Bioservices

A unified Python interface to 40+ bioinformatics web services including UniProt, KEGG, ChEMBL, and Reactome. This shines when you need to chain queries across multiple databases in a single workflow, like pulling a protein from UniProt, mapping its ID to KEGG, finding associated pathways, then cross-referencing compounds through UniChem to ChEMBL. The API consistency across services is the real win here. Note that it requires Python 3.9–3.12 and live internet access to all those APIs, so offline work is out. NCBI BLAST needs a contact email via environment variable. For quick single-database lookups, gget is faster. For local sequence manipulation, stick with BioPython.

skills.sh installs: 2.1K
GitHub stars: 56.6K
last updated: Aug 21, 2026

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Install

$ npx -y skills add k-dense-ai/scientific-agent-skills --skill bioservices --agent claude-code

Installs into .claude/skills of the current project.

Files

BioServices

When to use

Use BioServices when combining protein annotation, gene/pathway membership, compound cross-references, or genomic resources in Python. Its service clients share transport helpers, but their request parameters and return types differ. Use the service reference before composing clients; method names from PubChemPy, mygene, or older BioServices are not portable.

Targets bioservices 1.16.0, the current PyPI release at review. Package metadata allows Python >=3.9,<4; the bundled tests were run in an isolated Python 3.13 environment. The previous 3.12 upper bound was not a package requirement.