Given a Neo4j based KG engine, provides summary information in the form of
node counts, category counts across nodes, and relationship type counts.
General information about the graph is printed to the console, and a list of
dataframes describing node and edge counts is returned invisibly. Also returned
are cats and preds entries, containing lists of available node categories and
edge predicates, respectively, for convenient auto-completion in RStudio.
# S3 method for class 'neo4j_engine'
summary(object, ..., quiet = FALSE)A list of dataframes and named lists
# prints a readable summary and returns a list of dataframes
stats <- monarch_engine() |> summary()
#> Trying to connect to https://neo4j.monarchinitiative.org
#> Connected to https://neo4j.monarchinitiative.org
#>
#> A Neo4j-backed knowledge graph engine.
#> Gathering statistics, please wait...
#> Total nodes: 1124572
#> Total edges: 9394432
#>
#> Node category counts:
#> category count
#> biolink:NamedThing 1124572
#> biolink:Entity 1124572
#> biolink:BiologicalEntity 1077862
#> biolink:ThingWithTaxon 1077862
#> biolink:PhysicalEssenceOrOccurrent 870252
#> biolink:PhysicalEssence 804910
#> biolink:OntologyClass 779947
#> biolink:GenomicEntity 714605
#> biolink:ChemicalEntityOrGeneOrGeneProduct 605779
#> biolink:GeneOrGeneProduct 588713
#> biolink:MacromolecularMachineMixin 588713
#> biolink:Gene 563624
#> biolink:DiseaseOrPhenotypicFeature 199273
#> biolink:PhenotypicFeature 169051
#> biolink:Genotype 136237
#> biolink:SubjectOfInvestigation 73553
#> biolink:OrganismalEntity 73553
#> biolink:AnatomicalEntity 73239
#> biolink:BiologicalProcessOrActivity 65342
#> biolink:Occurrent 65342
#> biolink:BiologicalProcess 52688
#> biolink:ChemicalEntityOrProteinOrPolypeptide 42155
#> biolink:Disease 30222
#> biolink:Polypeptide 25089
#> biolink:Protein 25089
#> biolink:GeneProductMixin 25089
#> biolink:Pathway 21946
#> biolink:ChemicalOrDrugOrTreatment 17066
#> biolink:ChemicalEntity 17066
#> biolink:SequenceVariant 14744
#> biolink:MolecularActivity 12654
#> biolink:CellularComponent 4525
#> biolink:Cell 3122
#> biolink:OrganismTaxon 1974
#> biolink:MolecularEntity 529
#> biolink:LifeStage 314
#>
#> Edge type counts:
#> predicate count
#> biolink:interacts_with 2480332
#> biolink:has_phenotype 1492755
#> biolink:expressed_in 1228812
#> biolink:orthologous_to 1067913
#> biolink:actively_involved_in 659331
#> biolink:subclass_of 593050
#> biolink:enables 455769
#> biolink:related_to 393758
#> biolink:located_in 317598
#> biolink:participates_in 275046
#> biolink:is_active_in 146927
#> biolink:acts_upstream_of_or_within 133635
#> biolink:part_of 59047
#> biolink:causes 16019
#> biolink:is_sequence_variant_of 14873
#> biolink:model_of 9339
#> biolink:treats_or_applied_or_studied_to_treat 8634
#> biolink:has_mode_of_inheritance 8616
#> biolink:gene_associated_with_condition 8047
