{"slug":"k-dense-ai-bioservices","name":"bioservices","description":"Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.","long_description":"---\nname: bioservices\ndescription: Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.\nlicense: GPLv3 license\nallowed-tools: Read Write Edit Bash\ncompatibility: Requires Python 3.9–3.12 and internet access to 40+ bioinformatics web APIs. NCBI BLAST requires a contact email (`NCBI_EMAIL` env var or explicit parameter).\nmetadata:\n version: \"1.3\"\n skill-author: K-Dense Inc.\n openclaw:\n envVars:\n - name: NCBI_EMAIL\n required: false\n description: Email for NCBI service identification.\n---\n\n# BioServices\n\n## Overview\n\nBioServices is a Python package providing programmatic access to approximately 40 bioinformatics web services and databases. Retrieve biological data, perform cross-database queries, map identifiers, analyze sequences, and integrate multiple biological resources in Python workflows. The package handles both REST and SOAP/WSDL protocols transparently.\n\n**Version note:** Examples target **bioservices 1.16.0** (PyPI, Mar 2026). Requires **Python 3.9–3.12**. UniProt REST changes in mid-2022 (bioservices ≥1.10) mainly affect tabular `columns` names — see upstream `_legacy_names` if parsing breaks. ChEMBL wrappers changed at 1.6.0 (2018 API); use `get_similarity`, `get_substructure`, `get_molecule` instead of pre-1.6 method names.\n\n## When to Use This Skill\n\nThis skill should be used when:\n- Retrieving protein sequences, annotations, or structures from UniProt, PDB, Pfam\n- Analyzing metabolic pathways and gene functions via KEGG or Reactome\n- Searching compound databases (ChEBI, ChEMBL, PubChem) for chemical information\n- Converting identifiers between different biological databases (KEGG↔UniProt, compound IDs)\n- Running sequence similarity searches (BLAST, MUSCLE alignment)\n- Querying gene ontology terms (QuickGO, GO annotations)\n- Accessing protein-protein interaction data (PSICQUIC, IntactComplex)\n- Mining genomic data (BioMart, ArrayExpress, ENA)\n- Integrating data from multiple bioinformatics resources in a single workflow\n\n## Core Capabilities\n\n### 1. Protein Analysis\n\nRetrieve protein information, sequences, and functional annotations:\n\n```python\nfrom bioservices import UniProt\n\nu = UniProt(verbose=False)\n\n# Search for protein by name\nresults = u.search(\"ZAP70_HUMAN\", frmt=\"tab\", columns=\"id,genes,organism\")\n\n# Retrieve FASTA sequence\nsequence = u.retrieve(\"P43403\", \"fasta\")\n\n# Map identifiers between databases\nkegg_ids = u.mapping(fr=\"UniProtKB_AC-ID\", to=\"KEGG\", query=\"P43403\")\n```\n\n**Key methods:**\n- `search()`: Query UniProt with flexible search terms\n- `retrieve()`: Get protein entries in various formats (FASTA, XML, tab)\n- `mapping()`: Convert identifiers between databases\n\nReference: `references/services_reference.md` for complete UniProt API details.\n\n### 2. Pathway Discovery and Analysis\n\nAccess KEGG pathway information for genes and organisms:\n\n```python\nfrom bioservices import KEGG\n\nk = KEGG()\nk.organism = \"hsa\" # Set to human\n\n# Search for organisms\nk.lookfor_organism(\"droso\") # Find Drosophila species\n\n# Find pathways by name\nk.lookfor_pathway(\"B cell\") # Returns matching pathway IDs\n\n# Get pathways containing specific genes\npathways = k.get_pathway_by_gene(\"7535\", \"hsa\") # ZAP70 gene\n\n# Retrieve and parse pathway data\ndata = k.get(\"hsa04660\")\nparsed = k.parse(data)\n\n# Extract pathway interactions\ninteractions = k.parse_kgml_pathway(\"hsa04660\")\nrelations = interactions['relations'] # Protein-protein interactions\n\n# Convert to Simple Interaction Format\nsif_data = k.pathway2sif(\"hsa04660\")\n```\n\n**Key methods:**\n- `lookfor_organism()`, `lookfor_pathway()`: Search by name\n- `get_pathway_by_gene()`: Find pathways containing genes\n- `parse_kgml_pathway()`: Extract structured pathway data\n- `pathway2sif()`: Get protein interaction networks\n\nReference: `references/workflow_patterns.md` for complete pathway analysis workflows.\n\n### 3. Compound Database Searches\n\nSearch and cross-reference compounds across multiple databases:\n\n```python\nfrom bioservices import KEGG, UniChem\n\nk = KEGG()\n\n# Search compounds by name\nresults = k.find(\"compound\", \"Geldanamycin\") # Returns cpd:C11222\n\n# Get compound information with database links\ncompound_info = k.get(\"cpd:C11222\") # Includes ChEBI links\n\n# Cross-reference KEGG → ChEMBL using UniChem\nu = UniChem()\nchembl_id = u.get_compound_id_from_kegg(\"C11222\") # Returns CHEMBL278315\n```\n\n**Version caveat:** the per-source `get_compound_id_from_*` helpers are gone from\nbioservices 1.16.0 — check `hasattr(u, \"get_compound_id_from_kegg\")` first, and\notherwise use the current UniChem API (`u.get_compounds(compound, source_type)`\nand read `res[\"compounds\"][0][\"sources\"]`). ChEMBL lookups follow the same rule:\n`get_molecule`, not the pre-1.6 `get_compound_by_chemblId`.\n\n**Common workflow:**\n1. Search compound by name in KEGG\n2. Extract KEGG compound ID\n3. Use UniChem for KEGG → ChEMBL mapping\n4. ChEBI IDs are often provided in KEGG entries\n\nReference: `references/identifier_mapping.md` for complete cross-database mapping guide.