maziyarpanahi/openmed

maziyarpanahi/openmed · AGENTS.md

maziyarpanahi/openmed · skills/annotating-variants/SKILL.md · Annotates VCF variants and normalizes HGVS nomenclature with public, license-free annotators (Ensembl VEP REST…

maziyarpanahi/openmed · skills/ask-openmed/SKILL.md · Choose the first OpenMed workflow skill for an intake, privacy, extraction, exchange, or verification request using…

maziyarpanahi/openmed · skills/assembling-fhir-bundles/SKILL.md · Package multiple FHIR R4 resources produced from OpenMed output into a single valid transaction Bundle ready to POST to…

maziyarpanahi/openmed · skills/auditing-deid-leakage/SKILL.md · Adversarially scan already-de-identified clinical text for residual identifiers and emit a leakage report that blocks…

maziyarpanahi/openmed · skills/auditing-deidentification-runs/SKILL.md · Produce a signed, reproducible, no-PHI audit trail for an OpenMed de-identification run via deidentify(audit=True). Use…

maziyarpanahi/openmed · skills/auditing-part11-trails/SKILL.md · Generates and verifies 21 CFR Part 11-style audit trails — who/what/when, electronic signatures, and tamper-evidence —…

maziyarpanahi/openmed · skills/auditing-safe-harbor-checklist/SKILL.md · Verify OpenMed de-identified output against all 18 HIPAA Safe Harbor identifier categories and report residual…

maziyarpanahi/openmed · skills/auditing-subgroup-fairness/SKILL.md · Audit an OpenMed NER or de-identification model for performance disparities across demographic subgroups (sex, age…

maziyarpanahi/openmed · skills/authoring-model-cards/SKILL.md · Generate a model card for an OpenMed clinical NER or de-identification model documenting intended use, quantitative…

maziyarpanahi/openmed · skills/batch-processing-clinical-text/SKILL.md · Run large-scale batch NER, PII extraction, or de-identification over many clinical notes on-device with OpenMed, with…

maziyarpanahi/openmed · skills/benchmark-pii-recall/SKILL.md · Benchmark an OpenMed PII model with synthetic gold spans and report label-aware exact-span and grapheme recall without…

maziyarpanahi/openmed · skills/benchmarking-clinical-ner/SKILL.md · Score an OpenMed clinical or biomedical NER model against a user-supplied gold corpus with entity-level precision…

maziyarpanahi/openmed · skills/bridging-presidio-and-spacy/SKILL.md · Combine OpenMed clinical NLP with Microsoft Presidio, spaCy, or LangChain through OpenMed's built-in interop adapter…

maziyarpanahi/openmed · skills/building-gold-corpus/SKILL.md · Scaffold a synthetic gold-standard annotation project for evaluating OpenMed NER and de-identification models — label…

maziyarpanahi/openmed · skills/building-patient-timelines/SKILL.md · Assemble a chronological patient timeline from OpenMed-extracted clinical events, normalizing dates and resolving…

maziyarpanahi/openmed · skills/building-with-openmed/SKILL.md · Orient and bootstrap any project that uses OpenMed, the on-device clinical and biomedical NLP library, for named-entity…

maziyarpanahi/openmed · skills/checking-hipaa-compliance/SKILL.md · Runs a HIPAA Privacy and Security Rule checklist over a data pipeline and produces a gap report before deploying…

maziyarpanahi/openmed · skills/choosing-openmed-models/SKILL.md · Discover and pick the right OpenMed model for a clinical or biomedical task, domain, or language. Use when the user…

maziyarpanahi/openmed · skills/coding-hcc-risk-adjustment/SKILL.md · Maps chronic conditions extracted by OpenMed to CMS-HCC V28 risk-adjustment categories and estimates a RAF (Risk…

maziyarpanahi/openmed · skills/coding-icd10/SKILL.md · Suggests candidate ICD-10-CM diagnosis codes (and ICD-10-PCS procedure codes) for diagnoses and procedures extracted by…

maziyarpanahi/openmed · skills/computing-ecqms/SKILL.md · Compute electronic clinical quality measures (eCQMs) over structured data using CQL/QDM logic, lifting note-derived…

maziyarpanahi/openmed · skills/configuring-privacy-policies/SKILL.md · Select and customize OpenMed's seven bundled privacy policy profiles for de-identification, and build custom surrogate…

maziyarpanahi/openmed · skills/defining-cohort-phenotypes/SKILL.md · Authors computable phenotype and cohort definitions in the OHDSI ATLAS / CIRCE style over the OMOP CDM, combining…

maziyarpanahi/openmed · skills/deidentify-a-dataset/SKILL.md · De-identify selected free-text columns in a local CSV, JSONL, or Parquet dataset with OpenMed and produce a separate…

maziyarpanahi/openmed · skills/deidentifying-clinical-text/SKILL.md · Remove, mask, or replace PHI/PII in clinical free text on-device with OpenMed's deidentify(). Use when the user needs…

