SBGN bricks ontology as a tool to describe recurring concepts in molecular networks

Adrien Rougny, National Institute of Advanced Industrial Science and Technology
Vasundra Touré, Swiss Institute of Bioinformatics
John Albanese, Trinity College Hartford
Dagmar Waltemath, Universitätsmedizin Greifswald
Denis Shirshov, CNRS Centre National de la Recherche Scientifique
Anatoly Sorokin, Insitute of Cell Biophisics RAS
Gary D. Bader, University of Toronto Faculty of Medicine
Michael L. Blinov, School of Medicine
Alexander Mazein, École Normale Supérieure de Lyon


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