V. MAIZE GENOME DATABASE

MaizeDB-- www.agron.missouri.edu

New Data

In brief. MaizeDB has added over 84,000 new records this year, many with links to external databases. Of the new records, 50% are 'Probes', 16% references, 14% Gel Patterns and 7% Variations . Images of over 1000 agarose screening blots for SSR and RFLP markers are now available. MNL issues are now retroactive to 1988, and accessible to full-text searching as are abstracts for the Annual Maize Genetics Conference, retrospective to 1991. See also the Stock Center report; new stocks are entered into MaizeDB , largely by the staff at the Stock Center.

Data Sources

Data for SSR have been imported from the Missouri Maize Project, the Acemaz database , Pioneer, and Keith Edwards (UK). Clone data for ESTs are imported from dbEST, GenBank, and ZmDB. When SSR are found and mapped in an EST, the link from the SSR primer pair and map information is made to the EST clone, which also inherits the map information. In all cases, acknowledgment of sources, complete with links to the external database source, is entered into each record.

External Database Links

New databases added this year include ZmDB (www.zmdb.iastate.edu) and TIGR(www.tigr.org). EMBL records are now linked to MaizeDB. We continue to regularly update links to dbEST, dbSTS, GenBank; SwissProt; and Medline/PubMed. Some 12% of the non-MNL references have links to PubMed; PubMed provides abstracts, related articles and sequences. GRIN links for genetic stocks are kindly provided by Marty Sachs at the Stock Center. MaizeDB also links to the Plant Genome Database suite at Cornell for comparative map data in GrainGenes and RiceGenes. In response to community requests for files of mapped cDNA sequences, with map coordinates, a utility that creates files of map coordinates and/or accessions for retrieval from GenBank by formats provided at NCBI, has been installed on the database EST page.

Literature Annotation

The past 2-3 years MaizeDB has not had resources to keep up with the flow of literature; this year some additional funding to MaizeDB from the USDA-ARS is being used to enhance this effort. Literature citations are selected and entered automatically, with links to authors. Of 33,837 references, 9,614 are MNL or Maize Meeting Abstracts. Many are currently linked to database objects, such as loci, map data, PCR primers and agronomic traits.

Navigation aids

•A side-bar directory that is inherited on the main pages for the database. It is organized into 4 sections: (1) general information, (2) access styles and (3) category-specific access (Locus, Stocks, Trait, Person, etc.) listings, followed by (4) links to other resources.

•Category-specific navigation helps are available , linked to the sidebar categories and maintained by a staff member most expert in that area and listed on the page for contact . When multiple staff members are involved, users are encouraged to contact the staff, at db_request@teosinte.agron.missouri.edu.

•Enhanced 'table of contents' , called 'Browser' in the side-bar. Alphabetical lists of the individual items, organized by category, Locus, Probes, Stocks, Images, Persons, and References may be explored and are dynamically created from the underlying database tables. Many of the lists permit restriction of listings to items based on map location and, where applicable , provide information about map and sequence accessions. Lists are created dynamically . The lists may be saved to any desktop, using the browser utility to save as 'source' or 'html' and then imported into standard software, such as an Excel workbook, all-the-while maintaining hypertext links .

•Integrated EST and SSR compilations, with links to sequence and map data. These are accessible from the sidebar list of categories.

Works in Progress

The work described below is largely supported by NSF award # 9872655.

Interactive Maize Plant - 'a feel for the organism'

An interactive set of images of the maize plant, complete with glossary of terms for anatomical features, is being developed for different stages of the maize plant, complete with links to underlying MaizeDB records. One goal is to provide access to the underlying maize genome to any person interested in maize, including elementary-high school students or teachers, undergraduates and researchers in various disciplines. The sort of access to be provided may be viewed at Flybase, flybase.bio.indiana.edu, a Drosophila genome database that integrates community information similarly to MaizeDB. The glossary will be harmonize d with trait and phenotype terminology in the germplasm, and also in other related species, in particular the grasses.

Custom Table-Making

A copy of the database has been placed under OPM (Object Protocol Management), which provides a graphical display of data relationships, custom query access, as well as defaults. Access to the work-in-progress is provided on the 'about MaizeDB' page, accessible from the homepage sidebar. In progress, access to a glossary of all the fields in the database. The software is proprietary, and licensed to MaizeDB, free of charge, from Data Logic, www.genelogic.com. We thank Dr. I-Min Chen and her colleagues for providing support in this work.

Interaction with cereal genome databases

OPM (see above section) also permits interactive database query interfaces across platforms, such as Oracle and Sybase, and at different locations. This is distinct from the record-to-record linking typically employed. We are testing a prototype rice genes dataset in collaboration with our colleagues in Tsukuba , Japan , using distinct schema and database management softwares (Oracle, Sybase). We are in contact with the USDA-ARS database suite at Cornell regarding this utility for providing distributed queries across different databases. The OPM software also supports interactions with applications, such as BLAST.

Graphical Representation

Currently, maps are viewable by ACEDB software at the Cornell site and by postscript files, stored at MaizeDB . Viewers, such as that developed for the Japan Rice Genome Program , and also facile custom-map displays are works in progress.

User Statistics

Access to the database has approximately doubled over the past year, from 25,000-30,000 visitors/month to over 60,000. Some 17% of resolvable hits is US educational, 56 % US commercial or network. Data categories most accessed include References, Locus, Person, Maps, Variations, Stock, Probes, GelPatterns, Gene Products, Images; these, however, account for only 22% of hits. Other hits are to various entry pages; a major referral page is the Maize Genetics Stock Center, Urbana.

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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