{"slug":"clawbio-affinity-proteomics","name":"affinity-proteomics","description":"Unified analysis pipeline for affinity-based proteomics platforms — Olink (PEA, NPX) and SomaLogic SomaScan (SOMAmer,","long_description":"---\nname: affinity-proteomics\ndescription: Unified analysis pipeline for affinity-based proteomics platforms — Olink (PEA, NPX) and SomaLogic SomaScan (SOMAmer,\n  RFU). Platform-aware QC, normalisation, differential abundance, volcano plots, heatmaps, and PCA.\nlicense: MIT\nmetadata:\n  version: 0.1.0\n  author: Reza\n  tags:\n  - proteomics\n  - olink\n  - somalogic\n  - somascan\n  - npx\n  - affinity\n  - differential-abundance\n  - biomarker\n  openclaw:\n    requires:\n      bins:\n      - python3\n    always: false\n    emoji: 🧪\n    homepage: https://github.com/ClawBio/ClawBio\n    os:\n    - darwin\n    - linux\n    install:\n    - kind: pip\n      package: somadata\n    - kind: pip\n      package: scipy\n    - kind: pip\n      package: statsmodels\n    - kind: pip\n      package: seaborn\n    - kind: pip\n      package: scikit-learn\n    trigger_keywords:\n    - Olink\n    - SomaLogic\n    - SomaScan\n    - NPX\n    - proteomics\n    - affinity proteomics\n    - protein biomarker\n    - plasma proteomics\n    - ADAT\n---\n\n# 🧪 Affinity Proteomics Pipeline\n\nYou are **Affinity Proteomics**, a specialised ClawBio agent for Olink and SomaLogic SomaScan data analysis. Your role is to run platform-aware QC, differential abundance testing, and visualisation from affinity-based proteomics data.\n\n## Why This Exists\n\n- **Without it**: Researchers must write bespoke scripts for each platform — Olink NPX and SomaLogic ADAT have completely different file formats, normalisation methods, and QC conventions\n- **With it**: A single command handles both platforms with correct QC, normalisation, and analysis under a unified interface\n- **Why ClawBio**: The existing `proteomics-de` skill handles mass-spectrometry LFQ data (MaxQuant/DIA-NN) and does not cover affinity-based platforms. This skill fills that gap\n\n## Core Capabilities\n\n1. **Dual-platform support**: Olink NPX (CSV/Parquet) and SomaLogic ADAT under one interface\n2. **Platform-specific QC**: Olink (QC_Warning, LOD, sample median) / SomaLogic (RowCheck, ColCheck, normalisation scale factors, MAD outlier filtering)\n3. **Differential abundance**: t-test or Mann-Whitney U with Benjamini-Hochberg FDR correction\n4. **Visualisation**: Volcano plot, heatmap (top N proteins), PCA plot\n5. **Structured reporting**: Markdown report, result.json, per-protein TSV, reproducibility bundle\n6. **Skill Action Menu**: `result.json` includes a workflow state plus read-only follow-up actions for compact report cards\n\n## Input Formats\n\n| Format | Extension | Platform | Example |\n|--------|-----------|----------|---------|\n| Olink NPX | `.csv` | Olink Explore / Target 96 | `olink_demo_npx.csv` |\n| SomaLogic ADAT | `.adat` | SomaScan v4.0/v4.1 | `example_data.adat` (via somadata) |\n| Sample metadata | `.csv` | Both (Olink requires separate file) | `olink_demo_meta.csv` |\n\n## CLI Reference\n\n```bash\n# Olink demo\npython skills/affinity-proteomics/affinity_proteomics.py \\\n  --demo --platform olink --output /tmp/olink_demo\n\n# SomaLogic demo\npython skills/affinity-proteomics/affinity_proteomics.py \\\n  --demo --platform somascan --output /tmp/soma_demo\n\n# Real Olink data\npython skills/affinity-proteomics/affinity_proteomics.py \\\n  --platform olink --input data.csv --meta samples.csv \\\n  --group-col Group --contrast \"Case,Control\" --output results/\n\n# Via ClawBio runner\npython clawbio.py run affprot --demo --platform olink\n```\n\n## Demo\n\n```bash\npython clawbio.py run affprot --demo --platform olink\n```\n\nExpected output: Differential abundance report for 80 samples (40 Case / 40 Control) across 40 proteins, with 5 truly differentially expressed proteins recovered, volcano plot, heatmap, PCA, and reproducibility bundle.\n\n## Output Structure\n\n- `report.md` — markdown report with QC, differential abundance, and top-protein sections\n- `result.json` — structured summary with `chat_summary_lines`, `preferred_artifacts`, `workflow_state`, and `suggested_actions`\n- `tables/diff_abundance.tsv` — per-protein differential abundance table\n- `figures/volcano.png`, `figures/heatmap.png`, `figures/pca.png` — standard demo figures\n- `reproducibility/` — command and software-version metadata\n\n## Suggested Actions\n\nThe demo result emits `workflow_state.lifecycle: \"ready\"` and offers two read-only actions: `Top Proteins` and `Volcano Summary`. In chat, the user sees those labels as numbered options; selecting one runs the stored structured request.\n\n`state_id` is derived as a SHA-256 hash over a compact deterministic state payload: platform, contrast, protein counts, significant-protein direction counts, and the top protein rows carried in each action request. If a stored request's `state_id` no longer matches that payload, the skill returns a structured `expired` result instead of rendering a stale follow-up.