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: 1123059
#> Total edges: 8969089
#>
#> Node category counts:
#> category count
#> biolink:NamedThing 1123059
#> biolink:Entity 1123059
#> biolink:ThingWithTaxon 1080221
#> biolink:BiologicalEntity 1080221
#> biolink:PhysicalEssenceOrOccurrent 876393
#> biolink:PhysicalEssence 811051
#> biolink:OntologyClass 786167
#> biolink:GenomicEntity 720825
#> biolink:ChemicalEntityOrGeneOrGeneProduct 609877
#> biolink:MacromolecularMachineMixin 592806
#> biolink:GeneOrGeneProduct 592806
#> biolink:Gene 571154
#> biolink:DiseaseOrPhenotypicFeature 198941
#> biolink:PhenotypicFeature 168951
#> biolink:Genotype 135567
#> biolink:OrganismalEntity 73461
#> biolink:SubjectOfInvestigation 73461
#> biolink:AnatomicalEntity 73155
#> biolink:BiologicalProcessOrActivity 65342
#> biolink:Occurrent 65342
#> biolink:BiologicalProcess 52688
#> biolink:ChemicalEntityOrProteinOrPolypeptide 38723
#> biolink:Disease 29990
#> biolink:Pathway 21946
#> biolink:GeneProductMixin 21652
#> biolink:Polypeptide 21652
#> biolink:Protein 21652
#> biolink:ChemicalEntity 17071
#> biolink:ChemicalOrDrugOrTreatment 17071
#> biolink:SequenceVariant 14104
#> biolink:MolecularActivity 12654
#> biolink:CellularComponent 4525
#> biolink:Cell 3069
#> biolink:OrganismTaxon 1959
#> biolink:MolecularEntity 529
#> biolink:LifeStage 306
#>
#> Edge type counts:
#> predicate count
#> biolink:interacts_with 2458186
#> biolink:has_phenotype 1489349
#> biolink:expressed_in 1233656
#> biolink:orthologous_to 696758
#> biolink:actively_involved_in 659514
#> biolink:subclass_of 572463
#> biolink:enables 455373
#> biolink:related_to 385165
#> biolink:located_in 317053
#> biolink:participates_in 273655
#> biolink:is_active_in 147062
#> biolink:acts_upstream_of_or_within 133021
#> biolink:part_of 59011
#> biolink:causes 15818
#> biolink:is_sequence_variant_of 14183
#> biolink:model_of 9313
#> biolink:has_mode_of_inheritance 8616
#> biolink:treats_or_applied_or_studied_to_treat 8616
#> biolink:gene_associated_with_condition 8060
#> biolink:acts_upstream_of 7364
#> biolink:contributes_to 6376
#> biolink:genetically_associated_with 2924
#> biolink:colocalizes_with 2551
#> biolink:associated_with_increased_likelihood_of 2388
#> biolink:disease_has_location 1016
#> biolink:acts_upstream_of_positive_effect 493
#> biolink:acts_upstream_of_or_within_positive_effect 453
#> biolink:ameliorates_condition 296
#> biolink:acts_upstream_of_negative_effect 174
#> biolink:acts_upstream_of_or_within_negative_effect 153
#> biolink:preventative_for_condition 28
#> biolink:contraindicated_in 1
print(stats)
#> $node_summary
#> category count
#> 1 biolink:NamedThing 1123059
#> 2 biolink:Entity 1123059
#> 3 biolink:ThingWithTaxon 1080221
#> 4 biolink:BiologicalEntity 1080221
#> 5 biolink:PhysicalEssenceOrOccurrent 876393
#> 6 biolink:PhysicalEssence 811051
#> 7 biolink:OntologyClass 786167
#> 8 biolink:GenomicEntity 720825
#> 9 biolink:ChemicalEntityOrGeneOrGeneProduct 609877
#> 10 biolink:MacromolecularMachineMixin 592806
#> 11 biolink:GeneOrGeneProduct 592806
#> 12 biolink:Gene 571154
#> 13 biolink:DiseaseOrPhenotypicFeature 198941
#> 14 biolink:PhenotypicFeature 168951
#> 15 biolink:Genotype 135567
#> 16 biolink:OrganismalEntity 73461
#> 17 biolink:SubjectOfInvestigation 73461
#> 18 biolink:AnatomicalEntity 73155
#> 19 biolink:BiologicalProcessOrActivity 65342
#> 20 biolink:Occurrent 65342
#> 21 biolink:BiologicalProcess 52688
#> 22 biolink:ChemicalEntityOrProteinOrPolypeptide 38723
#> 23 biolink:Disease 29990
