Genomics Inform.  2015 Mar;13(1):7-14. 10.5808/GI.2015.13.1.7.

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

Affiliations
  • 1Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad 91775-1163, Iran. tahmoores@um.ac.ir
  • 2National Institute of Genetic Engineering and Biotechnology, Tehran 14965-161, Iran.

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 Protege 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.

Keyword

gene ontology; geographic information systems; linear referencing; rumen

MeSH Terms

Biology
Dataset
Gene Ontology
Genome
Genome, Microbial
Geographic Information Systems
Rumen*
Semantics
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