Reference Type: Journal Article Record Number: 5 Author: Jaiswal, P; Ni, J.; Yap, I.; Ware, D; Spooner, W.; Youens-Clark, K.; Ren, L.; Liang, C.; Hurwitz, B.; Zhao, W.; Ratnapu, K.; Faga, B.; Canaran, P.; Fogleman, M.; Hebbard, C.; Avraham, S; Schmidt, S.; Casstevens, T. M.; Buckler, E. S.; Stein, L; McCouch, S Year: 2006 Title: Gramene: A genomics and genetics resource for rice. Journal: Rice Genetics Newsletter Volume: 22 Issue: 1 Pages: 9-16 Short Title: Gramene: A genomics and genetics resource for rice. Abstract: Rice, maize, sorghum, wheat, barley and the other major crop grasses from the family Poaceae (Gramineae) are mankind's most important source of calories and contribute billions of dollars annually to the world economy (FAO 1999, http://www.fao.org). Therefore, continued improvement of Poaceae crops is necessary in order to continue to feed an ever-growing world population. The Gramene database (http://www.gramene.org) takes advantage of the known genetic colinearity (synteny) between rice and other major cereal crop genomes to provide researchers with the benefits of an annotated rice genome and to facilitate its comparisons with the other cereal genomes. Gramene is a one-stop online web resource that provides ready access to curated literature, genetic, physical and sequence based maps, markers, genes, genomes, proteins and QTL (Fig. 1) as well as comparative analysis tools. These datasets contribute to our understanding of the genome organization, as well as genes and gene families and their role in determining the anatomy, development, environmental responses and factors influencing agronomic performance of rice and other major cereal crop plants. As an information resource and public repository of curated rice datasets (Ware et al. 2002a, Ware et al. 2002b, Jaiswal et al. submitted to Nucleic Acids Res.), Gramene adds value to data that is initially contributed by numerous rice researchers, projects, databases and generic data repositories such as NCBI's Entrez (http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi?term=oryza). While Gramene database provides information on a range of grass species, the datasets and their presentation or accessibility via various modules described in this report are focused for rice only. The description is based on release #18 (September 2005) of the database. URL: http://www.shigen.nig.ac.jp/rice/rgn/vol22/v01.html Reference Type: Journal Article Record Number: 4 Author: Jaiswal, P.; Ni, J.; Yap, I.; Ware, D.; Spooner, W.; Youens-Clark, K.; Ren, L.; Liang, C.; Zhao, W.; Ratnapu, K.; Faga, B.; Canaran, P.; Fogleman, M.; Hebbard, C.; Avraham, S.; Schmidt, S.; Casstevens, T. M.; Buckler, E. S.; Stein, L.; McCouch, S. Year: 2006 Title: Gramene: a bird's eye view of cereal genomes Journal: Nucleic Acids Res. Volume: 34 Issue: Database issue Pages: D717-23. Short Title: Gramene: a bird's eye view of cereal genomes Accession Number: 16381966 Abstract: Rice, maize, sorghum, wheat, barley and the other major crop grasses from the family Poaceae (Gramineae) are mankind's most important source of calories and contribute tens of billions of dollars annually to the world economy (FAO 1999, http://www.fao.org; USDA 1997, http://www.usda.gov). Continued improvement of Poaceae crops is necessary in order to continue to feed an ever-growing world population. However, of the major crop grasses, only rice (Oryza sativa), with a compact genome of approximately 400 Mbp, has been sequenced and annotated. The Gramene database (http://www.gramene.org) takes advantage of the known genetic colinearity (synteny) between rice and the major crop plant genomes to provide maize, sorghum, millet, wheat, oat and barley researchers with the benefits of an annotated genome years before their own species are sequenced. Gramene is a one stop portal for finding curated literature, genetic and genomic datasets related to maps, markers, genes, genomes and quantitative trait loci. The addition of several new tools to Gramene has greatly facilitated the potential for comparative analysis among the grasses and contributes to our understanding of the anatomy, development, environmental responses and the factors influencing agronomic performance of cereal crops. Since the last publication on Gramene database by D. H. Ware, P. Jaiswal, J. Ni, I. V. Yap, X. Pan, K. Y. Clark, L. Teytelman, S. C. Schmidt, W. Zhao, K. Chang et al. [(2002), Plant Physiol., 130, 1606-1613], the database has undergone extensive changes that are described in this