GOCCPARENTS {GO} | R Documentation

## Annotation of GO Identifiers to their Cellular Component Parents

### Description

This data set describes associations between GO molecular function (CC) terms and their direct parent CC terms, based on the directed acyclic graph (DAG) defined by the Gene Ontology Consortium. The format is an R environment mapping the GO CC 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 CC term is mapped to a named vector of GO CC 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.

Cellular component is defined as the subcellular structures, locations, and macromolecular complexes; examples include nucleus, telomere, and origin recognition complex as defined b y Gene Ontology Consortium.

Mappings were based on data provided:

Gene Ontology:ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest. Built: Build Information not available

Package built: Mon Apr 7 09:09:39 2008

### References

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

### Examples

      require("GO", character.only = TRUE) || stop("GO unavailable")
      require("annotate", character.only = TRUE) || stop("annotate unavailable")
      # Convert the environment object to a list
      xx <- as.list(GOCCPARENTS)
      # Remove GO IDs that do not have any parent
      xx <- xx[!is.na(xx)]
      if(length(xx) > 0){
         goids <- xx[[1]]
         # Find out the GO terms for the first parent go ID
         GOID(GOTERM[[goids[1]]])
         Term(GOTERM[[goids[1]]])
         Synonym(GOTERM[[goids[1]]])
         Secondary(GOTERM[[goids[1]]])
         Definition(GOTERM[[goids[1]]])
         Ontology(GOTERM[[goids[1]]])
      }

[Package GO version 2.2.0 Index]