Skill UI

This skill scaffolds a gold-standard annotation project tailored for evaluating clinical NER and de-identification models (OpenMed). It guides users through defining label schemas, writing rigorous guidelines, configuring annotation tools (like BRAT/Label Studio), generating synthetic clinical text, and creating disciplined, non-leaking train/dev/test splits. It ensures that all committed data are synthetic fixtures for reproducible evaluation.

This skill facilitates the computation of Electronic Clinical Quality Measures (eCQMs) by leveraging CQL (Clinical Quality Language) logic against the QDM (Quality Data Model). It is designed to extract crucial facts—such as counseling provided, symptoms, or documented exclusions—from unstructured clinical notes. By lifting these facts, it supplements structured EHR data, ensuring that numerators and valid exclusions are accurately captured for quality measure evaluation. Note that this tool augments data capture and does not replace certified measure engines.

This tool de-identifies sensitive free-text columns (e.g., names, dates, identifiers) in local structured datasets (CSV, JSONL, Parquet) using advanced OpenMed models. It ensures strict privacy by generating a completely redacted dataset and a separate PHI-free aggregate summary, allowing for secure data sharing and analysis without compromising source privacy or logging sensitive values.

This skill performs the crucial ETL process of mapping OpenMed-extracted, terminology-coded clinical facts (conditions, drugs, measurements) into the OMOP Common Data Model (CDM) v5.4 tables. It is used downstream after entity extraction and source coding, transforming raw NLP findings into standardized, OMOP-conformant records for OHDSI analytics.

This skill maps free-text laboratory and clinical observation names to standardized LOINC codes. It resolves ambiguous terms by considering the full six-axis model: Component, Property, Time, System (specimen), Scale, and Method. It integrates with FHIR terminology services to ensure accuracy, supporting US Core Laboratory Results and UCUM units.