#> biolink:acts_upstream_of 7385
#> biolink:contributes_to 6382
#> biolink:genetically_associated_with 3203
#> biolink:colocalizes_with 2549
#> biolink:associated_with_increased_likelihood_of 2544
#> biolink:disease_has_location 1016
#> biolink:acts_upstream_of_positive_effect 493
#> biolink:ameliorates_condition 485
#> biolink:acts_upstream_of_or_within_positive_effect 457
#> biolink:acts_upstream_of_negative_effect 174
#> biolink:acts_upstream_of_or_within_negative_effect 154
#> biolink:preventative_for_condition 86
#> biolink:contraindicated_in 3
print(stats)
#> $node_summary
#> category count
#> 1 biolink:NamedThing 1124572
#> 2 biolink:Entity 1124572
#> 3 biolink:BiologicalEntity 1077862
#> 4 biolink:ThingWithTaxon 1077862
#> 5 biolink:PhysicalEssenceOrOccurrent 870252
#> 6 biolink:PhysicalEssence 804910
#> 7 biolink:OntologyClass 779947
#> 8 biolink:GenomicEntity 714605
#> 9 biolink:ChemicalEntityOrGeneOrGeneProduct 605779
#> 10 biolink:GeneOrGeneProduct 588713
#> 11 biolink:MacromolecularMachineMixin 588713
#> 12 biolink:Gene 563624
#> 13 biolink:DiseaseOrPhenotypicFeature 199273
#> 14 biolink:PhenotypicFeature 169051
#> 15 biolink:Genotype 136237
#> 16 biolink:SubjectOfInvestigation 73553
#> 17 biolink:OrganismalEntity 73553
#> 18 biolink:AnatomicalEntity 73239
#> 19 biolink:BiologicalProcessOrActivity 65342
#> 20 biolink:Occurrent 65342
#> 21 biolink:BiologicalProcess 52688
#> 22 biolink:ChemicalEntityOrProteinOrPolypeptide 42155
#> 23 biolink:Disease 30222
#> 24 biolink:Polypeptide 25089
#> 25 biolink:Protein 25089
#> 26 biolink:GeneProductMixin 25089
#> 27 biolink:Pathway 21946
#> 28 biolink:ChemicalOrDrugOrTreatment 17066
#> 29 biolink:ChemicalEntity 17066
#> 30 biolink:SequenceVariant 14744
#> 31 biolink:MolecularActivity 12654
#> 32 biolink:CellularComponent 4525
#> 33 biolink:Cell 3122
#> 34 biolink:OrganismTaxon 1974
#> 35 biolink:MolecularEntity 529
#> 36 biolink:LifeStage 314
#>
#> $edge_summary
#> predicate count
#> 1 biolink:interacts_with 2480332
#> 2 biolink:has_phenotype 1492755
#> 3 biolink:expressed_in 1228812
#> 4 biolink:orthologous_to 1067913
#> 5 biolink:actively_involved_in 659331
#> 6 biolink:subclass_of 593050
#> 7 biolink:enables 455769
#> 8 biolink:related_to 393758
#> 9 biolink:located_in 317598
#> 10 biolink:participates_in 275046
#> 11 biolink:is_active_in 146927
#> 12 biolink:acts_upstream_of_or_within 133635
#> 13 biolink:part_of 59047
#> 14 biolink:causes 16019
#> 15 biolink:is_sequence_variant_of 14873
#> 16 biolink:model_of 9339
#> 17 biolink:treats_or_applied_or_studied_to_treat 8634
#> 18 biolink:has_mode_of_inheritance 8616
#> 19 biolink:gene_associated_with_condition 8047
#> 20 biolink:acts_upstream_of 7385
#> 21 biolink:contributes_to 6382
#> 22 biolink:genetically_associated_with 3203
#> 23 biolink:colocalizes_with 2549
#> 24 biolink:associated_with_increased_likelihood_of 2544
