phenoml 17.7.0 → 17.9.0

package/reference.md

@@ -1627,6 +1627,9 @@ await client.construe.codeSystems.export("CUSTOM_CODES", {
 
 Converts natural language text into structured medical codes.
 
+Pass `system.version` to select a specific code system version, for example
+`umls-2026aa` for UMLS 2026AA-backed systems.
+
 Usage of CPT is subject to AMA requirements: see PhenoML Terms of Service.
 </dd>
 </dl>
@@ -1680,6 +1683,83 @@ await client.construe.codes.extract({
 </dl>
 
 
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.construe.codes.<a href="/src/api/resources/construe/resources/codes/client/Client.ts">phenocr</a>({ ...params }) -> phenoml.ExtractCodesResult</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**Alpha:** phenocr is an alpha feature. The API contract — request
+parameters and response shape — may change as its internals evolve, and
+results may vary between releases. Do not depend on it for production
+workloads yet.
+
+Extracts medical codes from natural language clinical text using phenocr.
+
+Supported code systems: HPO, ICD-10-CM, and SNOMED_CT_US. The code
+system name and version are both required.
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.construe.codes.phenocr({
+    text: "5-year-old male with seizures, severe intellectual disability, microcephaly, and hypotonia.",
+    system: {
+        name: "HPO",
+        version: "umls-2026AA"
+    }
+});
+
+```
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.construe.PhenoCrRequest` 
+    
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `CodesClient.RequestOptions` 
+    
+</dd>
+</dl>
+</dd>
+</dl>
+
+
 </dd>
 </dl>
 </details>
@@ -3340,8 +3420,8 @@ await client.fhirProvider.authConfig.remove("1716d214-de93-43a4-aa6b-a878d864e2a
 </dl>
 </details>
 
-## Lang2Fhir
-<details><summary><code>client.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">create</a>({ ...params }) -> phenoml.FhirResource</code></summary>
+## Implementation Guides
+<details><summary><code>client.implementationGuides.implementationGuides.<a href="/src/api/resources/implementationGuides/resources/implementationGuides/client/Client.ts">list</a>() -> phenoml.ImplementationGuideListResponse</code></summary>
 <dl>
 <dd>
 
@@ -3353,9 +3433,65 @@ await client.fhirProvider.authConfig.remove("1716d214-de93-43a4-aa6b-a878d864e2a
 <dl>
 <dd>
 
-Converts natural language text into a structured FHIR resource.
+Returns every implementation guide on this instance — both guides that
+have stored metadata (a profile_context) and guides referenced by at
+least one custom profile — with the number of profiles in each.
+</dd>
+</dl>
+</dd>
+</dl>
 
-**Patient identifier handling.** When generating a `patient` (or `patient-canvas`) resource, US Core requires `Patient.identifier` (a business identifier such as an MRN). When the source text contains an identifier, it is extracted with an appropriate URI system. When the source text does not contain a detectable identifier, a synthetic one is generated with `system: "urn:phenoml:lang2fhir-generated-id"` and a UUID `value` so the resource remains FHIR-valid and US Core conformant. Callers who need a tenant-specific namespace should rewrite the synthetic system after extraction.
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.implementationGuides.implementationGuides.list();
+
+```
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**requestOptions:** `ImplementationGuidesClient.RequestOptions` 
+    
+</dd>
+</dl>
+</dd>
+</dl>
+
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.implementationGuides.implementationGuides.<a href="/src/api/resources/implementationGuides/resources/implementationGuides/client/Client.ts">get</a>(name) -> phenoml.ImplementationGuideDetail</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Returns a single implementation guide, including its profile_context and
+the ids of the profiles that belong to it.
 </dd>
 </dl>
 </dd>
@@ -3370,11 +3506,7 @@ Converts natural language text into a structured FHIR resource.
 <dd>
 
 ```typescript
-await client.lang2Fhir.create({
-    version: "R4",
-    resource: "condition-encounter-diagnosis",
-    text: "Patient has severe persistent asthma with acute exacerbation"
-});
+await client.implementationGuides.implementationGuides.get("acme-cardiology");
 
 ```
 </dd>
@@ -3390,7 +3522,7 @@ await client.lang2Fhir.create({
 <dl>
 <dd>
 
-**request:** `phenoml.lang2Fhir.CreateRequest` 
+**name:** `string` — The implementation guide name.
     
