Question: Programmatically Obtain The Go Version From Go.Db
0
gravatar for Dave Bridges
4.0 years ago by
Dave Bridges1.3k
Ann Arbor, MI
Dave Bridges1.3k wrote:

I am annotating genes with GO.db but I would like to programmatically record the version/date of the gene ontology release that is used for that annotation. Is there any way to extract this from a function in GO.db. The same goes for KEGG/KEGG.db

R kegg go • 1.3k views
ADD COMMENTlink modified 3.6 years ago by Biostar ♦♦ 20 • written 4.0 years ago by Dave Bridges1.3k
3
gravatar for Neilfws
4.0 years ago by
Neilfws47k
Sydney, Australia
Neilfws47k wrote:

Does this help?

library(GO.db)
GO_dbInfo()

name                value
GOSOURCENAME        Gene Ontology
GOSOURCEURL         ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
GOSOURCEDATE        20130907
Db type             GODb
package             AnnotationDbi
DBSCHEMA            GO_DB
GOEGSOURCEDATE      2013-Sep12
GOEGSOURCENAME      Entrez Gene
GOEGSOURCEURL       ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
DBSCHEMAVERSION     2.1

library(KEGG.db)
KEGG_dbInfo()

name                      value
PATHNAMESOURCENAME        KEGG PATHWAY
PATHNAMESOURCEURL         ftp://ftp.genome.jp/pub/kegg/pathway
PATHNAMESOURCEDATE        2011-Mar14
KEGGSOURCENAME            KEGG GENOME
KEGGSOURCEURL             ftp://ftp.genome.jp/pub/kegg/genomes
KEGGSOURCEDATE            2011-Mar15
GOEXTSOURCEDATE           2012-Sepec2go24
GOEXTSOURCENAME           Gene Ontology External Link
GOEXTSOURCEURL            http://www.geneontology.org/external2go
DBSCHEMA                  KEGG_DB
Db type                   KEGGDb
DBSCHEMAVERSION           2.1
ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by Neilfws47k
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