLS/3537244"
        },
        {
          "entityId": "UMLS/3714501"
        },
        {
          "entityId": "UMLS/21641"
        },
        {
          "entityId": "UMLS/795635"
        },
        {
          "entityId": "UMLS/1533581"
        },
        {
          "entityId": "UMLS/4721402"
        }
      ],
      "temporalAssessment": {
        "value": "CURRENT",
        "confidence": 0.87631082534790039
      },
      "certaintyAssessment": {
        "value": "LIKELY",
        "confidence": 0.9999774694442749
      },
      "subject": {
        "value": "PATIENT",
        "confidence": 0.99999970197677612
      },
      "confidence": 0.41636556386947632
    },
    {
      "mentionId": "2",
      "type": "MED_DOSE",
      "text": {
        "content": "5 units",
        "beginOffset": 22
      },
      "confidence": 0.56910794973373413
    },
    {
      "mentionId": "3",
      "type": "MED_ROUTE",
      "text": {
        "content": "IV",
        "beginOffset": 30
      },
      "linkedEntities": [
        {
          "entityId": "UMLS/348016"
        }
      ],
      "confidence": 0.9180646538734436
    }
  ],
  "entities": [
    {
      "entityId": "UMLS/1533581",
      "preferredTerm": "Therapeutic Insulin",
      "vocabularyCodes": [
        "MTH/NOCODE",
        "NCI/C581"
      ]
    },
    {
      "entityId": "UMLS/21641",
      "preferredTerm": "Insulin",
      "vocabularyCodes": [
        "FMA/83365",
        "LNC/LA15805-7",
        "LNC/LP14676-8",
        "LNC/LP16325-0",
        "LNC/LP32542-0",
        "LNC/LP70329-5",
        "LNC/MTHU002108",
        "LNC/MTHU019392",
        "MSH/D007328",
        "MTH/NOCODE"
      ]
    },
    {
      "entityId": "UMLS/348016",
      "preferredTerm": "Intravenous",
      "vocabularyCodes": [
        "LNC/LA9437-0",
        "LNC/LP32453-0",
        "MTH/NOCODE",
        "NCI/C13346"
      ]
    },
    {
      "entityId": "UMLS/3537244",
      "preferredTerm": "Insulins",
      "vocabularyCodes": [
        "MSH/D061385",
        "MTH/NOCODE"
      ]
    },
    {
      "entityId": "UMLS/3714501",
      "preferredTerm": "Insulin Drug Class",
      "vocabularyCodes": [
        "MTH/NOCODE",
        "VANDF/4021631"
      ]
    },
    {
      "entityId": "UMLS/4721402",
      "preferredTerm": "INS protein, human",
      "vocabularyCodes": [
        "MTH/NOCODE",
        "NCI/C2271"
      ]
    },
    {
      "entityId": "UMLS/795635",
      "preferredTerm": "insulin, regular, human",
      "vocabularyCodes": [
        "LNC/LP17001-6",
        "MSH/D061386",
        "MTH/NOCODE",
        "NCI/C29125",
        "RXNORM/253182",
        "VANDF/4017559",
        "VANDF/4017569",
        "VANDF/4019786"
      ]
    }
  ],
  "relationships": [
    {
      "subjectId": "1",
      "objectId": "2",
      "confidence": 0.53775161504745483
    },
    {
      "subjectId": "1",
      "objectId": "3",
      "confidence": 0.95007365942001343
    }
  ]
}

Including licensed vocabularies

You can include the following licensed vocabularies in your requests to the Healthcare Natural Language API:

• International Classification of Diseases, Tenth Revision, Clinical Modification (ICD10CM): used to code and classify morbidity data from inpatient and outpatient records, physician offices, and most National Center for Health Statistics (NCHS) surveys.
• SNOMED Clinical Terms, US Version (SNOMEDCT_US): provides core general terminology for electronic health records.

Note: To use these two vocabularies, you must send your request to the us-central1 region. The request must also originate from the US. If your request does not include either of these two vocabularies, these location restrictions do not apply.

The following samples show how to make a POST request to the Healthcare Natural Language API and include both of the available licensed vocabularies in the licensedVocabularies object. You can specify one or more of the available licensed vocabularies.

curl

The following sample shows a POST request using curl:

curl -X POST \
    -H "Authorization: Bearer "$(gcloud auth application-default print-access-token) \
    -H "Content-Type:application/json" \
    --data "{
      'nlpService':'projects/PROJECT_ID/locations/us-central1/services/nlp',
       'documentContent':'Diabetes. Insulin regimen human 5 units IV administered.',
       'licensedVocabularies':['SNOMEDCT_US','ICD10CM']
    }" \
    "https://healthcare.googleapis.com/v1/projects/PROJECT_ID/locations/us-central1/services/nlp:analyzeEntities"

Replace PROJECT_ID with your Google Cloud project ID.

