Agent skill

Reidentifying Text

by maziyarpanahi in maziyarpanahi/openmed

Reversibly de-identify clinical text with OpenMed and later restore the original PHI from a saved mapping.

Apache-2.0Auto-check passedLegal & Compliance

Install Reidentifying Text

skills CLI

$ npx skills add maziyarpanahi/openmed --skill reidentifying-text -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install maziyarpanahi/openmed reidentifying-text --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/reidentifying-text .claude/skills/reidentifying-text && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "reidentifying-text" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/reidentifying-text into .claude/skills/reidentifying-text/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "reidentifying-text", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/maziyarpanahi/openmed/tree/master/skills/reidentifying-text

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add maziyarpanahi/openmed --skill reidentifying-text -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install maziyarpanahi/openmed reidentifying-text --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/reidentifying-text .agents/skills/reidentifying-text && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "reidentifying-text" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/reidentifying-text into .agents/skills/reidentifying-text/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "reidentifying-text", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add maziyarpanahi/openmed --skill reidentifying-text -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install maziyarpanahi/openmed reidentifying-text --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/reidentifying-text .cursor/skills/reidentifying-text && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "reidentifying-text" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/reidentifying-text into .cursor/skills/reidentifying-text/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "reidentifying-text", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/maziyarpanahi/openmed.git --path skills/reidentifying-text

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add maziyarpanahi/openmed --skill reidentifying-text -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install maziyarpanahi/openmed reidentifying-text --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/reidentifying-text .gemini/skills/reidentifying-text && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "reidentifying-text" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/reidentifying-text into .gemini/skills/reidentifying-text/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "reidentifying-text", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install maziyarpanahi/openmed reidentifying-text

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add maziyarpanahi/openmed --skill reidentifying-text -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/reidentifying-text .github/skills/reidentifying-text && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "reidentifying-text" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/reidentifying-text into .github/skills/reidentifying-text/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "reidentifying-text", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add maziyarpanahi/openmed --skill reidentifying-text -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install maziyarpanahi/openmed reidentifying-text --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/maziyarpanahi/openmed.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/reidentifying-text .opencode/skills/reidentifying-text && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "reidentifying-text" agent skill from https://github.com/maziyarpanahi/openmed/tree/master/skills/reidentifying-text into .opencode/skills/reidentifying-text/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "reidentifying-text", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: reidentifying-text
GitHub stars: 5.5k
Token cost: ~1.8k tokens
SKILL.md length: 519 words
Files: 1
Skills in repo: 74
Repo updated: Oct 9, 2026
First seen: Oct 7, 2026
Licence: Apache-2.0

At a glance

Reversibly de-identify clinical text with OpenMed and later restore the original PHI from a saved mapping.

The user needs pseudonymization rather than permanent anonymization
SKILL.md covers When to use, Install, Quick start: reversible… and Use consistent surrogates for…, plus 5 more sections
Calls pip
Wants to mask PHI now and re-link it later under authorization (e.g

What it does

Reidentifying Text is an agent skill from maziyarpanahi/openmed. 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), asks about deidentify keepmapping, reidentify, or how to store and protect the re-identification mapping. Covers when reversibility is and is not appropriate (pseudonymization vs HIPAA Safe Harbor anonymization)…

Its SKILL.md is about 1.8k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Legal & Compliance, covering Healthcare and finance regulation and Privacy and GDPR. The repository describes itself as: 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… The licence is Apache-2.0.

When your agent uses it

The user needs pseudonymization rather than permanent anonymization
Wants to mask PHI now and re-link it later under authorization (e.g

Example prompts

“/reidentifying-text”

Requirements

Python 3

What it can do on your machine

Read from SKILL.md and the folder at commit 9dca507. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Shell commands in SKILL.md call:
- pip
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
- gdpr-info.eu
- hhs.gov
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Reidentifying Text loads about 1.8k tokens when it runs. Until then it costs about 151 tokens; SKILL.md has 519 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~151
When it runs · the whole SKILL.md, loaded when a task matches: ~1.8k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from maziyarpanahi/openmed at commit 9dca507, republished under its Apache-2.0 licence (© maziyarpanahi). 519 words, ~1,809 tokens.

Download SKILL.mdSave it as .claude/skills/reidentifying-text/SKILL.md (or your agent's skills folder).

name: reidentifying-text
description: 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), asks about deidentify keep_mapping, reidentify, or how to store and protect the re-identification mapping. Covers when reversibility is and is not appropriate (pseudonymization vs HIPAA Safe Harbor anonymization). Pairs after extracting-pii-entities and deidentifying-clinical-text.
license: Apache-2.0
metadata.project: OpenMed
metadata.category: openmed-core
metadata.pairs: adjacent
metadata.version: 1.0

Reidentifying Text

Some workflows need to remove PHI for processing but keep the ability to restore it later under authorization — adjudication, patient recontact, linking results back to a record. That is pseudonymization (reversible), not anonymization (irreversible). OpenMed supports it with deidentify(..., keep_mapping=True) to capture a mapping, and reidentify to restore. Everything runs on-device.

