Skills bioservices

📦

bioservices

Name: bioservices
Author: davila7

Content revision r2 Safe ⚡ Contains scripts📁 Filesystem access⚙️ External commands🌐 Network access

Connect Bioinformatics Databases with BioServices

Bioinformatics research often requires separate interfaces for proteins, pathways, compounds, and identifiers. This skill guides unified BioServices workflows across major biological databases.

Supports: Claude Codex Code(CC)

🥈 82 Silver

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/davila7-bioservices.md and its manifest at https://skillstore.io/api/skills/davila7-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.

Markdown detail GET /skills/davila7-bioservices.md Signed manifest GET /api/skills/davila7-bioservices/manifest Signed lockfile GET /api/skills/davila7-bioservices/lockfile

Test it

Using "bioservices". Find human ZAP70 and summarize its major database links.

Expected outcome:

Primary UniProt record: P43403, with the matched protein name and organism.
Mapped KEGG gene identifiers and associated pathways are listed with source labels.
Missing or ambiguous links are marked for manual review.

Using "bioservices". Convert a UniProt identifier list to KEGG identifiers.

Expected outcome:

Successful mappings are grouped by source identifier.
One-to-many mappings remain separate instead of being collapsed.
Unmapped identifiers are listed for retry or manual investigation.

Using "bioservices". Cross-reference aspirin across compound databases.

Expected outcome:

A concise comparison lists available KEGG, ChEBI, and ChEMBL identifiers, selected properties, linked pathways, and unavailable fields.

Security Audit

Safe

v9 • 7/23/2026 Open versioned report

All 138 static findings are false positives caused by Markdown formatting, biological identifiers, harmless prose, and documented result exports. No dynamic execution, system reconnaissance, prompt injection, or malicious network intent was found. The workflows intentionally contact public biological services and may write user-selected output files.

Files scanned

3,937

Lines analyzed

Review items

False positives ignored

Risk Factors

⚡ Contains scripts (2)

references/services_reference.md:408 scripts/protein_analysis_workflow.py:327

📁 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 (50)

SKILL.md:31-44 SKILL.md:44-47 SKILL.md:47-48 SKILL.md:48-49 SKILL.md:49-51 SKILL.md:51-57 SKILL.md:57-82 SKILL.md:82-85 SKILL.md:85 SKILL.md:86-87 SKILL.md:87-88 SKILL.md:88-90 SKILL.md:90-96 SKILL.md:96-110 SKILL.md:110-118 SKILL.md:118-124 SKILL.md:124-141 SKILL.md:141-149 SKILL.md:149-167 SKILL.md:167-174 SKILL.md:174-180 SKILL.md:180-190 SKILL.md:190-196 SKILL.md:196-206 SKILL.md:206-218 SKILL.md:218-220 SKILL.md:220-233 SKILL.md:233-235 SKILL.md:235-247 SKILL.md:247-249 SKILL.md:249-261 SKILL.md:261-263 SKILL.md:263-279 SKILL.md:279-284 SKILL.md:284-290 SKILL.md:290-298 SKILL.md:298-303 SKILL.md:303-304 SKILL.md:304-305 SKILL.md:305-306 SKILL.md:306-308 SKILL.md:308 SKILL.md:325-326 SKILL.md:326-327 SKILL.md:327-328 SKILL.md:328-336 SKILL.md:336-337 SKILL.md:337-338 SKILL.md:338-344 SKILL.md:344-346

🌐 Network access (2)

SKILL.md:353 SKILL.md:354

No confirmed security findings were detected by the latest completed static and semantic audit. This does not prove the skill has no side effects.

Audited by: codex View Audit History →

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.

Open versioned report

Copy report link

https://skillstore.io/skills/davila7-bioservices/audits/9?utm_source=security_passport&utm_medium=share&utm_campaign=versioned_report

Markdown badge

[![Skillstore security assessment](https://skillstore.io/badges/skills/davila7-bioservices/security.svg)](https://skillstore.io/skills/davila7-bioservices?utm_source=security_passport_badge)

HTML badge

<a href="https://skillstore.io/skills/davila7-bioservices?utm_source=security_passport_badge"><img src="https://skillstore.io/badges/skills/davila7-bioservices/security.svg" alt="Skillstore security assessment" loading="lazy"></a>

Embed card

<iframe src="https://skillstore.io/embed/skills/davila7-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

davila7. (2026). bioservices security audit report (audit version 9) [Author version unspecified]. Skillstore. https://skillstore.io/skills/davila7-bioservices/audits/9

BibTeX citation

@techreport{davila7-davila7-bioservices-2026,
  author = {davila7},
  title = {bioservices security audit report (audit version 9)},
  institution = {Skillstore},
  year = {2026},
  number = {9},
  url = {https://skillstore.io/skills/davila7-bioservices/audits/9},
  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 9)"
version: "unspecified"
type: report
authors:
  - name: "davila7"
date-released: "2026-07-23"
url: "https://skillstore.io/skills/davila7-bioservices/audits/9"
identifiers:
  - type: other
    value: "skillstore:davila7-bioservices:audit:9"
    description: "Skillstore immutable audit report identifier"

Compare variants

2 installable variants

Each 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 Current

davila7-bioservices

Skillstore Score 82

Evidence Confidence High

Skillstore usage 9

Updated

2026-08-21

K-Dense-AI

k-dense-ai-bioservices

Skillstore Score 79

Evidence Confidence High

Skillstore usage 11

Updated

2026-08-21

Skillstore Score

Why this score Evidence Confidence: High

Architecture

Maintainability

Content

Community

Spec Compliance

What You Can Build

Characterize a Protein

Combine UniProt, BLAST, KEGG, interaction, and ontology results for an initial protein profile.

Map Identifier Collections

Convert large identifier lists between UniProt, KEGG, Ensembl, RefSeq, PDB, and related resources.

Build Research Data Pipelines

Integrate several biological services with chunking, export, error handling, and documented database links.

Try These Prompts

Retrieve a Protein Record

Use BioServices to find [protein name] in [organism]. Return the UniProt identifier, sequence length, and a concise annotation summary.

Map Identifier Batches

Convert these [source database] identifiers to [target database] identifiers: [list]. Report unmapped and one-to-many results separately.

Compare Compound Records

Search [compound name] across KEGG, ChEBI, and ChEMBL. Compare identifiers, formula, molecular weight, and linked pathways, noting unavailable fields.

Build an Integrated Protein Workflow

Design a reproducible BioServices workflow for [protein] covering UniProt, BLAST, KEGG pathways, interactions, and GO annotations. Include rate limits and failure handling.

Best Practices

Specify the organism and source database to reduce ambiguous identifiers.
Use small batches, delays, retries, and cached results for external service queries.
Validate important mappings against source records before drawing scientific conclusions.

Avoid

Do not treat the first search result as confirmed without checking the organism and record.
Do not collapse one-to-many mappings into a single identifier.
Do not run large unthrottled batches against public biological services.