APPLICATION OF SEMANTIC WEB TECHNOLOGY TO BIO-INFORMATICS

Nilavamuthan Chandrasekaran¹*, ShanmughavelPiramanayagam²*
¹Computational Biology and Bioinformatics Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore- 641046, Tamil Nadu, India
²Computational Biology and Bioinformatics Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore- 641046, Tamil Nadu, India
* Corresponding Author : shanvel_99@yahoo.com

Received : -     Accepted : -     Published : 15-06-2010
Volume : 2     Issue : 1       Pages : 67 - 71
Int J Bioinformatics Res 2.1 (2010):67-71
DOI : http://dx.doi.org/10.9735/0975-3087.2.1.67-71

Keywords : Integrative Bioinformatics, Systems integration, Semantic Web, Biological databases Oracle RDF Data Model, Seamark Navigator
Conflict of Interest : None declared
Acknowledgements/Funding : The authors gratefully acknowledge the facilities provided by DBT-BIF provided at Bharathiar University, Coimbatore, Tamil Nadu, India

The enormous amount of data resources are available on web, this makes integrative Bioinformatics research more important in life sciences research. Bioinformatics is about searching biological databases, comparing sequences, looking at protein structures, and solving biological and biomedical problems using a computer. Huge amount of online bioinformatics tools and data are available, so systems integration has become very important for further progress. Today, bioinformatics hosts heavily on the Web. But the Web is geared towards human interaction rather than automated processing. The approach of a Semantic Web facilitates this automation by annotating web content and by applying adequate reasoning languages. Semantic Web infrastructure utilizes the scalable Oracle Resource Description Framework (RDF) Data Model as the repository and Seamark Navigator for browsing and searching the data.

[1] Tim Berners-Lee, James Hendler and Ora Lassila (2008). Scientific American Magazine  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[2] W3C (2008) W3C Semantic Web Frequently Asked Questions,03-13  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[3] Ivan Herman, W3C Head.http://www.w3.org/2003/Talks/111 2-BeijingSW-IH  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[4] Loana Robu, Valentin Robu, Benoit Thirion. (2006) J Med Libr Assoc, 94(2): 198– 205  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[5] Sheth, Ramakrishnan et al. (2005)  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[6] Neumann E, Miller E., Wilbanks J:, (2004) Biosilico 228–236  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[7] Rebhan M., Chalifa-Caspi V., Prilusky J., Lancet D., (1998) Bioinformatics 14 656e664  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[8] Lenhard B., Hayes W.S., Wasserman W.W. (2001) Genome Research, (11), 2151- 2157  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[9] Diehn M., Sherlock G., Binkley G., Jin H., Matese J.C., Hernandez-Boussard T.,Rees C.A., Cherry J.M., Botstein D., Brown P.O., Alizadeh A.A., (2003) Nucleic Acids Research 31219e223  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[10] Su A.I., Cooke M.P., Ching K.A., Hakak Y., Walker J.R., Wiltshire T., Orth A.P., Vega R.G., Sapinoso L.M.,Moqrich A., Patapoutian A., Hampton G.M., Schultz P.G., Hogenesch J.B. (2002) Proceedings of the National Academy of Sciences 99 4465 - 4470  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[11] Pasquier, Institute of Developmental Biology and Cancer, CNRS e UMR 6543, University of Nice Sophia Antipolis, Parc Valrose, 06108 NICE Cedex 2, France  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[12] The UniProt Consortium (2007) Nucleic Acids Research 35 193 - 197.  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[13] Kerrien S., Alam-Faruque Y., Aranda B., Bancarz I., Bridge A., Derow C., Dimmer E., Feuermann M., Friedrichsen A., Huntley R., Kohler C., Khadake J., Leroy C., Liban A., Lieftink C., MontecchiPalazzi L., Orchard S., Risse J., Robbe K., Roechert B., Thorneycroft D., Zhang Y., Apweiler R. (2007) Nucleic Acids Research 35 D561 - D565.  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[14] Ashburner M., Ball C.A. , Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., Harris M.A., Hill L. Issel- Tarver D.P., Kasarskis A., Lewis S., Matese J.C., Richardson J.E., Ringwald M., Rubin G.M., Sherlock G. (2000) Nature Genetics 25 25e29  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[15] von Mering C., Jensen L.J., Kuhn M., Chaffron S., Doerks T., Kruger B., Snel B., Bork P. (2007) Nucleic Acids Research 35 358e362.  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[16] Kanehisa M., Goto S., Hattori M., Aoki- Kinoshita K.F., Itoh M., Kawashima S., Katayama T., Araki M., Hirakawa M., (2006) Nucleic Acids Research 34 D354eD357  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[17] Mitchell J.A., Aronson A.R., Mork J.G., Folk L.C., Humphrey S.M., Ward J.M. (2003) American Medical Informatics Association, Annual Symposium Proceedings, 460 - 464.  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[18] Camon E., Magrane M., Barrell D., Lee V., Dimmer E., Maslen J., Binns D., Harte N., Lopez R., Apweiler R. (2004) Nucleic Acids Research,32, 262 - 266  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[19] Maglott D., Ostell J., Pruitt K.D., Tatusova T. (2007) Nucleic Acids Research, 35, 26-31  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[20] Birney E., Andrews T.D., Bevan P., Caccamo M., Chen Y., Clarke L., Coates G., Cuff J., Curwen V., Cutts T., Down T., Eyras E., Fernandez-Suarez X.M., Gane P., Gibbins B., Gilbert J., Hammond M., Hotz H.-R., Iyer V., Jekosch K., Kahari A., Kasprzyk A., Keefe D., Keenan S., Lehvaslaiho H., McVicker G., Melsopp C., Meidl P., Mongin E., Pettett R., Potter S., Proctor G., Rae M., Searle S., Slater G., Smedley D., Smith J., Spooner W., Stabenau A., Stalker J., Storey R., Ureta-Vidal A., . Woodwark K.C., Cameron G., Durbin R., Cox A., Hubbard T., Clamp M. (2004) Genome Research,14, 925-928.  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[21] CheungKH., YipK Y., Smith A., deKnikker R., Masiar A., Gerstein M. (2005) Bioinformatics, 21, i85-i96  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[22] John M., Vinay C., Dimitris P., Adel S., Thodoros T. (1996) The VLDB Journal ,5, 238-263.  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[23] Guo Y., Pan Z., Heflin J. (2004) Proceedings of the Third International Semantic Web Conference  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[24] Chimezie Ogbuji, Eugene Blackstone, Chris Pierce, (2007) Cleveland Clinic  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus  

[25] Surajit C., Umeshwar D. (1997) ACM SIGMOD ,26, 65-74  
» CrossRef   » Google Scholar   » PubMed   » DOAJ   » CAS   » Scopus