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Format DOIDs

format_doid.Rd

Convert valid DOIDs and/or bare numbers to a specified DOID format. Input may be tested to ensure it matches a valid DOID format but no attempt is made to confirm bare numbers or DOIDs match actual diseases in the ontology.

Usage

format_doid(x, as = "CURIE", convert_bare = FALSE, validate_input = TRUE)

Arguments

x

A set of IDs, as a character vector.

as

The format to convert the DOIDs to, as a string. All valid formats are possible options: "CURIE" (default), "URI", "obo_CURIE", "basename".

convert_bare

Whether bare numbers should be converted to canonical DOIDs, TRUE or FALSE (default).

validate_input

Whether to ensure only valid DOIDs are included in x, TRUE (default) or FALSE. When FALSE, non-DOID input will be returned unchanged.

Caution

Be extra cautious when using format_doid() with validate_input = FALSE as unexpected text conversion may occur.

See also

Other format IDs: format_obo()

Examples

x <- c(
    "http://purl.obolibrary.org/obo/DOID_0001816",
    "DOID:4",
    "obo:DOID_14566",
    "DOID_0040001"
)

format_doid(x, as = "URI")
#> [1] "http://purl.obolibrary.org/obo/DOID_0001816"
#> [2] "http://purl.obolibrary.org/obo/DOID_4"      
#> [3] "http://purl.obolibrary.org/obo/DOID_14566"  
#> [4] "http://purl.obolibrary.org/obo/DOID_0040001"
format_doid(x, as = "CURIE")
#> [1] "DOID:0001816" "DOID:4"       "DOID:14566"   "DOID:0040001"
format_doid(x, as = "obo_CURIE")
#> [1] "obo:DOID_0001816" "obo:DOID_4"       "obo:DOID_14566"   "obo:DOID_0040001"
format_doid(x, as = "basename")
#> [1] "DOID_0001816" "DOID_4"       "DOID_14566"   "DOID_0040001"

# bare numbers can be converted to canonical DOIDs, if desired
w_bare <- c(x, "0050117")
format_doid(w_bare, convert_bare = TRUE)
#> [1] "DOID:0001816" "DOID:4"       "DOID:14566"   "DOID:0040001" "DOID:0050117"

# non-DOIDs can be passed as input, if desired
mixed_input <- c(x, "random_text", "obo:SYMP_0000000", "0050117")
format_doid(mixed_input, validate_input = FALSE)
#> [1] "DOID:0001816"     "DOID:4"           "DOID:14566"       "DOID:0040001"    
#> [5] "random_text"      "obo:SYMP_0000000" "0050117"         
format_doid(mixed_input, convert_bare = TRUE, validate_input = FALSE)
#> [1] "DOID:0001816"     "DOID:4"           "DOID:14566"       "DOID:0040001"    
#> [5] "random_text"      "obo:SYMP_0000000" "DOID:0050117"