Onco Phenotype model configuration
To interact with the Onco Phenotype model, you can provide several model configurations parameters that modify the outcome of the responses.
Important
Model configuration is applied to ALL the patients within a request.
"configuration": {
"checkForCancerCase": false,
"includeEvidence": false
}
Case finding
The Onco Phenotype model configuration helps you find if any cancer cases exist. The API allows you to explicitly check if a cancer case exists in the provided clinical documents.
| Check for cancer case | Did the model find a case? | Behavior |
|---|---|---|
| true | Yes | Inferences are returned |
| true | No | No inferences are returned |
| false | N/A | Inferences are always returned but they aren't meaningful if there's no cancer case. |
Set checkForCancerCase to false if
- you're sure that the provided clinical documents definitely contain a case
- the model is unable to find a case in a valid scenario
If a case is found in the provided clinical documents and the model is able to find that case, the inferences are always returned.
Case finding examples
With case finding
The following example represents a case finding. The checkForCancerCase has been set to true and includeEvidence has been set to false. Meaning the model checks for a cancer case but not include the evidence.
Request that contains a case:
{
"configuration": {
"checkForCancerCase": true,
"includeEvidence": false
},
"patients": [
{
"id": "patient1",
"data": [
{
"kind": "note",
"clinicalType": "pathology",
"id": "document1",
"language": "en",
"createdDateTime": "2022-01-01T00:00:00",
"content": {
"sourceType": "inline",
"value": "Laterality: Left \n Tumor type present: Invasive duct carcinoma; duct carcinoma in situ \n Tumor site: Upper inner quadrant \n Invasive carcinoma \n Histologic type: Ductal \n Size of invasive component: 0.9 cm \n Histologic Grade - Nottingham combined histologic score: 1 out of 3 \n In situ carcinoma (DCIS) \n Histologic type of DCIS: Cribriform and solid \n Necrosis in DCIS: Yes \n DCIS component of invasive carcinoma: Extensive \n"
}
}
]
}
]
}
Response:
{
"results": {
"patients": [
{
"id": "patient1",
"inferences": [
{
"kind": "tumorSite",
"value": "C50.2",
"description": "BREAST",
"confidenceScore": 0.9214
},
{
"kind": "histology",
"value": "8500",
"confidenceScore": 0.9973
},
{
"kind": "clinicalStageT",
"value": "T1",
"confidenceScore": 0.9956
},
{
"kind": "clinicalStageN",
"value": "N0",
"confidenceScore": 0.9931
},
{
"kind": "clinicalStageM",
"value": "None",
"confidenceScore": 0.5217
},
{
"kind": "pathologicStageT",
"value": "T1",
"confidenceScore": 0.9477
},
{
"kind": "pathologicStageN",
"value": "N0",
"confidenceScore": 0.7927
},
{
"kind": "pathologicStageM",
"value": "M0",
"confidenceScore": 0.9208
}
]
}
],
"modelVersion": "2023-03-01-preview"
},
"jobId": "385903b2-ab21-4f9e-a011-43b01f78f04e",
"createdDateTime": "2023-03-08T17:02:46Z",
"expirationDateTime": "2023-03-08T17:19:26Z",
"lastUpdateDateTime": "2023-03-08T17:02:53Z",
"status": "succeeded"
}
Request that does not contain a case:
{
"configuration": {
"checkForCancerCase": true,
"includeEvidence": false
},
"patients": [
{
"id": "patient1",
"data": [
{
"kind": "note",
"clinicalType": "pathology",
"id": "document1",
"language": "en",
"createdDateTime": "2022-01-01T00:00:00",
"content": {
"sourceType": "inline",
"value": "Test document"
}
}
]
}
]
}
Response:
{
"results": {
"patients": [
{
"id": "patient1",
"inferences": []
}
],
"modelVersion": "2023-03-01-preview"
},
"jobId": "abe71219-b3ce-4def-9e12-3dc511096c88",
"createdDateTime": "2023-03-08T17:05:23Z",
"expirationDateTime": "2023-03-08T17:22:03Z",
"lastUpdateDateTime": "2023-03-08T17:05:23Z",
"status": "succeeded"
}
Evidence
Through the model configuration, the API allows you to seek evidence from the provided clinical documents as part of the inferences.
| Include evidence | Behavior |
|---|---|
| true | Evidence is returned as part of each inference |
| false | No evidence is returned |
Evidence example
The following example represents a case finding. The checkForCancerCase has been set to true and includeEvidence has been set to true. Meaning the model checks for a cancer case and include the evidence.
