Glossary

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the Gene Ontology
GO website
controlled vocabulary
a set of selected terms—words and phrases—in which each concept is carefully defined to ensure it is unambiguous and used consistently. Concepts are described using only one term in the set and each term in the set describes only one concept.
ontology
a formal representation of knowledge within a domain using a set of concepts and the relationships between those concepts. It is used to reason about the properties of that domain, and may be used to describe the domain.
GO term
A biological concept in one of three domains: cellular component, molecular function or biological process. GO terms consist of a GO ID, in the form GO:nnnnnnn, and a term string. The majority of GO terms have a textual definition, and many have synonyms, database cross-references and/or a comment.
GO database
Consists of the ontology itself and annotation data
gene product
the shorthand used by the Gene Ontology project to refer to genes and the products of genes, such as proteins or functional RNAs
namespace
in GO, this designates which of the three ontologies (biological process, molecular function, cellular component) a term belongs to
synonym type
designates the relationship between the synonym and the GO term name
documentation
aspect
synonym for namespace
annotation
synonym for association
association
A piece of information linking a gene product to a GO term. Has four main parts: gene product, GO term, evidence code and reference
documentation
association qualifier
The Qualifier column is used for flags that modify the interpretation of an annotation. Allowable values are NOT, contributes_to, and colocalizes_with.
documentation
relation or relationship
documentation
relationship type
aka relation (also called "properties" in OWL). All relationships have a relationship type.
GO slim
Cut-down versions of the GO ontologies containing a subset of the terms in the whole GO. They give a broad overview of the ontology content without the detail of the specific fine grained terms.
documentation
evidence code
a shorthand code to describe the proof for a GO annotation
documentation
assigned by
Refers to the database that created the annotation
documentation