Browse > Article
http://dx.doi.org/10.5808/GI.2015.13.1.7

An Ontology-Based GIS for Genomic Data Management of Rumen Microbes  

Jelokhani-Niaraki, Saber (Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad)
Tahmoorespur, Mojtaba (Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad)
Minuchehr, Zarrin (National Institute of Genetic Engineering and Biotechnology)
Nassiri, Mohammad Reza (Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad)
Abstract
During recent years, there has been exponential growth in biological information. With the emergence of large datasets in biology, life scientists are encountering bottlenecks in handling the biological data. This study presents an integrated geographic information system (GIS)-ontology application for handling microbial genome data. The application uses a linear referencing technique as one of the GIS functionalities to represent genes as linear events on the genome layer, where users can define/change the attributes of genes in an event table and interactively see the gene events on a genome layer. Our application adopted ontology to portray and store genomic data in a semantic framework, which facilitates data-sharing among biology domains, applications, and experts. The application was developed in two steps. In the first step, the genome annotated data were prepared and stored in a MySQL database. The second step involved the connection of the database to both ArcGIS and $Prot{\acute{e}}g{\acute{e}}$ as the GIS engine and ontology platform, respectively. We have designed this application specifically to manage the genome-annotated data of rumen microbial populations. Such a GIS-ontology application offers powerful capabilities for visualizing, managing, reusing, sharing, and querying genome-related data.
Keywords
gene ontology; geographic information systems; linear referencing; rumen;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Selvi M. Bioinformatics: an information explosion arena: an overview. J Adv Libr Inform Sci 2012;1:192-196.
2 Benson DA, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res 2014;42:D32-D37.   DOI
3 Fernandez-Suarez XM, Galperin MY. The 2013 Nucleic Acids Research Database Issue and the online molecular biology database collection. Nucleic Acids Res 2013;41:D1-D7.   DOI
4 Kamra DN. Rumen microbial ecosystem. Curr Sci 2005;89: 124-135.
5 Hobson PN. The Rumen Microbial Eco-system. London: Elsevier Applied Science, 1989.
6 Edwards JE, McEwan NR, Travis AJ, Wallace RJ. 16S rDNA library- based analysis of ruminal bacterial diversity. Antonie Van Leeuwenhoek 2004;86:263-281.   DOI
7 Larue R, Yu Z, Parisi VA, Egan AR, Morrison M. Novel microbial diversity adherent to plant biomass in the herbivore gastrointestinal tract, as revealed by ribosomal intergenic spacer analysis and rrs gene sequencing. Environ Microbiol 2005;7: 530-543.   DOI
8 Yu Z, Yu M, Morrison M. Improved serial analysis of V1 ribosomal sequence tags (SARST-V1) provides a rapid, comprehensive, sequence-based characterization of bacterial diversity and community composition. Environ Microbiol 2006;8: 603-611.   DOI
9 Altman RB. Building successful biological databases. Brief Bioinform 2004;5:4-5.   DOI
10 Philippi S. Data and knowledge integration in the life sciences. Brief Bioinform 2008;9:451.   DOI
11 Olken F, Jagadish HV. Data management for integrative biology. OMICS 2003;7:1.   DOI
12 Field D, Sansone SA. A special issue on data standards. OMICS 2006;10:84-93.   DOI
13 Field D, Sansone SA, Garrity GM. Foreword to the special issue on the Fifth Genomic Standards Consortium Workshop. OMICS 2008;12:99.   DOI
14 Fischer MM, Nijkamp P. Geographic Information Systems, Spatial Modeling, and Policy Evaluation. Berlin: Springer-Verlag, 1993.
15 Kozak KH, Graham CH, Wiens JJ. Integrating GIS-based environmental data into evolutionary biology. Trends Ecol Evol 2008;23:141-148.   DOI
16 Dolan ME, Holden CC, Beard MK, Bult CJ. Genomes as geography: using GIS technology to build interactive genome feature maps. BMC Bioinformatics 2006;7:416.   DOI
17 Gasevic D, Djuric D, Devedzic V. Model Driven Architecture and Ontology Development. Berlin: Springer-Verlag, 2006.
18 Environmental Systems Research Institute. Network Analysis. Redlands: ESRI Press, 1995.
19 Hendler J. Agents and the semantic web. IEEE Intell Syst 2001;16:30-37.
20 Bard JB, Rhee SY. Ontologies in biology: design, applications and future challenges. Nat Rev Genet 2004;5:213-222.   DOI
21 Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000;25:25-29.   DOI
22 Environmental Systems Research Institute. Arcgis10. Redlands: ESRI Press, 2010.
23 SCBIR. Protege 3.4.8. Accessed 2015 Jan 2. Available from: http://smi-protegestanfordedu/repos/protege/owl/trunk.
24 Stalker J, Gibbins B, Meidl P, Smith J, Spooner W, Hotz HR, et al. The Ensembl Web site: mechanics of a genome browser. Genome Res 2004;14:951-955.   DOI
25 University of Maryland Libraries. Introduction to GIS using ArcGIS Desktop 10. College Park: University of Maryland Libraries, 2012. Accessed 2015 Jan 2. Available from: http://www.lib.umd.edu/gov/.
26 Sarajlic S. Contaminant Hydrogeology Knowledge Base (CHKb) of Georgia, USA. Atlanta: Georgia State University, 2013.
27 Medina I, Salavert F, Sanchez R, de Maria A, Alonso R, Escobar P, et al. Genome Maps, a new generation genome browser. Nucleic Acids Res 2013;41:W41-W46.   DOI
28 Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, et al. The human genome browser at UCSC. Genome Res 2002;12:996-1006.   DOI
29 Avraham S, Tung CW, Ilic K, Jaiswal P, Kellogg EA, McCouch S, et al. The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Res 2008;36:D449-D454.   DOI
30 Biswas S, Marwaha S, Malhotra PK, Wahi SD, Dhar DW, Singh R. Building and querying microbial ontology. Procedia Technol 2013;10:13-19.   DOI