NLP Sandbox Data Node API (1.2.0)

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NLP Sandbox Team: team@nlpsandbox.io URL: https://nlpsandbox.io License: Apache 2.0

Overview

The NLP Sandbox Data Node is a repository of data used to benchmark NLP Tools like the NLP Sandbox Date Annotator and Person Name Annotator.

The resources that can be stored in this Data Node and the operations supported are listed below:

Create and manage datasets - Create and manage FHIR stores
- Store and retrieve FHIR patient profiles
- Store and retrieve clinical notes
Create and manage annotation stores
- Store and retrieve text annotations

Annotation

Operations about annotations

Create an annotation

path Parameters

datasetId required	string (DatasetId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-dataset The ID of the dataset
annotationStoreId required	string (AnnotationStoreId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-annotation-store The ID of the annotation store

query Parameters

annotationId

required

string (AnnotationId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$

Example: annotationId=awesome-annotation

The ID of the annotation that is being created

Request Body schema: application/json

required	object (AnnotationSource) The source of an annotation record
	Array of objects (TextDateAnnotation) Date annotations in a text
	Array of objects (TextPersonNameAnnotation) Person name annotations in a text
	Array of objects (TextLocationAnnotation) Location annotations in a text
	Array of objects (TextIdAnnotation) ID annotations in a text
	Array of objects (TextContactAnnotation) Contact annotations in a text
	Array of objects (TextCovidSymptomAnnotation) COVID symptom annotations in a text

Responses

Request samples

Payload

Content type

application/json

{"annotationSource": {"resourceSource": {"name": "string"
}
},
"textDateAnnotations": [{"start": 42,
"length": 10,
"text": "10/26/2020",
"dateFormat": "MM/DD/YYYY",
"confidence": 95.5
}
],
"textPersonNameAnnotations": [{"start": 42,
"length": 11,
"text": "Chloe Price",
"confidence": 95.5
}
],
"textLocationAnnotations": [{"start": 42,
"length": 7,
"text": "Seattle",
"locationType": "city",
"confidence": 95.5
}
],
"textIdAnnotations": [{"start": 42,
"length": 11,
"text": "203-11-4535",
"idType": "ssn",
"confidence": 95.5
}
],
"textContactAnnotations": [{"start": 42,
"length": 11,
"text": "dave@uw.edu",
"contactType": "email",
"confidence": 95.5
}
],
"textCovidSymptomAnnotations": [{"start": 42,
"length": 9,
"text": "dry cough",
"condition": "cough",
"certainty": "positive",
"confidence": 95.5
}
]
}

Response samples

201
400
409
500

Content type

application/json

{"name": "datasets/awesome-dataset/annotationStores/awesome-annotation-store/annotations/awesome-annotation"
}

List the annotations in an annotation store

Returns the annotations in an annotation store

path Parameters

datasetId required	string (DatasetId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-dataset The ID of the dataset
annotationStoreId required	string (AnnotationStoreId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-annotation-store The ID of the annotation store

query Parameters

limit	integer (PageLimit) [ 10 .. 100 ] Default: 10 Maximum number of results returned
offset	integer (PageOffset) >= 0 Default: 0 Index of the first result that must be returned

Responses

Response samples

200
400
500

Content type

application/json

{"offset": 0,
"limit": 10,
"links": {"next": "http://example.com"
},
"totalResults": 0,
"annotations": [{"name": "datasets/awesome-dataset/annotationStores/awesome-annotation-store/annotations/awesome-annotation",
"annotationSource": {"resourceSource": {"name": "string"
}
},
"textDateAnnotations": [{"start": 42,
"length": 10,
"text": "10/26/2020",
"dateFormat": "MM/DD/YYYY",
"confidence": 95.5
}
],
"textPersonNameAnnotations": [{"start": 42,
"length": 11,
"text": "Chloe Price",
"confidence": 95.5
}
],
"textLocationAnnotations": [{"start": 42,
"length": 7,
"text": "Seattle",
"locationType": "city",
"confidence": 95.5
}
],
"textIdAnnotations": [{"start": 42,
"length": 11,
"text": "203-11-4535",
"idType": "ssn",
"confidence": 95.5
}
],
"textContactAnnotations": [{"start": 42,
"length": 11,
"text": "dave@uw.edu",
"contactType": "email",
"confidence": 95.5
}
],
"textCovidSymptomAnnotations": [{"start": 42,
"length": 9,
"text": "dry cough",
"condition": "cough",
"certainty": "positive",
"confidence": 95.5
}
]
}
]
}

