Package: minimalistGODB
Version: 1.1.0
Date: 2025-05-04
Title: Build a Minimalist Gene Ontology (GO) Database (GODB)
Authors@R: c(
          person("Barry", "Zeeberg", email = "barryz2013@gmail.com",
                role = c("aut", "cre")))
Maintainer: Barry Zeeberg <barryz2013@gmail.com>
Author: Barry Zeeberg [aut, cre]
Depends: R (>= 4.2.0)
LazyData: true
LazyDataCompression: xz
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 
 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>).
License: GPL (>= 2)
Encoding: UTF-8
VignetteBuilder: knitr
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
RoxygenNote: 7.3.2
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2025-05-04 13:35:56 UTC; barryzeeberg
Repository: CRAN
Date/Publication: 2025-05-04 14:00:02 UTC
Built: R 4.4.3; ; 2025-12-01 18:58:03 UTC; windows
