alterlab-bioservices

# 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. ## 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 ...