\n\n### 4. Sequence Analysis\n\nRun BLAST searches and sequence alignments. NCBI requires a contact email — prefer the `NCBI_EMAIL` environment variable (same convention as BioPython Entrez and other repo skills):\n\n```python\nimport os\nfrom bioservices import NCBIblast\n\ns = NCBIblast(verbose=False)\nemail = os.environ[\"NCBI_EMAIL\"] # set before running: export NCBI_EMAIL=you@lab.org\n\n# Run BLASTP against UniProtKB\njobid = s.run(\n program=\"blastp\",\n sequence=protein_sequence,\n stype=\"protein\",\n database=\"uniprotkb\",\n email=email,\n)\n\n# Check job status and retrieve results\ns.getStatus(jobid)\nresults = s.getResult(jobid, \"out\")\n```\n\n**Note:** BLAST jobs are asynchronous. Check status before retrieving results.\n\n### 5. Identifier Mapping\n\nConvert identifiers between different biological databases:\n\n```python\nfrom bioservices import UniProt, KEGG\n\n# UniProt mapping (many database pairs supported)\nu = UniProt()\nresults = u.mapping(\n fr=\"UniProtKB_AC-ID\", # Source database\n to=\"KEGG\", # Target database\n query=\"P43403\" # Identifier(s) to convert\n)\n\n# KEGG gene ID → UniProt\nkegg_to_uniprot = u.mapping(fr=\"KEGG\", to=\"UniProtKB_AC-ID\", query=\"hsa:7535\")\n\n# For compounds, use UniChem\nfrom bioservices import UniChem\nu = UniChem()\nchembl_from_kegg = u.get_compound_id_from_kegg(\"C11222\")\n```\n\n**Supported mappings (UniProt):**\n- UniProtKB ↔ KEGG\n- UniProtKB ↔ Ensembl\n- UniProtKB ↔ PDB\n- UniProtKB ↔ RefSeq\n- And many more (see `references/identifier_mapping.md`)\n\n### 6. Gene Ontology Queries\n\nAccess GO terms and annotations:\n\n```python\nfrom bioservices import QuickGO\n\ng = QuickGO(verbose=False)\n\n# Retrieve GO term information\nterm_info = g.Term(\"GO:0003824\", frmt=\"obo\")\n\n# Search annotations\nannotations = g.Annotation(protein=\"P43403\", format=\"tsv\")\n```\n\n### 7. Protein-Protein Interactions\n\nQuery interaction databases via PSICQUIC. **PSICQUIC is not shipped by every\nrelease — it is absent from 1.16.0** — so import it defensively and fall back to\n`IntactComplex`, `OmniPath`, or `STRING` when it is missing:\n\n```python\nfrom bioservices import PSICQUIC\n\ns = PSICQUIC(verbose=False)\n\n# Query specific database (e.g., MINT)\ninteractions = s.query(\"mint\", \"ZAP70 AND species:9606\")\n\n# List available interaction databases\ndatabases = s.activeDBs\n```\n\n**Available databases:** MINT, IntAct, BioGRID, DIP, and 30+ others.\n\n## Multi-Service Integration Workflows\n\nBioServices excels at combining multiple services for comprehensive analysis. Common integration patterns:\n\n### Complete Protein Analysis Pipeline\n\nExecute a full protein characterization workflow:\n\n```bash\nexport NCBI_EMAIL=your.email@example.com\npython scripts/protein_analysis_workflow.py ZAP70_HUMAN\n# Or pass email as optional second argument if NCBI_EMAIL is unset\npython scripts/protein_analysis_workflow.py ZAP70_HUMAN your.email@example.com\n```\n\nThis script demonstrates:\n1. UniProt search for protein entry\n2. FASTA sequence retrieval\n3. BLAST similarity search\n4. KEGG pathway discovery\n5. PSICQUIC interaction mapping\n\n### Pathway Network Analysis\n\nAnalyze all pathways for an organism:\n\n```bash\npython scripts/pathway_analysis.py hsa output_directory/\n```\n\nExtracts and analyzes:\n- All pathway IDs for organism\n- Protein-protein interactions per pathway\n- Interaction type distributions\n- Exports to CSV/SIF formats\n\n### Cross-Database Compound Search\n\nMap compound identifiers across databases:\n\n```bash\npython scripts/compound_cross_reference.py Geldanamycin\n```\n\nRetrieves:\n- KEGG compound ID\n- ChEBI identifier\n- ChEMBL identifier\n- Basic compound properties\n\n### Batch Identifier Conversion\n\nConvert multiple identifiers at once:\n\n```bash\npython scripts/batch_id_converter.py input_ids.txt --from UniProtKB_AC-ID --to KEGG\n```\n\n## Best Practices\n\n### Output Format Handling\n\nDifferent services return data in various formats:\n- **XML**: Parse using BeautifulSoup (most SOAP services)\n- **Tab-separated (TSV)**: Pandas DataFrames for tabular data\n- **Dictionary/JSON**: Direct Python manipulation\n- **FASTA**: BioPython integration for sequence analysis\n\n### Rate Limiting and Verbosity\n\nControl API request behavior:\n\n```python\nfrom bioservices import KEGG\n\nk = KEGG(verbose=False) # Suppress HTTP request details\nk.TIMEOUT = 30 # Adjust timeout for slow connections\n```\n\n### Error Handling\n\nWrap service calls in try-except blocks:\n\n```python\ntry:\n results = u.search(\"ambiguous_query\")\n if results:\n # Process results\n pass\nexcept Exception as e:\n print(f\"Search failed: {e}\")\n```\n\n### Organism Codes\n\nUse standard organism abbreviations:\n- `hsa`: Homo sapiens (human)\n- `mmu`: Mus musculus (mouse)\n- `dme`: Drosophila melanogaster\n- `sce`: Saccharomyces cerevisiae (yeast)\n\nList all organisms: `k.list(\"organism\")` or `k.organismIds`\n\n### Integration with Other Tools\n\nBioServices works well with:\n- **BioPython**: Sequence analysis on retrieved FASTA data\n- **Pandas**: Tabular data manipulation\n- **PyMOL**: 3D structure visualization (retrieve PDB IDs)\n- **NetworkX**: Network analysis of pathway interactions\n- **Galaxy**: Custom tool wrappers for workflow platforms\n\n## Resources\n\n### scripts/\n\nExecutable Python scripts demonstrating complete workflows:\n\n- `protein_analysis_workflow.py`: End-to-end protein characterization\n- `pathway_analysis.py`: KEGG pathway discovery and network extraction\n- `compound_cross_reference.py`: Multi-database compound searching\n- `batch_id_converter.py`: Bulk identifier mapping utility\n\nScripts can be executed directly or adapted for specific use cases.