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Drug-Target-Disease Knowledge Graph

Run the Drug-Target-Disease Knowledge Graph MicroSim Fullscreen

About This MicroSim

This MicroSim displays a heterogeneous knowledge graph connecting three entity types: drugs (blue circles), protein targets (green diamonds), and diseases (red squares). Labeled edges show the relationships: drugs "bind" targets, targets are "associated with" diseases, and drugs "treat" diseases.

Node Types and Shapes

  • Drugs (blue circles) — Pharmaceutical compounds
  • Protein Targets (green diamonds) — The molecular targets that drugs act on
  • Diseases (red squares) — Medical conditions

Relationship Types

  • binds (drug → target) — The drug physically interacts with the protein
  • associated_with (target → disease) — The protein is genetically or functionally linked to the disease
  • treats (drug → disease) — The drug is used clinically to treat the disease

Drug Repurposing Paths

The most interesting patterns are indirect paths: a drug binds a target that is associated with a disease the drug was NOT designed to treat. These paths suggest potential drug repurposing opportunities.

How to Use

  1. Click any node to highlight all its direct connections and see the path structure
  2. Hover for node details
  3. Trace paths — Follow Drug → binds → Target → associated_with → Disease to discover drug-target-disease relationships
  4. Look for triangles — When a Drug → Target → Disease path also has a direct Drug → treats → Disease edge, this validates the mechanism

Iframe Embed Code

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        height="550"
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        scrolling="no"></iframe>

Lesson Plan

Grade Level

College introductory bioinformatics

Duration

15-20 minutes

Prerequisites

  • Understanding of drug mechanisms of action
  • Basic knowledge of proteins as drug targets
  • Concept of knowledge graphs

Activities

  1. Exploration (5 min): Identify all three node types by shape and color. Click several drugs and trace their connections to diseases through protein targets.
  2. Path Analysis (5 min): Find a drug that binds a target associated with a disease the drug does NOT currently treat. This is a drug repurposing hypothesis. What additional evidence would you need?
  3. Discussion (5 min): Why is a knowledge graph more useful for drug discovery than three separate tables of drugs, targets, and diseases?
  4. Assessment (5 min): Answer the reflection questions below.

Assessment

  1. What are the three node types and three edge types in this knowledge graph?
  2. How can a Drug → Target → Disease path suggest a drug repurposing opportunity?
  3. Why might a drug that "binds" a target NOT "treat" the associated disease?
  4. What databases would you need to build a real drug-target-disease knowledge graph?

References

  1. Drug repositioning — Wikipedia
  2. Drug target — Wikipedia
  3. Knowledge graph — Wikipedia
  4. Pharmacology — Wikipedia