Abstract
Tripal community database construction toolkit utilizing the content management system Drupal. Tripal is used to make biological, genetic and genomic data more discoverable, shareable, searchable and standardized. As funding for community-level genomics databases declines, Tripal’s open-source codebase provides a means for sites to be built and maintained with a minimal investment in staff and new development. Tripal is ultimately as strong as the community of sites and developers that use it. We present a set of developer tools that will make building and maintaining Tripal 3 sites easier for new and returning users. These tools break down barriers to entry such as setting up developer and testing environments, acquiring and loading test datasets, working with controlled vocabulary terms and writing new Drupal classes.
Highlights
The rapid advancement in sequencing technology has resulted in a proliferation of genomic data
Allpurpose databases such as NCBI capture some of this data, but additional support is needed for manual annotation, specialized analyses and data integration, for groups not specializing in bioinformatics
Given that Tripal lives at the union of these disciplines, we identify challenges that a small development team is likely to face deploying a Tripal site and present a suite of developer tools to facilitate their resolution (Table 2), which we have developed in the course of our own work on the Tripal-based site Hardwood Genomics Project [18]
Summary
The rapid advancement in sequencing technology has resulted in a proliferation of genomic data. General, allpurpose databases such as NCBI capture some of this data, but additional support is needed for manual annotation, specialized analyses and data integration, for groups not specializing in bioinformatics. Community-level genomics databases fill this role, hosting a curated set of data from a species or multiple species of interest. To continue the critical role they play connecting researchers to tailored bioinformatic resources, community databases must formulate a plan to keep sites available and continue to add new data and services. The biological community database construction toolkit Tripal was created as a multifaceted solution to many of these problems [2]. Tripal utilizes the same system of modular code units that have
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