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

Abstract

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.

CorkOakDB—The Cork Oak Genome Database Portal

“…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 15 June 2020) framework ( 18 ), which greatly facilitates the development of new portals. Tripal is an open-source toolkit for biological databases that is part of the Generic Model Organism Database project tools and is the basis of several genome portals ( 13 , 14 ).…”

“…The CorkOakDB was developed using Tripal ( 18 ). In addition to the standard built-in Tripal modules, CorkOakDB is equipped with Tripal Extension Modules dedicated to data analysis, annotation and visualization, such as Tripal Analysis Expression, Tripal Analysis BLAST ( 17 ), Tripal Analysis InterPro and third-party Integration Extension Modules, including Tripal JBrowse—used for the integration of a pre-installed GMOD JBrowse instance ( 16 )—that extend the functionality and possibilities of the portal.…”

Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases

“…To this end, the Tripal ( 16–18 ) platform provides a mechanism by which online genomic, genetic and breeding databases can reduce duplication of effort, develop a common platform and improve the sustainability of their respective online databases. It is a software platform, developed using PHP, the Drupal content management system (CMS) and the Chado database schema ( 19 ).…”

Machado: open source genomics data integration framework

“…Its biological relational database schema named Chado (Mungall & Emmert, 2007) is widely adopted and many softwares are able connect to it eg. Jbrowse (Skinner et al, 2009), Gbrowse (Stein et al, 2002), Apollo (Lee et al, 2013), Intermine (Kalderimis et al, 2014), and Tripal (Spoor et al, 2019).…”