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The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes.

Sprague J, Bayraktaroglu L, Bradford Y, Conlin T, Dunn N, Fashena D, Frazer K, Haendel M, Howe DG, Knight J, Mani P, Moxon SA, Pich C, Ramachandran S, Schaper K, Segerdell E, Shao X, Singer A, Song P, Sprunger B, Van Slyke CE, Westerfield M - Nucleic Acids Res. (2007)

Bottom Line: ZFIN is the definitive source for zebrafish gene and allele nomenclature, the zebrafish anatomical ontology (AO) and for zebrafish gene ontology (GO) annotations.ZFIN plays an active role in the development of cross-species ontologies such as the phenotypic quality ontology (PATO) and the gene ontology (GO).Recent enhancements to ZFIN include (i) a new home page and navigation bar, (ii) expanded support for genotypes and phenotypes, (iii) comprehensive phenotype annotations based on anatomical, phenotypic quality and gene ontologies, (iv) a BLAST server tightly integrated with the ZFIN database via ZFIN-specific datasets, (v) a global site search and (vi) help with hands-on resources.

View Article: PubMed Central - PubMed

Affiliation: The Zebrafish Information Network, 5291 University of Oregon, Eugene, OR 97403-5291, USA. judys@cs.uoregon.edu

ABSTRACT
The Zebrafish Information Network (ZFIN, http://zfin.org), the model organism database for zebrafish, provides the central location for curated zebrafish genetic, genomic and developmental data. Extensive data integration of mutant phenotypes, genes, expression patterns, sequences, genetic markers, morpholinos, map positions, publications and community resources facilitates the use of the zebrafish as a model for studying gene function, development, behavior and disease. Access to ZFIN data is provided via web-based query forms and through bulk data files. ZFIN is the definitive source for zebrafish gene and allele nomenclature, the zebrafish anatomical ontology (AO) and for zebrafish gene ontology (GO) annotations. ZFIN plays an active role in the development of cross-species ontologies such as the phenotypic quality ontology (PATO) and the gene ontology (GO). Recent enhancements to ZFIN include (i) a new home page and navigation bar, (ii) expanded support for genotypes and phenotypes, (iii) comprehensive phenotype annotations based on anatomical, phenotypic quality and gene ontologies, (iv) a BLAST server tightly integrated with the ZFIN database via ZFIN-specific datasets, (v) a global site search and (vi) help with hands-on resources.

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The genotype page summarizes genotype specific data for mibta52b/ta52b and provides extensive cross-linking to all mibta52b/ta52b data in ZFIN.
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Figure 1: The genotype page summarizes genotype specific data for mibta52b/ta52b and provides extensive cross-linking to all mibta52b/ta52b data in ZFIN.

Mentions: This new page is the hub for genotype-specific data for the more than 5000 genotypes described in ZFIN (Figure 1). Genetic background, parental genotypes, affected genes and current sources for fish with this genotype are listed. Links to all phenotype and gene expression data associated with the genotype are included. A ‘Genotype Details’ section lists affected genes, zygosity, parental zygosity, mutation type, mutagen protocol, lab of origin and mapping information for each allele. Links to construct pages are provided for transgenic genotypes. Mutant/Transgenics query results, phenotype and gene expression details pages and gene pages link to the genotype page.Figure 1.


The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes.

Sprague J, Bayraktaroglu L, Bradford Y, Conlin T, Dunn N, Fashena D, Frazer K, Haendel M, Howe DG, Knight J, Mani P, Moxon SA, Pich C, Ramachandran S, Schaper K, Segerdell E, Shao X, Singer A, Song P, Sprunger B, Van Slyke CE, Westerfield M - Nucleic Acids Res. (2007)

The genotype page summarizes genotype specific data for mibta52b/ta52b and provides extensive cross-linking to all mibta52b/ta52b data in ZFIN.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238839&req=5

Figure 1: The genotype page summarizes genotype specific data for mibta52b/ta52b and provides extensive cross-linking to all mibta52b/ta52b data in ZFIN.
Mentions: This new page is the hub for genotype-specific data for the more than 5000 genotypes described in ZFIN (Figure 1). Genetic background, parental genotypes, affected genes and current sources for fish with this genotype are listed. Links to all phenotype and gene expression data associated with the genotype are included. A ‘Genotype Details’ section lists affected genes, zygosity, parental zygosity, mutation type, mutagen protocol, lab of origin and mapping information for each allele. Links to construct pages are provided for transgenic genotypes. Mutant/Transgenics query results, phenotype and gene expression details pages and gene pages link to the genotype page.Figure 1.

Bottom Line: ZFIN is the definitive source for zebrafish gene and allele nomenclature, the zebrafish anatomical ontology (AO) and for zebrafish gene ontology (GO) annotations.ZFIN plays an active role in the development of cross-species ontologies such as the phenotypic quality ontology (PATO) and the gene ontology (GO).Recent enhancements to ZFIN include (i) a new home page and navigation bar, (ii) expanded support for genotypes and phenotypes, (iii) comprehensive phenotype annotations based on anatomical, phenotypic quality and gene ontologies, (iv) a BLAST server tightly integrated with the ZFIN database via ZFIN-specific datasets, (v) a global site search and (vi) help with hands-on resources.

View Article: PubMed Central - PubMed

Affiliation: The Zebrafish Information Network, 5291 University of Oregon, Eugene, OR 97403-5291, USA. judys@cs.uoregon.edu

ABSTRACT
The Zebrafish Information Network (ZFIN, http://zfin.org), the model organism database for zebrafish, provides the central location for curated zebrafish genetic, genomic and developmental data. Extensive data integration of mutant phenotypes, genes, expression patterns, sequences, genetic markers, morpholinos, map positions, publications and community resources facilitates the use of the zebrafish as a model for studying gene function, development, behavior and disease. Access to ZFIN data is provided via web-based query forms and through bulk data files. ZFIN is the definitive source for zebrafish gene and allele nomenclature, the zebrafish anatomical ontology (AO) and for zebrafish gene ontology (GO) annotations. ZFIN plays an active role in the development of cross-species ontologies such as the phenotypic quality ontology (PATO) and the gene ontology (GO). Recent enhancements to ZFIN include (i) a new home page and navigation bar, (ii) expanded support for genotypes and phenotypes, (iii) comprehensive phenotype annotations based on anatomical, phenotypic quality and gene ontologies, (iv) a BLAST server tightly integrated with the ZFIN database via ZFIN-specific datasets, (v) a global site search and (vi) help with hands-on resources.

Show MeSH