GO(Gene Ontology) IDs for Homo sapiens in all three ontologies

Question

[nkhan.mscs15seecs]

Can somebody please tell me where I can download full list of GO IDs of homo sapiens. I actually want to create two tables of following structure

Table1

GO ID       Name



Table2 (GO IDs)

Sr    Biological   Molecular Cellular

where I can have full list?

regards

[Sej Modha]

Have you looked at: http://www.geneontology.org/

[Jean-Karim Heriche]

The Gene Ontology is generally species-agnostic so you should clarify what you mean. Are you looking for all GO terms that are currently used to annotate human genes ? If so, used in which resource ?

Answer 1

[Benn]

One way to get all human GO terms is with biomaRt in R. Here an example how to retrieve information from ensembl using biomaRt, the creation of the tables further is up to you.

library(biomaRt)

ensembl <- useMart("ENSEMBL_MART_ENSEMBL")

ensembl <- useDataset("hsapiens_gene_ensembl", mart = ensembl)

# First get all ensembl genes
all.ensemblgene <- unique(getBM(attributes = "ensembl_gene_id",
  values = "*", 
  mart = ensembl))

# Get all GO terms associated with the genes
GOs <- getBM(attributes=c('ensembl_gene_id', 'go_id', 'name_1006', 'namespace_1003'), 
      filters = 'ensembl_gene_id', 
      values = all.ensemblgene, 
      mart = ensembl)

dim(GOs)
[1] 420970      4

# Keep only unique terms
only.go.table <- unique(GOs[,2:4])

dim(only.go.table)
[1] 17911     3

head(only.go.table)
       go_id                                  name_1006     namespace_1003
1 GO:0005737                                  cytoplasm cellular_component
2 GO:0005829                                    cytosol cellular_component
3 GO:0005654                                nucleoplasm cellular_component
4 GO:0009967 positive regulation of signal transduction biological_process
5 GO:0005515                            protein binding molecular_function
6 GO:0005886                            plasma membrane cellular_component