bioservices

BioServices

When to use

Use BioServices when combining protein annotation, gene/pathway membership, compound cross-references, or genomic resources in Python. Its service clients share transport helpers, but their request parameters and return types differ. Use the service reference before composing clients; method names from PubChemPy, mygene, or older BioServices are not portable.

Targets bioservices 1.16.0, the current PyPI release at review. Package metadata allows Python >=3.9,<4; the bundled tests were run in an isolated Python 3.13 environment. The previous 3.12 upper bound was not a package requirement.

uv pip install "bioservices==1.16.0"

Workflow

1. Resolve the requested organism and entity to stable accessions. Review search hits before selecting one; gene symbols and compound names may be ambiguous.
2. Inspect the service's actual response type, including pagination and errors. BioServices can return an integer-like HTTP error or None, not only raise.
3. Preserve one-to-many mappings, failed identifiers, taxonomy, database release, query parameters, and retrieval date alongside derived tables.
4. Distinguish annotations and inferred associations from experimental evidence. Pathway membership alone is not an enrichment analysis or causal finding.
5. Run a small lookup before batching; honor provider limits and retain failures separately from confirmed empty results.

Protein search, sequence retrieval, and mapping

from bioservices import UniProt

u = UniProt(verbose=False)
u.services.TIMEOUT = 30
rows = u.search(
    "gene_exact:ZAP70 AND organism_id:9606 AND reviewed:true",
    frmt="tsv", columns="accession,gene_names,organism_name,length",
    limit=5, size=5,
)
if not isinstance(rows, str):
    raise RuntimeError("UniProt search failed")
print(rows)
fasta = u.retrieve("P43403", frmt="fasta")
record = u.retrieve("P43403", frmt="json")

mapping = u.mapping(fr="UniProtKB_AC-ID", to="KEGG", query="P43403")
if not isinstance(mapping, dict) or "results" not in mapping:
    raise RuntimeError("Mapping incomplete or failed")
kegg_ids = [row["to"] for row in mapping["results"] if row["from"] == "P43403"]
print(kegg_ids, mapping.get("failedIds", []))