\n\n### references/\n\nDetailed documentation loaded as needed:\n\n- `services_reference.md`: Comprehensive list of all 40+ services with methods\n- `workflow_patterns.md`: Detailed multi-step analysis workflows\n- `identifier_mapping.md`: Complete guide to cross-database ID conversion\n\nLoad references when working with specific services or complex integration tasks.\n\n## Installation\n\n```bash\nuv pip install \"bioservices==1.16.0\"\n```\n\nDependencies are installed automatically. Upstream CI tests Python 3.9–3.12 ([PyPI](https://pypi.org/project/bioservices/), [docs](https://bioservices.readthedocs.io/)).\n\n## Credentials\n\nMost services need no API key. Exceptions:\n\n| Service | Requirement |\n|---------|-------------|\n| NCBI BLAST | Contact email via `NCBI_EMAIL` or `email=` in `NCBIblast.run()` |\n| Some EBI services | Optional; check service docs if rate-limited |\n\nSet once per shell session:\n\n```bash\nexport NCBI_EMAIL=your.email@example.com\n```\n\nUse a real institutional or lab address — NCBI may contact you about heavy BLAST usage.\n\n## Additional Information\n\nFor detailed API documentation and advanced features, refer to:\n- Official documentation: https://bioservices.readthedocs.io/\n","tagline":"Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. 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it assumes the dependency is already available.","Permission surface needs review: secrets or environment access, shell or command execution","Dependency/runtime risk: command execution surface, credential or environment access","Permission surface: secrets or environment access, shell or command execution","No real agent outcome reports yet","Human review required before unattended installation"],"evidence":{"stars":"38K GitHub stars","repoActivity":"38K stars, 3.6K forks","lastPushed":"7d since push","license":"GPLv3 license","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bioservices","install":"npx skills add K-Dense-AI/scientific-agent-skills --skill bioservices","installSafety":"standard package or runtime install path","permissionSurface":"secrets or environment access, shell or command execution","documentation":"Strong README/SKILL.md context","agentOutcomes":"No agent outcome data yet","agentProvenScore":0,"outcomeConfidence":"0%","installPolicy":"human_review_before_install"},"installReadiness":{"ready":true,"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill bioservices","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","7d since push","Trust Score v5 requires review or sandbox-only use before install."]},"agentCompatibility":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"riskSummary":{"level":"medium","label":"Review before production","notes":["SKILL.md does not explicitly include a setup or installation step for the bioservices package; 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it assumes the dependency is already available.","Permission surface needs review: secrets or environment access, shell or command execution","Dependency/runtime risk: command execution surface, credential or environment access","Permission surface: secrets or environment access, shell or command execution"],"backward_compatible":{"trust_score_v4":{"version":"trust-score-v4","score":69,"tier":"review","label":"Manual review","summary":"Potentially useful, but at least one trust signal needs human inspection."}}},"trust_score_v4":{"version":"trust-score-v4","score":69,"tier":"review","label":"Manual review","summary":"Potentially useful, but at least one trust signal needs human inspection.","recommendedAction":"Inspect the repository, license, and recent activity before connecting it to agent workflows.","dimensions":[{"id":"github_adoption","label":"GitHub adoption","score":100,"weight":0.13,"status":"pass","detail":"38K GitHub stars"},{"id":"repo_activity","label":"Stars/forks activity","score":97,"weight":0.08,"status":"pass","detail":"38K stars, 3.6K forks; issue activity unavailable in current metadata"},{"id":"maintenance","label":"Recent maintenance","score":100,"weight":0.14,"status":"pass","detail":"7d since push"},{"id":"license","label":"License clarity","score":86,"weight":0.09,"status":"pass","detail":"GPLv3 license"},{"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":28,"weight":0.12,"status":"fail","detail":"command execution surface, credential or environment access"},{"id":"installability","label":"Install availability","score":92,"weight":0.1,"status":"pass","detail":"npx skills add K-Dense-AI/scientific-agent-skills --skill bioservices"},{"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":18,"weight":0.07,"status":"fail","detail":"secrets or environment access, shell or command execution"},{"id":"repository","label":"Repository evidence","score":86,"weight":0.04,"status":"pass","detail":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bioservices"},{"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":"38K GitHub stars"},{"status":"pass","label":"Stars/forks activity","detail":"38K stars, 3.6K forks; issue activity unavailable in current metadata"},{"status":"pass","label":"Recent