Agent skills by maziyarpanahi

Checks OpenMed de-identified clinical text against the 18 HIPAA Safe Harbor identifier categories and reports gaps and residual re-identification risk.

maziyarpanahi/openmed

Fills in a model card for an OpenMed clinical NER or de-identification model from its evaluation reports: intended use, metrics, subgroups and limitations.

maziyarpanahi/openmed

Walks a data pipeline against the HIPAA Privacy and Security Rule checklist and produces a gap report before it processes patient data.

maziyarpanahi/openmed

Suggests candidate ICD-10-CM diagnosis and ICD-10-PCS procedure codes for clinical text extracted by OpenMed, with rationale for a certified coder to review.

maziyarpanahi/openmed

Maps OpenMed-extracted, terminology-coded conditions, drugs and measurements into OMOP CDM v5.4 tables for OHDSI and ATLAS analytics.

maziyarpanahi/openmed

Finds social risks such as housing instability or food insecurity in clinical notes and proposes matching ICD-10-CM Z-codes for a coder to confirm.

maziyarpanahi/openmed

Converts scanned faxes, images, CSV/TSV exports and C-CDA XML into clean text on-device, ready for OpenMed de-identification and named-entity recognition.

maziyarpanahi/openmed

Annotates VCF variants and normalizes HGVS nomenclature with public, license-free annotators (Ensembl VEP REST, VEP/SnpEff/ANNOVAR offline) and links variants to gnomAD population frequencies and…

maziyarpanahi/openmed

Choose the first OpenMed workflow skill for an intake, privacy, extraction, exchange, or verification request using deterministic local routing.

maziyarpanahi/openmed

Packages standalone FHIR R4 resources from OpenMed output into one transaction Bundle with stable fullUrls and rewritten references, ready to post to a FHIR server.

maziyarpanahi/openmed

Scans text that has already been de-identified for leftover identifiers such as SSNs, card numbers, emails and dates, and blocks release if anything turns up.

maziyarpanahi/openmed

Produce a signed, reproducible, no-PHI audit trail for an OpenMed de-identification run via deidentify(audit=True).

maziyarpanahi/openmed

Generates and verifies 21 CFR Part 11-style audit trails — who/what/when, electronic signatures, and tamper-evidence — for OpenMed pipelines in GxP and clinical-trial (GCP) settings.

maziyarpanahi/openmed

Audit an OpenMed NER or de-identification model for performance disparities across demographic subgroups (sex, age band, race/ethnicity when available) using openmed.eval.fairnessreport.

maziyarpanahi/openmed

Run large-scale batch NER, PII extraction, or de-identification over many clinical notes on-device with OpenMed, with sharding, checkpointing, resumability, and append-only JSONL output.

maziyarpanahi/openmed

Benchmark an OpenMed PII model with synthetic gold spans and report label-aware exact-span and grapheme recall without emitting identifier surfaces.

maziyarpanahi/openmed

Score an OpenMed clinical or biomedical NER model against a user-supplied gold corpus with entity-level precision, recall, and F1, then break errors down per label.

maziyarpanahi/openmed

Combine OpenMed clinical NLP with Microsoft Presidio, spaCy, or LangChain through OpenMed's built-in interop adapter registry (openmed.interop).

maziyarpanahi/openmed

Scaffold a synthetic gold-standard annotation project for evaluating OpenMed NER and de-identification models — label schema, annotation guidelines, BRAT or Label Studio config, and disjoint…

maziyarpanahi/openmed

Assemble a chronological patient timeline from OpenMed-extracted clinical events, normalizing dates and resolving relative time expressions on-device.

maziyarpanahi/openmed

Orient and bootstrap any project that uses OpenMed, the on-device clinical and biomedical NLP library, for named-entity recognition, PHI de-identification, FHIR export, and evaluation.

maziyarpanahi/openmed

Discover and pick the right OpenMed model for a clinical or biomedical task, domain, or language.

maziyarpanahi/openmed

Maps chronic conditions extracted by OpenMed to CMS-HCC V28 risk-adjustment categories and estimates a RAF (Risk Adjustment Factor) score as decision support.

maziyarpanahi/openmed

Compute electronic clinical quality measures (eCQMs) over structured data using CQL/QDM logic, lifting note-derived numerator and exclusion facts from OpenMed to improve measure capture.

maziyarpanahi/openmed

Select and customize OpenMed's seven bundled privacy policy profiles for de-identification, and build custom surrogate generators.

maziyarpanahi/openmed

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.

maziyarpanahi/openmed

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.

maziyarpanahi/openmed

Remove, mask, or replace PHI/PII in clinical free text on-device with OpenMed's deidentify().

maziyarpanahi/openmed

De-identify non-English clinical text on-device with OpenMed by passing lang= and locale= to deidentify().

maziyarpanahi/openmed

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.

maziyarpanahi/openmed

Computes disproportionality signals — PRR, ROR, EBGM, and IC (BCPNN) — over FAERS / OpenFDA drug-event data to flag potential safety signals.

maziyarpanahi/openmed

Add a logging and telemetry guard that scrubs or blocks PHI from logs, traces, and error reports around an OpenMed deployment.

maziyarpanahi/openmed

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.

maziyarpanahi/openmed

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.

maziyarpanahi/openmed

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…

maziyarpanahi/openmed

Extract clinical entities from synthetic or already de-identified text with OpenMed and map them into deterministic FHIR R4 resources and a Bundle.

maziyarpanahi/openmed

Run clinical and biomedical named-entity recognition on medical text with OpenMed's analyzetext.

maziyarpanahi/openmed

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.

maziyarpanahi/openmed

Detects and extracts tabular laboratory panels from PDFs, scans, and images into structured rows ready for OpenMed and FHIR.

maziyarpanahi/openmed

Detect PHI/PII spans in clinical text with OpenMed's extractpii without altering the text.

maziyarpanahi/openmed

Fetches and pages FHIR R4 resources (Patient, DocumentReference, DiagnosticReport, Observation, Condition) from a FHIR REST server, decodes base64 attachments, and extracts clinical narrative for…

maziyarpanahi/openmed

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.

maziyarpanahi/openmed

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.

maziyarpanahi/openmed

Replace detected PHI with realistic, type-matched fake values in OpenMed so clinical notes stay readable and parseable instead of full of [REDACTED] markers.

maziyarpanahi/openmed

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.

maziyarpanahi/openmed

Load OpenMed clinical/biomedical NER models from the Hugging Face Hub or a local path and reuse them efficiently across calls.

maziyarpanahi/openmed

Maps laboratory and clinical observation names extracted by OpenMed to LOINC codes using the public Regenstrief LOINC and FHIR terminology APIs.

maziyarpanahi/openmed

Maps clinical concept spans extracted by OpenMed to SNOMED CT concepts through a USER-SUPPLIED terminology server (the user's own Ontoserver, Snowstorm, or UMLS/UTS), never a bundled vocabulary.

maziyarpanahi/openmed