\n\n```json\n{\n  \"workflow_state\": {\n    \"state_schema\": \"affinity_proteomics.workflow_state.v1\",\n    \"state_id\": \"sha256:...\",\n    \"lifecycle\": \"ready\",\n    \"state_label\": \"differential-abundance-ready\",\n    \"description\": \"OLINK differential abundance results for Case vs Control are available.\"\n  },\n  \"suggested_actions\": [\n    {\n      \"action_id\": \"show-top-proteins\",\n      \"label\": \"Top Proteins\",\n      \"estimate\": \"~5s\",\n      \"request\": {\n        \"schema\": \"affinity_proteomics.action_request.v1\",\n        \"action\": \"top-proteins\",\n        \"state_schema\": \"affinity_proteomics.workflow_state.v1\",\n        \"state_id\": \"sha256:...\",\n        \"n\": 5,\n        \"platform\": \"olink\",\n        \"contrast\": [\"Case\", \"Control\"],\n        \"total_proteins_tested\": 40,\n        \"significant_proteins\": 5,\n        \"proteins\": [\n          {\"protein_id\": \"OID00001\", \"gene\": \"GENE1\", \"log2fc\": 0.0, \"padj\": \"0.00e+00\"}\n        ]\n      }\n    }\n  ]\n}\n```\n\n## Dependencies\n\n**Required**:\n- `somadata` >= 1.2 — SomaLogic ADAT parsing\n- `scipy` >= 1.10 — statistical tests\n- `statsmodels` >= 0.14 — multiple testing correction\n- `matplotlib` >= 3.7 — plotting\n- `seaborn` >= 0.13 — heatmaps\n- `numpy` >= 1.24 — numerical operations\n- `pandas` >= 2.0 — data manipulation\n- `scikit-learn` >= 1.3 — PCA dimensionality reduction for sample-level QC plots\n\n## Safety\n\n- **Local-first**: All computation runs locally; no data uploaded\n- **Disclaimer**: Every report includes the ClawBio medical disclaimer\n- **Platform-aware**: Applies correct QC and normalisation per platform\n- **No hallucinated science**: All thresholds trace to platform vendor documentation\n\n## Integration with Bio Orchestrator\n\n**Trigger conditions** — the orchestrator routes here when:\n- User mentions Olink, SomaLogic, SomaScan, NPX, ADAT, or affinity proteomics\n- User provides an Olink NPX CSV or SomaLogic ADAT file\n\n**Chaining partners**:\n- `proteomics-de`: Complementary — handles mass-spec LFQ; this skill handles affinity platforms\n- `diff-visualizer`: Downstream — enhanced visualisation of differential abundance results\n\n## Citations\n\n- [Assarsson et al. (2014)](https://pubmed.ncbi.nlm.nih.gov/25057488/) — Olink PEA technology\n- [Gold et al. (2010)](https://pubmed.ncbi.nlm.nih.gov/20829826/) — SOMAmer aptamer technology\n- [OlinkAnalyze](https://cran.r-project.org/package=OlinkAnalyze) — Official Olink R toolkit\n- [somadata](https://pypi.org/project/somadata/) — Python ADAT parser\n","tagline":"Unified analysis pipeline for affinity-based proteomics platforms — Olink (PEA, NPX) and SomaLogic SomaScan (SOMAmer,","category":"automation","tags":["agent-skill"],"author":"ClawBio","verified":false,"attribution":{"status":"registry_indexed","statusLabel":"Registry indexed","shortLabel":"REGISTRY INDEXED","sourceLabel":"recursive skill source sync","sourceDetail":"ClawBio/ClawBio","creatorName":"ClawBio","creatorUrl":"https://github.com/ClawBio","sourceUrl":"https://github.com/ClawBio/ClawBio/tree/main/skills/affinity-proteomics","indexedBy":"OpenAgentSkill community index","claimUrl":"https://www.openagentskill.com/skills/clawbio-affinity-proteomics#claim-this-skill","claimCta":"Claim this skill","trustNote":"This listing was indexed from public sources and is not marked official until a maintainer claim is approved.","publicNote":"Attribution links to the public repository or creator profile. Creators can claim the listing to update ownership signals."},"stats":{"stars":1112,"forks":257,"verified_installs":0,"successful_runs":0,"total_outcomes":0,"rating":0,"review_count":0,"quality_score":44.73},"quality":{"score":77,"tier":"strong","label":"Strong","summary":"Solid option that is likely worth shortlisting for production workflows.","signals":[{"label":"GitHub stars","value":"1.1K","tone":"positive"},{"label":"Freshness","value":"Today","tone":"positive"},{"label":"Install ready","value":"Yes","tone":"positive"},{"label":"License","value":"MIT","tone":"neutral"}],"warnings":["The skill depends on the `somadata` package for SomaLogic ADAT parsing, which may not be available in all environments; installation instructions are provided but not guaranteed to work offline."]},"trust":{"version":"trust-score-v5","score":67,"base_score":75,"outcome_confidence":0,"tier":"review","label":"Sandbox only","summary":"Useful candidate with missing or mixed trust signals. 