Get direct edges in the ontology graph for a term
Value
data.frame with columns subject, subject_label,
predicate, predicate_label, object,
object_label.
Examples
goref <- semsql_connect(ontology = "go")
#> Connected to SemanticSQL database: /home/vincent/.cache/R/BiocFileCache/b24227f056f7_go.db
#> Primary ontology prefix: GO
get_direct_edges(goref, "GO:0006915")
#> subject subject_label predicate predicate_label object
#> 1 GO:0006915 apoptotic process RO:0002162 in taxon NCBITaxon:33154
#> 2 GO:0006915 apoptotic process RO:0002224 starts with GO:0097190
#> 3 GO:0006915 apoptotic process RO:0002224 starts with GO:0097190
#> 4 GO:0006915 apoptotic process RO:0002230 ends with GO:0097194
#> 5 GO:0006915 apoptotic process RO:0002230 ends with GO:0097194
#> 6 GO:0006915 apoptotic process rdfs:subClassOf <NA> GO:0012501
#> object_label
#> 1 Opisthokonta
#> 2 apoptotic signaling pathway
#> 3 apoptotic signaling pathway
#> 4 execution phase of apoptosis
#> 5 execution phase of apoptosis
#> 6 programmed cell death
get_direct_edges(goref, "GO:0006915", direction = "both")
#> subject subject_label
#> 1 GO:0006915 apoptotic process
#> 2 GO:0006915 apoptotic process
#> 3 GO:0006915 apoptotic process
#> 4 GO:0006915 apoptotic process
#> 5 GO:0006915 apoptotic process
#> 6 GO:0006915 apoptotic process
#> 7 GO:0006925 inflammatory cell apoptotic process
#> 8 GO:0008637 apoptotic mitochondrial changes
#> 9 GO:0008637 apoptotic mitochondrial changes
#> 10 GO:0010657 muscle cell apoptotic process
#> 11 GO:0016505 peptidase activator activity involved in apoptotic process
#> 12 GO:0016505 peptidase activator activity involved in apoptotic process
#> 13 GO:0033028 myeloid cell apoptotic process
#> 14 GO:0033668 symbiont-mediated suppression of host apoptosis
#> 15 GO:0033668 symbiont-mediated suppression of host apoptosis
#> 16 GO:0034349 glial cell apoptotic process
#> 17 GO:0042981 regulation of apoptotic process
#> 18 GO:0042981 regulation of apoptotic process
#> 19 GO:0043065 positive regulation of apoptotic process
#> 20 GO:0043065 positive regulation of apoptotic process
#> 21 GO:0043066 negative regulation of apoptotic process
#> 22 GO:0043066 negative regulation of apoptotic process
#> 23 GO:0043276 anoikis
#> 24 GO:0044346 fibroblast apoptotic process
#> 25 GO:0051402 neuron apoptotic process
#> 26 GO:0052150 symbiont-mediated perturbation of host apoptosis
#> 27 GO:0052151 symbiont-mediated activation of host apoptosis
#> 28 GO:0052151 symbiont-mediated activation of host apoptosis
#> 29 GO:0071839 apoptotic process in bone marrow cell
#> 30 GO:0071887 leukocyte apoptotic process
#> 31 GO:0072577 endothelial cell apoptotic process
#> 32 GO:0097152 mesenchymal cell apoptotic process
#> 33 GO:0097190 apoptotic signaling pathway
#> 34 GO:0097190 apoptotic signaling pathway
#> 35 GO:0097194 execution phase of apoptosis
#> 36 GO:0097194 execution phase of apoptosis
#> 37 GO:0140208 apoptotic process in response to mitochondrial fragmentation
#> 38 GO:1902362 melanocyte apoptotic process
#> 39 GO:1902489 hepatoblast apoptotic process
#> 40 GO:1902742 apoptotic process involved in development
#> 41 GO:1904019 epithelial cell apoptotic process
