Semantic Webs and Ontology-driven Biological Data Integration Methods for Bacteria
Abstract
Integrating data from distant heterogeneous data sources is a big challenge for research community. By putting semantic web into practice, a new framework is being presented for knowledge engineering, querying and information sharing. In present paper, we presented an ontology based effort for the development of a knowledge that would allow for semantically querying bacteria knowledge base.References
D. Rubin, N. Shah and F. Natalya, Biomedical Ontologies:
AFunctional Perspective, Briefings in Bioinformatics, 9 (2008)
-90.
C. Jonquet, M. A.Musen, and N. H. Shah, Building a biomedical
ontology recommender web service, J Biomed Semantics 1
(2010) 1-18.
G. Babnigg, C. Giometti, A Database of Unique Protein Sequence
Identifiers for Proteome Studies. J.Proteomics 6 (2006) 4514-4522.
A. Silvescu, J. Reinoso, and V. Honavar, Ontology-Driven
Information Extraction and Knowledge Acquisition from
Heterogeneous, Distributed, Autonomous Biological Data, 1-10,
Report submitted to Department of Computer Science 226 Atanasoff
Hall, Iowa State University Ames, Iowa 50011-1040 Menlo Park,
California. Simon, and E. Tomita (Eds.): ALT 2005, LNAI 3734,
Springer-Verlag Berlin Heidelberg (2005) pp. 13–44.
Y. Liu, A. Coulet, P. Pendu, and H. Shah, Using ontology-based
annotation to profile disease research; Stanford Centre for
Biomedical Informatics, 1265 Welch Road, Medical School Office
Building, Room X215 Mail Code 5479, Stanford, CA 94305, USA
(2012) doi:10.1186/2041-1480-4-S1-S8.
A. Musen, F.Noy and H. Shah, Division of Biomedical Statistics and
Informatics, Mayo Clinic, Rochester, Minnesota, USA, Department
of Computer Science, University of Victoria, Canada, (2011)
doi: 10.1136/amiajnl-2011-000631.
A.L. Battista, N.V. Rosales, M.P. Michel and D. Umontier, SMART:
A Web Based, Ontology-Driven, Semantic Web Query Answering
Application, School of Computer Science, Department of Biology,
Carleton University, Ottawa, Ontario, Canada. (2008) Technical
Report: FBI-HH-B-262/05.
E. Sirin, B. Parsia, B.C. Grau, A. Kalyanpur, and Y. Katz, Pellet:
A Practical Owl-dl Reasoner, 3rd International Semantic Web
Conference (ISWC2004) 2004) pp. 21-29.
G. Heja, P. Varga, P. Pallinger and G. Surjan, Restructuring the
Foundational Model of Anatomy, Stud Health Technol. Inform 124
(2006) 755-760.
V. Haarslev, R. Möller and M. Wessel M, Querying the Semantic
Web with Racer + nRQLin KI-04, Workshop on Applications on
Description Logics (Ulm, 2004) doi:biomedcentral.com/1471-
/8/S3/S4.
I. Foster,C. Kesselman, J. Nick and S. Tuecke, The Physiology of the
Grid: An Open Grid Services Architecture for Distributed Systems
Integration in Globus Project(2002.) doi = 10.1.1.14.8105
J. Luciano, PAX of Mind for Pathway Researchers. J. Drug Discov.
Today 10 (2005) 937-942.
J. Christopher, S. Arash, S. Xiao, H. Volker and B. Greg, Semantic
Web Infrastructure for Fungal Enzyme Biotechnologists. J. Web
Semantic 4 (2006) 168-180.
K. Wolstencroft, P. Lord, L. Tabernero, A. Brass, and R. Stevens,
Protein Classification using Ontology Classification, Bioinformatics
(2006) e530-538.
LR. Alan, Modularization of Domain Ontologies Implemented in
Description logics and Related Formalisms including OWL,KC2003
(Sanibel Island, FL, USA, 2003), ACM Press.doi:ceur-ws.org/Vol315/paper3.pdf
U. Consortium, The Gene Ontology (GO) Project in 2006. Nucleic
Acids Res 34 (2006) D322-326.
L. French, S. Lane, T. Law, L. Xu and Paul Pavlidis, Application and
Evaluation of Automated Semantic Annotation of Gene Expression
Experiments. Bioinformatics Graduate Program, Department of
Psychiatry and Centre for High-Throughput Biology, University of
British Columbia, Vancouver, BC, Canada (2009)
doi: 10.1093/bioinformatics/btp259
M. Idrees and M. U. G. Khan, SMGCD: Metrics for Biological
Sequence data, The Nucleus 51 (2014) 125-131.
LinkHub. http://hub.gerteinlab.org.
M.A. Remli, S. Deris and A. Abdullah, Ontology-based Semantic
Data Integration for Lactococcus Lactis (L.lactis): Connecting CrossReferences Heterogeneous Data Sources, 4th International
Conference on Bioinformatics and Biomedical Technology IPCBEE
(2012) pp.100-104.
P. Grenon, B. Smith and L. Goldberg, Biodynamic Ontology:
Applying BFO in the Biomedical Domain. Stud Health Technol.
Inform 102 (2004) 20-38.
M. Sabou, V. Lopez, E. Motta and V. Uren, Ontology Selection:
Ontology Evaluation on the Real Semantic Web. 4th International
EON Workshop, Evaluation of Ontologies for the Web, EON‟06,
Proceedings of CEUR Workshop 179 (2010) doi:10.1186/2041-
-1-S1-S1
M. Aranguren, Ontology Design Patterns for the Formalization of
Biological Ontologies, A Report submitted to the University of
Manchester, Degree of Philosophy, Faculty of Engineering and
Physical Sciences and Biological Sciences (2005) 1-67dissertation.
R. Hoehndorf, M. Dumontier and G. Gkoutos, Evaluation of
Research in Biomedical Ontologies, Briefings in Bioinformatics
(2012) 1-17.
N. Villanueva-Rosales, K. Osbahr and M. Dumontier, Towards a
Semantic Knowledge Base for Yeast Biologists, Copyright is held by
the Author/ Owner(s) May 8-12 2007, Banff, Canada. Dissertation.
P. Buitelaar, P. Cimiano, S. Racioppa and M. Siegel, Ontology-based
Information Extraction with SOBA, Saarbrücken, Kalrsruhe,
Germany (2006), Medical Information Science Reference, IGI
Global Data Mediation and Extraction at the 7th International
Semantic Web Conference, Karlsruhe, Germany.
T. Hussain and S. Asghar, Evaluation of Similarity Measuresfor
Categoricaldata; The Nucleus 50 (2013) 387-394.
S. Zhang, O. Bodenreider and C. Golbreich, Experience in
Reasoning with the Foundational Model of Anatomy in OWL DL.
Pac Symp Biocomput. (2006) pp. 200-211.
SS. Dwight, M. Harris, K. Dolinski and C.A. Ball, J. Nucleic Acids
Res. 30 (2002) 69-72.
S. Jupp, J. Klein, J. Schanstra and R. Stevens, Developing a Kidney
and Urinary Pathway Knowledge Base. J Biomed Semantics
semantic Applications in Life Sciences 2 (Suppl 2) 9-10 July (2010),
Boston, MA, USA.
S. Schulz, H. Stenzhorn and M. Boeker, Report: The ontology of
Biological Taxa. Institute of Medical Biometry and Medical
Informatics, National University of Ireland, Galway, University
Road, Galway, Ireland (2008) HG004028.
U. Consortium, J. Nucleic Acids Res. 40 (2012) D71-D75.
