Clinical text in.
Structured data out.

curl -X POST 'https://experiment.app.pheno.ml/auth/token' \
  -H 'Authorization: Bearer YOUR_API_KEY'

{
  "token": "eyJhbGciOiJSUzI1NiJ9..."
}

curl -X POST 'https://experiment.app.pheno.ml/v2/auth/token' \
  -H 'Authorization: Bearer YOUR_API_KEY' \
  -H 'Content-Type: application/json' \
  -d '{
  "client_id": "your_client_id",
  "client_secret": "your_client_secret"
}'

{
  "access_token": "eyJhbGciOiJSUzI1NiIsInR5cCI6IkpXVCJ9...",
  "token_type": "Bearer",
  "expires_in": 172800
}

curl -X POST 'https://experiment.app.pheno.ml/construe/feedback' \
  -H 'Authorization: Bearer YOUR_API_KEY' \
  -H 'Content-Type: application/json' \
  -d '{
  "text": "Patient has type 2 diabetes with hyperglycemia",
  "received_result": {
    "system": {
      "name": "SNOMED_CT_US_LITE",
      "version": "20240901"
    },
    "codes": [
      {
        "code": "195967001",
        "description": "Asthma",
        "valid": true,
        "reason": "example",
        "is_ancestor": true,
        "citations": [
          {
            "text": "Patient has type 2 diabetes",
            "begin_offset": 0,
            "end_offset": 27
          }
        ],
        "categories": [
          {
            "uri": "HP:0025142",
            "label": "Constitutional symptom"
          }
        ]
      }
    ]
  },
  "expected_result": {},
  "detail": "Expected code X instead because ..."
}'

{
  "id": "abc123def456"
}

curl 'https://experiment.app.pheno.ml/construe/codes/systems' \
  -H 'Authorization: Bearer YOUR_API_KEY'

{
  "systems": [
    {
      "name": "ICD-10-CM",
      "version": "2025",
      "code_count": 72750,
      "builtin": true
    }
  ]
}

curl 'https://experiment.app.pheno.ml/construe/codes/systems/ICD-10-CM?version=2025' \
  -H 'Authorization: Bearer YOUR_API_KEY'

{
  "name": "ICD-10-CM",
  "version": "2025",
  "code_count": 72750,
  "builtin": true,
  "status": "ready",
  "created_at": "2024-01-15T09:30:00Z",
  "updated_at": "2024-01-15T09:30:00Z"
}

curl -X DELETE 'https://experiment.app.pheno.ml/construe/codes/systems/CUSTOM_CODES?version=example' \
  -H 'Authorization: Bearer YOUR_API_KEY'

{
  "message": "code system deleted successfully"
}

curl 'https://experiment.app.pheno.ml/construe/codes/systems/CUSTOM_CODES/export?version=example' \
  -H 'Authorization: Bearer YOUR_API_KEY'

{
  "name": "CUSTOM_CODES",
  "version": "1.0",
  "format": "json",
  "codes": [
    {
      "code": "E11.65",
      "description": "Type 2 diabetes mellitus with hyperglycemia",
      "definition": "example"
    }
  ]
}

curl -X POST 'https://experiment.app.pheno.ml/construe/upload' \
  -H 'Authorization: Bearer YOUR_API_KEY' \
  -H 'Content-Type: application/json' \
  -d '{
  "name": "CUSTOM_CODES",
  "version": "1.0",
  "format": "json",
  "codes": [
    {
      "code": "X001",
      "description": "Example custom code 1"
    },
    {
      "code": "X002",
      "description": "Example custom code 2"
    }
  ]
}'

{
  "status": "processing",
  "name": "CUSTOM_CODES",
  "version": "1.0"
}

curl 'https://experiment.app.pheno.ml/construe/codes/ICD-10-CM?version=2025&limit=5' \
  -H 'Authorization: Bearer YOUR_API_KEY'

{
  "system": {
    "name": "ICD-10-CM",
    "version": "2025"
  },
  "codes": [
    {
      "code": "A00",
      "description": "Cholera"
    },
    {
      "code": "A000",
      "description": "Cholera due to Vibrio cholerae 01, biovar cholerae"
    },
    {
      "code": "A001",
      "description": "Cholera due to Vibrio cholerae 01, biovar eltor"
    },
    {
      "code": "A009",
      "description": "Cholera, unspecified"
    },
    {
      "code": "A01",
      "description": "Typhoid and paratyphoid fevers"
    }
  ],
  "next_cursor": "QTAx",
  "has_more": true
}

curl 'https://experiment.app.pheno.ml/construe/codes/ICD-10-CM/E1165' \
  -H 'Authorization: Bearer YOUR_API_KEY'

{
  "system": {
    "name": "ICD-10-CM",
    "version": "2025"
  },
  "code": "E1165",
  "description": "Type 2 diabetes mellitus with hyperglycemia"
}

curl 'https://experiment.app.pheno.ml/construe/codes/ICD-10-CM/search/semantic?text=patient%20has%20trouble%20breathing%20at%20night%20and%20wakes%20up%20gasping&limit=5' \
  -H 'Authorization: Bearer YOUR_API_KEY'

