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minimalistGODB  

Build a Minimalist Gene Ontology (GO) Database (GODB)
View on CRAN: Click here


Download and install minimalistGODB package within the R console
Install from CRAN:
install.packages("minimalistGODB")

Install from Github:
library("remotes")
install_github("cran/minimalistGODB")

Install by package version:
library("remotes")
install_version("minimalistGODB", "1.0")



Attach the package and use:
library("minimalistGODB")
Maintained by
Barry Zeeberg
[Scholar Profile | Author Map]
First Published: 2025-03-18
Latest Update: 2025-03-18
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 <https://geneontology.org/>). 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>).
How to cite:
Barry Zeeberg (2025). minimalistGODB: Build a Minimalist Gene Ontology (GO) Database (GODB). R package version 1.0, https://cran.r-project.org/web/packages/minimalistGODB. Accessed 09 May. 2025.
Previous versions and publish date:
1.0 (2025-03-18 16:20)
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Full minimalistGODB package functions and examples
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