 </dd>
 </dl>
@@ -3398,7 +3530,7 @@ await client.lang2Fhir.create({
 <dl>
 <dd>
 
-**requestOptions:** `Lang2FhirClient.RequestOptions` 
+**requestOptions:** `ImplementationGuidesClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -3410,7 +3542,7 @@ await client.lang2Fhir.create({
 </dl>
 </details>
 
-<details><summary><code>client.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">createMulti</a>({ ...params }) -> phenoml.CreateMultiResponse</code></summary>
+<details><summary><code>client.implementationGuides.implementationGuides.<a href="/src/api/resources/implementationGuides/resources/implementationGuides/client/Client.ts">update</a>(name, { ...params }) -> phenoml.ImplementationGuideSummary</code></summary>
 <dl>
 <dd>
 
@@ -3422,11 +3554,10 @@ await client.lang2Fhir.create({
 <dl>
 <dd>
 
-Analyzes natural language text and extracts multiple FHIR resources, returning them as a transaction Bundle.
-Automatically detects Patient, Condition, MedicationRequest, Observation, and other resource types from the text.
-Resources are linked with proper references (e.g., Conditions reference the Patient).
-
-**Patient identifier handling.** US Core requires `Patient.identifier` (a business identifier such as an MRN). When the source text contains an identifier, it is extracted with an appropriate URI system. When the source text does not contain a detectable identifier, a synthetic one is generated with `system: "urn:phenoml:lang2fhir-generated-id"` and a UUID `value` so the bundle remains FHIR-valid and US Core conformant. Callers who need a tenant-specific namespace should rewrite the synthetic system after extraction.
+Sets (or clears, with an empty value) the natural-language profile_context
+for an implementation guide. The context is injected into the LLM during
+resource detection to help select the right profiles from this guide.
+It applies to every profile in the guide.
 </dd>
 </dl>
 </dd>
@@ -3441,10 +3572,7 @@ Resources are linked with proper references (e.g., Conditions reference the Pati
 <dd>
 
 ```typescript
-await client.lang2Fhir.createMulti({
-    text: "John Smith, 45-year-old male, diagnosed with Type 2 Diabetes. Prescribed Metformin 500mg twice daily. Blood pressure 140/90.",
-    version: "R4"
-});
+await client.implementationGuides.implementationGuides.update("acme-cardiology");
 
 ```
 </dd>
@@ -3460,7 +3588,7 @@ await client.lang2Fhir.createMulti({
 <dl>
 <dd>
 
-**request:** `phenoml.lang2Fhir.CreateMultiRequest` 
+**name:** `string` — The implementation guide name.
     
 </dd>
 </dl>
@@ -3468,7 +3596,15 @@ await client.lang2Fhir.createMulti({
 <dl>
 <dd>
 
-**requestOptions:** `Lang2FhirClient.RequestOptions` 
+**request:** `phenoml.implementationGuides.UpdateImplementationGuideRequest` 
+    
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `ImplementationGuidesClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -3480,7 +3616,7 @@ await client.lang2Fhir.createMulti({
 </dl>
 </details>
 
-<details><summary><code>client.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">search</a>({ ...params }) -> phenoml.SearchResponse</code></summary>
+<details><summary><code>client.implementationGuides.implementationGuides.<a href="/src/api/resources/implementationGuides/resources/implementationGuides/client/Client.ts">delete</a>(name) -> void</code></summary>
 <dl>
 <dd>
 
