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Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment

Jill L. Wegrzyn, Margaret A. Staton, Nathaniel R. Street, Dorrie Main, Emily Grau, Nic Herndon, Sean Buehler, Taylor Falk, Sumaira Zaman, Risharde Ramnath, Peter Richter, Lang Sun (+6 others)
2019 Frontiers in Plant Science  
Although primary databases store genetic resources for just over 2,000 forest tree species, these are largely focused on sequence storage, basic genome assemblies, and functional assignment through existing  ...  The organism databases of today are no longer simply catalogs or containers of genetic information.  ...  GENOME DATABASE FOR ROSACEAE The Genome Database for Rosaceae (GDR 2 , Jung et al., 2013) was initiated in 2003 to provide curated and integrated, genomic, genetics and breeding (GGB) data alongside  ... 
doi:10.3389/fpls.2019.00813 pmid:31293610 pmcid:PMC6603172 fatcat:vpbwpe3sg5f3hmnzboiwaxanga

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  
This focus was paired with the development of tools to enable comparative genomics and data visualization.  ...  The database provides a curated archive for high-throughput genomics, including reference genomes, transcriptomes, genetic maps and variant data.  ...  implementing the Natural Diversity extensions in Tripal.  ... 
doi:10.1093/database/bay084 pmid:30239664 pmcid:PMC6146132 fatcat:o5a5wj5ylvdkdncttoebsk3ni4

Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases

Margaret Staton, Ethalinda Cannon, Lacey-Anne Sanderson, Jill Wegrzyn, Tavis Anderson, Sean Buehler, Irene Cobo-Simón, Kay Faaberg, Emily Grau, Valentin Guignon, Jessica Gunoskey, Blake Inderski (+8 others)
2021 Briefings in Bioinformatics  
least 31 publicly available databases spanning plants, animals and human data, primarily storing genomics, genetics and breeding data.  ...  With ongoing improvement since its first release in 2009, Tripal provides full functionality for searching, browsing, loading and curating numerous types of data and is a primary technology powering at  ...  The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.  ... 
doi:10.1093/bib/bbab238 pmid:34251419 pmcid:PMC8574961 fatcat:khqsm7dedrgupeu7h5iyaoi7wi

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

2019 Database: The Journal of Biological Databases and Curation  
These sites house genomic, transcriptomic, genetic, breeding and ancillary data for specific species, families or clades.  ...  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  ...  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 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  
These Tripal extension modules provide a holistic approach for importing, storage, display and analysis within a relational database schema.  ...  Tripal, an open-source toolkit for developing biological data web portals, uses the GMOD Chado database schema to achieve flexible, ontology-driven storage in PostgreSQL.  ...  Funding This work was supported by the 'Application of Genomics to Innovation in the Lentil Economy (AGILE)' project funded by Genome Canada and managed by Genome Prairie.  ... 
doi:10.1093/database/baab051 pmid:34389844 pmcid:PMC8363843 fatcat:mxstsjb64vfrvauxm3ssbyh5zu

Tripal MapViewer: A tool for interactive visualization and comparison of genetic maps

2019 Database: The Journal of Biological Databases and Curation  
Tripal is an open-source, resource-efficient toolkit for construction of genomic, genetic and breeding databases.  ...  Tripal MapViewer is a new interactive tool for visualizing genetic map data.  ...  Acknowledgements We acknowledge with thanks the Tripal and GMOD developer communities; the Rosaceae, cotton, citrus, cool season food legume, Conflict of interest. None declared.  ... 
doi:10.1093/database/baz100 pmid:31688940 pmcid:PMC6829499 fatcat:qnvm3ev7hzcsfo4jsvxkoi2kj4

Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops

Yi Zheng, Shan Wu, Yang Bai, Honghe Sun, Chen Jiao, Shaogui Guo, Kun Zhao, Jose Blanca, Zhonghua Zhang, Sanwen Huang, Yong Xu, Yiqun Weng (+17 others)
2018 Nucleic Acids Research  
During the past several years, genomic and genetic data have been rapidly accumulated for cucurbits.  ...  A set of analysis and visualization  ...  ACKNOWLEDGEMENTS We thank the Tripal community for developing, maintaining and updating the Tripal modules. FUNDING  ... 
doi:10.1093/nar/gky944 pmid:30321383 fatcat:3yw6vj25izentji7qntchuodja

Tripal: a construction toolkit for online genome databases

S. P. Ficklin, L.-A. Sanderson, C.-H. Cheng, M. E. Staton, T. Lee, I.-H. Cho, S. Jung, K. E. Bett, D. Main
2011 Database: The Journal of Biological Databases and Curation  
Lab and Clemson's Cyberinfrastructure and Technology Integration (CITI) Group who provided assistance with early developments of Tripal for the Marine Genomics Project.  ...  Acknowledgements Special thanks are extended to Scott Cain and Dave Clements of the GMOD project team for logistical support and consultation, as well as, to the Marine Genomics Group at the Hollings Marine  ...  and visualization of genomic, genetic and other biological data.  ... 
doi:10.1093/database/bar044 pmid:21959868 pmcid:PMC3263599 fatcat:elbmyqg3qzcflcl3l3277gk2oq

