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)
response = uc.get_compounds("CHEBI:15365", "chebi")  # aspirin
if not isinstance(response, dict) or "compounds" not in response:
    raise RuntimeError("UniChem request failed")
chembl_ids = sorted({source["compoundId"]
    for match in response["compounds"] for source in match.get("sources", [])
    if source.get("shortName") == "chembl"})
print(chembl_ids)

UniChem 2 uses POST /api/v1/compounds with a JSON body; BioServices assembles it. Discover source names through uc.source_ids; KEGG is absent at review. From a KEGG compound, preserve every ChEBI cross-reference and use only a uniquely resolved, structurally reviewed candidate. Check charge, stereochemistry, salts, and parent forms before merging data. Multiple unresolved name hits or mappings remain unresolved in the bundled compound script. Empty results do not prove absence.

QuickGO annotations

from bioservices import QuickGO

g = QuickGO(verbose=False)
terms = g.get_go_terms("GO:0003824")  # list of term dictionaries
page = g.Annotation(geneProductId="UniProtKB:P43403", includeFields="goName",
                    limit=100, page=1)
if not isinstance(page, dict) or "results" not in page:
    raise RuntimeError("QuickGO request failed")
for annotation in page["results"][:5]:
    print(annotation["goId"], annotation["goName"], annotation["goAspect"])
print(page["pageInfo"])  # current, total, resultsPerPage

Term, Annotation(protein=..., format="tsv"), and fixed TSV column offsets belong to the old API. Fetch pages 1 through pageInfo.total; the SDK permits 1–100 rows per page. Preserve qualifiers, evidence codes, references and taxon. The protein script summarizes distinct positive terms and excludes NOT assertions; its summary is not a raw annotation export or an enrichment test.

Sequence similarity and associations

NCBIblast wraps EMBL-EBI Job Dispatcher, not NCBI's BLAST URL API. The SDK's current methods are get_status, get_result, get_result_types, and get_parameter_details. Contact email is required by EMBL-EBI; this skill's NCBI_EMAIL variable is a local convention, not automatically read by the SDK. The submission example is illustrative; no live BLAST job was submitted in review.

import os
from bioservices import NCBIblast

blast = NCBIblast(verbose=False)
blast.services.url = "https://www.ebi.ac.uk/Tools/services/rest/ncbiblast"
# protein_sequence must contain the actual query sequence.
job_id = blast.run(program="blastp", sequence=protein_sequence, stype="protein",
                   database="uniprotkb", email=os.environ["NCBI_EMAIL"])
status = blast.get_status(job_id)
if status == "FINISHED":
    result_types = blast.get_result_types(job_id)
    report = blast.get_result(job_id, "out")

Poll with a delay and deadline. Stop on FAILURE, ERROR, or NOT_FOUND; only retrieve completed jobs. Retain the job ID when a local wait times out. Use the bundled script's bounded polling rather than an unbounded loop.

PSICQUIC is absent from 1.16.0. Use STRING.get_interaction_partners for scored associations and provide the verified taxonomy ID; this is a different evidence source, not an equivalent PSICQUIC replacement. STRING's default functional edges can be indirect and do not establish physical binding.

Bundled workflows

Run from this skill directory after installation:

python scripts/protein_analysis_workflow.py P43403 --skip-blast
python scripts/pathway_analysis.py hsa output_directory/ --limit 2
python scripts/compound_cross_reference.py Geldanamycin
python scripts/batch_id_converter.py input_ids.txt --from UniProtKB_AC-ID --to KEGG
python scripts/batch_id_converter.py --list-databases

• Protein analysis: UniProt, optional BLAST, all mapped KEGG genes, STRING associations, paginated QuickGO terms. Prefer a stable accession; free-text searches display and use the first hit.
• Pathway analysis: KGML entry/subtype counts and CSV/SIF exports. Missing KGML is reported and skipped.
• Compound lookup: unique exact KEGG name match (or sole hit), all ChEBI candidates, guarded UniChem mapping, ChEBI/ChEMBL properties.
• Batch converter: preserves multiple targets; CSV distinguishes Success, explicit Unmapped, and request/incomplete Failed.

See workflow patterns for integration examples. Network smoke tests covered the public core lookups; unit tests use current response fixtures. Genome-scale downloads, paid/authenticated resources, and live BLAST submissions were not tested. Service availability is not guaranteed.

Sources and service limits

Current signatures were checked against the 1.16.0 SDK documentation and installed source. Provider contracts: UniProt mapping fields, KEGG API, QuickGO API, Job Dispatcher, STRING API. Configure timeouts on the actual transport, e.g. k.services.TIMEOUT = 30; k.TIMEOUT = 30 merely creates an unused attribute on many wrapper classes. Use cache=True in supported constructors; CACHE/DELAY are not uniform BioServices controls. STRING 1.16.0 issues direct requests without the transport's timeout or rate limiter; bound large workflows externally and use provider bulk downloads when appropriate.