#> 42 GO:1904516 myofibroblast cell apoptotic process
#> 43 GO:1904606 fat cell apoptotic process
#> 44 GO:1990009 retinal cell apoptotic process
#> predicate predicate_label object
#> 1 RO:0002162 in taxon NCBITaxon:33154
#> 2 RO:0002224 starts with GO:0097190
#> 3 RO:0002224 starts with GO:0097190
#> 4 RO:0002230 ends with GO:0097194
#> 5 RO:0002230 ends with GO:0097194
#> 6 rdfs:subClassOf <NA> GO:0012501
#> 7 rdfs:subClassOf <NA> GO:0006915
#> 8 BFO:0000050 part of GO:0006915
#> 9 BFO:0000050 part of GO:0006915
#> 10 rdfs:subClassOf <NA> GO:0006915
#> 11 BFO:0000050 part of GO:0006915
#> 12 BFO:0000050 part of GO:0006915
#> 13 rdfs:subClassOf <NA> GO:0006915
#> 14 RO:0012014 negatively regulates in another organism GO:0006915
#> 15 RO:0012014 negatively regulates in another organism GO:0006915
#> 16 rdfs:subClassOf <NA> GO:0006915
#> 17 RO:0002211 regulates GO:0006915
#> 18 RO:0002211 regulates GO:0006915
#> 19 RO:0002213 positively regulates GO:0006915
#> 20 RO:0002213 positively regulates GO:0006915
#> 21 RO:0002212 negatively regulates GO:0006915
#> 22 RO:0002212 negatively regulates GO:0006915
#> 23 rdfs:subClassOf <NA> GO:0006915
#> 24 rdfs:subClassOf <NA> GO:0006915
#> 25 rdfs:subClassOf <NA> GO:0006915
#> 26 RO:0002010 regulates in another organism GO:0006915
#> 27 RO:0012013 positively regulates in another organism GO:0006915
#> 28 RO:0012013 positively regulates in another organism GO:0006915
#> 29 rdfs:subClassOf <NA> GO:0006915
#> 30 rdfs:subClassOf <NA> GO:0006915
#> 31 rdfs:subClassOf <NA> GO:0006915
#> 32 rdfs:subClassOf <NA> GO:0006915
#> 33 BFO:0000050 part of GO:0006915
#> 34 BFO:0000050 part of GO:0006915
#> 35 BFO:0000050 part of GO:0006915
#> 36 BFO:0000050 part of GO:0006915
#> 37 rdfs:subClassOf <NA> GO:0006915
#> 38 rdfs:subClassOf <NA> GO:0006915
#> 39 rdfs:subClassOf <NA> GO:0006915
#> 40 rdfs:subClassOf <NA> GO:0006915
#> 41 rdfs:subClassOf <NA> GO:0006915
#> 42 rdfs:subClassOf <NA> GO:0006915
#> 43 rdfs:subClassOf <NA> GO:0006915
#> 44 rdfs:subClassOf <NA> GO:0006915
#> object_label
#> 1 Opisthokonta
#> 2 apoptotic signaling pathway
#> 3 apoptotic signaling pathway
#> 4 execution phase of apoptosis
#> 5 execution phase of apoptosis
#> 6 programmed cell death
#> 7 apoptotic process
#> 8 apoptotic process
#> 9 apoptotic process
#> 10 apoptotic process
#> 11 apoptotic process
#> 12 apoptotic process
#> 13 apoptotic process
#> 14 apoptotic process
#> 15 apoptotic process
#> 16 apoptotic process
#> 17 apoptotic process
#> 18 apoptotic process
#> 19 apoptotic process
#> 20 apoptotic process
#> 21 apoptotic process
#> 22 apoptotic process
#> 23 apoptotic process
#> 24 apoptotic process
#> 25 apoptotic process
#> 26 apoptotic process
#> 27 apoptotic process
#> 28 apoptotic process
#> 29 apoptotic process
#> 30 apoptotic process
#> 31 apoptotic process
#> 32 apoptotic process
#> 33 apoptotic process
#> 34 apoptotic process
#> 35 apoptotic process
#> 36 apoptotic process
#> 37 apoptotic process
#> 38 apoptotic process
#> 39 apoptotic process
#> 40 apoptotic process
#> 41 apoptotic process
#> 42 apoptotic process
#> 43 apoptotic process
#> 44 apoptotic process
disconnect(goref)
#> Disconnected from 'b24227f056f7_go.db'