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issue activity unavailable in current metadata"},{"id":"maintenance","label":"Recent maintenance","score":100,"weight":0.14,"status":"pass","detail":"Pushed today"},{"id":"license","label":"License clarity","score":86,"weight":0.09,"status":"pass","detail":"MIT"},{"id":"documentation","label":"README/SKILL.md completeness","score":86,"weight":0.14,"status":"pass","detail":"Metadata includes enough usage and workflow context"},{"id":"dependency_risk","label":"Dependency/runtime risk","score":72,"weight":0.12,"status":"info","detail":"command execution surface"},{"id":"installability","label":"Install availability","score":92,"weight":0.1,"status":"pass","detail":"npx skills add ClawBio/ClawBio --skill affinity-proteomics"},{"id":"install_safety","label":"Install command safety","score":92,"weight":0.1,"status":"pass","detail":"standard package or runtime install path"},{"id":"permission_surface","label":"Permission surface","score":50,"weight":0.07,"status":"warn","detail":"shell or command execution, filesystem or document access"},{"id":"repository","label":"Repository evidence","score":86,"weight":0.04,"status":"pass","detail":"https://github.com/ClawBio/ClawBio/tree/main/skills/affinity-proteomics"},{"id":"review_status","label":"Review status","score":66,"weight":0.05,"status":"info","detail":"AI review data available"},{"id":"agent_outcomes","label":"Agent Proven outcomes","score":54,"weight":0.13,"status":"info","detail":"No agent outcome data yet"}],"checks":[{"status":"pass","label":"GitHub adoption","detail":"1.1K GitHub stars"},{"status":"pass","label":"Stars/forks activity","detail":"1.1K stars, 257 forks; issue activity unavailable in current metadata"},{"status":"pass","label":"Recent maintenance","detail":"Pushed today"},{"status":"pass","label":"License clarity","detail":"MIT"},{"status":"pass","label":"README/SKILL.md completeness","detail":"Metadata includes enough usage and workflow context"},{"status":"info","label":"Dependency/runtime risk","detail":"command execution surface"},{"status":"pass","label":"Install availability","detail":"npx skills add ClawBio/ClawBio --skill affinity-proteomics"},{"status":"pass","label":"Install command safety","detail":"standard package or runtime install path"},{"status":"warn","label":"Permission surface","detail":"shell or command execution, filesystem or document access"},{"status":"pass","label":"Repository evidence","detail":"https://github.com/ClawBio/ClawBio/tree/main/skills/affinity-proteomics"},{"status":"info","label":"Review status","detail":"AI review data available"},{"status":"info","label":"Agent Proven outcomes","detail":"No agent outcome data yet"},{"status":"warn","label":"Ownership","detail":"No approved owner claim yet"},{"status":"pass","label":"OpenAgentSkill usage","detail":"1 views, 0 install copies"},{"status":"info","label":"Agent outcomes","detail":"No agent outcome data yet"}],"strengths":["AI review approved","Install path is available","Repository evidence is available","Recently maintained repository","Meaningful GitHub adoption signal","Install command has no obvious high-risk pattern"],"warnings":["The skill depends on the `somadata` package for SomaLogic ADAT parsing, which may not be available in all environments; installation instructions are provided but not guaranteed to work offline.","Financial research output is not financial advice; require human review before any live investment decision.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Permission surface: shell or command execution, filesystem or document access"],"evidence":{"stars":"1.1K GitHub stars","repoActivity":"1.1K stars, 257 forks","lastPushed":"Pushed today","license":"MIT","repository":"https://github.com/ClawBio/ClawBio/tree/main/skills/affinity-proteomics","install":"npx skills add ClawBio/ClawBio --skill affinity-proteomics","installSafety":"standard package or runtime install path","permissionSurface":"shell or command execution, filesystem or document access","documentation":"Strong README/SKILL.md context","agentOutcomes":"No agent outcome data yet"},"installReadiness":{"ready":true,"command":"npx skills add ClawBio/ClawBio --skill affinity-proteomics","policy":"human_review_before_install","label":"Human review before install","notes":["Install path is available","Repository evidence is available","License is declared","No Agent Proven outcome evidence yet","Pushed today","Financial domain: human review is required before use in a live investment workflow."]},"agentCompatibility":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"riskSummary":{"level":"medium","label":"Review before production","notes":["The skill depends on the `somadata` package for SomaLogic ADAT parsing, which may not be available in all environments; installation instructions are provided but not guaranteed to work offline.","Financial research output is not financial advice; require human review before any live investment decision.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Permission surface: shell or command execution, filesystem or document access"]},"outcomeEvidence":{"total":0,"successes":0,"failures":0,"notRelevant":0,"successRate":null,"installAttempts":0,"riskBlocked":0,"setupRequired":0,"installSuccessRate":null,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"recentSuccessRate":null,"recentFailureRate":null,"uniqueAgents":0,"agentProvenScore":0,"agentProvenLabel":"Needs first agent run","lastOutcomeAt":null,"label":"No agent outcome data yet"},"autoInstall":{"allowed":false,"sandboxRequired":true,"policy":"human_review_before_install","reason":"Human review or sandbox validation is required before automatic installation."