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Tripal Developer Toolkit [article]

Bradford Condon, Abdullah Almsaeed, Joe West, Ming Chen, Margaret Staton
2018 bioRxiv   pre-print
Tripal is an open-source biological community database construction toolkit utilizing the content management system Drupal.  ...  Tripal is ultimately as strong as the community of sites and developers that use it.  ...  leadership of the core Tripal infrastructure and the community of Tripal software developers.  ... 
doi:10.1101/328641 fatcat:rmw6hhfc3fdefidqtuou6ddrx4

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

2019 Database: The Journal of Biological Databases and Curation  
The open-source Tripal database toolkit seeks to mitigate these challenges by creating both the software and an interactive community of developers for construction of online community databases.  ...  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

blend4php: a PHP API for galaxy

Connor Wytko, Brian Soto, Stephen P. Ficklin
2017 Database: The Journal of Biological Databases and Curation  
The blend4php library was specifically developed for the integration of Galaxy with Tripal, the open-source toolkit for the creation of online genomic and genetic web sites.  ...  Here we report the development of the blend4php library that wraps Galaxy's RESTful API into a PHP-based library.  ...  Acknowledgements We acknowledge the assistance of the Galaxy Team for providing help during the development of this library.  ... 
doi:10.1093/database/baw154 pmid:28077564 pmcid:PMC5225400 fatcat:a2xbof2gwncb5msce4fja6mcim

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.  ...  Tripal is an open-source, freely available, standards-based toolkit for storage, integration and dissemination of biological data.  ...  Tripal therefore provides a web interface for allowing the addition of custom tables by a site developer.  ... 
doi:10.1093/database/bat075 pmid:24163125 pmcid:PMC3808541 fatcat:khwlk7dc6zadpntbze5xskz7um

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  
of Tripal for the Marine Genomics Project.  ...  support and consultation, as well as, to the Marine Genomics Group at the Hollings Marine Lab and Clemson's Cyberinfrastructure and Technology Integration (CITI) Group who provided assistance with early developments  ...  In some cases it uses the Perl-based BioPerl (23, 24) toolkit.  ... 
doi:10.1093/database/bar044 pmid:21959868 pmcid:PMC3263599 fatcat:elbmyqg3qzcflcl3l3277gk2oq

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.  ...  Developed as a Tripal replacement for Comparative Map Viewer (CMap), it enables visualization of entire maps or linkage groups and features such as molecular markers, quantitative trait loci (QTLs) and  ...  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

Wheatgene: a genomics database for common wheat and its related species

Diego F. Garcia, Zhengyu Wang, Jiantao Guan, Lingjie Yin, Shuaifeng Geng, Aili Li, Long Mao
2021 Crop Journal  
WheatGene was developed with Drupal, a popular content management system and the toolkit Tripal managed the biological information.  ...  Long Mao conceptualized the database and supervised the entire development process. Diego Fernando Garcia executed and developed the database.  ...  Since Tripal toolkit does not have a feature for homologous gene pairs visualiztion, we developed a new Tripal module and was named Tripal Homologous.  ... 
doi:10.1016/j.cj.2021.04.011 fatcat:vldc7glrmbdtviscpafkdcgx2e

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.  ...  We discuss potential mapping challenges and solutions and provide suggestions for future development to further increase interoperability between these platforms.  ...  The opensource biological database toolkit Tripal serves as a common framework for community databases (5) .  ... 
doi:10.1093/database/baz143 pmid:31960040 pmcid:PMC6989756 fatcat:5t63iw7xqfdgvcg3hya5ucti34

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  
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  ...  Full integration of genetic maps and quantitative trait loci is imminent, and development of tools exploring structural variation is being explored.  ...  Over 100 plant and animal databases use Tripal (https://www. drupal.org/project/tripal; http://tripal.info/sites_using_tripal, Sanderson et al., 2013) , an open-source, highly customizable toolkit providing  ... 
doi:10.3389/fpls.2019.00965 pmid:31428111 pmcid:PMC6690010 fatcat:z37uayzokva6vovxfr7ozqsxoi

New extension software modules to enhance searching and display of transcriptome data in Tripal databases

Ming Chen, Nathan Henry, Abdullah Almsaeed, Xiao Zhou, Jill Wegrzyn, Stephen Ficklin, Margaret Staton
2017 Database: The Journal of Biological Databases and Curation  
Tripal is an open source software package for developing biological databases with a focus on genetic and genomic data.  ...  To expand the utility of the Tripal software system, particularly for RNASeq data, we developed two new extension modules.  ...  Acknowledgements We acknowledge the entire Tripal software developers community, particularly Stephen Ficklin (Washington State University) and Lacey-Anne Sanderson (University of Saskatchewan), for providing  ... 
doi:10.1093/database/bax052 pmid:29220446 pmcid:PMC5532966 fatcat:f3knlukwgbho3chigteszlb5v4

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  
TreeGenes recently migrated to Tripal, an integrated and open-source database schema and content management system.  ...  This focus was paired with the development of tools to enable comparative genomics and data visualization.  ...  implementing the Natural Diversity extensions in Tripal.  ... 
doi:10.1093/database/bay084 pmid:30239664 pmcid:PMC6146132 fatcat:o5a5wj5ylvdkdncttoebsk3ni4

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  
(CuGenDB; http://cucurbitgenomics.org) using the Tripal toolkit.  ...  To store, mine, analyze, integrate and disseminate these large-scale datasets and to provide a central portal for the cucurbit research and breeding community, we have developed the Cucurbit Genomics Database  ...  ACKNOWLEDGEMENTS We thank the Tripal community for developing, maintaining and updating the Tripal modules. FUNDING  ... 
doi:10.1093/nar/gky944 pmid:30321383 fatcat:3yw6vj25izentji7qntchuodja

CorkOakDB—The Cork Oak Genome Database Portal

Cirenia Arias-Baldrich, Marta Contreiras Silva, Filippo Bergeretti, Inês Chaves, Célia Miguel, Nelson J M Saibo, Daniel Sobral, Daniel Faria, Pedro M Barros
2020 Database: The Journal of Biological Databases and Curation  
In an effort to integrate this information in a comprehensive, accessible and intuitive format, we have developed The Cork Oak Genome Database Portal (CorkOakDB).  ...  One thing that has changed since the first genome portals arose is the availability of website content management systems and toolkits such as the Tripal ('Tripal | Tripal', https://tripal.info/, accessed  ...  The CorkOakDB portal The CorkOakDB was developed using Tripal (18) .  ... 
doi:10.1093/database/baaa114 pmid:33382885 fatcat:hmic5lcpnjcqzfvtt3srehseyy

SpinachBase: a central portal for spinach genomics

2019 Database: The Journal of Biological Databases and Curation  
A reference spinach genome has been recently released, and additional spinach genomic resources are being rapidly developed.  ...  To this end, we developed SpinachBase (http://spinachbase.org), which provides centralized public accesses to genomic data as well as analytical tools to assist research and breeding in spinach.  ...  SpinachBase has been implemented using Tripal, a widely used toolkit for constructing web-based genomic and genetic databases (6, 7) .  ... 
doi:10.1093/database/baz072 pmid:31211398 pmcid:PMC6580994 fatcat:etfdixa2vjcbhjaloupg45ijle

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  
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.  ...  Open-source software is uniquely positioned to fill this need through user-focused, crowd-sourced development.  ...  They were developed to be modular and highly configurable to facilitate sharing among the Tripal community.  ... 
doi:10.1093/database/baab051 pmid:34389844 pmcid:PMC8363843 fatcat:mxstsjb64vfrvauxm3ssbyh5zu
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