openmed-skills

Plugin openmed-skills from marketplace openmed-skills in maziyarpanahi/openmed. Commands read from the repo's manifest — yesterday.

Skills (74)

• annotating-variants

  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 the clinical context OpenMed extracts. Use when the user wants to predict variant consequences, map HGVS

• ask-openmed

  Choose the first OpenMed workflow skill for an intake, privacy, extraction, exchange, or verification request using deterministic local routing. Use when a goal is broad, spans several clinical-data stages, or leaves the data-sensitivity status unclear; the privacy gate is selected before downstream

• assembling-fhir-bundles

  Package multiple FHIR R4 resources produced from OpenMed output into a single valid transaction Bundle ready to POST to an EHR, using OpenMed's verified bundle assembler openmed.clinical.exporters.fhir.to_bundle. Covers deterministic urn:uuid fullUrls, automatic in-Bundle reference rewriting, reques

• auditing-deid-leakage

  Adversarially scan already-de-identified clinical text for residual identifiers and emit a leakage report that blocks release on any hit. Use after OpenMed de-identification when the user asks to verify a redaction, prove no PHI/PII leaked, gate a dataset before sharing, or run a second-pass detecto

• auditing-deidentification-runs

  Produce a signed, reproducible, no-PHI audit trail for an OpenMed de-identification run via deidentify(audit=True). Use when the user needs compliance evidence, a tamper-evident record of what was redacted and why, to verify nothing was changed, to retain proof for HIPAA/GDPR audits, or to review de

• auditing-part11-trails

  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. Use when the user runs OpenMed in a regulated/validated environment and needs an attributable, time-stamped, tamper-e

• auditing-safe-harbor-checklist

  Verify OpenMed de-identified output against all 18 HIPAA Safe Harbor identifier categories and report residual re-identification risk. Use when the user must confirm a note meets HIPAA Safe Harbor (45 CFR 164.514(b)(2)), needs a coverage checklist mapping detected entities to the 18 categories, want

• auditing-subgroup-fairness

  Audit an OpenMed NER or de-identification model for performance disparities across demographic subgroups (sex, age band, race/ethnicity when available) using openmed.eval.fairness_report. Use when the user wants per-subgroup recall and leakage, wants to check whether de-identification under-protects

• authoring-model-cards

  Generate a model card for an OpenMed clinical NER or de-identification model documenting intended use, quantitative metrics, subgroup performance, limitations, and a medical-device disclaimer for clinical AI governance. Use when the user wants to write or update a model card, a README model section,

• batch-processing-clinical-text

  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. Use when the user needs to process a corpus or folder of notes, de-identify a dataset, run NER over thousands of

• benchmark-pii-recall

  Benchmark an OpenMed PII model with synthetic gold spans and report label-aware exact-span and grapheme recall without emitting identifier surfaces. Use when an agent must compare a model, threshold, backend, or quantized artifact and enforce a recall floor before release.

• benchmarking-clinical-ner

  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. Use when the user wants a seqeval-style scorecard, strict vs partial (relaxed) span matching, a per-label confusion matrix, false-negat

• bridging-presidio-and-spacy

  Combine OpenMed clinical NLP with Microsoft Presidio, spaCy, or LangChain through OpenMed's built-in interop adapter registry (openmed.interop). Covers the lazy adapter registry (available_adapters, get_adapter, adapter_spec), the presidio/spacy/langchain pip extras, and the verified callables — Pre

• building-gold-corpus

  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 train/dev/test splits. Use when the user wants to create eval fixtures, set up annotation, define a label set

• building-patient-timelines

  Assemble a chronological patient timeline from OpenMed-extracted clinical events, normalizing dates and resolving relative time expressions on-device. Use when the user wants to build a patient timeline, order events from clinical notes, reconstruct a longitudinal history, plot a course of illness,

• building-with-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. Use when the user mentions OpenMed, wants to install it, asks which OpenMed capability or model fits a task, or is

