Semantic Webs and Ontology-driven Biological Data Integration Methods for Bacteria

M. U. G. Khan, M. Idrees, U. Hayat, A. Akram


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.

Full Text:



D. Rubin, N. Shah and F. Natalya, Biomedical Ontologies:

AFunctional Perspective, Briefings in Bioinformatics, 9 (2008)


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)


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 =

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

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.


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-


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.


  • There are currently no refbacks.