Cell system ontology: Representation for modeling, visualizing, and simulating biological pathways

In Silico Biology

Volumn 7, Issue 6, 2007, Pages 623-638

  Jeong, Euna ^a   Nagasaki, Masao ^a   Saito, Ayumu ^a   Miyano, Satoru ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

Biological pathway; Cell system ontology; CSO; Data exchange format; Dynamic simulation; HFPNe; Visualization

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; CAENORHABDITIS ELEGANS; CELL INTERACTION; CELL SYSTEM ONTOLOGY; COMPUTER LANGUAGE; COMPUTER SYSTEM; CYTOLOGY; INFORMATION SYSTEM; METABOLISM; NONHUMAN; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; SIGNAL TRANSDUCTION; SIMULATION; VALIDATION PROCESS;

CELL NUCLEUS; CELL PHYSIOLOGY; COMPUTER GRAPHICS; COMPUTER SIMULATION; CYTOPLASM; LANGUAGE; MODELS, BIOLOGICAL; MODELS, THEORETICAL; PROGRAMMING LANGUAGES;

EID: 41849092276     PISSN: 13866338     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (34)

1. Bader, G. and Cary, M. (2005). BioPAX - biological pathways exchange language level 2, version 1.0 documentation. http://www.biopax.org/ release/biopax-level2-documentation.pdf.
2. Bodenreider, O. and Stevens, R. (2006). Bio-ontologies: Current trends and future directions. Brief. Bioinform. 7, 256-274.
3. Bray, T., Paoli, J., Sperberg-McQueen, C., Maler, E., Yergeau, F. and Cowan, J. (2006). Extensible Markup Language (XML) 1.1. http://www.w3.org/TR/2006/REC-xm111-20060816/.
4. Burek, P., Hoehndorf, R., Loebe, F., Visagie, J., Herre, H. and Kelso, J. (2005). A top-level ontology of functions and its application in the Open Biomedical Ontologies. Bioinformatics 22, e66-e73.
5. Day-Richter, J. (2004). The OBO Flat File Format Specification, version 1.2. http://www.geneontology.org/GO.format.obo1-2.shtml.
6. Decker, S., van Harmelen, F., Broekstra, J., Erdmann, M., Fensel, D, Horrocks, I., Klein, M. and Melnik, S. (2000). The Semantic Web: The Roles of XML and RDF. Internet Computing 4(5), 63-74.
7. Fukuda, K. and Takagi, T. (2004). A pathway editor for literature-based knowledge curation. In: Yi-Ping Phoebe Chen (ed.), Proceedings of the second conference on Asia-Pacific bioinformatics, vol. 29, pp. 339-344.
8. Harris, M. A., et al.; Gene Ontology Consortium (2004). The gene ontology (GO) database and informatics, resource. Nucleic Acids Res. 32, D258-D261.
9. Hermjakob, H., et al. (2004). The HUPO PSI's molecular interaction format - a community standard for the representation of protein interaction data. Nat. Biotechnol. 22, 177-183.
10. Horrocks, I., Patel-Schneider, P.F. and van Harmelen, F. (2003). From SHIQ and RDF to OWL: The making of a web ontology language. Web Sernant. 1, 7-26.
11. Hucka, M., Finney, A., Hoops, S., Keating, S. and Le Novère, N. (2007). Systems biology markup language (SBML) Level 2: Structures and facilities for model definitions. http://nchc.dl.sourceforge.net/ sourceforge/sbml/sbml-level-2-version-3-rel-2.pdf.
12. Jeong, E., Nagasaki, M. and Miyano, S. (2007). Conversion from BioPAX to CSO for System Dynamics and Visualization of Biological Pathway. Genome Inform. 18, 225-236.
13. Joshi-Tope, G., Gillespie, M., Vastrik, I., D'Eustachio, P., Schmidt, E., de Bono, B., Jassal, B., Gopinath, G. R., Wu, G. R., Matthews, L., Lewis, S., Birney, E. and Stein, L. (2005). Reactome: A knowledgebase of biological pathways. Nucleic Acids Res. 33, D428-D432.
14. Kanehisa, M., Goto, S., Kawashima, S. and Nakaya, A. (2002). The KEGG databases at GenomeNet. Nucleic Acids Res. 30, 4246.