@@ -3492,14 +3628,11 @@ await client.lang2Fhir.createMulti({
 <dl>
 <dd>
 
-Converts natural language text into FHIR search parameters.
-Automatically identifies the appropriate FHIR resource type and generates valid search query parameters.
-
-Supported resource types include: AllergyIntolerance, Appointment, CarePlan, CareTeam, Condition,
-Coverage, Device, DiagnosticReport, DocumentReference, Encounter, Goal, Immunization, Location,
-Medication, MedicationRequest, Observation, Organization, Patient, PlanDefinition, Practitioner,
-PractitionerRole, Procedure, Provenance, Questionnaire, QuestionnaireResponse, RelatedPerson,
-Schedule, ServiceRequest, Slot, and Specimen.
+Deletes the stored metadata for an implementation guide — its
+profile_context and timestamps. Member profiles keep their
+implementation_guide assignment, so a guide still referenced by at least
+one profile continues to appear in listings, just without context or
+timestamps.
 </dd>
 </dl>
 </dd>
@@ -3514,9 +3647,7 @@ Schedule, ServiceRequest, Slot, and Specimen.
 <dd>
 
 ```typescript
-await client.lang2Fhir.search({
-    text: "Appointments between March 2-9, 2025"
-});
+await client.implementationGuides.implementationGuides.delete("acme-cardiology");
 
 ```
 </dd>
@@ -3532,7 +3663,7 @@ await client.lang2Fhir.search({
 <dl>
 <dd>
 
-**request:** `phenoml.lang2Fhir.SearchRequest` 
+**name:** `string` — The implementation guide name.
     
 </dd>
 </dl>
@@ -3540,7 +3671,7 @@ await client.lang2Fhir.search({
 <dl>
 <dd>
 
-**requestOptions:** `Lang2FhirClient.RequestOptions` 
+**requestOptions:** `ImplementationGuidesClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -3552,7 +3683,8 @@ await client.lang2Fhir.search({
 </dl>
 </details>
 
-<details><summary><code>client.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">uploadProfile</a>({ ...params }) -> phenoml.UploadProfileResponse</code></summary>
+## Lang2Fhir
+<details><summary><code>client.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">create</a>({ ...params }) -> phenoml.FhirResource</code></summary>
 <dl>
 <dd>
 
@@ -3564,16 +3696,9 @@ await client.lang2Fhir.search({
 <dl>
 <dd>
 
-Upload a custom FHIR StructureDefinition profile for use with the lang2fhir service.
-
-All metadata is derived from the StructureDefinition JSON itself. The lowercase `id` field
-from the StructureDefinition is used as the profile's unique identifier and lookup key.
-To use the uploaded profile with `/lang2fhir/create`, pass this id as the `resource` parameter.
+Converts natural language text into a structured FHIR resource.
 
-Uploads will be rejected if:
-- A built-in US Core or R4 base profile already exists with the same id
-- A custom profile with the same id has already been uploaded
-- A custom profile with the same url has already been uploaded
+**Patient identifier handling.** When generating a `patient` (or `patient-canvas`) resource, US Core requires `Patient.identifier` (a business identifier such as an MRN). When the source text contains an identifier, it is extracted with an appropriate URI system. When the source text does not contain a detectable identifier, a synthetic one is generated with `system: "urn:phenoml:lang2fhir-generated-id"` and a UUID `value` so the resource remains FHIR-valid and US Core conformant. Callers who need a tenant-specific namespace should rewrite the synthetic system after extraction.
 </dd>
 </dl>
 </dd>
@@ -3588,10 +3713,10 @@ Uploads will be rejected if:
 <dd>
 
 ```typescript
-await client.lang2Fhir.uploadProfile({
-    profile: "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",
-    implementation_guide: "acme-cardiology",
-    profile_context: "When clinical text describes cardiology-specific findings, prefer this profile over the generic US Core Condition."
+await client.lang2Fhir.create({
+    version: "R4",
+    resource: "condition-encounter-diagnosis",
+    text: "Patient has severe persistent asthma with acute exacerbation"
 });
 
 ```
@@ -3608,7 +3733,7 @@ await client.lang2Fhir.uploadProfile({
 <dl>
 <dd>
 
-**request:** `phenoml.lang2Fhir.ProfileUploadRequest` 
+**request:** `phenoml.lang2Fhir.CreateRequest` 
     
 </dd>
 </dl>
@@ -3628,7 +3753,7 @@ await client.lang2Fhir.uploadProfile({
 </dl>
 </details>
 
-<details><summary><code>client.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">document</a>({ ...params }) -> phenoml.FhirResource</code></summary>
+<details><summary><code>client.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">createMulti</a>({ ...params }) -> phenoml.CreateMultiResponse</code></summary>
 <dl>
 <dd>
 
@@ -3640,9 +3765,11 @@ await client.lang2Fhir.uploadProfile({
 <dl>
 <dd>
 
-Extracts text from a document (PDF or image) and converts it into a structured FHIR resource.
+Analyzes natural language text and extracts multiple FHIR resources, returning them as a transaction Bundle.
+Automatically detects Patient, Condition, MedicationRequest, Observation, and other resource types from the text.
+Resources are linked with proper references (e.g., Conditions reference the Patient).
 