maintenance","detail":"7d since push"},{"status":"pass","label":"License clarity","detail":"GPLv3 license"},{"status":"pass","label":"README/SKILL.md completeness","detail":"Metadata includes enough usage and workflow context"},{"status":"fail","label":"Dependency/runtime risk","detail":"command execution surface, credential or environment access"},{"status":"pass","label":"Install availability","detail":"npx skills add K-Dense-AI/scientific-agent-skills --skill bioservices"},{"status":"pass","label":"Install command safety","detail":"standard package or runtime install path"},{"status":"fail","label":"Permission surface","detail":"secrets or environment access, shell or command execution"},{"status":"pass","label":"Repository evidence","detail":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bioservices"},{"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":"5 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","Large GitHub adoption signal","Install command has no obvious high-risk pattern"],"warnings":["SKILL.md does not explicitly include a setup or installation step for the bioservices package; 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it assumes the dependency is already available.","Permission surface needs review: secrets or environment access, shell or command execution","Dependency/runtime risk: command execution surface, credential or environment access","Permission surface: secrets or environment access, shell or command execution"]},"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":["design-creative","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"],"knownRisks":["SKILL.md does not explicitly include a setup or installation step for the bioservices package; it assumes the dependency is already available.","Permission surface needs review: secrets or environment access, shell or command execution","Dependency/runtime risk: command execution surface, credential or environment access","Permission surface: secrets or environment access, shell or command execution"]},"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":38,"level":"avoid_auto_install","label":"Avoid automatic install","safety_tier":{"tier":"experimental","label":"Experimental","badge":"EXPERIMENTAL","summary":"Sparse or mixed signals. Useful for discovery, but not for autonomous installation.","recommended_action":"Test manually in an isolated workspace and compare against safer alternatives.","auto_install_policy":"review","reasons":["Metadata combines secrets access with shell or command execution","High-risk permission hints: Shell or command execution, Secrets or environment access","38/100 agent safety score"]},"auto_install_allowed":false,"human_review_required":true,"blocked":false,"audit_risk":"needs_review","permission_hints":[{"id":"shell","label":"Shell or command execution","reason":"Skill metadata references terminal, CLI, shell, subprocess, or command execution workflows.","severity":"high"},{"id":"network","label":"Network access","reason":"Skill likely fetches remote pages, APIs, repositories, or external services.","severity":"medium"},{"id":"filesystem","label":"Filesystem access","reason":"Skill may read or write project files, documents, generated artifacts, or local workspace state.","severity":"medium"},{"id":"secrets","label":"Secrets or environment access","reason":"Skill metadata references credentials, tokens, environment variables, or secret-bearing workflows.","severity":"high"},{"id":"database","label":"Database access","reason":"Skill may inspect schemas, query databases, or work with persistent stores.","severity":"medium"}],"policy_warnings":["High-risk permission hints: Shell or command execution, Secrets or environment access","Dependency or permission surface needs review"],"constraints_applied":{"max_risk":"medium","needs_install_command":true,"min_stars":0}},"safety_gate":{"tier":"experimental","label":"Experimental","badge":"EXPERIMENTAL","auto_install_policy":"review","auto_install_allowed":false,"blocked":false,"human_review_required":true,"recommended_action":"Test manually in an isolated workspace and compare against safer alternatives.","reasons":["Metadata combines secrets access with shell or command execution","High-risk permission hints: Shell or command execution, Secrets or environment access","38/100 agent safety score"]},"eval":{"version":"openagentskill-skill-eval-v1","status":"failed","score":72,"risk_level":"high","decision":{"recommendation":"do_not_auto_install","reason":"Permission surface: secrets or environment access, shell or command execution","auto_install_allowed":false,"policy":"block","human_review_required":true},"blockers":["Permission surface: secrets or environment access, shell or command execution"],"warnings":["Trust score: Potentially useful, but at least one trust signal needs human inspection.","Audit score: Needs review","Agent safety gate: Sparse or mixed signals. Useful for discovery, but not for autonomous installation.","High-risk permission hints: Shell or command execution, Secrets or environment access","Dependency or permission surface needs review","Permission surface may require sandboxing","SKILL.md does not explicitly include a setup or installation step for the bioservices package; it assumes the dependency is already available.","The documentation correctly warns about removed UniChem