When to use

You need to re-link redacted output to the original record later.
You are doing GDPR pseudonymization (Art. 4(5)): identifiers held separately, reversible under controlled conditions.
A reviewer must spot-check redactions against originals.

Do NOT use reversibility when:

The goal is HIPAA Safe Harbor anonymization or a true anonymous release — a re-identification mapping defeats anonymization. Use method="remove" and keep no mapping.
The redacted text leaves your trust boundary and the mapping might travel with it. The mapping is the secret; never co-locate it with the de-identified output.

Install

bash

pip install "openmed[hf]"

Quick start: reversible round-trip

python

import openmed

note = "Patient John Doe (MRN 00481726) seen on 2024-03-02 by Dr. Alice Smith."

# 1) De-identify AND capture the reversal mapping
deid = openmed.deidentify(
    note,
    method="mask",          # or "replace" for realistic surrogates
    keep_mapping=True,       # <-- required to enable reidentify()
    policy="gdpr_pseudonymization",
)

safe_text = deid.deidentified_text       # ship/process this
mapping   = deid.mapping                  # SECRET: store separately, encrypted

# 2) Later, under authorization, restore the original
restored = openmed.reidentify(safe_text, mapping)
assert restored == note

reidentify(deidentified_text, mapping) performs the inverse substitution. The mapping is a dict[str, str] of redacted → original text, produced only when keep_mapping=True.

Use `consistent` surrogates for stable pseudonyms

For replacement that maps the same identifier to the same surrogate across a document (and reproducibly across runs with a seed):

python

import openmed

deid = openmed.deidentify(
    "Mr. John Doe called. John Doe's MRN is 00481726.",
    method="replace",
    consistent=True,    # same input value -> same surrogate within the run
    seed=42,            # reproducible across runs (implies consistent=True)
    keep_mapping=True,
)
print(deid.deidentified_text)
restored = openmed.reidentify(deid.deidentified_text, deid.mapping)

consistent=True keeps surrogates stable so analytics on the pseudonymized text stay coherent; seed makes them reproducible. Either way, reversal still requires the saved mapping.

Store the mapping securely — separate from the text

The mapping is the re-identification key. Treat it like a secret:

Never write it to the same store/file/log as the de-identified text.
Encrypt at rest; restrict access; audit every reversal.
Key the store by an opaque document id, not by any patient identifier.

python

import json, os
import openmed

note = "Patient John Doe (MRN 00481726), DOB 1970-01-15."
deid = openmed.deidentify(note, method="mask", keep_mapping=True, seed=7)

doc_id = "doc-7f3a"   # opaque id, no PHI

# De-identified text -> general processing store (safe to share downstream)
with open(f"deid/{doc_id}.txt", "w", encoding="utf-8") as fh:
    fh.write(deid.deidentified_text)

# Mapping -> SEPARATE, access-controlled, encrypted vault (illustrative path)
os.makedirs("vault", exist_ok=True)
with open(f"vault/{doc_id}.map.json", "w", encoding="utf-8") as fh:
    json.dump(deid.mapping, fh)   # encrypt this store in production

To re-identify later, load only the mapping for the authorized doc_id:

python

import json, openmed
with open("vault/doc-7f3a.map.json", encoding="utf-8") as fh:
    mapping = json.load(fh)
with open("deid/doc-7f3a.txt", encoding="utf-8") as fh:
    safe_text = fh.read()
original = openmed.reidentify(safe_text, mapping)

Reversible vs irreversible: pick deliberately

Goal	Call	Mapping
GDPR pseudonymization (reversible)	`deidentify(..., keep_mapping=True, policy="gdpr_pseudonymization")`	keep, encrypted, separate
HIPAA Safe Harbor anonymization	`deidentify(..., method="remove", policy="hipaa_safe_harbor")`	none
Irreversible token linking	`deidentify(..., method="hash")`	none (one-way)

method="hash" yields consistent, one-way tokens — good for joining records without ever restoring the original. That is not reversible and needs no mapping.

Show full SKILL.md (185 more words)Show less

Hand-off to / from OpenMed

From extracting-pii-entities: preview the spans first if you want to confirm what will be masked before committing to a reversible run.
From deidentifying-clinical-text: that skill covers methods, policies, and the safety sweep; this one adds the keep_mapping + reidentify round-trip.
To downstream NER: run openmed.analyze_text on deid.deidentified_text; re-identify only the final, authorized output — never intermediate logs.

Edge cases & gotchas

keep_mapping=True is mandatory for reidentify to work; without it deid.mapping is None.
Result field is .deidentified_text (and .pii_entities, .mapping), not .text/.entities.
Mapping direction is redacted → original. reidentify substitutes those keys back into the text.
Mask collisions: with method="mask", identical placeholders (e.g. two [NAME]) cannot be distinguished on reversal. For lossless round-trips use method="replace" with consistent=True/seed, which produces distinct, reversible surrogates.
Never anonymize-and-keep-mapping. If the release must be anonymous, keep no mapping — a stored mapping makes it pseudonymous, not anonymous.
Authorization & audit. Re-identification is privileged; log who/when/why and keep the mapping out of general PHI logs.

