Reactions automatic layout with nested compartments

Up until now, we have placed existing regular pathway diagrams and textbook-style illustrations in our pathway detailed pages (e.g. Hemostasis, Platelet Adhesion to exposed collagen), leaving single reactions as the only type of events without a self-contained image. To fill the gap, an automatic algorithm to deterministically lay reactions out has been developed. It uses data directly from our graph-database to generate images without any kind of human intervention.

Long story short, the algorithm’s strategy places inputs on the left, outputs on the right, catalysts on top and regulators at the bottom. Each element is placed in its corresponding compartment, and these are nested following the Gene Ontology hierarchy. The algorithm supports normal and disease* reactions minimizing the space as well as avoiding lines to cross unnecessary elements in the display.

Finally, the reaction visualisation complies with the Systems Biology Graphical Notation (SBGN).

Some examples:

  1. Enzyme-bound ATP is released
  2. VCP-catalyzed ATP hydrolysis promotes the translocation of Hh-C into the cytosol
  3. Ubiquitination of PAK-2p34
  4. Defective ABCD1 does not transfer LCFAs from cytosol to peroxisomal matrix

*Disease reactions can either be classified as infectious, gain-of-function or lost-of-function. In the latter category some participants have to be crossed out.