A Holistic Approach for Metabolic Pathway Visualization

Information

• Publication Type: Master Thesis
• Workgroup(s)/Project(s): not specified
• Date: 2023
• Second Supervisor: Hsiang-Yun Wu
• Open Access: yes
• First Supervisor: Eduard Gröller
• Pages: 144
• Keywords: graph drawing, metabolic pathways, cluster visualization, multilevel layout, constraint-based layout, expand and collapse, complexity reduction, SBGN, graph quality metrics, motif simplification

Abstract

Metabolic pathways represent interconnected reactions of chemical entities, which take place within cells. These pathways are represented in domain-specific notations, which are used for knowledge exchange in the life sciences. Since they can contain thousands of nodes, automatic layouts are required that conserve the meaning of these pathways. There are many graph drawing algorithms including hierarchical, topology-shape-metric, force-directed, and constraint-based approaches. They typically consider only a subset of the requirements needed to faithfully visualize metabolic pathways and rarely support domain-specific notations. In this work, we present a holistic approach to visualize metabolic pathways compliant with the Systems Biology Graph Notation (SBGN). Our approach starts with loading a metabolic pathway and mapping it to a clustered graph structure to model the hierarchy of subcellular locations. The nodes are then arranged through vectorized stress majorization using domain-specific constraints in a multilevel setup. This leads to a SBGN-compliant layout. To distinguish certain reactions at subcellular locations, we developed a visualization technique that produces distinct shapes in analogy to an elastic band. To explore large pathways, we provide an expand and collapse interaction in combination with motif simplification. We determine the degree of the layout's compliance with the SBGN by proposing domain-specific quality metrics. Our results demonstrate that the formulation of SBGN-specific constraints in the framework of vectorized stress majorization is feasible. Finally, our evaluation corroborates that our layout approach can faithfully represent metabolic pathways.

Additional Files and Images

Weblinks

• Entry in reposiTUm (TU Wien Publication Database)
• DOI: 10.34726/hss.2023.86461

BibTeX

@mastersthesis{mistelbauer-2023-aha,
  title =      "A Holistic Approach for Metabolic Pathway Visualization",
  author =     "Stefanie Mistelbauer",
  year =       "2023",
  abstract =   "Metabolic pathways represent interconnected reactions of
               chemical entities, which take place within cells. These
               pathways are represented in domain-specific notations, which
               are used for knowledge exchange in the life sciences. Since
               they can contain thousands of nodes, automatic layouts are
               required that conserve the meaning of these pathways. There
               are many graph drawing algorithms including hierarchical,
               topology-shape-metric, force-directed, and constraint-based
               approaches. They typically consider only a subset of the
               requirements needed to faithfully visualize metabolic
               pathways and rarely support domain-specific notations. In
               this work, we present a holistic approach to visualize
               metabolic pathways compliant with the Systems Biology Graph
               Notation (SBGN). Our approach starts with loading a
               metabolic pathway and mapping it to a clustered graph
               structure to model the hierarchy of subcellular locations.
               The nodes are then arranged through vectorized stress
               majorization using domain-specific constraints in a
               multilevel setup. This leads to a SBGN-compliant layout. To
               distinguish certain reactions at subcellular locations, we
               developed a visualization technique that produces distinct
               shapes in analogy to an elastic band. To explore large
               pathways, we provide an expand and collapse interaction in
               combination with motif simplification. We determine the
               degree of the layout's compliance with the SBGN by proposing
               domain-specific quality metrics. Our results demonstrate
               that the formulation of SBGN-specific constraints in the
               framework of vectorized stress majorization is feasible.
               Finally, our evaluation corroborates that our layout
               approach can faithfully represent metabolic pathways.",
  pages =      "144",
  address =    "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria",
  school =     "Research Unit of Computer Graphics, Institute of Visual
               Computing and Human-Centered Technology, Faculty of
               Informatics, TU Wien",
  keywords =   "graph drawing, metabolic pathways, cluster visualization,
               multilevel layout, constraint-based layout, expand and
               collapse, complexity reduction, SBGN, graph quality metrics,
               motif simplification",
  URL =        "https://www.cg.tuwien.ac.at/research/publications/2023/mistelbauer-2023-aha/",
}