# Send Phenosnap Phenotype Extractor to your agent Hand the extracted package to your coding agent with a concrete install brief instead of figuring it out manually. ## Fast path - Download the package from Yavira. - Extract it into a folder your agent can access. - Paste one of the prompts below and point your agent at the extracted folder. ## Suggested prompts ### New install ```text I downloaded a skill package from Yavira. Read SKILL.md from the extracted folder and install it by following the included instructions. Then review README.md for any prerequisites, environment setup, or post-install checks. Tell me what you changed and call out any manual steps you could not complete. ``` ### Upgrade existing ```text I downloaded an updated skill package from Yavira. Read SKILL.md from the extracted folder, compare it with my current installation, and upgrade it while preserving any custom configuration unless the package docs explicitly say otherwise. Then review README.md for any prerequisites, environment setup, or post-install checks. Summarize what changed and any follow-up checks I should run. ``` ## Machine-readable fields ```json { "schemaVersion": "1.0", "item": { "slug": "phenoskill", "name": "Phenosnap Phenotype Extractor", "source": "tencent", "type": "skill", "category": "开发工具", "sourceUrl": "https://clawhub.ai/kaichop/phenoskill", "canonicalUrl": "https://clawhub.ai/kaichop/phenoskill", "targetPlatform": "OpenClaw" }, "install": { "downloadUrl": "/downloads/phenoskill", "sourceDownloadUrl": "https://wry-manatee-359.convex.site/api/v1/download?slug=phenoskill", "sourcePlatform": "tencent", "targetPlatform": "OpenClaw", "packageFormat": "ZIP package", "primaryDoc": "SKILL.md", "includedAssets": [ "CHANGELOG.md", "README.md", "SKILL.md" ], "downloadMode": "redirect", "sourceHealth": { "source": "tencent", "slug": "phenoskill", "status": "healthy", "reason": "direct_download_ok", "recommendedAction": "download", "checkedAt": "2026-05-07T01:46:21.484Z", "expiresAt": "2026-05-14T01:46:21.484Z", "httpStatus": 200, "finalUrl": "https://wry-manatee-359.convex.site/api/v1/download?slug=phenoskill", "contentType": "application/zip", "probeMethod": "head", "details": { "probeUrl": "https://wry-manatee-359.convex.site/api/v1/download?slug=phenoskill", "contentDisposition": "attachment; filename=\"phenoskill-0.1.1.zip\"", "redirectLocation": null, "bodySnippet": null, "slug": "phenoskill" }, "scope": "item", "summary": "Item download looks usable.", "detail": "Yavira can redirect you to the upstream package for this item.", "primaryActionLabel": "Download for OpenClaw", "primaryActionHref": "/downloads/phenoskill" }, "validation": { "installChecklist": [ "Use the Yavira download entry.", "Review SKILL.md after the package is downloaded.", "Confirm the extracted package contains the expected setup assets." ], "postInstallChecks": [ "Confirm the extracted package includes the expected docs or setup files.", "Validate the skill or prompts are available in your target agent workspace.", "Capture any manual follow-up steps the agent could not complete." ] } }, "links": { "detailUrl": "https://openagent3.xyz/skills/phenoskill", "downloadUrl": "https://openagent3.xyz/downloads/phenoskill", "agentUrl": "https://openagent3.xyz/skills/phenoskill/agent", "manifestUrl": "https://openagent3.xyz/skills/phenoskill/agent.json", "briefUrl": "https://openagent3.xyz/skills/phenoskill/agent.md" } } ``` ## Documentation ### When to use Use this skill when the user provides their own: clinical phenotypes / symptoms / diagnoses (free text, bullet lists, clinical note-like text), and/or drugs/medications (names, dosages, frequencies). Examples that should trigger: “Symptoms: ataxia, seizures, developmental delay. Meds: levetiracetam 500 mg BID.” “I’m taking metformin 500mg daily and have fatigue, polyuria, blurry vision.” ### When NOT to use Do not use this skill when: The user asks general questions (e.g., “What is HPO?”, “What is a phenotype?”, “What is GLP-1?”). The user provides text that is not personal clinical information (news articles, academic paragraphs, code, etc.). The user asks you to interpret someone else’s private clinical record (PHI) without clear permission. ### Safety & privacy Treat user input as potentially sensitive clinical information. Do not upload user text or extracted results anywhere (this skill is