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Reasoning with bio-ontologies: using relational closure rules to enable practical querying

Ward Blondé UGent, Vladimir Mironov, Aravind Venkatesan, Erick Zimar Antezana San Roman UGent, Bernard De Baets UGent and Martin Kuiper (2011) BIOINFORMATICS. 27(11). p.1562-1568
abstract
Motivation: Ontologies have become indispensable in the Life Sciences for managing large amounts of knowledge. The use of logics in ontologies ranges from sound modelling to practical querying of that knowledge, thus adding a considerable value. We conceive reasoning on bio-ontologies as a semi-automated process in three steps: (i) defining a logic-based representation language; (ii) building a consistent ontology using that language; and (iii) exploiting the ontology through querying. Results: Here, we report on how we have implemented this approach to reasoning on the OBO Foundry ontologies within BioGateway, a biological Resource Description Framework knowledge base. By separating the three steps in a manual curation effort on Metarel, a vocabulary that specifies relation semantics, we were able to apply reasoning on a large scale. Starting from an initial 401 million triples, we inferred about 158 million knowledge statements that allow for a myriad of prospective queries, potentially leading to new hypotheses about for instance gene products, processes, interactions or diseases.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
MANAGEMENT, DATABASE, RESOURCES, BIOLOGY, TOOL, GENE ONTOLOGY, SEMANTIC WEB, LIFE SCIENCES, INFORMATION
journal title
BIOINFORMATICS
Bioinformatics
volume
27
issue
11
pages
1562 - 1568
Web of Science type
Article
Web of Science id
000291062400016
JCR category
MATHEMATICAL & COMPUTATIONAL BIOLOGY
JCR impact factor
5.468 (2011)
JCR rank
1/46 (2011)
JCR quartile
1 (2011)
ISSN
1367-4803
DOI
10.1093/bioinformatics/btr164
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
2135604
handle
http://hdl.handle.net/1854/LU-2135604
date created
2012-06-07 10:28:19
date last changed
2013-02-27 09:11:07
@article{2135604,
  abstract     = {Motivation: Ontologies have become indispensable in the Life Sciences for managing large amounts of knowledge. The use of logics in ontologies ranges from sound modelling to practical querying of that knowledge, thus adding a considerable value. We conceive reasoning on bio-ontologies as a semi-automated process in three steps: (i) defining a logic-based representation language; (ii) building a consistent ontology using that language; and (iii) exploiting the ontology through querying. 
Results: Here, we report on how we have implemented this approach to reasoning on the OBO Foundry ontologies within BioGateway, a biological Resource Description Framework knowledge base. By separating the three steps in a manual curation effort on Metarel, a vocabulary that specifies relation semantics, we were able to apply reasoning on a large scale. Starting from an initial 401 million triples, we inferred about 158 million knowledge statements that allow for a myriad of prospective queries, potentially leading to new hypotheses about for instance gene products, processes, interactions or diseases.},
  author       = {Blond{\'e}, Ward and Mironov, Vladimir and Venkatesan, Aravind and Antezana San Roman, Erick Zimar and De Baets, Bernard and Kuiper, Martin},
  issn         = {1367-4803},
  journal      = {BIOINFORMATICS},
  keyword      = {MANAGEMENT,DATABASE,RESOURCES,BIOLOGY,TOOL,GENE ONTOLOGY,SEMANTIC WEB,LIFE SCIENCES,INFORMATION},
  language     = {eng},
  number       = {11},
  pages        = {1562--1568},
  title        = {Reasoning with bio-ontologies: using relational closure rules to enable practical querying},
  url          = {http://dx.doi.org/10.1093/bioinformatics/btr164},
  volume       = {27},
  year         = {2011},
}

Chicago
Blondé, Ward, Vladimir Mironov, Aravind Venkatesan, Erick Zimar Antezana San Roman, Bernard De Baets, and Martin Kuiper. 2011. “Reasoning with Bio-ontologies: Using Relational Closure Rules to Enable Practical Querying.” Bioinformatics 27 (11): 1562–1568.
APA
Blondé, W., Mironov, V., Venkatesan, A., Antezana San Roman, E. Z., De Baets, B., & Kuiper, M. (2011). Reasoning with bio-ontologies: using relational closure rules to enable practical querying. BIOINFORMATICS, 27(11), 1562–1568.
Vancouver
1.
Blondé W, Mironov V, Venkatesan A, Antezana San Roman EZ, De Baets B, Kuiper M. Reasoning with bio-ontologies: using relational closure rules to enable practical querying. BIOINFORMATICS. 2011;27(11):1562–8.
MLA
Blondé, Ward, Vladimir Mironov, Aravind Venkatesan, et al. “Reasoning with Bio-ontologies: Using Relational Closure Rules to Enable Practical Querying.” BIOINFORMATICS 27.11 (2011): 1562–1568. Print.