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Reference

Introduction Errors Common headers

Getting started

POSTRequest an access token POSTGenerate authentication token (legacy)

Understand

POSTSubmit feedback on extraction results GETList available code systems GETGet code system detail DELETEDelete custom code system GETExport custom code system POSTUpload custom code system GETList codes in a code system GETGet a specific code GETSemantic search (embedding-based)GETText search (keyword-based)POSTCrosswalk a code to target code systems POSTExtract medical codes from text POST[Alpha] Extract medical codes with phenocr

Structure

POSTAnalyze text for patient cohort criteria GETList batch jobs POSTCreate a batch job GETGet a batch job POSTCancel a batch job POSTFinalize a batch job POSTUpload one batch item GETList a batch job's results GETGet one batch item's result POSTCreate FHIR resource from text POSTExtract multiple FHIR resources from text POSTConvert document to FHIR resource POSTExtract multiple FHIR resources from a document POSTUpload custom FHIR profile (deprecated)POSTGenerate FHIR search parameters from text

POSTGenerate a summary from FHIR resources POSTCreate a new summary template GETGet a summary template by ID PUTUpdate a summary template DELETEDelete a summary template GETList all summary templates

POSTMap FHIR resources to OMOP CDM v5.4

Act

GETGet agent by ID PUTUpdate agent DELETEDelete agent PATCHPatch agent POSTCreate a new agent GETList agents POSTChat with agent GETGet chat messages POSTChat with agent (streaming)POSTCreate agent prompt GETGet prompt by ID PUTUpdate prompt DELETEDelete prompt PATCHPatch prompt GETList agent prompts

GETList all workflows POSTCreate new workflow GETGet workflow by ID PUTUpdate workflow DELETEDelete workflow POSTExecute workflow

POSTAnalyze patient cohorts POSTCreate FHIR resource from text and store it POSTExtract and store multiple FHIR resources POSTSearch FHIR resources from natural language GETGet MCP server by ID DELETEDelete MCP server by ID POSTCreate MCP server GETList MCP servers GETList MCP server tools GETGet MCP server tool by ID DELETEDelete MCP server tool by ID

Connect & store

POSTCreate FHIR provider GETGet FHIR provider by ID DELETEDelete FHIR provider POSTExecute FHIR bundle operation GETRead or search FHIR resources PUTUpsert FHIR resource POSTCreate FHIR resource DELETEDelete FHIR resource PATCHPatch FHIR resource GETList FHIR providers PATCHAdd authentication configuration PATCHRemove authentication configuration PATCHSet active authentication configuration

Other references

GETList implementation guides GETGet an implementation guide PUTSet an implementation guide's profile context DELETEDelete an implementation guide family POSTPublish an exact custom-profile package GETGet an exact custom-profile package GETList custom FHIR profiles POSTUpload a custom FHIR profile GETGet a custom FHIR profile PUTUpdate a custom FHIR profile DELETEDelete a custom FHIR profile GETList versions for a custom FHIR profile POSTAdd a retained version to a custom FHIR profile GETGet a retained custom FHIR profile version DELETEDelete a retained custom FHIR profile version

POSTTranscribe audio

Other references

Markdown index Full API export

FHIR2OMOP

Map FHIR R4 resources and bundles into OMOP Common Data Model (CDM v5.4) tables.

Endpoints

POST/fhir2omop/create