{
  "system": {
    "name": "ICD-10-CM",
    "version": "2025"
  },
  "results": [
    {
      "code": "R06.00",
      "description": "Dyspnea, unspecified"
    },
    {
      "code": "R06.01",
      "description": "Orthopnea"
    },
    {
      "code": "G47.33",
      "description": "Obstructive sleep apnea"
    },
    {
      "code": "R06.83",
      "description": "Snoring"
    },
    {
      "code": "J45.20",
      "description": "Mild intermittent asthma, uncomplicated"
    }
  ]
}

curl 'https://experiment.app.pheno.ml/construe/codes/ICD-10-CM/search/text?q=E11.65&limit=5' \
  -H 'Authorization: Bearer YOUR_API_KEY'

{
  "system": {
    "name": "ICD-10-CM",
    "version": "2025"
  },
  "results": [
    {
      "code": "E11.65",
      "description": "Type 2 diabetes mellitus with hyperglycemia"
    },
    {
      "code": "E11.649",
      "description": "Type 2 diabetes mellitus with hypoglycemia without coma"
    },
    {
      "code": "E11.69",
      "description": "Type 2 diabetes mellitus with other specified complication"
    }
  ],
  "found": 3
}

curl -X POST 'https://experiment.app.pheno.ml/construe/extract' \
  -H 'Authorization: Bearer YOUR_API_KEY' \
  -H 'Content-Type: application/json' \
  -d '{
  "text": "Patient is a 14-year-old female, previously healthy, who is here for evaluation of abnormal renal ultrasound with atrophic right kidney.",
  "system": {
    "name": "ICD-10-CM",
    "version": "2025"
  }
}'

{
  "system": {
    "name": "ICD-10-CM",
    "version": "2025"
  },
  "codes": [
    {
      "code": "Q60.3",
      "description": "Renal hypoplasia, unspecified",
      "valid": true
    },
    {
      "code": "R93.42",
      "description": "Abnormal findings on diagnostic imaging of kidney",
      "valid": true
    },
    {
      "code": "N28.1",
      "description": "Cyst of kidney, acquired",
      "valid": true
    }
  ]
}

curl -X POST 'https://experiment.app.pheno.ml/cohort' \
  -H 'Authorization: Bearer YOUR_API_KEY' \
  -H 'Content-Type: application/json' \
  -d '{
  "text": "female patients over 65 with diabetes but not hypertension"
}'

{
  "success": true,
  "message": "Successfully analyzed cohort criteria",
  "queries": [
    {
      "resource_type": "Patient",
      "search_params": "gender=female&birthdate=le1959-01-01",
      "concept": "female patients over 65",
      "exclude": false
    }
  ]
}

curl -X POST 'https://experiment.app.pheno.ml/lang2fhir/create' \
  -H 'Authorization: Bearer YOUR_API_KEY' \
  -H 'Content-Type: application/json' \
  -d '{
  "text": "Patient has severe persistent asthma with acute exacerbation",
  "version": "R4",
  "resource": "condition-encounter-diagnosis"
}'

{
  "resourceType": "Condition",
  "clinicalStatus": {
    "coding": [
      {
        "system": "http://terminology.hl7.org/CodeSystem/condition-clinical",
        "code": "active"
      }
    ]
  },
  "code": {
    "coding": [
      {
        "system": "http://snomed.info/sct",
        "code": "195967001",
        "display": "Asthma"
      }
    ],
    "text": "Severe persistent asthma with acute exacerbation"
  },
  "severity": {
    "coding": [
      {
        "system": "http://snomed.info/sct",
        "code": "24484000",
        "display": "Severe"
      }
    ]
  }
}

curl -X POST 'https://experiment.app.pheno.ml/lang2fhir/create/multi' \
  -H 'Authorization: Bearer YOUR_API_KEY' \
  -H 'Content-Type: application/json' \
  -d '{
  "text": "John Smith, 45-year-old male, diagnosed with Type 2 Diabetes. Prescribed Metformin 500mg twice daily. Blood pressure 140/90.",
  "version": "R4"
}'

{
  "success": true,
  "message": "Successfully extracted 3 resources",
  "bundle": {
    "resourceType": "Bundle",
    "type": "transaction",
    "entry": [
      {
        "fullUrl": "urn:uuid:patient-001",
        "resource": {
          "resourceType": "Patient",
          "name": [
            {
              "given": [
                "John"
              ],
              "family": "Smith"
            }
          ],
          "gender": "male"
        },
        "request": {
          "method": "POST",
          "url": "Patient"
        }
      },
      {
        "fullUrl": "urn:uuid:condition-001",
        "resource": {
          "resourceType": "Condition",
          "code": {
            "text": "Type 2 Diabetes"
          }
        },
        "request": {
          "method": "POST",
          "url": "Condition"
        }
      },
      {
        "fullUrl": "urn:uuid:medication-001",
        "resource": {
          "resourceType": "MedicationRequest",
          "medicationCodeableConcept": {
            "text": "Metformin 500mg"
          }
        },
        "request": {
          "method": "POST",
          "url": "MedicationRequest"
        }
      }
    ]
  }
}

curl -X POST 'https://experiment.app.pheno.ml/lang2fhir/document' \
  -H 'Authorization: Bearer YOUR_API_KEY' \
  -H 'Content-Type: application/json' \
  -d '{
  "version": "R4",
  "resource": "questionnaire",
  "content": "Example text content",
  "config": {
    "page_filter": {
      "context": "clinical notes, diagnoses, medications — not sample collection instructions or insurance forms"
    }
  }
}'

