bioservices

SUMMARY

What it does

This skill provides a unified Python interface to over 40 bioinformatics web services and databases, enabling retrieval of biological data, cross-database queries, identifier mapping, sequence analysis, and integration of multiple biological resources in Python workflows. It supports REST and SOAP/WSDL protocols. The skill includes capabilities for protein analysis (UniProt, PDB, Pfam), pathway discovery (KEGG, Reactome), compound database searches (ChEBI, ChEMBL, PubChem), sequence analysis (BLAST, MUSCLE), identifier mapping (UniProt, UniChem), gene ontology queries (QuickGO), and protein-protein interactions (PSICQUIC, IntactComplex, OmniPath, STRING). It also provides multi-service integration workflows and scripts for common tasks. The skill requires Python 3.9–3.12 and internet access. NCBI BLAST requires a contact email via NCBI_EMAIL environment variable or explicit parameter. Most services do not require API keys. The skill is part of the Scientific Agent Skills library by K-Dense and is distributed under the MIT license (as declared in the submitted record).