Gene Ontology - AbsoluteAstronomy.com

The Gene Ontology, or GO, is a major bioinformatics

Bioinformatics

Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...

initiative to unify the representation of gene

Gene

A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...

and gene product

Gene product

A gene product is the biochemical material, either RNA or protein, resulting from expression of a gene. A measurement of the amount of gene product is sometimes used to infer how active a gene is. Abnormal amounts of gene product can be correlated with disease-causing alleles, such as the...

attributes across all 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...

. More specifically, the project aims to:

Maintain and develop its controlled vocabulary
Controlled vocabulary
Controlled vocabularies provide a way to organize knowledge for subsequent retrieval. They are used in subject indexing schemes, subject headings, thesauri, taxonomies and other form of knowledge organization systems...

of gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...

and gene product
Gene product
A gene product is the biochemical material, either RNA or protein, resulting from expression of a gene. A measurement of the amount of gene product is sometimes used to infer how active a gene is. Abnormal amounts of gene product can be correlated with disease-causing alleles, such as the...

attributes;
Annotate gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...

s and gene product
Gene product
A gene product is the biochemical material, either RNA or protein, resulting from expression of a gene. A measurement of the amount of gene product is sometimes used to infer how active a gene is. Abnormal amounts of gene product can be correlated with disease-causing alleles, such as the...

s, and assimilate and disseminate annotation data;
Provide tools for easy access to all aspects of the data provided by the project.

The GO is part of a larger classification effort, the Open Biomedical Ontologies

Open Biomedical Ontologies

Open Biomedical Ontologies is an effort to create controlled vocabularies for shared use across different biological and medical domains. As of 2006, OBO forms part of the resources of the U.S...

(OBO).

GO terms and ontology

There is no universal standard terminology in biology and related domains, and term usages 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

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...

of defined terms representing gene product

Gene product

properties. The ontology covers three domains:

cellular component
Cellular component
Cellular component refers to the unique, highly organized substances and substances of which cells, and thus living organisms, are composed. Examples include membranes, organelles, proteins, and nucleic acids...

, the parts of a cell
Cell (biology)
The cell is the basic structural and functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life. The Alberts text discusses how the "cellular building blocks" move to shape developing embryos....

or its extracellular
Extracellular
In cell biology, molecular biology and related fields, the word extracellular means "outside the cell". This space is usually taken to be outside the plasma membranes, and occupied by fluid...

environment;
molecular function, the elemental activities of a gene product at the molecular level, such as binding or catalysis
Enzyme catalysis
Enzyme catalysis is the catalysis of chemical reactions by specialized proteins known as enzymes. Catalysis of biochemical reactions in the cell is vital due to the very low reaction rates of the uncatalysed reactions....

;
biological process
Biological process
A biological process is a process of a living organism. Biological processes are made up of any number of chemical reactions or other events that results in a transformation....

, operations or sets of molecular events with a defined beginning and end, pertinent to the functioning of integrated living units: cells, tissues
Tissue (biology)
Tissue is a cellular organizational level intermediate between cells and a complete organism. A tissue is an ensemble of cells, not necessarily identical, but from the same origin, that together carry out a specific function. These are called tissues because of their identical functioning...

, organs
Organ (anatomy)
In biology, an organ is a collection of tissues joined in structural unit to serve a common function. Usually there is a main tissue and sporadic tissues . The main tissue is the one that is unique for the specific organ. For example, main tissue in the heart is the myocardium, while sporadic are...

, and organism
Organism
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...

s.

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 a namespace 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 ontology is structured as a directed acyclic graph

Directed acyclic graph

In mathematics and computer science, a directed acyclic graph , is a directed graph with no directed cycles. That is, it is formed by a collection of vertices and directed edges, each edge connecting one vertex to another, such that there is no way to start at some vertex v and follow a sequence of...

, and each term has defined relationships

Relation (mathematics)

In set theory and logic, a relation is a property that assigns truth values to k-tuples of individuals. Typically, the property describes a possible connection between the components of a k-tuple...

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 prokaryote

Prokaryote

The prokaryotes are a group of organisms that lack a cell nucleus , or any other membrane-bound organelles. The organisms that have a cell nucleus are called eukaryotes. Most prokaryotes are unicellular, but a few such as myxobacteria have multicellular stages in their life cycles...

s and eukaryote

Eukaryote

A eukaryote is an organism whose cells contain complex structures enclosed within membranes. Eukaryotes may more formally be referred to as the taxon Eukarya or Eukaryota. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear...

s, single and multicellular organism

Multicellular organism

Multicellular organisms are organisms that consist of more than one cell, in contrast to single-celled organisms. Most life that can be seen with the the naked eye is multicellular, as are all animals and land plants.-Evolutionary history:Multicellularity has evolved independently dozens of times...

s.

The GO ontology 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 ontology file is 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.

Example GO term

id: GO:0000016
name: lactase activity
namespace: molecular_function
def: "Catalysis of the reaction: lactose + H2O = D-glucose + D-galactose." [EC:3.2.1.108]
synonym: "lactase-phlorizin hydrolase activity" BROAD [EC:3.2.1.108]
synonym: "lactose galactohydrolase activity" EXACT [EC:3.2.1.108]
xref: EC:3.2.1.108
xref: MetaCyc:LACTASE-RXN
xref: Reactome:20536
is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds

Data source:

Annotation

Genome annotation is the practice of capturing data about a gene product, and GO annotations use terms from the GO ontology to do so. The members of the GO Consortium submit their annotation for integration and dissemination on the GO website, where they can be downloaded directly or viewed online using AmiGO. In addition to the gene product identifier and the relevant GO term, GO annotations have the following data:

