Jan 9, 2008

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

BMC Bioinformatics
Michelle KnowltonStephen C Ekker

Abstract

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. 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...Continue Reading

  • References34
  • Citations10

References

  • References34
  • Citations10

Citations

Mentioned in this Paper

Vertebrates
Embryo
Twitter Messaging
Biochemical Pathway
Genome
Caenorhabditis elegans
Anatomic Structures
Science of Morphology
Candidate Disease Gene
Genetic Screening (Procedure)

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