Which databases are supported by the BioServices skill?

BioServices provides access to over 40 bioinformatics services, including major databases like UniProt, KEGG, ChEMBL, PubChem, Reactome, PDB, and QuickGO.

Can I use this skill to convert protein IDs?

Yes, the skill excels at identifier mapping, allowing you to convert IDs between formats like UniProtKB, KEGG, Ensembl, RefSeq, and PDB.

Does BioServices support BLAST sequence searches?

Yes, it includes programmatic access to NCBI BLAST, allowing you to run sequence similarity searches and retrieve results directly through Python workflows.

Do I need to manage REST and SOAP protocols manually?

No, BioServices handles both REST and SOAP/WSDL protocols transparently, providing a consistent Pythonic API regardless of the underlying service architecture.

How does it handle metabolic pathway data?

It can search for organisms, find pathways by gene ID, and extract structured interaction data from services like KEGG and Reactome, even converting them to Simple Interaction Format (SIF).

BioServices Bioinformatics Tool

Name: BioServices Bioinformatics Tool
Author: K-Dense-AI

byK-Dense-AI

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2,188

データサイエンスとML

Streamlines access to over 40 bioinformatics web services and databases for biological data retrieval and cross-database analysis.

概要

BioServices is a powerful Python-based skill for Claude that provides programmatic access to a vast ecosystem of over 40 bioinformatics resources including UniProt, KEGG, ChEMBL, and NCBI. It enables researchers and developers to automate complex scientific workflows such as retrieving protein sequences, mapping identifiers between disparate databases, performing metabolic pathway discovery, and executing BLAST searches. By offering a unified API for various REST and SOAP protocols, it eliminates the need to write individual scrapers for major biological data repositories.

主な機能

Metabolic pathway analysis and protein-protein interaction mapping
Unified interface for 40+ bioinformatics services (UniProt, KEGG, ChEMBL, etc.)
Programmatic NCBI BLAST searches and sequence similarity processing
Seamless cross-database identifier mapping (e.g., KEGG to UniProt)
2,188 GitHub stars
Automated protein sequence retrieval and functional annotation extraction

ユースケース

Mapping diverse biological identifiers across multiple scientific databases
Cross-referencing chemical compounds across ChEBI, ChEMBL, and PubChem
Automating high-throughput metabolic pathway and gene function analysis

概要

主な機能

Metabolic pathway analysis and protein-protein interaction mapping
Unified interface for 40+ bioinformatics services (UniProt, KEGG, ChEMBL, etc.)
Programmatic NCBI BLAST searches and sequence similarity processing
Seamless cross-database identifier mapping (e.g., KEGG to UniProt)
2,188 GitHub stars
Automated protein sequence retrieval and functional annotation extraction

ユースケース

Mapping diverse biological identifiers across multiple scientific databases
Cross-referencing chemical compounds across ChEBI, ChEMBL, and PubChem
Automating high-throughput metabolic pathway and gene function analysis