Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for
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Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for
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LanguagePython
LicenseMIT
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</> SKILL.md
bioservices.SKILL.md
---name: bioservices
description: Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.
license: GPLv3 license
allowed-tools: Read Write Edit Bash
compatibility: Requires Python 3.9–3.12 and internet access to 40+ bioinformatics web APIs. NCBI BLAST requires a contact email (`NCBI_EMAIL` env var or explicit parameter).
required_environment_variables: [{"name": "NCBI_EMAIL", "prompt": "Email for NCBI service identification.", "required_for": "optional features"}]
metadata: {"version": "1.2", "skill-author": "K-Dense Inc.", "openclaw": {"envVars": [{"name": "NCBI_EMAIL", "required": false, "description": "Email for NCBI service identification."}]}}
---# BioServices
## Overview
BioServices is a Python package providing programmatic access to approximately 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. The package handles both REST and SOAP/WSDL protocols transparently.
**Version note:** Examples target **bioservices 1.16.0** (PyPI, Mar 2026). Requires **Python 3.9–3.12**. UniProt REST changes in mid-2022 (bioservices ≥1.10) mainly affect tabular `columns` names — see upstream `_legacy_names` if parsing breaks. ChEMBL wrappers changed at 1.6.0 (2018 API); use `get_similarity`, `get_substructure`, `get_molecule` instead of pre-1.6 method names.
Reference: `references/identifier_mapping.md` for complete cross-database mapping guide.
### 4. Sequence Analysis
Run BLAST searches and sequence alignments. NCBI requires a contact email — prefer the `NCBI_EMAIL` environment variable (same convention as BioPython Entrez and other repo skills):
```python
import os
from bioservices import NCBIblast
s = NCBIblast(verbose=False)
email = os.environ["NCBI_EMAIL"] # set before running: export NCBI_EMAIL=you@lab.org
# Run BLASTP against UniProtKB
jobid = s.run(
program="blastp",
sequence=protein_sequence,
stype="protein",
database="uniprotkb",
email=email,
)
# Check job status and retrieve results
s.getStatus(jobid)
results = s.getResult(jobid, "out")
```
**Note:** BLAST jobs are asynchronous. Check status before retrieving results.
### 5. Identifier Mapping
Convert identifiers between different biological databases:
