BioGRID
Encyclopedia
The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database
of protein
-protein and genetic interactions created in 2003 (originally referred to as simply the General Repository for Interaction Datasets (GRID) by Mike Tyers, Bobby-Joe Breitkreutz, and Chris Stark at the Samuel Lunenfeld Research Institute
at Mount Sinai Hospital
. It strives to provide a comprehensive resource of protein–protein
and genetic
interactions for all major model organism
species
while attempting to remove redundancy to create a single mapping of interactions. Users of The BioGRID can search for their protein
of interest and retrieve annotation, as well as physical and genetic
interaction data as reported, by the primary literature and compiled by in house large-scale curation efforts. The BioGRID is hosted in Toronto
, Ontario
, Canada
and is partnered with the Saccharomyces Genome Database
. The BioGRID is funded by the BBSRC, NIH, and CIHR. BioGRID is a member of the International Molecular Exchange Consortium (IMEx).
specific databases, the newest version now provides a unified front end allowing for searches across several organisms simultaneously.
species. BioGRID currently contains over 335,000 interactions from 17 different species, as derived from both high-throughput studies and conventional focused studies. Through comprehensive curation efforts, BioGRID now includes a virtually complete set of interactions reported to date in the primary literature for budding yeast Saccharomyces cerevisiae
, thale cress Arabidopsis thaliana
and the fission yeast Schizosaccharomyces pombe
. A number of new features have been added to the BioGRID including an improved user interface to display interactions based on different attributes, a mirror site and a dedicated interaction management system to coordinate curation across different locations. The BioGRID provides interaction data with monthly updates to Saccharomyces Genome Database
, Flybase
, GeneDB, TAIR
and Entrez Gene. Source code for the BioGRID and the linked Osprey Network Visualization System is now freely available without restriction.
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 protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
-protein and genetic interactions created in 2003 (originally referred to as simply the General Repository for Interaction Datasets (GRID) by Mike Tyers, Bobby-Joe Breitkreutz, and Chris Stark at the Samuel Lunenfeld Research Institute
Samuel Lunenfeld Research Institute
The Samuel Lunenfeld Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada was established in 1985 by an endowment from the Lunenfeld and Kunin families. It comprises 36 principal investigators, has a budget of C$90 million , has over 200 trainees and approximately 600 staff...
at Mount Sinai Hospital
Mount Sinai Hospital (Toronto)
Mount Sinai Hospital is a hospital in Toronto, Ontario, Canada. Although it is physically linked by bridges and tunnels to two University Health Network hospitals , Mount Sinai is an independently operated facility...
. It strives to provide a comprehensive resource of protein–protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
and genetic
Genetics
Genetics , a discipline of biology, is the science of genes, heredity, and variation in living organisms....
interactions for all major 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...
species
Species
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...
while attempting to remove redundancy to create a single mapping of interactions. Users of The BioGRID can search for their protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
of interest and retrieve annotation, as well as physical and genetic
Genetics
Genetics , a discipline of biology, is the science of genes, heredity, and variation in living organisms....
interaction data as reported, by the primary literature and compiled by in house large-scale curation efforts. The BioGRID is hosted in Toronto
Toronto
Toronto is the provincial capital of Ontario and the largest city in Canada. It is located in Southern Ontario on the northwestern shore of Lake Ontario. A relatively modern city, Toronto's history dates back to the late-18th century, when its land was first purchased by the British monarchy from...
, Ontario
Ontario
Ontario is a province of Canada, located in east-central Canada. It is Canada's most populous province and second largest in total area. It is home to the nation's most populous city, Toronto, and the nation's capital, Ottawa....
, Canada
Canada
Canada is a North American country consisting of ten provinces and three territories. Located in the northern part of the continent, it extends from the Atlantic Ocean in the east to the Pacific Ocean in the west, and northward into the Arctic Ocean...
and is partnered with the Saccharomyces Genome Database
Saccharomyces Genome Database
The Saccharomyces Genome Database is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast....
. The BioGRID is funded by the BBSRC, NIH, and CIHR. BioGRID is a member of the International Molecular Exchange Consortium (IMEx).
History
The BioGRID was originally published and released as simply the General Repository for Interaction Datasets but was later renamed to the BioGRID in order to more concisely describe the project, and help distinguish it from several unrelated projects with a similar name. Originally separated into organismOrganism
In biology, an organism is any contiguous living system . In at least some form, all organisms are capable of response to stimuli, reproduction, growth and development, and maintenance of homoeostasis as a stable whole.An organism may either be unicellular or, as in the case of humans, comprise...
specific databases, the newest version now provides a unified front end allowing for searches across several organisms simultaneously.