The output is the following. The output from specifying the licensed vocabularies is in bold:

{
  "entityMentions": [
    {
      "mentionId": "1",
      "type": "PROBLEM",
      "text": {
        "content": "Diabetes"
      },
      "linkedEntities": [
        {
          "entityId": "UMLS/C0011847"
        },
        {
          "entityId": "UMLS/C0011849"
        },
        {
          "entityId": "UMLS/C0241863"
        }
      ],
      "temporalAssessment": {
        "value": "CURRENT",
        "confidence": 0.98781299591064453
      },
      "certaintyAssessment": {
        "value": "LIKELY",
        "confidence": 0.872421145439148
      },
      "subject": {
        "value": "PATIENT",
        "confidence": 0.99975031614303589
      },
      "confidence": 0.99663406610488892
    },
    {
      "mentionId": "2",
      "type": "MEDICINE",
      "text": {
        "content": "Insulin regimen",
        "beginOffset": 10
      },
      "linkedEntities": [
        {
          "entityId": "UMLS/C0795635"
        },
        {
          "entityId": "UMLS/C0021641"
        },
        {
          "entityId": "UMLS/C3537244"
        },
        {
          "entityId": "UMLS/C1533581"
        },
        {
          "entityId": "UMLS/C3714501"
        }
      ],
      "temporalAssessment": {
        "value": "CURRENT",
        "confidence": 0.91042423248291016
      },
      "certaintyAssessment": {
        "value": "LIKELY",
        "confidence": 0.99766635894775391
      },
      "subject": {
        "value": "PATIENT",
        "confidence": 0.999998152256012
      },
      "confidence": 0.716249406337738
    },
    {
      "mentionId": "3",
      "type": "MEDICINE",
      "text": {
        "content": "human",
        "beginOffset": 26
      },
      "temporalAssessment": {
        "value": "CURRENT",
        "confidence": 0.64570724964141846
      },
      "certaintyAssessment": {
        "value": "LIKELY",
        "confidence": 0.90325617790222168
      },
      "subject": {
        "value": "PATIENT",
        "confidence": 0.97613298892974854
      },
      "confidence": 0.57638454437255859
    },
    {
      "mentionId": "4",
      "type": "MED_DOSE",
      "text": {
        "content": "5 units",
        "beginOffset": 32
      },
      "confidence": 0.92076742649078369
    },
    {
      "mentionId": "5",
      "type": "MED_ROUTE",
      "text": {
        "content": "IV",
        "beginOffset": 40
      },
      "linkedEntities": [
        {
          "entityId": "UMLS/C0348016"
        }
      ],
      "confidence": 0.967033863067627
    }
  ],
  "entities": [
    {
      "entityId": "UMLS/C0011847",
      "preferredTerm": "Diabetes",
      "vocabularyCodes": [
        "ICD10CM/E11",
        "LNC/LA10529-8",
        "LNC/LP128793-9",
        "LNC/MTHU040702",
        "MTH/NOCODE",
        "OMIM/MTHU050182"
      ]
    },
    {
      "entityId": "UMLS/C0011849",
      "preferredTerm": "Diabetes Mellitus",
      "vocabularyCodes": [
        "HPO/HP:0000819",
        "ICD10CM/E08-E13",
        "ICD9CM/250",
        "LNC/LA14291-1",
        "LNC/LA27539-8",
        "LNC/MTHU020781",
        "MEDLINEPLUS/4",
        "MEDLINEPLUS/45",
        "MSH/D003920",
        "MTH/NOCODE",
        "MTH/U000263",
        "NCI/C2985",
        "NCI/OMFAQ",
        "NCI/TCGA",
        "OMIM/MTHU036798",
        "SNOMEDCT_US/73211009"
      ]
    },
    {
      "entityId": "UMLS/C0021641",
      "preferredTerm": "Insulin",
      "vocabularyCodes": [
        "FMA/83365",
        "LNC/LA15805-7",
        "LNC/LP14676-8",
        "LNC/LP16325-0",
        "LNC/LP32542-0",
        "LNC/LP70329-5",
        "LNC/MTHU002108",
        "LNC/MTHU019392",
        "MEDLINEPLUS/4935",
        "MSH/D007328",
        "MTH/NOCODE",
        "SNOMEDCT_US/39487003",
        "SNOMEDCT_US/412222002",
        "SNOMEDCT_US/67866001"
      ]
    },
    {
      "entityId": "UMLS/C0241863",
      "preferredTerm": "Diabetic",
      "vocabularyCodes": [
        "LNC/LA26134-9"
      ]
    },
    {
      "entityId": "UMLS/C0348016",
      "preferredTerm": "Intravenous",
      "vocabularyCodes": [
        "LNC/LA9437-0",
        "LNC/LP32453-0",
        "MTH/NOCODE",
        "NCI/C13346",
        "SNOMEDCT_US/255560000"
      ]
    },
    {
      "entityId": "UMLS/C0795635",
      "preferredTerm": "insulin, regular, human",
      "vocabularyCodes": [
        "LNC/LP17001-6",
        "MSH/D061386",
        "MTH/NOCODE",
        "NCI/C29125",
        "RXNORM/253182",
        "SNOMEDCT_US/126210001",
        "SNOMEDCT_US/417423002",
        "SNOMEDCT_US/420609005",
        "SNOMEDCT_US/96367001",
        "VANDF/4017559",
        "VANDF/4017569",
        "VANDF/4019786"
      ]
    },
    {
      "entityId": "UMLS/C1533581",
      "preferredTerm": "Therapeutic Insulin",
      "vocabularyCodes": [
        "MTH/NOCODE",
        "NCI/C581"
      ]
    },
    {
      "entityId": "UMLS/C3537244",
      "preferredTerm": "Insulins",
      "vocabularyCodes": [
        "MSH/D061385",
        "MTH/NOCODE"
      ]
    },
    {
      "entityId": "UMLS/C3714501",
      "preferredTerm": "Insulin Drug Class",
      "vocabularyCodes": [
        "MTH/NOCODE",
        "VANDF/4021631"
      ]
    }
  ],
  "relationships": [
    {
      "subjectId": "2",
      "objectId": "4",
      "confidence": 0.99827027320861816
    },
    {
      "subjectId": "2",
      "objectId": "5",
      "confidence": 0.99729859828948975
    },
    {
      "subjectId": "3",
      "objectId": "4",
      "confidence": 0.80851161479949951
    },
    {
      "subjectId": "3",
      "objectId": "5",
      "confidence": 0.67507040500640869
    }
  ]
}