-**Patient identifier handling.** When generating a `patient` (or `patient-canvas`) resource, US Core requires `Patient.identifier` (a business identifier such as an MRN). When the source text contains an identifier, it is extracted with an appropriate URI system. When the source text does not contain a detectable identifier, a synthetic one is generated with `system: "urn:phenoml:lang2fhir-generated-id"` and a UUID `value` so the resource remains FHIR-valid and US Core conformant. Callers who need a tenant-specific namespace should rewrite the synthetic system after extraction.
+**Patient identifier handling.** US Core requires `Patient.identifier` (a business identifier such as an MRN). When the source text contains an identifier, it is extracted with an appropriate URI system. When the source text does not contain a detectable identifier, a synthetic one is generated with `system: "urn:phenoml:lang2fhir-generated-id"` and a UUID `value` so the bundle remains FHIR-valid and US Core conformant. Callers who need a tenant-specific namespace should rewrite the synthetic system after extraction.
 </dd>
 </dl>
 </dd>
@@ -3657,10 +3784,9 @@ Extracts text from a document (PDF or image) and converts it into a structured F
 <dd>
 
 ```typescript
-await client.lang2Fhir.document({
-    version: "R4",
-    resource: "questionnaire",
-    content: "JVBERi0xLjQKJeLjz9MK...(base64-encoded PDF or image bytes)"
+await client.lang2Fhir.createMulti({
+    text: "John Smith, 45-year-old male, diagnosed with Type 2 Diabetes. Prescribed Metformin 500mg twice daily. Blood pressure 140/90.",
+    version: "R4"
 });
 
 ```
@@ -3677,7 +3803,7 @@ await client.lang2Fhir.document({
 <dl>
 <dd>
 
-**request:** `phenoml.lang2Fhir.DocumentRequest` 
+**request:** `phenoml.lang2Fhir.CreateMultiRequest` 
     
 </dd>
 </dl>
@@ -3697,7 +3823,7 @@ await client.lang2Fhir.document({
 </dl>
 </details>
 
-<details><summary><code>client.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">documentMulti</a>({ ...params }) -> phenoml.DocumentMultiResponse</code></summary>
+<details><summary><code>client.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">search</a>({ ...params }) -> phenoml.SearchResponse</code></summary>
 <dl>
 <dd>
 
@@ -3709,12 +3835,14 @@ await client.lang2Fhir.document({
 <dl>
 <dd>
 
-Extracts text from a document (PDF or image) and converts it into multiple FHIR resources,
-returned as a transaction Bundle. Combines document text extraction with multi-resource detection.
-Automatically detects Patient, Condition, MedicationRequest, Observation, and other resource types.
-Resources are linked with proper references (e.g., Conditions reference the Patient).
+Converts natural language text into FHIR search parameters.
+Automatically identifies the appropriate FHIR resource type and generates valid search query parameters.
 
-**Patient identifier handling.** US Core requires `Patient.identifier` (a business identifier such as an MRN). When the source text contains an identifier, it is extracted with an appropriate URI system. When the source text does not contain a detectable identifier, a synthetic one is generated with `system: "urn:phenoml:lang2fhir-generated-id"` and a UUID `value` so the bundle remains FHIR-valid and US Core conformant. Callers who need a tenant-specific namespace should rewrite the synthetic system after extraction.
+Supported resource types include: AllergyIntolerance, Appointment, CarePlan, CareTeam, Condition,
+Coverage, Device, DiagnosticReport, DocumentReference, Encounter, Goal, Immunization, Location,
+Medication, MedicationRequest, Observation, Organization, Patient, PlanDefinition, Practitioner,
+PractitionerRole, Procedure, Provenance, Questionnaire, QuestionnaireResponse, RelatedPerson,
+Schedule, ServiceRequest, Slot, and Specimen.
 </dd>
 </dl>
 </dd>
@@ -3729,10 +3857,8 @@ Resources are linked with proper references (e.g., Conditions reference the Pati
 <dd>
 
 ```typescript
-await client.lang2Fhir.documentMulti({
-    version: "R4",
-    content: "JVBERi0xLjQKJeLjz9MK...(base64-encoded PDF or image bytes)",
-    provider: "medplum"
+await client.lang2Fhir.search({
+    text: "Appointments between March 2-9, 2025"
 });
 