Abstract
The Biological General Repository for Interaction Datasets (BioGRID) database (http://www.thebiogrid.org) was developed to house and distribute collections of protein and genetic interactions from major model organismModel 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...
species. BioGRID currently contains over 335,000 interactions from 17 different species, as derived from both high-throughput studies and conventional focused studies. Through comprehensive curation efforts, BioGRID now includes a virtually complete set of interactions reported to date in the primary literature for budding yeast Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae is a species of yeast. It is perhaps the most useful yeast, having been instrumental to baking and brewing since ancient times. It is believed that it was originally isolated from the skin of grapes...
, thale cress Arabidopsis thaliana
Arabidopsis thaliana
Arabidopsis thaliana is a small flowering plant native to Europe, Asia, and northwestern Africa. A spring annual with a relatively short life cycle, arabidopsis is popular as a model organism in plant biology and genetics...
and the fission yeast Schizosaccharomyces pombe
Schizosaccharomyces pombe
Schizosaccharomyces pombe, also called "fission yeast", is a species of yeast. It is used as a model organism in molecular and cell biology. It is a unicellular eukaryote, whose cells are rod-shaped. Cells typically measure 3 to 4 micrometres in diameter and 7 to 14 micrometres in length...
. A number of new features have been added to the BioGRID including an improved user interface to display interactions based on different attributes, a mirror site and a dedicated interaction management system to coordinate curation across different locations. The BioGRID provides interaction data with monthly updates to Saccharomyces Genome Database
Saccharomyces Genome Database
The Saccharomyces Genome Database is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast....
, Flybase
FlyBase
FlyBase is an online bioinformatics database and the primary repository of genetic and molecular data for the insect family Drosophilidae. For the most extensively studied species and model organism, Drosophila melanogaster, a wide range of data are presented in different formats...
, GeneDB, TAIR
Tair
Tair is derived from "altair", the Arabic word for a bird.* Tair Airways* Tair Carn Uchaf* Tair , a Soviet telephoto prime lens series manufactured by Zenit.TAIR may refer to :...
and Entrez Gene. Source code for the BioGRID and the linked Osprey Network Visualization System is now freely available without restriction.
Supported Organisms
The following organisms are currently supported within the BioGRID, but not all may contain interactions in the most recent build:- Arabidopsis thalianaArabidopsis thalianaArabidopsis thaliana is a small flowering plant native to Europe, Asia, and northwestern Africa. A spring annual with a relatively short life cycle, arabidopsis is popular as a model organism in plant biology and genetics...
- Thale Cress - Bacillus subtilisBacillus subtilisBacillus subtilis, known also as the hay bacillus or grass bacillus, is a Gram-positive, catalase-positive bacterium commonly found in soil. A member of the genus Bacillus, B. subtilis is rod-shaped, and has the ability to form a tough, protective endospore, allowing the organism to tolerate...
- Bacillus subtilis - Bos taurus - Cow
- Caenorhabditis elegansCaenorhabditis elegansCaenorhabditis elegans is a free-living, transparent nematode , about 1 mm in length, which lives in temperate soil environments. Research into the molecular and developmental biology of C. elegans was begun in 1974 by Sydney Brenner and it has since been used extensively as a model...
- Nematode Worm - Canis familiaris - Dog
- Danio rerioDanio rerioThe zebrafish, Danio rerio, is a tropical freshwater fish belonging to the minnow family of order Cypriniformes. It is a popular aquarium fish, frequently sold under the trade name zebra danio, and is an important vertebrate model organism in scientific research.-Taxonomy:The zebrafish are...
- Zebrafish - Drosophila melanogasterDrosophila melanogasterDrosophila melanogaster is a species of Diptera, or the order of flies, in the family Drosophilidae. The species is known generally as the common fruit fly or vinegar fly. Starting from Charles W...
- Fruit Fly - Escherichia coliEscherichia coliEscherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms . Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans, and are occasionally responsible for product recalls...
- E. coli - Gallus gallus - Chicken
- Homo sapiens - Human
- Herpesvirus - Herpes Virus
- Macaca mulatta - Rhesus Monkey
- Mus musculus - House Mouse
- Rattus norvegicus - Norway Rat
- Saccharomyces cerevisiaeSaccharomyces cerevisiaeSaccharomyces cerevisiae is a species of yeast. It is perhaps the most useful yeast, having been instrumental to baking and brewing since ancient times. It is believed that it was originally isolated from the skin of grapes...
- Budding Yeast - Schizosaccharomyces pombeSchizosaccharomyces pombeSchizosaccharomyces pombe, also called "fission yeast", is a species of yeast. It is used as a model organism in molecular and cell biology. It is a unicellular eukaryote, whose cells are rod-shaped. Cells typically measure 3 to 4 micrometres in diameter and 7 to 14 micrometres in length...
- Fission Yeast - Xenopus laevis - African Clawed Frog