What biological databases does BioServices support?

BioServices provides access to over 40 major services, including UniProt, KEGG, ChEMBL, ChEBI, PubChem, Reactome, and the Protein Data Bank (PDB).

How does BioServices handle different data formats?

It transparently handles XML, JSON, and TSV responses, often integrating with Pandas for tabular data and BioPython for sequence objects.

Does this skill support sequence alignment tools?

Yes, it allows you to run NCBI BLAST jobs and retrieve results asynchronously directly within your Python environment.

Can I use this skill to convert gene or protein IDs?

Yes, it features robust identifier mapping capabilities to convert between formats like UniProt AC, KEGG IDs, Ensembl, and RefSeq.

BioServices Bioinformatics Toolkit

Name: BioServices Bioinformatics Toolkit
Author: Activer007

byActiver007

0•

Data Science & ML

Provides programmatic access to over 40 bioinformatics web services and databases for integrated biological data analysis.

BioServices is a comprehensive Python wrapper that simplifies access to essential bioinformatics resources like UniProt, KEGG, ChEMBL, and PubChem. It enables developers and researchers to perform complex multi-database workflows, including sequence retrieval, pathway analysis, identifier mapping, and compound searches, all through a unified API. By abstracting the complexities of REST and SOAP protocols, it allows Claude to efficiently integrate diverse biological datasets into automated discovery pipelines and data science workflows.

Key Features

01Asynchronous sequence similarity searching via NCBI BLAST

02Automated identifier mapping across heterogeneous biological databases

03Chemical compound searching across ChEMBL, PubChem, and ChEBI

04Unified access to 40+ bioinformatics services including UniProt and KEGG

05Advanced metabolic pathway discovery and network analysis

060 GitHub stars

Use Cases

01Cross-referencing chemical compounds across multiple pharmaceutical databases

02Extracting and exporting protein-protein interaction networks for systems biology

03Automating protein characterization and functional annotation pipelines

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add activer007/ordinary-claude-skills bioservices

For use in Claude.ai and ChatGPT

Download Skill