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drugmechdb-query

Query DrugMechDB for drug mechanism-of-action paths by entity names or identifiers.

130|4|Updated Mar 13, 2026
Search Tags:#research#bioinformatics#evidence#moa#drugmechdb#drug mechanism#graph paths
One-click install
npx skills add https://github.com/QSong-github/DrugClaw --skill drugmechdb-query
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: drugmechdb-query
Source: https://github.com/QSong-github/DrugClaw/tree/main/skills/drug_mechanism/drugmechdb
Command: npx skills add https://github.com/QSong-github/DrugClaw --skill drugmechdb-query

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Query DrugMechDB for drug mechanism-of-action paths by entity name or ID. Each path is a directed graph connecting a drug to a disease through intermediates, with typed nodes and labeled edges, enabling researchers to trace mechanisms and access supporting data.

Core Features & Use Cases

  • Entity auto-detection and flexible lookup (DrugBank IDs, MESH IDs, UniProt IDs, GO terms, and free-text queries).
  • API-style access: load, build_index, search, search_batch, summarize, and to_json to retrieve and summarize MoA paths.
  • Presentable results: structured paths with node/edge details and evidence sources for research reproducibility.

Quick Start

Run a sample query against DrugMechDB by supplying a drug name or identifier to retrieve mechanism paths.

Frequently Asked Questions about drugmechdb-query

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

FAQPage Schema
How do I find drug mechanism-of-action paths using a DrugBank ID or protein name?▼

You can find drug mechanism paths by querying with exact identifiers like DrugBank, MESH, UniProt, or GO terms. The tool also supports free-text lookups to retrieve structured MoA paths connecting drugs to diseases.

What is a mechanism-of-action path in DrugMechDB?▼

A mechanism-of-action path is a directed graph connecting a drug to a disease through intermediates. It features typed nodes, labeled edges, and evidence sources, enabling researchers to trace mechanisms and access supporting data.

Can I retrieve drug MoA paths in bulk for multiple entities?▼

Yes, you can retrieve drug MoA paths in bulk using the search_batch function. This allows you to input multiple entity names or identifiers and receive structured results for each.

Does the drug mechanism query tool support UniProt and GO term lookups?▼

Yes, the query tool supports UniProt and GO term lookups alongside DrugBank and MESH identifiers. It auto-detects entity types and performs flexible free-text searches to retrieve matching MoA paths.

How do I get structured JSON output with evidence sources for drug mechanism paths?▼

You can use the to_json and summarize functions to export structured JSON output. The results include complete node and edge details alongside evidence sources for research reproducibility.

What are the limitations of querying DrugMechDB for mechanism paths?▼

Querying relies on loading indication_paths.json and building an index for lookup. Results depend on the database's existing typed nodes and labeled edges, meaning mechanisms outside its curated coverage will not be returned.

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