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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, allow = "standard", ns_type = "obo")

is_valid_doid(x, allow = "standard", ns_type = "obo")

Arguments

x

A set of IDs, as a character vector.

allow

The OBO ID format(s) to consider valid; as a character vector. One or more of: "curie", "obo_curie" (e.g. obo:DOID_4), "uri", "<uri>" (URI in angle brackets), or "ns.lui" (i.e. an OBO CURIE without obo:).

"standard" (default) is a generic grouping that represents syntactically correct formats ("curie", "obo_curie", "uri" and "<uri>").

"ns.lui" will only be included if explicitly specified.

ns_type

The type of OBO namespaces to consider valid; as a character vector. One of: "obo" (default), "ont" (ontology primary namespaces only), or "prop" (ontology property namespaces only; may not be exhaustive).

Details

  • is_valid_obo() to determine if identifiers match an OBO Foundry ID.

  • is_valid_doid() to determine if identifiers match a DOID/doid.

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) AND correspond to a known namespace of an OBO Foundry ontology (see obo_prefix).

See also

Other ID predicates: is_curie(), is_uri()

Other predicates: all_duplicated(), char_val_predicates, iff_all_vals(), is_curie(), is_invariant(), is_uri(), lgl_predicates, num_val_predicates

Examples

# OBO formats
obo_id <- c(
    #### valid by default ####
    "http://purl.obolibrary.org/obo/DOID_0001816", # URI
    "<http://purl.obolibrary.org/obo/CL_0000066>", # angle-bracketed URI
    "DOID:4", # CURIE, standard version
    "obo:CL_0000066", # OBO CURIE
    #### valid OBO property ####
    "so:has_origin", # standard CURIE ~ OBO annotation property
    "obo:so#has_origin", # '#' separator ~ OBO annotation property
    ### conditionally valid -- only if "ns.lui" in `allow` ###
    "DOID_0040001", # namespace-separator-LUI (i.e. OBO CURIE w/'obo:' prefix removed)
    "so#has_origin", # namespace-lui separator must be '#' for properties
    #### invalid ####
    "0001816", # bare number without prefix
    "obo:DOID:14566", # namespace-lui separator must be '_' ('#' for properties)
    " obo:HP_0000001" # must have NO `[:space:]` characters
)

is_valid_obo(obo_id)
#>  [1]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE
is_valid_obo(obo_id, allow = c("standard", "ns.lui"))
#>  [1]  TRUE  TRUE  TRUE  TRUE  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
    # properties are recognized as valid (unless ns_type = 'ont')
    "doid:DO_IEDB_slim",
    "obo:doid#DO_IEDB_slim",
    # namespace-separator-LUI (valid if 'ns.lui' included in `allow`)
    "DOID_0040001",
    #### invalid ####
    "0001816", # bare number without prefix
    "obo:DOID_21 " # must have NO `[:space:]` characters
)

is_valid_doid(doid)
#> [1]  TRUE  TRUE  TRUE  TRUE  TRUE FALSE FALSE FALSE
is_valid_doid(doid, ns_type = "ont")
#> [1]  TRUE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE
is_valid_doid(doid, allow = c("standard", "ns.lui"), ns_type = "ont")
#> [1]  TRUE  TRUE  TRUE FALSE FALSE  TRUE FALSE FALSE