Identify Data Missing from an Ontology (DEPRECATED)

Identifies data missing from an ontology. Currently only works for mappings, includes both xrefs and skos matches. Requires ROBOT for comparison.

Usage

onto_missing(onto_path, input, what = "OMIM", report_present = TRUE)

Arguments

onto_path: The path to an ontology -edit file, as a string.
input: The path to a TSV/CSV file with data to compare against the data in the ontology, as a string.
what: What to compare between the two files, as a string.
report_present: Whether to report data present in the ontology (default) along with data missing, as a boolean.

Value

For report_present = TRUE (default), a list with two data.frames indicating data in the ontology (in_onto) and data missing (missing); otherwise, a single data.frame showing the missing data only.

Examples

if (FALSE) {
onto_missing(
    onto_path = "~/Ontologies/HumanDiseaseOntology/src/ontology/doid-edit.owl",
    input = "omimps.csv", # e.g. manually copied from https://www.omim.org/phenotypicSeries/PS609060
    "OMIM"
)
}