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curated-bio-datasets

Guide to accessing curated biological datasets for computational biology. COSMIC cancer data, GTEx expression, GWAS catalog, GeneBass exome variants, BioGRID interactions, MSigDB gene sets, DisGeNET disease-gene associations, and GO ontology. For specific database APIs use individual database skills (cosmic-database, gwas-database, etc.).

backend/cli/skills/biology/curated-bio-datasets/SKILL.md

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# Curated Bio-Datasets: Biological Datasets Guide

## Overview

Curated Bio-Datasets provides a comprehensive guide to accessing and working with major curated biological datasets. This skill covers COSMIC cancer genomics data, GTEx tissue expression data, GWAS Catalog SNP-trait associations, GeneBass exome-wide association results, BioGRID protein-protein interaction data, MSigDB gene set collections, DisGeNET disease-gene associations, and Gene Ontology resources. Each section includes download patterns, file formats, parsing code, and integration examples.

## When to Use This Skill

- Downloading and parsing COSMIC cancer gene census data
- Accessing GTEx tissue-level expression data (TPM matrices, eQTLs)
- Querying the GWAS Catalog for SNP-trait associations
- Working with GeneBass exome-wide burden test results
- Building protein-protein interaction networks from BioGRID
- Loading MSigDB gene sets for pathway enrichment analysis