PUBLICATION

ZFIN, the Zebrafish Model Organism Database: Updates and new directions

Authors
Ruzicka, L., Bradford, Y.M., Frazer, K., Howe, D.G., Paddock, H., Ramachandran, S., Singer, A., Toro, S., Van Slyke, C.E., Eagle, A.E., Fashena, D., Kalita, P., Knight, J., Mani, P., Martin, R., Moxon, S.A., Pich, C., Schaper, K., Shao, X., Westerfield, M.
ID
ZDB-PUB-150623-6
Date
2015
Source
Genesis (New York, N.Y. : 2000)   53(8): 498-509 (Other)
Registered Authors
Bradford, Yvonne, Eagle, Anne, Fashena, David, Frazer, K., Howe, Doug, Kalita, Patrick, Knight, Jonathan, Mani, Prita, Martin, Ryan, Moxon, Sierra (fka Taylor), Paddock, Holly, Pich, Christian, Ramachandran, Sridhar, Ruzicka, Leyla, Schaper, Kevin, Shao, Xiang, Singer, Amy, Toro, Sabrina, Van Slyke, Ceri E., Westerfield, Monte
Keywords
curation, data mining, human disease models, ontology
MeSH Terms
  • Animals
  • Computational Biology/methods
  • Data Curation/methods
  • Databases, Genetic*
  • Genetic Association Studies
  • Genomics/methods
  • Internet
  • Models, Animal
  • Zebrafish/genetics*
  • Zebrafish Proteins/genetics*
PubMed
26097180 Full text @ Genesis
Abstract
The Zebrafish Model Organism Database (ZFIN; http://zfin.org) is the central resource for genetic and genomic data from zebrafish (Danio rerio) research. ZFIN staff curate detailed information about genes, mutants, genotypes, reporter lines, sequences, constructs, antibodies, knockdown reagents, expression patterns, phenotypes, gene product function, and orthology from publications. Researchers can submit mutant, transgenic, expression, and phenotype data directly to ZFIN and use the ZFIN Community Wiki to share antibody and protocol information. Data can be accessed through topic-specific searches, a new site-wide search, and the data-mining resource ZebrafishMine (http://zebrafishmine.org). Data download and web service options are also available. ZFIN collaborates with major bioinformatics organizations to verify and integrate genomic sequence data, provide nomenclature support, establish reciprocal links and participate in the development of standardized structured vocabularies (ontologies) used for data annotation and searching. ZFIN-curated gene, function, expression, and phenotype data are available for comparative exploration at several multi-species resources. The use of zebrafish as a model for human disease is increasing. ZFIN is supporting this growing area with three major projects: adding easy access to computed orthology data from gene pages, curating details of the gene expression pattern changes in mutant fish, and curating zebrafish models of human diseases. This article is protected by copyright. All rights reserved.
Genes / Markers
Figures
Expression
Phenotype
Mutation and Transgenics
Human Disease / Model Data
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping
Errata and Notes