 ```
@@ -3749,7 +3875,7 @@ await client.lang2Fhir.documentMulti({
 <dl>
 <dd>
 
-**request:** `phenoml.lang2Fhir.DocumentMultiRequest` 
+**request:** `phenoml.lang2Fhir.SearchRequest` 
     
 </dd>
 </dl>
@@ -3765,6 +3891,581 @@ await client.lang2Fhir.documentMulti({
 </dl>
 
 
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">uploadProfile</a>({ ...params }) -> phenoml.UploadProfileResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**Deprecated — use `POST /fhir/profiles` instead.** This route continues to work
+and operates on the same custom profiles, so no migration is required; it
+will be removed in a future release. Note that `POST /fhir/profiles` does not
+accept `profile_context`; set implementation-guide context with
+`PUT /fhir/implementation-guides/{name}`.
+
+Upload a custom FHIR StructureDefinition profile for use with the lang2fhir service.
+
+All metadata is derived from the StructureDefinition JSON itself. The lowercase `id` field
+from the StructureDefinition is used as the profile's unique identifier and lookup key.
+To use the uploaded profile with `/lang2fhir/create`, pass this id as the `resource` parameter.
+
+Uploads will be rejected if:
+- A built-in US Core or R4 base profile already exists with the same id
+- A custom profile with the same id has already been uploaded
+- A custom profile with the same url has already been uploaded
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.lang2Fhir.uploadProfile({
+    profile: "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",
+    implementation_guide: "acme-cardiology",
+    profile_context: "When clinical text describes cardiology-specific findings, prefer this profile over the generic US Core Condition."
+});
+
+```
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.ProfileUploadRequest` 
+    
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Lang2FhirClient.RequestOptions` 
+    
+</dd>
+</dl>
+</dd>
+</dl>
+
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">document</a>({ ...params }) -> phenoml.FhirResource</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Extracts text from a document (PDF or image) and converts it into a structured FHIR resource.
+
+**Patient identifier handling.** When generating a `patient` (or `patient-canvas`) resource, US Core requires `Patient.identifier` (a business identifier such as an MRN). When the source text contains an identifier, it is extracted with an appropriate URI system. When the source text does not contain a detectable identifier, a synthetic one is generated with `system: "urn:phenoml:lang2fhir-generated-id"` and a UUID `value` so the resource remains FHIR-valid and US Core conformant. Callers who need a tenant-specific namespace should rewrite the synthetic system after extraction.
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.lang2Fhir.document({
+    version: "R4",
+    resource: "questionnaire",
+    content: "JVBERi0xLjQKJeLjz9MK...(base64-encoded PDF or image bytes)"
+});
+
+```
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.lang2Fhir.DocumentRequest` 
+    
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Lang2FhirClient.RequestOptions` 
+    
+</dd>
+</dl>
+</dd>
+</dl>
+
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">documentMulti</a>({ ...params }) -> phenoml.DocumentMultiResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Extracts text from a document (PDF or image) and converts it into multiple FHIR resources,
+returned as a transaction Bundle. Combines document text extraction with multi-resource detection.
+Automatically detects Patient, Condition, MedicationRequest, Observation, and other resource types.
+Resources are linked with proper references (e.g., Conditions reference the Patient).
+
+**Patient identifier handling.** US Core requires `Patient.identifier` (a business identifier such as an MRN). When the source text contains an identifier, it is extracted with an appropriate URI system. When the source text does not contain a detectable identifier, a synthetic one is generated with `system: "urn:phenoml:lang2fhir-generated-id"` and a UUID `value` so the bundle remains FHIR-valid and US Core conformant. Callers who need a tenant-specific namespace should rewrite the synthetic system after extraction.
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.lang2Fhir.documentMulti({
+    version: "R4",
+    content: "JVBERi0xLjQKJeLjz9MK...(base64-encoded PDF or image bytes)",
+    provider: "medplum"
+});
+
+```
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.lang2Fhir.DocumentMultiRequest` 
+    
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Lang2FhirClient.RequestOptions` 
+    
+</dd>
+</dl>
+</dd>
+</dl>
+
+
+</dd>
+</dl>
+</details>
+
+## Profiles