• checking-hipaa-compliance

  Runs a HIPAA Privacy and Security Rule checklist over a data pipeline and produces a gap report before deploying OpenMed on PHI. Use when the user is about to process protected health information, needs a pre-deployment compliance review, wants to know which administrative, physical, and technical s

• choosing-openmed-models

  Discover and pick the right OpenMed model for a clinical or biomedical task, domain, or language. Use when the user asks which OpenMed model to use, wants to list model categories, find a Disease vs Oncology vs Privacy/PII model, get a PII model for a specific language, search models by size or task

• coding-hcc-risk-adjustment

  Maps chronic conditions extracted by OpenMed to CMS-HCC V28 risk-adjustment categories and estimates a RAF (Risk Adjustment Factor) score as decision support. Use when the user wants to surface risk-adjustable diagnoses from notes, map ICD-10-CM codes to HCC categories, estimate or reconcile a patie

• coding-icd10

  Suggests candidate ICD-10-CM diagnosis codes (and ICD-10-PCS procedure codes) for diagnoses and procedures extracted by OpenMed, with rationale and a human-coder caveat. Use when the user wants to code a problem list, map a diagnosis span to a billable ICD-10-CM code, route a finding to the right ch

• computing-ecqms

  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. Use when the user wants to compute an eCQM, evaluate a CMS/ECQI quality measure, improve numerator capture from c

• configuring-privacy-policies

  Select and customize OpenMed's seven bundled privacy policy profiles for de-identification, and build custom surrogate generators. Use when the user asks which policy fits HIPAA Safe Harbor vs Expert Determination vs GDPR vs PIPEDA vs a research limited dataset vs strict no-leak, wants to pass polic

• defining-cohort-phenotypes

  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 Li

• deidentify-a-dataset

  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

• deidentifying-clinical-text

  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 ha

• deidentifying-multilingual-text

  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-sp

• deploying-openmed-mcp

  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

• detecting-pv-signals

  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

• enforcing-nophi-logging

  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 t

• etl-to-omop-cdm

  Map OpenMed-extracted, terminology-coded conditions, drugs, and measurements into OMOP CDM v5.4 clinical tables (condition_occurrence, drug_exposure, 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 note

• evaluating-with-leakage-gates

  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 RELEAS

• exporting-bulk-fhir

  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 Acc

• exporting-to-fhir

  Convert OpenMed NER output (entities from openmed.analyze_text) 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, codeable_concept, system_uri), de

• extract-clinical-entities-to-fhir

  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 ter

• extracting-clinical-entities

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

• extracting-dicom-metadata

  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 an

• extracting-lab-tables

  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 f

• extracting-pii-entities

  Detect PHI/PII spans in clinical text with OpenMed's extract_pii 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

• extracting-sdoh

  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 surfacin

• fetching-fhir-resources

  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, HA

• gating-deid-leakage

  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 ga

• generating-synthea-data

  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 hel

• generating-synthetic-surrogates

  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 documen

• ingesting-clinical-documents

  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.deident

• linking-umls-concepts

  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-

• loading-openmed-models

  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 cache_d

• mapping-loinc

  Maps laboratory and clinical observation names extracted by OpenMed to LOINC codes using the public Regenstrief LOINC and FHIR terminology APIs. Use when the user wants to code lab tests, vital signs, or observations to LOINC, resolve a test name plus specimen and method to the correct LOINC part-mo

• mapping-to-snomed

  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. Use when the user wants to code findings, disorders, procedures, body structures, or substances to SNOMED

• mining-pubmed-literature

  Searches and fetches PubMed and PMC via NCBI E-utilities (ESearch then EFetch/ESummary) to gather biomedical evidence and build text corpora. Use when the user wants citations for a condition or drug, abstracts to summarize, MeSH-based searches, or a corpus of literature to run NER over. Trigger key

