updated GO dataframe in R

Question

[lessismore]

Dear all,

I'm performing GO analyses with R I'd need to get the most updated gene ontology list of terms as a dataframe with ID, ontology (BP, CC, MF), description columns. Does anyone know the best way to do this, or a package having it as a dataset by default? or a way to convert an obo file from here http://geneontology.org/docs/download-ontology/ into a dataframe?

thanks in advance

Answer 1

[jv]

I like using the Org.XX.eg.db annotation packages from Bioconductor (where XX is an abbreviation for your model organism, e.g. the Homo sapiens annotation package is named Org.Hs.eg.db).

There's a package available for many of the common eukaryotic model organisms - go to https://bioconductor.org/packages/3.14/data/annotation/ and search in the page for "Org" and you'll find a list of different options.

[lessismore]

Thanks! This is a very cool way and I know it, but unfortunately I need to build my own package (with annotationforge package) as I'm working with a non model organism. The GO annotation I've found to build it doesn't display the ontology code (BP, CC, MF) but just the GO id and its description. So I was wandering the fastest way to add this column to my GO annotation dataframe.

Answer 2

[EagleEye]

GeneSCF (Gene Set Clustering based on Functional annotation): Most up-to-date and realtime information based gene enrichment analysis.

Updating GeneSCF with complete geneontology database or download the terms as simple text file for human

./geneSCF-master-vx.x/prepare_database -db=GO_all -org=goa_human

Note: Specific dabases can be also updated using 'GO_BP', 'GO_MF' and 'GO_CC'. The above command downloads complete geneontology ('GO_all') with corresponding genes per GO term as simple text file in following location, 'geneSCF-master-vx.x/class/lib/db/goa_human/'.