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Gramene QTL database: development, content and applications

Junjian Ni, Anuradha Pujar, Ken Youens-Clark, Immanuel Yap, Pankaj Jaiswal, Isaak Tecle, Chih-Wei Tung, Liya Ren, William Spooner, Xuehong Wei, Shuly Avraham, Doreen Ware (+2 others)
2009 Database: The Journal of Biological Databases and Curation  
Acknowledgements We appreciate the numerous authors of QTL publications who have kindly shared information with us on QTL, markers and maps by way of personal communication. .........................  ...  Applications of the QTL database in plant breeding and selection The QTL and trait-associated markers are crucially important for applications in plant breeding and selection.  ...  Database schema The schema developed for the QTL database and all QTL data are downloadable from the Gramene ftp site: ftp:// ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/ database_dump/mysql-dumps  ... 
doi:10.1093/database/bap005 pmid:20157478 pmcid:PMC2790302 fatcat:thesfvm7mbdefmpgm4qjtg7jva

Gramene database in 2010: updates and extensions

K. Youens-Clark, E. Buckler, T. Casstevens, C. Chen, G. DeClerck, P. Derwent, P. Dharmawardhana, P. Jaiswal, P. Kersey, A. S. Karthikeyan, J. Lu, S. R. McCouch (+6 others)
2010 Nucleic Acids Research  
ACKNOWLEDGEMENTS We would like to thank our users for their feedback and support as well as our collaborators and contributors who have supplied Gramene with data, especially NSF projects #0638566 Conflict  ...  Gramene has contributed all the 'core' databases for the fully sequenced plant genomes available at EG website (http://plants.ensembl.org), and both groups work on quality control, the integration of content  ...  For bioinformatics and software developers interested in installing a local copy of the Gramene database, we upgraded the internal web server to the most recent Apache version 2.  ... 
doi:10.1093/nar/gkq1148 pmid:21076153 pmcid:PMC3013721 fatcat:y5hesnoprzc53hzq264nppv25i

A genotypic and phenotypic information source for marker-assisted selection of cereals: the CEREALAB database

J. Milc, A. Sala, S. Bergamaschi, N. Pecchioni
2011 Database: The Journal of Biological Databases and Curation  
The CEREALAB database aims to store genotypic and phenotypic data obtained by the CEREALAB project and to integrate them with already existing data sources in order to create a tool for plant breeders  ...  The database can help them in unravelling the genetics of economically important phenotypic traits; in identifying and choosing molecular markers associated to key traits; and in choosing the desired parentals  ...  Authors wish to thank all partners of the CEREALAB laboratory for their suggestions about the database structure and queries and for the critical discussion of the obtained results.  ... 
doi:10.1093/database/baq038 pmid:21247929 pmcid:PMC3025694 fatcat:h5qs5ermtbdxfiffi7yehbx6om

QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice

Shuchi Smita, Sangram Keshari Lenka, Amit Katiyar, Pankaj Jaiswal, Justin Preece, Kailash Chander Bansal
2011 Database: The Journal of Biological Databases and Curation  
The authors thank Gramene (http://www.gramene.org), MSU_osa1 (http://rice.plantbiology.msu.edu/), KEGG (http://www.genome.jp/tools/kaas/) and other biological databases for sharing their data.  ...  Acknowledgement The authors are grateful to Mr Kamal Batra, Technical Officer, IARI for helpful discussion and suggestions.  ...  These QTLs, their corresponding gene loci, associated literature references and genomic information have been stored in a MySQL database (5) accessed via a powerful web application developed using the  ... 
doi:10.1093/database/bar037 pmid:21965557 pmcid:PMC3184618 fatcat:z47vbvz6kngwxlvw7epxaprlp4

CSGRqtl: A Comparative Quantitative Trait Locus Database for Saccharinae Grasses [chapter]

Dong Zhang, Andrew H. Paterson
2016 Msphere  
As an example, the wealth of rice QTL information in Gramene (Ware et al., 2002; http://www. gramene.org/qtl/) and genomic synteny data in the Plant Genome Duplication Database (Tang et al., 2008;  ...  Each QTL is allocated a proper trait accession, based on the Gramene Plant Trait Ontology.  ... 
doi:10.1007/978-1-4939-6658-5_15 pmid:27987176 fatcat:abeayy5koba2rp64jsuuapq7li

