V. MAIZE GENOME DATABASE

http://www.agron.missouri.edu

MaizeDB, http://www.agron.missouri.edu, started in 1991 and maintained by the ARS, is an integrated genome resource for the maize genetics community. In Oct 1998, the Missouri Maize Project received funding from the NSF Plant Genome Program to support new extensions and enhancements of the database, with particular emphasis on user access. The implementation has three phases: (1) upgrading user capabilities and interfaces of MaizeDB with better data analysis tools and map viewers; (2) development of a new object-oriented framework; (3) extension and enhancement of the current MaizeDB. The NSF funding complements the ARS commitment to support the curation and serving of the production database on the WWW. We are pleased to introduce a new cooperator, Dr. Su-Shing Chen, Chair and Professor of Computer Science and Engineering, University of Missouri-Columbia. Dr. Chen is a co-PI on the NSF project and will be taking the lead in development of new enhancements to the database.

Users throughout the community will be selected to test and comment on new design tools. In addition, we strongly encourage all cooperators to take a moment and try looking up something of interest and inform us where you have difficulty finding something. Feel strongly encouraged to let us know about anything you would like to see changed or added. Send email to db_request@teosinte.agron.missouri.edu or use the email link on our home page.

 

New Design 1998

1. Stock query form specific for MGCSC (Maize Genetics Cooperation Stock Center). This form now retrieves only Stocks available from the Stock Center. The search options are limited to a selected group, many of which are provided in menu format, rather than 'type into the blanks'.

2. SSR (Simple Sequence Repeats or microsatellite) tabulations (browse only, real time, linked to database for details). A copy of the tabulation, as extracted April 1999, is appended.

3. Person queries by name and city only. This form is a simplified version of the Person 'all attributes' query page, and retrieves only the address and phone information. It is linked to the full MaizeDB record for other information, such as references authored. We would greatly appreciate if you would check your entry and provide any updates or corrections to us.

4. Reorganization of pages so that form queries and browse lists are listed together by category of information, in addition to the options for style of query. For example, touching on Loci/Variations accesses query forms for all attributes, a simplified Locus query form, and various browsable listings of mutant Images, the MNL Gene List and nomenclature guidelines. Touching on Stocks/Probes will lead to the Stock center and its Catalogs and various Stock searching styles which include the full text of the entire database, any attribute, and names only. The Probes section of this page leads to lists of the Core markers, the SSR tabulations (see above), probes available from the UMC RFLP laboratory, and the various searching styles: full text, any attribute, names only.

Design Plans for the coming year.

1. Table making. Current users of MaizeDB may access a few tables but the columns allowed are predetermined. Examples include map scores by the bin; the gene list; SSR compilations; the core marker table; the stock center catalog. Typical form searches where the user may specify attributes will retrieve a list of names only. A table-making tool, with menu derived options, would permit additional columns to be selected, for example phenotypes and SSR probes, and map coordinates.

2. Graphical mapviewer. Current map displays are text only, and do not permit custom or comparative map displays. We plan to develop a new utility, building on current WWW map display software; it will extract data in real time, and support robust query, display and print options.

3. Interface for data entry by the community. Community includes the expert curator, such as at the Stock Center, high through-put projects in maize, and Cooperators at large. Stock Center curation is provided direct access to the entire database, while the Cooperator at large, updating address information for example, might have more limited access to the database.

 

Mary Polacco, Curator MaizeDB


Please Note: Notes submitted to the Maize Genetics Cooperation Newsletter may be cited only with consent of the authors.

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