| Version: | 1.1.0 |
| Date: | 2025-05-04 |
| Title: | Build a Minimalist Gene Ontology (GO) Database (GODB) |
| 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 | GPL-3 [expanded from: 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 |
minimalistGODB data set
Description
minimalistGODB data set generated by parseGOBASIC()
Usage
data(GO)
minimalistGODB data set
Description
minimalistGODB data set generated by parseGOA()
Usage
data(GOA)
minimalistGODB data set
Description
small version of minimalistGODB data set generated by buildGODatabase()
Usage
data(GOGOAsmall)
buildGODatabase
Description
driver to build GO database
Usage
buildGODatabase(goa, gobasic, dir = NULL, verbose = FALSE)
Arguments
goa |
character string path name to downloaded goa_human.gaf |
gobasic |
character string path name to downloaded go-basic.obo |
dir |
character string path name to directory to hold subdirectory GODB_RDATA |
verbose |
Boolean if TRUE print out some diagnostic info |
Details
download goa_human.gaf from https://current.geneontology.org/products/pages/downloads.html download go-basic.obo from https://geneontology.org/docs/download-ontology/ parameter dir should be omitted or NULL except for the developer harvesting the updated .RData DBs
The output GOGOA was saved as an .RData file. This was too large for CRAN. It is available from https://github.com/barryzee/GO/tree/main/databases
Value
returns no value but has side effect of saving GOGOA3 to a subdirectory
Examples
## Not run:
# replace my path names for goa and gobasic with your own!!
# these were obtained from the download sites listed in 'details' section
goa<-"~/goa_human.gaf"
gobasic<-"~/go-basic.obo"
buildGODatabase(goa,gobasic,dir="~/",verbose=TRUE)
# > dim(GOGOA)
# [1] 720139 5
# > GOGOA[1:5,]
# HGNC GO RELATION NAME ONTOLOGY
# [1,] "NUDT4B" "GO:0003723" "enables" "RNA binding" "molecular_function"
# [2,] "NUDT4B" "GO:0005515" "enables" "protein binding" "molecular_function"
# [3,] "NUDT4B" "GO:0046872" "enables" "metal ion binding" "molecular_function"
# [4,] "NUDT4B" "GO:0005829" "located_in" "cytosol" "cellular_component"
# [5,] "TRBV20OR9-2" "GO:0002376" "involved_in" "immune system process" "biological_process"
## End(Not run)
# here is a small example that you can run
f1<-system.file("extdata","goa_human.small.gaf",package="minimalistGODB")
f2<-system.file("extdata","go-basic.small.obo",package="minimalistGODB")
buildGODatabase(f1,f2,verbose=TRUE)
buildGODatabaseDriver
Description
driver to build multiple GO databases for many species
Usage
buildGODatabaseDriver(goaDir, gobasic, dir = NULL, verbose = FALSE)
Arguments
goaDir |
character string path name to directory containing downloaded goa .gaf files |
gobasic |
character string path name to downloaded go-basic.obo |
dir |
character string path name to directory to hold species database subdirectories |
verbose |
Boolean if TRUE print out some diagnostic info |
Details
download goa .gaf files from https://current.geneontology.org/products/pages/downloads.html download go-basic.obo from https://geneontology.org/docs/download-ontology/
The output GOGOA3 was saved as an .RData file. This was too large for CRAN. It is available from https://github.com/barryzee/GO/tree/main/databases
Value
returns GO database with columns c("HGNC","GO","RELATION","NAME","ONTOLOGY")