{}

curl -X POST 'https://experiment.app.pheno.ml/lang2fhir/document/multi' \
  -H 'Authorization: Bearer YOUR_API_KEY' \
  -H 'Content-Type: application/json' \
  -d '{
  "version": "R4",
  "content": "Example text content",
  "provider": "canvas",
  "implementation_guide": "acme-cardiology",
  "detection_effort": "standard",
  "validation_method": "none",
  "config": {
    "page_filter": {
      "context": "clinical notes, diagnoses, medications — not sample collection instructions or insurance forms"
    }
  }
}'

{
  "success": true,
  "message": "Successfully extracted FHIR resources from document",
  "bundle": {
    "resourceType": "Bundle",
    "type": "transaction",
    "entry": [
      {
        "fullUrl": "urn:uuid:a842c4bc-f6cb-4555-9741-ac3aec4ef0b8",
        "resource": {},
        "request": {
          "method": "POST",
          "url": "Patient"
        }
      }
    ]
  },
  "resources": [
    {
      "tempId": "urn:uuid:a842c4bc-f6cb-4555-9741-ac3aec4ef0b8",
      "resourceType": "Patient",
      "description": "John Smith (DOB 1980-05-12) was diagnosed with Type 2 Diabetes during office visit on 2025-03-01 with Dr. Chen",
      "originalText": "diagnosed with Type 2 Diabetes"
    }
  ],
  "validation": {
    "passes": [
      {
        "issues": [
          {
            "severity": "fatal",
            "code": "ABC123",
            "diagnostics": "example",
            "expression": [
              "example"
            ],
            "source": "example"
          }
        ],
        "stats": {
          "resource_type": "Patient",
          "profile_url": "https://example.com",
          "is_custom_profile": true,
          "duration_ms": 0.5
        }
      }
    ],
    "fixed": true,
    "attempts": 10,
    "summary": "example"
  },
  "page_classifications": [
    {
      "page_number": 1,
      "include": true,
      "reason": "clinical notes with diagnoses"
    }
  ]
}

curl -X POST 'https://experiment.app.pheno.ml/lang2fhir/profile/upload' \
  -H 'Authorization: Bearer YOUR_API_KEY' \
  -H 'Content-Type: application/json' \
  -d '{
  "profile": "(base64 encoded FHIR StructureDefinition JSON)",
  "implementation_guide": "acme-cardiology",
  "profile_context": "When clinical text describes phenotypic features, abnormalities, or findings that map to HPO terms, use the hpo-phenotype-observation profile instead of Condition."
}'

{
  "message": "Profile successfully uploaded",
  "id": "custom-patient",
  "type": "Patient",
  "url": "http://phenoml.com/fhir/StructureDefinition/custom-patient"
}

curl -X POST 'https://experiment.app.pheno.ml/lang2fhir/search' \
  -H 'Authorization: Bearer YOUR_API_KEY' \
  -H 'Content-Type: application/json' \
  -d '{
  "text": "Appointments between March 2-9, 2025"
}'

{
  "resource_type": "Appointment",
  "search_params": "date=ge2025-03-02&date=le2025-03-09"
}

curl -X POST 'https://experiment.app.pheno.ml/fhir2summary/create' \
  -H 'Authorization: Bearer YOUR_API_KEY' \
  -H 'Content-Type: application/json' \
  -d '{
  "mode": "narrative",
  "template_id": "a1b2c3d4-e5f6-7890-abcd-ef1234567890",
  "fhir_resources": {
    "resourceType": "Bundle",
    "type": "collection",
    "entry": [
      {
        "resource": {
          "resourceType": "Patient",
          "name": [
            {
              "given": [
                "John"
              ],
              "family": "Doe"
            }
          ],
          "gender": "male",
          "birthDate": "1979-03-15"
        }
      },
      {
        "resource": {
          "resourceType": "Condition",
          "code": {
            "text": "Type 2 Diabetes Mellitus"
          },
          "onsetDateTime": "2024-01-15"
        }
      }
    ]
  }
}'

{
  "success": true,
  "summary": "Patient John Doe is a 45-year-old male diagnosed with Type 2 Diabetes Mellitus on January 15, 2024. Current treatment plan includes lifestyle modifications and medication management.",
  "warnings": []
}

curl -X POST 'https://experiment.app.pheno.ml/fhir2summary/template' \
  -H 'Authorization: Bearer YOUR_API_KEY' \
  -H 'Content-Type: application/json' \
  -d '{
  "name": "Discharge Summary",
  "example_summary": "Patient John Doe, age 45, was admitted on 2024-01-10 with Type 2 Diabetes. Discharged on 2024-01-15 with Metformin 500mg BID.",
  "target_resources": [
    "Patient",
    "Condition",
    "MedicationRequest"
  ],
  "mode": "narrative"
}'

