BioServices

Overview

BioServices is a Python package providing programmatic access to roughly 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.

Recent changes that break old scripts (verified against bioservices 1.16.0):

• SOAP/WSDL support was removed in 1.15 — every active service is REST now, and the WSDLService class and its suds dependency are gone.
• PSICQUIC and BioGRID were removed in 1.14. For protein interactions use the STRING class (added in 1.14) or IntactComplex; from bioservices import PSICQUIC raises ImportError.
• UniProt.mapping() returns the raw UniProt job payload — {"results": [{"from": ..., "to": ...}, ...], "failedIds": [...]} — not a {source_id: [target_ids]} dict. See "Identifier Mapping" below.
• NCBIblast methods are snake_case (get_status, get_result, get_result_types, wait); the old getStatus/getResult camelCase names are gone. 1.16 also adds ncbiblastapi.NCBIBlastAPI, which submits to NCBI directly instead of EBI.