What databases does BioServices support?

BioServices provides programmatic access to over 40 services, including major databases like UniProt, KEGG, ChEMBL, PubChem, PDB, and Ensembl.

Can I use this skill for sequence alignment?

Yes, the BioServices skill includes wrappers for NCBI BLAST and other sequence analysis tools, allowing you to run similarity searches and retrieve results asynchronously.

Does it support metabolic pathway analysis?

Yes, it features deep integration with KEGG and Reactome, supporting pathway discovery, gene-to-pathway mapping, and the parsing of KGML files for interaction network analysis.

How does it handle biological identifier mapping?

It provides built-in methods for the UniProt mapping service and UniChem, enabling you to convert identifiers between databases like Ensembl, RefSeq, KEGG, and ChEMBL.

BioServices Bioinformatics Suite

Name: BioServices Bioinformatics Suite
Author: Microck

byMicrock

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Data Science & ML

Accesses and integrates data from over 40 bioinformatics web services and databases using a unified Python API.

BioServices is a comprehensive Python toolkit designed for researchers to programmatically interact with a vast array of biological databases including UniProt, KEGG, and ChEMBL. It simplifies complex workflows like cross-database identifier mapping, metabolic pathway analysis, and sequence alignment by providing a standardized interface for both REST and SOAP protocols. This skill is ideal for building automated biological data pipelines, performing large-scale protein analysis, and synchronizing information across disparate genomic and chemical resources directly within the Claude Code environment.

Key Features

01Seamless identifier mapping and cross-referencing between biological entities

02Unified API for 40+ biological databases including UniProt, KEGG, and PubChem

03Programmatic access to sequence similarity searches like NCBI BLAST

04Advanced metabolic pathway discovery and protein-protein interaction analysis

05Support for multiple data formats including FASTA, XML, JSON, and TSV

0681 GitHub stars

Use Cases

01Automating protein sequence retrieval and functional annotation pipelines

02Extracting and analyzing metabolic pathway networks for specific organisms

03Mapping compound IDs across chemical databases for drug discovery research

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add microck/ordinary-claude-skills bioservices

For use in Claude.ai and ChatGPT

Download Skill