{
  "success": true,
  "message": "Template created successfully",
  "template_id": "a1b2c3d4-e5f6-7890-abcd-ef1234567890",
  "template": {
    "id": "a1b2c3d4-e5f6-7890-abcd-ef1234567890",
    "name": "Discharge Summary",
    "template": "Patient <<Patient.name[0].text>>, age <<Patient.birthDate|age>>, was admitted on <<Encounter[0].period.start>> with <<Condition[0].code.coding[0].display>>. Discharged on <<Encounter[0].period.end>> with <<MedicationRequest[0].medicationCodeableConcept.coding[0].display>> <<MedicationRequest[0].dosageInstruction[0].text>>.",
    "target_resources": [
      "Patient",
      "Condition",
      "MedicationRequest"
    ],
    "mode": "narrative",
    "created_at": "2024-01-15T10:30:00Z",
    "updated_at": "2024-01-15T10:30:00Z"
  }
}

curl 'https://experiment.app.pheno.ml/fhir2summary/template/abc-123-def-456' \
  -H 'Authorization: Bearer YOUR_API_KEY'

{
  "success": true,
  "template": {
    "id": "550e8400-e29b-41d4-a716-446655440000",
    "name": "Example Name",
    "description": "An example description",
    "template": "{{resource.field}}",
    "target_resources": [
      "Patient"
    ],
    "mode": "narrative",
    "metadata": {},
    "created_at": "2024-01-15T09:30:00Z",
    "updated_at": "2024-01-15T09:30:00Z"
  }
}

curl -X PUT 'https://experiment.app.pheno.ml/fhir2summary/template/%7Bid%7D' \
  -H 'Authorization: Bearer YOUR_API_KEY' \
  -H 'Content-Type: application/json' \
  -d '{
  "name": "Example Name",
  "description": "An example description",
  "template": "{{resource.field}}",
  "target_resources": [
    "Patient"
  ],
  "mode": "narrative"
}'

{
  "success": true,
  "message": "Template updated successfully",
  "template": {
    "id": "550e8400-e29b-41d4-a716-446655440000",
    "name": "Example Name",
    "description": "An example description",
    "template": "{{resource.field}}",
    "target_resources": [
      "Patient"
    ],
    "mode": "narrative",
    "metadata": {},
    "created_at": "2024-01-15T09:30:00Z",
    "updated_at": "2024-01-15T09:30:00Z"
  }
}

curl -X DELETE 'https://experiment.app.pheno.ml/fhir2summary/template/abc-123-def-456' \
  -H 'Authorization: Bearer YOUR_API_KEY'

{
  "success": true,
  "message": "Template deleted successfully"
}

curl 'https://experiment.app.pheno.ml/fhir2summary/templates' \
  -H 'Authorization: Bearer YOUR_API_KEY'

{
  "success": true,
  "templates": [
    {
      "id": "550e8400-e29b-41d4-a716-446655440000",
      "name": "Example Name",
      "description": "An example description",
      "template": "{{resource.field}}",
      "target_resources": [
        "Patient"
      ],
      "mode": "narrative",
      "metadata": {},
      "created_at": "2024-01-15T09:30:00Z",
      "updated_at": "2024-01-15T09:30:00Z"
    }
  ]
}

curl -X POST 'https://experiment.app.pheno.ml/fhir2omop/create' \
  -H 'Authorization: Bearer YOUR_API_KEY' \
  -H 'Content-Type: application/json' \
  -d '{
  "fhir_resources": {
    "resourceType": "Bundle",
    "type": "collection",
    "entry": [
      {
        "resource": {
          "resourceType": "Patient",
          "id": "patient-1",
          "gender": "female",
          "birthDate": "1985-07-22"
        }
      },
      {
        "resource": {
          "resourceType": "Condition",
          "id": "condition-1",
          "subject": {
            "reference": "Patient/patient-1"
          },
          "code": {
            "coding": [
              {
                "system": "http://snomed.info/sct",
                "code": "44054006",
                "display": "Type 2 diabetes mellitus"
              }
            ]
          },
          "onsetDateTime": "2024-01-15"
        }
      },
      {
        "resource": {
          "resourceType": "MedicationRequest",
          "id": "medreq-1",
          "status": "active",
          "subject": {
            "reference": "Patient/patient-1"
          },
          "medicationReference": {
            "reference": "#med0"
          },
          "authoredOn": "2024-01-16",
          "contained": [
            {
              "resourceType": "Medication",
              "id": "med0",
              "code": {
                "coding": [
                  {
                    "system": "http://www.nlm.nih.gov/research/umls/rxnorm",
                    "code": "860975",
                    "display": "metformin hydrochloride 500 MG"
                  }
                ]
              }
            }
          ]
        }
      }
    ]
  }
}'

