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The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data

S. Jung, N. Menda, S. Redmond, R. M. Buels, M. Friesen, Y. Bendana, L.-A. Sanderson, H. Lapp, T. Lee, B. MacCallum, K. E. Bett, S. Cain (+3 others)
2011 Database: The Journal of Biological Databases and Curation  
The ND module was developed with plant breeding data (Solanaceae, Rosaceae and legume species) and large-scale natural diversity data (mosquitoes) in mind.  ...  Discussion The ND Module was developed to store large-scale phenotyping, genotyping and breeding data.  ... 
doi:10.1093/database/bar051 pmid:22120662 pmcid:PMC3225077 fatcat:5of5hkmxtjg7lcdwqvm5p4573q

A PostgreSQL Tripal solution for large-scale genotypic and phenotypic data

Lacey-Anne Sanderson, Carolyn T Caron, Reynold L Tan, Kirstin E Bett
2021 Database: The Journal of Biological Databases and Curation  
Researchers are seeking cost-effective solutions for management and analysis of large-scale genotypic and phenotypic data.  ...  We describe here a fully relational PostgreSQL solution to handle large-scale genotypic and phenotypic data that is implemented as a collection of freely available, open-source modules.  ...  Supplementary data Supplementary data are available at Database Online.  ... 
doi:10.1093/database/baab051 pmid:34389844 pmcid:PMC8363843 fatcat:mxstsjb64vfrvauxm3ssbyh5zu

Chado use case: storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado

Sook Jung, Taein Lee, Stephen Ficklin, Jing Yu, Chun-Huai Cheng, Dorrie Main
2016 Database: The Journal of Biological Databases and Curation  
These online databases use Chado, an open-source, generic and ontology-driven database schema for biological data, as the primary data storage platform.  ...  These data include whole genome sequence and annotation, transcripts, molecular markers, genetic maps, Quantitative Trait Loci, Mendelian Trait Loci, traits, germplasm, pedigrees, large scale phenotypic  ...  Genotypic data Large scale genotypic data from projects such as germplasm evaluation and breeding are also stored using the project, genotype and natural diversity modules of Chado similar to phenotypic  ... 
doi:10.1093/database/baw058 pmid:27141090 pmcid:PMC4852396 fatcat:ag5724tx6ndezh3qhs45l5eom4

Chado use case: storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado

Sook Jung, Taein Lee, Stephen Ficklin, Jing Yu, Chun-Huai Cheng, Dorrie Main
2016 Database: The Journal of Biological Databases and Curation  
These online databases use Chado, an open-source, generic and ontology-driven database schema for biological data, as the primary data storage platform.  ...  These data include whole genome sequence and annotation, transcripts, molecular markers, genetic maps, Quantitative Trait Loci, Mendelian Trait Loci, traits, germplasm, pedigrees, large scale phenotypic  ...  Genotypic data Large scale genotypic data from projects such as germplasm evaluation and breeding are also stored using the project, genotype and natural diversity modules of Chado similar to phenotypic  ... 
doi:10.1093/database/baw010 pmid:26989146 pmcid:PMC4795932 fatcat:ulmoo7j3gvhync3j3lipxvbtgq

Addition of a breeding database in the Genome Database for Rosaceae

Kate Evans, Sook Jung, Taein Lee, Lisa Brutcher, Ilhyung Cho, Cameron Peace, Dorrie Main
2013 Database: The Journal of Biological Databases and Curation  
The infrastructure was built using the software Chado and Drupal, making use of the Natural Diversity module to accommodate large-scale phenotypic and genotypic data.  ...  Development of new infrastructure in the Genome Database for Rosaceae (GDR) was designed and implemented to enable secure and efficient storage, management and analysis of large datasets from the Washington  ...  part of the web search pages and implemented Organic Group to use for data access control and group home page development.  ... 
doi:10.1093/database/bat078 pmid:24247530 pmcid:PMC3831303 fatcat:uifw43ssczgyxpuyovqmf42vjy

