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", []))

Use frmt="tsv", not "tab"; current field names include accession, gene_names, organism_name, protein_name, go_id, and xref_pdb. mapping() returns a results/failedIds envelope, not a source-to-list dictionary. Mapping to UniProt uses to="UniProtKB" and returns full records in row["to"]; extract primaryAccession. UniProtKB_AC-ID is a source code. See identifier mapping for allowed pairs, normalization, and limits. For bounded searches set size=limit (at most 500); 1.16.0 mixes the two values in its pagination loop.

KEGG pathways and networks

from bioservices import KEGG

k = KEGG(verbose=False)
k.services.url = "https://rest.kegg.jp"
pathway_names = k.get_pathway_by_gene("7535", "hsa")  # dict: pathway ID -> name
print(pathway_names)
kgml = k.parse_kgml_pathway("hsa04660")
entries = {entry["id"]: entry for entry in kgml["entries"]}
for relation in kgml["relations"][:5]:
    print(entries[relation["entry1"]]["name"], relation["name"],
          entries[relation["entry2"]]["name"])

The reviewed /list/organism endpoint returned HTTP 400 despite remaining in the manual. SDK methods that validate against that catalogue can fail. The bundled compound and pathway-list scripts use the documented scoped endpoints through k.services.http_get to avoid that unrelated catalogue dependency.

KEGG get permits at most ten entries; KGML permits one pathway per request. Keep requests at or below three per second. list/find return TSV strings; get returns a flat-file string unless an option changes the representation. KGML entries include genes, compounds, groups, and maps. A relation can produce several subtype records; those counts are neither unique genes nor independent physical interactions. Entry IDs are local to each pathway. The bundled SIF export namespaces them as pathway#entry so combining pathways cannot merge unrelated nodes. pathway2sif(..., uniprot=False) is an optional lossy projection of gene-to-gene activation/inhibition, not a complete pathway network.

Compound cross-references

from bioservices import UniChem

uc = UniChem(verbose=False)

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