Bioinformatics Advance Access originally published online on September 3, 2004
Bioinformatics 2005 21(3):399-401; doi:10.1093/bioinformatics/bti002
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Bioinformatics vol. 21 issue 3 © Oxford University Press 2005; all rights reserved.
BarleyExpress: a web-based submission tool for enriched microarray database annotations
1 Electrical and Computer Engineering Department, Iowa State University Ames, IA 50011-3060, USA
2 Virtual Reality Applications Center, Iowa State University Ames, IA, 50011-2274, USA
*To whom correspondence should be addressed.
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Abstract |
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Summary: BarleyExpress is a web-based microarray experiment data submission tool for BarleyBase, a public data resource of Affymetrix GeneChip® data for plants. BarleyExpress uses the Plant Ontology vocabularies and enhances the MIAME guidelines to standardize the annotation of microarray gene expression experiments. In addition, BarleyExpress provides explicit support for factorial experiment design and template loading methods to ease the submission process for large experiments.
Availability: http://barleybase.org
Contact: julied{at}iastate.edu
Supplementary information: BarleyExpress Users Manual.
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INTRODUCTION |
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TOPAbstractINTRODUCTIONDESCRIPTIONDISCUSSIONREFERENCES |
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BarleyBase serves as a public repository for raw and normalized expression data from Barley1 and other plant GeneChips. The Barley1 GeneChip is a community-designed, Affymetrix 22K probe array (Close et al., 2004) which is a model for plants without a fully sequenced genome. To make valid comparisons, the experiment annotations must be standardized using community-defined vocabularies. BarleyExpress is a web-based data submission tool that enriches the MIAME (Brazma et al., 2001) guidelines by promoting best practices in experiment design and extending the experimental definitions to the plant community. BarleyExpress also enforces usage of the growth stage, anatomy and trait-controlled vocabularies from the Plant Ontology to annotate microarray gene expression experiment metadata (The Plant OntologyTM Consortium, 2002). This leads the experimental data in BarleyBase into a biological context and enables valuable insights into biological processes. Exemplar data in BarleyBase are annotated with Gene Ontology information as it becomes available (Gene Ontology Consortium, 2000).
There are several prominent public databases that provide access to microarray data. These include general repositories, such as the Gene Expression Omnibus (GEO) (Edgar et al., 2002) the Stanford Microarray Database (Gollub et al., 2003) and ArrayExpress (Brazma et al., 2003). These repositories are intended to act as central data distribution hubs for download and local processing, and not as online analysis tools for related datasets. Currently, only ArrayExpress has a validated MIAME-compliant, web-based submission tool, MIAMExpress (EMBL-EBI, 2004). GEO is currently implementing such a system. None of these systems requires ontology information to specify key biological information on tissue type and development stages.
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DESCRIPTION |
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BarleyBase stores four basic types of information: GeneChip and/or microarray structure data, experimental and labeling protocols, actual measured gene expression data and annotations, and analysis results in both MAS 5.0 (Affymetrix Inc., 2001) and Robust Multichip Average (RMA) (Gautier et al., 2004) normalized formats. BarleyBase shares links with external bioinformatics databases, including Gramene (Ware et al., 2002) GrainGenes (Matthews et al., 2003) PlantGDB (Dong et al., 2004) and TAIR (Rhee et al., 2003) for annotation information integration and linking to sequenced plants such as rice and Arabidopsis. Links between databases make the use of controlled vocabularies from the Gene and Plant Ontologies critical.
Design of BarleyExpress
BarleyExpress follows the MIAME guidelines in organizing microarray data on an experimental basis. BarleyExpress was initially modeled on MIAMExpress which implemented the MIAME guidelines (EMBL-EBI, 2004). It is also customized to meet the needs of users in the plant community as described below.
