bioservices
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.
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BioServices - Unified Bioinformatics Database Interface
Skills Overview
BioServices is a Python package that provides a unified interface to access 40+ bioinformatics databases and web services, including UniProt, KEGG, ChEMBL, Reactome, and more. It supports cross-database queries, ID mapping, and sequence analysis.
Applicable Scenarios
1. Cross-database Protein Analysis
When you need to integrate data from multiple bioinformatics databases—such as querying UniProt for protein sequences, KEGG for pathway information, and PSICQUIC for interaction data—BioServices offers a consistent API so you don't need to learn each database's calling methods separately.
2. Bio-database Identifier Conversion
When mapping identifiers between different databases—such as converting UniProt IDs to KEGG IDs, or converting compound IDs among ChEMBL, ChEBI, and KEGG—BioServices' built-in mapping features can handle batch conversion tasks.
3. Sequence and Compound Data Retrieval
When you need to run BLAST sequence searches, query protein structure information, or search compound information across databases, BioServices wraps services like NCBI BLAST, PDB, and UniChem, simplifying data retrieval workflows.
Core Features
1. Protein and Sequence Analysis
Search proteins via the UniProt service, retrieve FASTA sequences and functional annotations, use NCBI BLAST for sequence similarity searches, and support fetching protein structure information from PDB.
2. Pathway and Gene Function Analysis
Access KEGG and Reactome databases, search metabolic pathways by gene or pathway name, extract protein interaction networks within pathways, and support parsing pathway data in KGML format.
3. Cross-database ID Mapping
Perform bidirectional identifier conversion among UniProt, KEGG, Ensembl, PDB, RefSeq, and other databases, support batch ID conversion, and map compound IDs among ChEMBL, ChEBI, and KEGG via the UniChem service.
Frequently Asked Questions
Which bioinformatics databases does BioServices support?
BioServices supports 40+ bioinformatics services, including: UniProt (proteins), KEGG (pathways), ChEMBL/ChEBI (compounds), PDB (structures), Reactome (pathways), PSICQUIC (interactions), QuickGO (Gene Ontology), BioMart, ArrayExpress, ENA, and more. See the official documentation for the full list.
What’s the difference between BioServices, gget, and BioPython?
These tools can be used complementarily: retrieve data with BioServices and perform sequence analysis with BioPython.
How to batch-convert protein IDs?
Use the UniProt service's mapping method to perform batch conversions. For example, to convert UniProt IDs to KEGG IDs:
from bioservices import UniProt
u = UniProt()
results = u.mapping(fr="UniProtKB_AC-ID", to="KEGG", query="P43403,P12345")Compound ID conversions can be done using the UniChem service. See the project's batch_id_converter.py script for detailed batch conversion examples.