Introduction:

"Oryzabase" is a combination of the words "Oryza" (genus name of rice) and "database". Oryzabase was constructed and maintained by the Rice Genetic Resource Committee in Japan, which inherited the previous "Rice Genetic Resources Database in Japan"
(Yamazaki et al. 2000). The objectives of the database are:

(1) to serve as a portal site which provides researchers with information on available resources
(2) to provide as much information on research related to rice
(3) to provide a starting point for those beginning to conduct rice research
(4) to serve as an archive of sites related to rice research worldwide.

Oryzabase is available online at http://www.shigen.nig.ac.jp/rice/oryzabase/top/top.jsp.

This project is funded by the Ministry of Education, Culture, Sports, Science and Technology in Japan (MEXT), and organized by the rice genetic resources committee under MEXT.

Contents:

Oryzabase consists mainly of the following six components:

1. Rice Genetic Resources developed and maintained by Japanese researchers

Current database compiles around 11,000 strains maintained by 25 stock centers in Japan, which are mainly universities and research institutes. Stock strains are classified into 10 groups according to their genetic properties. Most informations are kept up-to-date by joint work with maintainers. While all stocks belonging to the same group share the same basic data format, some stocks have more data about their characteristics, which is important for breeding science. Oryzabase also provides a "Core Collection of Wild Rice" to show representative wild rice accessions, which covers nine different genomes (AA, BB, CC, BBCC, CCDD, EE, FF, GG, and HHJJ) and 19 different species. All collections have been characterized and included image data. To promote accumulation of useful information on the designated accessions, we recommend researchers to use core collections, from rank 1 to rank 3, for their future research.

2. Mutant phenotype collection

The mutant phenotype collection is a database of phenotype images that are currently classified into five major groups of Coloration, Heterochrony, Reproductive Organ, Seed and Vegetative Organ. Each accession includes the causal gene with one or more alleles, its chromosomal location, linkage map information, citations and character description. To allow the continued growth of this collection, a web-based submission system was established. Users can upload new mutant phenotype image files, and submit them to the database from their personal computers. Anyone who published a mutant(s) in any journal including RGN can register the mutant phenotype and characteristics on Oryzabase. Oryzabase will acknowledge it and refer the depositor and the journal on each mutant site.

3. Gene dictionary

The gene information in Oryzabase is based on the report of the Committee on Gene Symbolization, Nomenclature and Linkage Groups. New gene data, including recently sequenced genes, are now being processed to add into the database. The current dictionary contains a mixture of sequenced genes and phenotypic trait genes. Source references are also presented for all genes in the database. Genomic information and strain information are linked.

4. Genetic maps

Oryzabase provides several linkage maps and physical maps, including the latest information published by the Rice Genome Project. Common genes and/or markers located on two or more maps are automatically updated with the link to new release genomic sequences. Linkage maps, including both trait genes and DNA markers, will give useful information on both functional and comparative genomics.

5. Rice basic information

In addition to serving as an archive of rice research information, a major gal of Oryzabase is to promote studies on rice by encouraging the next generation of rice researchers. To this end, Oryzabase will continue to provide introductory data to those just beginning their studies. A key portion of this project is a strong introduction to the study on wild rice which serves as a powerful gene resources rarely found in the current cultivated strains. An additional project to establish rice development/anatomy database in accordance with ontology movement is ongoing.

6. Rice related information sites

There are several useful rice databases worldwide, including RGP (Rice Genome Research Program, Japan), IRRI (Philippine), Gramene (USA), and Genome database of Chinese Super Hybrid Rice (China). However, the organization that manages these databases, and the locations of the databases themselves, can frequently changed due to their rapid reconstruction. Therefore, Oryzabase plans to ensure an up-to-date information through automated URL-checking, which is supplemented by manual checking of the sites it refers.

Current activities

Ontology is a powerful idea used to specify certain concepts consistently. It is especially useful in comparing common concepts between different fields. Among the many biological ontology projects recently established, the gene ontology (GO) project is the most popular and widespread because major databases such as Flybase (Drosophila), SGD (Yeast), MGI (Mouse), TAIR (Arabidopsis), WormBase (C.elagans), PomBase (Yeast), RGD (Rat), EBI, TIGR have already joined. Recently the Gramene database maintained by Cornell University joined the GO project prior to other Rice databases. The Gramene database now proposes three rice ontologies, gene ontology (GO), traits ontology (TO) and plant ontology (PO), which defines plant anatomy and/ or plant growth stages. Coordinating Gramene's efforts, Oryzabase started an internal ontology project for all genes of the dictionary assigned to the above ontologies. The new version of Oryzabase includes a GO browser by which users can easily have an access to GO data. Japanese researchers have just started discussion on nomenclature and will work on all ontologies in collaboration with overseas rice researchers. Since the ontology project is difficult for experimental researchers to join, Oryzabase is preparing a tool which will offer researchers with a conceptual data view to present an overview of database contents, as well as a more focused view for those interested in more specific concepts.

Future plans:

We are expecting a complete japonica rice genome sequence by the end of this year. Oryzabase will relate such genomic information with existing data. In the near future, spatial and temporal gene expression pattern in various organs will be added to the database. We are also planning to implement many links to external databases, not only Japanese databases but also international databases, and even across species.

Reference

Yamazaki, Y., A. Yoshimura, Y. Nagato and N. Kurata: Oryzabase-Integrated map and mutant database-. Plant & Animal Genome VIII Abstract 54p (2000)