#> 25 biolink:disease_has_location 1016
#> 26 biolink:acts_upstream_of_positive_effect 493
#> 27 biolink:ameliorates_condition 485
#> 28 biolink:acts_upstream_of_or_within_positive_effect 457
#> 29 biolink:acts_upstream_of_negative_effect 174
#> 30 biolink:acts_upstream_of_or_within_negative_effect 154
#> 31 biolink:preventative_for_condition 86
#> 32 biolink:contraindicated_in 3
#>
#> $total_nodes
#> [1] 1124572
#>
#> $total_edges
#> [1] 9394432
#>
#> $cats
#> $cats$`biolink:NamedThing`
#> [1] "biolink:NamedThing"
#>
#> $cats$`biolink:Entity`
#> [1] "biolink:Entity"
#>
#> $cats$`biolink:BiologicalEntity`
#> [1] "biolink:BiologicalEntity"
#>
#> $cats$`biolink:ThingWithTaxon`
#> [1] "biolink:ThingWithTaxon"
#>
#> $cats$`biolink:PhysicalEssenceOrOccurrent`
#> [1] "biolink:PhysicalEssenceOrOccurrent"
#>
#> $cats$`biolink:PhysicalEssence`
#> [1] "biolink:PhysicalEssence"
#>
#> $cats$`biolink:OntologyClass`
#> [1] "biolink:OntologyClass"
#>
#> $cats$`biolink:GenomicEntity`
#> [1] "biolink:GenomicEntity"
#>
#> $cats$`biolink:ChemicalEntityOrGeneOrGeneProduct`
#> [1] "biolink:ChemicalEntityOrGeneOrGeneProduct"
#>
#> $cats$`biolink:GeneOrGeneProduct`
#> [1] "biolink:GeneOrGeneProduct"
#>
#> $cats$`biolink:MacromolecularMachineMixin`
#> [1] "biolink:MacromolecularMachineMixin"
#>
#> $cats$`biolink:Gene`
#> [1] "biolink:Gene"
#>
#> $cats$`biolink:DiseaseOrPhenotypicFeature`
#> [1] "biolink:DiseaseOrPhenotypicFeature"
#>
#> $cats$`biolink:PhenotypicFeature`
#> [1] "biolink:PhenotypicFeature"
#>
#> $cats$`biolink:Genotype`
#> [1] "biolink:Genotype"
#>
#> $cats$`biolink:SubjectOfInvestigation`
#> [1] "biolink:SubjectOfInvestigation"
#>
#> $cats$`biolink:OrganismalEntity`
#> [1] "biolink:OrganismalEntity"
#>
#> $cats$`biolink:AnatomicalEntity`
#> [1] "biolink:AnatomicalEntity"
#>
#> $cats$`biolink:BiologicalProcessOrActivity`
#> [1] "biolink:BiologicalProcessOrActivity"
#>
#> $cats$`biolink:Occurrent`
#> [1] "biolink:Occurrent"
#>
#> $cats$`biolink:BiologicalProcess`
#> [1] "biolink:BiologicalProcess"
#>
#> $cats$`biolink:ChemicalEntityOrProteinOrPolypeptide`
#> [1] "biolink:ChemicalEntityOrProteinOrPolypeptide"
#>
#> $cats$`biolink:Disease`
#> [1] "biolink:Disease"
#>
#> $cats$`biolink:Polypeptide`
#> [1] "biolink:Polypeptide"
#>
#> $cats$`biolink:Protein`
#> [1] "biolink:Protein"
#>
#> $cats$`biolink:GeneProductMixin`
#> [1] "biolink:GeneProductMixin"
#>
#> $cats$`biolink:Pathway`
#> [1] "biolink:Pathway"
#>
#> $cats$`biolink:ChemicalOrDrugOrTreatment`
#> [1] "biolink:ChemicalOrDrugOrTreatment"
#>
#> $cats$`biolink:ChemicalEntity`
#> [1] "biolink:ChemicalEntity"
#>
#> $cats$`biolink:SequenceVariant`
#> [1] "biolink:SequenceVariant"
#>
#> $cats$`biolink:MolecularActivity`
#> [1] "biolink:MolecularActivity"
#>
#> $cats$`biolink:CellularComponent`
#> [1] "biolink:CellularComponent"
#>
#> $cats$`biolink:Cell`
