Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2013 Oct 25;2013:bat075.
doi: 10.1093/database/bat075. Print 2013.

Tripal v1.1: A Standards-Based Toolkit for Construction of Online Genetic and Genomic Databases

Affiliations
Free PMC article

Tripal v1.1: A Standards-Based Toolkit for Construction of Online Genetic and Genomic Databases

Lacey-Anne Sanderson et al. Database (Oxford). .
Free PMC article

Abstract

Tripal is an open-source freely available toolkit for construction of online genomic and genetic databases. It aims to facilitate development of community-driven biological websites by integrating the GMOD Chado database schema with Drupal, a popular website creation and content management software. Tripal provides a suite of tools for interaction with a Chado database and display of content therein. The tools are designed to be generic to support the various ways in which data may be stored in Chado. Previous releases of Tripal have supported organisms, genomic libraries, biological stocks, stock collections and genomic features, their alignments and annotations. Also, Tripal and its extension modules provided loaders for commonly used file formats such as FASTA, GFF, OBO, GAF, BLAST XML, KEGG heir files and InterProScan XML. Default generic templates were provided for common views of biological data, which could be customized using an open Application Programming Interface to change the way data are displayed. Here, we report additional tools and functionality that are part of release v1.1 of Tripal. These include (i) a new bulk loader that allows a site curator to import data stored in a custom tab delimited format; (ii) full support of every Chado table for Drupal Views (a powerful tool allowing site developers to construct novel displays and search pages); (iii) new modules including 'Feature Map', 'Genetic', 'Publication', 'Project', 'Contact' and the 'Natural Diversity' modules. Tutorials, mailing lists, download and set-up instructions, extension modules and other documentation can be found at the Tripal website located at http://tripal.info. DATABASE URL: http://tripal.info/.

Figures

Figure 1.
Figure 1.
Tripal modules are organized in a hierarchical structure. The Tripal Core module, Chado-specific modules, the Tripal Views and Bulk Loader modules comprise the base Tripal package. Extension modules and applications build on the Tripal API provided by the base modules, but are available separately. The Tripal theme is a separate entity, but is dependent on the Tripal Core module. The Tripal Theme provides all templates for the base modules.
Figure 2.
Figure 2.
Screenshots of the project page. (A) The project details page provide the project name and a description. (B) Publications associated with the project. This information is available by clicking the ‘Publications’ link in the right sidebar.
Figure 3.
Figure 3.
Screenshots of the contact page. (A) The contact details provide the name, contact type and a brief description. Additional details are available by clicking the ‘More Details’ link on the right sidebar (not shown). (B) If the contact is associated with publications those are shown by clicking the ‘Publications’ link on the right sidebar.
Figure 4.
Figure 4.
Screenshots of a genetic map page. (A) The map details provide the name of the map, the map units and a brief description. Additional details are available by clicking the ‘More Details’ link on the right sidebar (not shown). (B) If features (e.g. genetic markers) are associated with a map, they are listed by clicking on the ‘Properties’ link of the right sidebar.
Figure 5.
Figure 5.
Screenshots of a publication page. (A) The publication details provide information about a publication including the title, authors, journal (book or conference, etc.) name, citation and other relevant details. (B) Additional details are available by clicking the ‘More Details’ link on the right sidebar.
Figure 6.
Figure 6.
Screenshot of the publication edit page. Here a content manager for the site can edit details about the publication and add any number of properties.
Figure 7.
Figure 7.
Screenshot of the publication importer. The Tripal publication importer allows a content manager to create a set of search criteria to remotely query a remote publication database such as PubMed. The manager can test the importer query before saving.
Figure 8.
Figure 8.
Screenshot of the germplasm (stock) page with associated genotypes. The Natural Diversity Module of Tripal adds genotype information to stocks and features. Here are SNP genotype calls for the germplasm ‘Basmati’.
Figure 9.
Figure 9.
Screenshot of the Custom Table interface. Here a site developer can create custom tables not found in Chado using the Drupal Schema API array structure to define the table.
Figure 10.
Figure 10.
Screenshot of the Bulk Loader interface. This example shows one record with an ‘insert’ operation and four fields: genus, species, common_name and abbreviation. Each field is set to a specific column in the input file. This template can be used for loading organisms into the database.
Figure 11.
Figure 11.
The relationship diagram between stock, cvterm, cv and organism tables. These tables are all needed for storing entries in the stock table. The stock table requires a type, which is stored in the cvterm table. It also requires an organism, which is stored in the organism table. Both are associated to the stock via foreign key constraints with the cvterm_id and organism_id fields, respectively. Fields used in foreign key relationships are bold.
Figure 12.
Figure 12.
A screenshot of the Drupal Views UI. This screenshot shows the settings for the Feature module default view that allows site users to search for features. The ‘Basic Settings’ section sets some display and behavior criteria for the View. The ‘Fields’ section indicates which fields are to be displayed in the resulting page, and the ‘Sort criteria’ section specifies the order in which features should be displayed. The ‘Filters’ section specifies which features should be displayed. There are three filter criteria: common name, type id and name. While not shown, these fields are exported to the user and appear as form elements when searching (see Figure 13).
Figure 13.
Figure 13.
A screenshot of the default feature search View. This search form, with accompanying results is the result of the view described in Figure 12. The form elements for selecting a common name and type are present because they were configured as exposed filters.
Figure 14.
Figure 14.
A screenshot of the Views Integration interface. 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. Note that for the name field, the filer handler is set to be ‘tripal_views_handler_filter_file_upload’. This handler will provide a form element for uploading feature names when the field is used as a filter and exposed to the site user.

Similar articles

See all similar articles

Cited by 26 articles

See all "Cited by" articles

References

    1. Schmutz J, Wheeler J, Grimwood J, et al. Quality assessment of the human genome sequence. Nature. 2004;429:365–368. - PubMed
    1. Drysdale R. FlyBase:a database for the Drosophila research community. Methods Mol. Biol. 2008;420:45–59. - PubMed
    1. Harris TW, Antoshechkin I, Bieri T, et al. WormBase: a comprehensive resource for nematode research. Nucleic Acids Res. 2010;38:D463–D467. - PMC - PubMed
    1. Jaiswa P. Gramene database: a hub for comparative plant genomics. Methods Mol. Biol. 2011;678:247–275. - PubMed
    1. Ouyang S, Zhu W, Hamilton J, et al. The TIGR rice genome annotation resource: improvements and new features. Nucleic Acids Res. 2007;35:D883–D887. - PMC - PubMed

Publication types

Feedback