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cPath: open source software for collecting, storing, and querying biological pathways
Open accessAbstract
BACKGROUND: Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. RESULTS: We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. CONCLUSION: cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling.
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BioPAX can be used to aggregate large pathway datasets by reducing required collection and translation effort.
“BioPAX can be used to help aggregate large pathway datasets by reducing the required collection and translation effort, for instance using software such as cPath43.”
From The BioPAX community standard for pathway data sharing (2010) · cites this paper as [43]
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References 41 · Cited by 125
Metadata
- Authors
- Cerami, E. G., Bader, G. D., Gross, B. E., & Sander, C.
- Affiliations
- Memorial Sloan Kettering Cancer Center (US)
- University of Toronto (CA)
- Corresponding author
- Cerami, Ethan G
- Bader, Gary D
- Gross, Benjamin E
- Sander, Chris
- Venue
- BMC Bioinformatics
- Published
- 2006-11-13
- Volume
- 7
- Issue
- 1
- Pages
- 497-497
- ISSN
- 1471-2105 (ISSN-L)
- OpenAlex
- W1597403892
- Cited by
- 125
- References
- 41
- Citations by year
- 2026: 1 · 2023: 3 · 2022: 2 · 2021: 2 · 2020: 1 · 2019: 2 · 2017: 3 · 2016: 2 · 2015: 7 · 2014: 5 · 2013: 14 · 2012: 8
- FWCI
- 6.25
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- BMC Bioinformatics (publishedVersion, cc-by)
- PubMed (publishedVersion)
- TSpace (University of Toronto) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- GlaxoSmithKline
- Oregon Health and Science University
- National Cancer Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Health Sciences › Medicine › Health Informatics › Biomedical Text Mining and Ontologies
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Keywords
- biological pathway databases, BioPAX, identifier mapping, pathway visualization, open source software, metabolic pathways, protein-protein interaction network, signaling pathways, gene regulatory networks
- MeSH terms
- Computer Graphics, Humans, Programming Languages, Software, Software Design, User-Computer Interface, Signal Transduction, Databases, Factual, Information Storage and Retrieval, Systems Integration, Computational Biology, Internet
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