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Hub AI
Gene Ontology AI simulator
(@Gene Ontology_simulator)
Hub AI
Gene Ontology AI simulator
(@Gene Ontology_simulator)
Gene Ontology
The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and gene product attributes; 2) annotate genes and gene products, and assimilate and disseminate annotation data; and 3) provide tools for easy access to all aspects of the data provided by the project, and to enable functional interpretation of experimental data using the GO, for example via enrichment analysis. GO is part of a larger classification effort, the Open Biomedical Ontologies, being one of the Initial Candidate Members of the OBO Foundry.
Whereas gene nomenclature focuses on gene and gene products, the Gene Ontology focuses on the function of the genes and gene products. The GO also extends the effort by using a markup language to make the data (not only of the genes and their products but also of curated attributes) machine readable, and to do so in a way that is unified across all species (whereas gene nomenclature conventions vary by biological taxon).
The Gene Ontology was originally constructed in 1998 by a consortium of researchers studying the genomes of three model organisms: Drosophila melanogaster (fruit fly), Mus musculus (mouse), and Saccharomyces cerevisiae (brewer's or baker's yeast). Many other Model Organism Databases have joined the Gene Ontology Consortium, contributing not only to annotation data, but also to the development of ontologies and tools to view and apply the data. Many major plant, animal, and microorganism databases make a contribution towards this project. As of July 2019, the GO contains 44,945 terms; there are 6,408,283 annotations to 4,467 different biological organisms. There is a significant body of literature on the development and use of the GO, and it has become a standard tool in the bioinformatics arsenal. Their objectives have three aspects: building gene ontology, assigning ontology to gene/gene products, and developing software and databases for the first two objects.
Several analyses of the Gene Ontology using formal, domain-independent properties of classes (the metaproperties) are also starting to appear. For instance, there is now an ontological analysis of biological ontologies.
From a practical view, an ontology is a representation of something we know about. "Ontologies" consist of representations of things that are detectable or directly observable and the relationships between those things. There is no universal standard terminology in biology and related domains, and term usage may be specific to a species, research area, or even a particular research group. This makes communication and sharing of data more difficult. The Gene Ontology project provides an ontology of defined terms representing gene product properties. The ontology covers three domains:
Each GO term within the ontology has a term name, which may be a word or string of words; a unique alphanumeric identifier; a definition with cited sources; and an ontology indicating the domain to which it belongs. Terms may also have synonyms, which are classed as being exactly equivalent to the term name, broader, narrower, or related; references to equivalent concepts in other databases; and comments on term meaning or usage. The GO is structured as a directed acyclic graph, and each term has defined relationships to one or more other terms in the same domain, and sometimes to other domains. The GO vocabulary is designed to be species-neutral and includes terms applicable to prokaryotes and eukaryotes, single and multicellular organisms.
GO is not static, and additions, corrections, and alterations are suggested by and solicited from members of the research and annotation communities, as well as by those directly involved in the GO project. For example, an annotator may request a specific term to represent a metabolic pathway, or a section of the ontology may be revised with the help of community experts (e.g.). Suggested edits are reviewed by the ontology editors, and implemented where appropriate.
The GO and annotation files are freely available from the GO website in a number of formats or can be accessed online using the GO browser AmiGO. The Gene Ontology project also provides downloadable mappings of its terms to other classification systems.
Gene Ontology
The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and gene product attributes; 2) annotate genes and gene products, and assimilate and disseminate annotation data; and 3) provide tools for easy access to all aspects of the data provided by the project, and to enable functional interpretation of experimental data using the GO, for example via enrichment analysis. GO is part of a larger classification effort, the Open Biomedical Ontologies, being one of the Initial Candidate Members of the OBO Foundry.
Whereas gene nomenclature focuses on gene and gene products, the Gene Ontology focuses on the function of the genes and gene products. The GO also extends the effort by using a markup language to make the data (not only of the genes and their products but also of curated attributes) machine readable, and to do so in a way that is unified across all species (whereas gene nomenclature conventions vary by biological taxon).
The Gene Ontology was originally constructed in 1998 by a consortium of researchers studying the genomes of three model organisms: Drosophila melanogaster (fruit fly), Mus musculus (mouse), and Saccharomyces cerevisiae (brewer's or baker's yeast). Many other Model Organism Databases have joined the Gene Ontology Consortium, contributing not only to annotation data, but also to the development of ontologies and tools to view and apply the data. Many major plant, animal, and microorganism databases make a contribution towards this project. As of July 2019, the GO contains 44,945 terms; there are 6,408,283 annotations to 4,467 different biological organisms. There is a significant body of literature on the development and use of the GO, and it has become a standard tool in the bioinformatics arsenal. Their objectives have three aspects: building gene ontology, assigning ontology to gene/gene products, and developing software and databases for the first two objects.
Several analyses of the Gene Ontology using formal, domain-independent properties of classes (the metaproperties) are also starting to appear. For instance, there is now an ontological analysis of biological ontologies.
From a practical view, an ontology is a representation of something we know about. "Ontologies" consist of representations of things that are detectable or directly observable and the relationships between those things. There is no universal standard terminology in biology and related domains, and term usage may be specific to a species, research area, or even a particular research group. This makes communication and sharing of data more difficult. The Gene Ontology project provides an ontology of defined terms representing gene product properties. The ontology covers three domains:
Each GO term within the ontology has a term name, which may be a word or string of words; a unique alphanumeric identifier; a definition with cited sources; and an ontology indicating the domain to which it belongs. Terms may also have synonyms, which are classed as being exactly equivalent to the term name, broader, narrower, or related; references to equivalent concepts in other databases; and comments on term meaning or usage. The GO is structured as a directed acyclic graph, and each term has defined relationships to one or more other terms in the same domain, and sometimes to other domains. The GO vocabulary is designed to be species-neutral and includes terms applicable to prokaryotes and eukaryotes, single and multicellular organisms.
GO is not static, and additions, corrections, and alterations are suggested by and solicited from members of the research and annotation communities, as well as by those directly involved in the GO project. For example, an annotator may request a specific term to represent a metabolic pathway, or a section of the ontology may be revised with the help of community experts (e.g.). Suggested edits are reviewed by the ontology editors, and implemented where appropriate.
The GO and annotation files are freely available from the GO website in a number of formats or can be accessed online using the GO browser AmiGO. The Gene Ontology project also provides downloadable mappings of its terms to other classification systems.