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Unified Python interface to 40+ bioinformatics web services: UniProt proteins, KEGG pathways, ChEMBL/ChEBI/PubChem, BLAST, cross-database ID mapping, GO annotations, PPI. For deep single-DB queries use dedicated tools (gget for Ensembl, pubchempy for PubChem); bioservices excels at cross-database workflows.
Passed 20 of 22 test cases with the skill, and 13 of 22 without it.
and 8 more in the full report
8 fixed12 passed either way1 still failing1 broke
Tokens, turns and time describe resource use, not a dollar price.
One of 8 test cases the skill fixed. Same model, same prompt, with and without the skill.
Write a Python snippet to convert the ChEMBL identifier CHEMBL25 to cross-referenced external compound identifiers using UniChem. What source database ID represents ChEMBL in UniChem mapping calls?
| Checked | Without skill | With skill |
|---|---|---|
| Calls get_mapping on the UniChem service instance. | Missed | Passed |
| Passes source database identifier 1 to indicate ChEMBL as the origin database. | Passed | Passed |
The instructions your model reads when the skill loads.
BioServices provides a unified Python interface to 40+ bioinformatics web services including UniProt, KEGG, ChEMBL, ChEBI, PubChem, UniChem, PSICQUIC, QuickGO, and BLAST. Each service is accessed through a consistent object-oriented API with built-in caching, rate limiting, and output format handling.
pip install bioservices
# Optional: pandas for tabular output, matplotlib for visualization
pip install pandas matplotlib
API Rate Limits: Most services have rate limits. bioservices handles basic throttling internally, but for batch operations add explicit delays:
from bioservices import UniProt, KEGG
import time
# Protein lookup
test cases passed, vs 13 / 22 without
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