What is gene ontology exactly?

Question

[nemo]

I am new to the bio informatic field. In a script a retrieved all gene ontology terms. But I don't fully understand what gene ontology is. I know that its purpose is to standardize the representation of the properties of genes and the gene products. But it doesn't exactly explain what the gene ontology terms are. Are they properties the gene contains like biological properties, are they the function of the gene? Or is it something else?

[Jean-Karim Heriche]

In addition to the answers about specifics of the Gene Ontology, I think you may also need to understand what an ontology is. An ontology organizes a controlled vocabulary using a formal language to capture relationships between the terms (and concepts they represent). A controlled vocabulary simply lists terms that are to be used to describe a particular context but doesn't relate them. An ontology takes the form of a directed acyclic graph whose edges represent the relationships between concepts represented by the nodes. For example, a controlled vocabulary to describe the cell cycle could contain the terms 'cell cycle', 'mitosis' and 'chromosome segregation'. A cell cycle ontology would organize these terms by specifying that 'chromosome segregation' is part of 'mitosis' and 'mitosis' is part of 'cell cycle'.

[Kevin Blighe]

Yet further information for you, if you are going to delve into the Gene Ontology: A: Go annotation reliability ?

Answer 1

[Emily]

My super-shorthand: Biological process is what the protein does. Molecular function is how it does it. Cellular component is where in the cell it does it.

Answer 2

[arta]

"Three categories of GO

Biological process refers to a biological objective to which the gene or gene product contributes. A process is accomplished via one or more ordered assemblies of molecular functions. Processes often involve a chemical or physical transformation, in the sense that something goes into a process and something different comes out of it. Examples of broad (high level) biological process terms are ‘cell growth and maintenance’ or ‘signal transduction’. Examples of more specific (lower level) process terms are ‘translation', ‘pyrimidine metabolism’ or ‘cAMP biosynthesis’.

Molecular function is defined as the biochemical activity (including specific binding to ligands or structures) of a gene product. This definition also applies to the capability that a gene product (or gene product complex) carries as a potential. It describes only what is done without specifying where or when the event actually occurs. Examples of broad functional terms are ‘enzyme', ‘transporter’ or ‘ligand’. Examples of narrower functional terms are ‘adenylate cyclase’ or ‘Toll receptor ligand’.

Cellular component refers to the place in the cell where a gene product is active. These terms reflect our understanding of eukaryotic cell structure. As is true for the other ontologies, not all terms are applicable to all organisms; the set of terms is meant to be inclusive. Cellular component includes such terms as ‘ribosome’ or ‘proteasome’, specifying where multiple gene products would be found. It also includes terms such as ‘nuclear membrane’ or ‘Golgi apparatus’."

You can find more from the published paper.

Answer 3

[Benn]

Quote from http://www.geneontology.org/page/about

"The Gene Ontology (GO) project is a major bioinformatics initiative to develop a computational representation of our evolving knowledge of how genes encode biological functions at the molecular, cellular and tissue system levels."

Read more about it on their website.

Answer 4

[EagleEye]

In-short and simple terms, Gene predicted or validated to play a role in particular/many biological function(s), example this information can be derived from available literatures and compiled in single database: Genes to BiologicalFunctions relationship (in this case, Gene Ontology). In case of Gene Ontology, these derived functions are divided under three major categories 'biological process (BP)', cellular components (CC) and 'molecular functions (MF)'

These articles will give you brief introduction about why and how gene ontology play a role in interpreting your data:

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1250-z

http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003343

Answer 5

[Joe]

I prefer to think of it outside of it's bioinformatics context:

ontology

noun

1. the branch of metaphysics dealing with the nature of being.

2. a set of concepts and categories in a subject area or domain that shows their properties and the relations between them.

Put simply, as others have said, its literally just a representation of some things and how they interact with other things.

In a biological context, this usually means proteins that are known to be in the same biochemical pathway for instance.