{
  "success": true,
  "message": "Operation completed successfully",
  "tables": {
    "location": [
      {
        "location_id": 10,
        "address_1": "123 Main St",
        "address_2": "123 Main St",
        "city": "San Francisco",
        "state": "example",
        "zip": "example",
        "county": "example",
        "location_source_value": "example",
        "country_concept_id": 10,
        "country_source_value": "US",
        "latitude": 0.5,
        "longitude": 0.5
      }
    ],
    "care_site": [
      {
        "care_site_id": 10,
        "care_site_name": "Example Name",
        "place_of_service_concept_id": 10,
        "location_id": 10,
        "care_site_source_value": "example",
        "place_of_service_source_value": "example"
      }
    ],
    "provider": [
      {
        "provider_id": 10,
        "provider_name": "Example Name",
        "npi": "example",
        "dea": "example",
        "specialty_concept_id": 10,
        "care_site_id": 10,
        "year_of_birth": 10,
        "gender_concept_id": 10,
        "provider_source_value": "example",
        "specialty_source_value": "example",
        "specialty_source_concept_id": 10,
        "gender_source_value": "example",
        "gender_source_concept_id": 10
      }
    ],
    "person": [
      {
        "person_id": 10,
        "gender_concept_id": 10,
        "year_of_birth": 10,
        "month_of_birth": 10,
        "day_of_birth": 10,
        "birth_datetime": "example",
        "race_concept_id": 10,
        "ethnicity_concept_id": 10,
        "location_id": 10,
        "person_source_value": "example",
        "gender_source_value": "example",
        "race_source_value": "example",
        "ethnicity_source_value": "San Francisco"
      }
    ],
    "death": [
      {
        "person_id": 10,
        "death_date": "example",
        "death_datetime": "example",
        "death_type_concept_id": 10,
        "cause_concept_id": 10,
        "cause_source_value": "example",
        "cause_source_concept_id": 10
      }
    ],
    "observation_period": [
      {
        "observation_period_id": 10,
        "person_id": 10,
        "observation_period_start_date": "example",
        "observation_period_end_date": "example",
        "period_type_concept_id": 10
      }
    ],
    "visit_occurrence": [
      {
        "visit_occurrence_id": 10,
        "person_id": 10,
        "visit_concept_id": 10,
        "visit_start_date": "example",
        "visit_start_datetime": "example",
        "visit_end_date": "example",
        "visit_end_datetime": "example",
        "visit_type_concept_id": 10,
        "provider_id": 10,
        "care_site_id": 10,
        "visit_source_value": "example"
      }
    ],
    "condition_occurrence": [
      {
        "condition_occurrence_id": 10,
        "person_id": 10,
        "condition_concept_id": 10,
        "condition_start_date": "example",
        "condition_start_datetime": "example",
        "condition_end_date": "example",
        "condition_type_concept_id": 10,
        "visit_occurrence_id": 10,
        "provider_id": 10,
        "condition_source_value": "example",
        "condition_source_concept_id": 10,
        "condition_status_source_value": "active"
      }
    ],
    "drug_exposure": [
      {
        "drug_exposure_id": 10,
        "person_id": 10,
        "drug_concept_id": 10,
        "drug_exposure_start_date": "example",
        "drug_exposure_start_datetime": "example",
        "drug_exposure_end_date": "example",
        "drug_type_concept_id": 10,
        "stop_reason": "example",
        "sig": "example",
        "visit_occurrence_id": 10,
        "provider_id": 10,
        "drug_source_value": "example",
        "drug_source_concept_id": 10
      }
    ],
    "procedure_occurrence": [
      {
        "procedure_occurrence_id": 10,
        "person_id": 10,
        "procedure_concept_id": 10,
        "procedure_date": "example",
        "procedure_datetime": "example",
        "procedure_type_concept_id": 10,
        "visit_occurrence_id": 10,
        "provider_id": 10,
        "procedure_source_value": "example",
        "procedure_source_concept_id": 10
      }
    ],
    "measurement": [
      {
        "measurement_id": 10,
        "person_id": 10,
        "measurement_concept_id": 10,
        "measurement_date": "example",
        "measurement_datetime": "example",
        "measurement_type_concept_id": 10,
        "value_as_number": 0.5,
        "operator_concept_id": 10,
        "value_as_concept_id": 10,
        "unit_concept_id": 10,
        "range_low": 0.5,
        "range_high": 0.5,
        "visit_occurrence_id": 10,
        "provider_id": 10,
        "measurement_source_value": "example",
        "measurement_source_concept_id": 10,
        "unit_source_value": "example",
        "value_source_value": "example"
      }
    ],
    "observation": [
      {
        "observation_id": 10,
        "person_id": 10,
        "observation_concept_id": 10,
        "observation_date": "example",
        "observation_datetime": "example",
        "observation_type_concept_id": 10,
        "value_as_number": 0.5,
        "value_as_string": "example",
        "value_as_concept_id": 10,
        "unit_concept_id": 10,
        "visit_occurrence_id": 10,
        "provider_id": 10,
        "observation_source_value": "example",
        "observation_source_concept_id": 10,
        "unit_source_value": "example",
        "value_source_value": "example"
      }
    ]
  },
  "mappings": [
    {
      "resource_type": "Patient",
      "resource_id": "abc-123-def-456",
      "omop_table": "example",
      "omop_id": 10,
      "source_system": "example",
      "source_code": "ABC123",
      "source_name": "Example Name",
      "target_vocabulary": "example",
      "target_code": "ABC123",
      "target_name": "Example Name",
      "mapping_status": "active",
      "note": "example"
    }
  ],
  "dropped": [
    {
      "resource_type": "Patient",
      "resource_id": "abc-123-def-456",
      "reason": "example"
    }
  ],
  "vocab_version": "example",
  "summary": {
    "codes_already_standard": 10,
    "codes_normalized": 10,
    "codes_unmapped": 10,
    "off_vocab_rate": 0.5
  }
}

curl 'https://experiment.app.pheno.ml/agent/abc-123-def-456' \
  -H 'Authorization: Bearer YOUR_API_KEY'