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  
and for opportunities to participate in outreach programs associated with GMOD.  ...  Conflict of interest. None declared. Page 17 of 18  ...  A key role of Tripal is to reduce the time and costs for deployment of data-rich genome databases. Tripal uses the GMOD Chado database schema (8, 9) for storage of biological data.  ... 
doi:10.1093/database/bat075 pmid:24163125 pmcid:PMC3808541 fatcat:khwlk7dc6zadpntbze5xskz7um

15 years of GDR: New data and functionality in the Genome Database for Rosaceae

Sook Jung, Taein Lee, Chun-Huai Cheng, Katheryn Buble, Ping Zheng, Jing Yu, Jodi Humann, Stephen P Ficklin, Ksenija Gasic, Kristin Scott, Morgan Frank, Sushan Ru (+11 others)
2018 Nucleic Acids Research  
The Genome Database for Rosaceae (GDR, https://www.rosaceae.org) is an integrated web-based community database resource providing access to publicly available genomics, genetics and breeding data and data-mining  ...  Significantly more quantitative trait loci, genetic maps and markers are available in MapViewer, a new visualization tool that better integrates with other pages in GDR.  ...  ACKNOWLEDGEMENTS The authors acknowledge with thanks their funding sources, the Rosaceae research community for providing data, support and feedback, the Tripal and GMOD community of developers for developing  ... 
doi:10.1093/nar/gky1000 pmid:30357347 pmcid:PMC6324069 fatcat:mwwos4ljmnekvl4u6penvw2joa

Kiwifruit Genome Database (KGD): a comprehensive resource for kiwifruit genomics

Junyang Yue, Jiacheng Liu, Wei Tang, Ya Qing Wu, Xiaofeng Tang, Wei Li, Ying Yang, Lihuan Wang, Shengxiong Huang, Congbing Fang, Kun Zhao, Zhangjun Fei (+2 others)
2020 Horticulture Research  
A set of user-friendly query interfaces, analysis tools and visualization modules have been implemented in KGD to facilitate translational and applied research in kiwifruit, which include JBrowse, a popular  ...  Since the release of the first kiwifruit reference genome sequence in 2013, large volumes of genome and transcriptome data have been rapidly accumulated for a handful of kiwifruit species.  ...  Acknowledgements This study was supported by grants from the National Natural Science Conflict of interest The authors declare that they have no conflict of interest.  ... 
doi:10.1038/s41438-020-0338-9 pmid:32821400 pmcid:PMC7395147 fatcat:hrkefpgi2vdgdpv233fuqse75q

KnowPulse: A Web-Resource Focused on Diversity Data for Pulse Crop Improvement

Lacey-Anne Sanderson, Carolyn T. Caron, Reynold Tan, Yichao Shen, Ruobin Liu, Kirstin E. Bett
2019 Frontiers in Plant Science  
It is also summarized on genetic marker and sequence variant pages. Phenotypic data is visualized in trait distribution plots: violin plots for quantitative data and histograms for qualitative data.  ...  KnowPulse is built using the open-source Tripal toolkit and utilizes open-source tools including, but not limited to, species-specific JBrowse instances, a BLAST interface, and whole-genome CViTjs visualizations  ...  KnowPulse is built using Tripal, with the purpose of serving as a reliable data storage solution with metadata preservation.  ... 
doi:10.3389/fpls.2019.00965 pmid:31428111 pmcid:PMC6690010 fatcat:z37uayzokva6vovxfr7ozqsxoi

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  
The Genome Database for Rosaceae (GDR) and CottonGen are comprehensive online data repositories that provide access to integrated genomic, genetic and breeding data through search, visualization and analysis  ...  Therefore, Chado is flexible such that it has been used to house genomic, genetic and breeding data for GDR and CottonGen.  ...  The Genome Database for Rosaceae (GDR) and CottonGen are (25) one of the first, if not the only, databases that adopted Chado/Tripal solely to store integrated genetic, genomic and breeding data comprised  ... 
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  
The Genome Database for Rosaceae (GDR) and CottonGen are comprehensive online data repositories that provide access to integrated genomic, genetic and breeding data through search, visualization and analysis  ...  Therefore, Chado is flexible such that it has been used to house genomic, genetic and breeding data for GDR and CottonGen.  ...  The Genome Database for Rosaceae (GDR) and CottonGen are (25) one of the first, if not the only, databases that adopted Chado/Tripal solely to store integrated genetic, genomic and breeding data comprised  ... 
doi:10.1093/database/baw010 pmid:26989146 pmcid:PMC4795932 fatcat:ulmoo7j3gvhync3j3lipxvbtgq

Tripal EUtils: a Tripal module to increase exchange and reuse of genome assembly metadata

2019 Database: The Journal of Biological Databases and Curation  
We present mappings for multiple NCBI data structures and introduce a Tripal software module, Tripal EUtils, to pull metadata from NCBI into a Tripal/Chado database.  ...  Data and metadata interoperability between data storage systems is a critical component of the FAIR data principles.  ...  Acknowledgements We thank Ethalinda Cannon, Gerard Lazo and three anonymous reviewers for the thoughtful reviews of this manuscript.  ... 
doi:10.1093/database/baz143 pmid:31960040 pmcid:PMC6989756 fatcat:5t63iw7xqfdgvcg3hya5ucti34
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