P atika: an integrated visual environment for collaborative construction and analysis of cellular pathways
Open accessAbstract
Motivation: Availability of the sequences of entire genomes shifts the scientific curiosity towards the identification of function of the genomes in large scale as in genome studies. In the near future, data produced about cellular processes at molecular level will accumulate with an accelerating rate as a result of proteomics studies. In this regard, it is essential to develop tools for storing, integrating, accessing, and analyzing this data effectively. Results: We define an ontology for a comprehensive representation of cellular events. The ontology presented here enables integration of fragmented or incomplete pathway information and supports manipulation and incorporation of the stored data, as well as multiple levels of abstraction. Based on this ontology, we present the architecture of an integrated environment named Patika (Pathway Analysis Tool for Integration and Knowledge Acquisition). Patika is composed of a server-side, scalable, object-oriented database and client-side editors to provide an integrated, multi-user environment for visualizing and manipulating network of cellular events. This tool features automated pathway layout, functional computation support, advanced querying and a user-friendly graphical interface. We expect that Patika will be a valuable tool for rapid knowledge acquisition, microarray generated large-scale data interpretation, disease gene identification, and drug development. Availability: A prototype of Patika is available upon request from the authors. Contact: patika@cs.bilkent.edu.tr * To whom correspondence should be addressed.
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Over 300 pathway or molecular interaction related data resources and many visualization and analysis software tools have been developed.
“Over 300 pathway or molecular interaction related data resources17 and many visualization and analysis software tools3,20-22 have been developed.”
From The BioPAX community standard for pathway data sharing (2010) · cites this paper as [3]
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- Authors
- Demir, E., Babur, O., Dogrusoz, U., Gursoy, A., Nisanci, G., Cetin-Atalay, R., & Ozturk, M.
- Affiliations
- Bilkent University (TR)
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2002-07-01
- Volume
- 18
- Issue
- 7
- Pages
- 996-1003
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2121905803
- Cited by
- 156
- References
- 27
- Citations by year
- 2025: 1 · 2024: 3 · 2023: 1 · 2022: 1 · 2021: 5 · 2020: 1 · 2019: 1 · 2018: 5 · 2017: 6 · 2016: 1 · 2015: 1 · 2014: 5 · 2013: 9 · 2012: 10
- FWCI
- 3.82
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- Bilkent University Institutional Repository (Bilkent University) (submittedVersion)
- Funders
- Weizmann Institute of Science
- Türkiye Bilimsel ve Teknolojik Araştırma Kurumu
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- pathway visualization, network layout, proteomics data integration, object-oriented databases, microarray data interpretation, disease gene identification, drug development, knowledge acquisition
- MeSH terms
- Cell Physiological Phenomena, Computer Graphics, Database Management Systems, Software Design, User-Computer Interface, Databases, Factual, Information Storage and Retrieval, Internet
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