CSGRqtl, a Comparative Quantitative Trait Locus Database for Saccharinae Grasses

D. Zhang, H. Guo, C. Kim, T.-H. Lee, J. Li, J. Robertson, X. Wang, Z. Wang, A. H. Paterson
2012 Plant Physiology  
As an example, the wealth of rice QTL information in Gramene (Ware et al., 2002; http://www. gramene.org/qtl/) and genomic synteny data in the Plant Genome Duplication Database (Tang et al., 2008;  ...  Each QTL is allocated a proper trait accession, based on the Gramene Plant Trait Ontology.  ... 
doi:10.1104/pp.112.206870 pmid:23370713 pmcid:PMC3561006 fatcat:v4bwuwbfhzfe5ogwt5wpyzu3tm

A Statistical Procedure for Genome-wide Detection of QTL Hotspots Using Public Databases with Application to Rice [article]

Chen-Hung Kao, Man-Hsia Yang, Dong-Hong Wu
2018 bioRxiv   pre-print
Depending on the thresholds used, more than 100 hotspots are detected in GRAMENE rice database.  ...  In this article, we propose a statistical procedure for QTL hotspot detection by using the summarized QTL (interval) data collected in public web-accessible databases.  ...  The GRAMENE rice database example The GRAMENE database and Q-TARO database: Both the GRAMENE database and Q-TARO database are web-accessible and common reference databases for rice research.  ... 
doi:10.1101/479725 fatcat:g6wpbwklp5fodl76vjzryeu6di

A Statistical Procedure for Genome-Wide Detection of QTL Hotspots Using Public Databases with Application to Rice

Man-Hsia Yang, Dong-Hong Wu, Chen-Hung Kao
2018 G3: Genes, Genomes, Genetics  
Depending on the thresholds used, more than 100 hotspots are detected in GRAMENE rice database.  ...  In this article, we propose a statistical procedure for QTL hotspot detection by using the summarized QTL (interval) data collected in public web-accessible databases.  ...  ACKNOWLEDGMENTS We are grateful to the associate editor and the three referees for their valuable comments and suggestions.  ... 
doi:10.1534/g3.118.200922 fatcat:noaidlgscjehni3kqqal573t2a

The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations

Shulamit Avraham, Chih-Wei Tung, Katica Ilic, Pankaj Jaiswal, Elizabeth A. Kellogg, Susan McCouch, Anuradha Pujar, Leonore Reiser, Seung Y Rhee, Martin M Sachs, Mary Schaeffer, Lincoln Stein (+4 others)
2008 Nucleic Acids Research  
The Consortium has also implemented new functionalities to facilitate the application of PO in genomic research and updated the website to keep the contents current.  ...  meaningful crossspecies and database comparisons.  ...  We also thank all database groups, annotation contributors, researchers, curators, reviewers, collaborators, specifically Alice Clare Augustine from Monsanto and David Selinger and Arthur Lane from Pioneer  ... 
doi:10.1093/nar/gkm908 pmid:18194960 pmcid:PMC2238838 fatcat:4pct3qkkrzabbgrud45bpbwroy

Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases

Julien Wollbrett, Pierre Larmande, Frédéric de Lamotte, Manuel Ruiz
2013 BMC Bioinformatics  
Results: We developed a framework, named BioSemantic, for the creation of Semantic Web Services that are applicable to relational biological databases.  ...  A common approach involves the development of wrapper systems that map a relational database schema onto existing domain ontologies.  ...  Acknowledgements We would like to acknowledge Isabelle Mougenot and Guilhem Sempere for their assistance. This work was supported by Région Languedoc-Roussillon and CIRAD.  ... 
doi:10.1186/1471-2105-14-126 pmid:23586394 pmcid:PMC3680174 fatcat:htd6pjkckzdg5dr3lf7koh37fa

Choosing a genome browser for a Model Organism Database: surveying the Maize community

