Location: National Germplasm Resources Laboratory2009 Annual Report
1a. Objectives (from AD-416)
Serve as the information system for the documentation of plant, insect, animal, and microbial germplasm maintained by the U.S. National Genetic Resources program. Operate and enhance existing databases, create and improve linkages to other genetic resources databases, and share information and technology on documentation of genetic resources collections.
1b. Approach (from AD-416)
Support will be provided to the existing GRIN databases that serve the National Genetic Resources Program to ensure that they are functional and relevant to the needs of collection managers and curators and to the germplasm user community. Upgrades will be made to the highly specialized application software, as appropriate, to ensure that it remains compatible with hardware upgrades and that it meets the requirements for germplasm maintenance and documentation and information exchange. Appropriate measures will be taken to ensure security of the databases and the data they contain. Develop the next version of the GRIN software as a scalable portable system capable of being transfered to other genebanks in addition to allowing greater interoperability between genetic resources and biodiversity databases.
3. Progress Report
The Database Management Unit (DBMU) supports NP 301 by providing a central database for the germplasm collections within the National Plant Germplasm System (NPGS). This central database provides curator tools for managing the collections as well as a portal for public access and ordering of material. An essential task for the DBMU is to maintain near 24/7 availability of the system. A 98% availability target was met. A new application server was purchased and installed. Preparations were made to move from a 10 Mb commercial internet service provider to the 600 Mb USDA telecommunications network. In addition to maintaining the servers and current GRIN software, the DBMU is contributing to the development of a new version of the GRIN software (GRIN-Global) with collaborators from ARS, Global Crop Diversity Trust and Bioversity International. This will be a scalable version of GRIN using open source technology to better service the needs of the NPGS and the breeding and research community. In addition, it will be made available to interested genetic resource managers worldwide, especially in the developing countries where there is a serious need for a genebank management system. The initial phases of the project that have been completed are: designation of the development team, several team meetings, selection of the Technical Steering Committee, conversion of the Oracle database to open source MySQL, training and initialization of the development work.
1. GRIN Availability. The GRIN database was available on a nearly 24/7 basis throughout 2009. Access to the web pages for GRIN averaged over 1.5 million hits per month for 2009. As of July 2009 over 140,000 samples of germplasm have been distributed from the NPGS genebanks, most of them requested on the basis of information made available through GRIN.
2. GRIN Molecular Data. The molecular marker section of GRIN was put into full production and 9 marker datasets have been added to the database (Blueberry, Cacao, Rhubarb, Pea, Hops, Pear, Apple, Grape, and Hazelnut). GRIN is now capable of storing and presenting datasets with both phenotypic (trait) and genotypic (marker) information. Links were established between molecular studies registered in NCBI that were based upon accessions from the NPGS and GRIN. Users searching the NCBI site can link to GRIN and vice versa, users querying GRIN can link to the relevant NCBI dataset where applicable.
3. GRIN Enhancements. Improvements were made to the existing GRIN curator and public software, including the ability to download an entire evaluation (all traits), improved marker data displays and additional query options on the crop query pages. Hardware and network enhancements include purchase and installation of a new application server and movement from a commercial internet server to the USDA network. In order to comply with the International Treaty, a Standard Material Transfer Agreement (SMTA) module was added to GRIN. The SMTA module allows NPGS curators to track and manage covered accessions in compliance with the international law.