Tripal: a construction toolkit for online genome databases

As the availability, affordability and magnitude of genomics and genetics research increases so does the need to provide online access to resulting data and analyses. Availability of a tailored online database is the desire for many investigators or research communities; however, managing the Information Technology infrastructure needed to create such a database can be an undesired distraction from primary research or potentially cost prohibitive. Tripal provides simplified site development by merging the power of Drupal, a popular web Content Management System with that of Chado, a community-derived database schema for storage of genomic, genetic and other related biological data. Tripal provides an interface that extends the content management features of Drupal to the data housed in Chado. Furthermore, Tripal provides a web-based Chado installer, genomic data loaders, web-based editing of data for organisms, genomic features, biological libraries, controlled vocabularies and stock collections. Also available are Tripal extensions that support loading and visualizations of NCBI BLAST, InterPro, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses, as well as an extension that provides integration of Tripal with GBrowse, a popular GMOD tool. An Application Programming Interface is available to allow creation of custom extensions by site developers, and the look-and-feel of the site is completely customizable through Drupal-based PHP template files. Addition of non-biological content and user-management is afforded through Drupal. Tripal is an open source and freely available software package found at http://tripal.sourceforge.net

[1]  Robert M. Buels,et al.  The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl , 2010, Nucleic Acids Res..

[2]  Jason E Stajich,et al.  An Introduction to BioPerl. , 2007, Methods in molecular biology.

[3]  Peili Zhang,et al.  Using Chado to store genome annotation data. , 2006, Current protocols in bioinformatics.

[4]  A. Nekrutenko,et al.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences , 2010, Genome Biology.

[5]  Scott Cain,et al.  GMODWeb: a web framework for the generic model organism database , 2008, Genome Biology.

[6]  Douglas Thain,et al.  Distributed computing in practice: the Condor experience , 2005, Concurr. Pract. Exp..

[7]  R. Drysdale.  FlyBase : a database for the Drosophila research community. , 2008, Methods in molecular biology.

[8]  Matthew R. Pocock,et al.  The Bioperl toolkit: Perl modules for the life sciences. , 2002, Genome research.

[9]  Pankaj Jaiswal,et al.  Gramene database: a hub for comparative plant genomics. , 2011, Methods in molecular biology.

[10]  Jonathan Crabtree,et al.  Ergatis: a web interface and scalable software system for bioinformatics workflows , 2010, Bioinform..

[11]  Chris Mungall,et al.  A Chado case study: an ontology-based modular schema for representing genome-associated biological information , 2007, ISMB/ECCB.

[12]  Rolf Apweiler,et al.  InterProScan - an integration platform for the signature-recognition methods in InterPro , 2001, Bioinform..

[13]  Juan Miguel García-Gómez,et al.  BIOINFORMATICS APPLICATIONS NOTE Sequence analysis Manipulation of FASTQ data with Galaxy , 2005 .

[14]  Jill L. Wegrzyn,et al.  TreeGenes: A Forest Tree Genome Database , 2008, International journal of plant genomics.

[15]  Alex Bateman,et al.  The InterPro database, an integrated documentation resource for protein families, domains and functional sites , 2001, Nucleic Acids Res..

[16]  Akiyasu C. Yoshizawa,et al.  KAAS: an automatic genome annotation and pathway reconstruction server , 2007, Environmental health perspectives.

[17]  S. Lewis,et al.  The generic genome browser: a building block for a model organism system database. , 2002, Genome research.

[18]  Qunfeng Dong,et al.  MaizeGDB, the community database for maize genetics and genomics , 2004, Nucleic Acids Res..

[19]  Stefan Götz,et al.  Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics , 2007, International journal of plant genomics.

[20]  Dorrie Main,et al.  GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data , 2007, Nucleic Acids Res..

[21]  Stephen P. Ficklin,et al.  GDR (Genome Database for Rosaceae): integrated web resources for Rosaceae genomics and genetics research , 2004, BMC Bioinform..

[22]  Kara Dolinski,et al.  The Saccharomyces Genome Database provides comprehensive information about the biology of S. cerevisiae and tools for studies in comparative genomics , 2007 .

[23]  Carolyn J. Lawrence,et al.  MaizeGDB: The Maize Model Organism Database for Basic, Translational, and Applied Research , 2008, International journal of plant genomics.

[24]  E. Birney,et al.  Apollo: a sequence annotation editor , 2002, Genome Biology.

[25]  Yoshihiro Yamanishi,et al.  KEGG for linking genomes to life and the environment , 2007, Nucleic Acids Res..

[26]  Maureen J Donlin,et al.  Using the Generic Genome Browser (GBrowse) , 2007, Current protocols in bioinformatics.

[27]  Kimberly Van Auken,et al.  WormBase: a comprehensive resource for nematode research , 2009, Nucleic Acids Res..

[28]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[29]  Yian A Chen,et al.  Marine Genomics: A clearing-house for genomic and transcriptomic data of marine organisms , 2005, BMC Genomics.

[30]  Alexie Papanicolaou,et al.  The GMOD Drupal Bioinformatic Server Framework , 2010, Bioinform..

[31]  Matthew R. Pocock,et al.  Taverna: a tool for the composition and enactment of bioinformatics workflows , 2004, Bioinform..

[32]  L. Stein,et al.  JBrowse: a next-generation genome browser. , 2009, Genome research.