The Zebrafish Information Network: the zebrafish model organism database

By Judy Sprague, L. Bayraktaroglu, D. Clements, Tom Conlin, D. Fashena, K. Frazer, Melissa A. Haendel, D. Howe, Prita Mani, S. Ramachandran and 7 more. Nucleic Acids Res., 2005

378 citations recorded by the source corpus.

The Zebrafish Information Network (ZFIN; ) is a web based community resource that implements the curation of zebrafish genetic, genomic and developmental data. ZFIN provides an integrated representation of mutants, genes, genetic markers, mapping panels, publications and community resources such as meeting announcements and contact information. Recent enhancements to ZFIN include (i) comprehensive curation of gene expression data from the literature and from directly submitted data, (ii) increased support and annotation of the genome sequence, (iii) expanded use of ontologies to support curation and query forms, (iv) curation of morpholino data from the literature, and (v) increased versatility of gene pages, with new data types, links and analysis tools.

Subfields: Molecular Biology

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Citations in the corpus

Database resources of the National Center for Biotechnology Information (2006, methodology): “HomoloGene reports include homology and phenotype information drawn from Online Mendelian Inheritance in Man (30), Mouse Genome Informatics (31), Zebrafish Information Network (32), Saccharomyces Genome Database (33) and FlyBase (34).”
The zebrafish (Danio rerio) as a model organism, with emphasis on applications for finfish aquaculture research (2014, background): “In these websites, it is possible to find the latest versions of genetic, genomic or developmental data of zebrafish resources and continuous updates of mutants, genes or genetic markers are available (Sprague et al. 2006; Bradford et al. 2011).”
Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species (2008, methodology): “Several databases provide species-specific ontologies that describe anatomical features for a species, such as ZFIN [8] for the zebrafish.”
Biomedical ontologies: a functional perspective (2007, background): “Many groups are creating ontologies, from biologists and bench researchers [6–8] to clinical researchers and clinical practitioners [9–12].”
Ensembl 2016 (2015, background): “Eight sources are incorporated for other species including RGD (25), OMIA (26), AnimalQTL (27), ZFIN (28).”
Functional Annotation of the Arabidopsis Genome Using Controlled Vocabularies1 (2004, background): “The GO vocabularies are gaining widespread acceptance within the scientiﬁc community as the standard set of terms to use for functional annotation (Dwight et al., 2002; Camon et al., 2003; Hazbun et al., 2003; Hennig et al., 2003; Kanapin et al., 2003; King et al., 2003; Sprague et al., 2003).”
Database resources of the National Center for Biotechnology Information (2009, background): “HomoloGene reports include homology and phenotype information drawn from OMIM (21), Mouse Genome Informatics (22), Zebrafish Information Network (23), Saccharomyces Genome Database (24), Clusters of Orthologous Groups (COGs) (25) and FlyBase (26).”
Zebrafish: Development of a Vertebrate Model Organism (2018, background): “The Zebrafish Information Network (ZFIN; Sprague, 2006) also contains information about many different aspects of zebrafish including genomic information, gene expression data, available constructs, etc. and can be found at https://zfin.org.”
Database resources of the National Center for Biotechnology Information (2011, methodology): “HomoloGene reports include homology and phenotype information drawn from Online Mendelian Inheritance in Man (OMIM) (26), Mouse Genome Informatics (MGI) (27), Zebrafish Information Network (ZFIN) (28), Saccharomyces Genome Database (SGD) (29), Clusters of Orthologous Groups (COG) (30) and FlyBase (3”
Database resources of the National Center for Biotechnology Information (2014, methodology): “HomoloGene reports include homology and phenotype information drawn from Online Mendelian Inheritance in Man (OMIM) (33), Mouse Genome Informatics (MGI) (34), the Zebrafish Information Network (ZFIN) (35), the Saccharomyces Genome Database (SGD) (36) and FlyBase (37).”
Database resources of the National Center for Biotechnology Information: update (2004, background): “Homolo-Gene reports include homology and phenotype information drawn from Online Mendelian Inheritance in Man (OMIM) (33) , Mouse Genome Informatics (MGI) (34), the Zebrafish Information Network (ZFIN) (35) , the Saccharomyces Genome Database (SGD) (36) and FlyBase (37) .”
Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes (2013, methodology): “Phenotype and disease data from SGD [77], MGI [78], Wormbase [79], Flybase [80], GSEA [20], Zfin [81] were incorporated into our functional networks by summing the cooccurrences of gene pairs in all phenotypes/diseases and normalizing by the size of the phenotype/disease.”