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

Michelle N Knowlton,Brent R Bill,Tongbin Li,Stephen C Ekker,Lynda Bm Ellis,Yongliang Ren

doi:10.1186/1471-2105-9-7

Abstract

BackgroundThe 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.DescriptionThe 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.ConclusionMODB 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.

Highlights

The zebrafish is a powerful model vertebrate amenable to high throughput in vivo genetic analyses
Given the intent of our database to display the large amount of data generated from our on-going collaborative screens, we have developed of a scalable, centralized yet accessible worldwide, MOrpholino DataBase (MODB) [3] to store and facilitate retrieval of zebrafish morpholino screening results
To utilize the data entered into MODB in a meaningful manner, we developed a variety of search functions

Summary

Conclusion

By offering public access to our schema and the data contained within MODB, we hope to aid in the advancement of functional genetic studies and gene annotation as well as improvements in morpholino analysis and design. To be added as an authorized user, contact the corresponding author M.K. or S.C.E. Morpholinos are readily available for purchase through Gene Tools [34] or Open Biosystems [35]. The authors have no affiliation, financial or otherwise, with either corporate entity. MK designed, tested and managed the database. BB aided in the conception, design and testing of the database. EL and SE aided in the conception and design of the database and coordinated the project as a whole. All authors read and approved the final manuscript

Background

Discussion