Get an annotation

Returns the annotation specified

path Parameters

datasetId required	string (DatasetId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-dataset The ID of the dataset
annotationStoreId required	string (FhirStoreId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-fhir-store The ID of the annotation store
annotationId required	string (AnnotationId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-annotation The ID of the annotation

Responses

Response samples

200
404
500

Content type

application/json

{"name": "datasets/awesome-dataset/annotationStores/awesome-annotation-store/annotations/awesome-annotation",
"annotationSource": {"resourceSource": {"name": "string"
}
},
"textDateAnnotations": [{"start": 42,
"length": 10,
"text": "10/26/2020",
"dateFormat": "MM/DD/YYYY",
"confidence": 95.5
}
],
"textPersonNameAnnotations": [{"start": 42,
"length": 11,
"text": "Chloe Price",
"confidence": 95.5
}
],
"textLocationAnnotations": [{"start": 42,
"length": 7,
"text": "Seattle",
"locationType": "city",
"confidence": 95.5
}
],
"textIdAnnotations": [{"start": 42,
"length": 11,
"text": "203-11-4535",
"idType": "ssn",
"confidence": 95.5
}
],
"textContactAnnotations": [{"start": 42,
"length": 11,
"text": "dave@uw.edu",
"contactType": "email",
"confidence": 95.5
}
],
"textCovidSymptomAnnotations": [{"start": 42,
"length": 9,
"text": "dry cough",
"condition": "cough",
"certainty": "positive",
"confidence": 95.5
}
]
}

Delete an annotation

Deletes the annotation specified

path Parameters

datasetId required	string (DatasetId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-dataset The ID of the dataset
annotationStoreId required	string (FhirStoreId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-fhir-store The ID of the annotation store
annotationId required	string (AnnotationId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-annotation The ID of the annotation

Responses

Response samples

200
404
500

Content type

application/json

{ }

AnnotationStore

Operations about annotation stores

Create an annotation store

Create an annotation store with the ID specified

path Parameters

datasetId

required

string (DatasetId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$

Example: awesome-dataset

The ID of the dataset

query Parameters

annotationStoreId

required

string (AnnotationStoreId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$

Example: annotationStoreId=awesome-annotation-store

The ID of the annotation store that is being created.

Request Body schema: application/json

object (AnnotationStoreCreateRequest)

An empty object

Responses

Request samples

Payload

Content type

application/json

{ }

Response samples

201
400
409
500

Content type

application/json

{"name": "datasets/awesome-dataset/annotationStores/awesome-annotation-store"
}

List the annotation stores in a dataset

Returns the annotation stores

path Parameters

datasetId

required

string (DatasetId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$

Example: awesome-dataset

The ID of the dataset

query Parameters

limit	integer (PageLimit) [ 10 .. 100 ] Default: 10 Maximum number of results returned
offset	integer (PageOffset) >= 0 Default: 0 Index of the first result that must be returned

Responses

Response samples

200
400
500

Content type

application/json

{"offset": 0,
"limit": 10,
"links": {"next": "http://example.com"
},
"totalResults": 0,
"annotationStores": [{"name": "datasets/awesome-dataset/annotationStores/awesome-annotation-store"
}
]
}

Get an annotation store

Returns the annotation store specified

path Parameters

datasetId required	string (DatasetId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-dataset The ID of the dataset
annotationStoreId required	string (AnnotationStoreId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-annotation-store The ID of the annotation store

Responses

Response samples

200
404
500

Content type

application/json

{"name": "datasets/awesome-dataset/annotationStores/awesome-annotation-store"
}

Delete an annotation store

Deletes the annotation store specified

path Parameters

datasetId required	string (DatasetId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-dataset The ID of the dataset
annotationStoreId required	string (AnnotationStoreId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-annotation-store The ID of the annotation store

