Skills bioservices
🧬

bioservices

Safe ⚙️ External commands🌐 Network access📁 Filesystem access

Access bioinformatics databases from Python

Also available from: davila7

Query 40+ biological databases including UniProt, KEGG, and ChEMBL with a consistent Python API. Simplifies cross-database analysis and identifier conversion for bioinformatics research.

Supports: Claude Codex Code(CC)
🥈 77 Silver
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Using "bioservices". Find information about protein P43403

Expected outcome:

  • UniProt ID: P43403
  • Gene: ZAP70
  • Organism: Homo sapiens (Human)
  • KEGG ID: hsa:7535
  • Pathways: hsa04660 (B cell receptor signaling), hsa04650

Using "bioservices". Convert compound IDs from KEGG to ChEMBL

Expected outcome:

  • KEGG ID: C11222
  • ChEMBL ID: CHEMBL278315
  • ChEBI ID: CHEBI:17957
  • Compound: Geldanamycin

Security Audit

Safe
v4 • 1/17/2026

All 521 static findings are false positives. Scanner misidentified markdown code block delimiters as shell commands, biological database identifiers as cryptographic algorithms, and legitimate API queries to bioinformatics databases as system reconnaissance. The skill is a legitimate scientific library interface.

9
Files scanned
4,227
Lines analyzed
3
findings
4
Total audits

Risk Factors

⚙️ External commands (4)
SKILL.md:34 references/identifier_mapping.md:33 references/services_reference.md:12 references/workflow_patterns.md:25
🌐 Network access (1)
SKILL.md:356-357
📁 Filesystem access (2)
scripts/batch_id_converter.py:168 scripts/pathway_analysis.py:114
Audited by: claude View Audit History →

Quality Score

68
Architecture
100
Maintainability
85
Content
22
Community
100
Security
91
Spec Compliance

What You Can Build

Cross-database protein analysis

Retrieve protein data from UniProt, map to KEGG pathways, and analyze interactions in one workflow.

Compound identifier mapping

Convert compound IDs between KEGG, ChEMBL, and ChEBI databases for chemical research.

Pathway network extraction

Extract protein interaction networks from KEGG pathways for downstream network analysis.

Try These Prompts

Find protein sequence 
Use BioServices to find the UniProt entry for protein ZAP70 and retrieve its FASTA sequence.
Map gene identifiers 
Convert the UniProt ID P43403 to its corresponding KEGG gene ID using BioServices mapping.
Analyze pathways 
Use BioServices to get all pathways for human containing gene 7535 and extract the interaction network.
Cross-reference compounds 
Search KEGG for compound Geldanamycin, then use UniChem to find its ChEMBL and ChEBI identifiers.

Best Practices

  • Set verbose=False to reduce logging output for cleaner results
  • Add delays between batch requests to respect API rate limits
  • Always specify organism codes to avoid ambiguity

Avoid

  • Making thousands of requests without rate limiting
  • Using ambiguous gene names without specifying organism
  • Skipping error handling for network-dependent operations

Frequently Asked Questions

Which databases are supported?
40+ databases including UniProt, KEGG, ChEMBL, ChEBI, PDB, Reactome, BioMart, and ArrayExpress.
Do I need API keys?
Most databases are free. NCBI services require a valid email address for BLAST searches.
How to handle rate limits?
Add time.sleep between requests and use chunk_size parameter for batch operations.
Can I convert batch identifiers?
Yes, use the batch_id_converter.py script or implement chunked mapping with 50-100 IDs per request.
What output formats are supported?
FASTA, XML, tab-separated, JSON, and database-specific formats depending on the service.
How to get pathway interactions?
Use KEGG.pathway2sif() or parse_kgml_pathway() to extract protein-protein interaction networks.

Developer Details

Author

K-Dense-AI

License

GPLv3 license

Repository

https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/bioservices

Ref

main

File structure

📁 references/

📄 identifier_mapping.md

📄 services_reference.md

📄 workflow_patterns.md

📁 scripts/

📄 batch_id_converter.py

📄 compound_cross_reference.py

📄 pathway_analysis.py

📄 protein_analysis_workflow.py

📄 SKILL.md