{"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.","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. For quick single-database lookups use gget; for ","category":"design-creative","tags":["agent-skill"],"author":{"name":"K-Dense-AI","verified":false,"url":"https://github.com/K-Dense-AI"},"attribution":{"status":"registry_indexed","statusLabel":"Registry indexed","shortLabel":"REGISTRY INDEXED","sourceLabel":"recursive skill source sync","sourceDetail":"K-Dense-AI/scientific-agent-skills","creatorName":"K-Dense-AI","creatorUrl":"https://github.com/K-Dense-AI","sourceUrl":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bioservices","indexedBy":"OpenAgentSkill community index","claimUrl":"https://www.openagentskill.com/skills/k-dense-ai-bioservices#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":38487,"forks":3607,"verified_installs":0,"install_attempts":0,"successful_runs":0,"total_outcomes":0,"downloads":0,"rating":0,"review_count":0,"quality_score":55.05},"quality":{"score":92,"tier":"excellent","label":"Excellent","summary":"High-confidence pick with strong adoption and healthy maintenance signals.","signals":[{"label":"GitHub stars","value":"38K","tone":"positive"},{"label":"Freshness","value":"7d ago","tone":"positive"},{"label":"Install ready","value":"Yes","tone":"positive"},{"label":"License","value":"GPLv3 license","tone":"neutral"}],"warnings":["SKILL.md does not explicitly include a setup or installation step for the bioservices package; it assumes the dependency is already available."]},"trust":{"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":"info","label":"OpenAgentSkill usage","detail":"No local usage activity yet"},{"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; 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"],"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"},"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"]},"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; 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"]},"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,"human_review_required":true,"blocked":false,"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"]},"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","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."]},"decision":{"readiness_score":100,"readiness_label":"Production-ready","headline":"Primary pick for Workflow automation","role":"Primary pick","primary_fit":"Workflow automation","best_for":["Workflow automation workflows","Claude Code teams","teams that value GitHub adoption signals"],"risks":["SKILL.md does not explicitly include a setup or installation step for the bioservices package; it assumes the dependency is already available.","No OpenAgentSkill engagement data yet"],"next_steps":["Install it in a sandbox agent and run one Workflow automation task end to end.","Compare output quality, latency, and failure behavior against at least one alternative.","Promote it into production only after reviewing repository permissions, license, and maintenance signals."]},"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_<unique-id>\",\"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_<unique-id>\",\"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_<unique-id>\",\"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.","No OpenAgentSkill engagement data yet","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."],"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":"<install_receipt.outcome_feedback.event_id or feedback.event_id from /api/agent/resolve>","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_<unique-id>\",\"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_<unique-id>\",\"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_<unique-id>\",\"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.","No OpenAgentSkill engagement data yet","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."],"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":"<install_receipt.outcome_feedback.event_id or feedback.event_id from /api/agent/resolve>","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"}},"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"}],"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_<unique-id>\",\"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_<unique-id>\",\"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_<unique-id>\",\"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","updated_at":"2026-09-01T11:59:28.941454+00:00","canonical_key":"k-dense-ai/scientific-agent-skills#skills/bioservices","recommendation_reasons":["Strong GitHub adoption: 38,487 stars","Install handoff is available","Repository freshness signal is available"],"urls":{"web":"https://www.openagentskill.com/skills/k-dense-ai-bioservices","api":"https://www.openagentskill.com/api/agent/skills/k-dense-ai-bioservices","install_api":"https://www.openagentskill.com/api/skills/k-dense-ai-bioservices/install","audit":"https://www.openagentskill.com/skills/k-dense-ai-bioservices/audit","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/bioservices"},"meta":{"endpoint":"/api/registry/manifest/{slug}","canonical_agent_endpoint":"/api/agent/skills/k-dense-ai-bioservices","agent_friendly":true,"api_version":"1.0","generated_at":"2026-09-06T13:27:40.400Z"}}