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ZFIN


NAR Molecular Biology Database Collection entry number 101
Howe, Doug; Bradford, Yvonne; Conlin, Tom; Eagle, Anne; Fashena, David; Frazer, Ken; Knight, Jonathan; Mani, Prita; Martin, Ryan; Moxon, Sierra; Paddock, Holly; Pich, Christian; Ramachandran, Sridhar; Ruef, Barbara; Ruzicka, Leyla; Schaper, Kevin; Shao, Xiang; Singer, Amy; Sprunger, Brock; Van Slyke, Ceri; Westerfield, Monte
The Zebrafish Information Network, The University of Oregon, Eugene, OR 97403-5291, USA.

Database Description

ZFIN, the zebrafish model organism database (http://zfin.org), provides a centralized source of curated and integrated zebrafish genomic, genetic and phenotypic data. Searchable interfaces are provided for finding mutant, gene, molecular segment, mapping and expression data.

Recent Developments

Recent enhancements of ZFIN facilitate integrated studies of zebrafish functional genomics. Gene Ontology (GO) annotations are provided to describe gene products and to facilitate comparisons of genes and gene products in different organisms. GO annotations are made through an automated electronic annotation pipeline, as well as during our manual literature curation process. ZFIN has also increased the detail of curation of gene expression data. Incorporation of high-quality annotated images of gene expression submitted by researchers has continued at a high rate. Gene expression curation from the literature now includes images and captions (when permitted), the expressed genes, fish genotype, assay, experimental conditions, developmental stage, and anatomical structures. The zebrafish anatomical ontology continues to be expanded, and is used to support curation and queries at ZFIN. The integration and cross-linking of ZFIN with the genome sequencing effort at Sanger has been expanded, and analysis tools have been added to the gene pages.

Acknowledgements

Funds for the development of the Zebrafish Information Network are provided by the NIH (P41 HG002659).

References

1. Sprague J, Clements D, Conlin T, Edwards P, Frazer K, Schaper K, Segerdell E, Song P, Sprunger B, Westerfield M. The Zebrafish Information Network (ZFIN): the zebrafish model organism database. Nucleic Acids Res. 2003 Jan 1;31(1):241-243.
2.The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D258-D261.


Go to the abstract in the NAR 2008 Database Issue.
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