An Integrated Korean Biodiversity and Genetic Information Retrieval System

Plant and animal specimen data with surveys and observational data stored in museums and herbaria provide a vast information resource; these data include not only the historic information going back several hundred years, but also present day information on the locations of these entities [1]. The availability of this specimen data in on-line databases is greatly improving science and reducing cost and effort by providing for more efficient and effective biological surveys, which allow scientists to spend more time on research [2].

Traditionally, collections in museums and herbaria were made with only one main purpose in mind, taxonomic study, but their long-term mission has been to document biodiversity and its distribution through time and space for research, education, and service to the public [3]. The introduction of computer databases has opened up this vast data storage to many new uses [4]. These uses include biogeographic studies [5], conservation planning [6], reserve selection [7], climate change studies [8, 9], species translocation studies [10], etc.

The Internet's development has allowed new opportunities for interchanging data. Until the Species Analyst project [11], which began in the late 90's, there had been few successful electronic data interchange projects that utilized the Internet. Since then, a number of distributed projects have been initiated: the Mammal Networked Information System (MaNIS) [12], the World Network on Biodiversity (CONABIO) [13], the Australian Virtual Herbarium (AVH) [14], and the European Natural History Specimen Information Network (ENHSIN) [15]. Furthermore, a number of international cooperative projects (e.g., GBIF data portal, Species 2000, Consortium for the Barcode of Life (CBOL), Encyclopedia of Life (EOL), Ocean Biogeographic Information System (OBIS), Scratchpads [16], and WikiSpecies [17]) have recently begun to link and distribute biodiversity data among countries and international organizations. A general trend in bioscience is that advanced bioinformatics analysis and link-up tools are overcoming the challenges of different database types [18, 19]. For example, NCBI's databases contain information from molecular to species in different layers [20]. These layers are now becoming linked and integrated through genetic information from fast sequencing projects such as metagenomics; this process also accelerates biotechnological applications. The most important aspect of integration is that once these systems are deployed world wide, it will be possible for machines to process biodiversity information automatically, assuming the data are accurate. This will also accelerate standardization and raise the efficiency of the process of applying biodiversity studies by many magnitudes.

The biodiversity databases in Korea have been scattered among several institutes and local natural history museums, and the data were made up of heterogeneous types of databases with different formats and properties; a centralized standardized portal that enabled access to biodiversity information was necessary. A web portal will be able to speed up the investigation of complicated biological inquiries, allow researchers to develop new knowledge by analyzing large data sets, and provide the appropriate analytical tools [21]. For example, identification studies of predominant areas for conservation [22] and impacts of climate change across natural systems [23] will be increased through the accessibility of large, integrated databases.

We built NARIS, a database and national website for biodiversity, to manage and utilize the biodiversity resources in Korea and beyond. This system can be used in other nations with minimum modifications and language translations. At its core, NARIS is a biodiversity database, but it includes links to molecular and genetic information from the NCBI databases. NARIS aims to promote conservation, management, education, research, and industrial applications in biodiversity. In particular, with the advancements in fast genome sequencing technology, we expect that most of the common species will be completely sequenced before 2015. An integrated biodiversity management system such as NARIS will provide a platform that directly integrates the vast amount of genetic diversity information in the existing species diversity information.

With the advancement of information technology, the Internet, and rapid gene sequencers, managing biodiversity information in association with genetic information is becoming a global issue. Sharing and disseminating biodiversity information among different countries through relevant international organizations is becoming the standard practice.

In this paper, we presented an effective data management system, NARIS, which is a centralized data portal enabling an integrated information retrieval of the distributed biodiversity data and is linked with genetic information from NCBI. NARIS was specifically developed in Korea but is applicable to other nations. NARIS uses the DiGIR protocol with Darwin Core2.0 format as its metadata standard for data exchange to integrate and share the biodiversity data among organizations in Korea and abroad and to play an important role as a data node of the GBIF as well.

Considering the growing importance of biodiversity resources as the original source of bio-industry, establishing this integrated biodiversity information system is expected to be integral in protecting valuable national natural resources. Also, the system will be useful for the study of species and their distributions, conservation, scientific research, education, natural resource management, climate change, social and political uses, and medicinal studies.