Skip to contents

Format OBO Foundry IDs

format_obo.Rd

Convert valid OBO Foundry ontology IDs to a specified format. Input may be tested to ensure it matches a valid OBO ID format but no attempt is made to confirm IDs match actual terms in any OBO Foundry ontology.

Usage

format_obo(x, as = "CURIE", validate_input = TRUE)

Arguments

x

A set of IDs, as a character vector.

as

The format to convert the OBO IDs to, as a string. The following formats are possible options:

  • "CURIE" (default)

  • "URI"

  • "bracketed_URI": e.g. "<http://purl.obolibrary.org/obo/CL_0000066>"

  • "ns_lui": namespace with local unique identifier (preserves separator).

  • "ns": namespace of ontology only

As valid OBO formats, the first three formats may be modified repeatedly by format_obo(). The 'ns' formats, on the other hand, are not valid OBO formats and cannot be formatted again by format_obo().

validate_input

Whether to ensure only valid OBO IDs are included in x,TRUE (default) or FALSE. When FALSE, non-OBO ID input will most likely be returned unchanged.

Caution

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

See also

Other format IDs: format_doid()

Examples

x <- c(
    "http://purl.obolibrary.org/obo/DOID_0001816",
    "<http://purl.obolibrary.org/obo/CL_0000066>",
    "obo:SYMP_0000000",
    "obo:so#has_origin"
)

# reversible
format_obo(x, as = "CURIE")
#> [1] "obo:DOID_0001816"  "obo:CL_0000066"    "obo:SYMP_0000000" 
#> [4] "obo:so#has_origin"
format_obo(x, as = "URI")
#> [1] "http://purl.obolibrary.org/obo/DOID_0001816" 
#> [2] "http://purl.obolibrary.org/obo/CL_0000066"   
#> [3] "http://purl.obolibrary.org/obo/SYMP_0000000" 
#> [4] "http://purl.obolibrary.org/obo/so#has_origin"
format_obo(x, as = "bracketed_URI")
#> [1] "<http://purl.obolibrary.org/obo/DOID_0001816>" 
#> [2] "<http://purl.obolibrary.org/obo/CL_0000066>"   
#> [3] "<http://purl.obolibrary.org/obo/SYMP_0000000>" 
#> [4] "<http://purl.obolibrary.org/obo/so#has_origin>"

# irreversible
format_obo(x, as = "ns_lui")
#> [1] "DOID_0001816"  "CL_0000066"    "SYMP_0000000"  "so#has_origin"
format_obo(x, as = "ns")
#> [1] "DOID" "CL"   "SYMP" "so#" 

# non-OBO IDs can be passed as input with caution, if desired
mixed_input <- c(x, "random_text", "0050117", "obo:SYMP:0000000")
format_obo(mixed_input, validate_input = FALSE)
#> [1] "obo:DOID_0001816"  "obo:CL_0000066"    "obo:SYMP_0000000" 
#> [4] "obo:so#has_origin" "random_text"       "0050117"          
#> [7] "obo:SYMP:0000000"