Gene Ontology

The Gene Ontology (GO) is a big project in bioinformatics that helps scientists understand genes and what they do in all kinds of living things. It creates a special set of words and ideas to describe the jobs that genes and their products have. This makes it easier for scientists to 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 produce. Third, it offers tools so scientists can use this information to understand their experiments better.

Unlike systems that name genes, the Gene Ontology looks at what those genes actually do. It also uses a special kind of markup language so computers can easily read and use this information. 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 started in 1998 when researchers studying fruit flies, mice, and yeast worked together. They created a way to describe what genes do in living things. Many databases for different plants, animals, and tiny organisms have joined this project, helping to add more information and tools. By July 2019, the Gene Ontology had over 44,000 terms and had been used to describe genes in more than 4,000 different types of living things. It has become an important tool in studying biological data.

The project has three main goals: creating descriptions for genes, connecting these descriptions to actual genes, and making software and databases to help people use this information. Researchers also study the qualities of these descriptions to better understand biology.

Terms and ontology

An ontology is a way to describe things we know about and how they are connected. The Gene Ontology project helps scientists describe what genes do by providing a list of special terms that everyone can use. These terms cover three main areas: parts of a cell, what a gene product does at the molecular level, and the bigger processes that happen in living things.

Each term has a name, a special number, a clear meaning, and can be linked to other terms. This helps scientists talk to each other and share their discoveries. The Gene Ontology keeps growing, with new terms added based on feedback from scientists. You can find all these terms online for free.

Annotation

Genome annotation is about collecting information about genes and their products. The Gene Ontology (GO) uses special terms to describe these genes. These annotations are shared on the GO website and can be viewed online or downloaded. Each annotation includes important details like the source of the information, the type of evidence used, the date, and who made the annotation.

Evidence codes show how the annotation was made. Some come from reading scientific papers, while others are based on computer predictions. Over time, more annotations have been checked by humans. The GO Consortium offers workshops to help new groups learn how to make these annotations. Many computer programs have also been created to help predict Gene Ontology annotations.

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

There are many tools that use information from the Gene Ontology project. Most of these tools are made by other groups, but the Gene Ontology Consortium has created two important tools: AmiGO and OBO-Edit.

AmiGO is a website where users can search, explore, and see information about genes and their functions. It also includes a BLAST tool for comparing genes, ways to study big sets of data, and a way to ask questions directly to the Gene Ontology database. AmiGO can be used online or downloaded for personal use on any database that follows the Gene Ontology style. It is free open source software.

OBO-Edit is a free tool that helps people edit and view sets of information about genes. It is made to work 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 can find connections between pieces of information based on what is already known. Even though it was made for biological 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 group of scientists and databases working together on the Gene Ontology project. It includes databases for studying different living things, groups that create software, and a special office for editing the information.