maziyarpanahi

maziyarpanahi/openmed

Plugin Claude Code

Plugin marketplace listing 1 plugin: openmed-skills.

maziyarpanahi/openmed

Instructions file CodexOpenCode

Instructions for maziyarpanahi/openmed, covering repository guidelines, project structure & module organization, build, test, and development commands, linting and formatting and coding style & architecture rules.

maziyarpanahi/openmed

Skill Claude CodeCodex

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 to genomic…

maziyarpanahi/openmed

Skill Claude CodeCodex

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 work when raw…

maziyarpanahi/openmed

Skill Claude CodeCodex

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.tobundle. Covers deterministic urn:uuid fullUrls, automatic in-Bundle reference rewriting, request blocks…

maziyarpanahi/openmed

Skill Claude CodeCodex

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 detector. Covers format…

maziyarpanahi/openmed

Skill Claude CodeCodex

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-id decisions…

maziyarpanahi/openmed

Skill Claude CodeCodex

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-evident record of…

maziyarpanahi/openmed

Skill Claude CodeCodex

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, wants to flag gaps like…

maziyarpanahi/openmed

Skill Claude CodeCodex

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. Use when the user wants per-subgroup recall and leakage, wants to check whether de-identification under-protects a group, wants to…

maziyarpanahi/openmed

Skill Claude CodeCodex

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, or governance…

maziyarpanahi/openmed

Skill Claude CodeCodex

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 documents, build a…

maziyarpanahi/openmed

Skill Claude CodeCodex

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.

maziyarpanahi/openmed

Skill Claude CodeCodex

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-negative /…

maziyarpanahi/openmed

Skill Claude CodeCodex

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 (availableadapters, getadapter, adapterspec), the presidio/spacy/langchain pip extras, and the verified callables — Presidio…

maziyarpanahi/openmed

Skill Claude CodeCodex

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, write guidelines…

maziyarpanahi/openmed

Skill Claude CodeCodex

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, or turn…

maziyarpanahi/openmed

Skill Claude CodeCodex

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 starting to build a…

maziyarpanahi/openmed

Skill Claude CodeCodex

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 safeguards apply, is…

maziyarpanahi/openmed

Skill Claude CodeCodex

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, or inspect a…

maziyarpanahi/openmed

Skill Claude CodeCodex

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 patient/panel RAF, find…

maziyarpanahi/openmed

Skill Claude CodeCodex

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 chapter, cross-walk…

maziyarpanahi/openmed

Skill Claude CodeCodex

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 clinical notes…

maziyarpanahi/openmed

Skill Claude CodeCodex

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 policy= to deidentify()…