Skill UI

This module provides a lazy adapter registry to seamlessly integrate OpenMed's clinical PII detection with major NLP frameworks like Microsoft Presidio, spaCy, and LangChain. It allows users to use OpenMed for enhanced PII recall, merge spans, or implement on-device PHI redaction guardrails without rewriting entire pipelines.

This skill acts as a comprehensive map for developing clinical and biomedical NLP pipelines using OpenMed. OpenMed is a local-first Python library that performs named-entity recognition (NER), protected health information (PHI) de-identification, and FHIR export, all running fully on-device without cloud calls. Use this guide when starting a new clinical text project, needing to select the appropriate capability (e.g., zero-shot NER, auditing, or FHIR conversion), or requiring an entry point for the core OpenMed features.

This skill helps developers programmatically discover, filter, and inspect the entire OpenMed model registry. It allows users to find the correct model key for specific clinical tasks (e.g., diseases, oncology, PII detection), filter by language, size, or task, and review model metadata before loading. It pairs with `loading-openmed-models`.

Converts raw OpenMed NER outputs (text spans) into structured, standards-compliant FHIR R4 resources (e.g., Condition, Observation, MedicationStatement). It provides mechanical helpers for building CodeableConcepts using major coding systems like SNOMED, LOINC, and ICD-10, ensuring high interoperability with EHR systems and registries.

Utilizes OpenMed's analyze_text to perform sophisticated Named-Entity Recognition (NER) on clinical and biomedical text. This tool extracts structured entities such as diseases, drugs, anatomy, genes, and proteins. It provides precise character spans and model confidence scores, making it essential for building robust, privacy-first clinical Natural Language Processing (NLP) pipelines.

Use openmed.extract_pii to detect and retrieve specific types of Protected Health Information (PHI) or Personally Identifiable Information (PII) spans (names, dates, MRNs, etc.) from clinical text. Unlike deidentification, this function returns the original text and the detected spans, allowing users to audit, preview redactions, normalize labels, or route spans to a custom anonymizer without altering the source data. It is ideal for pre-processing and policy enforcement.

Synthea generates statistically realistic, fully synthetic patient records in multiple standards (FHIR R4, C-CDA, CSV). This tool is essential for developers and researchers needing safe, shareable test data for OpenMed pipelines, CI fixtures, or specialized de-identification leakage gate test sets. It ensures zero risk of exposing real Protected Health Information (PHI).

This skill maps clinical concept spans (disorders, anatomy, procedures, etc.) extracted by OpenMed to SNOMED CT concept IDs (SCTID). It performs complex, out-of-process terminology resolution using standard FHIR R4 endpoints ($lookup, $translate, ValueSet/$expand) against a user-supplied, licensed terminology server (e.g., Ontoserver, UTS). Ideal for generating rich, hierarchy-aware clinical codes, performing subsumption queries (ECL), or translating codes between clinical standards (like ICD-10 to SNOMED CT).

This skill facilitates the crucial grounding step for clinical coding by interacting with external FHIR terminology servers. It supports core operations such as `$validate-code`, `$expand` (for ValueSets), `$lookup`, and `$translate` (ConceptMaps). It ensures that raw text spans are converted into validated, coded `CodeableConcept` resources using industry standards like SNOMED CT, LOINC, and ICD-10, maintaining interoperability.

This skill guides users on deploying OpenMed models completely on-device for maximum privacy and edge computing. It details running workflows using three backends: MLX (Apple Silicon), CoreML (iOS/macOS), and ONNX/WebGPU (cross-platform/browser). The process involves converting, optionally quantizing, and running models locally, ensuring PHI never leaves the host device.

A comprehensive guide for embedding OpenMed-powered tools into Electronic Health Records (EHRs) like Epic or Cerner. It covers the entire SMART on FHIR workflow, including OAuth2 PKCE authorization, granular scoping (e.g., patient/DocumentReference.rs), secure token handling, and processing clinical notes locally on-device for de-identification and Named Entity Recognition (NER).