Taner Z. Sen, Lisa C. Harper, Mary L. Schaeffer, Carson M. Andorf, Trent E. Seigfried, Darwin A. Campbell, Carolyn J. Lawrence
2010 Database: The Journal of Biological Databases and Curation  
Acknowledgements We thank USDA-ARS for its sustained funding, past and present members of the MaizeGDB Working Group (Volker Brendel Wang, and Cesar Alvarez-Mejia), without whose comments and suggestions  ...  Last, but not least, we deeply appreciate and thank the maize community for their continuous support. Conflict of interest. None declared.  ...  A developer can modify GBrowse at the following three different layers: the database layer, the data model layer and the application layer.  ... 
doi:10.1093/database/baq007 pmid:20627860 pmcid:PMC2911842 fatcat:6ihbvxcmdnfypo2clanjfma5vq

OGRO: The Overview of functionally characterized Genes in Rice online database

Eiji Yamamoto, Jun-ichi Yonemaru, Toshio Yamamoto, Masahiro Yano
2012 Rice  
The database has two interfaces: a table containing gene information, and a genome viewer that allows users to compare the locations of QTLs and functionally characterized genes.  ...  To facilitate the application of gene function information to the study of natural variation in rice, we comprehensively searched for articles related to rice functional genomics and extracted information  ...  Namiki, and S. Takeshita for construction of the Web-based interfaces for the database.  ... 
doi:10.1186/1939-8433-5-26 pmid:27234245 pmcid:PMC5520837 fatcat:5rnudzl3zfcp3c77owz6crsn3a

PeanutMap: an online genome database for comparative molecular maps of peanut

Arun M Jesubatham, Mark D Burow
2006 BMC Bioinformatics  
Molecular maps have been developed for many species, and are of particular importance for varietal development and comparative genomics.  ...  However, despite the existence of multiple sets of linkage maps, databases of these data are lacking for many species, including peanut.  ...  Acknowledgements This work was supported by an award "Accelerating Development of Peanut Varieties through Molecular Markers" from the National Peanut Board to M. B.  ... 
doi:10.1186/1471-2105-7-375 pmid:16904007 pmcid:PMC1564155 fatcat:nzwyw7dnk5ctpk5fcmm22y6oey

Plant Genome DataBase Japan (PGDBj): A Portal Website for the Integration of Plant Genome-Related Databases

Erika Asamizu, Hisako Ichihara, Akihiro Nakaya, Yasukazu Nakamura, Hideki Hirakawa, Takahiro Ishii, Takuro Tamura, Kaoru Fukami-Kobayashi, Yukari Nakajima, Satoshi Tabata
2014 Plant and Cell Physiology  
The Plant Genome DataBase Japan (PGDBj, http://pgdbj. jp/?ln=en) is a portal website that aims to integrate plant genome-related information from databases (DBs) and the literature.  ...  The PGDBj is comprised of three component DBs and a cross-search engine, which provides a seamless search over the contents of the DBs. The three DBs are as follows.  ...  Hideki Hatanaka, Asuka Bandoh and Junichi Onami of the NBDC for their helpful comments. We also thank Ms./Mr.  ... 
doi:10.1093/pcp/pct189 pmid:24363285 pmcid:PMC3894704 fatcat:kmyxi626pnd2jpticw3hcku5fm

GrainGenes: a data-rich repository for small grains genetics and genomics

Eric Yao, Victoria C Blake, Laurel Cooper, Charlene P Wight, Steve Michel, H Busra Cagirici, Gerard R Lazo, Clay L Birkett, David J Waring, Jean-Luc Jannink, Ian Holmes, Amanda J Waters (+2 others)
2022 Database: The Journal of Biological Databases and Curation  
Interactive and linked content is paramount for successful biological databases and GrainGenes now has 2917 manually curated gene records, including 289 genes and 254 alleles from the Wheat Gene Catalogue  ...  GrainGenes accomplishes its mission by continually enriching its cross-linked data content following the findable, accessible, interoperable and reusable principles, enhancing and maintaining an intuitive  ...  USDA is an equal opportunity provider and employer.  ... 
doi:10.1093/database/baac034 pmid:35616118 pmcid:PMC9216595 fatcat:zdbhbx32vfcpdejmxovf7uyhce
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