{
  "success": true,
  "message": "Agent retrieved successfully",
  "data": {
    "id": "agent_123",
    "name": "Medical Assistant",
    "description": "An AI assistant for medical information processing",
    "prompts": [
      "prompt_123",
      "prompt_456"
    ],
    "tools": [
      "mcp_server_123",
      "mcp_server_456"
    ],
    "workflows": [
      "workflow_123",
      "workflow_456"
    ],
    "tags": [
      "medical",
      "fhir"
    ],
    "provider": "7002b0b4-8d09-445a-bf65-0fafdaf26c35"
  }
}

curl -X PUT 'https://experiment.app.pheno.ml/agent/%7Bid%7D' \
  -H 'Authorization: Bearer YOUR_API_KEY' \
  -H 'Content-Type: application/json' \
  -d '{
  "name": "Example Name",
  "description": "An AI assistant for medical information processing",
  "prompts": [
    "prompt_123",
    "prompt_456"
  ],
  "tools": [
    "mcp_server_123",
    "mcp_server_456"
  ],
  "workflows": [
    "workflow_123",
    "workflow_456"
  ],
  "tags": [
    "medical",
    "fhir"
  ],
  "provider": "7002b0b4-8d09-445a-bf65-0fafdaf26c35"
}'

{
  "success": true,
  "message": "Agent updated successfully",
  "data": {
    "id": "agent_123",
    "name": "Medical Assistant",
    "description": "An AI assistant for medical information processing",
    "prompts": [
      "prompt_123",
      "prompt_456"
    ],
    "tools": [
      "mcp_server_123",
      "mcp_server_456"
    ],
    "workflows": [
      "workflow_123",
      "workflow_456"
    ],
    "tags": [
      "medical",
      "fhir"
    ],
    "provider": "7002b0b4-8d09-445a-bf65-0fafdaf26c35"
  }
}

curl -X DELETE 'https://experiment.app.pheno.ml/agent/abc-123-def-456' \
  -H 'Authorization: Bearer YOUR_API_KEY'

{
  "success": true,
  "message": "Agent deleted successfully"
}

curl -X PATCH 'https://experiment.app.pheno.ml/agent/%7Bid%7D' \
  -H 'Authorization: Bearer YOUR_API_KEY' \
  -H 'Content-Type: application/json' \
  -d '[
  {
    "op": "replace",
    "path": "/name",
    "value": "Updated Agent Name"
  },
  {
    "op": "add",
    "path": "/tags/-",
    "value": "new-tag"
  },
  {
    "op": "remove",
    "path": "/description"
  }
]'

{
  "success": true,
  "message": "Agent patched successfully",
  "data": {
    "id": "agent_123",
    "name": "Medical Assistant",
    "description": "An AI assistant for medical information processing",
    "prompts": [
      "prompt_123",
      "prompt_456"
    ],
    "tools": [
      "mcp_server_123",
      "mcp_server_456"
    ],
    "workflows": [
      "workflow_123",
      "workflow_456"
    ],
    "tags": [
      "medical",
      "fhir"
    ],
    "provider": "7002b0b4-8d09-445a-bf65-0fafdaf26c35"
  }
}

curl -X POST 'https://experiment.app.pheno.ml/agent/create' \
  -H 'Authorization: Bearer YOUR_API_KEY' \
  -H 'Content-Type: application/json' \
  -d '{
  "name": "Example Name",
  "description": "An AI assistant for medical information processing",
  "prompts": [
    "prompt_123",
    "prompt_456"
  ],
  "tools": [
    "mcp_server_123",
    "mcp_server_456"
  ],
  "workflows": [
    "workflow_123",
    "workflow_456"
  ],
  "tags": [
    "medical",
    "fhir"
  ],
  "provider": "7002b0b4-8d09-445a-bf65-0fafdaf26c35"
}'

{
  "success": true,
  "message": "Agent created successfully",
  "data": {
    "id": "agent_123",
    "name": "Medical Assistant",
    "description": "An AI assistant for medical information processing",
    "prompts": [
      "prompt_123",
      "prompt_456"
    ],
    "tools": [
      "mcp_server_123",
      "mcp_server_456"
    ],
    "workflows": [
      "workflow_123",
      "workflow_456"
    ],
    "tags": [
      "medical",
      "fhir"
    ],
    "provider": "7002b0b4-8d09-445a-bf65-0fafdaf26c35"
  }
}

curl 'https://experiment.app.pheno.ml/agent/list?tags=example' \
  -H 'Authorization: Bearer YOUR_API_KEY'

