Agent skill · research science · k-dense-ai
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.
Why this skill is useful
Provides access to 40+ bioinformatics APIs with specific methods for cross-database queries and data retrieval that the AI wouldn't reliably generate on its own.
What it needs
Requires python installed locally. About 6k tokens when loaded. Last updated 2026-08-03. 32,849 stars on the source repository.
What this skill does
BioServices Overview BioServices is a Python package providing programmatic access to approximately 40 bioinformatics web services and databases. Retrieve biological data, perform cross-database queries, map identifiers, analyze sequences, and integrate multiple biological resources in Python workflows. The package handles both REST and SOAP/WSDL protocols transparently. Version note: Examples target bioservices 1.16.0 (PyPI, Mar 2026). Requires Python 3.9–3.12. UniProt REST changes in mid-2022 (bioservices ≥1.10) mainly affect tabular columns names — see upstream legacynames if parsing breaks. ChEMBL wrappers changed at 1.6.0 (2018 API); use getsimilarity, getsubstructure, getmolecule instead of pre-1.6 method names. When to Use This Skill This skill should be used when: Retrieving protein sequences, annotations, or structures from UniProt, PDB, Pfam Analyzing metabolic pathways and gene functions via KEGG or Reactome Searching compound databases (ChEBI, ChEMBL, PubChem) for chemical information Converting identifiers between different biological databases (KEGG↔UniProt, compound IDs) Running sequence similarity searches (BLAST, MUSCLE alignment) Querying gene ontology terms (QuickGO, GO annotations) Accessing protein-protein interaction data (PSICQUIC, IntactComplex) Mining genomic data (BioMart, ArrayExpress, ENA) Integrating data from multiple bioinformatics resources in a single workflow Core Capabilities 1. Protein Analysis Retrieve protein information, sequences, and functional annotations: Key methods: search(): Query UniProt with flexible search terms retrieve(): Get protein entries in various formats (FASTA, XML, tab) mapping(): Convert identifiers between databases Reference: references/servicesreference.md for complete UniProt API details. 2. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills k-dense-ai/bioservices