Background Biological pathways represent chains of molecular interactions in biological systems that jointly form complex dynamic networks. The network structure changes from the significance of biological experiments and layout algorithms often sacrifice low-level details to maintain high-level information, which complicates the entire image to large biochemical systems such as human metabolic pathways. Results Our work is inspired by concepts from urban planning since we create a visual hierarchy of biological pathways, which is analogous to city blocks and grid-like road networks in an urban area. We automatize the manual drawing process of biologists by first partitioning the map domain into multiple sub-blocks, and then building the corresponding pathways by routing edges schematically, to maintain the global and local context simultaneously. Our system incorporates constrained floor-planning and network-flow algorithms to optimize the layout of sub-blocks and to distribute the edge density along the map domain. We have developed the approach in close collaboration with domain experts and present their feedback on the pathway diagrams based on selected use cases. Conclusions We present a new approach for computing biological pathway maps that untangles visual clutter by decomposing large networks into semantic sub-networks and bundling long edges to create space for presenting relationships systematically.
Bibliographical noteKAUST Repository Item: Exported on 2020-04-23
Acknowledged KAUST grant number(s): BAS/1/1680-01-01
Acknowledgements: The authors would like to thank the members from KEGG , ReconMap , and CellDesigner  who have provided valuable comments to our system. The project leading to this submission has received funding from the European Union Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 747985, from the Vienna Science and Technology Fund (WWTF) through projects VRG11-010 and VRG15-007, from the Austrian Science Fund (FWF) through project P31119, and from King Abdullah University of Science and Technology (KAUST) through award BAS/1/1680-01-01.
- Biological pathways
- Edge routing
- Floor planning
- Graph drawing
- Map metaphor
- Orthogonal layout
ASJC Scopus subject areas
- Structural Biology
- Molecular Biology
- Computer Science Applications
- Applied Mathematics