15. Karp, P. D. (2000). An ontology for biological function based on molecular interactions. Bioinformatics 16, 269-285.
16. Keseler, I. M., Collado-Vides, J., Gama-Castro, S., Ingraham, J., Paley, S., Paulsen I. T., Peralta-Gil, M.and Karp, P. D. (2005). EcoCyc: A comprehensive database resource for Escherichia coli. Nucleic Acids Res. 33, D334-D337.
17. Kohn, K. W., Aladjem, M. I., Weinstein, J. N. and Pommier, Y. (2006). Molecular interaction maps of bioregulatory networks: A general rubric for systems biology. Mol. Biol. Cell 17, 1-13.
18. Kojima, K., Nagasaki, M., Jeong, E., Kato, M. and Miyano, S. (2007). An efficient grid layout algorithm for biological networks utilizing various biological attributes. BMC Bioinformatics 8, 76.
19. Küffner, R., Zimmer, R. and Lengauer, T. (2000). Pathway analysis in metabolic databases via differential metabolic display (DMD). Bioinformatics 16, 825-836.
20. Kushida, T., Takagi, T. and Fukuda, K. I. (2006). Event ontology: A pathway-centric ontology for biological processes Pac. Symp. Biocomput 11, 152-163.
21. Lloyd, C. M., Halstead, M. D. and Nielsen, P. F. (2004). CellML: Its future, present and past Prog. Biophys. Mol. Biol. 85, 433-450.
22. Mizoguchi, R. and Kitamura, Y. (2000). Foundation of knowledge systematization. role of ontological engineering. In: Industrial knowledge management - a micro level approach, Roy, R. (ed.), Springer-Verlag, London, pp. 17-36.
23. Nagasaki, M., Doi, A., Matsuno, H. and Miyano, S. (2003). Qenomic Object Net: I. A platform for modeling and simulating biopathways. Appl. Bioinformatics 2, 181-184.
24. Nagasaki, M., Doi, A., Matsuno, H. and Miyano, S. (2004). A versatile-petri net based architecture for modeling and simulation of complex biological processes. Genome Inform. 15, 180-197.
25. Noy, N., Crubezy, M., Fergerson, R., Knublauch, H., Tu, S., Vendetti, J. and Musen, M. (2003). Protégé-2000: An open-source ontology-development and knowledge-acquisition environment. AMIA Annu. Symp. Proc. 2003, 953.
26. Saito, A., Nagasaki, M., Doi, A., Ueno, K. and Miyano, S. (2006). Cell fate simulation model of gustatory neurons with microRNAs double-negative feedback loop by hybrid function petri net with extension. Genome Inform, 17, 100-111.
27. Schomburg, I., Chang, A., Ebeling, C., Gremse, M., Heldt, C., Huhn, G. and Schomburg, P. (2000), Enzyme data and metabolic information: BRENDA, a resource for research in biology, biochemistry and medicine. Nucleic Acids Res. 32, D431-D433.
28. Schulze-Kremer, S. (2002). Ontologies for molecular biology and bioinformatics. In Silico Biol. 2, 0017.
29. Smith, B., Ceusters, W., Klagges, B., Uhler, J., Kumar, A., Lomax, J., Mungall, C, Neuhaus, F., Rector, A. L. and Rosse, C. (2005). Relations in biomedical ontologies. Genome Biol. 6, R46.
30. Smith, M., Welty, C. and McGuinness, D. (2004). OWL Web Ontology Language Guide. http://www.w3.org/TR/owl-guide/.
31. Stevens, R., Goble, C. A. and Bechhofer, S. (2000). Ontology-based knowledge representation for bioinformatics, Brief. Bioinform. 1, 398-416.
32. Strömbäck, L. and Lambrix, P. (2005). Representations of molecular pathways: An evaluation of SBML, PSI MI and BioPAX. Bioinformatics 21 4401-4407.
33. Takai-Igarashi, T. and Mizoguchi, R. (2003). Cell signaling networks ontology, In Silico Biology 4, 0008.
34. Wroe, C. J., Stevens, R., Goble, C. A. and Ashburner, M. (2003). A methodology to migrate the gene ontology to a description logic environment using DAML+OIL. Pac. Symp. Biocomput. 8, 624-635.