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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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A typical published figure with curated phenotype annotations. ‘Whole organism’, ‘shield’, ‘germ ring’, ‘notochord’ and ‘somite’ are entities derived from the zebrafish AO. ‘Gastrulation’ and ‘embryonic morphogenesis’ are entities derived from the GO. ‘Increased thickness’, ‘decreased length’, ‘malformed’, ‘fused with’, ‘arrested’, ‘disrupted’ and ‘abnormal’ are PATO qualities. Links are provided to the genotype page, stage description, anatomy term pages, GO details page and the full text of the publication. Figure reproduced from Reim and Brand (11).
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Figure 3: A typical published figure with curated phenotype annotations. ‘Whole organism’, ‘shield’, ‘germ ring’, ‘notochord’ and ‘somite’ are entities derived from the zebrafish AO. ‘Gastrulation’ and ‘embryonic morphogenesis’ are entities derived from the GO. ‘Increased thickness’, ‘decreased length’, ‘malformed’, ‘fused with’, ‘arrested’, ‘disrupted’ and ‘abnormal’ are PATO qualities. Links are provided to the genotype page, stage description, anatomy term pages, GO details page and the full text of the publication. Figure reproduced from Reim and Brand (11).

Mentions: Phenotypes are tightly integrated into many parts of ZFIN and can be found on gene, genotype and anatomy pages. Comparisons of curated phenotypes at ZFIN are supported through the specification of ‘affected anatomy’ on the Mutants/Transgenics query form (http://zfin.org/cgi-bin/webdriver?MIval=aa-fishselect.apg&line_type=mutant). Phenotype annotations are associated with individual published figures and displayed on phenotype figure pages (Figure 3). Images and figure captions are included when consistent with journal copyright permissions. Ultimately, the use of PATO and other ontologies will provide a means for more complex queries at ZFIN and for comparisons with other organisms, specifically for the determination of animal models of human disease.Figure 3.


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)

A typical published figure with curated phenotype annotations. ‘Whole organism’, ‘shield’, ‘germ ring’, ‘notochord’ and ‘somite’ are entities derived from the zebrafish AO. ‘Gastrulation’ and ‘embryonic morphogenesis’ are entities derived from the GO. ‘Increased thickness’, ‘decreased length’, ‘malformed’, ‘fused with’, ‘arrested’, ‘disrupted’ and ‘abnormal’ are PATO qualities. Links are provided to the genotype page, stage description, anatomy term pages, GO details page and the full text of the publication. Figure reproduced from Reim and Brand (11).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 3: A typical published figure with curated phenotype annotations. ‘Whole organism’, ‘shield’, ‘germ ring’, ‘notochord’ and ‘somite’ are entities derived from the zebrafish AO. ‘Gastrulation’ and ‘embryonic morphogenesis’ are entities derived from the GO. ‘Increased thickness’, ‘decreased length’, ‘malformed’, ‘fused with’, ‘arrested’, ‘disrupted’ and ‘abnormal’ are PATO qualities. Links are provided to the genotype page, stage description, anatomy term pages, GO details page and the full text of the publication. Figure reproduced from Reim and Brand (11).
Mentions: Phenotypes are tightly integrated into many parts of ZFIN and can be found on gene, genotype and anatomy pages. Comparisons of curated phenotypes at ZFIN are supported through the specification of ‘affected anatomy’ on the Mutants/Transgenics query form (http://zfin.org/cgi-bin/webdriver?MIval=aa-fishselect.apg&line_type=mutant). Phenotype annotations are associated with individual published figures and displayed on phenotype figure pages (Figure 3). Images and figure captions are included when consistent with journal copyright permissions. Ultimately, the use of PATO and other ontologies will provide a means for more complex queries at ZFIN and for comparisons with other organisms, specifically for the determination of animal models of human disease.Figure 3.

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