bioservices-multi-database
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.
npx skills add BioTender-max/awesome-bio-agent-skills --skill bioservices-multi-database --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
What it does
The skill offers a unified Python API to access multiple bioinformatics services (UniProt, KEGG, ChEMBL, ChEBI, PubChem, UniChem, PSICQUIC, QuickGo, BLAST, and more) with built-in caching, rate limiting, and output format handling. It supports protein queries, pathway discovery, cross-database identifier mappings, GO annotations, protein interactions, and batch identifier conversion across databases.
How it works
- Provides initialization and usage patterns for services such as UniProt, KEGG, ChEMBL, ChEBI, UniChem, NCBIblast, PSICQUIC, QuickGO, and KEGG parsing.
- Demonstrates typical operations: search/retrieve UniProt data, map identifiers, list and parse KEGG pathways, KGML parsing, cross-database compound lookups, PubChem/ChEMBL/ChEBI lookups, BLAST job submission and polling, and batch ID mapping.
- Includes example code blocks for core API interactions, including mapping, pathway discovery, and GO annotations.
- Shows how to perform cross-database workflows and batch processing with rate-limiting guidance.
When to use it
- For protein information from UniProt (search, retrieve, ID mapping)
- For discovering KEGG pathways and extracting networks
- For cross-referencing compounds across ChEMBL, ChEBI, PubChem, and KEGG
- For BLAST sequence similarity searches against UniProtKB
- For mapping identifiers between databases (UniProt, Ensembl, KEGG, RefSeq, PDB)
- For GO annotations via QuickGO and protein interactions via PSICQUIC
- For batch converting thousands of identifiers with error handling
- When performing cross-database workflows and needing a consistent API across services
What it can touch
- Uses service clients like UniProt, KEGG, ChEMBL, ChEBI, UniChem, NCBIblast, PSICQUIC, QuickGO, and others as shown in examples.
- The code examples call methods such as
retrieve,mapping,get_pathway_by_gene,parse,get,Annotation, andqueryacross these services.
Caveats
- API rate limits are noted for several services (e.g., UniProt mapping ~1 request/second; KEGG 10 requests/second; ChEMBL/ChEBI 5-10; BLAST ~1 job at a time with async polling).
- Requires installation of
bioservicesand optionallypandasandmatplotlibfor certain outputs. - Some sections mention using dedicated tools for deep single-DB queries (gget for Ensembl, pubchempy for PubChem).
- Licensing shown as GPLv3 in the skill description; license field in metadata indicates NOASSERTION.
# BioServices Multi-Database Access ## Overview 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. ## When to Use - Querying protein information from UniProt (search, retrieve, ID mapping) - Discovering KEGG pathways and extracting gene/interaction networks - Cross-referencing compounds across ChEMBL, ChEBI, PubChem, and KEGG - Running BLAST sequence similarity searches against UniProtKB - Mapping identifiers between biological databases (UniProt, Ensembl, KEGG, RefSeq, PDB) - Retrieving Gene Ontology annotations via QuickGO - Finding protein-protein interactions via PSICQUIC (IntAct, MINT, BioGRID) - Batch converting thousands of biological identifiers with error handling - For single-database deep queries → use gget (Ensembl), pubchempy (PubChem), or chembl-database skill - For pathway visualization → use pathway analysis tools (Cytoscape, NetworkX) after retrieving data with bioservices ## Prerequisites ```bash pip install bioservi
- Overview
- When to Use
- Prerequisites
- Quick Start
- Core API
- 1. Protein Analysis (UniProt)
- 2. Pathway Discovery (KEGG)
- 3. Compound Databases (ChEMBL, ChEBI, UniChem, PubChem)
- 4. Sequence Analysis (BLAST)
- 5. Identifier Mapping
- 6. Gene Ontology & Protein Interactions
- Key Concepts
- Service Initialization & Verbosity
- Output Format Handling
pip install bioservices pip install pandas matplotlib
What does the bioservices-multi-database skill do?
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.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill bioservices-multi-database --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.