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

doi:10.1093/database/bat075

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Tripal v1.1: A standards-based toolkit for construction of online genetic and genomic databases

Journal article

Open access

Peer reviewed

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 and Dorrie Main

Database : the journal of biological databases and curation, Vol.2013, pp.bat075-bat075

2013

DOI: https://doi.org/10.1093/database/bat075

Handle:

https://hdl.handle.net/2376/114008

PMCID: PMC3808541

PMID: 24163125

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https://doi.org/10.1093/database/bat075View

Published (Version of record) Open

Abstract

User-Computer Interface

Publications

Seeds - genetics

Genome - genetics

Genomics - standards

Databases, Genetic

Genotype

Genetic Variation

Reference Standards

Plants - genetics

Internet

Genomics - methods

Software

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/.

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Title: Tripal v1.1: A standards-based toolkit for construction of online genetic and genomic databases
Creators: Lacey-Anne Sanderson - Department of Plant Sciences, University of Saskatchewan. Saskatoon, SK Canada, Department of Horticulture, Washington State University. Pullman, WA, USA and Department of Genetics and Biochemistry, Clemson University. Clemson, SC, USA
Stephen P Ficklin
Chun-Huai Cheng
Sook Jung
Frank A Feltus
Kirstin E Bett
Dorrie Main
Publication Details: Database : the journal of biological databases and curation, Vol.2013, pp.bat075-bat075
Academic Unit: Horticulture, Department of
Publisher: England
Identifiers: 99900547634101842
Language: English
Resource Type: Journal article