GOMFPARENTS: Annotation of GO Identifiers to their Molecular Function...

In VincentL5201/GO.db: A set of annotation maps describing the entire Gene Ontology

Description

This data set describes associations between GO molecular function (MF) terms and their direct parent MF terms, based on the directed acyclic graph (DAG) defined by the Gene Ontology Consortium. The format is an R object mapping the GO MF terms to all direct parent terms, where a direct parent term is a more general GO term that immediately precedes the given GO term in the DAG.

Details

Each GO MF term is mapped to a named vector of GO MF terms. The name associated with the parent term will be either isa, hasa or partof, where isa indicates that the child term is a more specific version of the parent, and hasa and partof indicate that the child term is a part of the parent. For example, a telomere is part of a chromosome.

Molecular function is defined as the tasks performed by individual gene products; examples are transcription factor and DNA helicase as defined by the Gene Ontology Consortium.

Mappings were based on data provided by: Gene Ontology ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/ With a date stamp from the source of: 2018-Mar28

References

http://www.geneontology.org/ and https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene

See Also

• AnnotationDb-class for use of the select() interface.

Examples

## select() interface:
## Objects in this package can be accessed using the select() interface
## from the AnnotationDbi package. See ?select for details.

## Bimap interface:
# Convert the object to a list
xx <- as.list(GOMFPARENTS)
# Remove GO identifiers that do not have any parent
xx <- xx[!is.na(xx)]
if(length(xx) > 0){
    # Get the parent GO identifiers for the first elents of xx
    goids <- xx[[1]]
    # Find out the GO terms for the first parent goid
    GOID(GOTERM[[goids[1]]])
    Term(GOTERM[[goids[1]]])
    Synonym(GOTERM[[goids[1]]])
    Secondary(GOTERM[[goids[1]]])
    Definition(GOTERM[[goids[1]]])
    Ontology(GOTERM[[goids[1]]])
}

VincentL5201/GO.db documentation built on May 31, 2019, 5:10 p.m.