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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  ...  Each release of the database contains new and updated annotations. Since our last publication, Gramene has added or updated many plant genomes listed in Table 1 .  ...  Gramene is a free online database for comparative plant genomics that began as an extension of the RiceGenes project (1, 2) and now holds many large and varied data sets that are used extensively by  ... 
doi:10.1093/nar/gkq1148 pmid:21076153 pmcid:PMC3013721 fatcat:y5hesnoprzc53hzq264nppv25i

The Gene Ontology in 2010: extensions and refinements

2009 Nucleic Acids Research  
The GO ontologies are expanding both in content and in structure.  ...  Gene product annotation using GO continues to increase both in the number of total annotations and in species coverage.  ...  ACKNOWLEDGEMENTS The GO Consortium thanks the community researchers who have participated in content-related meetings or provided valuable feedback on ontology content and annotations.  ... 
doi:10.1093/nar/gkp1018 pmid:19920128 pmcid:PMC2808930 fatcat:coftgdrxfbad7imo4qgcgxgp6q

Applications and methods utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for bioinformatics resource discovery and disparate data and service integration

Rex T Nelson, Shulamit Avraham, Randy C Shoemaker, Gregory D May, Doreen Ware, Damian DG Gessler
2010 BioData Mining  
We used SSWAP to express these offerings in OWL Web Ontology Language (OWL), Resource Description Framework (RDF) and eXtensible Markup Language (XML) documents, which are appropriate for their semantic  ...  This process is made more difficult by the separate and independent construction of biological databases, which makes the exchange of data between information resources difficult and labor intensive.  ...  We also thank Ken Youens-Clark and Jim Thomason for critical review of the manuscript.  ... 
doi:10.1186/1756-0381-3-3 pmid:20525377 pmcid:PMC2894815 fatcat:vkueo2wbrjem7ihqgrqziz2fyy

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.  ...  Page 5 of 9 Database, Vol. 2010, Article ID baq007, doi:10.1093/database/baq007 Original article ... .... at DigiTop USDA's Digital Desktop Library on August 30, 2010  ... 
doi:10.1093/database/baq007 pmid:20627860 pmcid:PMC2911842 fatcat:6ihbvxcmdnfypo2clanjfma5vq

RoBuST: an integrated genomics resource for the root and bulb crop families Apiaceae and Alliaceae

Ashwini Bhasi, Doug Senalik, Philipp W Simon, Brajendra Kumar, Vinu Manikandan, Philge Philip, Periannan Senapathy
2010 BMC Plant Biology  
genetic maps, delineation of taxonomic relationships, and investigation of molecular aspects of gene expression in biochemical pathways and disease responses.  ...  Description: The RoBuST database has been developed to initiate a platform for collecting and organizing genomic information useful for RBV researchers.  ...  Sreedharan and Bipin Balan for providing technical support and Anup Viswanathan for designing the RobuST logo for the web interface. Author  ... 
doi:10.1186/1471-2229-10-161 pmid:20691054 pmcid:PMC3017783 fatcat:jto24dbjevfpdeanjtm34c4dga

agriGO: a GO analysis toolkit for the agricultural community

Zhou Du, Xin Zhou, Yi Ling, Zhenhai Zhang, Zhen Su
2010 Nucleic Acids Research  
Gene Ontology (GO), the de facto standard in gene functionality description, is used widely in functional annotation and enrichment analysis.  ...  EasyGO is valuable for its proficiency, and has proved useful in uncovering biological knowledge in massive data sets from high-throughput experiments.  ...  The authors thank anonymous reviewers for their valuable contributions and comments on an earlier version of this article.  ... 
doi:10.1093/nar/gkq310 pmid:20435677 pmcid:PMC2896167 fatcat:coxlqmeu4zaxvp7smfbpwt5svq

A database and API for variation, dense genotyping and resequencing data

Daniel Rios, William M McLaren, Yuan Chen, Ewan Birney, Arne Stabenau, Paul Flicek, Fiona Cunningham
2010 BMC Bioinformatics  
project in a number of database and application environments.  ...  The database and software system is easily expanded to integrate both public and non-public data sources in the context of an Ensembl software installation and is already being used outside of the Ensembl  ...  Acknowledgements The authors acknowledge the following individuals and organisations: Graham McVicker for his early work on the variation database design and schema; Solexa for access to resequencing data  ... 
doi:10.1186/1471-2105-11-238 pmid:20459810 pmcid:PMC2882931 fatcat:2yosg4clebgefb3oql3iqbfr2i

Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature

Rosemary Shrestha, Elizabeth Arnaud, Ramil Mauleon, Martin Senger, Guy F. Davenport, David Hancock, Norman Morrison, Richard Bruskiewich, Graham McLaren
2010 AoB Plants  
and aims Agricultural crop databases maintained in gene banks of the Consultative Group on International Agricultural Research (CGIAR) are valuable sources of information for breeders.  ...  The use of ontology terms to describe agronomic phenotypes and the accurate mapping of these descriptions into databases will be important steps in comparative phenotypic and genotypic studies across species  ...  Acknowledgements We would like to thank Genevieve Mae Aquino and Jeffrey Detras of IRRI for their contribution in indexing of GCP crop ontology.  ... 
doi:10.1093/aobpla/plq008 pmid:22476066 pmcid:PMC3000699 fatcat:4k6ksed3pbgn5mip3hfg24jt5e

