Gene Ontology

The Gene Ontology (GO) is a big project in bioinformatics. It helps scientists learn about genes and what they do in all kinds of living things.

It makes a list of words and ideas to explain the jobs that genes and what they make do. This helps scientists share and compare their work, no matter which plants, animals, or tiny organisms they study.

The Gene Ontology does three main things. First, it keeps a list of clear descriptions for gene functions. Second, it connects these descriptions to real genes and what they make. Third, it gives tools so scientists can use this information to understand their experiments better.

Unlike systems that just name genes, the Gene Ontology looks at what those genes actually do. It also uses a special kind of markup language so computers can read and use this information easily. This helps scientists all over the world work together, even when they study very different kinds of life, because the Gene Ontology works the same way for every species. It is part of a bigger group called the Open Biomedical Ontologies and is one of the first members of the OBO Foundry.

History

The Gene Ontology began in 1998 when scientists studying fruit flies, mice, and yeast decided to work together. They made a way to explain what genes do in living things. Many databases about different plants, animals, and tiny organisms joined this project, adding more information and tools. By July 2019, the Gene Ontology had over 44,000 terms and helped describe genes in more than 4,000 types of living things. It is now a very useful tool for studying biology.

The project has three main goals: making descriptions for genes, linking these descriptions to real genes, and creating software and databases to help people use this information. Scientists also study these descriptions to learn more about biology.

Terms and ontology

An ontology is a way to describe things and how they are connected. The Gene Ontology project helps scientists explain what genes do. It gives them a list of special terms to use. These terms cover three main areas: parts of a cell, what a gene product does, and the big processes in living things.

Each term has a name, a number, and a clear meaning. Terms can be linked to other terms. This helps scientists share ideas and discoveries. The Gene Ontology grows with new terms from scientists. You can find all these terms online for free.

Annotation

Genome annotation is about finding out information about genes and what they do. The Gene Ontology (GO) uses special words to explain these genes. These notes about genes can be seen online or downloaded from the GO website. Each note includes useful details such as where the information came from, how we know it is true, the date, and who wrote it down.

Evidence codes tell us how the note was created. Some notes come from reading science papers, while others are guesses made by computers. As time goes by, more of these notes are checked by scientists. The GO Consortium holds classes to teach new groups how to make these notes. Many computer tools have also been made to help guess Gene Ontology notes.

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 (https://pubmed.ncbi.nlm.nih.gov/17611253)

Assigned by: UniProtKB, June 6, 2008

Data source:

Tools

Many tools use information from the Gene Ontology project. The Gene Ontology Consortium has made two important tools: AmiGO and OBO-Edit.

AmiGO is a website where you can search and learn about genes and what they do. It also has a BLAST tool for comparing genes, ways to study large groups of data, and a way to ask questions to the Gene Ontology database. AmiGO can be used online or downloaded for personal use. It is free open source software.

OBO-Edit is a free tool that helps people edit and view information about genes. It works on any computer and uses Java. OBO-Edit has strong search and filtering options, and users can change how it looks. It also includes a reasoner that finds connections between pieces of information. OBO-Edit can be used with any kind of information set. It is available to download for free.

Consortium

The Gene Ontology Consortium is a team of scientists and databases. They work together on the Gene Ontology project. The group includes databases that study different living things, teams that make software, and a special office for editing the information.