ZFIN is a curated resource for zebrafish biology comprised of the following primary data types: genes, phenotypes, genotypes, gene expression, functional and phenotypic annotations, anatomical structures, orthology, nucleotide and protein sequence associations and reagents such as morpholinos and antibodies. lists ZFIN data contents as of July 2010. A tabular presentation of ZFIN’s growth over the years can be accessed from the database (http://zfin.org/zf_info/zfin_stats.html
). ZFIN data can be accessed using any of the data-type specific search forms, site search, BLAST, or GBrowse. A comprehensive suite of download files provide a means of accessing large quantities of data for further analysis. Special requests for data reports can be requested from firstname.lastname@example.org.
Summary of ZFIN data content (July 2010)
ZFIN participates in regularly scheduled data exchanges, ranging from daily to monthly, with major bioinformatics organizations, such as the Welcome Trust Sanger Institute, Ensembl, NCBI and UniProt resulting in reciprocal links that provide valuable cross-site data integration. These exchanges enhance data accuracy and consistency because curators work continuously to resolve identified discrepancies. In addition, we provide links to many community resources on our home page.
ZFIN’s curation process utilizes bioinformatics community-supported best practices to ensure data are described accurately and consistently. One such practice is the use of standardized nomenclature. ZFIN, in conjunction with the Zebrafish Nomenclature Committee, serves as the authoritative source of gene and allele nomenclature. Standardized nomenclature is essential to unambiguous communication. Zebrafish nomenclature guidelines are coordinated with guidelines used for human and mouse genes. Similarly, standardization of functional and phenotypic gene annotations promotes robust searching and comparisons within and among species. ZFIN’s annotations are based on the structured vocabularies and relationships defined by biological ontologies. These ontologies are evolving resources that require community input to ensure completeness and accuracy. ZFIN collaborates with the bioinformatics community on the development of several ontologies including Gene Ontology [GO; (1
)], Cell Ontology [CL; (2
)] and Phenotype Quality Ontology [PATO; (3
)]. ZFIN also develops and maintains the Zebrafish Anatomical Ontology [ZFA; (4
)]. ZFIN is the authoritative source for zebrafish GO annotations. Standardized evidence codes are used to support GO and orthology annotations. All data are attributed to their original sources.
ZFIN encourages comments and suggestions from the community. A ‘Your Input Welcome’ button is provided on every ZFIN data page to facilitate communication. ZFIN curators address incoming questions and data submissions. Requests for new features and enhancements, combined with annual user surveys results, play a key role in determining future directions.