Fetch and parse the 'psi-ms.obo' and some metadata from the usual sources to use as ontology.

If use_local_fallback is TRUE, this function will never fail. Otherwise, it may fail if the internet connection is flawed or internal URLs related to GitHubs API become stale.

Usage

getCVDictionary(
  source = c("latest", "local", "custom"),
  custom_uri = NULL,
  use_local_fallback = TRUE
)

Arguments

source: Where to get the PSI-MS CV from: - 'latest' will download 'psi-ms.obo' from https://api.github.com/repos/HUPO-PSI/psi-ms-CV/releases/latest - 'local' will use rmzqc/cv/psi-ms.obo' (which might be outdated, if you need the latest terms) - 'custom' uses a user-defined URI in 'custom_uri'
custom_uri: Used when 'source' is set to 'custom'. The URI can be local or remote, e.g. 'c:/obo/my.obo' or 'https://www.abc.com/my.obo'
use_local_fallback: When downloading a file from a URI fails, should we fall back to the local psi-ms.obo shipped with rmzqc?

Value

A list with 'CV', 'URI' and 'version', where 'CV' is a data.frame with columns 'id', 'name', 'def', 'parents', 'children' (and many more) which contains the CV entries

Details

A 'pato.obo', and 'uo.obo' from the 'rmzqc/cv/' folder are automatically merged into the result.

See CV_ class to use this function efficiently.