{
  "success": true,
  "message": "Agents retrieved successfully",
  "agents": [
    {
      "id": "agent_123",
      "name": "Medical Assistant",
      "description": "An AI assistant for medical information processing",
      "prompts": [
        "prompt_123",
        "prompt_456"
      ],
      "tools": [
        "mcp_server_123",
        "mcp_server_456"
      ],
      "workflows": [
        "workflow_123",
        "workflow_456"
      ],
      "tags": [
        "medical",
        "fhir"
      ],
      "provider": "7002b0b4-8d09-445a-bf65-0fafdaf26c35"
    }
  ]
}

curl -X POST 'https://experiment.app.pheno.ml/agent/chat' \
  -H 'Authorization: Bearer YOUR_API_KEY' \
  -H 'Content-Type: application/json' \
  -d '{
  "message": "What is the patient'\''s current condition?",
  "agent_id": "agent-123",
  "session_id": "session-abc123"
}'

{
  "success": true,
  "message": "Response generated successfully",
  "response": "Based on the patient records, they have been diagnosed with Type 2 Diabetes Mellitus (ICD-10: E11.65) and Essential Hypertension (ICD-10: I10). Current medications include Metformin 500mg BID and Lisinopril 10mg daily. Most recent HbA1c was 7.2% on 2024-12-15.",
  "session_id": "session-abc123"
}

curl 'https://experiment.app.pheno.ml/agent/chat/messages?role=user' \
  -H 'Authorization: Bearer YOUR_API_KEY'

{
  "messages": [
    {
      "id": "message_123",
      "session_id": "session_123",
      "role": "user",
      "content": "Hello, how are you?",
      "created": "2021-01-01T00:00:00Z",
      "updated": "2021-01-01T00:00:00Z",
      "function_name": "get_patient_info",
      "function_args": {
        "patient_id": "123"
      },
      "function_result": {
        "name": "John Doe"
      },
      "message_order": 1
    }
  ],
  "total": 10,
  "session_id": "session_123"
}

curl -X POST 'https://experiment.app.pheno.ml/agent/stream-chat' \
  -H 'Authorization: Bearer YOUR_API_KEY' \
  -H 'Content-Type: application/json' \
  -d '{
  "message": "What is the patient'\''s current condition?",
  "context": "Respond concisely and with clear rationale",
  "session_id": "session-abc123",
  "agent_id": "agent-123",
  "enhanced_reasoning": false
}'

{
  "type": "content_delta",
  "session_id": "session_123",
  "content": "I'll create a patient record...",
  "success": true,
  "message": "Streaming chat response. Each frame is a standard SSE record\n(`event:` line + `data:` JSON line). The example shows a single\n`content_delta` payload — multiple frames stream until `message_end`.",
  "function_name": "lang2fhir_search",
  "function_args": {},
  "function_result": {}
}

curl -X POST 'https://experiment.app.pheno.ml/agent/prompts' \
  -H 'Authorization: Bearer YOUR_API_KEY' \
  -H 'Content-Type: application/json' \
  -d '{
  "name": "Medical Assistant System Prompt",
  "description": "System prompt for medical assistant agent",
  "content": "You are a helpful medical assistant specialized in FHIR data processing...",
  "is_default": false,
  "tags": [
    "medical",
    "system"
  ]
}'

{
  "success": true,
  "message": "Prompt created successfully",
  "data": {
    "id": "prompt_123",
    "name": "Medical Assistant System Prompt",
    "description": "System prompt for medical assistant agent",
    "content": "You are a helpful medical assistant...",
    "is_default": false,
    "tags": [
      "medical",
      "system"
    ]
  }
}

curl 'https://experiment.app.pheno.ml/agent/prompts/abc-123-def-456' \
  -H 'Authorization: Bearer YOUR_API_KEY'

{
  "success": true,
  "message": "Prompt retrieved successfully",
  "data": {
    "id": "prompt_123",
    "name": "Medical Assistant System Prompt",
    "description": "System prompt for medical assistant agent",
    "content": "You are a helpful medical assistant...",
    "is_default": false,
    "tags": [
      "medical",
      "system"
    ]
  }
}

curl -X PUT 'https://experiment.app.pheno.ml/agent/prompts/%7Bid%7D' \
  -H 'Authorization: Bearer YOUR_API_KEY' \
  -H 'Content-Type: application/json' \
  -d '{
  "name": "Medical Assistant System Prompt",
  "description": "System prompt for medical assistant agent",
  "content": "You are a helpful medical assistant specialized in FHIR data processing...",
  "is_default": false,
  "tags": [
    "medical",
    "system"
  ]
}'

{
  "success": true,
  "message": "Prompt updated successfully",
  "data": {
    "id": "prompt_123",
    "name": "Medical Assistant System Prompt",
    "description": "System prompt for medical assistant agent",
    "content": "You are a helpful medical assistant...",
    "is_default": false,
    "tags": [
      "medical",
      "system"
    ]
  }
}

curl -X DELETE 'https://experiment.app.pheno.ml/agent/prompts/abc-123-def-456' \
  -H 'Authorization: Bearer YOUR_API_KEY'

{
  "success": true,
  "message": "Prompt deleted successfully"
}

curl -X PATCH 'https://experiment.app.pheno.ml/agent/prompts/%7Bid%7D' \
  -H 'Authorization: Bearer YOUR_API_KEY' \
  -H 'Content-Type: application/json' \
  -d '[
  {
    "op": "replace",
    "path": "/name",
    "value": "Updated Agent Name"
  },
  {
    "op": "add",
    "path": "/tags/-",
    "value": "new-tag"
  },
  {
    "op": "remove",
    "path": "/description"
  }
]'