#> 24 biolink:Pathway 21946
#> 25 biolink:GeneProductMixin 21652
#> 26 biolink:Polypeptide 21652
#> 27 biolink:Protein 21652
#> 28 biolink:ChemicalEntity 17071
#> 29 biolink:ChemicalOrDrugOrTreatment 17071
#> 30 biolink:SequenceVariant 14104
#> 31 biolink:MolecularActivity 12654
#> 32 biolink:CellularComponent 4525
#> 33 biolink:Cell 3069
#> 34 biolink:OrganismTaxon 1959
#> 35 biolink:MolecularEntity 529
#> 36 biolink:LifeStage 306
#>
#> $edge_summary
#> predicate count
#> 1 biolink:interacts_with 2458186
#> 2 biolink:has_phenotype 1489349
#> 3 biolink:expressed_in 1233656
#> 4 biolink:orthologous_to 696758
#> 5 biolink:actively_involved_in 659514
#> 6 biolink:subclass_of 572463
#> 7 biolink:enables 455373
#> 8 biolink:related_to 385165
#> 9 biolink:located_in 317053
#> 10 biolink:participates_in 273655
#> 11 biolink:is_active_in 147062
#> 12 biolink:acts_upstream_of_or_within 133021
#> 13 biolink:part_of 59011
#> 14 biolink:causes 15818
#> 15 biolink:is_sequence_variant_of 14183
#> 16 biolink:model_of 9313
#> 17 biolink:has_mode_of_inheritance 8616
#> 18 biolink:treats_or_applied_or_studied_to_treat 8616
#> 19 biolink:gene_associated_with_condition 8060
#> 20 biolink:acts_upstream_of 7364
#> 21 biolink:contributes_to 6376
#> 22 biolink:genetically_associated_with 2924
#> 23 biolink:colocalizes_with 2551
#> 24 biolink:associated_with_increased_likelihood_of 2388
#> 25 biolink:disease_has_location 1016
#> 26 biolink:acts_upstream_of_positive_effect 493
#> 27 biolink:acts_upstream_of_or_within_positive_effect 453
#> 28 biolink:ameliorates_condition 296
#> 29 biolink:acts_upstream_of_negative_effect 174
#> 30 biolink:acts_upstream_of_or_within_negative_effect 153
#> 31 biolink:preventative_for_condition 28
#> 32 biolink:contraindicated_in 1
#>
#> $total_nodes
#> [1] 1123059
#>
#> $total_edges
#> [1] 8969089
#>
#> $cats
#> $cats$`biolink:NamedThing`
#> [1] "biolink:NamedThing"
#>
#> $cats$`biolink:Entity`
#> [1] "biolink:Entity"
#>
#> $cats$`biolink:ThingWithTaxon`
#> [1] "biolink:ThingWithTaxon"
#>
#> $cats$`biolink:BiologicalEntity`
#> [1] "biolink:BiologicalEntity"
#>
#> $cats$`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:MacromolecularMachineMixin`
#> [1] "biolink:MacromolecularMachineMixin"
#>
#> $cats$`biolink:GeneOrGeneProduct`
#> [1] "biolink:GeneOrGeneProduct"
#>
#> $cats$`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:OrganismalEntity`
#> [1] "biolink:OrganismalEntity"
#>
#> $cats$`biolink:SubjectOfInvestigation`
#> [1] "biolink:SubjectOfInvestigation"
#>
#> $cats$`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:Pathway`
#> [1] "biolink:Pathway"
#>
#> $cats$`biolink:GeneProductMixin`
#> [1] "biolink:GeneProductMixin"
#>
#> $cats$`biolink:Polypeptide`
#> [1] "biolink:Polypeptide"
#>
#> $cats$`biolink:Protein`
#> [1] "biolink:Protein"
#>
#> $cats$`biolink:ChemicalEntity`
#> [1] "biolink:ChemicalEntity"
#>
#> $cats$`biolink:ChemicalOrDrugOrTreatment`
#> [1] "biolink:ChemicalOrDrugOrTreatment"
#>
#> $cats$`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:has_mode_of_inheritance`
#> [1] "biolink:has_mode_of_inheritance"
#>
#> $preds$`biolink:treats_or_applied_or_studied_to_treat`
#> [1] "biolink:treats_or_applied_or_studied_to_treat"
#>
#> $preds$`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:acts_upstream_of_or_within_positive_effect`
#> [1] "biolink:acts_upstream_of_or_within_positive_effect"
#>
#> $preds$`biolink:ameliorates_condition`
#> [1] "biolink:ameliorates_condition"
#>
#> $preds$`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"
#>
#>