local-only). Before writing any input to disk, redact obvious identifiers: emails, phone numbers, street addresses MRN-like long numeric identifiers (e.g., 8+ digits) names when clearly presented as “Name: …” If the message appears to include highly identifying PHI (e.g., name + DOB + address, or name + MRN), pause and ask for confirmation to proceed, recommending the user remove identifiers first. ### Requirements / setup Python: python3 available on PATH. Network access (only for initial PhenoSnap download if missing). HPO OBO file: Default expected path: {baseDir}/resources/hp.obo Override path via environment variable: HPO_OBO_PATH This skill does not auto-download hp.obo. You must supply it. Recommended (best practice): Use a virtual environment (venv/conda) before running this skill, because it may install Python packages via pip. ### Inputs & outputs Input text file (redacted): {baseDir}/artifacts/phenosnap_inputs/input_.txt Output JSON file (timestamped): {baseDir}/artifacts/phenosnap_outputs/phenotypes_.json Third-party download cache: {baseDir}/third_party/phenosnap_main.zip {baseDir}/third_party/get-pip.py ### Detection heuristic (activation check) Trigger if the user message contains any of: phenotype cues: symptom(s), phenotype(s), Dx, diagnosis, PMH, Hx, history of, or a symptom-like list medication cues: meds, medications, taking, prescribed, plus patterns like: dosages: \\b\\d+(\\.\\d+)?\\s?(mg|mcg|g|ml|units)\\b frequencies: qd, q.d., bid, b.i.d., tid, t.i.d., qhs, qAM, qPM, daily, weekly Do not trigger for purely informational questions without user-provided phenotype/medication content. ### 0) Create required directories Create if missing: {baseDir}/PhenoSnap/ {baseDir}/artifacts/phenosnap_inputs/ {baseDir}/artifacts/phenosnap_outputs/ {baseDir}/resources/ {baseDir}/third_party/ ### 1) Confirm / redact sensitive identifiers Scan the user message for identifiers (email/phone/address/MRN/name fields). If strongly identifying PHI is present (name + DOB/address/MRN): Ask the user to confirm proceeding and recommend removing identifiers. Produce a redacted version of the user text: Replace emails with [REDACTED_EMAIL] Replace phone numbers with [REDACTED_PHONE] Replace long numeric IDs with [REDACTED_ID] Replace address-like patterns with [REDACTED_ADDRESS] Replace explicit “Name: …” fields with Name: [REDACTED_NAME] ### 2) Ensure PhenoSnap exists locally Target location: {baseDir}/PhenoSnap/ ### 2A) If {baseDir}/PhenoSnap/ exists and contains extract_phenotypes.py Proceed to dependency self-test. ### 2B) If {baseDir}/PhenoSnap/ does NOT exist (or missing extract_phenotypes.py) Prefer git; fallback to zip. If git is available Run: git clone https://github.com/WGLab/PhenoSnap.git "{baseDir}/PhenoSnap" If git is NOT available Download zip: URL: https://github.com/WGLab/PhenoSnap/archive/refs/heads/main.zip Destination: {baseDir}/third_party/phenosnap_main.zip Download method (pick first available): If curl exists: curl -L "https://github.com/WGLab/PhenoSnap/archive/refs/heads/main.zip" -o "{baseDir}/third_party/phenosnap_main.zip" Else on Windows PowerShell: Invoke-WebRequest -Uri "https://github.com/WGLab/PhenoSnap/archive/refs/heads/main.zip" -OutFile "{baseDir}/third_party/phenosnap_main.zip" Unzip (choose by OS/tools): Windows PowerShell: Expand-Archive -Path "{baseDir}/third_party/phenosnap_main.zip" -DestinationPath "{baseDir}/third_party/phenosnap_unzip" -Force macOS/Linux with unzip: unzip -o "{baseDir}/third_party/phenosnap_main.zip" -d "{baseDir}/third_party/phenosnap_unzip" If neither unzip nor Expand-Archive is available, use Python: python3 -c "import zipfile; z=zipfile.ZipFile(r'{baseDir}/third_party/phenosnap_main.zip'); z.extractall(r'{baseDir}/third_party/phenosnap_unzip')" Then rename/move the extracted folder to {baseDir}/PhenoSnap/: The extracted folder is typically {baseDir}/third_party/phenosnap_unzip/PhenoSnap-main Move/rename to {baseDir}/PhenoSnap/ Final check: Verify {baseDir}/PhenoSnap/extract_phenotypes.py exists. If not found, stop and report the directory listing of {baseDir}/PhenoSnap/ and {baseDir}/third_party/phenosnap_unzip/. ### 3) Dependency self-test and auto-install Run from inside {baseDir}/PhenoSnap/. ### 3A) Smoke test importability Run: python3 -c "import importlib.util; spec=importlib.util.spec_from_file_location('extract_phenotypes','extract_phenotypes.py'); m=importlib.util.module_from_spec(spec); spec.loader.exec_module(m); print('ok')" If