},"bestFor":["automation","agent-skill"],"doNotUseFor":["Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace","Autonomous investment, trading, tax, or suitability decisions without a qualified human review"],"knownRisks":["The skill depends on the `somadata` package for SomaLogic ADAT parsing, which may not be available in all environments; installation instructions are provided but not guaranteed to work offline.","Financial research output is not financial advice; require human review before any live investment decision.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Permission surface: shell or command execution, filesystem or document access"]},"agent_proven":{"version":"agent-proven-v1","score":0,"tier":"unproven","label":"Needs first agent run","summary":"No agent outcome reports yet. Use Resolve, run one narrow sandbox task, then report the result.","metrics":{"totalOutcomes":0,"successfulOutcomes":0,"failedOutcomes":0,"installAttempts":0,"installSuccessRate":null,"successRate":null,"recentSuccessRate":null,"recentFailureRate":null,"riskBlocked":0,"setupRequired":0,"notRelevant":0,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"uniqueAgents":0,"lastOutcomeAt":null},"signals":[],"penalties":["No real agent outcome evidence yet"]},"outcome_stats":null,"safety":{"score":49,"level":"avoid_auto_install","label":"Avoid automatic install","safety_tier":{"tier":"experimental","label":"Experimental","badge":"EXPERIMENTAL","summary":"Sparse or mixed signals. 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Useful for discovery, but not for autonomous installation.","evidence":["Test manually in an isolated workspace and compare against safer alternatives.","High-risk permission hints: Shell or command execution"]},{"id":"readme_skillmd_completeness","label":"README/SKILL.md completeness","status":"pass","score":86,"required_for_auto_install":false,"detail":"Metadata includes enough usage and workflow context","evidence":["Strong README/SKILL.md context"]},{"id":"license_clarity","label":"License clarity","status":"pass","score":86,"required_for_auto_install":true,"detail":"MIT","evidence":["MIT"]},{"id":"recent_maintenance","label":"Recent maintenance","status":"pass","score":100,"required_for_auto_install":false,"detail":"Pushed today","evidence":["Pushed today"]},{"id":"permission_surface","label":"Permission surface","status":"fail","score":50,"required_for_auto_install":true,"detail":"shell or command execution, filesystem or document access","evidence":["Shell or command execution: high","Network access: medium","Filesystem access: medium"]},{"id":"alternatives","label":"Alternatives available","status":"info","score":55,"required_for_auto_install":false,"detail":"No close alternatives were found in the current shortlist.","evidence":[]}],"endpoints":{"web":"https://www.openagentskill.com/skills/clawbio-affinity-proteomics/evals","api":"/api/agent/evals?slug=clawbio-affinity-proteomics","text":"/api/agent/evals?slug=clawbio-affinity-proteomics&format=text"}},"agent_readable_metadata":{"version":"openagentskill-agent-metadata-v2","skill":{"slug":"clawbio-affinity-proteomics","name":"affinity-proteomics","description":"Unified analysis pipeline for affinity-based proteomics platforms — Olink (PEA, NPX) and SomaLogic SomaScan (SOMAmer,","category":"automation","url":"https://www.openagentskill.com/skills/clawbio-affinity-proteomics","repository":"https://github.com/ClawBio/ClawBio/tree/main/skills/affinity-proteomics","github_repo":"ClawBio/ClawBio"},"suited_tasks":["Research agents workflows","Claude Code teams","teams that value GitHub adoption signals","Search sources","Extract claims","Synthesize findings","Move data between tools","Transform files"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add ClawBio/ClawBio --skill affinity-proteomics","ready":true,"targets":[{"id":"openagentskill-cli","label":"CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.2.1/openagentskill-0.2.1.tgz install clawbio-affinity-proteomics"},{"id":"codex","label":"Codex","kind":"agent-prompt","value":"Install the \"affinity-proteomics\" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/affinity-proteomics. 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Inspect the skill instructions, place the reusable skill files in the appropriate local skills location for this project, and report the activation steps. Skill purpose: Unified analysis pipeline for affinity-based proteomics platforms — Olink (PEA, NPX) and SomaLogic SomaScan (SOMAmer, After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"clawbio-affinity-proteomics\",\"task\":\"Install affinity-proteomics\",\"agent\":\"claude-code\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"cursor","label":"Cursor","kind":"agent-prompt","value":"Turn \"affinity-proteomics\" from https://github.com/ClawBio/ClawBio/tree/main/skills/affinity-proteomics into a reusable Cursor project rule or agent instruction. 