helper methods in bioservices 1.16.0, but the included scripts should be audited to ensure they do not still call deprecated methods like get_compound_id_from_kegg.","No explicit input validation or data-handling guidance is given for untrusted compound names, identifiers, or web API responses, which is relevant for a network-connected bioinformatics skill.","Permission surface needs review: secrets or environment access, shell or command execution","Dependency/runtime risk: command execution surface, credential or environment access","Permission surface: secrets or environment access, shell or command execution"],"validation_plan":["Inspect repository, README/SKILL.md, license, and recent commits before production use.","Install in an isolated workspace or sandbox with no production secrets available.","Run the smallest representative task and record files touched, commands run, network access, and outputs.","Compare the selected skill against at least one alternative when the eval status is review or failed.","Promote only after the agent reports a successful verification result and unresolved warnings are accepted."],"checks":[{"id":"task_fit","label":"Task fit","status":"pass","score":84,"required_for_auto_install":true,"detail":"Task wording matches this skill metadata.","evidence":["Evaluate bioservices before installing it in an agent workflow","design-creative","Workflow automation workflows; Claude Code teams; teams that value GitHub adoption signals"]},{"id":"install_path","label":"Install path","status":"pass","score":92,"required_for_auto_install":true,"detail":"Install handoff is available.","evidence":["npx skills add K-Dense-AI/scientific-agent-skills --skill bioservices"]},{"id":"install_safety","label":"Install command safety","status":"pass","score":92,"required_for_auto_install":true,"detail":"standard package or runtime install path","evidence":["npx skills add K-Dense-AI/scientific-agent-skills --skill bioservices"]},{"id":"trust_score","label":"Trust score","status":"warn","score":69,"required_for_auto_install":true,"detail":"Potentially useful, but at least one trust signal needs human inspection.","evidence":["Manual review","38K GitHub stars","GPLv3 license"]},{"id":"audit_score","label":"Audit score","status":"warn","score":82,"required_for_auto_install":true,"detail":"Needs review","evidence":["Dependency or permission surface needs review"]},{"id":"agent_safety_gate","label":"Agent safety gate","status":"warn","score":38,"required_for_auto_install":true,"detail":"Sparse or mixed signals. Useful for discovery, but not for autonomous installation.","evidence":["Test manually in an isolated workspace and compare against safer alternatives.","Metadata combines secrets access with 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":"GPLv3 license","evidence":["GPLv3 license"]},{"id":"recent_maintenance","label":"Recent maintenance","status":"pass","score":100,"required_for_auto_install":false,"detail":"7d since push","evidence":["7d since push"]},{"id":"permission_surface","label":"Permission surface","status":"fail","score":18,"required_for_auto_install":true,"detail":"secrets or environment access, shell or command execution","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/k-dense-ai-bioservices/evals","api":"/api/agent/evals?slug=k-dense-ai-bioservices","text":"/api/agent/evals?slug=k-dense-ai-bioservices&format=text"}},"agent_readable_metadata":{"version":"openagentskill-agent-metadata-v2","skill":{"slug":"k-dense-ai-bioservices","name":"bioservices","description":"Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.","category":"design-creative","url":"https://www.openagentskill.com/skills/k-dense-ai-bioservices","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bioservices","github_repo":"K-Dense-AI/scientific-agent-skills"},"suited_tasks":["Workflow automation workflows","Claude Code teams","teams that value GitHub adoption signals","Move data between tools","Transform files","Trigger repeatable actions","Read uploaded files","Extract structured fields"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill bioservices","ready":true,"targets":[{"id":"openagentskill-cli","label":"CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.3.0/openagentskill-0.3.0.tgz add k-dense-ai-bioservices"},{"id":"codex","label":"Codex","kind":"agent-prompt","value":"Install the \"bioservices\" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bioservices. 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 Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_\",\"skill_slug\":\"k-dense-ai-bioservices\",\"task\":\"Install bioservices\",\"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 \"bioservices\" as a Claude Code skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bioservices. 