publication. URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16381966 Author Address: Department of Plant Breeding, 240 Emerson Hall, Cornell University, Ithaca, NY 14853, USA. Reference Type: Journal Article Record Number: 3 Author: Jaiswal, P; Ni, J.; Yap, I.; Ware, D; Spooner, W.; Youens-Clark, K.; Ren, L.; Wei, X.; Liang, C.; Pasternak, S.; Zhao, W.; Tecle, I.; Faga, B.; Canaran, P.; Ravenscroft, D.; Hebbard, C.; Avraham, S; Casstevens, T. M.; Buckler, E. S.; Stein, L; McCouch, S Year: 2006 Title: Gramene: A Genomics and Genetics Resources for Maize. Journal: Maize Genetics Cooperation Newsletter Volume: 80 Pages: 99-107 Short Title: Gramene: A Genomics and Genetics Resources for Maize. URL: http://www.agron.missouri.edu/mnl/80/gramene80.htm Link to PDF: Maize Genetics Cooperation Newsletter Reference Type: Journal Article Record Number: 2 Author: Jaiswal, P.; Ware, D.; Ni, J.; Chang, K.; Zhao, W.; Schmidt, S.; Pan, X.; Clark, K.; Teytelman, L.; Cartinhour, S.; Stein, L.; McCouch, S. Year: 2002 Title: Gramene: development and integration of trait and gene ontologies for rice Journal: Comparative and Functional Genomics Volume: 3 Issue: 2 Pages: 132-136 Short Title: Gramene: development and integration of trait and gene ontologies for rice Abstract: Gramene (http://www.gramene.org/) is a comparative genome database for cereal crops and a community resource for rice. We are populating and curating Gramene with annotated rice (Oryza sativa) genomic sequence data and associated biological information including molecular markers, mutants, phenotypes, polymorphisms and Quantitative Trait Loci (QTL). In order to support queries across various data sets as well as across external databases, Gramene will employ three related controlled vocabularies. The specific goal of Gramene is, first to provide a Trait Ontology (TO) that can be used across the cereal crops to facilitate phenotypic comparisons both within and between the genera. Second, a vocabulary for plant anatomy terms, the Plant Ontology (PO) will facilitate the curation of morphological and anatomical feature information with respect to expression, localization of genes and gene products and the affected plant parts in a phenotype. The TO and PO are both in the early stages of development in collaboration with the International Rice Research Institute, TAIR and MaizeDB as part of the Plant Ontology Consortium. Finally, as part of another consortium comprising macromolecular databases from other model organisms, the Gene Ontology Consortium, we are annotating the confirmed and predicted protein entries from rice using both electronic and manual curation. Copyright © 2002 John Wiley & Sons, Ltd. URL: http://www3.interscience.wiley.com/cgi-bin/abstract/91016047/ABSTRACT Reference Type: Journal Article Record Number: 7 Author: Ware, D.; Jaiswal, P.; Ni, J.; Pan, X.; Chang, K.; Clark, K.; Teytelman, L.; Schmidt, S.; Zhao, W.; Cartinhour, S.; McCouch, S.; Stein, L. Year: 2002 Title: Gramene: a resource for comparative grass genomics Journal: Nucleic Acids Res Volume: 30 Issue: 1 Pages: 103-5. Short Title: Gramene: a resource for comparative grass genomics Accession Number: 11752266 Keywords: Chromosome Mapping Computer Graphics Database Management Systems *Databases, Genetic Forecasting Genes, Plant Genetic Markers *Genome, Plant Information Storage and Retrieval Internet Mutation Oryza sativa/*genetics Poaceae/*genetics Quantitative Trait, Heritable Research Support, U.S. Gov't, Non-P.H.S. Sequence Homology Abstract: Gramene (http://www.gramene.org) is a comparative genome mapping database for grasses and a community resource for rice. Rice, in addition to being an economically important crop, is also a model monocot for understanding other agronomically important grass genomes. Gramene replaces the existing AceDB database 'RiceGenes' with a relational database based on Oracle. Gramene provides curated and integrative information about maps, sequence, genes, genetic markers, mutants, QTLs, controlled vocabularies and publications. Its aims are to use the rice genetic, physical and sequence maps as fundamental organizing units, to provide a common denominator for moving from one crop grass to another and is to serve as a portal for interconnecting with other web-based crop grass resources. This paper describes the initial steps we have taken towards realizing these goals. URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11752266 Author Address: Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA. Reference Type: Journal Article Record Number: 6 Author: