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BioServices Unified Bioinformatics Access

Query 40+ bioinformatics databases (UniProt, KEGG, ChEMBL, Reactome) through one consistent Python interface.

Data & AnalyticsIntermediate★ 41,485⑂ 3,824AI score 9/10Last updated: Aug 31, 2026

What it does

  • Uses the BioServices Python package to access ~40 bioinformatics web services (UniProt, KEGG, ChEBI, ChEMBL, PDB, Reactome, QuickGO, PSICQUIC, BioMart) with one consistent API, handling REST and SOAP transparently.
  • Provides working code for protein search and retrieval, KEGG pathway parsing and interaction network export (SIF), compound cross-referencing, asynchronous NCBI BLAST jobs, and cross-database ID mapping.
  • Ships runnable scripts: protein_analysis_workflow.py, pathway_analysis.py, compound_cross_reference.py, batch_id_converter.py, plus reference docs on services, workflows, and identifier mapping.
  • Documents version pitfalls (UniProt 2022 column renames, ChEMBL 1.6 method changes, PSICQUIC/UniChem helpers missing in 1.16.0) and defensive fallbacks.

Who it's for

  • Bioinformatics researchers and grad students combining data across multiple biological databases.
  • Data analysts who need bulk gene/protein/compound identifier conversion.
  • Developers building reproducible Python pipelines over public biology APIs.

Example uses

  1. "Find ZAP70_HUMAN in UniProt, pull the FASTA, BLAST it, and list its KEGG pathways" → full protein characterization pipeline.
  2. "Map Geldanamycin to its KEGG, ChEBI, and ChEMBL IDs" → UniChem-based compound cross-reference.
  3. "Convert 500 UniProt accessions to KEGG gene IDs" → batch identifier conversion script.

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/bioservices/SKILL.md

What I want: (describe your task here)

If Claude can't open the link, open it yourself and paste the contents instead.

↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the skills/bioservices folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/bioservices/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/bioservices ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Open a terminal and confirm you're on Python 3.9–3.12 (python --version).
  2. Clone the repository: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  3. Copy the skill folder: mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/bioservices ~/.claude/skills/
  4. Install the library: uv pip install "bioservices==1.16.0" (or pip install "bioservices==1.16.0").
  5. If you plan to use NCBI BLAST, set a contact email: export NCBI_EMAIL=your.email@example.com
  6. Restart Claude Code and try a prompt like "Retrieve the FASTA sequence for P43403 from UniProt" to trigger the skill.
View source on GitHub ↗License: MIT