Given a Neo4j based KG engine, provides summary information in the form of
node counts, category counts across nodes, relationship type counts, and available properties.
General information about the graph is printed to the console, and a list of
dataframes with this information is returned invisibly. Also returned
are cats, preds, and props entries, containing lists of available
categories/predicates/properties 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: 1346185
#> Total edges: 14621271
#>
#> Node category counts:
#> category count
#> biolink:Gene 581682
#> biolink:SequenceVariant 209865
#> biolink:PhenotypicFeature 169316
#> biolink:Genotype 137639
#> biolink:AnatomicalEntity 66029
#> biolink:BiologicalProcess 30769
#> biolink:Disease 30384
#> biolink:NamedThing 27656
#> biolink:Protein 25098
#> biolink:Pathway 22254
#> biolink:ChemicalEntity 22231
#> biolink:MolecularActivity 12723
#> biolink:CellularComponent 4538
#> biolink:Cell 3171
#> biolink:OrganismTaxon 1987
#> biolink:MolecularEntity 529
#> biolink:LifeStage 314
#>
#> Edge type counts:
#> predicate count
#> biolink:interacts_with 2797006
#> biolink:expressed_in 2379934
#> biolink:has_phenotype 2077069
#> biolink:orthologous_to 1506263
#> biolink:enables 1239419
#> biolink:actively_involved_in 1103592
#> biolink:located_in 994683
#> biolink:subclass_of 612920
#> biolink:related_to 520067
#> biolink:participates_in 329190
#> biolink:acts_upstream_of_or_within 295324
#> biolink:is_active_in 188945
#> biolink:is_sequence_variant_of 181003
#> biolink:has_sequence_variant 157143
#> biolink:part_of 129977
#> biolink:treats_or_applied_or_studied_to_treat 18934
#> biolink:causes 18203
#> biolink:acts_upstream_of 17896
#> biolink:model_of 10069
#> biolink:contributes_to 9837
#> biolink:has_mode_of_inheritance 8829
#> biolink:gene_associated_with_condition 8089
#> biolink:associated_with_increased_likelihood_of 4394
#> biolink:colocalizes_with 4251
#> biolink:genetically_associated_with 3484
#> biolink:disease_has_location 1020
#> biolink:acts_upstream_of_positive_effect 992
#> biolink:acts_upstream_of_or_within_positive_effect 826
#> biolink:ameliorates_condition 786
#> biolink:acts_upstream_of_negative_effect 336
#> biolink:acts_upstream_of_or_within_negative_effect 279
#> biolink:has_participant 269
#> biolink:preventative_for_condition 145
#> biolink:disrupts 89
#> biolink:caused_by 5
#> biolink:contraindicated_in 3
#>
#> Available node and edge properties:
#> [1] "category" "name"
#> [3] "provided_by" "in_taxon"
#> [5] "in_taxon_label" "namespace"
#> [7] "id" "description"
#> [9] "synonym" "exact_synonyms"
#> [11] "iri" "deprecated"
#> [13] "full_name" "symbol"
#> [15] "xref" "type"
#> [17] "narrow_synonyms" "broad_synonyms"
#> [19] "related_synonyms" "subsets"
#> [21] "has_gene" "predicate"
#> [23] "agent_type" "aggregator_knowledge_source"
#> [25] "knowledge_level" "primary_knowledge_source"
#> [27] "publications" "subject"
#> [29] "object" "original_subject"
#> [31] "original_object" "has_evidence"
#> [33] "disease_context_qualifier" "has_count"
#> [35] "has_percentage" "has_quotient"
#> [37] "has_total" "frequency_qualifier"
#> [39] "qualifiers" "stage_qualifier"
#> [41] "original_predicate" "subject_specialization_qualifier"
#> [43] "qualifier" "object_specialization_qualifier"
#> [45] "negated" "onset_qualifier"
#> [47] "sex_qualifier" "species_context_qualifier"
#>
#>
#> For more information about Biolink node (Class) and edge (Association) properties, see https://biolink.github.io/biolink-model/.
