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: 1128872
#> Total edges: 9432564
#>
#> Node category counts:
#> category count
#> biolink:Entity 1128872
#> biolink:NamedThing 1128872
#> biolink:ThingWithTaxon 1076490
#> biolink:BiologicalEntity 1076490
#> biolink:PhysicalEssenceOrOccurrent 876727
#> biolink:PhysicalEssence 811322
#> biolink:OntologyClass 780621
#> biolink:GenomicEntity 715216
#> biolink:ChemicalEntityOrGeneOrGeneProduct 609150
#> biolink:GeneOrGeneProduct 586392
#> biolink:MacromolecularMachineMixin 586392
#> biolink:Gene 563625
#> biolink:DiseaseOrPhenotypicFeature 199440
#> biolink:PhenotypicFeature 169147
#> biolink:Genotype 136735
#> biolink:OrganismalEntity 73662
#> biolink:SubjectOfInvestigation 73662
#> biolink:AnatomicalEntity 73348
#> biolink:Occurrent 65405
#> biolink:BiologicalProcessOrActivity 65405
#> biolink:BiologicalProcess 52702
#> biolink:ChemicalEntityOrProteinOrPolypeptide 45525
#> biolink:Disease 30293
#> biolink:Polypeptide 22767
#> biolink:Protein 22767
#> biolink:GeneProductMixin 22767
#> biolink:ChemicalEntity 22758
#> biolink:ChemicalOrDrugOrTreatment 22758
#> biolink:Pathway 21946
#> biolink:SequenceVariant 14856
#> biolink:MolecularActivity 12703
#> biolink:CellularComponent 4536
#> biolink:Cell 3136
#> biolink:OrganismTaxon 1982
#> biolink:MolecularEntity 529
#> biolink:LifeStage 314
#>
#> Edge type counts:
#> predicate count
#> biolink:interacts_with 2480332
#> biolink:has_phenotype 1494613
#> biolink:expressed_in 1228812
#> biolink:orthologous_to 1067896
#> biolink:actively_involved_in 642840
#> biolink:subclass_of 607367
#> biolink:enables 452649
#> biolink:related_to 404848
#> biolink:located_in 315774
#> biolink:participates_in 288255
#> biolink:is_active_in 148277
#> biolink:acts_upstream_of_or_within 142265
#> biolink:part_of 57892
#> biolink:treats_or_applied_or_studied_to_treat 18846
#> biolink:causes 16051
#> biolink:is_sequence_variant_of 14981
#> biolink:model_of 9357
#> biolink:has_mode_of_inheritance 8616
#> biolink:gene_associated_with_condition 8047
#> biolink:acts_upstream_of 7414
#> biolink:contributes_to 6241
#> biolink:genetically_associated_with 3242
#> biolink:associated_with_increased_likelihood_of 2584
#> biolink:colocalizes_with 2499
#> biolink:disease_has_location 1016
#> biolink:acts_upstream_of_positive_effect 490
#> biolink:ameliorates_condition 485
#> biolink:acts_upstream_of_or_within_positive_effect 457
#> biolink:acts_upstream_of_negative_effect 173
#> biolink:acts_upstream_of_or_within_negative_effect 156
#> biolink:preventative_for_condition 86
#> biolink:contraindicated_in 3
print(stats)
#> $node_summary
#> category count
#> 1 biolink:Entity 1128872
#> 2 biolink:NamedThing 1128872
#> 3 biolink:ThingWithTaxon 1076490
#> 4 biolink:BiologicalEntity 1076490
#> 5 biolink:PhysicalEssenceOrOccurrent 876727
#> 6 biolink:PhysicalEssence 811322
#> 7 biolink:OntologyClass 780621
#> 8 biolink:GenomicEntity 715216
#> 9 biolink:ChemicalEntityOrGeneOrGeneProduct 609150
#> 10 biolink:GeneOrGeneProduct 586392
#> 11 biolink:MacromolecularMachineMixin 586392
#> 12 biolink:Gene 563625
#> 13 biolink:DiseaseOrPhenotypicFeature 199440
#> 14 biolink:PhenotypicFeature 169147
#> 15 biolink:Genotype 136735
#> 16 biolink:OrganismalEntity 73662
#> 17 biolink:SubjectOfInvestigation 73662
#> 18 biolink:AnatomicalEntity 73348
#> 19 biolink:Occurrent 65405