Request that contains a case:
{
"configuration": {
"checkForCancerCase": true,
"includeEvidence": true
},
"patients": [
{
"id": "patient1",
"data": [
{
"kind": "note",
"clinicalType": "pathology",
"id": "document1",
"language": "en",
"createdDateTime": "2022-01-01T00:00:00",
"content": {
"sourceType": "inline",
"value": "Laterality: Left \n Tumor type present: Invasive duct carcinoma; duct carcinoma in situ \n Tumor site: Upper inner quadrant \n Invasive carcinoma \n Histologic type: Ductal \n Size of invasive component: 0.9 cm \n Histologic Grade - Nottingham combined histologic score: 1 out of 3 \n In situ carcinoma (DCIS) \n Histologic type of DCIS: Cribriform and solid \n Necrosis in DCIS: Yes \n DCIS component of invasive carcinoma: Extensive \n"
}
}
]
}
]
}
Response:
{
"results": {
"patients": [
{
"id": "patient1",
"inferences": [
{
"type": "tumorSite",
"evidence": [
{
"patientDataEvidence": {
"id": "document1",
"text": "Upper inner",
"offset": 108,
"length": 11
},
"importance": 0.5563
},
{
"patientDataEvidence": {
"id": "document1",
"text": "duct",
"offset": 68,
"length": 4
},
"importance": 0.0156
}
],
"value": "C50.2",
"description": "BREAST",
"confidenceScore": 0.9214
},
{
"type": "histology",
"evidence": [
{
"patientDataEvidence": {
"id": "document1",
"text": "Ductal",
"offset": 174,
"length": 6
},
"importance": 0.2937
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Invasive duct",
"offset": 43,
"length": 13
},
"importance": 0.2439
},
{
"patientDataEvidence": {
"id": "document1",
"text": "invasive",
"offset": 193,
"length": 8
},
"importance": 0.1588
},
{
"patientDataEvidence": {
"id": "document1",
"text": "duct",
"offset": 68,
"length": 4
},
"importance": 0.1483
},
{
"patientDataEvidence": {
"id": "document1",
"text": "solid",
"offset": 368,
"length": 5
},
"importance": 0.0694
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Cribriform",
"offset": 353,
"length": 10
},
"importance": 0.043
}
],
"value": "8500",
"confidenceScore": 0.9973
},
{
"type": "clinicalStageT",
"evidence": [
{
"patientDataEvidence": {
"id": "document1",
"text": "Invasive duct carcinoma; duct",
"offset": 43,
"length": 29
},
"importance": 0.2613
},
{
"patientDataEvidence": {
"id": "document1",
"text": "invasive",
"offset": 193,
"length": 8
},
"importance": 0.1341
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Laterality: Left",
"offset": 0,
"length": 17
},
"importance": 0.0874
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Invasive",
"offset": 133,
"length": 8
},
"importance": 0.0722
},
{
"patientDataEvidence": {
"id": "document1",
"text": "situ",
"offset": 86,
"length": 4
},
"importance": 0.0651
}
],
"value": "T1",
"confidenceScore": 0.9956
},
{
"type": "clinicalStageN",
"evidence": [
{
"patientDataEvidence": {
"id": "document1",
"text": "Invasive duct carcinoma; duct carcinoma in situ",
"offset": 43,
"length": 47
},
"importance": 0.1529
},
{
"patientDataEvidence": {
"id": "document1",
"text": "invasive carcinoma: Extensive",
"offset": 423,
"length": 30
},
"importance": 0.0782
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Invasive",
"offset": 133,
"length": 8
},
"importance": 0.0715
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Tumor",
"offset": 95,
"length": 5
},
"importance": 0.0513
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Left",
"offset": 13,
"length": 4
},
"importance": 0.0325
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Tumor",
"offset": 22,
"length": 5
},
"importance": 0.0174
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Histologic",
"offset": 156,
"length": 10
},
"importance": 0.0066
}
],
"value": "N0",
"confidenceScore": 0.9931
},
{
"type": "clinicalStageM",
"evidence": [
{
"patientDataEvidence": {
"id": "document1",
"text": "Laterality: Left",
"offset": 0,
"length": 17
},
"importance": 0.1579
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Invasive duct",
"offset": 43,
"length": 13
},
"importance": 0.1493
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Histologic Grade - Nottingham",
"offset": 225,
"length": 29
},
"importance": 0.1038
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Invasive",
"offset": 133,
"length": 8
},
"importance": 0.089
},
{
"patientDataEvidence": {
