bioservices

1# BioServices
2 
3## When to use
4 
5Use BioServices when combining protein annotation, gene/pathway membership,
6compound cross-references, or genomic resources in Python. Its service clients
7share transport helpers, but their request parameters and return types differ.
8Use [the service reference](references/services_reference.md) before composing
9clients; method names from PubChemPy, mygene, or older BioServices are not portable.
10 
11Targets **bioservices 1.16.0**, the current PyPI release at review. Package metadata
12allows Python >=3.9,<4; the bundled tests were run in an isolated Python 3.13
13environment. The previous 3.12 upper bound was not a package requirement.
14 
15```bash
16uv pip install "bioservices==1.16.0"
17```
18 
19## Workflow
20 
211. Resolve the requested organism and entity to stable accessions. Review search
22   hits before selecting one; gene symbols and compound names may be ambiguous.
232. Inspect the service's actual response type, including pagination and errors.
24   BioServices can return an integer-like HTTP error or `None`, not only raise.
253. Preserve one-to-many mappings, failed identifiers, taxonomy, database release,
26   query parameters, and retrieval date alongside derived tables.
274. Distinguish annotations and inferred associations from experimental evidence.
28   Pathway membership alone is not an enrichment analysis or causal finding.
295. Run a small lookup before batching; honor provider limits and retain failures
30   separately from confirmed empty results.
31…