Growing and cultivating the forest genomics database, TreeGenes

Taylor Falk, Nic Herndon, Emily Grau, Sean Buehler, Peter Richter, Sumaira Zaman, Eliza M Baker, Risharde Ramnath, Stephen Ficklin, Margaret Staton, Frank A Feltus, Sook Jung (+2 others)
2018 Database: The Journal of Biological Databases and Curation  
The database provides a curated archive for high-throughput genomics, including reference genomes, transcriptomes, genetic maps and variant data.  ...  Examining the relationships among genetic, phenotypic and environmental factors for these species provides insight on the areas of concern for breeders and researchers alike.  ...  implementing the Natural Diversity extensions in Tripal.  ... 
doi:10.1093/database/bay084 pmid:30239664 pmcid:PMC6146132 fatcat:o5a5wj5ylvdkdncttoebsk3ni4

Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases

Lacey-Anne Sanderson, Stephen P. Ficklin, Chun-Huai Cheng, Sook Jung, Frank A. Feltus, Kirstin E. Bett, Dorrie Main
2013 Database: The Journal of Biological Databases and Curation  
Here a site developer can change the viewable name for a field, the table on which a field can join and set sort, field and filter handlers.  ...  This handler will provide a form element for uploading feature names when the field is used as a filter and exposed to the site user. . ................................................................  ...  The Natural Diversity module The 'Natural Diversity' module provides a set of templates for display of genotypic, phenotypic or other large-scale assays involving multiple features or stocks (such as germplasm  ... 
doi:10.1093/database/bat075 pmid:24163125 pmcid:PMC3808541 fatcat:khwlk7dc6zadpntbze5xskz7um

ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data

Sergio Gonzalez, Bernardo Clavijo, Máximo Rivarola, Patricio Moreno, Paula Fernandez, Joaquín Dopazo, Norma Paniego
2017 BMC Bioinformatics  
This new application simplifies data exploration, visualization, and integration for a better comprehension of the results.  ...  The large and complex datasets resulting from functional genomic experiments represent a challenge in data processing, management, and analysis.  ...  Acknowledgments We would like to acknowledge Julia Sabio Y Garcia for the manuscript correction. Funding  ... 
doi:10.1186/s12859-017-1494-2 pmid:28222698 pmcid:PMC5320735 fatcat:f6dspf444fespbpnjwa56qkvvu

Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases

2019 Database: The Journal of Biological Databases and Curation  
A new site developer can use Tripal to develop a basic site with little to no programming, with the ability to integrate other data types using extension modules and the Tripal application programming  ...  Tripal uses the community-developed Chado database as a default data store, but now provides tools to support other data stores, while ensuring that CVs remain the central organizational structure for  ...  Funding Tripal is developed by an international group of researchers and programmers. Conflict of interest. None declared.  ... 
doi:10.1093/database/baz077 pmid:31328773 pmcid:PMC6643302 fatcat:ybq2vbsqsngotlu4tubpqhjhem

A Chado case study: an ontology-based modular schema for representing genome-associated biological information

Christopher J. Mungall, David B. Emmert
2007 Computer applications in the biosciences : CABIOS  
Motivation: A few years ago, FlyBase undertook to design a new database schema to store Drosophila data.  ...  It would fully integrate genomic sequence and annotation data with bibliographic, genetic, phenotypic and molecular data from the literature representing a distillation of the first 100 years of research  ...  ); the Daphnia Water Flea Genome Database Indiana University; VectorBase for A. gambiae at Notre Dame University; the University of Wisconsin at the Wicell Research Institute; Infobiogen in France; and  ... 
doi:10.1093/bioinformatics/btm189 pmid:17646315 fatcat:uzrlncl35bbqbd6zqizswt4ruy

ImageBreed: Open‐access plant breeding web–database for image‐based phenotyping

Nicolas Morales, Nicholas S. Kaczmar, Nicholas Santantonio, Michael A. Gore, Lukas A. Mueller, Kelly R. Robbins
2020 tppj  
To facilitate routine analyses and to drive breeding decisions, data integration is critical for effective management of germplasm, field experiment design, phenotyping, tissue sampling, genotyping, aerial-phenotyping  ...  Plot-polygon images are queryable against genotypic, phenotypic, and experimental design information for training of machine learning models and  ...  Breedbase employs the Chado database schema, the Natural Diversity (ND) module, and controlled vocabulary driven data models, allowing for a highly extensible system (Jung et al., 2011; Mungall, Emmert  ... 
doi:10.1002/ppj2.20004 fatcat:xiu73ee47ndtphkswgqb3igqky