print(stats)
#> $node_summary
#> category count
#> 1 biolink:Gene 581682
#> 2 biolink:SequenceVariant 209865
#> 3 biolink:PhenotypicFeature 169316
#> 4 biolink:Genotype 137639
#> 5 biolink:AnatomicalEntity 66029
#> 6 biolink:BiologicalProcess 30769
#> 7 biolink:Disease 30384
#> 8 biolink:NamedThing 27656
#> 9 biolink:Protein 25098
#> 10 biolink:Pathway 22254
#> 11 biolink:ChemicalEntity 22231
#> 12 biolink:MolecularActivity 12723
#> 13 biolink:CellularComponent 4538
#> 14 biolink:Cell 3171
#> 15 biolink:OrganismTaxon 1987
#> 16 biolink:MolecularEntity 529
#> 17 biolink:LifeStage 314
#>
#> $edge_summary
#> predicate count
#> 1 biolink:interacts_with 2797006
#> 2 biolink:expressed_in 2379934
#> 3 biolink:has_phenotype 2077069
#> 4 biolink:orthologous_to 1506263
#> 5 biolink:enables 1239419
#> 6 biolink:actively_involved_in 1103592
#> 7 biolink:located_in 994683
#> 8 biolink:subclass_of 612920
#> 9 biolink:related_to 520067
#> 10 biolink:participates_in 329190
#> 11 biolink:acts_upstream_of_or_within 295324
#> 12 biolink:is_active_in 188945
#> 13 biolink:is_sequence_variant_of 181003
#> 14 biolink:has_sequence_variant 157143
#> 15 biolink:part_of 129977
#> 16 biolink:treats_or_applied_or_studied_to_treat 18934
#> 17 biolink:causes 18203
#> 18 biolink:acts_upstream_of 17896
#> 19 biolink:model_of 10069
#> 20 biolink:contributes_to 9837
#> 21 biolink:has_mode_of_inheritance 8829
#> 22 biolink:gene_associated_with_condition 8089
#> 23 biolink:associated_with_increased_likelihood_of 4394
#> 24 biolink:colocalizes_with 4251
#> 25 biolink:genetically_associated_with 3484
#> 26 biolink:disease_has_location 1020
#> 27 biolink:acts_upstream_of_positive_effect 992
#> 28 biolink:acts_upstream_of_or_within_positive_effect 826
#> 29 biolink:ameliorates_condition 786
#> 30 biolink:acts_upstream_of_negative_effect 336
#> 31 biolink:acts_upstream_of_or_within_negative_effect 279
#> 32 biolink:has_participant 269
#> 33 biolink:preventative_for_condition 145
#> 34 biolink:disrupts 89
#> 35 biolink:caused_by 5
#> 36 biolink:contraindicated_in 3
#>
#> $total_nodes
#> [1] 1346185
#>
#> $total_edges
#> [1] 14621271
#>
#> $cats
#> $cats$`biolink:Gene`
#> [1] "biolink:Gene"
#>
#> $cats$`biolink:SequenceVariant`
#> [1] "biolink:SequenceVariant"
#>
#> $cats$`biolink:PhenotypicFeature`
#> [1] "biolink:PhenotypicFeature"
#>
#> $cats$`biolink:Genotype`
#> [1] "biolink:Genotype"
#>
#> $cats$`biolink:AnatomicalEntity`
#> [1] "biolink:AnatomicalEntity"
#>
#> $cats$`biolink:BiologicalProcess`
#> [1] "biolink:BiologicalProcess"
#>
#> $cats$`biolink:Disease`
#> [1] "biolink:Disease"
#>
#> $cats$`biolink:NamedThing`
#> [1] "biolink:NamedThing"
#>
#> $cats$`biolink:Protein`
#> [1] "biolink:Protein"
#>
#> $cats$`biolink:Pathway`
#> [1] "biolink:Pathway"
#>
#> $cats$`biolink:ChemicalEntity`
#> [1] "biolink:ChemicalEntity"
#>
#> $cats$`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:expressed_in`
#> [1] "biolink:expressed_in"
#>
#> $preds$`biolink:has_phenotype`
#> [1] "biolink:has_phenotype"
#>
#> $preds$`biolink:orthologous_to`
#> [1] "biolink:orthologous_to"
#>
#> $preds$`biolink:enables`
#> [1] "biolink:enables"
#>
#> $preds$`biolink:actively_involved_in`
#> [1] "biolink:actively_involved_in"
#>
#> $preds$`biolink:located_in`
#> [1] "biolink:located_in"
#>
#> $preds$`biolink:subclass_of`
#> [1] "biolink:subclass_of"
#>
#> $preds$`biolink:related_to`
#> [1] "biolink:related_to"
#>
#> $preds$`biolink:participates_in`
#> [1] "biolink:participates_in"
#>
#> $preds$`biolink:acts_upstream_of_or_within`
#> [1] "biolink:acts_upstream_of_or_within"
#>
#> $preds$`biolink:is_active_in`
