oneilsh
commented
1 week ago Making some progress on this one with a summary() method for engines; it prints some summary info (unless quiet = TRUE is passed) and returns a list of the summary info invisibly:
> res <- monarch_engine() |> summary()
A Neo4j-backed knowledge graph engine.
Gathering statistics, please wait...
Total nodes: 1032366
Total edges: 8626674
Node category counts:
category count
biolink:Entity 1032366
biolink:NamedThing 1032366
biolink:ThingWithTaxon 999620
biolink:BiologicalEntity 999602
biolink:PhysicalEssenceOrOccurrent 845454
biolink:OntologyClass 783717
biolink:PhysicalEssence 779441
biolink:GenomicEntity 717557
biolink:ChemicalEntityOrGeneOrGeneProduct 577339
biolink:MacromolecularMachineMixin 574363
biolink:GeneOrGeneProduct 572248
biolink:Gene 571124
biolink:DiseaseOrPhenotypicFeature 153897
biolink:Genotype 133380
biolink:PhenotypicFeature 124544
biolink:Occurrent 66013
biolink:BiologicalProcessOrActivity 66009
biolink:SubjectOfInvestigation 58906
biolink:OrganismalEntity 58905
biolink:AnatomicalEntity 56807
biolink:Disease 29353
biolink:BiologicalProcess 26268
biolink:Cell 26159
biolink:Pathway 22331
biolink:GrossAnatomicalStructure 17122
biolink:SequenceVariant 13028
biolink:ChemicalEntityOrProteinOrPolypeptide 6209
biolink:CellularComponent 5319
biolink:ChemicalOrDrugOrTreatment 5095
biolink:ChemicalEntity 5094
biolink:MolecularEntity 4723
biolink:MacromolecularComplex 2115
biolink:MolecularActivity 1560
biolink:CellularOrganism 1532
biolink:GeneProductMixin 1124
biolink:Polypeptide 1115
biolink:Protein 1114
biolink:Vertebrate 561
biolink:Virus 322
biolink:BehavioralFeature 297
biolink:LifeStage 238
biolink:PathologicalProcess 231
biolink:PathologicalEntityMixin 231
biolink:ChemicalMixture 104
biolink:Drug 100
biolink:MolecularMixture 100
biolink:SmallMolecule 72
biolink:Attribute 50
biolink:InformationContentEntity 49
biolink:ClinicalAttribute 44
biolink:Onset 44
biolink:ClinicalCourse 44
biolink:OrganismTaxon 41
biolink:NucleicAcidEntity 18
biolink:Transcript 16
biolink:EvidenceType 16
biolink:RNAProduct 10
biolink:Plant 4
biolink:Publication 4
biolink:Fungus 4
biolink:ExposureEvent 3
biolink:PlanetaryEntity 3
biolink:ProcessedMaterial 3
biolink:Activity 3
biolink:ActivityAndBehavior 3
biolink:Mammal 3
biolink:GeneGroupingMixin 3
biolink:BiologicalSex 3
biolink:RegulatoryRegion 3
biolink:ChemicalExposure 2
biolink:EnvironmentalFeature 2
biolink:ConfidenceLevel 2
biolink:Dataset 2
biolink:AdministrativeEntity 2
biolink:Agent 2
biolink:Invertebrate 2
biolink:ProteinFamily 2
biolink:GeneticInheritance 2
biolink:Haplotype 2
biolink:PopulationOfIndividualOrganisms 2
biolink:NoncodingRNAProduct 2
biolink:DrugExposure 1
biolink:Patent 1
biolink:CellLine 1
biolink:EnvironmentalProcess 1
biolink:WebPage 1
biolink:DatasetDistribution 1
biolink:IndividualOrganism 1
biolink:Bacterium 1
biolink:ProteinDomain 1
biolink:StudyVariable 1
biolink:Human 1
biolink:Event 1
biolink:Study 1
biolink:Zygosity 1
biolink:ReagentTargetedGene 1
biolink:MaterialSample 1
biolink:PhysicalEntity 1
biolink:Treatment 1
biolink:PhenotypicSex 1
biolink:GenotypicSex 1
biolink:Exon 1
biolink:TranscriptionFactorBindingSite 1
biolink:MicroRNA 1
biolink:SiRNA 1
biolink:Genome 1
biolink:Snv 1
biolink:AccessibleDnaRegion 1
biolink:DiagnosticAid 1
Edge type counts:
predicate count
biolink:interacts_with 2483429
biolink:has_phenotype 1460300
biolink:expressed_in 1229152
biolink:actively_involved_in 632984
biolink:orthologous_to 551358
biolink:subclass_of 522698
biolink:enables 431854
biolink:located_in 312598
biolink:related_to 298633
biolink:participates_in 268302
biolink:acts_upstream_of_or_within 145303
biolink:active_in 144810
biolink:part_of 63174
biolink:causes 15628
biolink:is_sequence_variant_of 13050
biolink:model_of 9242
biolink:has_mode_of_inheritance 8577
biolink:gene_associated_with_condition 7971
biolink:acts_upstream_of 7095
biolink:contributes_to 6334
biolink:treats_or_applied_or_studied_to_treat 5945
biolink:colocalizes_with 2653
biolink:associated_with_increased_likelihood_of 2199
biolink:genetically_associated_with 2155
biolink:acts_upstream_of_positive_effect 473
biolink:acts_upstream_of_or_within_positive_effect 440
biolink:acts_upstream_of_negative_effect 165
biolink:acts_upstream_of_or_within_negative_effect 152
> str(res)
List of 4
$ node_summary:'data.frame': 109 obs. of 2 variables:
..$ category: chr [1:109] "biolink:Entity" "biolink:NamedThing" "biolink:ThingWithTaxon" "biolink:BiologicalEntity" ...
..$ count : int [1:109] 1032366 1032366 999620 999602 845454 783717 779441 717557 577339 574363 ...
$ edge_summary:'data.frame': 28 obs. of 2 variables:
..$ predicate: chr [1:28] "biolink:interacts_with" "biolink:has_phenotype" "biolink:expressed_in" "biolink:actively_involved_in" ...
..$ count : int [1:28] 2483429 1460300 1229152 632984 551358 522698 431854 312598 298633 268302 ...
$ total_nodes : int 1032366
$ total_edges : int 8626674Not 100% happy, but it's a start.
It would be nice to have a small set of functions to help users orient to a KGs (ie, handled by an engine) contents for effective querying. Some ideas:
summarize_nodes - count nodes in the KG, broken out by category. This is somewhat complicated by overlapping categories; e.g. the count for GeneOrGeneProduct would subsume the count for Gene, and it's hard to know when a category is fully subsumed by another or something else. Counting by
pcategorywould be nice, may require some fancy cypher since those are defined post-fetchsummarize_edges - summarize the relationships in a KG, counts of different kinds, and maybe with some counts of the categories of nodes they connect? (e.g. there are N "biolink:has_phenotype" edges, N1 of which connect Disease -> Phenotype, N2 of which connect Gene -> Phenotype, etc)
sample - sample a set of nodes and edges. Perhaps filtered to specific categories or relationships of interest