bioservices
Provides a Python interface to bioinformatics services including UniProt, KEGG
by k-dense-aiFree
Description
bioservices is an agent skill that gives a Python interface to bioinformatics web services, including UniProt, KEGG, ChEMBL, Reactome, QuickGO and UniChem. It is used when you need to combine protein annotation, gene and pathway membership, compound cross-references or genomic resources in one workflow. The skill warns that the service clients share transport helpers, but their request parameters and return types differ, so you should read the service reference before composing calls. It also warns that method names from PubChemPy, mygene or older BioServices versions are not portable. The skill targets bioservices 1.16.0, the current PyPI release at the time of its review. Its package metadata allows Python 3.9 up to 4, and its bundled tests were run in an isolated Python 3.13 environment. The install command is uv pip install with bioservices pinned to 1.16.0. The skill is part of the k-dense-ai scientific agent skills repository on GitHub, which has about 49,600 stars. The listing shows it as free, and it has about 1,800 installs. Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.…
Highlights
- One Python interface to several biology databases
- UniProt, KEGG, ChEMBL, Reactome, QuickGO and UniChem
- Cross-database protein annotation
- Service reference before composing calls
- Pinned to bioservices 1.16.0
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bioservices FAQ
Which services does it cover?
UniProt, KEGG, ChEMBL, Reactome, QuickGO and UniChem, among others, through one Python interface.
When is it useful?
When combining protein annotation, gene and pathway membership, compound cross-references or genomic resources.
Are method names the same as other libraries?
No. The skill warns that names from PubChemPy, mygene or older BioServices versions are not portable.
Which version does it target?
bioservices 1.16.0, the current PyPI release at the time of review, tested on Python 3.13.
How do I install it?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill bioservices, then install the library with uv pip install bioservices==1.16.0.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.
What are the best bioservices alternatives?
Popular alternatives to bioservices include database-lookup, gget and fastapi-patterns. See all bioservices alternatives