Extract mappings from ORDO
extract_ordo_mappings.Rd
Extract mappings from the Orphanet Rare Disease Ontology (ORDO). ORDO uses
oboInOwl:hasDbXref
for mapping with annotations to indicate
exact/broad/narrow-ness. Utilizes robot()
.
Arguments
- ordo_path
The path to the ORDO file, as a string.
- as_skos
Whether to convert ORDO's annotated
oboInOwl:hasDbXref
mappings to their Simple Knowledge Organization System (SKOS) equivalents, as a boolean (default:TRUE
).The ORDO-skos equivalent predicates are as follows:
"BTNT"
-skos:narrowMatch
"NTBT"
-skos:broadMatch
"E"
-skos:exactMatch
"ND"
-doid:undefinedMatch
(supplements SKOS)"W"
-doid:notMatch
(supplements SKOS)
- output
The path where output will be written, as a string, or
NULL
(default) to load data directly.- tidy_what
The elements of a SPARQL-created data.frame to tidy, as a character vector. One or more of the following:
"everything"
to apply all tidy operations (has precedence over"nothing"
)."header"
to remove leading?
from header labels."unnest"
to unnest list columns withunnest_cross()
."uri_to_curie"
to convert all URIs recognized by DO.utils to CURIEs withto_curie()
."lgl_NA_false"
to replaceNA
in logical columns withFALSE
."as_tibble"
to make the output a tibble."nothing"
to prevent all tidying.
Value
If output
is specified, the path to the output file with the data.
Otherwise, the data as a tibble.
ORDO mappings data will be formatted according to the
SSSOM specification,
with an additional status
column indicating the status (active, deprecated,
etc.) of each ORPHA term.
If as_skos = FALSE
, ORDO's text-based oboInOwl:hasDbXref
annotations
denoting the type of relationship the Xref represents (simple text code only)
will be included in the predicate_modifier
column.