• normalizing-rxnorm

  Normalizes drug mentions extracted by OpenMed to RxNorm RxCUIs using the free public RxNav/RxNorm REST API. Use when the user wants to code, standardize, or de-duplicate medication names, resolve a brand/generic/ingredient to a stable RxCUI, link strength+dose-form to an SCD/SBD, attach NDCs, or bui

• parsing-ccda-documents

  Parses C-CDA / CCD XML clinical documents to extract human-readable section narrative plus coded entries, keyed by section LOINC codes and templateIds. Use before OpenMed processing when ingesting C-CDA R2.1 documents (CCD, Discharge Summary, H&P, Consultation Note) exported from an EHR and you need

• parsing-hl7v2-messages

  Decodes pipe-delimited HL7 v2.x messages (ADT, ORU, MDM, ORM) into structured segments/fields/components and surfaces OBX-5 and NTE-3 free-text narrative for OpenMed. Use before OpenMed processing when ingesting HL7 v2 feeds from an interface engine, lab/results system, or ADT stream and you need th

• parsing-lab-values

  Parse laboratory values and reference ranges from clinical text and flag results as low, normal, high, or critical with OpenMed. Use when the user needs to interpret lab results, compute abnormal flags, parse reference ranges like \"135-145\" or \"<5\", honor an originating-lab flag (H/L/critical),

• parsing-trial-eligibility

  Parses free-text clinical-trial eligibility criteria into structured inclusion and exclusion logic, then matches them against patient facts that OpenMed extracted. Use when the user wants to turn a ClinicalTrials.gov eligibility block into machine-readable rules, screen a synthetic patient for trial

• pick-a-pii-model

  Select an on-device OpenMed PII model from the committed registry by language, runtime format, and size budget, then require recall validation before deployment. Use when an agent must choose a local PII detector for CPU, Apple Silicon, or a mobile export without relying on live model discovery.

• pseudonymizing-for-gdpr

  Apply GDPR-grade pseudonymization to clinical or personal text with OpenMed, keeping a separately-held re-linkage key so the data can be controlled-re-linked later. Use when the user must process EU personal/health data under GDPR, asks for pseudonymization vs anonymization, needs Art. 4(5) / Art. 9

• querying-openfda-labels

  Looks up FDA drug labels, NDC directory entries, indications, boxed warnings, and recalls/enforcement actions via the free public OpenFDA API to enrich drugs that OpenMed extracts. Use when the user wants the prescribing information for a drug, its boxed warning, approved indications, dosage forms a

• querying-terminology-service

  Call a user-supplied FHIR terminology server ($validate-code, $expand, $lookup, $translate) to validate and expand clinical codes without bundling restricted vocabulary (SNOMED CT, RxNorm, LOINC, ICD-10) into OpenMed. Covers a thin local client, ValueSet $expand with filters/ECL, CodeSystem $lookup,

• reconciling-problem-lists

  Deduplicate and reconcile OpenMed-extracted conditions into one clean active problem list with clinical status (active / resolved / historical). Use after NER and context resolution when the user wants a problem list, condition reconciliation, dedup of synonymous diagnosis mentions, or active-vs-res

• reidentifying-text

  Reversibly de-identify clinical text with OpenMed and later restore the original PHI from a saved mapping. Use when the user needs pseudonymization rather than permanent anonymization, wants to mask PHI now and re-link it later under authorization (e.g. recontact, adjudication, GDPR pseudonymization

• reporting-adverse-events

  Structures adverse-event mentions that OpenMed extracts into FAERS / ICH E2B(R3) reportable fields — suspect drug, reaction (MedDRA PT), seriousness criteria, and outcome. Use when the user needs to build an individual case safety report (ICSR), populate a FAERS submission, map a narrative to E2B(R3