#> [1] "biolink:Cell"
#>
#> $cats$`biolink:OrganismTaxon`
#> [1] "biolink:OrganismTaxon"
#>
#> $cats$`biolink:MolecularEntity`
#> [1] "biolink:MolecularEntity"
#>
#> $cats$`biolink:LifeStage`
#> [1] "biolink:LifeStage"
#>
#>
#> $preds
#> $preds$`biolink:interacts_with`
#> [1] "biolink:interacts_with"
#>
#> $preds$`biolink:has_phenotype`
#> [1] "biolink:has_phenotype"
#>
#> $preds$`biolink:expressed_in`
#> [1] "biolink:expressed_in"
#>
#> $preds$`biolink:orthologous_to`
#> [1] "biolink:orthologous_to"
#>
#> $preds$`biolink:actively_involved_in`
#> [1] "biolink:actively_involved_in"
#>
#> $preds$`biolink:subclass_of`
#> [1] "biolink:subclass_of"
#>
#> $preds$`biolink:enables`
#> [1] "biolink:enables"
#>
#> $preds$`biolink:related_to`
#> [1] "biolink:related_to"
#>
#> $preds$`biolink:located_in`
#> [1] "biolink:located_in"
#>
#> $preds$`biolink:participates_in`
#> [1] "biolink:participates_in"
#>
#> $preds$`biolink:is_active_in`
#> [1] "biolink:is_active_in"
#>
#> $preds$`biolink:acts_upstream_of_or_within`
#> [1] "biolink:acts_upstream_of_or_within"
#>
#> $preds$`biolink:part_of`
#> [1] "biolink:part_of"
#>
#> $preds$`biolink:causes`
#> [1] "biolink:causes"
#>
#> $preds$`biolink:is_sequence_variant_of`
#> [1] "biolink:is_sequence_variant_of"
#>
#> $preds$`biolink:model_of`
#> [1] "biolink:model_of"
#>
#> $preds$`biolink:treats_or_applied_or_studied_to_treat`
#> [1] "biolink:treats_or_applied_or_studied_to_treat"
#>
#> $preds$`biolink:has_mode_of_inheritance`
#> [1] "biolink:has_mode_of_inheritance"
#>
#> $preds$`biolink:gene_associated_with_condition`
#> [1] "biolink:gene_associated_with_condition"
#>
#> $preds$`biolink:acts_upstream_of`
#> [1] "biolink:acts_upstream_of"
#>
#> $preds$`biolink:contributes_to`
#> [1] "biolink:contributes_to"
#>
#> $preds$`biolink:genetically_associated_with`
#> [1] "biolink:genetically_associated_with"
#>
#> $preds$`biolink:colocalizes_with`
#> [1] "biolink:colocalizes_with"
#>
#> $preds$`biolink:associated_with_increased_likelihood_of`
#> [1] "biolink:associated_with_increased_likelihood_of"
#>
#> $preds$`biolink:disease_has_location`
#> [1] "biolink:disease_has_location"
#>
#> $preds$`biolink:acts_upstream_of_positive_effect`
#> [1] "biolink:acts_upstream_of_positive_effect"
#>
#> $preds$`biolink:ameliorates_condition`
#> [1] "biolink:ameliorates_condition"
#>
#> $preds$`biolink:acts_upstream_of_or_within_positive_effect`
#> [1] "biolink:acts_upstream_of_or_within_positive_effect"
#>
#> $preds$`biolink:acts_upstream_of_negative_effect`
#> [1] "biolink:acts_upstream_of_negative_effect"
#>
#> $preds$`biolink:acts_upstream_of_or_within_negative_effect`
#> [1] "biolink:acts_upstream_of_or_within_negative_effect"
#>
#> $preds$`biolink:preventative_for_condition`
#> [1] "biolink:preventative_for_condition"
#>
#> $preds$`biolink:contraindicated_in`
#> [1] "biolink:contraindicated_in"
#>
#>