Programmatically Obtain The Go Version From Go.Db
1
0
Entering edit mode
11.1 years ago
Dave Bridges ★ 1.4k

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 go kegg • 2.5k views
ADD COMMENT
3
Entering edit mode
11.1 years ago
Neilfws 49k

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 COMMENT

Login before adding your answer.

Traffic: 2122 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6