Assess whether OMIM susceptibilities are in the DO — inventory_omim

Assesses whether OMIM entries are present in the Human Disease Ontology as susceptibilities (in the omim_susc_import.owl file). Utilizes robot() for comparison.

Usage

inventory_omim_susc(
  susc_path,
  omim_input,
  do_path = NULL,
  keep_mim = c("#", "%")
)

Arguments

susc_path

The path to the omim_susc_import.owl 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 susceptibility classes in the ontology.

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

do_path

The path to a Human Disease Ontology file, as a string, or NULL (default). If provided, additional information about the DOIDs (labels, deprecated status) that are related to the susceptibilities will be included in the output.

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
`#`	descriptive entry, not unique locus; usually a phenotype
`%`	phenotype / phenotypic locus, unknown molecular basis
`^`	deprecated
`none`	phenotype (usually), suspected or possibly overlapping

Value

The omim_input with 4 additional columns:

exists: Logical indicating whether an OMIM ID is present in the DO as a susceptibility.
susc_label: The label of the susceptibility.
susc_dep: Logical indicating whether the susceptibility is deprecated or not.
related_doid: All disease(s) related to a given OMIM susceptibility (delimited by " | "). If do_path is provided, the data will be formatted as "label (DOID; deprecated)" for each related disease; otherwise, only the DOID(s) will be included.

Output will have the class omim_susc_inventory.

Examples

if (FALSE) { # \dontrun{
# execute within the HumanDiseaseOntology repository and download data from
# https://www.omim.org/phenotypicSeries/PS145600 to omimps.tsv
inventory_omim_susc(
  susc_path = "src/ontology/omim_susc_import.owl",
  omim_input = "omimps.tsv",
  do_path = "src/ontology/doid-edit.owl"
)
} # }