minimalistGODB: Build a Minimalist Gene Ontology (GO) Database (GODB)
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
was originally restricted to human genes as designated by the HUGO Gene Nomenclature
Committee (HGNC) (see <https://geneontology.org/>). I have now added about two dozen
additional species, namely all species represented on the Gene Ontology
download page <https://current.geneontology.org/products/pages/downloads.html>.
This covers most of the model organisms that are commonly used in bio-medical
and basic research (assuming that anyone still has a grant to do such research).
This can be built in a matter of seconds from 2 easily
downloaded files (see <https://current.geneontology.org/products/pages/downloads.html>
and <https://geneontology.org/docs/download-ontology/>), 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)<doi:10.1186/gb-2003-4-4-r28>).
Relevant .RData files are available from GitHub (<https://github.com/barryzee/GO/tree/main/databases>).
Documentation:
Downloads:
Reverse dependencies:
Linking:
Please use the canonical form
https://CRAN.R-project.org/package=minimalistGODB
to link to this page.