PowerShell

The following sample shows a POST request using Windows PowerShell:

$cred = gcloud auth application-default print-access-token
$headers = @{ Authorization = "Bearer $cred" }

Invoke-WebRequest `
  -Method Post `
  -Headers $headers `
  -ContentType: "application/json; charset=utf-8" `
  -Body "{
    'nlpService':'projects/PROJECT_ID/locations/us-central1/services/nlp',
    'documentContent': 'Diabetes. Insulin regimen human 5 units IV administered.',
    'licensedVocabularies': ['SNOMEDCT_US','ICD10CM']
   }" `
   -Uri "https://healthcare.googleapis.com/v1/projects/PROJECT_ID/locations/us-central1/services/nlp:analyzeEntities"  | Select-Object -Expand Content

Replace PROJECT_ID with your Google Cloud project ID.

The output is the following. The output from specifying the licensed vocabularies is in bold:

{
  "entityMentions": [
    {
      "mentionId": "1",
      "type": "PROBLEM",
      "text": {
        "content": "Diabetes"
      },
      "linkedEntities": [
        {
          "entityId": "UMLS/C0011847"
        },
        {
          "entityId": "UMLS/C0011849"
        },
        {
          "entityId": "UMLS/C0241863"
        }
      ],
      "temporalAssessment": {
        "value": "CURRENT",
        "confidence": 0.98781299591064453
      },
      "certaintyAssessment": {
        "value": "LIKELY",
        "confidence": 0.872421145439148
      },
      "subject": {
        "value": "PATIENT",
        "confidence": 0.99975031614303589
      },
      "confidence": 0.99663406610488892
    },
    {
      "mentionId": "2",
      "type": "MEDICINE",
      "text": {
        "content": "Insulin regimen",
        "beginOffset": 10
      },
      "linkedEntities": [
        {
          "entityId": "UMLS/C0795635"
        },
        {
          "entityId": "UMLS/C0021641"
        },
        {
          "entityId": "UMLS/C3537244"
        },
        {
          "entityId": "UMLS/C1533581"
        },
        {
          "entityId": "UMLS/C3714501"
        }
      ],
      "temporalAssessment": {
        "value": "CURRENT",
        "confidence": 0.91042423248291016
      },
      "certaintyAssessment": {
        "value": "LIKELY",
        "confidence": 0.99766635894775391
      },
      "subject": {
        "value": "PATIENT",
        "confidence": 0.999998152256012
      },
      "confidence": 0.716249406337738
    },
    {
      "mentionId": "3",
      "type": "MEDICINE",
      "text": {
        "content": "human",
        "beginOffset": 26
      },
      "temporalAssessment": {
        "value": "CURRENT",
        "confidence": 0.64570724964141846
      },
      "certaintyAssessment": {
        "value": "LIKELY",
        "confidence": 0.90325617790222168
      },
      "subject": {
        "value": "PATIENT",
        "confidence": 0.97613298892974854
      },
      "confidence": 0.57638454437255859
    },
    {
      "mentionId": "4",
      "type": "MED_DOSE",
      "text": {
        "content": "5 units",
        "beginOffset": 32
      },
      "confidence": 0.92076742649078369
    },
    {
      "mentionId": "5",
      "type": "MED_ROUTE",
      "text": {
        "content": "IV",
        "beginOffset": 40
      },
      "linkedEntities": [
        {
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