Can I perform pathway analysis with this skill?

Absolutely. You can retrieve pathway data from KEGG or Reactome, find pathways associated with specific genes, and extract structured protein-protein interaction data.

What databases does the BioServices skill support?

BioServices provides access to over 40 major biological services including UniProt, KEGG, ChEMBL, Reactome, PDB, NCBI BLAST, and QuickGO.

Does BioServices handle SOAP and REST protocols?

Yes, the skill transparently handles both REST and SOAP/WSDL protocols, providing a consistent Pythonic interface regardless of the underlying service architecture.

Can I use this skill to map identifiers between different databases?

Yes, BioServices is specifically designed for cross-database mapping, allowing you to convert IDs between services like UniProt, KEGG, Ensembl, and RefSeq.

How does BioServices differ from Biopython?

While Biopython is excellent for local sequence manipulation and file parsing, BioServices focuses on programmatic access to remote web services and database integration.

BioServices Bioinformatics Toolkit

Name: BioServices Bioinformatics Toolkit
Author: Yezez9

byYezez9

0•

数据科学与机器学习

Provides a unified Python interface to over 40 bioinformatics web services and databases for integrated biological data analysis.

BioServices is a comprehensive Python library that streamlines programmatic access to major biological databases, including UniProt, KEGG, ChEMBL, and Reactome. This skill enables researchers and developers to perform complex, multi-service workflows such as protein characterization, metabolic pathway discovery, and cross-database identifier mapping without managing individual API protocols. It serves as an essential tool for bioinformatics pipelines requiring automated data integration from disparate biological resources, providing a consistent API for both REST and SOAP/WSDL services.

主要功能

01Unified access to 40+ bioinformatics web services including UniProt, KEGG, and ChEMBL

02Cross-database identifier mapping (e.g., KEGG to UniProt, ChEMBL to PubChem)

03Asynchronous sequence similarity searches using NCBI BLAST and MUSCLE alignment

04Advanced protein sequence retrieval and functional annotation mapping

05Metabolic pathway discovery and protein interaction network extraction

060 GitHub stars

使用场景

01Extracting and analyzing protein-protein interaction networks for specific metabolic pathways

02Automating multi-step protein characterization pipelines from sequence to pathway analysis

03Batch converting biological identifiers across diverse genomic and proteomic databases

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add yezez9/research-agent bioservices

For use in Claude.ai and ChatGPT