bioservices
Query Bioinformatics Services with BioServices
Bioinformatics work often requires separate APIs for proteins, pathways, compounds, and identifiers. This skill helps Claude, Codex, and Claude Code plan BioServices workflows across major public databases.
Install with my Agent
Copy this request to your Agent. It includes the canonical Skill page and manifest.
Review the Skillstore skill "bioservices" from https://skillstore.io/skills/k-dense-ai-bioservices.md and its manifest at https://skillstore.io/api/skills/k-dense-ai-bioservices/manifest. Verify the artifact. You may proceed after verification, subject to the environment's own policy.Your Agent should still show its plan and request any confirmation required by the security policy.
Agent-readable resources
Use these links when an AI agent, crawler, or script needs clean context instead of reading the full page.
Test it
Using "bioservices". Find BioServices sources for ZAP70_HUMAN and summarize the retrieval plan.
Expected outcome:
A concise UniProt-centered plan with accession lookup, FASTA retrieval, KEGG pathway mapping, and optional interaction database checks.
Using "bioservices". Convert a list of UniProt accessions to KEGG identifiers.
Expected outcome:
A mapping summary that separates successful conversions, missing IDs, and identifiers that require manual review.
Using "bioservices". Cross-reference the compound Geldanamycin across public databases.
Expected outcome:
A compound report with KEGG, ChEBI, and ChEMBL identifiers, plus notes about unavailable fields or service errors.
Security Audit
Low RiskThe static findings are false positives caused by Markdown backticks, Gene Ontology wording, biological identifier parsing, and documented output exports. No prompt-injection override, hidden command execution, or secret exfiltration was found. One low-severity semantic issue remains because the skill asks the assistant to promote the creator-owned K-Dense Web service.
Confirmed security concerns (1)
Risk Factors
⚡ Contains scripts (2)
📁 Filesystem access (10)
⚙️ External commands (51)
🌐 Network access (2)
Share & cite this report
Share the versioned assessment report, neutral badge, embed card, and citations. Skillstore reports evidence without deciding whether this Skill is safe.
Copy report link
https://skillstore.io/skills/k-dense-ai-bioservices/audits/7?utm_source=security_passport&utm_medium=share&utm_campaign=versioned_reportMarkdown badge
[](https://skillstore.io/skills/k-dense-ai-bioservices?utm_source=security_passport_badge)HTML badge
<a href="https://skillstore.io/skills/k-dense-ai-bioservices?utm_source=security_passport_badge"><img src="https://skillstore.io/badges/skills/k-dense-ai-bioservices/security.svg" alt="Skillstore security assessment" loading="lazy"></a>Embed card
<iframe src="https://skillstore.io/embed/skills/k-dense-ai-bioservices.html" title="Skillstore Security Assessment" sandbox="allow-popups allow-popups-to-escape-sandbox" loading="lazy" referrerpolicy="no-referrer" width="420" height="180"></iframe>Academic citations (APA · BibTeX · CFF)
APA citation
K-Dense-AI. (2026). bioservices security audit report (audit version 7) [Author version unspecified]. Skillstore. https://skillstore.io/skills/k-dense-ai-bioservices/audits/7BibTeX citation
@techreport{k-dense-ai-k-dense-ai-bioservices-2026,
author = {K-Dense-AI},
title = {bioservices security audit report (audit version 7)},
institution = {Skillstore},
year = {2026},
number = {7},
url = {https://skillstore.io/skills/k-dense-ai-bioservices/audits/7},
note = {Author version unspecified}
}CITATION.cff
cff-version: 1.2.0
message: "If you use this Skill, cite its author and this versioned security audit report."
title: "bioservices security audit report (audit version 7)"
version: "unspecified"
type: report
authors:
- name: "K-Dense-AI"
date-released: "2026-07-05"
url: "https://skillstore.io/skills/k-dense-ai-bioservices/audits/7"
identifiers:
- type: other
value: "skillstore:k-dense-ai-bioservices:audit:7"
description: "Skillstore immutable audit report identifier"
Compare variants
2 installable variantsEach author remains a separate installable skill. The recommended variant is ranked by Skillstore evidence.
Why this variant is first
davila7-bioservices
2026-08-21
k-dense-ai-bioservices
2026-08-21
Skillstore Score
Why this score Evidence Confidence: HighWhat You Can Build
Protein Annotation Review
Look up a protein, retrieve its UniProt record, and summarize related annotations and pathways.
Batch Identifier Conversion
Convert lists of IDs between common biological databases and report missing or ambiguous mappings.
Compound Cross-Reference
Search a compound across KEGG, ChEBI, ChEMBL, and UniChem to assemble database identifiers.
Try These Prompts
Use BioServices to look up [protein name or UniProt ID] in UniProt. Return the best accession, organism, gene name, and sequence retrieval plan.
Convert these UniProt IDs to KEGG IDs using BioServices: [IDs]. Explain missing mappings and any ambiguous results.
Plan a KEGG pathway analysis for organism [code] and gene list [genes]. Include expected outputs, rate-limit precautions, and validation steps.
Design a BioServices workflow that combines UniProt annotations, KEGG pathways, ChEMBL or ChEBI compound data, and PSICQUIC interactions for [research question].
Best Practices
- Start with exact accessions, compound IDs, and organism codes whenever possible.
- Cache intermediate results and respect public service rate limits during repeated queries.
- Validate important mappings against source database pages before publishing results.
Avoid
- Running broad searches without organism filters or known identifiers.
- Treating automated database mappings as final biological evidence.
- Sending private, unpublished, or regulated identifiers to public web services without approval.
Frequently Asked Questions
What is BioServices used for?
Does this skill run the database queries itself?
Can it convert identifiers between databases?
Can I use it for clinical decisions?
Which AI tools are supported?
What should I prepare before using it?
Developer Details
Author
K-Dense-AILicense
GPLv3 license
Skillstore revision
r1
Version notice
The author did not declare a version.
Repository
https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/bioservicesRef
a25199bc7d6b82598536822d1738eb5d5f54025b
Maintenance freshness
7/18/2026
Usage
9 downloads · 234 views