Using process diagrams for the graphical representation of biological networks
Abstract
With the increased interest in understanding biological networks, such as protein-protein interaction networks and gene regulatory networks, methods for representing and communicating such networks in both human- and machine-readable form have become increasingly important. Although there has been significant progress in machine-readable representation of networks, as exemplified by the Systems Biology Mark-up Language (SBML) (http://www.sbml.org) issues in human-readable representation have been largely ignored. This article discusses human-readable diagrammatic representations and proposes a set of notations that enhances the formality and richness of the information represented. The process diagram is a fully state transition-based diagram that can be translated into machine-readable forms such as SBML in a straightforward way. It is supported by CellDesigner, a diagrammatic network editing software (http://www.celldesigner.org/), and has been used to represent a variety of networks of various sizes (from only a few components to several hundred components).
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Pathway Tools software and CellDesigner pathway editor are developing support for BioPAX-based data exchange.
“The Pathway Tools software21 and CellDesigner pathway editor54 are developing support for BioPAX-based data exchange.”
From The BioPAX community standard for pathway data sharing (2010) · cites this paper as [54]
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- Authors
- Kitano, H., Funahashi, A., Matsuoka, Y., & Oda, K.
- Affiliations
- Systems Biology Institute (JP)
- Keio University (JP)
- Japan Science and Technology Agency (JP)
- Corresponding author
- Kitano, Hiroaki
- Venue
- Nature Biotechnology
- Published
- 2005-08
- Volume
- 23
- Issue
- 8
- Pages
- 961-966
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2045478141
- Cited by
- 483
- References
- 12
- Citations by year
- 2026: 3 · 2025: 6 · 2024: 8 · 2023: 5 · 2022: 8 · 2021: 10 · 2020: 20 · 2019: 17 · 2018: 24 · 2017: 30 · 2016: 12 · 2015: 18 · 2014: 18 · 2013: 35 · 2012: 23
- FWCI
- 14.31
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Ministry of Education, Culture, Sports, Science and Technology
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Keywords
- process diagrams, state diagrams, SBML, CellDesigner, protein-protein interaction network, gene regulatory networks, diagrammatic notation
- MeSH terms
- Animals, Computer Graphics, Computer Simulation, Gene Expression Regulation, Humans, Models, Biological, Transcription Factors, User-Computer Interface, Signal Transduction, Systems Biology
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