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OBO ID predicates

obo_ID_predicates.Rd

These predicates are designed to identify and validate common ID formats defined within OBO Foundry ontologies.

Usage

is_valid_obo(x)

is_valid_doid(x)

Arguments

x

A set of IDs, as a character vector.

Details

  • is_valid_obo() to determine if identifiers match the OBO Foundry IRI pattern or are an obo:LUI CURIE.

  • is_valid_doid() to determine if identifiers match DO's IRI or CURIE pattern.

Notes

These predicates do not attempt to confirm any ID actually exists in an OBO Foundry ontology, but only test if the IDs are syntactically formatted correctly (see OBO Foundry ID Policy and OBO File Specification).

Not all OBO formats are valid DOID formats and vice versa.

See also

Other ID predicates: is_curie()

Other predicates: char_val_predicates, is_curie(), is_invariant(), lgl_predicates, num_val_predicates

Examples

# OBO formats
obo_id <- c(
    #### valid ####
    "http://purl.obolibrary.org/obo/DOID_0001816", # URI
    "<http://purl.obolibrary.org/obo/CL_0000066>", # bracketed_URI
    "obo:DOID_4", # CURIE, standard version
    "obo:so#has_origin", # '#' separator ~ OBO annotation properties
    #### invalid ####
    "0001816", # bare number without prefix
    "obo:DOID:14566", # namespace-lui separator must be '_' or '#'
    " obo:HP_0000001" # must have NO `[:space:]` characters
)

is_valid_obo(obo_id)
#> [1]  TRUE  TRUE  TRUE  TRUE FALSE FALSE FALSE

# DOID formats
doid <- c(
    #### valid ####
    "http://purl.obolibrary.org/obo/DOID_0001816", # URI
    "DOID:4", # CURIE, standard version
    "obo:DOID_4", # OBO CURIE, less common
    "DOID_0040001", # basename (OBO prefix removed)
    #### invalid ####
    "0001816", # bare number without prefix
    "doid#DO_IEDB_slim", # namespace-lui separator must be '_'
    "obo:doid#DO_IEDB_slim",
    "obo:DOID_21 " # must have NO `[:space:]` characters
)

is_valid_doid(doid)
#> [1]  TRUE  TRUE  TRUE  TRUE FALSE FALSE FALSE FALSE