SBGN Bricks Ontology As a Tool to Describe Recurring Concepts in Molecular Networks

Overview

Journal Brief Bioinform

Publisher Oxford University Press

Specialty Biology

Date 2021 Mar 24

PMID 33758926

Citations 5

Authors

Adrien Rougny

Vasundra Toure

John Albanese

Dagmar Waltemath

Denis Shirshov

Anatoly Sorokin

Gary D Bader

Michael L Blinov

Alexander Mazein

Affiliations

Soon will be listed here.

Abstract

A comprehensible representation of a molecular network is key to communicating and understanding scientific results in systems biology. The Systems Biology Graphical Notation (SBGN) has emerged as the main standard to represent such networks graphically. It has been implemented by different software tools, and is now largely used to communicate maps in scientific publications. However, learning the standard, and using it to build large maps, can be tedious. Moreover, SBGN maps are not grounded on a formal semantic layer and therefore do not enable formal analysis. Here, we introduce a new set of patterns representing recurring concepts encountered in molecular networks, called SBGN bricks. The bricks are structured in a new ontology, the Bricks Ontology (BKO), to define clear semantics for each of the biological concepts they represent. We show the usefulness of the bricks and BKO for both the template-based construction and the semantic annotation of molecular networks. The SBGN bricks and BKO can be freely explored and downloaded at sbgnbricks.org.

Citing Articles

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Mazein I, Rougny A, Mazein A, Henkel R, Gutebier L, Michaelis L Brief Bioinform. 2024; 25(6).

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Vega C, Ostaszewski M, Groues V, Schneider R, Satagopam V Database (Oxford). 2024; 2024.

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A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance.

Mazein A, Acencio M, Balaur I, Rougny A, Welter D, Niarakis A Front Bioinform. 2023; 3:1197310.

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