kegg-database
Query KEGG database for pathways and genes
Também disponível em: davila7
Researchers need efficient access to KEGG bioinformatics data for pathway analysis and gene mapping. This skill provides Python helper functions for all KEGG REST API operations including pathway retrieval, gene-pathway mapping, compound searches, and ID conversion between databases.
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A utilizar "kegg-database". Find pathways associated with the glycolysis gene hsa:10458
Resultado esperado:
- Pathway hsa00010: Glycolysis / Gluconeogenesis
- Pathway hsa01100: Metabolic pathways
- Pathway hsa01200: Carbon metabolism
- Pathway hsa01210: 2-Oxocarboxylic acid metabolism
- Pathway hsa01230: Biosynthesis of amino acids
A utilizar "kegg-database". Get information about drug D00001
Resultado esperado:
- Drug: D00001
- Name: Theophylline
- Class: Purine alkaloids
- Formula: C7H8N4O2
- Target: Adenosine receptors
A utilizar "kegg-database". Convert human gene KEGG ID to UniProt
Resultado esperado:
- hsa:10458 -> Q9Y5K8
- hsa:10459 -> Q9Y5K9
- hsa:10572 -> Q8NHW6
Auditoria de Segurança
SeguroAll 253 static findings are false positives. The scanner incorrectly flags Markdown backticks as Ruby shell execution, KEGG API URLs as suspicious network targets, and bioinformatics identifiers (pathway IDs, gene names) as weak crypto algorithms. This is a legitimate bioinformatics research tool that uses standard urllib for HTTP requests to the official KEGG REST API. No malicious code, command injection, or data exfiltration present.
Fatores de risco
⚙️ Comandos externos (4)
🌐 Acesso à rede (3)
📁 Acesso ao sistema de arquivos (2)
Pontuação de qualidade
O Que Você Pode Construir
Pathway enrichment analysis
Map genes of interest to KEGG pathways and retrieve detailed pathway information for enrichment studies.
Cross-database integration
Convert KEGG gene IDs to UniProt, NCBI Gene IDs, or PubChem for integration with other analysis pipelines.
Drug interaction screening
Search drug databases and check potential drug-drug interactions using KEGG DDI endpoint.
Tente Estes Prompts
Use kegg_list to retrieve all KEGG pathways for human (hsa) and show the first 10 pathway IDs and names.
Search the KEGG genes database for entries matching 'p53' using kegg_find and display the results.
Use kegg_link to find all KEGG pathways that contain the TP53 gene (hsa:7157) and retrieve basic info for each.
Convert all human gene KEGG IDs to NCBI Gene IDs using kegg_conv and show the first 5 mapping pairs.
Melhores Práticas
- Cache API results locally to reduce redundant requests and respect rate limits.
- Check HTTP status codes (200=success, 400=bad request, 404=not found) for error handling.
- Use specific organism codes (hsa, mmu, eco) to narrow results and improve performance.
Evitar
- Making rapid-fire requests without delays - violates KEGG API usage guidelines.
- Ignoring HTTP error responses - always handle 400/404 errors appropriately.
- Requesting more than 10 entries in a single call - KEGG limits batch operations.
Perguntas Frequentes
What is KEGG?
Is this skill free to use?
What organisms are supported?
Can I get sequence data?
How do I convert gene IDs?
What are the API limits?
Detalhes do Desenvolvedor
Autor
K-Dense-AILicença
Non-academic use of KEGG requires a commercial license
Repositório
https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/kegg-databaseReferência
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Estrutura de arquivos