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Flexibility and utility of the Cell Cycle Ontology

Vladimir Mironov, Erick Zimar Antezana San Roman UGent, Mikel Egaña, Ward Blondé UGent, Bernard De Baets UGent, Martin Kuiper and Robert Stevens (2011) APPLIED ONTOLOGY. 6(3). p.247-261
abstract
The Cell Cycle Ontology (CCO) has the aim to provide a 'one stop shop' for scientists interested in the biology of the cell cycle that would like to ask questions from a molecular and/or systems perspective: what are the genes, proteins, and so on involved in the regulation of cell division? How do they interact to produce the effects observed in the regulation of the cell cycle? To answer these questions, the CCO must integrate a large amount of knowledge from diverse sources; the irregularity and incompleteness of this information suggests an ontology can act as the means of this integration. The volatility and continued expansion of biological knowledge means the content and modelling of the CCO will have to be frequently changed and updated. The CCO is generated from the input data automatically once every two months. This makes it easy to change the representation to enable certain queries; incorporate new knowledge; and consistently apply design patterns across the CCO. The automatic process also allows the CCO to be delivered in a variety of representations that suit the needs of various CCO customers and the abilities of existing toolsets. In this paper we present the CCO and its characteristics of utility and flexibility, that, from our perspective, make it a beautiful ontology.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
Bio-ontology, knowledge management, cell cycle, utility, flexibility, OWL, OBO, standardisation, SEMANTIC-WEB, DESIGN PATTERNS, BIO-ONTOLOGIES, GENE ONTOLOGY, KNOWLEDGE, EVOLUTION, RESOURCE, DATABASE, UNIPROT, BIOLOGY
journal title
APPLIED ONTOLOGY
Appl. Ontol.
volume
6
issue
3
pages
247 - 261
Web of Science type
Article
Web of Science id
000298743500004
JCR category
COMPUTER SCIENCE, THEORY & METHODS
JCR impact factor
1.105 (2011)
JCR rank
29/99 (2011)
JCR quartile
2 (2011)
ISSN
1570-5838
DOI
10.3233/AO-2011-0097
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
2135720
handle
http://hdl.handle.net/1854/LU-2135720
date created
2012-06-07 10:50:34
date last changed
2013-02-27 09:11:07
@article{2135720,
  abstract     = {The Cell Cycle Ontology (CCO) has the aim to provide a 'one stop shop' for scientists interested in the biology of the cell cycle that would like to ask questions from a molecular and/or systems perspective: what are the genes, proteins, and so on involved in the regulation of cell division? How do they interact to produce the effects observed in the regulation of the cell cycle? To answer these questions, the CCO must integrate a large amount of knowledge from diverse sources; the irregularity and incompleteness of this information suggests an ontology can act as the means of this integration. The volatility and continued expansion of biological knowledge means the content and modelling of the CCO will have to be frequently changed and updated. The CCO is generated from the input data automatically once every two months. This makes it easy to change the representation to enable certain queries; incorporate new knowledge; and consistently apply design patterns across the CCO. The automatic process also allows the CCO to be delivered in a variety of representations that suit the needs of various CCO customers and the abilities of existing toolsets. In this paper we present the CCO and its characteristics of utility and flexibility, that, from our perspective, make it a beautiful ontology.},
  author       = {Mironov, Vladimir and Antezana San Roman, Erick Zimar and Ega{\~n}a, Mikel and Blond{\'e}, Ward and De Baets, Bernard and Kuiper, Martin and Stevens, Robert},
  issn         = {1570-5838},
  journal      = {APPLIED ONTOLOGY},
  keyword      = {Bio-ontology,knowledge management,cell cycle,utility,flexibility,OWL,OBO,standardisation,SEMANTIC-WEB,DESIGN PATTERNS,BIO-ONTOLOGIES,GENE ONTOLOGY,KNOWLEDGE,EVOLUTION,RESOURCE,DATABASE,UNIPROT,BIOLOGY},
  language     = {eng},
  number       = {3},
  pages        = {247--261},
  title        = {Flexibility and utility of the Cell Cycle Ontology},
  url          = {http://dx.doi.org/10.3233/AO-2011-0097},
  volume       = {6},
  year         = {2011},
}

Chicago
Mironov, Vladimir, Erick Zimar Antezana San Roman, Mikel Egaña, Ward Blondé, Bernard De Baets, Martin Kuiper, and Robert Stevens. 2011. “Flexibility and Utility of the Cell Cycle Ontology.” Applied Ontology 6 (3): 247–261.
APA
Mironov, V., Antezana San Roman, E. Z., Egaña, M., Blondé, W., De Baets, B., Kuiper, M., & Stevens, R. (2011). Flexibility and utility of the Cell Cycle Ontology. APPLIED ONTOLOGY, 6(3), 247–261.
Vancouver
1.
Mironov V, Antezana San Roman EZ, Egaña M, Blondé W, De Baets B, Kuiper M, et al. Flexibility and utility of the Cell Cycle Ontology. APPLIED ONTOLOGY. 2011;6(3):247–61.
MLA
Mironov, Vladimir, Erick Zimar Antezana San Roman, Mikel Egaña, et al. “Flexibility and Utility of the Cell Cycle Ontology.” APPLIED ONTOLOGY 6.3 (2011): 247–261. Print.