Database Management of Plant Genetic Resources
Authors: Data Base Management of Plant Genetic Resources
Utpal Roy1, Nabarun Roy2
1Department of Plant Breeding and Genetics, Assam Agricultural University, Jorhat, Assam, India-785013
2Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India-785013
The conservation and management of plant genetic resources contain various inter-related activities that generate a large amount of data. The usefulness of the data generated can only be fully realized if they are transformed into meaningful information, for the benefit of both the conservationists and the users. The information can be used to make critical decisions on what germplasm needs to be collected, how much material is in store, when to regenerate accessions in the collection, which of the collection may have potential for utilization.
A documentation system must therefore be able to reliably store, retrieve and process data, and generate information from across all activities. Correct information can be retrieved if reliable data storage and information retrieval system, or more technically, a documentation system, is available.
Usefulness of a germplasm database system
The usefulness of a germplasm database system can be influenced by the following factors:
♦ information quality - refers to accuracy, precision, completeness, timeliness and source.
♦ information accessibility - refers to the relative ease in obtaining and manipulating information.
♦ information presentation - pertains to the capability of the system to format and summarize information the way users want it.
To facilitate data gathering and allow accurate observation, the data collector must have knowledge of the descriptors being scored. Bioversity International issues a compendium of descriptive information and traits that characterize a particular accession of a certain plant group called a descriptors list. It provides a comprehensive list of characters and aims to standardize plant characterization by setting an international format. Included in a descriptors list are passport data, characterization and evaluation.
If there are no published descriptors, the researchers can formulate their own, following the standard format and using the published Bioversity descriptors as model. In most cases, users of the documentation system looking for information are normally interested only in a fraction and very specific information out of the entire documentation system. Therefore, the PGR documentation system must be equipped with an effective search function.
• The search function should execute according to the specification supplied by the user, i.e. which tables should be searched, and how the search output should be organized.
• The nature of data and information that each user requires depends largely on the specific interest of the user.
• The report function is the output component of the documentation system or the end-result of the search execution. It is then subsequently visualized either on-screen or printed directly as a hardcopy or softcopy as a system file.
• This user-friendly feature should extend to data manipulation needs such as statistical and geographic information system (GIS) analyses; during file transfer from the database to another application; and for sharing information through the Internet.
• The usefulness of germplasm databases is magnified in direct proportion to the number of users who can access it. Putting germplasm databases on the web can increase access to them many times over.
• Some outstanding examples are the databases of the United States Department of Agriculture (USDA) (www.ars-grin.gov), the Center for Genetic Resources The Netherlands (CGN) (www.cgn.wur.nl), the Nordic Genebank (www.ordgen.org), the Asian Vegetable Research and Development Center (AVRDC) http://220.127.116.11/avgris), the Ministry of Agriculture, Forestry and Fisheries of Japan (www.gene.affrc.go.jp) and the CGIAR centers which can be accessed from their own websites or through the System-Wide Genetic Resources Program (SGRP) of the CGIAR.
Germplasm Resource Information System (GRIN)
Germplasm Resource Information System (GRIN) is the new version of GRIN-Global Project, providing the world’s crop genebanks with a powerful, but easy-to-use plant genetic resource (PGR) information management system. GRIN-Global accommodates commercial and open-source programming tools and requires no licensing fees. Programming strategies support continuous evaluation and refinement; advanced prototypes will be extensively beta-tested. Bioversity International will deploy GRIN-Global worldwide, working cooperatively with users to document the system in Arabic, English, French, Russian and Spanish, translate its interface, and implement it in developing countries. The system uses a .NET (“dot net”) framework and Visual Studio development environment. This technology allows data to be stored locally or on networks. Centralized data can be distributed to off-site systems.
A. GRIN and the Need for GRIN-Global
The USDA-ARS developed, supported and enhanced GRIN throughout its 22 year history. Widely recognized as a superior genebank management system, GRIN information content has been invaluable to researchers and genebank personnel, but its inherent complexity and licensing fees prevented some genebanks from adopting it. The Global Crop Diversity Trust initiated the GRIN-Global project to meet their common needs and reduce redundancies of effort being expended by the genebanks and independent consortia. GRIN-Global is being developed jointly by the USDA Agricultural Research Service, Bioversity International, and the Global Crop Diversity Trust. Core development team personnel are from:
♦ Plant Introduction Research Unit, Ames
♦ Database Management Unit, Beltsville
♦ National Clonal Germplasm Repository, Corvallis
♦ Subtropical Horticultural Research Station, Miami
♦ Bioversity International, Rome
B. Three-tier Design
- Presentation - It can assume different forms. For example, the GRIN-Global website retrieves PGR data from the database using the Business Tier’s web services. Also third-party applications, such as MaizeGDB or SoyBase, or websites connecting to the Business Tier web services, can retrieve data.
- Business - It contains a full complement of software modules which accessible to any computer connected to the internet via standard protocols. Such as current web services use the SOAP protocol, providing data in XML format.
- Data - It is having database where PGR data is permanently stored.
• GRIN-Global will be continually maintained and updated
• It is customizable to meet local system administrator requirements
• It is capable of data exporting & importing between spreadsheets and GRIN-Global’s database including customizable screen views, forms, and menus and a search engine that is “Google-like”
- Genebank Use
It Can be implemented different ways, ranging from a simple genebank inventory application to a widely distributed system supporting on-line user searching and germplasm ordering. It is operating over a network or on “stand-alone” personal computers. It supports PostgreSQL, MS SQL Server, Oracle, and MySQL databases and enables maximum flexibility in delegating user rights.
It provides immediate access to PGR information for researchers which incorporate an easy-to-use interface for extracting and manipulating PGR information. It facilitates germplasm ordering to meet specific research needs.
About Author / Additional Info:
I am currently pursuing PhD in Plant Breeding and Genetics from Assam Agricultural University, Jorhat, Assam, India.