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 Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_\",\"skill_slug\":\"k-dense-ai-bioservices\",\"task\":\"Install bioservices\",\"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 \"bioservices\" from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bioservices 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 Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_\",\"skill_slug\":\"k-dense-ai-bioservices\",\"task\":\"Install bioservices\",\"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/k-dense-ai-bioservices/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/k-dense-ai-bioservices"},"trust":{"score":69,"label":"Manual review","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"38K GitHub stars","repoActivity":"38K stars, 3.6K forks","lastPushed":"7d since push","license":"GPLv3 license","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bioservices","install":"npx skills add K-Dense-AI/scientific-agent-skills --skill bioservices","installSafety":"standard package or runtime install path","permissionSurface":"secrets or environment access, shell or command execution","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":["design-creative","agent-skill"],"known_risks":["SKILL.md does not explicitly include a setup or installation step for the bioservices package; it assumes the dependency is already available.","Permission surface needs review: secrets or environment access, shell or command execution","Dependency/runtime risk: command execution surface, credential or environment access","Permission surface: secrets or environment access, shell or command execution"]},"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":82,"risk_level":"needs_review","risk_label":"Needs review","warnings":["Dependency or permission surface needs review","Permission surface may require sandboxing","SKILL.md does not explicitly include a setup or installation step for the bioservices package; it assumes the dependency is already available.","The documentation correctly warns about removed UniChem helper methods in bioservices 1.16.0, but the included scripts should be audited to ensure they do not still call deprecated methods like get_compound_id_from_kegg.","No explicit input validation or data-handling guidance is given for untrusted compound names, identifiers, or web API responses, which is relevant for a network-connected bioinformatics skill.","Permission surface needs review: secrets or environment access, shell or command execution","Dependency/runtime risk: command execution surface, credential or environment access","Permission surface: secrets or environment access, shell or command execution"]},"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":92,"label":"Excellent"},"supply":{"track":"Research and knowledge work","scenario":"Document processing","maintenance":"7d since push","risk":"Needs review"},"alternative_skills":[],"do_not_use_when":["teams that need a vendor-supported SLA","production agents without a repository review","SKILL.md does not explicitly include a setup or installation step for the bioservices package; it assumes the dependency is already available.","High-risk permission hints: Shell or command execution, Secrets or environment access","Dependency or permission surface needs review","Permission surface may require sandboxing","The documentation correctly warns about removed UniChem helper methods in bioservices 1.16.0, but the included scripts should be audited to ensure they do not still call deprecated methods like get_compound_id_from_kegg.","No explicit input validation or data-handling guidance is given for untrusted compound names, identifiers, or web API responses, which is relevant for a network-connected bioinformatics skill."],"agent_contract":{"task_input":"Use bioservices 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: 69/100 Manual review","Audit: 82/100 Needs review","Safety: 38/100 Avoid automatic install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"k-dense-ai-bioservices (bioservices)","install_command":"npx skills add K-Dense-AI/scientific-agent-skills --skill bioservices","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":"","skill_slug":"k-dense-ai-bioservices","task":"Use bioservices 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/k-dense-ai-bioservices","api":"https://www.openagentskill.com/api/agent/skills/k-dense-ai-bioservices","audit":"https://www.openagentskill.com/skills/k-dense-ai-bioservices/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=k-dense-ai-bioservices&task=Use%20bioservices%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20bioservices%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20bioservices%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/k-dense-ai-bioservices/install","manifest":"https://www.openagentskill.com/api/registry/manifest/k-dense-ai-bioservices"}},"machine_metadata":{"version":"openagentskill-agent-metadata-v2","skill":{"slug":"k-dense-ai-bioservices","name":"bioservices","description":"Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.","category":"design-creative","url":"https://www.openagentskill.com/skills/k-dense-ai-bioservices","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bioservices","github_repo":"K-Dense-AI/scientific-agent-skills"},"suited_tasks":["Workflow automation workflows","Claude Code teams","teams that value GitHub adoption signals","Move data between tools","Transform files","Trigger repeatable actions","Read uploaded files","Extract structured fields"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill bioservices","ready":true,"targets":[{"id":"openagentskill-cli","label":"CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.3.0/openagentskill-0.3.0.tgz add k-dense-ai-bioservices"},{"id":"codex","label":"Codex","kind":"agent-prompt","value":"Install the \"bioservices\" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bioservices. 