it prints ok, proceed. ### 3B) If smoke test fails with missing module (ModuleNotFoundError / ImportError) Step 1: Ensure pip exists for python3 Check: python3 -m pip --version If that fails, try: python3 -m ensurepip --upgrade Check again: python3 -m pip --version If still failing, bootstrap pip via get-pip.py: Download https://bootstrap.pypa.io/get-pip.py to {baseDir}/third_party/get-pip.py with curl: curl -L "https://bootstrap.pypa.io/get-pip.py" -o "{baseDir}/third_party/get-pip.py" or PowerShell: Invoke-WebRequest -Uri "https://bootstrap.pypa.io/get-pip.py" -OutFile "{baseDir}/third_party/get-pip.py" Install: python3 "{baseDir}/third_party/get-pip.py" Verify: python3 -m pip --version If pip still cannot be used, stop and report the error output. Step 2: Install PhenoSnap dependencies From {baseDir}/PhenoSnap/, run: python3 -m pip install -r requirements.txt Step 3: Re-run smoke test once Re-run: python3 -c "import importlib.util; spec=importlib.util.spec_from_file_location('extract_phenotypes','extract_phenotypes.py'); m=importlib.util.module_from_spec(spec); spec.loader.exec_module(m); print('ok')" If still failing, stop and return: the missing module name (from error) the command output recommended fix (use a venv/conda env; verify python3/pip; rerun pip install) ### 4) Prepare HPO OBO path Resolve HPO OBO path in this order: If env var HPO_OBO_PATH is set and file exists, use that. Else use {baseDir}/resources/hp.obo if it exists. If the resolved file does not exist: Stop and tell the user to place hp.obo at {baseDir}/resources/hp.obo or set HPO_OBO_PATH to its full path. ### 5) Write input file (redacted) Timestamp format: YYYYMMDD_HHMMSS (local time). Write redacted user text to: {baseDir}/artifacts/phenosnap_inputs/input_.txt ### 6) Run extraction From {baseDir}/PhenoSnap/, run: python3 extract_phenotypes.py --input-file "{baseDir}/artifacts/phenosnap_inputs/input_.txt" --hpo-obo "" --output "{baseDir}/artifacts/phenosnap_outputs/phenotypes_.json" --format json Validate: Output file exists Output file is non-empty If validation fails: Return stderr/stdout Provide troubleshooting steps (missing hp.obo, permission issues, dependency issues) ### 7) Respond to user Return a concise confirmation: Detected content: “phenotypes” and/or “medications” Input file path (redacted) Output file path (timestamped JSON) Note: no data uploaded; local-only Any warnings (e.g., missing hp.obo, PHI redaction/confirmation) ### Troubleshooting PhenoSnap folder exists but script missing: confirm {baseDir}/PhenoSnap/extract_phenotypes.py exists. No git: zip fallback should run; ensure curl/PowerShell is available for download. Unzip fails: use Python zipfile fallback. pip missing: ensurepip then get-pip.py steps above; consider installing Python with “pip” included. Permission errors installing packages: use a virtual environment: python3 -m venv .venv then activate and rerun skill. hp.obo missing: place file at {baseDir}/resources/hp.obo or set HPO_OBO_PATH. ### Example 1 (phenotypes + meds) User: “Symptoms: developmental delay, seizures, ataxia. Meds: valproate 250 mg BID.” Action: Write redacted input → run PhenoSnap → output phenotypes_.json ### Example 2 (meds only) User: “Current meds: metformin 500mg daily, atorvastatin 20 mg qhs.” Action: Extract medication entities/phenotype-related terms supported by PhenoSnap → output JSON ### Example 3 (should NOT trigger) User: “What is the Human Phenotype Ontology and how is it used?” Action: Do not run extraction; answer informationally outside this skill. ## Trust - Source: tencent - Verification: Indexed source record - Publisher: kaichop - Version: 0.1.1 ## Source health - Status: healthy - Item download looks usable. - Yavira can redirect you to the upstream package for this item. - Health scope: item - Reason: direct_download_ok - Checked at: 2026-05-07T01:46:21.484Z - Expires at: 2026-05-14T01:46:21.484Z - Recommended action: Download for OpenClaw ## Links - [Detail page](https://openagent3.xyz/skills/phenoskill) - [Send to Agent page](https://openagent3.xyz/skills/phenoskill/agent) - [JSON manifest](https://openagent3.xyz/skills/phenoskill/agent.json) - [Markdown brief](https://openagent3.xyz/skills/phenoskill/agent.md) - [Download page](https://openagent3.xyz/downloads/phenoskill)