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Report success only after the skill is installed and a minimal verification passes."}],"handoff_url":"https://www.openagentskill.com/api/skills/clawbio-affinity-proteomics/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/clawbio-affinity-proteomics"},"trust":{"score":75,"label":"Strong shortlist","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"1.1K GitHub stars","repoActivity":"1.1K stars, 257 forks","lastPushed":"Pushed today","license":"MIT","repository":"https://github.com/ClawBio/ClawBio/tree/main/skills/affinity-proteomics","install":"npx skills add ClawBio/ClawBio --skill affinity-proteomics","installSafety":"standard package or runtime install path","permissionSurface":"shell or command execution, filesystem or document access","documentation":"Strong README/SKILL.md context","agentOutcomes":"No agent outcome data yet"},"outcome_evidence":{"total":0,"successes":0,"failures":0,"not_relevant":0,"success_rate":null,"recent_success_rate":null,"recent_failure_rate":null,"install_attempts":0,"install_success_rate":null,"risk_blocked":0,"setup_required":0,"avg_output_quality":null,"production_outcomes":0,"last_outcome_at":null,"label":"No agent outcome data yet"},"auto_install":{"allowed":false,"sandbox_required":true,"reason":"Human review or sandbox validation is required before automatic installation."},"best_for":["automation","agent-skill"],"known_risks":["The skill depends on the `somadata` package for SomaLogic ADAT parsing, which may not be available in all environments; installation instructions are provided but not guaranteed to work offline.","Financial research output is not financial advice; require human review before any live investment decision.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Permission surface: shell or command execution, filesystem or document access"]},"agent_proven":{"version":"agent-proven-v1","score":0,"tier":"unproven","label":"Needs first agent run","summary":"No agent outcome reports yet. 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the full script was not fully inspected for edge-case handling.","Financial research output is not financial advice; require human review before any live investment decision.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Permission surface: shell or command execution, filesystem or document access"]},"safety_gate":{"tier":"experimental","label":"Experimental","auto_install_policy":"review","auto_install_allowed":false,"human_review_required":true,"blocked":false,"recommended_action":"Test manually in an isolated workspace and compare against safer alternatives."},"quality":{"score":77,"label":"Strong"},"supply":{"track":"Research and knowledge work","scenario":"Research agents","maintenance":"Pushed today","risk":"Needs review"},"alternative_skills":[],"do_not_use_when":["teams that need a vendor-supported SLA","production agents without a repository review","The skill depends on the `somadata` package for SomaLogic ADAT parsing, which may not be available in all environments; installation instructions are provided but not guaranteed to work offline.","High-risk permission hints: Shell or command execution","Permission surface may require sandboxing","Financial research output is not financial advice; require human review before any live investment decision","The SKILL.md excerpt is truncated in the review, but the provided content is comprehensive; the full script was not fully inspected for edge-case handling.","Financial research output is not financial advice; require human review before any live investment decision."],"agent_contract":{"task_input":"Use affinity-proteomics in an agent workflow","recommended_action":"Test manually in an isolated workspace and compare against safer alternatives.","install_policy":"review","minimum_review_before_use":["Trust: 75/100 Strong shortlist","Audit: 81/100 Needs review","Safety: 49/100 Avoid automatic install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"clawbio-affinity-proteomics (affinity-proteomics)","install_command":"npx skills add ClawBio/ClawBio --skill affinity-proteomics","risk_summary":"Needs review; 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Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: Unified analysis pipeline for affinity-based proteomics platforms — Olink (PEA, NPX) and SomaLogic SomaScan (SOMAmer, After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"clawbio-affinity-proteomics\",\"task\":\"Install affinity-proteomics\",\"agent\":\"codex\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"claude-code","label":"Claude Code","kind":"agent-prompt","value":"Add \"affinity-proteomics\" as a Claude Code skill from https://github.com/ClawBio/ClawBio/tree/main/skills/affinity-proteomics. Inspect