Annotation of GO Identifiers to their Cellular Component Children

Description

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

Details

Each GO CC term is mapped to a vector of children GO CC terms.

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

Mappings were based on data provided: Gene Ontology ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/ With a date stamp from the source of: 20160305

References

http://www.geneontology.org/ and http://www.ncbi.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(GOCCCHILDREN)
# Remove GO IDs that do not have any children
xx <- xx[!is.na(xx)]
if(length(xx) > 0){
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]]])
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(GO.db)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums


> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GO.db/GOCCCHILDREN.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GOCCCHILDREN
> ### Title: Annotation of GO Identifiers to their Cellular Component
> ###   Children
> ### Aliases: GOCCCHILDREN
> ### Keywords: datasets
> 
> ### ** 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(GOCCCHILDREN)
> # Remove GO IDs that do not have any children
> xx <- xx[!is.na(xx)]
> if(length(xx) > 0){
+ 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]]])
+ }
[1] "CC"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>