Individual skill

bioservices

Unified Python access to 40+ bioinformatics web services; use when you need to query multiple databases (e.g., UniProt/KEGG/ChEMBL/Reactome) with one consistent API in a single workflow, especially for cross-database analysis and identifier mapping.

scientific-skills/Data Analysis/bioservices/SKILL.md

Read pinned source

Source commit 686e09dfdb45d9fa1a08664f06bb93769b3c9d91

What was checked

Matches the observed repository HEAD: Yes
Scanner rules are current: Yes
Repository scan complete: No
Skill scan complete: No
Observed behavior: Network or broad shell
Last checked: Nov 9, 2026

These are observations at the recorded commit, not a guarantee of safety. Review the source before running it.

Install this skill

Choose an agent in your Stack or copy a command below. Commands fetch the pinned commit and copy only this skill directory. Existing destinations are refused. Copying a command does not install anything.

An install command is unavailable: current rules, complete repository and skill scans, an eligible behavior level and a permitted license are required.

Repository context

Repository stars (not skill ratings): 2,039
Repository last updated: Sep 17, 2026
License: MIT

Observed agent integration: No specific integration evidence. Standard SKILL.md installation does not imply verified compatibility.

bioinformatics Repository topic
computational-biology Repository topic
data-analysis Repository topic
ai Repository topic
biology Repository topic
cancer-genomics Repository topic
data-visualization Repository topic
differential-expression Repository topic
genomics Repository topic
medical Repository topic
operations Derived category
data Derived category
data-databases Derived category

Files and excerpt

File metadata and permitted, redacted excerpts come from the recorded scan. Source links are pinned to that commit.

Browse files

SKILL.mdcore · 6,954 bytes
SKILL.mdcore · 6,954 bytes
bioservices_audit_result_v1.jsonasset · 12,364 bytes
references/identifier_mapping.mddoc · 18,407 bytes
references/services_reference.mddoc · 13,941 bytes
references/workflow_patterns.mddoc · 21,051 bytes
scripts/batch_id_converter.pyruns · 11,239 bytes
scripts/compound_cross_reference.pyruns · 11,667 bytes
scripts/pathway_analysis.pyruns · 9,856 bytes
scripts/protein_analysis_workflow.pyruns · 12,857 bytes

Read excerpt

> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)

## When to Use

- You need to **retrieve and combine biological data from multiple databases** (e.g., UniProt + KEGG + GO) in one Python workflow.
- You need **cross-database identifier mapping** (e.g., UniProt ↔ KEGG, KEGG compound ↔ ChEMBL) as part of downstream analysis.
- You want to **programmatically explore pathways and networks** (e.g., KEGG pathway parsing, exporting interactions to SIF).
- You need **service-agnostic access** across many providers (REST and SOAP/WSDL) without writing custom clients per service.
- You are building **integrated bioinformatics pipelines** (protein → sequence → BLAST → pathways → interactions) that span multiple resources.

## Key Features

- **Unified API** for ~40+ bioinformatics services (single Python package, consistent patterns).
- **Transparent protocol handling** (REST and SOAP/WSDL).
- **Protein-centric workflows** via UniProt (search, retrieve, ID mapping).