Terms and concepts

Drug–target network

A bipartite graph composed of approved drugs and proteins linked by drug–target binary associations.

Drug repurposing

A strategy for identifying new indications for approved or investigational (including clinically failed) drugs that have not been originally approved or dedicated (also termed drug repositioning, reprofiling or re-tasking).

Disease module

Represents a group of nodes (ie, proteins or genes) whose perturbation can be linked to a particular disease (eg, COVID-19) phenotype.

Systems pharmacology

An inter-discipline that applies systems biology principles and data science techniques in pharmacology.

Human interactome

The set of physical protein–protein interactions (the interactome) in human cells.

Network medicine

A discipline that seeks to redefine disease and therapeutics from an integrated perspective using systems biology and network science methodologies, offering important applications to drug design.

Node or vertex

The basic unit of graphs. Usually visualised as circles (or in other shapes), nodes represent basic entities, such as drugs and proteins.

Edge or link

A basic unit of graphs that connects two nodes. Usually visualised as lines (with arrows if directed), edges represent the relationships (eg, protein interaction) between the nodes.

Network proximity

Measures the distances between two modules, such as drug–target and disease–gene modules. Several proximity measures have been defined, such as shortest, closest, separation, kernel, and centre measures.

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  • Cheng F
  • Desai RJ
  • Handy DE
  • et al.
Network-based approach to prediction and population-based validation of in silico drug repurposing.