Assess whether OMIM Data is in DO — inventory

Assesses whether OMIM identifiers are present in the Human Disease Ontology as mappings (either xrefs or skos mappings). Utilizes robot() for comparison.

Usage

inventory_omim(
  onto_path,
  omim_input,
  keep_mim = c("#", "%"),
  include_pred = c("skos:exactMatch", "skos:closeMatch", "oboInOwl:hasDbXref"),
  when_pred_NA = "error"
)

Arguments

onto_path

The path to an ontology file, as a string.

omim_input

An omim_tbl created by read_omim() or the path to a .tsv or .csv file (possibly compressed) that can be read by read_omim() and includes OMIM data to compare against the mappings in the ontology.

NOTE: If an omim_tbl is provided, keep_mim will be ignored.

keep_mim

[OMIM search data only] The MIM symbols representing the data types to keep, as a character vector, or NULL to retain all (default: "#" and "%").

The OMIM defined MIM symbols are:

MIM symbol	MIM type
`*`	gene
`+`	gene, includes phenotype
`#`	phenotype
`%`	phenotype, unknown molecular basis
`^`	deprecated
`none`	phenotype, suspected/overlap

include_pred

The predicates to include when testing for one-to-multiple mappings, as a character vector (default: skos:exactMatch, skos:closeMatch, and oboInOwl:hasDbXref). All other predicates are ignored.

when_pred_NA

What to do when missing predicates are detected, as a string; one of "error" (default), "warn", or NULL (do nothing). NA predicates are always ignored when no mapping exists (i.e. one or both corresponding values of x or y is/are also NA).

Value

The omim_input with 5 additional columns:

exists: Logical indicating whether an OMIM ID is present in the DO.
mapping_type: The mapping predicate(s) of this OMIM ID to a disease, if present. Multiple predicate(s) between the same OMIM and DOID will be pipe delimited.
doid: The DOID of the disease mapped to this OMIM ID, if present.
do_label: The label of the disease mapped to this OMIM ID, if present.
do_dep: Logical indicating whether a disease is deprecated or not, if present.
multimaps: The direction in which an OMIM or DO term maps to multiple terms in the other resource, as "omim_to_doid", "doid_to_omim", "both_ways" or NA.

Output will have the class omim_inventory, a type of class mapping_inventory.

Examples

if (FALSE) {
# manually copy or download data from https://www.omim.org/phenotypicSeries/PS609060
inventory_omim(
    onto_path = "~/Ontologies/HumanDiseaseOntology/src/ontology/doid-edit.owl",
    omim_input = "omimps.csv",
)
}