Standard predicate CURIEs used in OBO ontologies

A named list of commonly used predicate CURIEs in OBO-format ontologies, for use with get_ancestors, get_descendants, and related functions.

Usage

PREDICATES

Format

A named list with elements subclass_of, part_of, has_part, develops_from, located_in, has_characteristic.

Examples

goref <- semsql_connect(ontology = "go")
#> Connected to SemanticSQL database: /home/vincent/.cache/R/BiocFileCache/b24227f056f7_go.db
#> Primary ontology prefix: GO
# apoptotic process (GO:0006915) ancestors via is-a and part-of
anc <- get_ancestors(goref, "GO:0006915",
  predicates = c(PREDICATES$subclass_of, PREDICATES$part_of))
head(anc)
#>            id                 label       predicate
#> 2  GO:0008150    biological_process rdfs:subClassOf
#> 3  GO:0008219            cell death rdfs:subClassOf
#> 4  GO:0009987      cellular process rdfs:subClassOf
#> 5 BFO:0000003             occurrent rdfs:subClassOf
#> 6 BFO:0000015               process rdfs:subClassOf
#> 7  GO:0012501 programmed cell death rdfs:subClassOf
disconnect(goref)
#> Disconnected from 'b24227f056f7_go.db'