#> [1] "biolink:is_active_in"
#>
#> $preds$`biolink:is_sequence_variant_of`
#> [1] "biolink:is_sequence_variant_of"
#>
#> $preds$`biolink:has_sequence_variant`
#> [1] "biolink:has_sequence_variant"
#>
#> $preds$`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:acts_upstream_of`
#> [1] "biolink:acts_upstream_of"
#>
#> $preds$`biolink:model_of`
#> [1] "biolink:model_of"
#>
#> $preds$`biolink:contributes_to`
#> [1] "biolink:contributes_to"
#>
#> $preds$`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:associated_with_increased_likelihood_of`
#> [1] "biolink:associated_with_increased_likelihood_of"
#>
#> $preds$`biolink:colocalizes_with`
#> [1] "biolink:colocalizes_with"
#>
#> $preds$`biolink:genetically_associated_with`
#> [1] "biolink:genetically_associated_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: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:has_participant`
#> [1] "biolink:has_participant"
#>
#> $preds$`biolink:preventative_for_condition`
#> [1] "biolink:preventative_for_condition"
#>
#> $preds$`biolink:disrupts`
#> [1] "biolink:disrupts"
#>
#> $preds$`biolink:caused_by`
#> [1] "biolink:caused_by"
#>
#> $preds$`biolink:contraindicated_in`
#> [1] "biolink:contraindicated_in"
#>
#>
#> $props
#> $props$category
#> [1] "category"
#>
#> $props$name
#> [1] "name"
#>
#> $props$provided_by
#> [1] "provided_by"
#>
#> $props$in_taxon
#> [1] "in_taxon"
#>
#> $props$in_taxon_label
#> [1] "in_taxon_label"
#>
#> $props$namespace
#> [1] "namespace"
#>
#> $props$id
#> [1] "id"
#>
#> $props$description
#> [1] "description"
#>
#> $props$synonym
#> [1] "synonym"
#>
#> $props$exact_synonyms
#> [1] "exact_synonyms"
#>
#> $props$iri
#> [1] "iri"
#>
#> $props$deprecated
#> [1] "deprecated"
#>
#> $props$full_name
#> [1] "full_name"
#>
#> $props$symbol
#> [1] "symbol"
#>
#> $props$xref
#> [1] "xref"
#>
#> $props$type
#> [1] "type"
#>
#> $props$narrow_synonyms
#> [1] "narrow_synonyms"
#>
#> $props$broad_synonyms
#> [1] "broad_synonyms"
#>
#> $props$related_synonyms
#> [1] "related_synonyms"
#>
#> $props$subsets
#> [1] "subsets"
#>
#> $props$has_gene
#> [1] "has_gene"
#>
#> $props$predicate
#> [1] "predicate"
#>
#> $props$agent_type
#> [1] "agent_type"
#>
#> $props$aggregator_knowledge_source
#> [1] "aggregator_knowledge_source"
#>
#> $props$knowledge_level
#> [1] "knowledge_level"
#>
#> $props$primary_knowledge_source
#> [1] "primary_knowledge_source"
#>
#> $props$publications
#> [1] "publications"
#>
#> $props$subject
#> [1] "subject"
#>
#> $props$object
#> [1] "object"
#>
#> $props$original_subject
#> [1] "original_subject"
#>
#> $props$original_object
#> [1] "original_object"
#>
#> $props$has_evidence
#> [1] "has_evidence"
#>
#> $props$disease_context_qualifier
#> [1] "disease_context_qualifier"
#>
#> $props$has_count
#> [1] "has_count"
#>
#> $props$has_percentage
#> [1] "has_percentage"
#>
#> $props$has_quotient
#> [1] "has_quotient"
#>
#> $props$has_total
#> [1] "has_total"
#>
#> $props$frequency_qualifier
#> [1] "frequency_qualifier"
#>
#> $props$qualifiers
#> [1] "qualifiers"
#>
#> $props$stage_qualifier
#> [1] "stage_qualifier"
#>
#> $props$original_predicate
#> [1] "original_predicate"
#>
#> $props$subject_specialization_qualifier
#> [1] "subject_specialization_qualifier"
#>
#> $props$qualifier
#> [1] "qualifier"
#>
#> $props$object_specialization_qualifier
#> [1] "object_specialization_qualifier"
#>
#> $props$negated
#> [1] "negated"
#>
#> $props$onset_qualifier
#> [1] "onset_qualifier"
#>
#> $props$sex_qualifier
#> [1] "sex_qualifier"
#>
#> $props$species_context_qualifier
#> [1] "species_context_qualifier"
#>
#>