Zebrafish Information Network
Encyclopedia
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. 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. 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).
guide, and anatomy information; and (2) 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). Information in ZFIN is tightly linked to the web resources of the Zebrafish International Resource Center (ZIRC), which maintains and provides research resources and materials.
ZFIN's relational database interface provides query forms and display pages for the following biological data types:
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.
Biological database
Biological databases are libraries of life sciences information, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analyses. They contain information from research areas including genomics, proteomics, metabolomics, microarray...
of information about the zebrafish (Danio rerio). The zebrafish is a widely used model organism
Model organism
A model organism is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the organism model will provide insight into the workings of other organisms. Model organisms are in vivo models and are widely used to...
for genetic
Genetics
Genetics , a discipline of biology, is the science of genes, heredity, and variation in living organisms....
, genomic
Genomics
Genomics is a discipline in genetics concerning the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis,...
, and developmental
Developmental biology
Developmental biology is the study of the process by which organisms grow and develop. Modern developmental biology studies the genetic control of cell growth, differentiation and "morphogenesis", which is the process that gives rise to tissues, organs and anatomy.- Related fields of study...
studies, and ZFIN provides an integrated interface for querying and displaying the large volume of data generated by this research. To facilitate use of the zebrafish as a model of human
Human
Humans are the only living species in the Homo genus...
biology, ZFIN links these data to corresponding information about other model organisms (e.g., mouse) and to human disease databases. Abundant links to external sequence
DNA sequence
The sequence or primary structure of a nucleic acid is the composition of atoms that make up the nucleic acid and the chemical bonds that bond those atoms. Because nucleic acids, such as DNA and RNA, are unbranched polymers, this specification is equivalent to specifying the sequence of...
databases (e.g., GenBank
GenBank
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. This database is produced and maintained by the National Center for Biotechnology Information as part of the International Nucleotide Sequence...
) and to genome browsers are included. Gene product, gene expression, and phenotype data are annotated with terms from biomedical ontologies
Ontology (computer science)
In computer science and information science, an ontology formally represents knowledge as a set of concepts within a domain, and the relationships between those concepts. It can be used to reason about the entities within that domain and may be used to describe the domain.In theory, an ontology is...
. ZFIN is based at the University of Oregon
University of Oregon
-Colleges and schools:The University of Oregon is organized into eight schools and colleges—six professional schools and colleges, an Arts and Sciences College and an Honors College.- School of Architecture and Allied Arts :...
in the United States, with funding provided by the National Institutes of Health
National Institutes of Health
The National Institutes of Health are an agency of the United States Department of Health and Human Services and are the primary agency of the United States government responsible for biomedical and health-related research. Its science and engineering counterpart is the National Science Foundation...
(NIH).
Contents
ZFIN consists of two principal parts: (1) a website of community news and announcements, as well as biological resources such as laboratory protocols, a gene nomenclatureGene nomenclature
Gene nomenclature is the scientific naming of genes, the units of heredity in living organisms. An international committee published recommendations for genetic symbols and nomenclature in 1957. The need to develop formal guidelines for human gene names and symbols was recognized in the 1960s and...
guide, and anatomy information; and (2) a relational database
Relational database
A relational database is a database that conforms to relational model theory. The software used in a relational database is called a relational database management system . Colloquial use of the term "relational database" may refer to the RDBMS software, or the relational database itself...
containing biological data that are curated
Biocurator
A biocurator is a professional scientist who collects, annotates, and validates information that is disseminated by biological and model organism databases...
from the scientific literature and that are directly submitted by zebrafish research laboratories (e.g., Thisse high-throughput gene expression analysis). Information in ZFIN is tightly linked to the web resources of the Zebrafish International Resource Center (ZIRC), which maintains and provides research resources and materials.
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 (BLASTBLASTIn bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
) - 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
Google
Google Inc. is an American multinational public corporation invested in Internet search, cloud computing, and advertising technologies. Google hosts and develops a number of Internet-based services and products, and generates profit primarily from advertising through its AdWords program...
-like global site search.
ZFIN's community wiki
Wiki
A wiki is a website that allows the creation and editing of any number of interlinked web pages via a web browser using a simplified markup language or a WYSIWYG text editor. Wikis are typically powered by wiki software and are often used collaboratively by multiple users. Examples include...
gives zebrafish researchers the ability to share information about laboratory protocols and antibodies.
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 BiologyInstitute of Genomics and Integrative BiologyInstitute of Genomics and Integrative Biology is a scientific research institute devoted primarily to integrated biological research. It is a part of Council of Scientific and Industrial Research , India....