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Geographical Bioinformatics Systems 237 Geographical Bioinformatics Systems 237 Geographical Bioinformatics Systems Tariq Rahim Soomro, Fujairah College, Fujairah, UAE, [email protected] Ghassan Al-Qaimari, Fujairah College, Fujairah, UAE, [email protected] Hassan Wahba, Al-Ain University of Science & Technology, Al-Ain, UAE, [email protected] Abstract store, analyze and integrate biological and genetic Geographical Bioinformatics Systems (GBS) information. represent the marriage between two distinct and well established fields, GIS & Bioinformatics. The collaboration of these two distinct fields, GIS Bioinformatics refer to the use of computers to and Bioinformatics was initiated by Virginia Tech handle biological information—that is, the use Office of GIS and Remote Sensing (OGIS) and the computers to store , compare , retrieve , analyze and Virginia Bioinformatics Institute (VBI), in 2001, predict the composition or structure of bio- when a conference focused on the interface between molecules. On the other hand, the term Geographic GIS and Bioinformatics was organized to study the Information Systems (GIS) refers to the prospects of research in these two fields. The computerized database management system for the participants of conference strongly indorsed the capture, storage, retrieval, analysis, and display of merger between the two fields, as GIS and spatial data. GIS is no longer restricted to the Bioinformatics have much in common, most notably fields of computer science, geography, cartography digital maps, large databases, and research involving or environmental science, but nowadays GIS tools visualization, pattern recognition, and most and techniques are successfully used and significantly analysis of data [3]. implemented in many other fields of life, such as advertising, agribusiness, banking, entertainment, This paper explores the future research in this new estate management, finance, food services, health multidisciplinary field. The paper is organized as services, insurance, manufacturing, pharmaceutical follow: section 2 reviews the applications of GBS; services, retail and utilities, social services, travel section 3 highlights future research trends in GBS; services and many more. This paper explores the section 4 discusses future directions and concluding merger of these two distinct fields GIS & remarks. Bioinformatics, and also explores the prospect for research and development in these two areas. 2. Applications of GBS 1. Introduction The authors propose the term Geographical In this paper we use the term Geographical Bioinformatics Systems (GBS) to describe a new Bioinformatics Systems (GBS) to describe the field of research and development that utilizes merger between GIS and Bioinformatics. expertise from two well-established fields, GIS and Geographical Information Systems (GIS) refer to a Bioinformatics. The term GBS refers to the complex technology, starting with the digital application of computer science in the management representation of landscapes captured by cameras, of biological information using the spatial and digitizers or scanners, in some cases transmitted by temporal maps and databases to collect and study satellite, and then with the help of computer the complex patterns and analyze its effects. systems, storing, checking, manipulating and Researchers in [3] agreed to use GIS applications to enhancing images to be analyzed and displayed as find and track large pattern, for example, geographic data referenced to the earth. GIS today is a well distribution of cancer and other diseases in human, established field with many practical applications. animal and plant populations etc. They are also The power of GIS lies not only in the ability to exploring the potential of using GIS to visualize and visualize spatial relationship, but beyond the space enhance the presentation of Bioinformatics data, and to a holistic view of the world with its many to identify the opportunities Bioinformatics presents interconnected subsystems and complex relationship to the GIS research community. They are also [1]. Bioinformatics on the other hand is an exciting exploring from another perspective the use of and rapidly growing field that uses computer Bioinformatics methodologies in GIS aiming at technology and information science to study enhancing current GIS techniques, and identifying biological information and structures. More new approaches to pattern recognition and data specifically, it is the science of developing computer analysis that could be used specifically for GBS databases and algorithms to facilitate and expedite purposes. biological research, particularly in genomics [2]. In simple terms, it is an application of computer The following is a short review of GIS applications technology to the management of biological that analyze and visualize Bioinformatics data to information. Computers here are used to gather, help Bioinformatics experts study biological Communications of the IBIMA Volume 5, 2008 238 Tariq Rahim Soomro, Ghassan Al-Qaimari and Hassan Wahba phenomena. These applications represent the a biomedical text-mining system focused on four solution for various Bioinformatics databases from types of gene-related information: biological GIS perspectives. functions, associated diseases, related genes and gene-gene relations. The aim of this system is to READ-IT (Research, Education, and Dissemination provide researchers with a user-friendly bio- via Information Technology) is a information service [8]. Bioinformatics/GIS program aimed at protecting chimpanzees. It is a system for the integration of Fungi is designed at University of Michigan to technology; research and education, through a explore spatial relationships between specimen data project designed to study and protect chimpanzees and other data using a GIS as one of the in Tanzania. This research is designed to develop bioinformatics method. This project makes it “interesting and compelling content for integrated possible to create maps showing the relationship research and educational opportunities for between the location of specimens and political undergraduate, graduate and professional students at units (states and counties of USA), major highways, Virginia Tech.” Some of those are involved with major lakes and rivers, and federal land ownership the “Bush to Base Bio-Informatics” and the GIS [9]. components of the program. In this program, field researchers gather physiological data on the chimps, Map Viewer is a tool designed at the National and code and process the data using handheld Center for Biotechnology Information (NCBI) that modules with Global Positioning Systems (GPS) allows a user to view an organism’s complete capability. The modules are designed to interface genome, integrated maps for each chromosome with a Virginia Tech-based Web-enabled server (when available), and/or sequence data for a designed to share information with authorized users genomic region of interest [10]. [4]. MultiStore is a research infrastructure designed at Micro-Mar is a database designed especially for University of Buffalo for supporting integrated dynamic representation of marine microbial research in specific targeted areas of computer biodiversity. It is created to collect DNA diversity science in the fields including Multimedia, information form marine prokaryotes for bio- Visualization, GIS and Bioinformatics. The research geographical and ecological analysis. The database objectives is to develop computational theories and aims to integrate molecular data and taxonomic algorithms for storing, managing, analyzing, affiliation with bio-geographical and ecological querying, and visualizing multi-dimensional data features that will allow experts to have dynamic sets that are generated from the related fields [11]. representation of the marine microbial diversity embedded in a user friendly web interface. In this ETI Projects at ETI Bioinformatics, in Amsterdam, program, GIS option provides an interface for is an NGO in operational relations with UNESCO, selecting a particular sampling location on the world participating in two GIS projects funded by NWO, map and getting all the sequences from the location the Dutch national science foundation. The first and their details [5]. project records and identifies the impact of global change on the biological diversity of the North Sea GenoSIS (Genome Data Interpretation Using GIS) and second project monitors climate changes in the is a genome spatial information system based on the Indonesian coral reef biotas. For these projects, ETI idea of “spatial genomics”, applying concepts and is building databases, programming queries and tools of spatial analysis and GIS to the interpretation preparing maps and map layers, using MapIt of genome data. It uses “off the shelf” GIS software package [12]. software, for example, ESRI’s ArcGIS and Orcale Spatial, to reuse existing spatial analysis, The majority of the above applications in classification, querying, and visualization tools for Bioinformatics are in the form of sequence analysis genome data analysis [6]. (e.g. DNA), genome annotation, computational evolutionary biology, measuring biodiversity, GEOBASE is a simple geographical information analysis of gene expression, analysis of regulations, system designed for personal computers. This analysis of protein expression, analysis of mutations system allows representation and elementary in cancer, prediction of protein structure, analysis of geographically coded information, and comparative genomics, modeling biological
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