Zebrafish Information Network - Wiki slovník

ZFIN
Content
Description	Zebrafish Model Organism Database.
Organisms	Zebrafish
Contact
Research center	University of Oregon
Primary citation	Bradford & al. (2011)
Release date	2010
Access
Website	http://zfin.org

The Zebrafish Information Network (ZFIN) is an online biological database of information about the zebrafish (Danio rerio). The zebrafish is a widely used model organism for genetic, genomic, and developmental studies, and ZFIN provides an integrated interface for querying and displaying the large volume of data generated by this research.^[2] To facilitate use of the zebrafish as a model of human biology, ZFIN links these data to corresponding information about other model organisms (e.g., mouse) and to human disease databases.^[3] Abundant links to external sequence databases (e.g., GenBank) and to genome browsers are included. Gene product, gene expression, and phenotype data are annotated with terms from biomedical ontologies. ZFIN is based at the University of Oregon in the United States, with funding provided by the National Institutes of Health (NIH).

a website of community news and announcements, as well as biological resources such as laboratory protocols, a gene nomenclature guide, and anatomy information
a relational database containing biological data that are curated from the scientific literature and that are directly submitted by zebrafish research laboratories (e.g., Thisse high-throughput gene expression analysis^[4]).

Information in ZFIN is tightly linked to the web resources of the Zebrafish International Resource Center (ZIRC), the China Zebrafish Resource Center (CZRC), and so on, which maintain and provide zebrafish-related research resources, materials and services.

ZFIN's relational database interface provides query forms and display pages for the following biological data types:

Genes, markers, and clones
Gene expression
Antibodies
Sequence alignments (BLAST)
Mutants and transgenic lines
Anatomy
Genetic maps

ZFIN also maintains a database of zebrafish-related publications, laboratories, people, and companies.

In addition to its specialized search interfaces, ZFIN provides a Google-like global site search.

ZFIN's community wiki gives zebrafish researchers the ability to share information about laboratory protocols and antibodies.

Notes and references

^ Bradford, Yvonne; Conlin, Tom; Dunn, Nathan; Fashena, David; Frazer, Ken; Howe, Douglas G; Knight, Jonathan; Mani, Prita; Martin, Ryan; Moxon, Sierra A. T.; Paddock, Holly; Pich, Christian; Ramachandran, Sridhar; Ruef, Barbara J; Ruzicka, Leyla; Bauer Schaper, Holle; Schaper, Kevin; Shao, Xiang; Singer, Amy; Sprague, Judy; Sprunger, Brock; Van Slyke, Ceri; Westerfield, Monte (Jan 2011). "ZFIN: enhancements and updates to the Zebrafish Model Organism Database". Nucleic Acids Res. 39 (Database issue). England: D822-9. doi:10.1093/nar/gkq1077. PMC 3013679. PMID 21036866.
^ Sprague et al. (2008). The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Res 36:D768.
^ The Zebrafish Database Project
^ B. Thisse; C. Thisse (2004). "Fast release clones: a high throughput expression analysis". ZFIN Direct Data Submission (Unpublished).

External links

ZFIN The Zebrafish Model Organism Database
Vega Zebrafish Genome Annotation
FishMap : The Zebrafish Community Genomics Browser maintained at the Institute of Genomics and Integrative Biology
Zebrafish GenomeWiki Beta Preview maintained at the Institute of Genomics and Integrative Biology

v t e Bioinformatics
Databases	Sequence databases: GenBank, European Nucleotide Archive, DNA Data Bank of Japan and China National GeneBank Secondary databases: UniProt, database of protein sequences grouping together Swiss-Prot, TrEMBL and Protein Information Resource Other databases: BioNumbers, Protein Data Bank, Ensembl, InterPro, KEGG, and Gene Ontology Specialised genomic databases: BOLD, Saccharomyces Genome Database, FlyBase, VectorBase, WormBase, Rat Genome Database, PHI-base, Arabidopsis Information Resource, GISAID and Zebrafish Information Network
Software	BLAST Bowtie Clustal EMBOSS HMMER MUSCLE PANGOLIN SAMtools SOAP suite TopHat
Other	Server: ExPASy Rosalind (education platform)
Institutions	Broad Institute Computational Biology Department (CBD) Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI) Database Center for Life Science (DBCLS) DNA Data Bank of Japan (DDBJ) European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory (EMBL) Flatiron Institute J. Craig Venter Institute (JCVI) Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) US National Center for Biotechnology Information (NCBI) Japanese Institute of Genetics Netherlands Bioinformatics Centre (NBIC) Philippine Genome Center (PGC) Scripps Research Swiss Institute of Bioinformatics (SIB) Wellcome Sanger Institute Whitehead Institute
Organizations	African Society for Bioinformatics and Computational Biology (ASBCB) Australia Bioinformatics Resource (EMBL-AR) European Molecular Biology network (EMBnet) International Nucleotide Sequence Database Collaboration (INSDC) International Society for Biocuration (ISB) International Society for Computational Biology (ISCB) Student Council (ISCB-SC) Institute of Genomics and Integrative Biology (CSIR-IGIB) Japanese Society for Bioinformatics (JSBi)
Meetings	Basel Computational Biology Conference‎ () European Conference on Computational Biology (ECCB) Intelligent Systems for Molecular Biology (ISMB) International Conference on Bioinformatics (InCoB) International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB) ISCB Africa ASBCB Conference on Bioinformatics Pacific Symposium on Biocomputing (PSB) Research in Computational Molecular Biology (RECOMB)
File formats	CRAM format FASTA format FASTQ format NeXML format Nexus format Pileup format SAM format Stockholm format VCF format GFF format GTF format
Related topics	Computational biology List of biobanks List of biological databases Molecular phylogenetics Sequencing Sequence database Sequence alignment
Category Commons

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Notes and references

External links

See also