Skill Claude CodeCodex
Authors computable phenotype and cohort definitions in the OHDSI ATLAS / CIRCE style over the OMOP CDM, combining standard concept sets with NLP-derived features that OpenMed extracts. Use when the user wants to define a patient cohort, write a computable phenotype, reuse PheKB or OHDSI Phenotype Library logic, build…
Skill Claude CodeCodex
De-identify selected free-text columns in a local CSV, JSONL, or Parquet dataset with OpenMed and produce a separate redacted dataset plus a PHI-free aggregate summary. Use when an agent must prepare a clinical dataset for analysis or sharing without overwriting the source or exposing cell values in logs.
Skill Claude CodeCodex
Remove, mask, or replace PHI/PII in clinical free text on-device with OpenMed's deidentify(). Use when the user needs to de-identify medical notes, strip patient identifiers, redact PHI before sharing or analysis, anonymize discharge summaries, or pick a de-id method (mask vs remove vs replace vs hash vs shiftdates).…
Skill Claude CodeCodex
De-identify non-English clinical text on-device with OpenMed by passing lang= and locale= to deidentify(). Use when the user has Spanish, German, French, Italian, Portuguese, Dutch, Hindi, Telugu, Arabic, Japanese, or Turkish medical notes, needs locale-aware fake surrogates, must handle language-specific national IDs…
Skill Claude CodeCodex
Run OpenMed's Model Context Protocol (MCP) server so coding agents (Claude Code, Codex) and chat clients can call clinical NER, PII extraction, and de-identification as tools, on-device. Use when the user wants to add OpenMed to an agent's MCP config, expose de-id/NER as MCP tools, run an MCP server over stdio or…
Skill Claude CodeCodex
Computes disproportionality signals — PRR, ROR, EBGM, and IC (BCPNN) — over FAERS / OpenFDA drug-event data to flag potential safety signals. Use when the user wants to mine spontaneous-report data for drug-reaction associations, build a 2x2 contingency table, compute a Proportional Reporting Ratio or Reporting Odds…
Skill Claude CodeCodex
Add a logging and telemetry guard that scrubs or blocks PHI from logs, traces, and error reports around an OpenMed deployment. Use when the user wants a Python logging.Filter that redacts protected health information before records are emitted, wants to keep PHI out of OpenTelemetry spans or error trackers, needs…
Skill Claude CodeCodex
Map OpenMed-extracted, terminology-coded conditions, drugs, and measurements into OMOP CDM v5.4 clinical tables (conditionoccurrence, drugexposure, measurement) for OHDSI/ATLAS analytics. Use when the user wants to load NLP-derived facts into an OMOP database, build an OHDSI ETL from clinical notes, populate…
Skill Claude CodeCodex
Evaluate an OpenMed de-identification or clinical NER model against the leakage-first release gates G1a through G8, which gate releases on residual PHI leakage rather than on F1. Use when the user wants to run the OpenMed eval harness on a synthetic golden set, decide whether a de-id model is RELEASABLE or…
Skill Claude CodeCodex
Kick off and harvest a FHIR Bulk Data $export (system-, group-, or patient-level) and stream the resulting NDJSON into a batch OpenMed de-identification + NER pipeline at cohort scale. Covers the async kickoff (Prefer respond-async) -> poll Content-Location -> download NDJSON flow, the Bulk Data Access IG, type/since…
Skill Claude CodeCodex
Convert OpenMed NER output (entities from openmed.analyzetext) into FHIR R4 resources — Condition, MedicationStatement, Observation — using OpenMed's built-in FHIR R4 export helpers in openmed.clinical.exporters. Covers the verified CodeableConcept builder (coding, codeableconcept, systemuri), deterministic fullUrl…
Skill Claude CodeCodex
Extract clinical entities from synthetic or already de-identified text with OpenMed and map them into deterministic FHIR R4 resources and a Bundle. Use when an agent must turn local clinical NER output into Conditions, MedicationStatements, Observations, or other FHIR resources without inventing terminology codes.
