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SkillsMP a collecté 74 skills depuis maziyarpanahi/openmed. Ouvrez un skill pour examiner sa source et ses détails.
Affichage de 40 skills collectés sur 74.
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,…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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,…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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,…
Langue du texte source : anglais
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,…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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…
Langue du texte source : anglais
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,…
Langue du texte source : anglais
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…
Langue du texte source : anglais