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Bioinformatics Advance Access originally published online on December 21, 2004
Bioinformatics 2005 21(8):1727-1729; doi:10.1093/bioinformatics/bti231
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Bloader—a batch loader application for MIAMExpress

Christian Schwager * and Jonathon Blake

EMBL Meyerhofstrasse 1, 67117 Heidelberg, Germany

*To whom correspondence should be addressed.


   Abstract
TOP
 Abstract
INTRODUCTION
 FEATURES
 IMPLEMENTATION
 REFERENCES
 

Summary: BLoader is a client server application for annotating and loading large amounts of Microarray data into a local installation of the MIAMExpress database. A set of nested spreadsheets is used to collect the required MIAME annotation. Controlled vocabularies are downloaded from MIAMExpress and ArrayExpress databases to guarantee MIAME compliance.

Availability: The application is available from the author at http://www.ansorge-group.embl.de/bloader

Contact: schwager{at}embl.de

Supplementary information: For more details on BLoader visit the above web page.


   INTRODUCTION
TOP
 Abstract
 INTRODUCTION
FEATURES
 IMPLEMENTATION
 REFERENCES
 
In recent years, many scientific publishers require submission of Microarray data to public repositories (ArrayExpress, EBI; GEO, NCBI; CIBEX, DDBJ) prior to publication. The data can be submitted as MAGE-ML (Spellman et al., 2002) formatted documents or the respective submission tools may be used.

For the ArrayExpress (Brazma et al., 2003) repository the EBI has developed the web based MIAMExpress tool (http://www.ebi.ac.uk/miamexpress/) For each database submission object a web form has to be filled out. This is easy and straightforward for a small set of microarray hybridizations (~10). When larger numbers of hybridizations (dozens or hundreds) are to be submitted, this becomes very time-consuming and error prone.

To overcome this problem, we have developed BLoader to generate the annotation information rapidly and submit the entire set in one batch.


   FEATURES
TOP
 Abstract
 INTRODUCTION
 FEATURES
IMPLEMENTATION
 REFERENCES
 
According to MIAME standards (Brazma et al., 2001), for each Sample, Extract, Labeled Extract and Hybridization annotations have to be submitted. In large datasets (time courses, drug treatments, disease samples, etc.) annotations are very similar between individual samples. Thus a spreadsheet-based tool can help to generate the annotations in a fast and clear way.

BLoader uses a set of nested spreadsheets, which contain a single line for each object. For Samples, Extracts, Labeled Extracts and Hybridizations a specific spreadsheet reflects required annotations for MIAME compliance. Controlled vocabularies as defined by the MGED society are downloaded from MIAMExpress and ArrayExpress databases and may be selected by the users from context specific pop-up selection lists. This guarantees compliance to MIAME recommendations. For example, once a single sample is created it can be easily copy/pasted or replicated. Auto increment functions enable fast generation of annotation data for time courses or dose–response series. Sample pools for Extracts or selection of Labeled Extracts as well as selection of data files for the respective Hybridizations are created with the help of permanent selections lists via drag and drop (Fig. 1). Already linked objects are marked to allow easy, consistent checking. Of course, any field may be edited or copy/pasted from external applications as in any other spreadsheet program.



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  		Fig. 1 A snapshot of the sample annotation page, showing 14 of the 20 sample hybridizations. The selection list shows all existing Labeled Extracts. Those, which are already linked to hybridization, are marked with asterisks (‘*’).

 
The submission can be saved at any time to a local data file. In a similar way the controlled vocabularies may be stored locally (Fig. 2). This allows production of a submission without online access to MIAMExpress database. BLoader submission data files may even be exchanged between different users or different installations of BLoader/MIAMExpress. BLoader data files can also be used as template submissions: commonly used parameters like protocols, organism, sample source, etc. can be generated as generic Bloader data submission files and easily customized for a specific experiment.



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  		Fig. 2 A snapshot of the sample annotation page. Ten samples have been created. Columns with blue headers contain controlled vocabularies. The selection list box offers the available controlled ‘Organism’ vocabulary.

 
Additional sheets allow generation of MIAMExpress users, Experiment information and all protocols required for a MIAMExpress submission.

Finally, data is loaded into a MIAMExpress database. Each object is loaded using a handshake-based protocol. Successfully loaded objects are marked and thus a broken or interrupted submission can be resumed easily.

The submitted data can be reviewed or edited with the standard MIAMExpress web GUI. MAGE-ML is generated using the experiment_mageml.pl script provided with MIAMExpress.


   IMPLEMENTATION
TOP
 Abstract
 INTRODUCTION
 FEATURES
 IMPLEMENTATION
REFERENCES
 
BLoader consists of a Perl/CGI web server, which communicates to the MIAMExpress database on one side and to the BLoader client on the other side. BLoader server requires an installation of the MIAMExpress database, which was installed on Red Hat Linux 9.0 using Apache Web server and MySQL database server.

BLoader client is a MS Windows application and runs on all recent Windows versions (Win95/98se, Millennium, NT, 2000 and XP). It offers the standard touch and feel of the rich Windows GUI.

For more details about BLoader application visit http://www.ansorge-group.embl.de/bloader


   Acknowledgments
 
BLoader application was implemented in the course of the EU funded TEMBLOR/DESPRAD grant.

Received on November 18, 2004; revised on December 15, 2004; accepted on December 15, 2004

   REFERENCES
TOP
 Abstract
 INTRODUCTION
 FEATURES
 IMPLEMENTATION
 REFERENCES
 

    Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., Aach, J., Ansorge, W., Ball, C.A., Causton, H.C., et al. (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat. Genet., 29, 365–371[CrossRef][ISI][Medline].

    Brazma, A., Parkinson, H., Sarkans, U., Shojatalab, M., Vilo, J., Abeygunawardena, N., Holloway, E., Kapushesky, M., Kemmeren, P., Lara, G.G., et al. (2003) ArrayExpress—a public repository for microarray gene expression data at the EBI. Nucleic Acids Res., 31, 68–71[Abstract/Free Full Text].

    Spellman, P.T., Miller, M., Stewart, J., Troup, C., Sarkans, U., Chervitz, S., Bernhart, D., Sherlock, G., Ball, C., Lepage, M., et al. (2002) Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol., 3, research0046.1–0046.9.


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This Article
Right arrow Abstract Freely available
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