Ware, D. H.; Jaiswal, P.; Ni, J.; Yap, I. V.; Pan, X.; Clark, K. Y.; Teytelman, L.; Schmidt, S. C.; Zhao, W.; Chang, K.; Cartinhour, S.; Stein, L. D.; McCouch, S. R. Year: 2002 Title: Gramene, a tool for grass genomics Journal: Plant Physiol Volume: 130 Issue: 4 Pages: 1606-13. Short Title: Gramene, a tool for grass genomics Accession Number: 12481044 Keywords: Avena sativa/genetics Comparative Study Computational Biology/methods Databases, Genetic Expressed Sequence Tags *Genome, Plant Genomics/*methods Hordeum/genetics Internet Oryza sativa/genetics Phenotype Physical Chromosome Mapping/methods Plant Proteins/genetics Poaceae/classification/*genetics Research Support, U.S. Gov't, Non-P.H.S. Triticum/genetics Abstract: Gramene (http://www.gramene.org) is a comparative genome mapping database for grasses and a community resource for rice (Oryza sativa). It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, and publications, with a curated database of rice mutants (genes and alleles), molecular markers, and proteins. Gramene curators read and extract detailed information from published sources, summarize that information in a structured format, and establish links to related objects both inside and outside the database, providing seamless connections between independent sources of information. Genetic, physical, and sequence-based maps of rice serve as the fundamental organizing units and provide a common denominator for moving across species and genera within the grass family. Comparative maps of rice, maize (Zea mays), sorghum (Sorghum bicolor), barley (Hordeum vulgare), wheat (Triticum aestivum), and oat (Avena sativa) are anchored by a set of curated correspondences. In addition to sequence-based mappings found in comparative maps and rice genome displays, Gramene makes extensive use of controlled vocabularies to describe specific biological attributes in ways that permit users to query those domains and make comparisons across taxonomic groups. Proteins are annotated for functional significance using gene ontology terms that have been adopted by numerous model species databases. Genetic variants including phenotypes are annotated using plant ontology terms common to all plants and trait ontology terms that are specific to rice. In this paper, we present a brief overview of the search tools available to the plant research community in Gramene. URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12481044 Author Address: Cold Spring Harbor Laboratory, New York 11724, USA. Reference Type: Journal Article Record Number: 1 Author: Yamazaki, Y.; Jaiswal, P. Year: 2005 Title: Biological ontologies in rice databases. An introduction to the activities in Gramene and Oryzabase Journal: Plant Cell Physiol Volume: 46 Issue: 1 Pages: 63-8. Epub 2005 Jan 19. Short Title: Biological ontologies in rice databases. An introduction to the activities in Gramene and Oryzabase Accession Number: 15659431 Keywords: *Databases, Genetic Gene Expression Regulation, Developmental Gene Expression Regulation, Plant Genes, Plant Mutation Oryza sativa/*genetics/growth & development Quantitative Trait Loci Abstract: An enormous amount of information and materials in the field of biology has been accumulating, such as nucleotide and amino acid sequences, gene and protein functions, mutants and their phenotypes, and literature references, produced by the rapid development in this field. Effective use of the information may strongly promote biological studies, and may lead to many important findings. It is, however, time-consuming and laborious for individual researchers to collect information from individual original sites and to rearrange it for their own purpose. A concept, ontology, has been introduced in biology to support and encourage researchers to share and reuse information among biological databases. Ontology has a glossary, named dynamic controlled vocabulary, in which relationships between terms are defined. Since each term is strictly defined and identified with an ID number, a set of data represented in biological ontology is easily accessible to automated information processing, even if the data sets are across several databases and/or different organisms. In this mini-review, we introduce activities in Gramene and Oryzabase, which provide biological ontologies for Oryza sativa (rice). URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15659431 Author Address: Center for Genetic Resource Information, National Institute of Genetics, Mishima, Shizuoka, 411-8540 Japan. yyamazak@lab.nig.ac.jp