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Gramene database in 2010: updates and extensions
2010
Nucleic Acids Research
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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
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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
2010
BioData Mining
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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
2010
Database: The Journal of Biological Databases and Curation
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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
http://database.oxfordjournals.org ...
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
2010
BMC Plant Biology
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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
2010
Nucleic Acids Research
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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
2010
BMC Bioinformatics
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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
2010
AoB Plants
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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
2010
Plant and Cell Physiology
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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
2020
Breeding Science
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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
2010
Journal of Horticultural Sciences
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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
2010
Interdisciplinary Bio Central
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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
2010
BMC Bioinformatics
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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
2013
The Plant Genome
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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
2019
Rice
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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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