{
  "success": true,
  "message": "Prompt patched successfully",
  "data": {
    "id": "prompt_123",
    "name": "Medical Assistant System Prompt",
    "description": "System prompt for medical assistant agent",
    "content": "You are a helpful medical assistant...",
    "is_default": false,
    "tags": [
      "medical",
      "system"
    ]
  }
}

curl 'https://experiment.app.pheno.ml/agent/prompts/list' \
  -H 'Authorization: Bearer YOUR_API_KEY'

{
  "success": true,
  "message": "Prompts retrieved successfully",
  "prompts": [
    {
      "id": "prompt_123",
      "name": "Medical Assistant System Prompt",
      "description": "System prompt for medical assistant agent",
      "content": "You are a helpful medical assistant...",
      "is_default": false,
      "tags": [
        "medical",
        "system"
      ]
    }
  ]
}

curl 'https://experiment.app.pheno.ml/workflows?verbose=true' \
  -H 'Authorization: Bearer YOUR_API_KEY'

{
  "success": true,
  "message": "Successfully retrieved workflows",
  "workflows": [
    {
      "id": "550e8400-e29b-41d4-a716-446655440001",
      "name": "Patient Data Mapping Workflow",
      "workflow_instructions": "Given diagnosis data, find the patient and create condition record",
      "sample_data": {
        "diagnosis_code": "I10",
        "diagnosis_date": "2025-01-01",
        "patient_first_name": "Clay",
        "patient_last_name": "Rippin"
      },
      "config": {
        "fhir_provider_ids": [
          "550e8400-e29b-41d4-a716-446655440000"
        ],
        "dynamic_generation": false
      },
      "graph": {
        "steps": [
          {
            "id": "step_1_id",
            "name": "Find Patient",
            "description": "Search for an existing patient by first name and last name",
            "type": "search",
            "provider_id": "550e8400-e29b-41d4-a716-446655440000"
          }
        ]
      },
      "created_at": "2024-01-15T10:30:00Z",
      "updated_at": "2024-01-15T15:45:00Z"
    }
  ],
  "workflow_details": [
    {
      "id": "550e8400-e29b-41d4-a716-446655440001",
      "name": "Patient Data Mapping Workflow",
      "workflow_instructions": "Given diagnosis data, find the patient and create condition record",
      "sample_data": {
        "diagnosis_code": "I10",
        "diagnosis_date": "2025-01-01",
        "patient_first_name": "Clay",
        "patient_last_name": "Rippin"
      },
      "config": {},
      "graph": {
        "steps": [
          {
            "id": "1",
            "name": "Create Patient Resource",
            "description": "Create a FHIR Patient resource from input data",
            "type": "create",
            "operation": {
              "search_definition": {
                "original_query": "find patient {{patient_first_name}} {{patient_last_name}} by first name and last name",
                "resource_type": "Patient",
                "search_parameters": {
                  "family": "{{patient_last_name}}",
                  "given": "{{patient_first_name}}"
                },
                "required_fields": [
                  "id",
                  "name",
                  "identifier"
                ],
                "runtime_placeholders": {
                  "{{patient_first_name}}": "input.patient_first_name",
                  "{{patient_last_name}}": "input.patient_last_name"
                }
              },
              "create_definition": {
                "original_description": "create condition with diagnosis code {{diagnosis_code}} and diagnosis date 2025-01-01",
                "resource_type": "Condition",
                "resource_template": {
                  "resourceType": "Condition",
                  "code": {
                    "coding": [
                      {
                        "code": "{{diagnosis_code}}",
                        "system": "http://hl7.org/fhir/sid/icd-10"
                      }
                    ]
                  },
                  "subject": {
                    "reference": "Patient/{{step_1_id}}"
                  }
                },
                "runtime_placeholders": {
                  "{{diagnosis_code}}": "input.diagnosis_code",
                  "{{diagnosis_date}}": "input.diagnosis_date"
                }
              },
              "workflow_definition": {
                "workflow_id": "550e8400-e29b-41d4-a716-446655440002",
                "input": {
                  "patient_id": "{{step_1_id}}",
                  "additional_context": "laboratory_results"
                },
                "runtime_placeholders": {
                  "{{step_1_id}}": "step_1.result.id",
                  "{{patient_data}}": "input.patient_data"
                }
              },
              "decision_definition": {
                "expression": "input.patient_age >= 18",
                "paths": {
                  "true": "step_adult_workflow",
                  "false": "step_pediatric_workflow",
                  "default": "step_error_handler"
                },
                "runtime_placeholders": {
                  "{{patient_age}}": "input.patient_age",
                  "{{diagnosis_type}}": "step_2.result.diagnosis_category"
                }
              }
            },
            "provider_id": "550e8400-e29b-41d4-a716-446655440000",
            "dependencies": [],
            "dynamic_generation": false
          }
        ]
      },
      "created_at": "2024-01-15T10:30:00Z",
      "updated_at": "2024-01-15T15:45:00Z"
    }
  ]
}