scholarly journals Developing a biocuration workflow for AgBase, a non-model organism database

Database ◽  
2012 ◽  
Vol 2012 (0) ◽  
pp. bas038-bas038 ◽  
Author(s):  
L. Pillai ◽  
P. Chouvarine ◽  
C. O. Tudor ◽  
C. J. Schmidt ◽  
K. Vijay-Shanker ◽  
...  
Keyword(s):  
Model Organism ◽  
Model Organism Database

scholarly journals MaizeGDB update: new tools, data and interface for the maize model organism database

2015 ◽  
Vol 44 (D1) ◽  
pp. D1195-D1201 ◽  
Author(s):  
Carson M. Andorf ◽  
Ethalinda K. Cannon ◽  
John L. Portwood ◽  
Jack M. Gardiner ◽  
Lisa C. Harper ◽  
...  
Keyword(s):  
Model Organism ◽  
Model Organism Database

scholarly journals ZFIN, The zebrafish model organism database: Updates and new directions

genesis ◽  
2015 ◽  
Vol 53 (8) ◽  
pp. 498-509 ◽  
Author(s):  
Leyla Ruzicka ◽  
Yvonne M. Bradford ◽  
Ken Frazer ◽  
Douglas G. Howe ◽  
Holly Paddock ◽  
...  
Keyword(s):  
Model Organism ◽  
Model Organism Database ◽  
Zebrafish Model ◽  
Database Updates ◽  
New Directions

scholarly journals MaizeGDB: The Maize Model Organism Database for Basic, Translational, and Applied Research

2008 ◽  
Vol 2008 ◽  
pp. 1-10 ◽  
Author(s):  
Carolyn J. Lawrence ◽  
Lisa C. Harper ◽  
Mary L. Schaeffer ◽  
Taner Z. Sen ◽  
Trent E. Seigfried ◽  
...  
Keyword(s):  
Model Organism ◽  
Basic Research ◽  
Model Organism Database ◽  
High Productivity ◽  
Group Activities ◽  
Food And Agriculture ◽  
Food And Agriculture Organization ◽  
Genetics And Genomics ◽  
Excellent Source ◽  
By Products

In 2001 maize became the number one production crop in the world with the Food and Agriculture Organization of the United Nations reporting over 614 million tonnes produced. Its success is due to the high productivity per acre in tandem with a wide variety of commercial uses. Not only is maize an excellent source of food, feed, and fuel, but also its by-products are used in the production of various commercial products. Maize's unparalleled success in agriculture stems from basic research, the outcomes of which drive breeding and product development. In order for basic, translational, and applied researchers to benefit from others' investigations, newly generated data must be made freely and easily accessible. MaizeGDB is the maize research community's central repository for genetics and genomics information. The overall goals of MaizeGDB are to facilitate access to the outcomes of maize research by integrating new maize data into the database and to support the maize research community by coordinating group activities.

scholarly journals ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics

2012 ◽  
Vol 41 (D1) ◽  
pp. D854-D860 ◽  
Author(s):  
Douglas G. Howe ◽  
Yvonne M. Bradford ◽  
Tom Conlin ◽  
Anne E. Eagle ◽  
David Fashena ◽  
...  
Keyword(s):  
Model Organism ◽  
Model Organism Database ◽  
Zebrafish Model

scholarly journals BeetleBase: the model organism database for Tribolium castaneum

2007 ◽  
Vol 35 (Database) ◽  
pp. D476-D479 ◽  
Author(s):  
L. Wang ◽  
S. Wang ◽  
Y. Li ◽  
M. S. R. Paradesi ◽  
S. J. Brown
Keyword(s):  
Tribolium Castaneum ◽  
Model Organism ◽  
Model Organism Database

scholarly journals The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching

2016 ◽  
Vol 45 (D1) ◽  
pp. D758-D768 ◽  
Author(s):  
Douglas G. Howe ◽  
Yvonne M. Bradford ◽  
Anne Eagle ◽  
David Fashena ◽  
Ken Frazer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Human Disease ◽  
Model Organism ◽  
Disease Models ◽  
Model Organism Database ◽  
Zebrafish Model

scholarly journals JaponicusDB: Rapid deployment of a model organism database for an emerging model species

Genetics ◽  
2021 ◽  
Author(s):  
Kim M Rutherford ◽  
Midori A Harris ◽  
Snezhana Oliferenko ◽  
Valerie Wood
Keyword(s):  
Fission Yeast ◽  
Model Organism ◽  
Full Potential ◽  
Model Species ◽  
Model Organism Database ◽  
Cellular Processes ◽  
Growing Body ◽  
Central Resource ◽  
Ready Access ◽  
Rapid Deployment

Abstract The fission yeast Schizosaccharomyces japonicus has recently emerged as a powerful system for studying the evolution of essential cellular processes, drawing on similarities as well as key differences between S. japonicus and the related, well-established model Schizosaccharomyces pombe. We have deployed the open-source, modular code and tools originally developed for PomBase, the S. pombe model organism database (MOD), to create JaponicusDB (www.japonicusdb.org), a new MOD dedicated to S. japonicus. By providing a central resource with ready access to a growing body of experimental data, ontology-based curation, seamless browsing and querying, and the ability to integrate new data with existing knowledge, JaponicusDB supports fission yeast biologists to a far greater extent than any other source of S. japonicus data. JaponicusDB thus enables S. japonicus researchers to realise the full potential of studying a newly emerging model species, and illustrates the widely applicable power and utility of harnessing reusable PomBase code to build a comprehensive, community-maintainable repository of species-relevant knowledge.

scholarly journals The EcoCyc Database in 2021

2021 ◽  
Vol 12 ◽  
Author(s):  
Ingrid M. Keseler ◽  
Socorro Gama-Castro ◽  
Amanda Mackie ◽  
Richard Billington ◽  
César Bonavides-Martínez ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Regulation Of Gene Expression ◽  
Model Organism ◽  
Web Interface ◽  
Model Organism Database ◽  
Manual Curation ◽  
Genome Viewer ◽  
User Access ◽  
Visualization Tools ◽  
K 12

The EcoCyc model-organism database collects and summarizes experimental data for Escherichia coli K-12. EcoCyc is regularly updated by the manual curation of individual database entries, such as genes, proteins, and metabolic pathways, and by the programmatic addition of results from select high-throughput analyses. Updates to the Pathway Tools software that supports EcoCyc and to the web interface that enables user access have continuously improved its usability and expanded its functionality. This article highlights recent improvements to the curated data in the areas of metabolism, transport, DNA repair, and regulation of gene expression. New and revised data analysis and visualization tools include an interactive metabolic network explorer, a circular genome viewer, and various improvements to the speed and usability of existing tools.

scholarly journals ChlamBase: a curated model organism database for the Chlamydia research community

Database ◽  
2019 ◽  
Vol 2019 ◽  
Author(s):  
Tim Putman ◽  
Kevin Hybiske ◽  
Derek Jow ◽  
Cyrus Afrasiabi ◽  
Sebastien Lelong ◽  
...  
Keyword(s):  
Model Organism ◽  
Research Community ◽  
Model Organism Database
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