+<details><summary><code>client.profiles.profiles.<a href="/src/api/resources/profiles/resources/profiles/client/Client.ts">list</a>({ ...params }) -> phenoml.ProfileListResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Returns metadata for every custom (uploaded) FHIR profile on this
+instance, across all implementation guides. The full StructureDefinition
+JSON is omitted from each entry; fetch a single profile by id to retrieve it.
+
+The `url` query parameter filters by canonical URL. The canonical URL is the
+stable key other platform features use to reference a profile (FHIR's
+`meta.profile`, `baseDefinition`), since StructureDefinition ids are only
+unique within a package. A non-matching filter returns an empty list, not a 404.
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.profiles.profiles.list({
+    url: "http://phenoml.com/fhir/StructureDefinition/custom-patient|1.0.0"
+});
+
+```
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.profiles.ListRequest` 
+    
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `ProfilesClient.RequestOptions` 
+    
+</dd>
+</dl>
+</dd>
+</dl>
+
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.profiles.profiles.<a href="/src/api/resources/profiles/resources/profiles/client/Client.ts">create</a>({ ...params }) -> phenoml.ProfileSummary</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Creates a custom profile from a FHIR StructureDefinition supplied as a JSON
+object. All metadata (version, resource type, id, url) is derived from the
+StructureDefinition; the lowercase StructureDefinition id becomes the
+profile's lookup key. Code system configuration is auto-extracted from the
+snapshot. Optionally group the profile under a named implementation guide.
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.profiles.profiles.create({
+    structure_definition: {
+        "key": "value"
+    }
+});
+
+```
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.ProfileUploadRequest` 
+    
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `ProfilesClient.RequestOptions` 
+    
+</dd>
+</dl>
+</dd>
+</dl>
+
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.profiles.profiles.<a href="/src/api/resources/profiles/resources/profiles/client/Client.ts">get</a>(id) -> phenoml.ProfileGetResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Returns a single custom profile by id, including its full StructureDefinition JSON.
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.profiles.profiles.get("custom-patient");
+
+```
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**id:** `string` — The lowercase StructureDefinition id of the custom profile.
+    
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `ProfilesClient.RequestOptions` 
+    
+</dd>
+</dl>
+</dd>
+</dl>
+
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.profiles.profiles.<a href="/src/api/resources/profiles/resources/profiles/client/Client.ts">update</a>(id, { ...params }) -> phenoml.ProfileSummary</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Replaces an existing custom profile with a new StructureDefinition. The
+`id` path parameter is authoritative: if the StructureDefinition includes
+an `id` it must match the path parameter, and if it omits one the path
+parameter is used. The FHIR resource type of the profile cannot change.
+Code system configuration is
+re-derived from the new StructureDefinition. When `implementation_guide` is
+omitted, the profile keeps its existing implementation guide. The instance
+stores a single version per canonical URL, so this replaces it in place.
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.profiles.profiles.update("custom-patient", {
+    structure_definition: {
+        "key": "value"
+    }
+});
+
+```
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**id:** `string` — The lowercase StructureDefinition id of the custom profile.
+    
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**request:** `phenoml.ProfileUploadRequest` 
+    
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `ProfilesClient.RequestOptions` 
+    
+</dd>
+</dl>
+</dd>
+</dl>
+
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.profiles.profiles.<a href="/src/api/resources/profiles/resources/profiles/client/Client.ts">delete</a>(id) -> void</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Permanently deletes a custom profile by id.
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.profiles.profiles.delete("custom-patient");
+
+```
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**id:** `string` — The lowercase StructureDefinition id of the custom profile.
+    
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `ProfilesClient.RequestOptions` 
+    
+</dd>
+</dl>
+</dd>
+</dl>
+
+
 </dd>
 </dl>
 </details>