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

Yes, it excels at identifier mapping between various databases like UniProtKB, KEGG, Ensembl, RefSeq, and chemical databases via UniChem.

Does it support sequence alignment tools like BLAST?

Yes, the skill provides programmatic methods to run NCBI BLAST jobs and other sequence alignment tools like MUSCLE.

How does BioServices handle different API protocols?

It transparently manages both REST and SOAP/WSDL protocols, providing a consistent, high-level Pythonic interface for all integrated services.

What databases are supported by the BioServices skill?

BioServices supports over 40 services, including UniProt, KEGG, ChEMBL, PubChem, PDB, Reactome, QuickGO, and BioMart.

Is an email address required for NCBI services?

Yes, many services like NCBI BLAST require a valid email address as a parameter to track usage and communicate about job status.

BioServices Bioinformatics Toolkit

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

byK-Dense-AI

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3,717

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Data Science & ML

Accesses over 40 bioinformatics web services and databases through a unified Python API for biological data retrieval and analysis.

BioServices is a comprehensive scientific skill that provides programmatic access to approximately 40 major bioinformatics databases, including UniProt, KEGG, ChEMBL, and PubChem. It simplifies complex biological research workflows by handling REST and SOAP/WSDL protocols transparently, allowing researchers to perform cross-database queries, map identifiers between different standards, and conduct pathway or sequence analysis directly within their coding environment without manually navigating multiple web interfaces.

Key Features

01Unified programmatic access to 40+ bioinformatics databases

02Automated biological pathway discovery and network extraction via KEGG

03Integrated sequence analysis tools including NCBI BLAST and MUSCLE

04Support for chemical compound searches across ChEBI and PubChem

05Robust identifier mapping between UniProt, KEGG, Ensembl, and RefSeq

063,717 GitHub stars

Use Cases

01Mapping biological identifiers across multiple genomic and proteomic databases

02Automating protein sequence retrieval and functional annotation workflows

03Analyzing metabolic pathways and extracting protein-protein interaction networks

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add k-dense-ai/claude-scientific-skills bioservices

For use in Claude.ai and ChatGPT

Download Skill