Tripal Developer Toolkit

Condon, Bradford; Almsaeed, Abdullah; Chen, Ming; West, Joe; Staton, Margaret

doi:10.1093/database/bay099

Cited by 3 publications

(3 citation statements)

References 18 publications

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“…The instructions provided on the Tripal v3 Developer’s Handbook help developers implement their own fields. In addition, the Tripal Fields Generator package (36), available at https://github.com/tripal/fields_generator, will help automate initial setup of these field classes.…”

Section: Methodsmentioning

confidence: 99%

“…However, implementing it in Drupal 7 has been historically difficult due to the lack of core infrastructure. Tripal Test Suite (36) bootstraps a Tripal site to use PHPUnit and lessen the development time needed to add PHPUnit tests to any Tripal extension module. Tripal v3 core package uses Tripal Test Suite to provide core tests.…”

Section: Resources For Site Developersmentioning

confidence: 99%

See 1 more Smart Citation

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

et al. 2019

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Community biological databases provide an important online resource for both public and private data, analysis tools and community engagement. These sites house genomic, transcriptomic, genetic, breeding and ancillary data for specific species, families or clades. Due to the complexity and increasing quantities of these data, construction of online resources is increasingly difficult especially with limited funding and access to technical expertise. Furthermore, online repositories are expected to promote FAIR data principles (findable, accessible, interoperable and reusable) that presents additional challenges. 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. Additionally, through coordinated, distributed co-development, Tripal sites encourage community-wide sustainability. Here, we report the release of Tripal version 3 that improves data accessibility and data sharing through systematic use of controlled vocabularies (CVs). 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 the data. 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 interface. A thorough online User’s Guide and Developer’s Handbook are available at http://tripal.info, providing download, installation and step-by-step setup instructions.

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Section: Methodsmentioning

confidence: 99%

Section: Resources For Site Developersmentioning

confidence: 99%

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

et al. 2019

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“…Both the Tripal and PlantGenIE platforms provide cross-site search capabilities and a core framework that allows rapid development of a new instance. Tripal implements cross-site search with an Elastic Search module that removes dependence on a uniform database schema(Condon, Almsaeed, Chen, West, & Staton, 2018). For example, all of the Tripal tree databases are currently run-ning the Elastic Search module, which allows a visitor to TreeGenes to search a specific gene and request that matching results are returned from Hardwood Genomics Web, CitrusDB, and Genome Database for Rosaceae.…”

mentioning

confidence: 99%

Cyberinfrastructure and resources to enable an integrative approach to studying forest trees

Wegrzyn

Falk

Grau

et al. 2019

Evolutionary Applications

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Sequencing technologies and bioinformatic approaches are now available to resolve the challenges associated with complex and heterozygous genomes. Increased access to less expensive and more effective instrumentation will contribute to a wealth of high‐quality plant genomes in the next few years. In the meantime, more than 370 tree species are associated with public projects in primary repositories that are interrogating expression profiles, identifying variants, or analyzing targeted capture without a high‐quality reference genome. Genomic data from these projects generates sequences that represent intermediate assemblies for transcriptomes and genomes. These data contribute to forest tree biology, but the associated sequence remains trapped in supplemental files that are poorly integrated in plant community databases and comparative genomic platforms. Successful implementation of life science cyberinfrastructure is improving data standards, ontologies, analytic workflows, and integrated database platforms for both model and non‐model plant species. Unique to forest trees with large populations that are long‐lived, outcrossing, and genetically diverse, the phenotypic and environmental metrics associated with georeferenced populations are just as important as the genomic data sampled for each individual. To address questions related to forest health and productivity, cyberinfrastructure must keep pace with the magnitude of genomic and phenomic sampling of larger populations. This review examines the current landscape of cyberinfrastructure, with an emphasis on best practices and resources to align community data with the Findable, Accessible, Interoperable, and Reusable (FAIR) guidelines.

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OUP accepted manuscript

et al. 2021

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Researchers are seeking cost-effective solutions for management and analysis of large-scale genotypic and phenotypic data. Open-source software is uniquely positioned to fill this need through user-focused, crowd-sourced development. 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. Tripal also aids research-focused web portals in providing data according to findable, accessible, interoperable, reusable (FAIR) principles. 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. These Tripal extension modules provide a holistic approach for importing, storage, display and analysis within a relational database schema. Furthermore, they embody the Tripal approach to FAIR data by providing multiple search tools and ensuring metadata is fully described and interoperable. Our solution focuses on data integrity, as well as optimizing performance to provide a fully functional system that is currently being used in the production of Tripal portals for crop species. We fully describe the implementation of our solution and discuss why a PostgreSQL-powered web portal provides an efficient environment for researcher-driven genotypic and phenotypic data analysis.

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Tripal Developer Toolkit

Cited by 3 publications

References 18 publications

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

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

Cyberinfrastructure and resources to enable an integrative approach to studying forest trees

OUP accepted manuscript

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