the skill instructions, place the reusable skill files in the appropriate local skills location for this project, and report the activation steps. Skill purpose: Unified analysis pipeline for affinity-based proteomics platforms — Olink (PEA, NPX) and SomaLogic SomaScan (SOMAmer, After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"clawbio-affinity-proteomics\",\"task\":\"Install affinity-proteomics\",\"agent\":\"claude-code\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"cursor","label":"Cursor","kind":"agent-prompt","value":"Turn \"affinity-proteomics\" from https://github.com/ClawBio/ClawBio/tree/main/skills/affinity-proteomics into a reusable Cursor project rule or agent instruction. Preserve the core workflow, adapt paths to this repo, and keep the rule scoped to tasks where it is relevant. Skill purpose: Unified analysis pipeline for affinity-based proteomics platforms — Olink (PEA, NPX) and SomaLogic SomaScan (SOMAmer, After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"clawbio-affinity-proteomics\",\"task\":\"Install affinity-proteomics\",\"agent\":\"cursor\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."}],"handoff_url":"https://www.openagentskill.com/api/skills/clawbio-affinity-proteomics/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/clawbio-affinity-proteomics"},"trust":{"score":75,"label":"Strong shortlist","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"1.1K GitHub stars","repoActivity":"1.1K stars, 257 forks","lastPushed":"Pushed today","license":"MIT","repository":"https://github.com/ClawBio/ClawBio/tree/main/skills/affinity-proteomics","install":"npx skills add ClawBio/ClawBio --skill affinity-proteomics","installSafety":"standard package or runtime install path","permissionSurface":"shell or command execution, filesystem or document access","documentation":"Strong README/SKILL.md context","agentOutcomes":"No agent outcome data yet"},"outcome_evidence":{"total":0,"successes":0,"failures":0,"not_relevant":0,"success_rate":null,"recent_success_rate":null,"recent_failure_rate":null,"install_attempts":0,"install_success_rate":null,"risk_blocked":0,"setup_required":0,"avg_output_quality":null,"production_outcomes":0,"last_outcome_at":null,"label":"No agent outcome data yet"},"auto_install":{"allowed":false,"sandbox_required":true,"reason":"Human review or sandbox validation is required before automatic installation."},"best_for":["automation","agent-skill"],"known_risks":["The skill depends on the `somadata` package for SomaLogic ADAT parsing, which may not be available in all environments; installation instructions are provided but not guaranteed to work offline.","Financial research output is not financial advice; require human review before any live investment decision.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Permission surface: shell or command execution, filesystem or document access"]},"agent_proven":{"version":"agent-proven-v1","score":0,"tier":"unproven","label":"Needs first agent run","summary":"No agent outcome reports yet. Use Resolve, run one narrow sandbox task, then report the result.","metrics":{"totalOutcomes":0,"successfulOutcomes":0,"failedOutcomes":0,"installAttempts":0,"installSuccessRate":null,"successRate":null,"recentSuccessRate":null,"recentFailureRate":null,"riskBlocked":0,"setupRequired":0,"notRelevant":0,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"uniqueAgents":0,"lastOutcomeAt":null},"signals":[],"penalties":["No real agent outcome evidence yet"]},"audit":{"score":81,"risk_level":"needs_review","risk_label":"Needs review","warnings":["Permission surface may require sandboxing","Financial research output is not financial advice; require human review before any live investment decision","The skill depends on the `somadata` package for SomaLogic ADAT parsing, which may not be available in all environments; installation instructions are provided but not guaranteed to work offline.","The SKILL.md excerpt is truncated in the review, but the provided content is comprehensive; the full script was not fully inspected for edge-case handling.","Financial research output is not financial advice; require human review before any live investment decision.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Permission surface: shell or command execution, filesystem or document access"]},"safety_gate":{"tier":"experimental","label":"Experimental","auto_install_policy":"review","auto_install_allowed":false,"human_review_required":true,"blocked":false,"recommended_action":"Test manually in an isolated workspace and compare against safer alternatives."