Genomics and Bioinformatics Resources for Crop Improvement

K. Mochida, K. Shinozaki
2010 Plant and Cell Physiology  
We review recent advances in research platforms and resources in plant omics together with related databases and advances in technology.  ...  Recent remarkable innovations in platforms for omics-based research and application development provide crucial resources to promote research in model and applied plant species.  ...  Center for their valuable suggestions and comments.  ... 
doi:10.1093/pcp/pcq027 pmid:20208064 pmcid:PMC2852516 fatcat:7kkmabdhpfer5a6b5b3pp6u4pe

Current status of genomic resources on wild relatives of rice

Richa Kamboj, Balwant Singh, Tapan Kumar Mondal, Deepak Singh Bisht
2020 Breeding Science  
In this review, we introduce the key features of these databases focusing on their utility in rice breeding programs.  ...  Presently, there are several generic and specialized databases harboring genome-wide information on wild species of rice, and are acting as a useful resource for identification of novel genes and alleles  ...  Gramene Database Gramene is an integrated database developed for the comparative functional genomics in various plant species.  ... 
doi:10.1270/jsbbs.19064 pmid:32523396 pmcid:PMC7272243 fatcat:tn7j2ighmvaupmdiszssa5pzgy

Statistical Genomics and Bioinformatics

Prem Narain
2010 Journal of Horticultural Sciences  
In the second part, generation of databases, annotation, annotated sequence databases, and sequence similarity search have been described.  ...  Some important and interesting topics in the newly emerging disciplines of Statistical genomics andbioinformatics have been discussed briefly in relation to plants with possible references to fruit crops  ...  Besides PlantGDB database, there are speciesspecific databases like The Arabidopsis Information Resource (TAIR), MaizeGDB, Gramene, a tool for grass genomics, and the Stanford Microarray Database.  ... 
doaj:25cef78dd9fe4896ad16f19676081853 fatcat:donrvzfho5bpblfsj32iljncty

Cereal Resources in National BioResource Project of Japan

Kazuhiro Sato, Takashi R. Endo, Nori Kurata
2010 Interdisciplinary Bio Central  
Oryzabase also has links to two external databases: Gramene 30 (genetic information) and IRRI database (wild rice information at International Rice Information System 31 ) to share and confirm the rice  ...  Cultivated barley is a true diploid and has been extensively studied genetically.  ... 
doi:10.4051/ibc.2010.2.4.0013 fatcat:sqwuyiblrbbfhhnl27rzuw5snu

The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services

Martijn P van Iersel, Alexander R Pico, Thomas Kelder, Jianjiong Gao, Isaac Ho, Kristina Hanspers, Bruce R Conklin, Chris T Evelo
2010 BMC Bioinformatics  
BridgeDb provides its own ready-to-go mapping services, both in webservice and local database forms.  ...  All described software is open source and available at van Iersel et al.  ...  TK developed the first derby databases. AP developed the Ensembl ETL process for MySQL and derby database production. MI and JG designed the BridgeDb API.  ... 
doi:10.1186/1471-2105-11-5 pmid:20047655 pmcid:PMC2824678 fatcat:yvtvz7pffjg7nmcw6oaargq64m

Maize Metabolic Network Construction and Transcriptome Analysis

Marcela K. Monaco, Taner Z. Sen, Palitha D. Dharmawardhana, Liya Ren, Mary Schaeffer, Sushma Naithani, Vindhya Amarasinghe, Jim Thomason, Lisa Harper, Jack Gardiner, Ethalinda K.S. Cannon, Carolyn J. Lawrence (+2 others)
2013 The Plant Genome  
in maize.  ...  The MaizeCyc pathway database was created by running a library of evidences collected from the maize genome annotation, gene based phylogeny trees, and comparison to known genes and pathways from rice  ...  Peter Karp, Markus Krummenacker, and Suzanne Paley from SRI for excellent Pathway Tools support;  ... 
doi:10.3835/plantgenome2012.09.0025 fatcat:jwvh2brlyzcvbd6uymhqrm27iu

Infrastructures of systems biology that facilitate functional genomic study in rice

Woo-Jong Hong, Yu-Jin Kim, Anil Kumar Nalini Chandran, Ki-Hong Jung
2019 Rice  
Through the integration of those data, systems biology in rice is becoming more advanced.To facilitate such systemic approaches, we have summarized current resources, such as databases and tools, for systems  ...  We provide the names, websites, references, working states, and number of citations for each individual database or tool and discuss future prospects for the integrated understanding of rice gene functions  ...  It has facilitated the extensive mapping of genome-wide methylation patterns in rice (Chen and Zhou 2013) .  ... 
doi:10.1186/s12284-019-0276-z pmid:30874968 pmcid:PMC6419666 fatcat:zfqydgycnrahxjftpyg6cxd2v4
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