Comparing Classical Pathways and Modern Networks: Towards the Development of an Edge Ontology

TL;DR

This paper explores integrating classical biological pathways with modern network data, highlighting the need for a standardized edge ontology to better represent pathway interactions and crosstalk.

Contribution

It proposes a prototype for an edge ontology to unify pathway representations and improve the integration of classical and modern network data.

Findings

Embedding pathways in large-scale networks reveals crosstalk.

Current edge representations are inadequate for detailed pathway information.

A prototype edge ontology is proposed as a foundational step.

Abstract

Pathways are integral to systems biology. Their classical representation has proven useful but is inconsistent in the meaning assigned to each arrow (or edge) and inadvertently implies the isolation of one pathway from another. Conversely, modern high-throughput experiments give rise to standardized networks facilitating topological calculations. Combining these perspectives, we can embed classical pathways within large-scale networks and thus demonstrate the crosstalk between them. As more diverse types of high-throughput data become available, we can effectively merge both perspectives, embedding pathways simultaneously in multiple networks. However, the original problem still remains - the current edge representation is inadequate to accurately convey all the information in pathways. Therefore, we suggest that a standardized, well-defined, edge ontology is necessary and propose a prototype here, as a starting point for reaching this goal.