## File: GOBPPARENTS.Rd

package info (click to toggle)
r-bioc-go.db 3.12.1-1
• links: PTS, VCS
• area: main
• in suites: bullseye
• size: 88,960 kB
• sloc: makefile: 2
 file content (66 lines) | stat: -rw-r--r-- 2,249 bytes parent folder | download
 123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566 \name{GOBPPARENTS} \alias{GOBPPARENTS} \title{Annotation of GO Identifiers to their Biological Process Parents} \description{ This data set describes associations between GO molecular function (BP) terms and their direct parent BP terms, based on the directed acyclic graph (DAG) defined by the Gene Ontology Consortium. The format is an R object mapping the GO BP 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 BP term is mapped to a named vector of GO BP terms. The name associated with the parent term will be either \emph{isa}, \emph{hasa} or \emph{partof}, where \emph{isa} indicates that the child term is a more specific version of the parent, and \emph{hasa} and \emph{partof} indicate that the child term is a part of the parent. For example, a telomere is part of a chromosome. Biological process is defined as the broad biological goals, such as mitosis or purine metabolism, that are accomplished by ordered assemblies of molecular functions as defined by Gene Ontology Consortium. Mappings were based on data provided: Gene Ontology http://current.geneontology.org/ontology/go-basic.obo With a date stamp from the source of: 2020-09-10 } \references{ \url{http://www.geneontology.org/} and \url{https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene} } \seealso{ \itemize{ \item \code{\link[AnnotationDbi]{AnnotationDb-class}} for use of the \code{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(GOBPPARENTS) # Remove GO IDs that do not have any parent xx <- xx[!is.na(xx)] if(length(xx) > 0){ # Get the children GO IDs 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]]]) } } \keyword{datasets}