by Takako Takai-igarashi, Riichiro Mizoguchi
http://www.jsbi.org/journal/GIW04/GIW04F026.pdf
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Abstract:
Databases have collected masses of information concerning cell signaling pathways that includes information on pathways, molecular interactions as well as molecular complexes. However we have no general data model to represent comprehensive properties of cell signaling pathways, so that this type of information has been represented by two different data models that we call ‘binary relation’ and ‘state transition’. The disagreement between the existing models derives from lack of consensus about a factor of causality in reactions in cell signaling pathways, which is often called ‘signal’. We developed an ontology named CSNO (Cell Signaling Networks Ontology) based on device ontology. As device ontology is a research product of knowledge engineering, CSNO is the first application of it to biological knowledge. CSNO defines the factor of causality called ‘signal’, offers an integrative viewpoint for the two different data models, explicates intrinsic distinctions between signaling and metabolic pathways, and eliminates ambiguity from representation of complex molecules.
Citations
|
159
|
The large-scale organization of metabolic networks
– Jeong, Tombor, et al.
- 2000
|
|
106
|
BIND: The Biomolecular Interaction Network Database. Nucleic Acids Res
– Bader, Betel, et al.
- 2003
|
|
60
|
The database of interacting proteins: 2004 update
– Salwinski, Miller, et al.
|
|
40
|
MIPS: analysis and annotation of proteins from whole genomes
– Mewes, Amid, et al.
- 2004
|
|
19
|
Ontology-based description of functional design knowledge and its use in a functional way server, Expert Systems with Application
– Kitamura, Mizoguchi
- 2003
|
|
18
|
Kinase Pathway Database: An Integrated Protein-Kinase and NLP-Based Protein-Interaction Resource. Genome Res
– Koike, Kobayashi, et al.
- 2003
|
|
17
|
Prebind and Textomy–mining the biomedical literature for protein-protein interactions using a support vector machine
– Donaldson, Martin, et al.
|
|
16
|
A Pathway Finding System for the Cell Signaling Networks Database
– Takai-Igarashi, Kaminuma
- 1999
|
|
14
|
TRANSPATH: an integrated database on signal transduction and a tool for array analysis
– Krull, Voss, et al.
- 2003
|
|
13
|
Development of an Environment for Building Ontologies which is based on a Fundamental Consideration of "Relationship" and "Role
– Kozaki, Kitamura, et al.
- 2000
|
|
12
|
Knowledge representation of signaling transduction pathways
– Fukuda, Takagi
- 2001
|
|
12
|
InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes
– Ng, Zhuo, et al.
- 2003
|
|
12
|
From molecular activities and processes to biological function
– Helden, Naim, et al.
- 2001
|
|
6
|
An ontology for collaborative construction and analysis of cellular pathways
– Demir, Babur, et al.
- 2004
|
|
6
|
Cell signaling networks ontology
– Takai-Igarashi, Mizoguchi
- 2004
|
|
3
|
Physical Chemistry with Applications to the Life
– Eisenberg, Crothers
- 1979
|
|
3
|
Foundation of Knowledge Systematization: Role of Ontological Engineering
– Mizoguchi, Kitamura
- 2000
|
|
2
|
KDBI: Kinetic data of bio-molecular interactions database
– Ji, Chen, et al.
- 2003
|
|
2
|
FBRL:a function and behavior representation language
– Sasajima, Kitamura, et al.
- 1995
|
|
1
|
Mechanisms of TGF-beta signaling from cell membrane to the nucleus
– Shi, Massague
|
