annotating-variants
Annotates VCF variants and normalizes HGVS nomenclature with public, license-free annotators…
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
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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
name: setup-openmed description: "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 begins." license: Apache-2.0 metadata: project: OpenMed category: de-identification pairs: adjacent version: "1.0"
Use this skill before a de-identification pipeline when the privacy decisions are not already recorded. It creates a small policy document; it does not inspect, transform, upload, or retain clinical data. The setup is local-first, deterministic, and has **no mandatory network call**.
The output is a draft configuration contract, not a compliance certification, legal opinion, or guarantee of de-identification. A human must review and approve the draft before it controls a run.
Use it when a project needs to turn implicit privacy choices into a reviewable `DEID-POLICY.md` file. Use the focused de-identification skills afterward to apply or audit the selected policy.
Do not use this skill to collect a note, dataset row, identifier, model output, secret, credential, or any other source payload. The setup questions accept policy choices only. Keep logs, exceptions, reports, and fixtures free of raw sensitive values.
Collect these five decisions, one at a time. Do not invent a sixth field or silently choose a value. The value written to the artifact must be the lowercase canonical value in the right-hand column.
| Decision | Bounded choices (canonical value) | | --- | --- | | Jurisdiction or operating context | `us`, `eu`, `canada`, `research`, `organization-defined` | | Recall floor | `0.90`, `0.95`, `0.99` | | Surrogate strategy | `mask`, `remove`, `replace`, `hash` | | Model policy | `local-preinstalled`, `local-user-supplied`, `rules-only` | | Audit location | `separate-local-directory`, `controlled-artifact-store`, `no-retention` |
The jurisdiction choices are context labels, not findings that a law applies. For example, `us` may be used for a US/HIPAA-context workflow and `eu` for an EU/GDPR-context workflow, but the generated document must not claim that the workflow is compliant. `research` and `organization-defined` require the project's own governance review.
The recall floor is a release target, not an observed score. Do not write a metric, benchmark result, dataset name, or model claim into this artifact. `replace` must use deterministic, synthetic surrogates when it is later implemented; any re-identification mapping remains a separately protected secret. `hash` is one-way for this policy document, but hashes can still be sensitive linkage material.
Follow this order exactly:
1. Explain that the result is a draft configuration and that human approval is required. Ask only for the five decisions in the table. 2. Normalize each answer for comparison by trimming surrounding whitespace, folding case, and treating spaces or underscores as hyphens. Match the normalized answer against the bounded choices exactly. Do not accept a free-form value, and do not infer a jurisdiction from prose. 3. If an answer is missing or invalid, stop before writing the artifact. Report only the field name and the allowed canonical choices; never echo the answer, a source value, or exception text. 4. Read the local [DEID-POLICY.template.md](assets/DEID-POLICY.template.md) and replace only its five decision placeholders:
Before substitution, require `Template version: 1.0`, `Policy schema: 1`, and exactly one occurrence of each listed placeholder with no other placeholder. If that contract differs, stop before writing and report only that the template contract is invalid. Preserve the template version, section order, checkboxes, and line endings. Do not add a timestamp, random identifier, machine path, user identity, source text, detected span, model output, or free-form rationale. 5. Resolve the user-requested project directory and require it to be an existing local directory. The output target is exactly its direct child `DEID-POLICY.md`; do not accept a different filename or derive one from an answer. Refuse a symlink or any existing non-regular target. If a regular file already exists, ask for explicit permission before replacing it; never overwrite it implicitly or write through a symlink. Render to a uniquely created sibling temporary file, flush and sync its bytes, recheck the resolved parent and target immediately before replacement, and atomically replace the target. If the target appeared after the first check and no replacement was approved, stop. Clean up the temporary file on every failure. 6. Report only that `DEID-POLICY.md` was written in the requested project directory and that review is pending. Never print the absolute or parent directory path, the collected answers, a source payload, or exception text.
The same five canonical choices and the same template version must produce byte-for-byte identical output. Do not use the current time, environment variables, network responses, or machine-specific paths in the artifact.
This setup does not download a model or call a hosted service. With `local-preinstalled`, stop and ask the project owner to install or provide the approved local model if it is absent. With `local-user-supplied`, record no secret or personal path in `DEID-POLICY.md`; the caller supplies the model outside the artifact. `rules-only` must remain deterministic and local. A later pipeline may have its own explicitly approved setup step, but it is not pa
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
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