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tooluniverse-kegg-disease-drug

Maps disease-gene-drug-variant networks using KEGG curated databases.

1.7k|254|Updated Mar 3, 2025
Search Tags:#bioinformatics#pathway analysis#drug repurposing#kegg#drug targets#variant annotation#disease genes
One-click install
npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-kegg-disease-drug
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: tooluniverse-kegg-disease-drug
Source: https://github.com/mims-harvard/ToolUniverse/tree/main/plugins/tooluniverse/skills/tooluniverse-kegg-disease-drug
Command: npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-kegg-disease-drug

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires tooluniverse.

What problem does it solve?

Researchers investigating drug repurposing or disease mechanisms need to connect diseases to causal genes, drugs to molecular targets, and variants to pathways, but these relationships are scattered across KEGG's separate databases and ID namespaces. This Skill orchestrates lookups across KEGG Disease, Drug, Network, Variant, and Pathway to build mechanistic disease-gene-drug networks.

Core Features & Use Cases

  • Disease-Gene-Drug Network Exploration: Search KEGG disease entries, retrieve associated genes, find drugs, and resolve their molecular targets across 12 dedicated tools.
  • ID Conversion & Cross-Linking: Convert identifiers between KEGG and external databases (NCBI Gene, UniProt) and retrieve cross-database relationships such as all genes in a pathway or all drugs linked to a disease.
  • Evidence Grading: Distinguish direct drug-target binding from indirect pathway co-membership, with a grading framework for interpreting result strength.
  • Use Case: Find drugs targeting BRAF variants in cancer by searching KEGG diseases for melanoma, retrieving disease genes, searching for BRAF inhibitors like vemurafenib, and confirming targets and variant annotations.

Quick Start

Ask the agent to find KEGG drugs targeting BRAF variants in melanoma and show the disease-gene-drug network.

Frequently Asked Questions about tooluniverse-kegg-disease-drug

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I find drugs targeting a specific gene in KEGG?▼

Search KEGG drug entries with KEGG_search_drug using the gene or drug name, then call KEGG_get_drug_targets with the drug ID to retrieve confirmed molecular targets. Use KEGG_link_entries to find all drugs linked to a disease or pathway.

How to convert NCBI Gene IDs to KEGG gene IDs?▼

Use KEGG_convert_ids with source_db set to ncbi-geneid and target_db set to hsa for human genes. KEGG uses its own namespace such as hsa:7157 for TP53, so conversion is required before querying KEGG-specific tools.

What is the difference between direct and indirect drug-target relationships in KEGG?▼

A direct relationship means the drug binds the gene product, confirmed in KEGG Network entries. An indirect relationship means the drug affects a pathway containing the gene, inferred from co-membership. Direct relationships are stronger evidence for repurposing hypotheses.

Does KEGG cover all disease-gene associations?▼

No, KEGG coverage is not exhaustive and absence from KEGG does not mean absence of biological involvement. Cross-reference with Reactome, WikiPathways, CTD, ClinVar, or CIViC for broader coverage of diseases and variants.

Why does my KEGG query return no results for a known gene?▼

The most common cause is using external IDs instead of KEGG's own namespace. Convert identifiers first with KEGG_convert_ids, and note that failed conversions may indicate the gene is not in KEGG's curated set.

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