The Sol Genomics Network (SGN)—from genotype to phenotype to breeding

Noe Fernandez-Pozo, Naama Menda, Jeremy D. Edwards, Surya Saha, Isaak Y. Tecle, Susan R. Strickler, Aureliano Bombarely, Thomas Fisher-York, Anuradha Pujar, Hartmut Foerster, Aimin Yan, Lukas A. Mueller
2014 Nucleic Acids Research  
With the growing genomic and phenotypic data in the database, SGN is now advancing to develop new web-based breeding tools and implement the code and database structure for other species or clade-specific  ...  The Sol Genomics Network (SGN, http: //solgenomics.net) is a web portal with genomic and phenotypic data, and analysis tools for the Solanaceae family and close relatives.  ...  Phenotypes are stored in the Chado Natural Diversity schema (30) that was codeveloped by a group of MODs, including SGN and the Genome Database for Rosaceae (31) .  ... 
doi:10.1093/nar/gku1195 pmid:25428362 pmcid:PMC4383978 fatcat:524lfl7zyba6vnfjuxiyw364o4

GnpIS: an information system to integrate genetic and genomic data from plants and fungi

Delphine Steinbach, Michael Alaux, Joelle Amselem, Nathalie Choisne, Sophie Durand, Raphaël Flores, Aminah-Olivia Keliet, Erik Kimmel, Nicolas Lapalu, Isabelle Luyten, Célia Michotey, Nacer Mohellibi (+5 others)
2013 Database: The Journal of Biological Databases and Curation  
GnpIS: an information system to integrate genetic and genomic data from plants and fungi.  ...  Acknowledgements We are very grateful to all our INRA and Genoplante colleagues for their submissions of data and for their participation in bioinformatics meetings to help define and enrich the GnpIS  ...  Modifying such a database is complex, as the normalized schema may involve hundreds of tables and a large amount of data would need to be transformed to fit the new normalized schema.  ... 
doi:10.1093/database/bat058 pmid:23959375 pmcid:PMC3746681 fatcat:kdk4jjbmavcm5lradzvo42nxjy

A Community-Based Annotation Framework for Linking Solanaceae Genomes with Phenomes

N. Menda, R. M. Buels, I. Tecle, L. A. Mueller
2008 Plant Physiology  
Here we describe the background, features, implementation, results, and development road map of SGN's community annotation tools for curating genotypes and phenotypes.  ...  The SOL Genomics Network (SGN; http://www.sgn.cornell.edu) is a clade-oriented database (COD), which provides a more scalable and comparative framework for biological information.  ...  ACKNOWLEDGMENTS We would like to thank Esther Van Der Knaap, Roger Chetelat, and Dani Zamir and all submitters for contributing data to the phenotyped populations and locus database, and Anuradha Pujar  ... 
doi:10.1104/pp.108.119560 pmid:18539779 pmcid:PMC2492603 fatcat:idtk3vqar5he7j5756socytbiy

The Genome Database for Rosaceae (GDR): year 10 update

Sook Jung, Stephen P. Ficklin, Taein Lee, Chun-Huai Cheng, Anna Blenda, Ping Zheng, Jing Yu, Aureliano Bombarely, Ilhyung Cho, Sushan Ru, Kate Evans, Cameron Peace (+4 others)
2013 Nucleic Acids Research  
Phenotype and genotype data from breeding projects and genetic diversity projects are also included.  ...  The Genome Database for Rosaceae (GDR, http:/ www.rosaceae.org), the long-standing central repository and data mining resource for Rosaceae research, has been enhanced with new genomic, genetic and breeding  ...  ACKNOWLEDGEMENTS The authors thank their funding sources, the Rosaceae research community for providing data and feedback and the Tripal community of developers for developing and sharing Tripal modules  ... 
doi:10.1093/nar/gkt1012 pmid:24225320 pmcid:PMC3965003 fatcat:rkn52cq5avdjxlafga3l5o57aq
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