- BarleyExpress captures MIAME-compliant experiment annotation information required for unambiguous interpretation of microarray experiment results. In BarleyExpress, the MIAME guidelines were customized for Barley and other cereal crops when appropriate plant-based definitions did not exist. For example, some requirements that are specific for mammals were not considered when designing BarleyBase, but descriptions relating to plants were added instead such as ‘pathogen isolates’ as an experimental factor. The help files were also changed to reflect plant terminology.
- The goal of the Plant Ontology is to produce structured controlled vocabularies to describe plant features, such as phenotypes, traits, developmental stages and anatomical parts (The Plant OntologyTM Consortium, 2002). A structured ontology enables accurate queries and comparative analysis across different databases. BarleyExpress uses the Growth Stage Ontology and Plant Anatomy Ontology for barley (from Gramene) and Arabidopsis thaliana (from TAIR), respectively. These terms are stored in the fields, ‘growth stage’ and ‘organism part’ for each hybridization. Users may also upload pictures of the biomaterial used in the experiments from the ‘Sample preparation’ page. This visual information aids in interpreting experimental results.
- Information on experimental factors and factor levels is explicitly required by BarleyExpress. This is not required in the MIAME standards, but it is essential for effective organization of the microarray experiment results. Currently, BarleyExpress assumes that a factorial design will be used (Trochim, 2000). Users specify the experimental factors and factor levels and then the entire experiment design is laid out in a factorial tabular format. Each treatment is the combination of different experimental factors and factor levels. Unused combinations can be deleted.
- Secure and flexible account and data access management allows data owners to protect their data before publication and enable dispersed collaboration. It also allows reviewers to anonymously access datasets referenced by a manuscript to verify the conclusions. The submitter can specify the accessibility to data of an experiment as public, private or group accessible. Registered users can create their own groups, add selected users to the groups for data access and analysis.
Implementation and usage
BarleyExpress is a step-by-step submission wizard that leads users through the process. After all experimental information is input and reviewed, user finalizes the submission. The BarleyBase curator processes the submitted data and makes them available for online access. A unique accession number is assigned to the experiment after curation.
The submission process has three parts: experiment information, data upload, and hybridization or sample information. The first part inputs general experiment information and specifies the experimental factors and factor levels. Annotations for the ‘Experiment’ package of MIAME standards are recorded and enhanced with experiment factorial design information. Users can control the order of experimental factors, so that the experiment hybridization data will be organized and presented appropriately (Fig. 1).
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Next, users upload raw microarray data through a Java upload applet. Affymetrix CEL, DAT and EXP files are required; CEL and DAT files store raw expression and image data and EXP store information on parameters of the hybridization, washing, staining and scanning protocols.
In the third section, the individual data files are assigned to the hybridizations. Sample preparation information is input for each hybridization. Hybridizations sharing the same sample information are treated as technical replicates of the sample. Experiment protocols can be submitted if the protocols do not exist in BarleyBase yet. Template functions help to avoid repetition in data entry. For example, experimental samples may only differ slightly in a few fields, such as in experiment factor levels. BarleyExpress lets the user choose a previously submitted entry as a template and copy values of the old entry into a new entry. The user can edit the new entry. Template data entry exists for experiment design, sample preparation and all the five types of protocols submissions. Users may stop at any step of the submission process and resume at a later time.
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DISCUSSION |
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BarleyExpress makes supporting biologist users its main consideration. BarleyExpress enhances the submission process by capturing all applicable MIAME-compliant information and applying factorial experiment design specifications. The use of controlled vocabularies aids in accurate comparisons between experimental conditions. BarleyExpress is under active development and several enhancements, such as adding Plant Ontologies for a wide variety of plant species, are planned.
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Acknowledgments |
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The authors would like to thank our biological collaborators Roger P. Wise and Rico A. Caldo for their efforts in improving the BarleyExpress project. The BarleyBase projected is funded by the USDA-NRIprogram (grant no. 2002-03582) and USDA-CSREES North American Barley Genome Project. BarleyBase is hosted at Iowa State University Virtual Reality Applications Center.
Received on May 13, 2004; revised on August 4, 2004; accepted on August 23, 2004
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