• resolving-clinical-context

  Assign negation, temporality, and uncertainty (the ConText axes) to clinical entities extracted by OpenMed, so \"denies chest pain\" is not counted as chest pain and \"history of MI\" is not counted as an active MI. Use after NER when the user needs assertion status, negation detection, family-histo

• reviewing-reidentification-risk

  Run expert-determination-style quasi-identifier risk scoring (k-anonymity, l-diversity) plus OpenMed's empirical re-identification attack on a de-identified dataset, then document residual risk in a defensible memo. Use when the user needs HIPAA Expert Determination (45 CFR 164.514(b)(1)) support, a

• running-openmed-ondevice

  Run OpenMed models fully on-device with the MLX (Apple Silicon), CoreML (iOS/macOS), or ONNX/WebGPU (cross-platform/browser) backends, including convert-quantize-run workflows. Use when the user wants to deploy OpenMed at the edge, run NER/de-id on Apple Silicon, target iPhone/iPad/Mac, export to ON

• running-zeroshot-ner

  Extract arbitrary, custom entity types from clinical or biomedical text with no fine-tuning using OpenMed's GLiNER / GLiNER2 zero-shot support. Use when the user wants to define their own labels on the fly (e.g. Drug, Symptom, Device, Procedure), has no labelled data or a label set not covered by a

• scaffolding-smart-on-fhir

  Scaffold a SMART-on-FHIR app (SMART App Launch v2 — EHR launch and standalone launch, OAuth2 PKCE, scopes, token handling, fhirContext) so an OpenMed-powered tool can run inside Epic or Cerner/Oracle Health. Covers the .well-known/smart-configuration discovery, authorize/token sequence, scopes like

• searching-clinicaltrials

  Searches ClinicalTrials.gov for studies by condition, intervention, and recruitment status using the modern v2 REST API with cursor (pageToken) pagination. Use when the user wants to find trials for a diagnosis or drug, screen patients against open studies, build a trial-matching feature, or pull a

• segmenting-clinical-sections

  Split a clinical note into canonical sections (Chief Complaint, HPI, PMH, Medications, Allergies, Assessment & Plan, etc.) before running OpenMed NER or de-identification, so section context sharpens downstream precision. Use when the user has a free-text note or discharge summary and wants section-

• serving-openmed-rest-api

  Stand up OpenMed's FastAPI REST service for clinical NER, PII extraction, and de-identification, with health checks, model keep-alive/unload, optional dynamic batching, and no-PHI logging. Use when the user wants to serve OpenMed over HTTP, deploy a de-id/NER REST API, run an inference endpoint for

• setup-openmed

  Collect a bounded set of de-identification policy decisions and write a deterministic, reviewable DEID-POLICY.md from the versioned local template. Use when a project needs explicit jurisdiction, recall floor, surrogate strategy, model policy, audit location, and human approval before privacy work b

• shifting-clinical-dates

  Apply consistent per-patient date shifting in OpenMed that preserves intervals between events while satisfying HIPAA Safe Harbor's date rule. Use when the user needs to de-identify dates but keep temporal structure for research, shift all dates by the same offset per patient, preserve days-between-e

• structuring-radiology-reports

  Converts free-text radiology narratives into structured findings and impression — with measurements, laterality, anatomy, and follow-up recommendations — after OpenMed NER. Use when the user has a CT/MRI/X-ray/ultrasound/mammography report and needs the sections split (technique, comparison, finding

• summarizing-clinical-notes

  Produces structured, citation-anchored summaries of clinical notes — one-liner, hospital course, and problem-oriented views — where every claim cites a source span so nothing is hallucinated. Use after de-identifying notes when the user wants a discharge summary draft, handoff/SBAR, problem list, or

• validating-us-core

  Validate FHIR R4 resources and Bundles against US Core / USCDI profiles with the official HL7 FHIR validator before submitting to an EHR. Covers running validator_cli.jar (or the public validator.fhir.org), declaring meta.profile, must-support elements, common conformance gaps (missing code/category