Responses

Response samples

200
404
500

Content type

application/json

{ }

Dataset

Operations about datasets

Create a dataset

Create a dataset with the name specified

query Parameters

datasetId

required

string (DatasetId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$

Example: datasetId=awesome-dataset

The ID of the dataset that is being created

Request Body schema: application/json

object (DatasetCreateRequest)

An empty object

Responses

Request samples

Payload

Content type

application/json

{ }

Response samples

201
400
409
500

Content type

application/json

{"name": "datasets/awesome-dataset"
}

Get all datasets

Returns the datasets

query Parameters

limit	integer (PageLimit) [ 10 .. 100 ] Default: 10 Maximum number of results returned
offset	integer (PageOffset) >= 0 Default: 0 Index of the first result that must be returned

Responses

Response samples

200
400
500

Content type

application/json

{"offset": 0,
"limit": 10,
"links": {"next": "http://example.com"
},
"totalResults": 0,
"datasets": [{"name": "datasets/awesome-dataset"
}
]
}

Get a dataset by ID

Returns the dataset for a given ID

path Parameters

datasetId

required

string (DatasetId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$

Example: awesome-dataset

The ID of the dataset

Responses

Response samples

200
404
500

Content type

application/json

{"name": "datasets/awesome-dataset"
}

Delete a dataset by ID

Deletes the dataset for a given ID

path Parameters

datasetId

required

string (DatasetId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$

Example: awesome-dataset

The ID of the dataset

Responses

Response samples

200
404
500

Content type

application/json

{ }

FhirStore

Operations about FHIR stores

Create a FHIR store

Create a FHIR store with the ID specified

path Parameters

datasetId

required

string (DatasetId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$

Example: awesome-dataset

The ID of the dataset

query Parameters

fhirStoreId

required

string (FhirStoreId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$

Example: fhirStoreId=awesome-fhir-store

The ID of the FHIR store that is being created.

Request Body schema: application/json

object (FhirStoreCreateRequest)

An empty object

Responses

Request samples

Payload

Content type

application/json

{ }

Response samples

201
400
409
500

Content type

application/json

{"name": "datasets/awesome-dataset/fhirStores/awesome-fhir-store"
}

List the FHIR stores in a dataset

Returns the FHIR stores

path Parameters

datasetId

required

string (DatasetId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$

Example: awesome-dataset

The ID of the dataset

query Parameters

limit	integer (PageLimit) [ 10 .. 100 ] Default: 10 Maximum number of results returned
offset	integer (PageOffset) >= 0 Default: 0 Index of the first result that must be returned

Responses

Response samples

200
400
500

Content type

application/json

{"offset": 0,
"limit": 10,
"links": {"next": "http://example.com"
},
"totalResults": 0,
"fhirStores": [{"name": "datasets/awesome-dataset/fhirStores/awesome-fhir-store"
}
]
}

Get a FHIR store

Returns the FHIR store specified

path Parameters

datasetId required	string (DatasetId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-dataset The ID of the dataset
fhirStoreId required	string (FhirStoreId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-fhir-store The ID of the FHIR store

Responses

Response samples

200
404
500

Content type

application/json

{"name": "datasets/awesome-dataset/fhirStores/awesome-fhir-store"
}

Delete a FHIR store

Deletes the FHIR store specified

path Parameters

datasetId required	string (DatasetId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-dataset The ID of the dataset
fhirStoreId required	string (FhirStoreId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-fhir-store The ID of the FHIR store

Responses

Response samples

200
404
500

Content type

application/json

{ }

HealthCheck

Operations about health checks

Get health check information

Get information about the health of the service

Responses

Response samples

200
404
500

Content type

application/json

{"status": "pass"
}

Note

Operations about notes

Create a note

path Parameters

datasetId required	string (DatasetId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-dataset The ID of the dataset
fhirStoreId required	string (FhirStoreId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-fhir-store The ID of the FHIR store

query Parameters

noteId

required

string (NoteId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$

Example: noteId=awesome-note

The ID of the note that is being created

Request Body schema: application/json

text required	string The content of the clinical note
type required	string The note type (LOINC concept)
patientId required	string (PatientId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ The ID of the FHIR patient

Responses

Request samples

Payload

Content type

application/json

{"text": "On 12/26/2020, Ms. Chloe Price met with Dr. Prescott in Seattle.",
"type": "loinc:LP29684-5",
"patientId": "awesome-patient"
}

