annotating-variants
Annotates VCF variants and normalizes HGVS nomenclature with public, license-free annotators…
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
$ npx -y skills add maziyarpanahi/openmed --skill ask-openmed --agent claude-codeHow it fires
How this skill gets triggered: by you, by Claude, or both.
/ask-openmedContext preview
The summary Claude sees to decide when to auto-load this skill.
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
name: ask-openmed description: "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 clinical or personal content may be present." license: Apache-2.0 metadata: project: OpenMed category: openmed-core pairs: adjacent version: "1.0"
Use this skill as the first pass when a request does not name a focused OpenMed workflow. It selects an existing skill identifier; it does not process input, download a model, call a service, or make a clinical decision. No mandatory network call is part of this route.
Apply these rules in order:
1. Normalize only the stated goal: lowercase it, trim surrounding whitespace, and collapse repeated whitespace. Do not inspect or copy the data payload. 2. Apply the intake boundary. If the goal matches an Intake row, select the first matching intake skill even when the goal also names a later stage. If sensitivity is unclear, its next handoff is the **privacy gate**: [deidentifying-clinical-text](../deidentifying-clinical-text/SKILL.md), before extraction, exchange, or verification sees the parsed content. 3. For a goal with no intake cue, apply the privacy override. If it asks to analyze, extract, exchange, share, upload, or verify clinical or personal content and is not explicitly marked safe, start at the privacy gate. The only safe markers are `synthetic input`, `synthetic note`, `synthetic record`, `synthetic dataset`, `input is synthetic`, `data is synthetic`, `already de-identified`, and `already deidentified`. A marker does not count when `no`, `not`, `never`, `unknown`, or `uncertain` occurs in the four normalized words before it. Treat every ambiguous safety statement as sensitive. 4. Otherwise inspect the remaining tables in the fixed handoff order shown below. Treat each comma-separated cue as a case-insensitive substring of the normalized goal, and select the first matching row. Every cue cell is a comma-separated list of alternatives; conjunctions have no special meaning. Do not add synonyms or infer cues from the payload. This stage order and row order break every tie. 5. If no row matches, use [building-with-openmed](../building-with-openmed/SKILL.md) as the orientation fallback.
Route output should contain only the selected category, skill identifier, matched rule index, and next handoff. Never echo the request, input values, exception text, or detected spans into a log or report.
For a multi-stage request, route one stage at a time in this fixed handoff order: **intake → privacy → extraction → exchange → verification**. A later stage does not bypass the privacy gate merely because it was named first.
Choose the first skill for turning an external document or record format into local, processable input.
| Goal cues | First skill | Continue with | | --- | --- | --- | | laboratory table, lab table | [extracting-lab-tables](../extracting-lab-tables/SKILL.md) | privacy, then verification | | scan, fax, image, PDF, CSV, table, document OCR | [ingesting-clinical-documents](../ingesting-clinical-documents/SKILL.md) | privacy, then extraction | | C-CDA, CCD, CDA XML | [parsing-ccda-documents](../parsing-ccda-documents/SKILL.md) | privacy, then extraction | | HL7 v2, ADT, ORU, MDM, OBX, pipe-delimited feed | [parsing-hl7v2-messages](../parsing-hl7v2-messages/SKILL.md) | privacy, then extraction | | DICOM header, DICOM-SR metadata | [extracting-dicom-metadata](../extracting-dicom-metadata/SKILL.md) | privacy, then extraction | | pull FHIR records, page FHIR records, FHIR server | [fetching-fhir-resources](../fetching-fhir-resources/SKILL.md) | privacy, then extraction |
Use the privacy table both for an explicit privacy goal and for the privacy override. The first row is the default gate for unspecified sensitive input.
| Goal cues | First skill | Continue with | | --- | --- | --- | | remove clinical identifiers, mask clinical identifiers, redact clinical text, anonymize clinical text, de-identify clinical text | [deidentifying-clinical-text](../deidentifying-clinical-text/SKILL.md) | extraction or exchange | | find identifiers, detect identifiers, PII entities | [extracting-pii-entities](../extracting-pii-entities/SKILL.md) | de-identification or review | | privacy policy, privacy profile | [configuring-privacy-policies](../configuring-privacy-policies/SKILL.md) | de-identification | | PHI in logs, PHI in errors, PHI in telemetry, no-PHI logging | [enforcing-nophi-logging](../enforcing-nophi-logging/SKILL.md) | verification | | de-identify non-English text, multilingual de-identification | [deidentifying-multilingual-text](../deidentifying-multilingual-text/SKILL.md) | extraction | | stable pseudonyms, approved linkage pseudonyms | [pseudonymizing-for-gdpr](../pseudonymizing-for-gdpr/SKILL.md) | verification |
Choose the focused skill after intake and privacy handling when the request is about finding or structuring clinical meaning.
| Goal cues | First skill | Continue with | | --- | --- | --- | | diseases, drugs, anatomy, genes, clinical NER | [extracting-clinical-entities](../extracting-clinical-entities/SKILL.md) | exchange or verification | | custom entity labels, zero-shot extraction | [running-zeroshot-ner](../running-zeroshot-ner/SKILL.md) | exchange or verification | | housing, food, work, transport, SDOH | [extracting-sdoh](../extracting-sdoh/SKILL.md) | verification | | lab values, units, reference ranges, abnormal flags | [parsing-lab-values](../parsing-lab-values/SKILL.md) | terminology or exchange | | radiology findings, radiology measurements, radiology impression | [structuring-radiology-reports](../structuring-rad
Local-first healthcare AI: clinical NER and HIPAA PII de-identification on hardware you control. 2,200+ medical models, 35 model-backed PII languages, and Python, MLX, Android and browser runtimes. Apache-2.0 SDK.
Repo: maziyarpanahi/openmed
Annotates VCF variants and normalizes HGVS nomenclature with public, license-free annotators…
Package multiple FHIR R4 resources produced from OpenMed output into a single valid…
Adversarially scan already-de-identified clinical text for residual identifiers and emit a…
Produce a signed, reproducible, no-PHI audit trail for an OpenMed de-identification run via…
Generates and verifies 21 CFR Part 11-style audit trails — who/what/when, electronic…
Verify OpenMed de-identified output against all 18 HIPAA Safe Harbor identifier categories…