Examples
## Not run:
# replace my path names for goa and gobasic with your own!!
# these were obtained from the download sites listed in 'details' section
goaDir<-"/Users/barryzeeberg/Downloads/gaf/"
gobasic<-"~/go-basic.obo"
buildGODatabaseDriver(goaDir,gobasic,dir="~/personal",verbose=TRUE)
## End(Not run)
# here is a small example that you can run
goaDir<-system.file("extdata",package="minimalistGODB")
gobasic<-system.file("extdata","go-basic.small.obo",package="minimalistGODB")
dir<-tempdir()
buildGODatabaseDriver(goaDir,gobasic,dir,verbose=TRUE)
grepList
Description
determine the correct pattern to grep for depending on the species
Usage
grepList(gaf)
Arguments
gaf |
character string containing the basename of the gaf file downloaded from https://current.geneontology.org/products/pages/downloads.html |
Value
returns the correct pattern to grep for
Examples
pattern<-grepList("tair.gaf")
joinGO
Description
join the outputs of parseGOA and parseGOBASIC to add the GO category name and the ontology to GOA
Usage
joinGO(GOA, GO)
Arguments
GOA |
output of parseGOA() |
GO |
output of parseGOBASIC() |
Value
returns a matrix with columns c("HGNC","GO","RELATION","NAME","ONTOLOGY")
Examples
GOGOA<-joinGO(GOA,GO)
# GOGOA[1:5,]
# HGNC GO RELATION NAME ONTOLOGY
# [1,] "NUDT4B" "GO:0003723" "enables" "RNA binding" "molecular_function"
# [2,] "NUDT4B" "GO:0005515" "enables" "protein binding" "molecular_function"
# [3,] "NUDT4B" "GO:0046872" "enables" "metal ion binding" "molecular_function"
# [4,] "NUDT4B" "GO:0005829" "located_in" "cytosol" "cellular_component"
# v[5,] "TRBV20OR9-2" "GO:0002376" "involved_in" "immune system process" "biological_process"
# GO_NAME
# [1,] "GO_0003723__RNA_binding"
# [2,] "GO_0005515__protein_binding"
# [3,] "GO_0046872__metal_ion_binding"
# [4,] "GO_0005829__cytosol"
# [5,] "GO_0002376__immune_system_process"
# querying GOGOA to compute gene enrichment of some GO categories
hgncList<-GOGOA[1:1000,"HGNC"]
ontology<-"biological_process"
w<-which(GOGOA[,"ONTOLOGY"] == ontology)
GOGOA<-GOGOA[w,]
w<-which(GOGOA[,"HGNC"] %in% hgncList)
t<-sort(table(GOGOA[w,"NAME"]),decreasing=TRUE)[1:10]
parseGOA
Description
parse goa_human.gaf
Usage
parseGOA(goa)
Arguments
goa |
character string path name to downloaded goa_human.gaf |
Details
download goa_human.gaf from https://current.geneontology.org/products/pages/downloads.html
Value
returns matrix with columns c("HGNC","GO","RELATION")
Examples
## Not run:
# replace my path name for goa with your own!!
# this was obtained from the download sites listed in 'details' section
GOA<-parseGOA("~/goa_human.gaf")
# GOA[1:5,]
# HGNC GO RELATION
# [1,] "NUDT4B" "GO:0003723" "enables"
# [2,] "NUDT4B" "GO:0005515" "enables"
# [3,] "NUDT4B" "GO:0046872" "enables"
# [4,] "NUDT4B" "GO:0005829" "located_in"
# [5,] "TRBV20OR9-2" "GO:0002376" "involved_in"
## End(Not run)
# here is a small example that you can run
f<-system.file("extdata","goa_human.small.gaf",package="minimalistGODB")
GOAsmall<-parseGOA(f)
parseGOBASIC
Description
parse go-basic.obo
Usage
parseGOBASIC(gobasic, verbose = FALSE)
Arguments
gobasic |
character string path name to downloaded go-basic.obo |
verbose |
Boolean if TRUE print out some diagnostic info |
Details
download go-basic.obo from https://geneontology.org/docs/download-ontology/
Value
returns a list whose components are c("m", "bp", "mf", "cc")
Examples
## Not run:
# replace my path name for gobasic with your own!!
# this was obtained from the download sites listed in 'details' section
GO<-parseGOBASIC("~/go-basic.obo",verbose=FALSE)
# GO$bp[1:5,]
# GO NAME ONTOLOGY
# GO:0000001 "GO:0000001" "mitochondrion inheritance" "biological_process"
# GO:0000002 "GO:0000002" "mitochondrial genome maintenance" "biological_process"
# GO:0000011 "GO:0000011" "vacuole inheritance" "biological_process"
# GO:0000012 "GO:0000012" "single strand break repair" "biological_process"
# GO:0000017 "GO:0000017" "alpha-glucoside transport" "biological_process"
## End(Not run)
# here is a small example that you can run
f<-system.file("extdata","go-basic.small.obo",package="minimalistGODB")
GOsmall<-parseGOBASIC(f)
restrictGOA
Description
restrict GO categories in GOA to those in GO
Usage
restrictGOA(GOA, GO)
Arguments
GOA |
output of parseGOA() |
GO |
output of parseGOBASIC() |
Value
returns a restricted version of GOA
Examples
GOA<-restrictGOA(GOA,GO)
subsetGOGOA
Description
split GOGOA into 3 separate ontologies
Usage
subsetGOGOA(GOGOA)
Arguments
GOGOA |
return value of minimalistGODB::joinGO() |
Value
returns a list containing subsets of GOGOA for each ontology, unique gene and cat lists, and stats
Examples
#load("data/GOGOAsmall.RData")
GOGOA3small<-subsetGOGOA(GOGOAsmall)