The reference used to make the annotation (e.g. a journal article)
An evidence code denoting the type of evidence upon which the annotation is based
The date and the creator of the annotation

The evidence code comes from the Evidence Code Ontology, a controlled vocabulary

Controlled vocabulary

Controlled vocabularies provide a way to organize knowledge for subsequent retrieval. They are used in subject indexing schemes, subject headings, thesauri, taxonomies and other form of knowledge organization systems...

of codes covering both manual and automated annotation methods. For example, Traceable Author Statement (TAS) means a curator has read a published scientific paper and the metadata for that annotation bears a citation to that paper; Inferred from Sequence Similarity (ISS) means a human curator has reviewed the output from a sequence similarity search and verified that it is biologically meaningful. Annotations from automated processes (for example, remapping annotations created using another annotation vocabulary) are given the code Inferred from Electronic Annotation (IEA). As of April 1st, 2010, over 98% of all GO annotations were inferred computationally, not by curators. As these annotations are not checked by a human, the GO Consortium considers them to be less reliable and includes only a subset in the data available online in AmiGO. Full annotation data sets can be downloaded from the GO website. To support the development of annotation, the GO Consortium provides study camps and mentors to new groups of developers.

Example annotation

Gene product: Actin, alpha cardiac muscle 1, UniProtKB:P68032
GO term: heart contraction ; GO:0060047 (biological process)
Evidence code: Inferred from Mutant Phenotype (IMP)
Reference: PMID 17611253
Assigned by: UniProtKB, June 6, 2008

Data source:

Tools

There are a large number of tools available both online and to download that use the data provided by the GO project. The vast majority of these come from third parties; the GO Consortium develops and supports two tools, AmiGO and OBO-Edit.

AmiGO is a web-based application that allows users to query, browse and visualize ontologies and gene product annotation data. In addition, it also has a BLAST

BLAST

In 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...

tool, tools allowing analysis of larger data sets, and an interface to query the GO database directly..

AmiGO can be used online at the GO website to access the data provided by the GO Consortium, or can be downloaded and installed for local use on any database employing the GO database schema (e.g. ). It is free open source software and is available as part of the go-dev software distribution.

OBO-Edit is an open source, platform-independent ontology editor developed and maintained by the Gene Ontology Consortium. It is implemented in Java

Java (programming language)

Java is a programming language originally developed by James Gosling at Sun Microsystems and released in 1995 as a core component of Sun Microsystems' Java platform. The language derives much of its syntax from C and C++ but has a simpler object model and fewer low-level facilities...

, and uses a graph-oriented

Graph theory

In mathematics and computer science, graph theory is the study of graphs, mathematical structures used to model pairwise relations between objects from a certain collection. A "graph" in this context refers to a collection of vertices or 'nodes' and a collection of edges that connect pairs of...

approach to display and edit ontologies. OBO-Edit includes a comprehensive search and filter interface, with the option to render subsets of terms to make them visually distinct; the user interface can also be customized according to user preferences. OBO-Edit also has a reasoner

Semantic reasoner

A semantic reasoner, reasoning engine, rules engine, or simply a reasoner, is a piece of software able to infer logical consequences from a set of asserted facts or axioms. The notion of a semantic reasoner generalizes that of an inference engine, by providing a richer set of mechanisms to work with...

that can infer links that have not been explicitly stated, based on existing relationships and their properties. Although it was developed for biomedical ontologies, OBO-Edit can be used to view, search and edit any ontology. It is freely available to download.

GO Consortium

The GO Consortium is the set of biological database

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...

s and research groups actively involved in the GO project. This includes a number of 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...

databases and multi-species protein databases, software development groups, and a dedicated editorial office.

History

The Gene Ontology was originally constructed in 1998 by a consortium of researchers studying the genome of three model organism

Model organism

s: Drosophila melanogaster
Drosophila melanogaster
Drosophila 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), Mus musculus (mouse), and 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...

(brewers' or bakers' yeast). Many other model organism databases have joined the Gene Ontology consortium, contributing not only annotation data, but also contributing to the development of the ontologies and tools to view and apply the data. Until now, most of major databases in plant, animal and microorganism make a contribution towards this project. As of January 2008, GO contains over 24,500 terms applicable to a wide variety of biological organisms. There is a significant body of literature on the development and use of GO, and it has become a standard tool in the bioinformatics

Bioinformatics

arsenal. Their objectives have three aspects, building gene ontology, assigning ontology to gene/gene products and develop software and database for first two objects.

External links

Gene Ontology Consortium — Provides access to the ontologies, software tools, annotated gene product lists, and reference documents describing the GO and its uses.
The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration, Nature Biotechnology, 25 (11), 2007.
OBO Foundry library of interoperable gold standard reference ontologies.
GONUTS Wiki — Third party GO term documentation, including links to GO annotations at many 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...

databases.
GOCat - An Automatic GO Categorizer/Browser to help Functional Annotation of Biomedical Texts; also useful to functionally characterize protein and gene names lists generated by high-throughput experiments http://www.geneontology.org/GO.tools.annotation.shtml#gocat
Protein Ontology Project — Provides access to the Protein Ontology (PO) and reference documents describing the PO and its uses.
EAGLi - A Terminology-powered (Gene Ontology, Swiss-Prot keywords...) biomedical question answering engine for MEDLINE http://eagl.unige.ch/EAGLi/
PubOnto Medline Exploration based on Gene Ontology and other ontologies.
Semantic Systems Biology
National Center for Biomedical Ontology
WikiProfessional - Disambiguation, knowledge generation and collaborative intelligence - genes and proteins.

The source of this article is wikipedia, the free encyclopedia. The text of this article is licensed under the GFDL.

GO terms and ontology

Example GO term

Annotation

Example annotation

Tools

GO Consortium

History

See also

External links