Question

source of GO ontology and GO annotations in Bioconductor for GO.db

1

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marcinjoachimiak ▴ 10

@marcinjoachimiak-17331

Last seen 7.2 years ago

Hello,

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,

marcin

GO ontology GO.db • 1.6k views

ADD COMMENT • link updated 7.2 years ago by apkmirrorproject • 0 • written 7.2 years ago by marcinjoachimiak ▴ 10

score 1 · Answer 1 · 2018-09-13

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James W. MacDonald 68k

@james-w-macdonald-5106

Last seen 1 day ago

United States

This package is simply a re-packaging of data from geneontology.org, 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"
 [9] "GOBPOFFSPRING" "GOBPPARENTS"   "GOCCANCESTOR"  "GOCCCHILDREN"
[13] "GOCCOFFSPRING" "GOCCPARENTS"   "GOMAPCOUNTS"   "GOMFANCESTOR"
[17] "GOMFCHILDREN"  "GOMFOFFSPRING" "GOMFPARENTS"   "GOOBSOLETE"   
[21] "GOSYNONYM"     "GOTERM"

and then, as an example,

> ?GOTERM

Under the Details section there is this:

    Mappings were based on data provided by: Gene Ontology
     ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
     With a date stamp from the source of: 2018-Mar28

Which I believe answers your question?

ADD COMMENT • link 7.2 years ago James W. MacDonald 68k

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And alternately you could do

> GO_dbInfo()
              name                                                             value
1     GOSOURCENAME                                                     Gene Ontology
2      GOSOURCEURL ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
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                              ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
10 DBSCHEMAVERSION                                                               2.1

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

ADD REPLY • link 7.2 years ago James W. MacDonald 68k