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CURIE (RDF ID) Predicate

is_curie.Rd

This predicate is designed to validate CURIEs, compact URIs conforming to the W3C CURIE Syntax 1.0 standard (or stricter as allowed by that standard).

Usage

is_curie(x, def = "obo_generic")

Arguments

x

A set of CURIEs, as a character vector.

def

The definition of CURIEs to test against; as a string. One of "obo", "obo_generic" (default), "w3c", or "w3c_safe" (see Notes section for details).

Notes

The W3C CURIE Syntax 1.0 standard defines the most general CURIE syntax allowed (def = "w3c"; not a perfect implementation, e.g. U+3000 non-breaking space is not accepted). Note that by definition URIs will be identified as CURIEs. If it is desirable to distinguish these use def = "w3c_safe" and wrap CURIEs in brackets (as defined in the standard. Alternatively, use the stricter OBO Foundry-based standards (as stated in that standard, more strict definitions for CURIEs can be defined).

"obo" corresponds to the official OBO Foundry definition of a CURIE as stated in the OBO Foundry ID Policy. This should work for most class CURIEs from OBO Foundry ontologies but will not recognize obo:IDSPACE_LOCALID formatted CURIEs or CURIEs with letters or symbols in their local unique identifier. To allow these in the set while still restricting to CURIE patterns found in OBO Foundry ontologies, use "obo_generic".

See also

Other ID predicates: obo_ID_predicates

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

Examples

id <- c(
    #### pass all ####
    "DOID:0001816", "CL:0000066",
    #### pass "obo_generic" & "w3c" ####
    "obo:DOID_4", "obo:so#has_origin", # obo prefixed CURIEs
    "oboInOwl:hasDbXref", "skos:exactMatch", # obo object properties
    "alfred:LO362836C", # not OBO but conforms to `"obo_generic"` pattern
    #### pass only "w3c" ####
    "4dn.biosource:4DNSR73BT2A2", "aceview.worm:aap-1",
    #### always fail ####
    "0001816", # bare number without prefix
    " obo:HP_0000001", # must have NO `[:space:]` characters
    "http://purl.obolibrary.org/obo/DOID_0001816" # URI
)