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

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.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.Advances in scientific technology and the availability of genomic sequence for an increasing number of species have led to a paradigm shift from identifying sequence to gene product function. Large functional genetic screens are becoming increasingly prevalent and require a new way of thinking about data to facilitate cross-species comparison and deciphering gene product function in different organisms. Zebrafish are particularly amenable to large screens as they have a tremendous ability to reproduce, and their embryos finish the development of most organ rudiments by 2 days post-fertilization [1]. Their semi-transparent embryos and the ready availability of transgenic lines facilitate functional annotation of th