"id": "document1",
"text": "duct carcinoma",
"offset": 68,
"length": 14
},
"importance": 0.0807
},
{
"patientDataEvidence": {
"id": "document1",
"text": "invasive",
"offset": 423,
"length": 8
},
"importance": 0.057
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Extensive",
"offset": 444,
"length": 9
},
"importance": 0.0494
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Tumor",
"offset": 22,
"length": 5
},
"importance": 0.0311
}
],
"value": "None",
"confidenceScore": 0.5217
},
{
"type": "pathologicStageT",
"evidence": [
{
"patientDataEvidence": {
"id": "document1",
"text": "Invasive duct",
"offset": 43,
"length": 13
},
"importance": 0.3125
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Left",
"offset": 13,
"length": 4
},
"importance": 0.201
},
{
"patientDataEvidence": {
"id": "document1",
"text": "invasive",
"offset": 193,
"length": 8
},
"importance": 0.1244
},
{
"patientDataEvidence": {
"id": "document1",
"text": "invasive",
"offset": 423,
"length": 8
},
"importance": 0.0961
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Invasive",
"offset": 133,
"length": 8
},
"importance": 0.0623
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Tumor",
"offset": 22,
"length": 5
},
"importance": 0.0583
}
],
"value": "T1",
"confidenceScore": 0.9477
},
{
"type": "pathologicStageN",
"evidence": [
{
"patientDataEvidence": {
"id": "document1",
"text": "invasive component:",
"offset": 193,
"length": 19
},
"importance": 0.1402
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Nottingham combined histologic score:",
"offset": 244,
"length": 37
},
"importance": 0.1096
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Invasive carcinoma",
"offset": 133,
"length": 18
},
"importance": 0.1067
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Ductal",
"offset": 174,
"length": 6
},
"importance": 0.0896
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Invasive duct carcinoma;",
"offset": 43,
"length": 24
},
"importance": 0.0831
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Histologic",
"offset": 156,
"length": 10
},
"importance": 0.0447
},
{
"patientDataEvidence": {
"id": "document1",
"text": "in situ",
"offset": 83,
"length": 7
},
"importance": 0.042
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Tumor",
"offset": 22,
"length": 5
},
"importance": 0.0092
}
],
"value": "N0",
"confidenceScore": 0.7927
},
{
"type": "pathologicStageM",
"evidence": [
{
"patientDataEvidence": {
"id": "document1",
"text": "In situ carcinoma (DCIS)",
"offset": 298,
"length": 24
},
"importance": 0.1111
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Nottingham combined histologic",
"offset": 244,
"length": 30
},
"importance": 0.0999
},
{
"patientDataEvidence": {
"id": "document1",
"text": "invasive carcinoma:",
"offset": 423,
"length": 19
},
"importance": 0.0787
},
{
"patientDataEvidence": {
"id": "document1",
"text": "invasive",
"offset": 193,
"length": 8
},
"importance": 0.0617
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Invasive duct carcinoma;",
"offset": 43,
"length": 24
},
"importance": 0.0594
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Tumor",
"offset": 22,
"length": 5
},
"importance": 0.0579
},
{
"patientDataEvidence": {
"id": "document1",
"text": "of DCIS:",
"offset": 343,
"length": 8
},
"importance": 0.0483
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Laterality:",
"offset": 0,
"length": 11
},
"importance": 0.0324
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Invasive carcinoma",
"offset": 133,
"length": 18
},
"importance": 0.0269
},
{
"patientDataEvidence": {
"id": "document1",
"text": "carcinoma in",
"offset": 73,
"length": 12
},
"importance": 0.0202
},
{
"patientDataEvidence": {
"id": "document1",
"text": "Tumor",
"offset": 95,
"length": 5
},
"importance": 0.0112
}
],
"value": "M0",
"confidenceScore": 0.9208
}
]
}
],
"modelVersion": "2023-03-01-preview"
},
"jobId": "5f975105-6f11-4985-b5cd-896215fb5cd3",
"createdDateTime": "2023-03-08T17:10:39Z",
"expirationDateTime": "2023-03-08T17:27:19Z",
"lastUpdateDateTime": "2023-03-08T17:10:41Z",
"status": "succeeded"
}
Next steps
Refer to the following page to get better insights into the request and responses:
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