maziyarpanahi/openmed · skills/deidentifying-multilingual-text/SKILL.md · De-identify non-English clinical text on-device with OpenMed by passing lang= and locale= to deidentify(). Use when the…

maziyarpanahi/openmed · skills/deploying-openmed-mcp/SKILL.md · Run OpenMed's Model Context Protocol (MCP) server so coding agents (Claude Code, Codex) and chat clients can call…

maziyarpanahi/openmed · skills/detecting-pv-signals/SKILL.md · Computes disproportionality signals — PRR, ROR, EBGM, and IC (BCPNN) — over FAERS / OpenFDA drug-event data to flag…

maziyarpanahi/openmed · skills/enforcing-nophi-logging/SKILL.md · Add a logging and telemetry guard that scrubs or blocks PHI from logs, traces, and error reports around an OpenMed…

maziyarpanahi/openmed · skills/etl-to-omop-cdm/SKILL.md · Map OpenMed-extracted, terminology-coded conditions, drugs, and measurements into OMOP CDM v5.4 clinical tables…

maziyarpanahi/openmed · skills/evaluating-with-leakage-gates/SKILL.md · Evaluate an OpenMed de-identification or clinical NER model against the leakage-first release gates G1a through G8…

maziyarpanahi/openmed · skills/exporting-bulk-fhir/SKILL.md · Kick off and harvest a FHIR Bulk Data $export (system-, group-, or patient-level) and stream the resulting NDJSON into…

maziyarpanahi/openmed · skills/exporting-to-fhir/SKILL.md · Convert OpenMed NER output (entities from openmed.analyze_text) into FHIR R4 resources — Condition…

maziyarpanahi/openmed · skills/extract-clinical-entities-to-fhir/SKILL.md · Extract clinical entities from synthetic or already de-identified text with OpenMed and map them into deterministic…

maziyarpanahi/openmed · skills/extracting-clinical-entities/SKILL.md · Run clinical and biomedical named-entity recognition on medical text with OpenMed's analyze_text. Use when the user…

maziyarpanahi/openmed · skills/extracting-dicom-metadata/SKILL.md · Reads DICOM file headers and DICOM-SR (Structured Report) content to pull study/series metadata and embedded report…

maziyarpanahi/openmed · skills/extracting-lab-tables/SKILL.md · Detects and extracts tabular laboratory panels from PDFs, scans, and images into structured rows ready for OpenMed and…

maziyarpanahi/openmed · skills/extracting-pii-entities/SKILL.md · Detect PHI/PII spans in clinical text with OpenMed's extract_pii without altering the text. Use when the user wants to…

maziyarpanahi/openmed · skills/extracting-sdoh/SKILL.md · Extracts social determinants of health (SDOH) — housing instability, food insecurity, unemployment, transportation…

maziyarpanahi/openmed · skills/fetching-fhir-resources/SKILL.md · Fetches and pages FHIR R4 resources (Patient, DocumentReference, DiagnosticReport, Observation, Condition) from a FHIR…

maziyarpanahi/openmed · skills/gating-deid-leakage/SKILL.md · Add a CI gate that fails the build when an OpenMed de-identification model's recall on a held-out PHI set drops below…

maziyarpanahi/openmed · skills/generating-synthea-data/SKILL.md · Generates synthetic but realistic patient records (FHIR R4 bundles, C-CDA documents, CSV) with MITRE Synthea for…

maziyarpanahi/openmed · skills/generating-synthetic-surrogates/SKILL.md · Replace detected PHI with realistic, type-matched fake values in OpenMed so clinical notes stay readable and parseable…

maziyarpanahi/openmed · skills/ingesting-clinical-documents/SKILL.md · Turn scanned faxes, images, and CSV/CDA exports into clean text ready for OpenMed de-identification and NER, fully…

maziyarpanahi/openmed · skills/linking-umls-concepts/SKILL.md · Links entities extracted by OpenMed to UMLS Metathesaurus CUIs using the USER'S OWN UTS API key, with nothing from the…

maziyarpanahi/openmed · skills/loading-openmed-models/SKILL.md · Load OpenMed clinical/biomedical NER models from the Hugging Face Hub or a local path and reuse them efficiently across…

maziyarpanahi/openmed · skills/mapping-loinc/SKILL.md · Maps laboratory and clinical observation names extracted by OpenMed to LOINC codes using the public Regenstrief LOINC…

maziyarpanahi/openmed · skills/mapping-to-snomed/SKILL.md · Maps clinical concept spans extracted by OpenMed to SNOMED CT concepts through a USER-SUPPLIED terminology server (the…

maziyarpanahi/openmed · skills/mining-pubmed-literature/SKILL.md · Searches and fetches PubMed and PMC via NCBI E-utilities (ESearch then EFetch/ESummary) to gather biomedical evidence…

