Question: source of GO ontology and GO annotations in Bioconductor for GO.db
gravatar for marcinjoachimiak
8 days ago by
marcinjoachimiak10 wrote:


I started using a package called GO.db which is part of bioconductor, along the way I needed to find out the source of the GO ontology used by GO.db.

As far as I an tell based on the package source, GO.db is relying on bioconductor to provide the GO data file? However, I have not been able to find the corresponding code in bioconductor install files etc. If you could point me to where this occurs I would be very grateful. It looks like the GO.db package is maintained by bioconductor...

many thanks,


ADD COMMENTlink modified 5 days ago by apkmirrorproject0 • written 8 days ago by marcinjoachimiak10
gravatar for James W. MacDonald
8 days ago by
United States
James W. MacDonald47k wrote:

This package is simply a re-packaging of data from, into a format that is a bit more user friendly. It's not that obvious how one would find that out, but if you do something like

> library(GO.db)

> ls(2)
 [1] "GO"            "GO.db"         "GO_dbconn"     "GO_dbfile"    
 [5] "GO_dbInfo"     "GO_dbschema"   "GOBPANCESTOR"  "GOBPCHILDREN"
[21] "GOSYNONYM"     "GOTERM"  

and then, as an example,


Under the Details section there is this:

    Mappings were based on data provided by: Gene Ontology
     With a date stamp from the source of: 2018-Mar28

Which I believe answers your question?

ADD COMMENTlink written 8 days ago by James W. MacDonald47k

And alternately you could do

> GO_dbInfo()
              name                                                             value
1     GOSOURCENAME                                                     Gene Ontology
3     GOSOURCEDATE                                                        2018-Mar28
4          Db type                                                              GODb
5          package                                                     AnnotationDbi
6         DBSCHEMA                                                             GO_DB
7   GOEGSOURCEDATE                                                         2018-Apr4
8   GOEGSOURCENAME                                                       Entrez Gene
9    GOEGSOURCEURL                    
10 DBSCHEMAVERSION                                                               2.1

Which tells you some other stuff, but is maybe too 'inside baseball' to be useful?

ADD REPLYlink written 8 days ago by James W. MacDonald47k
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