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 Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_\",\"skill_slug\":\"k-dense-ai-bioservices\",\"task\":\"Install bioservices\",\"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 \"bioservices\" as a Claude Code skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bioservices. 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 Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_\",\"skill_slug\":\"k-dense-ai-bioservices\",\"task\":\"Install bioservices\",\"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 \"bioservices\" from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bioservices 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 Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_\",\"skill_slug\":\"k-dense-ai-bioservices\",\"task\":\"Install bioservices\",\"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/k-dense-ai-bioservices/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/k-dense-ai-bioservices"},"trust":{"score":69,"label":"Manual review","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"38K GitHub stars","repoActivity":"38K stars, 3.6K forks","lastPushed":"7d since push","license":"GPLv3 license","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bioservices","install":"npx skills add K-Dense-AI/scientific-agent-skills --skill bioservices","installSafety":"standard package or runtime install path","permissionSurface":"secrets or environment access, shell or command execution","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":["design-creative","agent-skill"],"known_risks":["SKILL.md does not explicitly include a setup or installation step for the bioservices package; it assumes the dependency is already available.","Permission surface needs review: secrets or environment access, shell or command execution","Dependency/runtime risk: command execution surface, credential or environment access","Permission surface: secrets or environment access, shell or command execution"]},"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":82,"risk_level":"needs_review","risk_label":"Needs review","warnings":["Dependency or permission surface needs review","Permission surface may require sandboxing","SKILL.md does not explicitly include a setup or installation step for the bioservices package; it assumes the dependency is already available.","The documentation correctly warns about removed UniChem helper methods in bioservices 1.16.0, but the included scripts should be audited to ensure they do not still call deprecated methods like get_compound_id_from_kegg.","No explicit input validation or data-handling guidance is given for untrusted compound names, identifiers, or web API responses, which is relevant for a network-connected bioinformatics skill.","Permission surface needs review: secrets or environment access, shell or command execution","Dependency/runtime risk: command execution surface, credential or environment access","Permission surface: secrets or environment access, shell or command execution"]},"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":92,"label":"Excellent"},"supply":{"track":"Research and knowledge work","scenario":"Document processing","maintenance":"7d since push","risk":"Needs review"},"alternative_skills":[],"do_not_use_when":["teams that need a vendor-supported SLA","production agents without a repository review","SKILL.md does not explicitly include a setup or installation step for the bioservices package; it assumes the dependency is already available.","High-risk permission hints: Shell or command execution, Secrets or environment access","Dependency or permission surface needs review","Permission surface may require sandboxing","The documentation correctly warns about removed UniChem helper methods in bioservices 1.16.0, but the included scripts should be audited to ensure they do not still call deprecated methods like get_compound_id_from_kegg.","No explicit input validation or data-handling guidance is given for untrusted compound names, identifiers, or web API responses, which is relevant for a network-connected bioinformatics skill."],"agent_contract":{"task_input":"Use bioservices 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: 69/100 Manual review","Audit: 82/100 Needs review","Safety: 38/100 Avoid automatic install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"k-dense-ai-bioservices (bioservices)","install_command":"npx skills add K-Dense-AI/scientific-agent-skills --skill bioservices","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":"","skill_slug":"k-dense-ai-bioservices","task":"Use bioservices 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/k-dense-ai-bioservices","api":"https://www.openagentskill.com/api/agent/skills/k-dense-ai-bioservices","audit":"https://www.openagentskill.com/skills/k-dense-ai-bioservices/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=k-dense-ai-bioservices&task=Use%20bioservices%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20bioservices%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20bioservices%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/k-dense-ai-bioservices/install","manifest":"https://www.openagentskill.com/api/registry/manifest/k-dense-ai-bioservices"}},"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":"Document processing","description":"I