minimalistGODB (version 1.0)
Build a Minimalist Gene Ontology (GO) Database (GODB)
Description
Normally building a GODB is fairly complicated, involving downloading
multiple database files and using these to build e.g. a 'mySQL' database.
Accessing this database is also complicated, involving an intimate knowledge
of the database in order to construct reliable queries.
Here we have a more modest goal, generating GOGOA3, which is a stripped down
version of the GODB that
is restricted to human genes as designated by the HUGO Gene Nomenclature
Committee (HGNC) (see ). This can be built in
a matter of seconds from 2 easily
downloaded files (see
and ), and it can be queried by e.g.
w<-which(GOGOA3[,"HGNC"] %in% hgncList) where GOGOA3
is a matrix representing the minimalist GODB and hgncList is a list of
gene identifiers. This database will be used in my upcoming package 'GoMiner'
which is based on my previous publication (see Zeeberg, B.R., Feng, W., Wang, G. et al. (2003)).
Relevant .RData files are available from GitHub ().