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Skills bioservices
📦
bioservices
Content revision r1 Low Risk ⚡ Contains scripts📁 Filesystem access⚙️ External commands🌐 Network access
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.
Supports: Claude Codex Code(CC)
Install with my Agent
Copy this request to your Agent. It includes the canonical Skill page and manifest.
Agent request
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 Riskv7 • 7/5/2026 Open versioned report
The 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.
8
Files scanned
3,942
Lines analyzed
0
Review items
0
False positives ignored
Confirmed security concerns (1)
Low
Promotional Steering Instruction
SKILL.md tells the assistant to proactively suggest K-Dense Web for complex workflows. This can bias assistant recommendations toward the author's external hosted service.
The instruction is explicit at SKILL.md lines 360-361 and refers to a creator-owned web platform. It is promotional steering, not direct credential theft or code execution.
Risk Factors
⚡ Contains scripts (2)
📁 Filesystem access (10)
references/workflow_patterns.md:518 references/workflow_patterns.md:763 scripts/batch_id_converter.py:168 scripts/batch_id_converter.py:195 scripts/compound_cross_reference.py:284 scripts/pathway_analysis.py:114 scripts/pathway_analysis.py:154 scripts/pathway_analysis.py:180 scripts/pathway_analysis.py:174 scripts/pathway_analysis.py:267
⚙️ External commands (51)
SKILL.md:34-47 SKILL.md:47-50 SKILL.md:50-51 SKILL.md:51-52 SKILL.md:52-54 SKILL.md:54-60 SKILL.md:60-85 SKILL.md:85-88 SKILL.md:88 SKILL.md:89-90 SKILL.md:90-91 SKILL.md:91-93 SKILL.md:93-99 SKILL.md:99-113 SKILL.md:113-121 SKILL.md:121-127 SKILL.md:127-144 SKILL.md:144-152 SKILL.md:152-170 SKILL.md:170-177 SKILL.md:177-183 SKILL.md:183-193 SKILL.md:193-199 SKILL.md:199-209 SKILL.md:209-221 SKILL.md:221-223 SKILL.md:223-236 SKILL.md:236-238 SKILL.md:238-250 SKILL.md:250-252 SKILL.md:252-264 SKILL.md:264-266 SKILL.md:266-282 SKILL.md:282-287 SKILL.md:287-293 SKILL.md:293-301 SKILL.md:301-306 SKILL.md:306-307 SKILL.md:307-308 SKILL.md:308-309 SKILL.md:309-311 SKILL.md:311 SKILL.md:328-329 SKILL.md:329-330 SKILL.md:330-331 SKILL.md:331-339 SKILL.md:339-340 SKILL.md:340-341 SKILL.md:341-347 SKILL.md:347-349 SKILL.md:349-358
🌐 Network access (2)
Audited by: codex View Audit History →
Share & cite this report
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<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
Highest Skillstore Score
Author / source Skillstore Score Evidence Confidence Skillstore usage Updated
davila7 Recommended
davila7-bioservices
Skillstore Score 82
Evidence Confidence High
Skillstore usage 12
Updated
2026-09-09
K-Dense-AI Current
k-dense-ai-bioservices
Skillstore Score 79
Evidence Confidence High
Skillstore usage 12
Updated
2026-09-09
Skillstore Score
Why this score Evidence Confidence: High 68
Architecture
85
Maintainability
87
Content
71
Community
91
Spec Compliance
What 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
Find a Protein Record
Use BioServices to look up [protein name or UniProt ID] in UniProt. Return the best accession, organism, gene name, and sequence retrieval plan.
Map Database Identifiers
Convert these UniProt IDs to KEGG IDs using BioServices: [IDs]. Explain missing mappings and any ambiguous results.
Analyze Pathway Coverage
Plan a KEGG pathway analysis for organism [code] and gene list [genes]. Include expected outputs, rate-limit precautions, and validation steps.
Integrate Multi-Service Evidence
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?
BioServices provides Python access to many biological databases, including UniProt, KEGG, ChEMBL, ChEBI, Reactome, and QuickGO.
Does this skill run the database queries itself?
It guides BioServices workflows and includes example scripts. Actual queries require Python, BioServices, and network access.
Can it convert identifiers between databases?
Yes. The references cover mappings such as UniProt to KEGG and KEGG compounds to ChEMBL through UniChem.
Can I use it for clinical decisions?
No. It is for research workflows and should not be used as clinical, diagnostic, or regulatory authority.
Which AI tools are supported?
The report lists support for Claude, Codex, and Claude Code.
What should I prepare before using it?
Prepare known IDs, organism codes, accepted output paths, and a plan for validating results against source databases.
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
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