Response samples

201
400
409
500

Content type

application/json

{"name": "datasets/awesome-dataset/fhirStores/awesome-fhir-store/Note/awesome-note"
}

List notes

Returns the notes in a FHIR store

path Parameters

datasetId required	string (DatasetId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-dataset The ID of the dataset
fhirStoreId required	string (FhirStoreId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-fhir-store The ID of the FHIR store

query Parameters

limit	integer (PageLimit) [ 10 .. 100 ] Default: 10 Maximum number of results returned
offset	integer (PageOffset) >= 0 Default: 0 Index of the first result that must be returned

Responses

Response samples

200
400
500

Content type

application/json

{"offset": 0,
"limit": 10,
"links": {"next": "http://example.com"
},
"totalResults": 0,
"notes": [{"identifier": "awesome-note",
"text": "On 12/26/2020, Ms. Chloe Price met with Dr. Prescott in Seattle.",
"type": "loinc:LP29684-5",
"patientId": "awesome-patient"
}
]
}

Get a note

Returns the note specified

path Parameters

datasetId required	string (DatasetId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-dataset The ID of the dataset
fhirStoreId required	string (FhirStoreId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-fhir-store The ID of the FHIR store
noteId required	string (NoteId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-note The ID of the note

Responses

Response samples

200
404
500

Content type

application/json

{"identifier": "awesome-note",
"text": "On 12/26/2020, Ms. Chloe Price met with Dr. Prescott in Seattle.",
"type": "loinc:LP29684-5",
"patientId": "awesome-patient"
}

Delete a note

Deletes the note specified

path Parameters

datasetId required	string (DatasetId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-dataset The ID of the dataset
fhirStoreId required	string (FhirStoreId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-fhir-store The ID of the FHIR store
noteId required	string (NoteId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-note The ID of the note

Responses

Response samples

200
404
500

Content type

application/json

{ }

Patient

Operations about patients

Create a FHIR patient

path Parameters

datasetId required	string (DatasetId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-dataset The ID of the dataset
fhirStoreId required	string (FhirStoreId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-fhir-store The ID of the FHIR store

query Parameters

patientId

required

string (PatientId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$

Example: patientId=awesome-patient

The ID of the patient that is being created

Request Body schema: application/json

gender

string

Enum: "male" "female" "other" "unknown"

Gender of the patient

Responses

Request samples

Payload

Content type

application/json

{"gender": "male"
}

Response samples

201
400
409
500

Content type

application/json

{"name": "datasets/awesome-dataset/fhirStores/awesome-fhir-store/Patient/507f1f77bcf86cd799439011"
}

List the Patients in a FHIR store

Returns the Patients in a FHIR store

path Parameters

datasetId required	string (DatasetId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-dataset The ID of the dataset
fhirStoreId required	string (FhirStoreId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-fhir-store The ID of the FHIR store

query Parameters

limit	integer (PageLimit) [ 10 .. 100 ] Default: 10 Maximum number of results returned
offset	integer (PageOffset) >= 0 Default: 0 Index of the first result that must be returned

Responses

Response samples

200
400
500

Content type

application/json

{"offset": 0,
"limit": 10,
"links": {"next": "http://example.com"
},
"totalResults": 0,
"patients": [{"identifier": "awesome-patient",
"gender": "male"
}
]
}

Get a FHIR patient

Returns the FHIR patient specified

path Parameters

datasetId required	string (DatasetId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-dataset The ID of the dataset
fhirStoreId required	string (FhirStoreId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-fhir-store The ID of the FHIR store
patientId required	string (PatientId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-patient The ID of the FHIR patient

Responses

Response samples

200
404
500

Content type

application/json

{"identifier": "awesome-patient",
"gender": "male"
}

Delete a FHIR patient

Deletes the FHIR patient specified

path Parameters

datasetId required	string (DatasetId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-dataset The ID of the dataset
fhirStoreId required	string (FhirStoreId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-fhir-store The ID of the FHIR store
patientId required	string (PatientId) [ 3 .. 60 ] characters ^[a-z0-9]+(?:-[a-z0-9]+)*$ Example: awesome-patient The ID of the FHIR patient

Responses

Response samples

200
404
500

Content type

application/json

{ }