ZFIN ID: ZDB-PUB-080124-15
A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information
Knowlton, M.N., Li, T., Ren, Y., Bill, B.R., Ellis, L.B., and Ekker, S.C.
Date: 2008
Source: BMC Bioinformatics 9(1): 7 (Journal)
Registered Authors: Bill, Brent, Ekker, Stephen C., Knowlton, Michelle
Keywords: none
MeSH Terms:
  • Animals
  • Antisense Elements (Genetics)*
  • Chromosome Mapping/methods
  • Computational Biology
  • Database Management Systems*
  • Databases, Genetic*
  • Embryo, Nonmammalian
  • Gene Expression
  • Gene Expression Profiling
  • Genomics
  • Internet
  • Oligonucleotides
  • Phenotype
  • Species Specificity
  • User-Computer Interface*
  • Vocabulary, Controlled
  • Zebrafish/embryology
  • Zebrafish/genetics*
PubMed: 18179718 Full text @ BMC Bioinformatics
BACKGROUND: The zebrafish is a powerful model vertebrate amenable to high throughput in vivo genetic analyses. For example, we have used this system for reverse genetic screens using morpholino knockdown, expression-based screening using enhancer trapping and forward genetic screening using transposon insertional mutagenesis. We created a comprehensive database to facilitate the unlocking of the large amount of data generated by these kinds of genetic studies for access around the world. Description The MOrpholino DataBase is a MySQL relational database with an online, PHP interface. Multiple security levels allow differential access to data in raw and finished formats. MODB 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). A fixed-vocabulary defect ontology allows 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 offers users the ability to retrieve morpholino data by sequence of morpholino or target, name of morpholino or target, anatomical structure affected and defect produced. CONCLUSIONS: MODB data can be used for functional genomic analysis of morpholino design to increased efficacy and decreased 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.