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[[Category: GOC Overview]] | |||
; the Gene Ontology | ; the Gene Ontology | ||
: [http://www.geneontology.org/ GO website] | : [http://www.geneontology.org/ GO website] | ||
; controlled vocabulary | ; 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. | : 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 | ; 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 | ; 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. | : 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 | ; GO database | ||
: Consists of the ontology itself and annotation data | : Consists of the ontology itself and annotation data | ||
; gene product | ; 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 | : the shorthand used by the Gene Ontology project to refer to genes and the products of genes, such as proteins or functional RNAs | ||
; annotation | |||
; 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 | |||
: [http://www.geneontology.org/GO.ontology.structure.shtml#synonyms 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 | : A piece of information linking a gene product to a GO term. Has four main parts: gene product, GO term, evidence code and reference | ||
: [http://www.geneontology.org/GO.annotation.shtml documentation] | : [http://www.geneontology.org/GO.annotation.shtml documentation] | ||
; association qualifier | ; 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. | : The Qualifier column is used for flags that modify the interpretation of an annotation. Allowable values are NOT, contributes_to, and colocalizes_with. | ||
: [http://www.geneontology.org/GO.annotation.shtml#qual documentation] | : [http://www.geneontology.org/GO.annotation.shtml#qual documentation] | ||
; relationship | |||
; relation or relationship | |||
: [http://www.geneontology.org/GO.usage.shtml#relationships documentation] | : [http://www.geneontology.org/GO.usage.shtml#relationships documentation] | ||
; relationship type | ; relationship type | ||
: aka relation (also called "properties" in OWL). All relationships have a relationship type. | : aka relation (also called "properties" in OWL). All relationships have a relationship type. | ||
; GO slim | ; 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. | : 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. | ||
: [http://www.geneontology.org/GO.slims.shtml documentation] | : [http://www.geneontology.org/GO.slims.shtml documentation] | ||
; evidence code | ; evidence code | ||
: a shorthand code to describe the proof for a GO annotation | : a shorthand code to describe the proof for a GO annotation | ||
: evidence | : [http://www.geneontology.org/GO.evidence.shtml documentation] | ||
; assigned by | ; assigned by | ||
: Refers to the database that created the annotation | : Refers to the database that created the annotation | ||
: [http://www.geneontology.org/GO.format.annotation.shtml documentation] | : [http://www.geneontology.org/GO.format.annotation.shtml documentation] | ||
Latest revision as of 09:02, 12 April 2019
- 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