BIOINFORMATICS Vol. 19 Suppl. 1 2003, pages i63–i65 DOI: 10.1093/bioinformatics/btg1006 Linking genotype to phenotype: the International Rice Information System (IRIS) Richard M. Bruskiewich 1, ∗ , Alexander B. Cosico 1 , William Eusebio 1 , Arllet M. Portugal 1 , Luralyn M. Ramos 1 , Ma. Teresa Reyes 1 , May Ann B. Sallan 1 , Victor Jun M. Ulat 1 , Xusheng Wang 1, 3 , Kenneth L. McNally 2 , Ruaraidh Sackville Hamilton 2 and Christopher Graham McLaren 1 1 Biometrics and Bioinformatics Unit, 2 Genetic Resources Center, International Rice Research Institute (IRRI), PO Box DAPO 7777, Metro Manila, Philippines and 3 Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310029, People’s Republic of China Received on January 6, 2003; accepted on February 20, 20003 ABSTRACT The International Rice Information System (IRIS, http://www.iris.irri.org) is the rice implementation of the International Crop Information System (ICIS, http://www.icis.cgiar.org), a database system for the management and integration of global information on genetic resources and germplasm improvement for any crop. Building upon the germplasm genealogy and field data components of ICIS, IRIS is being extended to handle diverse rice genomics data including: genetic mapping, genome annotation, genotype, mutant, transcripteome, proteome and metabolomic data. Users can access infor- mation in the database through stand-alone programs and WWW interfaces offering specialist views to researchers with different interests. Availability: http://bioinformatics.org/project/?group id= 141 Contact: r.bruskiewich@cgiar.org Keywords: database, crop, rice, germplasm, genotype, phenotype, genomics INTRODUCTION International germplasm exchange was the engine of the Green Revolution. In the past, however, much of the im- portant information produced from this exchange was only accessible locally, i.e. in field books or researchers’ files. Although major international initiatives for germplasm collection and conservation followed the Green Revolu- tion, much collected material is still not used because it is difficult to access. As a result, the full potential impact upon agriculture has not yet been realized. In 1995, the international agricultural research centers ∗ To whom correspondence should be addressed. CIMMYT and IRRI partnered with other CGIAR centers to establish a project to develop an International Crop Information System (ICIS; Fox and Skovmand, 1996 to overcome these deficiencies in crop data management. Since that time, the project has undergone a quiet evo- lution in design and implementation, and expansion to embrace many different crops, collaborative partners and categories of related information, including newly available molecular and genomic data. ICIS ARCHITECTURE A group of international scientists are collaborating to develop ICIS as a generic system that will accommodate all data sources for any crop and breeding system. The goals of ICIS are, firstly, to integrate different data types in both private and public datasets into a single information system and, secondly, to provide specialist views and applications that operate on this integrated platform. To achieve the first goal, the database is partitioned into a ‘Central’ (public) and ‘Local’ (private) installation, with a full user authentication and data ownership model built into the architecture. To achieve the second goal, a middleware layer was designed to provide a high-level data model and application program interface to insulate the details of the database schema from user applications. This has enabled the development of several independent standalone for ICIS, and also, provided modularity for the WWW interface. The system architecture is modular. A ‘Genealogy Management System’ (GMS) manages information concerning breeding methodology and chronology for germplasm. The GMS is also structured to assign a single unique ‘Germplasm Identifier’ (or GID) to each Bioinformatics 19(Suppl. 1) c  Oxford University Press 2003; all rights reserved. i63