Human-like layout algorithms for signalling hypergraphs: outlining requirements

Abstract The use of signalling pathway hypergraphs represented as process description diagrams is steadily becoming more pervasive in the field of biology. This makes ever more evident the necessity for an effective automated layout that can replicate high-quality manually drawn diagrams. The comple...

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Bibliographic Details
Published in:Briefings in bioinformatics 2020-01, Vol.21 (1), p.62-72
Main Authors: Siebenhaller, Martin, Nielsen, Sune S, McGee, Fintan, Balaur, Irina, Auffray, Charles, Mazein, Alexander
Format: Article
Language:English
Subjects:
Algorithms
Automation
Computer applications
End users
Graph theory
Graphs
Layouts
Signal transduction
Signaling
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Summary:Abstract The use of signalling pathway hypergraphs represented as process description diagrams is steadily becoming more pervasive in the field of biology. This makes ever more evident the necessity for an effective automated layout that can replicate high-quality manually drawn diagrams. The complexity and idiosyncrasies of these diagrams, as well as the specific tasks the end users perform with them, mean that a layout must meet many requirements beyond the simple metrics used in existing automated computational approaches. In this paper we outline these requirements, examine existing ones and describe new ones. We demonstrate state-of-the-art layout techniques enhanced with novel functionalities to meet part of the requirements. For comparatively small signalling pathways our enhanced algorithm provides results close to manually drawn layouts. In addition, we suggest technical approaches that may be suited for fulfilling the identified requirements currently not covered.
ISSN:1467-5463
1477-4054
DOI:10.1093/bib/bby099