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Pascual Lorente (1), Konstantinos Sidiropoulos (1), Guilherme Viteri(1), Lincoln Stein (2,3), Guanming Wu (4), Peter d’Eustachio (5), Henning Hermjakob (1,6), Antonio Fabregat (1,7) (1) EMBL-EBI, UK 2) OICR, Canada 3) Dept of Molecular Genetics, University of Toronto, Canada 4) OHSU, USA. 5) NYU Langone Medical Center, USA 6) State Key Lab. of Proteomics, China 7) Open Targets, UK)
Reactome (https://reactome.org) is a free, open-source, open-data, open-graphics, curated and peer-reviewed knowledgebase of biomolecular pathways. Reactions are the basic building blocks and pathways are the result of concatenating two or more reactions. Both pathways and reactions are considered events and are organised in a hierarchical way. Navigating through different events is a common exercise to further understand the studied phenomena. Previously, we have placed existing regular pathway diagrams and textbook-style illustrations in the pathway detailed pages, leaving single reactions as the only events without a self-contained image. Therefore, an automatic algorithm to deterministically lay reactions out was developed. It uses data directly from the database to generate images without human intervention. The algorithm’s strategy complies with the Systems Biology Graphical Notation (SBGN). Each element is placed in its corresponding compartment, and these are nested following Gene Ontology hierarchy. It supports disease reactions, minimizes space and avoids unnecessary crossings. This method constitutes the first milestone to lay out pathways automatically.