Which databases does the BioServices skill support?

It supports over 40 major bioinformatics services, including UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO, PDB, and Ensembl.

Does it support sequence alignment tools?

Yes, it provides programmatic interfaces for sequence similarity searches such as NCBI BLAST and MUSCLE alignment through their respective web service wrappers.

How does BioServices handle different data formats?

BioServices provides built-in parsers and methods to handle various biological data formats, including XML, JSON, Tab-separated (TSV), and FASTA sequences.

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

Yes, BioServices excels at identifier mapping, allowing you to convert IDs between sources like UniProt, KEGG, and ChEMBL using unified mapping methods and UniChem.

BioServices

Name: BioServices
Author: x-cmd

byx-cmd

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Data Science & ML

Provides programmatic Python access to over 40 bioinformatics web services for biological data retrieval and pathway analysis.

BioServices is a comprehensive Python library designed for bioinformatics researchers and developers, offering a unified interface to interact with major biological databases like UniProt, KEGG, and ChEMBL. It simplifies complex workflows involving protein sequence retrieval, metabolic pathway discovery, identifier mapping across multiple databases, and sequence similarity searches. By abstracting the complexities of REST and SOAP protocols, this skill enables seamless integration of diverse biological data sources into automated Python pipelines for scientific research, genomic analysis, and drug discovery.

Key Features

01Automated identifier mapping across disparate biological and chemical databases

02Asynchronous execution of sequence similarity searches like BLAST and MUSCLE

03Advanced metabolic pathway discovery and protein interaction network analysis

048 GitHub stars

05Unified access to 40+ bioinformatics services including UniProt, KEGG, and ChEMBL

06Comprehensive protein sequence retrieval and functional annotation tools

Use Cases

01Automating cross-database identifier conversion for large-scale genomic datasets

02Building automated drug discovery pipelines for chemical compound search and cross-referencing

03Performing integrated pathway analysis to map protein interactions in specific organisms

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add x-cmd/skill bioservices

For use in Claude.ai and ChatGPT