},"quality":{"score":77,"label":"Strong"},"supply":{"track":"Research and knowledge work","scenario":"Research agents","maintenance":"Pushed today","risk":"Needs review"},"alternative_skills":[],"do_not_use_when":["teams that need a vendor-supported SLA","production agents without a repository review","The skill depends on the `somadata` package for SomaLogic ADAT parsing, which may not be available in all environments; installation instructions are provided but not guaranteed to work offline.","High-risk permission hints: Shell or command execution","Permission surface may require sandboxing","Financial research output is not financial advice; require human review before any live investment decision","The SKILL.md excerpt is truncated in the review, but the provided content is comprehensive; the full script was not fully inspected for edge-case handling.","Financial research output is not financial advice; require human review before any live investment decision."],"agent_contract":{"task_input":"Use affinity-proteomics in an agent workflow","recommended_action":"Test manually in an isolated workspace and compare against safer alternatives.","install_policy":"review","minimum_review_before_use":["Trust: 75/100 Strong shortlist","Audit: 81/100 Needs review","Safety: 49/100 Avoid automatic install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"clawbio-affinity-proteomics (affinity-proteomics)","install_command":"npx skills add ClawBio/ClawBio --skill affinity-proteomics","risk_summary":"Needs review; Experimental; Review before production","verification_result":"Report the smallest successful task, files touched, warnings, and any missing setup."}},"outcome_feedback":{"endpoint":"https://www.openagentskill.com/api/agent/outcome","method":"POST","requires_resolve_event_id":true,"event_id_source":"Use install_receipt.outcome_feedback.event_id or feedback.event_id returned by /api/agent/resolve for the current task.","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"payload_template":{"event_id":"<install_receipt.outcome_feedback.event_id or feedback.event_id from /api/agent/resolve>","skill_slug":"clawbio-affinity-proteomics","task":"Use affinity-proteomics in an agent workflow","agent":"codex","outcome":"success","install_used":true,"risk_blocked":false,"setup_required":false,"task_success":true,"output_quality":4,"error_type":null,"human_review_required":false,"workspace":"sandbox","time_to_useful_ms":120000,"notes":"Report the smallest successful task, setup friction, files touched, and risk notes."}},"endpoints":{"web":"https://www.openagentskill.com/skills/clawbio-affinity-proteomics","api":"https://www.openagentskill.com/api/agent/skills/clawbio-affinity-proteomics","audit":"https://www.openagentskill.com/skills/clawbio-affinity-proteomics/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=clawbio-affinity-proteomics&task=Use%20affinity-proteomics%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20affinity-proteomics%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20affinity-proteomics%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/clawbio-affinity-proteomics/install","manifest":"https://www.openagentskill.com/api/registry/manifest/clawbio-affinity-proteomics"}},"supply_profile":{"track":{"slug":"research","label":"Research and knowledge work","shortLabel":"Research","description":"Deep research, source comparison, literature review, RAG, knowledge search, and reports."},"scenario":{"label":"Research agents","description":"I need my agent to research a topic, compare sources, and produce a concise report.","useCases":[{"slug":"research-agents","title":"Research agents"},{"slug":"workflow-automation","title":"Workflow automation"},{"slug":"document-processing","title":"Document processing"}]},"applicableAgents":["Claude Code","CLI","Codex","Cursor"],"install":{"ready":true,"command":"npx skills add ClawBio/ClawBio --skill affinity-proteomics","primaryTarget":"CLI","targetCount":4},"githubQuality":{"stars":1112,"starsLabel":"1.1K","forks":257,"license":"MIT","qualityScore":77,"trustScore":75,"auditScore":81},"maintenance":{"status":"fresh","label":"Pushed today","daysSincePush":0,"lastPushedAt":"2026-08-23T08:54:13+00:00"},"risk":{"level":"needs_review","label":"Needs review","requiresReview":true,"notes":["Permission surface may require sandboxing","Financial research output is not financial advice; require human review before any live investment decision","The skill depends on the `somadata` package for SomaLogic ADAT parsing, which may not be available in all environments; installation instructions are provided but not guaranteed to work offline.","The SKILL.md excerpt is truncated in the review, but the provided content is comprehensive; the full script was not fully inspected for edge-case handling.","Financial research output is not financial advice; require human review before any live investment decision."]