PAG-IX: MAIZEDB: COPING WITH THE DELUGE, NEW ACCESSES AND LINKAGES.

PAG-IX   Plant & Animal Genome IX Conference

Town & Country Hotel, San Diego, CA, January 13-17, 2001.

Workshop: Databases, Gene Systematics, and Nomenclature
W22_04.html

MAIZEDB: COPING WITH THE DELUGE, NEW ACCESSES AND LINKAGES.

MARY L POLACCO1, Denis Hancock2, Steve Schroeder2, Hector Sanchez-Villeda2, Zhiwei Fang3, Leszek Vincent2, Heike Kross2, Su-Shing Chen3, Edward Coe1,

1 USDA-ARS, Plant Genetics Unit, Curtis Hall & Dept Agronomy, Curtis Hall, University of Missouri, Columbia, MO 65211 USA
2 Dept Agronomy, University of Missouri, Columbia, MO 65211 USA
3 Dept Computer Engineering and Electrical Engineering, Univeristy of Missouri, Columbia, MO 65211 USA

MaizeDB, www.agron.missouri.edu, has historically served as a central resource for maize genome information, complete with linkages to related data repositories. Data reside in an industry standard relational database management system, Sybase. Datatypes include maps, loci, probes, genetic stocks, agronomic traits, mutant phenotypes, and images along with documentation, including references, raw map data, QTL analyses, source laboratories and persons, complete with address information. Database schema are suitably robust to support addition of new marker types, such as SSR (simple sequence repeats) with modest changes. New interfaces to the database have been created to provide rapid access to main data categories, including (1) browse lists, with a map constraint capability (2) library or map-location specified sequence accessions (3) graphical map comparisons, inter and intra-species. These are dynamic, and read the central curated database. In addition, there is a development copy of the database, under Object Protocol Management, which permits retrieval of custom tables, from any field in the database and displays entity relationship diagrams on the WWW. We are developing trait and phenotype ontologies; these will be compatible with those for other species and databases, for example GRIN, and interact with the Gene Ontology project initiated by FlyBase. The Interactive Maize Plant (IMP), underway, builds on this ontology, and graphical depicts maize developmental biology at a level understandable to K-12 classrooms.

Funded by the USDA-ARS, the NSF and the University of Missouri.

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