need my agent to read PDFs, extract tables, and turn documents into structured data.","useCases":[{"slug":"workflow-automation","title":"Workflow automation"},{"slug":"document-processing","title":"Document processing"},{"slug":"rag-knowledge","title":"RAG and knowledge"}]},"applicableAgents":["Claude Code","CLI","Codex","Cursor"],"install":{"ready":true,"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill bioservices","primaryTarget":"CLI","targetCount":4},"githubQuality":{"stars":38487,"starsLabel":"38K","forks":3607,"license":"GPLv3 license","qualityScore":92,"trustScore":69,"auditScore":82},"maintenance":{"status":"fresh","label":"7d since push","daysSincePush":7,"lastPushedAt":"2026-08-30T13:19:27+00:00"},"risk":{"level":"needs_review","label":"Needs review","requiresReview":true,"notes":["Dependency or permission surface needs review","Permission surface may require sandboxing","SKILL.md does not explicitly include a setup or installation step for the bioservices package; it assumes the dependency is already available.","The documentation correctly warns about removed UniChem helper methods in bioservices 1.16.0, but the included scripts should be audited to ensure they do not still call deprecated methods like get_compound_id_from_kegg.","No explicit input validation or data-handling guidance is given for untrusted compound names, identifiers, or web API responses, which is relevant for a network-connected bioinformatics skill."]},"coverageTags":["Research","Document processing","design-creative","agent-skill"]},"audit":{"audit_score":82,"risk_level":"needs_review","risk_label":"Needs review","quality_score":92,"trust_score":69,"maintenance_score":100,"security_score":69,"install_score":92,"warnings":["Dependency or permission surface needs review","Permission surface may require sandboxing","SKILL.md does not explicitly include a setup or installation step for the bioservices package; it assumes the dependency is already available.","The documentation correctly warns about removed UniChem helper methods in bioservices 1.16.0, but the included scripts should be audited to ensure they do not still call deprecated methods like get_compound_id_from_kegg.","No explicit input validation or data-handling guidance is given for untrusted compound names, identifiers, or web API responses, which is relevant for a network-connected bioinformatics skill.","Permission surface needs review: secrets or environment access, shell or command execution","Dependency/runtime risk: command execution surface, credential or environment access","Permission surface: secrets or environment access, shell or command execution"]},"quality_signals":{"model":"v2","star_score":32.1,"usage_score":0,"review_score":4.95,"metadata_score":3,"freshness_score":15},"platforms":["Claude Code"],"use_cases":[{"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":"rag-knowledge","title":"RAG and knowledge","url":"https://www.openagentskill.com/use-cases/rag-knowledge"},{"slug":"browser-automation","title":"Browser automation","url":"https://www.openagentskill.com/use-cases/browser-automation"}],"stacks":[{"slug":"content-growth-agent","title":"Content growth agent","url":"https://www.openagentskill.com/collections/content-growth-agent"},{"slug":"rag-knowledge-base","title":"RAG knowledge base","url":"https://www.openagentskill.com/collections/rag-knowledge-base"},{"slug":"browser-qa-agent","title":"Browser QA agent","url":"https://www.openagentskill.com/collections/browser-qa-agent"}],"install":"npx skills add K-Dense-AI/scientific-agent-skills --skill bioservices","install_targets":[{"id":"openagentskill-cli","label":"CLI","title":"OpenAgentSkill CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.3.0/openagentskill-0.3.0.tgz add k-dense-ai-bioservices","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 \"bioservices\" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bioservices. 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 Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_\",\"skill_slug\":\"k-dense-ai-bioservices\",\"task\":\"Install bioservices\",\"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 \"bioservices\" as a Claude Code skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bioservices. 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 Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_\",\"skill_slug\":\"k-dense-ai-bioservices\",\"task\":\"Install bioservices\",\"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 \"bioservices\" from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bioservices 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 Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_\",\"skill_slug\":\"k-dense-ai-bioservices\",\"task\":\"Install bioservices\",\"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/K-Dense-AI/scientific-agent-skills/tree/main/skills/bioservices","github_repo":"K-Dense-AI/scientific-agent-skills","version":"1.0.0","license":"GPLv3 license","urls":{"web":"https://www.openagentskill.com/skills/k-dense-ai-bioservices","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bioservices","api":"/api/agent/skills/k-dense-ai-bioservices","install_api":"/api/skills/k-dense-ai-bioservices/install"},"meta":{"created_at":"2026-08-30T13:23:35.993494+00:00","updated_at":"2026-09-01T11:59:28.941454+00:00","agent_friendly":true}}