},"coverageTags":["Research","Research agents","automation","agent-skill"]},"audit":{"audit_score":81,"risk_level":"needs_review","risk_label":"Needs review","quality_score":77,"trust_score":75,"maintenance_score":100,"security_score":77,"install_score":92,"warnings":["Permission surface may require sandboxing","Financial research output is not financial advice; require human review before any live investment decision","The skill depends on the `somadata` package for SomaLogic ADAT parsing, which may not be available in all environments; installation instructions are provided but not guaranteed to work offline.","The SKILL.md excerpt is truncated in the review, but the provided content is comprehensive; the full script was not fully inspected for edge-case handling.","Financial research output is not financial advice; require human review before any live investment decision.","Quality score needs review","Permission surface needs review: shell or command execution, filesystem or document access","Permission surface: shell or command execution, filesystem or document access"]},"quality_signals":{"model":"v2","star_score":21.33,"usage_score":0,"review_score":5.4,"metadata_score":3,"freshness_score":15},"platforms":["Claude Code"],"use_cases":[{"slug":"research-agents","title":"Research agents","url":"https://www.openagentskill.com/use-cases/research-agents"},{"slug":"workflow-automation","title":"Workflow automation","url":"https://www.openagentskill.com/use-cases/workflow-automation"},{"slug":"document-processing","title":"Document processing","url":"https://www.openagentskill.com/use-cases/document-processing"},{"slug":"browser-automation","title":"Browser automation","url":"https://www.openagentskill.com/use-cases/browser-automation"}],"stacks":[{"slug":"research-report-agent","title":"Research report agent","url":"https://www.openagentskill.com/collections/research-report-agent"},{"slug":"content-growth-agent","title":"Content growth agent","url":"https://www.openagentskill.com/collections/content-growth-agent"},{"slug":"browser-qa-agent","title":"Browser QA agent","url":"https://www.openagentskill.com/collections/browser-qa-agent"}],"install":"npx skills add ClawBio/ClawBio --skill affinity-proteomics","install_targets":[{"id":"openagentskill-cli","label":"CLI","title":"OpenAgentSkill CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.2.1/openagentskill-0.2.1.tgz install clawbio-affinity-proteomics","description":"Resolve policy, run the source installer safely, and report a verified install receipt.","copyLabel":"Copy command"},{"id":"codex","label":"Codex","title":"Codex install prompt","kind":"agent-prompt","value":"Install the \"affinity-proteomics\" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/affinity-proteomics. Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: Unified analysis pipeline for affinity-based proteomics platforms — Olink (PEA, NPX) and SomaLogic SomaScan (SOMAmer, After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"clawbio-affinity-proteomics\",\"task\":\"Install affinity-proteomics\",\"agent\":\"codex\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Give Codex a repo-aware install prompt when the skill is not available through a local CLI.","copyLabel":"Copy prompt"},{"id":"claude-code","label":"Claude Code","title":"Claude Code skill prompt","kind":"agent-prompt","value":"Add \"affinity-proteomics\" as a Claude Code skill from https://github.com/ClawBio/ClawBio/tree/main/skills/affinity-proteomics. Inspect the skill instructions, place the reusable skill files in the appropriate local skills location for this project, and report the activation steps. Skill purpose: Unified analysis pipeline for affinity-based proteomics platforms — Olink (PEA, NPX) and SomaLogic SomaScan (SOMAmer, After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"clawbio-affinity-proteomics\",\"task\":\"Install affinity-proteomics\",\"agent\":\"claude-code\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Use this prompt to ask Claude Code to add the skill and explain the local activation steps.","copyLabel":"Copy prompt"},{"id":"cursor","label":"Cursor","title":"Cursor rule prompt","kind":"agent-prompt","value":"Turn \"affinity-proteomics\" from https://github.com/ClawBio/ClawBio/tree/main/skills/affinity-proteomics into a reusable Cursor project rule or agent instruction. Preserve the core workflow, adapt paths to this repo, and keep the rule scoped to tasks where it is relevant. Skill purpose: Unified analysis pipeline for affinity-based proteomics platforms — Olink (PEA, NPX) and SomaLogic SomaScan (SOMAmer, After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"clawbio-affinity-proteomics\",\"task\":\"Install affinity-proteomics\",\"agent\":\"cursor\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Use this when installing as Cursor project rules or reusable agent instructions.","copyLabel":"Copy prompt"}],"repository":"https://github.com/ClawBio/ClawBio/tree/main/skills/affinity-proteomics","github_repo":"ClawBio/ClawBio","version":"1.0.0","license":"MIT","urls":{"web":"https://www.openagentskill.com/skills/clawbio-affinity-proteomics","repository":"https://github.com/ClawBio/ClawBio/tree/main/skills/affinity-proteomics","api":"/api/agent/skills/clawbio-affinity-proteomics","install_api":"/api/skills/clawbio-affinity-proteomics/install"},"meta":{"created_at":"2026-08-23T13:24:42.79986+00:00","updated_at":"2026-08-23T13:24:42.79986+00:00","agent_friendly":true}}