Skill Claude CodeCodex
Run clinical and biomedical named-entity recognition on medical text with OpenMed's analyzetext. Use when the user wants to extract diseases, drugs, anatomy, genes, or other biomedical entities from notes; needs NER output as dict/json/html/csv; wants to filter by confidence, group entities, toggle sentence detection…
Skill Claude CodeCodex
Reads DICOM file headers and DICOM-SR (Structured Report) content to pull study/series metadata and embedded report text, and flags PHI carried in header tags. Use before OpenMed processing when ingesting imaging data (CT/MR/CR/US, radiology SR) and you need the report narrative de-identified and analyzed, plus a list…
Skill Claude CodeCodex
Detects and extracts tabular laboratory panels from PDFs, scans, and images into structured rows ready for OpenMed and FHIR. Use when the user has a CBC, CMP, lipid panel, or other lab report as a scanned image / PDF / spreadsheet and needs the test name, value, unit, reference range, and abnormal flag as clean rows.…
Skill Claude CodeCodex
Detect PHI/PII spans in clinical text with OpenMed's extractpii without altering the text. Use when the user wants to find names, dates, MRNs, phone numbers, addresses, SSNs, or other identifiers and get their offsets and labels (not redact them), inspect what would be removed before de-identifying, route spans to a…
Skill Claude CodeCodex
Extracts social determinants of health (SDOH) — housing instability, food insecurity, unemployment, transportation barriers, social isolation, financial strain — from clinical narrative and maps the spans to ICD-10-CM Z-codes (Z55–Z65). Use after running OpenMed NER when the user wants SDOH surfacing, Z-code…
Skill Claude CodeCodex
Fetches and pages FHIR R4 resources (Patient, DocumentReference, DiagnosticReport, Observation, Condition) from a FHIR REST server, decodes base64 attachments, and extracts clinical narrative for OpenMed. Use before OpenMed processing when pulling charts from an EHR FHIR API (Epic, Cerner/Oracle, HAPI, or any US Core…
Skill Claude CodeCodex
Add a CI gate that fails the build when an OpenMed de-identification model's recall on a held-out PHI set drops below threshold or any critical identifier leaks. Use when the user wants a pytest test or CLI step that exits nonzero on de-id regression, wants to wire OpenMed's leakage-first release gates into GitHub…
Skill Claude CodeCodex
Generates synthetic but realistic patient records (FHIR R4 bundles, C-CDA documents, CSV) with MITRE Synthea for development, CI fixtures, demos, and leakage-gate test sets — zero real PHI. Use when you need safe, shareable test data for an OpenMed pipeline, reproducible fixtures for tests, or a held-out set for…
Skill Claude CodeCodex
Replace detected PHI with realistic, type-matched fake values in OpenMed so clinical notes stay readable and parseable instead of full of [REDACTED] markers. Use when the user wants surrogate names, MRNs, addresses, or dates rather than opaque masks, needs consistent fake identities across a document, must keep notes…
Skill Claude CodeCodex
Turn scanned faxes, images, and CSV/CDA exports into clean text ready for OpenMed de-identification and NER, fully on-device. Use when the user has clinical documents (image scans, photographed/faxed notes, tabular CSV/TSV exports, C-CDA XML) and needs OCR or structured intake before openmed.deidentify and…
Skill Claude CodeCodex
Links entities extracted by OpenMed to UMLS Metathesaurus CUIs using the USER'S OWN UTS API key, with nothing from the Metathesaurus bundled or cached. Use when the user wants to normalize concepts across vocabularies to a single CUI, resolve synonyms via the UMLS, filter by semantic type, or cross-walk between SNOMED…
Skill Claude CodeCodex
Load OpenMed clinical/biomedical NER models from the Hugging Face Hub or a local path and reuse them efficiently across calls. Use when the user wants to load an OpenMed model, control the model cache, run fully offline after a one-time download, reuse a ModelLoader to avoid reloading, set a cachedir or device, or…