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 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>).

install.packages("minimalistGODB")

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