GOBPPARENTS {GO}R Documentation

Annotation of GO identifiers by the GO identifiers of their direct parents

Description

This is an R environment (hash table) mapping GO ids to the GO ids of their direct parents under biological process (BP). Direct parents of a given GO id are those GO ids correponding to all the parents nodes that have direct link to the node for the GO id of concern based on the directed acyclic graph defined by Gene Ontology Consortium. GO terms for parent nodes are more general than that of the child nods

Details

GO ids are keys and the corresponding parent GO ids are values. Values are named vectors of length 1 or greater depending on whether the GO id of concern has only one or more parents. The name(s) of value(s) is(are) the association code (isa or partof) between the GO id and its direct parents.GO ids that do not have any parent node are assigned NA as the values.

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://www.godatabase.org/dev/database/archive/2004-07-01/go_200407-termdb.xml.gz. Built: 2004-07-01

Package built: Tue Sep 28 11:27:36 2004

References

http://www.geneontology.org/ and http://www.ncbi.nlm.nih.gov/LocusLink

Examples

  require("GO", character.only = TRUE) || stop("GO unavailable")
  require("annotate", character.only = TRUE) || stop("annoate unavailable")
  # Convert the environment 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
        GOTERM[[goids[1]]][["GOID"]]
        GOTERM[[goids[1]]][["Term"]]
        GOTERM[[goids[1]]][["Synonym"]]
        GOTERM[[goids[1]]][["Secondary"]]
        GOTERM[[goids[1]]][["Definition"]]
        GOTERM[[goids[1]]][["Ontology"]]
  }

[Package GO version 1.6.5 Index]