maziyarpanahi/openmed · skills/normalizing-rxnorm/SKILL.md · Normalizes drug mentions extracted by OpenMed to RxNorm RxCUIs using the free public RxNav/RxNorm REST API. Use when…

maziyarpanahi/openmed · skills/parsing-ccda-documents/SKILL.md · Parses C-CDA / CCD XML clinical documents to extract human-readable section narrative plus coded entries, keyed by…

maziyarpanahi/openmed · skills/parsing-hl7v2-messages/SKILL.md · Decodes pipe-delimited HL7 v2.x messages (ADT, ORU, MDM, ORM) into structured segments/fields/components and surfaces…

maziyarpanahi/openmed · skills/parsing-lab-values/SKILL.md · Parse laboratory values and reference ranges from clinical text and flag results as low, normal, high, or critical with…

maziyarpanahi/openmed · skills/parsing-trial-eligibility/SKILL.md · Parses free-text clinical-trial eligibility criteria into structured inclusion and exclusion logic, then matches them…

maziyarpanahi/openmed · skills/pick-a-pii-model/SKILL.md · Select an on-device OpenMed PII model from the committed registry by language, runtime format, and size budget, then…

maziyarpanahi/openmed · skills/pseudonymizing-for-gdpr/SKILL.md · Apply GDPR-grade pseudonymization to clinical or personal text with OpenMed, keeping a separately-held re-linkage key…

maziyarpanahi/openmed · skills/querying-openfda-labels/SKILL.md · Looks up FDA drug labels, NDC directory entries, indications, boxed warnings, and recalls/enforcement actions via the…

maziyarpanahi/openmed · skills/querying-terminology-service/SKILL.md · Call a user-supplied FHIR terminology server ($validate-code, $expand, $lookup, $translate) to validate and expand…

maziyarpanahi/openmed · skills/reconciling-problem-lists/SKILL.md · Deduplicate and reconcile OpenMed-extracted conditions into one clean active problem list with clinical status (active…

maziyarpanahi/openmed · skills/reidentifying-text/SKILL.md · Reversibly de-identify clinical text with OpenMed and later restore the original PHI from a saved mapping. Use when the…

maziyarpanahi/openmed · skills/reporting-adverse-events/SKILL.md · Structures adverse-event mentions that OpenMed extracts into FAERS / ICH E2B(R3) reportable fields — suspect drug…

maziyarpanahi/openmed · skills/resolving-clinical-context/SKILL.md · Assign negation, temporality, and uncertainty (the ConText axes) to clinical entities extracted by OpenMed, so "denies…

maziyarpanahi/openmed · skills/reviewing-reidentification-risk/SKILL.md · Run expert-determination-style quasi-identifier risk scoring (k-anonymity, l-diversity) plus OpenMed's empirical…

maziyarpanahi/openmed · skills/running-openmed-ondevice/SKILL.md · Run OpenMed models fully on-device with the MLX (Apple Silicon), CoreML (iOS/macOS), or ONNX/WebGPU…

maziyarpanahi/openmed · skills/running-zeroshot-ner/SKILL.md · Extract arbitrary, custom entity types from clinical or biomedical text with no fine-tuning using OpenMed's GLiNER /…

maziyarpanahi/openmed · skills/scaffolding-smart-on-fhir/SKILL.md · Scaffold a SMART-on-FHIR app (SMART App Launch v2 — EHR launch and standalone launch, OAuth2 PKCE, scopes, token…

maziyarpanahi/openmed · skills/searching-clinicaltrials/SKILL.md · Searches ClinicalTrials.gov for studies by condition, intervention, and recruitment status using the modern v2 REST API…

maziyarpanahi/openmed · skills/segmenting-clinical-sections/SKILL.md · Split a clinical note into canonical sections (Chief Complaint, HPI, PMH, Medications, Allergies, Assessment & Plan…

maziyarpanahi/openmed · skills/serving-openmed-rest-api/SKILL.md · Stand up OpenMed's FastAPI REST service for clinical NER, PII extraction, and de-identification, with health checks…

maziyarpanahi/openmed · skills/setup-openmed/SKILL.md · Collect a bounded set of de-identification policy decisions and write a deterministic, reviewable DEID-POLICY.md from…

maziyarpanahi/openmed · skills/shifting-clinical-dates/SKILL.md · Apply consistent per-patient date shifting in OpenMed that preserves intervals between events while satisfying HIPAA…

maziyarpanahi/openmed · skills/structuring-radiology-reports/SKILL.md · Converts free-text radiology narratives into structured findings and impression — with measurements, laterality…

maziyarpanahi/openmed · skills/summarizing-clinical-notes/SKILL.md · Produces structured, citation-anchored summaries of clinical notes — one-liner, hospital course, and problem-oriented…

maziyarpanahi/openmed · skills/validating-us-core/SKILL.md · Validate FHIR R4 resources and Bundles against US Core / USCDI profiles with the official HL7 FHIR validator before…