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Open Access Highly Accessed Database

A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information

Michelle N Knowlton16*, Tongbin Li2, Yongliang Ren2, Brent R Bill1, Lynda BM Ellis34 and Stephen C Ekker145

Author Affiliations

1 Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA

2 Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA

3 Department of Laboratory Medicine and Pathology, University of Minneapolis, Minneapolis, MN 55455, USA

4 University of Minnesota Arnold and Mabel Beckman Center for Transposon Research, Minneapolis, MN 55455, USA

5 Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA

6 Box 45, The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA

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BMC Bioinformatics 2008, 9:7  doi:10.1186/1471-2105-9-7

Published: 7 January 2008

Abstract

Background

The zebrafish is a powerful model vertebrate amenable to high throughput in vivo genetic analyses. Examples include reverse genetic screens using morpholino knockdown, expression-based screening using enhancer trapping and forward genetic screening using transposon insertional mutagenesis. We have created a database to facilitate web-based distribution of data from such genetic studies.

Description

The MOrpholino DataBase is a MySQL relational database with an online, PHP interface. Multiple quality control levels allow differential access to data in raw and finished formats. MODBv1 includes sequence information relating to almost 800 morpholinos and their targets and phenotypic data regarding the dose effect of each morpholino (mortality, toxicity and defects). To improve the searchability of this database, we have incorporated a fixed-vocabulary defect ontology that allows for the organization of morpholino affects based on anatomical structure affected and defect produced. This also allows comparison between species utilizing Phenotypic Attribute Trait Ontology (PATO) designated terminology. MODB is also cross-linked with ZFIN, allowing full searches between the two databases. MODB offers users the ability to retrieve morpholino data by sequence of morpholino or target, name of target, anatomical structure affected and defect produced.

Conclusion

MODB data can be used for functional genomic analysis of morpholino design to maximize efficacy and minimize toxicity. MODB also serves as a template for future sequence-based functional genetic screen databases, and it is currently being used as a model for the creation of a mutagenic insertional transposon database.