Source: IOWA STATE UNIVERSITY submitted to
DATABASE OF MAIZE GENOME INFORMATION (DBMGI) - A NEW GENERATION MAIZE GENOME DATABASE
Sponsoring Institution
Agricultural Research Service/USDA
Project Status
TERMINATED
Funding Source
USDA COOPERATIVE AGREEMENT
Reporting Frequency
Annual
Accession No.
0404984
Grant No.
(N/A)
Project No.
3625-21000-045-01S
Proposal No.
(N/A)
Multistate No.
(N/A)
Program Code
(N/A)
Project Start Date
Sep 25, 2001
Project End Date
Sep 24, 2006
Grant Year
(N/A)
Project Director
LAWRENCE C J
Recipient Organization
IOWA STATE UNIVERSITY
2229 Lincoln Way
AMES,IA 50011
Performing Department
GENETICS
Non Technical Summary
(N/A)
Animal Health Component
(N/A)
Research Effort Categories
Basic
90%
Applied
10%
Developmental
0%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
20115101080100%
Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1510 - Corn;

Field Of Science
1080 - Genetics;
Goals / Objectives
The objective of this project is to develop a next-generation maize genome database, which will be publicly accessible to users via the Web and serve as a model for data integration and database architecture for other species.
Project Methods
(1) Working with the USDA/ARS, we will review near-term bioinformatics needs for the reposition, curation, and analysis of maize genetic and genomic data; (2) Seeking to anticipate future requirements, particularly with respect to high-throughput genomic data that is being generated by NSF-funded maize genome projects; (3) Reviewing the current state of the art in genomic software to identify a suite of software that best matches the above requirements for maize; (4) Addressing near-term requirements for middleware and user interface tools for the existing USDA/ARS database for maize (MaizeDB); (5) Longer term, addressing the need for data integration across heterogeneous repositories; (6) Training graduate and postdoctoral students and short-term visitors in the application of bioinformatics and data-mining approaches to enhance their maize research projects; and (7) Working closely with technical and user advisory groups convened by USDA/ARS and NSF to insure that the project deliverables meet current and anticipated user needs.

Progress 09/25/01 to 09/24/06

Outputs
Progress Report 4d Progress report. This report serves to document research conducted under a specific cooperative agreement between ARS and Iowa State University. Additional details of research can be found in the report for the parent project #3625-21000-045-00D, Database of Maize Genome Information. The original purpose of the SCA was to develop a new maize community genetics and genomics database (MaizeGDB), integrating data sources previously held by the now superseded MaizeDB (http://www.agron.missouri.edu/) and ZmDB (http://www.zmdb.iastate.edu/) projects into a single resource. This task was completed in FY 2004: the transition from MaizeDB and ZmDB to MaizeGDB has been accomplished. The current purpose of this agreement is to automatically update sequences at the MaizeGDB site. This dataset is of particular interest because the genome of the maize inbred B73 and chromosome 10 of Mo17 are being sequenced. A pipeline by which sequences are made available to workers at MaizeGDB and the method of linking sequence records at MaizeGDB to the Iowa State University PlantGDB maize genome sequence assembly have been developed over the course of the past year. The sequence upload pipeline runs once monthly, and a new sequence set is made available to maize geneticists on or about the first Tuesday of each month. Currently, the SCA supports work to add capabilities to the MaizeGDB Community Curation Tools that would enable researchers to associate ontology terms with records of various types. These ontology terms are used at various online data repositories and can serve as a link to enable database interoperability.

Impacts
(N/A)

Publications

  • Lawrence, C., Seigfried, T.E., Brendel, V. 2005. The maize genetics and genomics database. The community resource for access to diverse maize data. Plant Physiology. 138(1):55-58.


Progress 10/01/04 to 09/30/05

Outputs
4d Progress report. This report serves to document research conducted under a specific cooperative agreement between ARS and Iowa State University. Additional details of research can be found in the report for the parent project #3625-21000-045-00D, Database of Maize Genome Information. The original purpose of the SCA was to develop a new maize community genetics and genomics database (MaizeGDB), integrating data sources previously held in MaizeDB (http://www.agron.missouri.edu/) and ZmDB (http://www.zmdb. iastate.edu/) into a single resource. This task was completed in FY 2004: the transition from MaizeDB and ZmDB to MaizeGDB has been accomplished. During the past year, a QTL data entry module was developed, which will be made available for general use in the very near future. New datasets including maps (genetic, cytogenetic, and recombination nodule) were incorporated into the database during the past year, and technical support was given for the Annual Maize Genetics Conference and the research activities of maize researchers around the world. Three curation tool training sessions were conducted: one at the International Plant and Animal Genome Conference, another on the Iowa State University campus, and a third concomitant with poster viewing at the Annual Maize Genetics Conference. Presently, the purpose of this agreement is to create a process to automatically make available an up-to-date set of all publicly available maize sequences (with associated ontological annotations) through the MaizeGDB site. This dataset is of particular interest because the genome of the maize inbred B73 is slated for complete sequencing in the very near future. Development of the method by which sequences are made available to workers at MaizeGDB and the method of linking sequence records at MaizeGDB to the PlantGDB maize genome sequence assembly are currently under development.

Impacts
(N/A)

Publications

  • Lawrence, C., Seigfried, T.E., Brendel, V. 2005. The maize genetics and genomics database. The community resource for access to diverse maize data. Plant Physiology. 138(1):55-58.


Progress 10/01/03 to 09/30/04

Outputs
4. What were the most significant accomplishments this past year? D. Progress Report. This report serves to document research conducted under a Specific Cooperative Agreement between ARS and Iowa State University (SCA No. 58- 3625-1-192). Additional details of research can be found in the report for the parent CRIS 3625-21000-045-00D "Database of Maize Genome Information". The purpose of the SCA was to develop a new maize community genetics and genomics database, integrating in particular data sources previously held in MaizeDB (http://www.agron.missouri.edu/) and ZmDB (http://www.zmdb.iastate.edu/). This task has been accomplished: MaizeGDB (http://www.maizegdb.org/) is now fully operational, encompassing all the data types previously stored elsewhere. The transition from MaizeDB and ZmDB to MaizeGDB is complete. New curation tools have been developed and tested. MaizeGDB provides a centralized web-based resource for maize genome information, supporting the annual Maize Genetics Conference and the research activities of maize researchers around the world. 7. List your most important publications in the popular press and presentations to organizations and articles written about your work. Lawrence, C.J., Q. Dong, M.L. Polacco, T.E. Seigfried, and V. Brendel. 2004. MaizeGDB, the community database for maize genetics and genomics. Nucleic Acids Research. 32:D393-397.

Impacts
(N/A)

Publications