In vjcitn/ontoProc: processing of ontologies of anatomy, cell lines, and so on

We'll start by setting up some package attachments and ontology objects. These examples use legacy versions of ontologies because certain terms and relationships were removed in more modern versions, and our tooling has not kept up with the changes.

library(knitr)
library(ontoProc)

library(ontoProc)
library(ontologyPlot)
library(BiocStyle)  # for package references
cl = getOnto("cellOnto", "2021") # for continuity --    has_high_plasma_membrane_amount: list
go = getOnto("goOnto", "2021")  # if updated, some assertions will fail...
pr = getOnto("Pronto", "2021")  # important case change
str(cl)

Legacy approaches

The following table describes the most up-to-date resources available with getOnto.

data(packDesc2023)
kable(packDesc2023[,-c(1,7)])

Other resources are listed in packDesc202x and packDesc2019.

vjcitn/ontoProc documentation built on March 29, 2025, 9:53 p.m.