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Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment
2019
Frontiers in Plant Science
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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
2018
Database: The Journal of Biological Databases and Curation
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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
2021
Briefings in Bioinformatics
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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
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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
2021
Database: The Journal of Biological Databases and Curation
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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
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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
2018
Nucleic Acids Research
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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
2011
Database: The Journal of Biological Databases and Curation
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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
2013
Database: The Journal of Biological Databases and Curation
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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
2018
Nucleic Acids Research
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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
2020
Horticulture Research
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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
2019
Frontiers in Plant Science
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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
2016
Database: The Journal of Biological Databases and Curation
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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
2016
Database: The Journal of Biological Databases and Curation
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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
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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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