#> 20 biolink:BiologicalProcessOrActivity 65405
#> 21 biolink:BiologicalProcess 52702
#> 22 biolink:ChemicalEntityOrProteinOrPolypeptide 45525
#> 23 biolink:Disease 30293
#> 24 biolink:Polypeptide 22767
#> 25 biolink:Protein 22767
#> 26 biolink:GeneProductMixin 22767
#> 27 biolink:ChemicalEntity 22758
#> 28 biolink:ChemicalOrDrugOrTreatment 22758
#> 29 biolink:Pathway 21946
#> 30 biolink:SequenceVariant 14856
#> 31 biolink:MolecularActivity 12703
#> 32 biolink:CellularComponent 4536
#> 33 biolink:Cell 3136
#> 34 biolink:OrganismTaxon 1982
#> 35 biolink:MolecularEntity 529
#> 36 biolink:LifeStage 314
#>
#> $edge_summary
#> predicate count
#> 1 biolink:interacts_with 2480332
#> 2 biolink:has_phenotype 1494613
#> 3 biolink:expressed_in 1228812
#> 4 biolink:orthologous_to 1067896
#> 5 biolink:actively_involved_in 642840
#> 6 biolink:subclass_of 607367
#> 7 biolink:enables 452649
#> 8 biolink:related_to 404848
#> 9 biolink:located_in 315774
#> 10 biolink:participates_in 288255
#> 11 biolink:is_active_in 148277
#> 12 biolink:acts_upstream_of_or_within 142265
#> 13 biolink:part_of 57892
#> 14 biolink:treats_or_applied_or_studied_to_treat 18846
#> 15 biolink:causes 16051
#> 16 biolink:is_sequence_variant_of 14981
#> 17 biolink:model_of 9357
#> 18 biolink:has_mode_of_inheritance 8616
#> 19 biolink:gene_associated_with_condition 8047
#> 20 biolink:acts_upstream_of 7414
#> 21 biolink:contributes_to 6241
#> 22 biolink:genetically_associated_with 3242
#> 23 biolink:associated_with_increased_likelihood_of 2584
#> 24 biolink:colocalizes_with 2499
#> 25 biolink:disease_has_location 1016
#> 26 biolink:acts_upstream_of_positive_effect 490
#> 27 biolink:ameliorates_condition 485
#> 28 biolink:acts_upstream_of_or_within_positive_effect 457
#> 29 biolink:acts_upstream_of_negative_effect 173
#> 30 biolink:acts_upstream_of_or_within_negative_effect 156
#> 31 biolink:preventative_for_condition 86
#> 32 biolink:contraindicated_in 3
#>
#> $total_nodes
#> [1] 1128872
#>
#> $total_edges
#> [1] 9432564
#>
#> $cats
#> $cats$`biolink:Entity`
#> [1] "biolink:Entity"
#>
#> $cats$`biolink:NamedThing`
#> [1] "biolink:NamedThing"
#>
#> $cats$`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: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:OrganismalEntity`
#> [1] "biolink:OrganismalEntity"
#>
#> $cats$`biolink:SubjectOfInvestigation`
#> [1] "biolink:SubjectOfInvestigation"
#>
#> $cats$`biolink:AnatomicalEntity`
#> [1] "biolink:AnatomicalEntity"
#>
#> $cats$`biolink:Occurrent`
#> [1] "biolink:Occurrent"
#>
#> $cats$`biolink:BiologicalProcessOrActivity`
#> [1] "biolink:BiologicalProcessOrActivity"
#>
#> $cats$`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:ChemicalEntity`
#> [1] "biolink:ChemicalEntity"
#>
#> $cats$`biolink:ChemicalOrDrugOrTreatment`
#> [1] "biolink:ChemicalOrDrugOrTreatment"
#>
#> $cats$`biolink:Pathway`
#> [1] "biolink:Pathway"
#>
#> $cats$`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:treats_or_applied_or_studied_to_treat`
#> [1] "biolink:treats_or_applied_or_studied_to_treat"
#>
#> $preds$`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: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:associated_with_increased_likelihood_of`
#> [1] "biolink:associated_with_increased_likelihood_of"
#>
#> $preds$`biolink:colocalizes_with`
#> [1] "biolink:colocalizes_with"
#>
#> $preds$`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"
#>
#>