Standards & references

GDPR pseudonymization: Regulation (EU) 2016/679, Art. 4(5) & Recital 26 — https://gdpr-info.eu/art-4-gdpr/
HIPAA de-identification (Safe Harbor / Expert Determination): https://www.hhs.gov/hipaa/for-professionals/privacy/special-topics/de-identification/
See also OpenMed policy profiles gdpr_pseudonymization and hipaa_safe_harbor (configuring-privacy-policies).

Files

Just SKILL.md in skills/reidentifying-text of maziyarpanahi/openmed.

Open the folder on GitHubat commit 9dca507

Compare with similar skills

Reidentifying Text next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Reidentifying Text compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Reidentifying Text this skillmaziyarpanahi/openmed	5.5k	—	~1.8k	Automated safety check: Pass	Apache-2.0	yesterday
Hipaa ComplianceSushegaad/Claude-Skills-Governance-Risk-and-Compliance	946	1 repos	~2.3k	Automated safety check: Pass	MIT	yesterday
Audit Reportharness/harness-skills	115	—	~1.3k	Automated safety check: Pass	Apache-2.0	4 days ago
Anne WojcickiK-Dense-AI/mimeographs	129	—	~1.5k	Automated safety check: Pass	MIT	1 mo ago
Dpa Checklist ReviewLegalQuants/lq-ai	150	—	~3.7k	Automated safety check: Pass	Apache-2.0	yesterday
Healthcare Phi Complianceaffaan-m/ECC	276k	1 repos	~1.4k	Automated safety check: Pass	MIT	yesterday

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Questions about Reidentifying Text

What does Reidentifying Text do?

Reversibly de-identify clinical text with OpenMed and later restore the original PHI from a saved mapping. Reidentifying Text is an agent skill from maziyarpanahi/openmed. Reversibly de-identify clinical text with OpenMed and later restore the original PHI from a saved mapping.

When should I use Reidentifying Text?

Reidentifying Text fits situations like: the user needs pseudonymization rather than permanent anonymization; wants to mask PHI now and re-link it later under authorization (e.g.

How do I install Reidentifying Text in Claude Code?

Run `npx skills add maziyarpanahi/openmed --skill reidentifying-text -a claude-code`. Or copy the skill folder (skills/reidentifying-text in maziyarpanahi/openmed) into .claude/skills/reidentifying-text in your project. Claude Code loads it when a task matches its description.

How do I install Reidentifying Text in Codex?

Run `npx skills add maziyarpanahi/openmed --skill reidentifying-text -a codex`. Or copy the skill folder (skills/reidentifying-text in maziyarpanahi/openmed) into .agents/skills/reidentifying-text in your project. Codex loads it when a task matches its description.

Can I use Reidentifying Text in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add maziyarpanahi/openmed --skill reidentifying-text -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/reidentifying-text, .gemini/skills/reidentifying-text, .github/skills/reidentifying-text and .opencode/skills/reidentifying-text in your project.

What does Reidentifying Text need to run?

Going by SKILL.md and its folder, Reidentifying Text needs the command-line tools its instructions call (pip). Our summary lists: Python 3.

Does Reidentifying Text access the network?

SKILL.md names 2 domains. As links in the text: gdpr-info.eu and hhs.gov. This is read from the text; nothing was executed.

Is Reidentifying Text safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Reidentifying Text use?

Reidentifying Text is published under the Apache-2.0 licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Reidentifying Text use?

About 1.8k tokens (SKILL.md is roughly 7.2k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Reidentifying Text?

Skills that share tags, products or a category with Reidentifying Text: Hipaa Compliance (Sushegaad/Claude-Skills-Governance-Risk-and-Compliance, 946 stars), Audit Report (harness/harness-skills, 115 stars), Anne Wojcicki (K-Dense-AI/mimeographs, 129 stars) and Dpa Checklist Review (LegalQuants/lq-ai, 150 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Reidentifying Text?

maziyarpanahi (a GitHub user) maintains it in maziyarpanahi/openmed, which has 5,500 GitHub stars. The repository holds 74 skills in this directory. The repository was last updated on October 9, 2026.

Source: maziyarpanahi/openmed on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Reidentifying Text

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

Reidentifying Text

When to use

Install

Quick start: reversible round-trip

Use consistent surrogates for stable pseudonyms

Store the mapping securely — separate from the text

Reversible vs irreversible: pick deliberately

Hand-off to / from OpenMed

Edge cases & gotchas

Standards & references

Files

Compare with similar skills

Similar skills

More from maziyarpanahi/openmed

Related

Questions about Reidentifying Text

Use `consistent` surrogates for stable pseudonyms