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Sprague, J., Clements, D., Conlin, T., Edwards, P., Frazer, K., Schaper, K., Segerdell, E., Song, P., Sprunger, B., Westerfield, M.
The Zebrafish International Resource Center, University of Oregon, Eugene, OR 97403-5274 USA.
Contact judys@cs.uoregon.edu
The Zebrafish Information Network (ZFIN) is a web based community resource that serves as a centralized location for the curation and integration of zebrafish genetic, genomic and developmental data (1). ZFIN is publicly accessible at http://zfin.org. ZFIN provides an integrated representation of mutants, genes, genetic markers, mapping panels, publications and community contact data. Recent enhancements to ZFIN include: 1) an anatomical dictionary that provides a controlled vocabulary of anatomical terms, grouped by developmental stages, that may be used to annotate and query gene expression data; 2) gene expression data; 3) expanded support for genome sequence; 4) gene annotation using the standardized vocabulary of Gene Ontology (GO) terms that can be used to elucidate relationships between gene products in zebrafish and other organisms; 5) collaborations with other databases (NCBI, Sanger Institute and SWISS-PROT) to provide standardization and interconnections based on shared curation.
Anatomical Dictionary ZFIN serves as the focal point for the development and the dissemination of the zebrafish anatomical dictionary. The dictionary organizes anatomical terms, for a series of developmental stages and the adult, in a hierarchical manner. The dictionary provides a standard vocabulary for annotating gene expression and phenotype thus providing a link between these two types of data commonly used to study gene function. The use of standard anatomical nomenclature enables comparisons of data among organisms. Anatomical dictionary terms may be used to query gene expression data found in ZFIN (http://zfin.org/cgi-bin/webdriver?MIval=aa-xpat select.apg). Sequence The zebrafish whole-genome sequencing initiative began in February 2001 by the Sanger Institute. ZFIN and the Sanger Institute collaborate to identify locations of known genes and markers and to identify novel genes. The long term plan is for ZFIN to serve as the repository for this information, integrating annotated sequence with ZFIN genotype, phenotype and gene expression data. To this end, ZFIN has begun to create an infrastructure that will take advantage of the genome sequence information. Curator annotated EMBL records of molecular segments sequenced and submitted by the Sanger Institute are incorporated into ZFIN and linked to other ZFIN objects. Gene Ontology One of ZFIN's major goals is to add information about gene products in a manner that will aid in the elucidation of relationships among genes in zebrafish and between zebrafish and other organisms. To this end, ZFIN has begun automated annotation of gene records with Gene Ontology (GO;http://geneontology.org) terms, a dynamic controlled vocabulary developed by the gene ontology consortium that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing (2)
Funds for the development of the Zebrafish Information Network are provided by the NIH (RR/HD 12546).
1.Sprague, J., Doerry, E., Douglas, S.,
Westerfield, M., and ZFIN GRP, (Conlin, T.,
Clements, D., Edwards, P., Frazer, K.,
Schaper, K., Segerdell, E.) (2001) The
Zebrafish Information Network (ZFIN): a
resource for genetic, genomic and
developmental research. Nucleic Acids Res.
29(1):87-90.
2.The Gene Ontology Consortium (2001)
Creating the Gene Ontology Resource:design
and implementation. Genome Res., 11,
1425-1433.
Category Genomic Databases
Go to the abstract in the NAR 2003 Database Issue.