What databases are supported by BioServices?

BioServices supports over 40 services, including major repositories like UniProt, KEGG, ChEMBL, PubChem, PDB, Reactome, and Ensembl.

How does BioServices handle different data formats?

The package handles REST and SOAP protocols transparently and provides methods to parse XML, JSON, and tabular data into Python-friendly structures.

Does it support sequence analysis like BLAST?

Yes, the skill includes interfaces for NCBIblast to run sequence similarity searches and retrieve alignment results programmatically.

Is an email address required for these services?

Some specific services, such as NCBI BLAST, require a user email address as part of their API usage policy to prevent abuse.

Can I use this for identifier mapping?

Yes, it provides robust tools to convert identifiers between various databases, such as mapping UniProtKB IDs to KEGG or Ensembl.

BioServices Bioinformatics Toolbox

Name: BioServices Bioinformatics Toolbox
Author: BbgnsurfTech

byBbgnsurfTech

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データサイエンスとML

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

概要

BioServices is a comprehensive Python interface designed to simplify the retrieval and analysis of biological data from major databases like UniProt, KEGG, ChEMBL, and PubChem. It enables researchers and developers to perform complex cross-database queries, map identifiers between disparate resources, analyze metabolic pathways, and run sequence alignments through a unified API. By abstracting the complexities of REST and SOAP protocols, it serves as an essential bridge for creating reproducible bioinformatics pipelines and integrating heterogeneous biological information into data science and machine learning workflows.

主な機能

Automated identifier mapping between major biological databases (KEGG, Ensembl, PDB)
Support for multiple data formats including XML, JSON, TSV, and FASTA
Programmatic sequence similarity searches (BLAST) and alignments
Metabolic pathway discovery and protein interaction network analysis
3 GitHub stars
Unified access to 40+ bioinformatics services including UniProt, KEGG, and ChEMBL

ユースケース

Cross-referencing chemical compounds across drug discovery databases
Building automated pipelines for protein characterization and functional annotation
Mapping gene lists to biological pathways and interaction networks

概要

主な機能

Automated identifier mapping between major biological databases (KEGG, Ensembl, PDB)
Support for multiple data formats including XML, JSON, TSV, and FASTA
Programmatic sequence similarity searches (BLAST) and alignments
Metabolic pathway discovery and protein interaction network analysis
3 GitHub stars
Unified access to 40+ bioinformatics services including UniProt, KEGG, and ChEMBL

ユースケース

Cross-referencing chemical compounds across drug discovery databases
Building automated pipelines for protein characterization and functional annotation
Mapping gene lists to biological pathways and interaction networks