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rtx-kg2-gateway-kuzu-database-details.md

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RTX-KG2-gateway Kuzu Database Schema Details

Please see below for details on the Kuzu database associated with RTX-KG2 created as part of this project.

Table types

Tables below are provided as either NODE or REL_GROUP tables. REL_GROUPS are specialized tables within Kuzu databases that are collections of NODE type pairs. REL_GROUPS are shown by name below which can be referenced as part of Cypher queries (instead of the more verbose and many NODE type pairs).

NODE Tables

Example NODE Data and JSON Schema

Example data Example data JSON schema 
{
  "node.id": "UMLS:C2459634",
  "node.name": "Oral Peripheral Mechanism Assessment using Other Equipment",
  "node.all_categories": [
    "biolink:Procedure"
  ],
  "node.category": "biolink:Procedure"
}
 
{
  "$schema": "http://json-schema.org/schema#",
  "type": "object",
  "properties": {
    "node.id": {
      "type": "string"
    },
    "node.name": {
      "type": "string"
    },
    "node.all_categories": {
      "type": "array",
      "items": {
        "type": "string"
      }
    },
    "node.category": {
      "type": "string"
    }
  },
  "required": [
    "node.all_categories",
    "node.category",
    "node.id",
    "node.name"
  ]
}

NODE Names

name type
Activity NODE
Agent NODE
AnatomicalEntity NODE
Behavior NODE
BehavioralFeature NODE
BiologicalEntity NODE
BiologicalProcess NODE
Cell NODE
CellLine NODE
CellularComponent NODE
ChemicalEntity NODE
ChemicalMixture NODE
ClinicalAttribute NODE
ClinicalIntervention NODE
Cohort NODE
ComplexMolecularMixture NODE
Device NODE
Disease NODE
DiseaseOrPhenotypicFeature NODE
Drug NODE
EnvironmentalFeature NODE
Event NODE
Exon NODE
Food NODE
GenomicEntity NODE
GeographicLocation NODE
IndividualOrganism NODE
LifeStage NODE
MolecularActivity NODE
MolecularEntity NODE
MolecularMixture NODE
NoncodingRNAProduct NODE
NucleicAcidEntity NODE
OrganismAttribute NODE
PathologicalProcess NODE
Protein NODE
ProteinDomain NODE
Transcript NODE
EnvironmentalProcess NODE
Gene NODE
GrossAnatomicalStructure NODE
MaterialSample NODE
Pathway NODE
PhenotypicFeature NODE
SmallMolecule NODE
GeneFamily NODE
GeneticInheritance NODE
InformationContentEntity NODE
MicroRNA NODE
Phenomenon NODE
PhysicalEntity NODE
PhysiologicalProcess NODE
Polypeptide NODE
Publication NODE
NamedThing NODE
OrganismTaxon NODE
OrganismalEntity NODE
PopulationOfIndividualOrganisms NODE
ProteinFamily NODE
RNAProduct NODE
Procedure NODE
RetrievalSource NODE
Treatment NODE

REL_GROUP Tables

Example REL_GROUP Data and JSON Schema

Example data Example data JSON schema 
{
  "r.qualified_object_aspect": "",
  "r.predicate": "biolink:treats",
  "r.domain_range_exclusion": "True",
  "r.qualified_object_direction": "",
  "r.id": 19799062,
  "r.primary_knowledge_source": "infores:semmeddb",
  "r.qualified_predicate": ""
}
 
{
  "$schema": "http://json-schema.org/schema#",
  "type": "object",
  "properties": {
    "r.qualified_object_aspect": {
      "type": "string"
    },
    "r.predicate": {
      "type": "string"
    },
    "r.domain_range_exclusion": {
      "type": "string"
    },
    "r.qualified_object_direction": {
      "type": "string"
    },
    "r.id": {
      "type": "integer"
    },
    "r.primary_knowledge_source": {
      "type": "string"
    },
    "r.qualified_predicate": {
      "type": "string"
    }
  },
  "required": [
    "r.domain_range_exclusion",
    "r.id",
    "r.predicate",
    "r.primary_knowledge_source",
    "r.qualified_object_aspect",
    "r.qualified_object_direction",
    "r.qualified_predicate"
  ]
}

REL_GROUP Names

name type
biomarker_for REL_GROUP
chemically_similar_to REL_GROUP
close_match REL_GROUP
associated_with REL_GROUP
actively_involved_in REL_GROUP
catalyzes REL_GROUP
composed_primarily_of REL_GROUP
affects REL_GROUP
capable_of REL_GROUP
causes REL_GROUP
coexists_with REL_GROUP
colocalizes_with REL_GROUP
contraindicated_for REL_GROUP
contributes_to REL_GROUP
disease_has_basis_in REL_GROUP
correlated_with REL_GROUP
directly_physically_interacts_with REL_GROUP
derives_from REL_GROUP
develops_from REL_GROUP
diagnoses REL_GROUP
disease_has_location REL_GROUP
disrupts REL_GROUP
enables REL_GROUP
exacerbates REL_GROUP
expressed_in REL_GROUP
gene_associated_with_condition REL_GROUP
gene_product_of REL_GROUP
has_decreased_amount REL_GROUP
has_increased_amount REL_GROUP
has_input REL_GROUP
has_member REL_GROUP
has_participant REL_GROUP
has_metabolite REL_GROUP
has_output REL_GROUP
has_part REL_GROUP
has_phenotype REL_GROUP
has_plasma_membrane_part REL_GROUP
homologous_to REL_GROUP
overlaps REL_GROUP
in_taxon REL_GROUP
indirectly_physically_interacts_with REL_GROUP
is_sequence_variant_of REL_GROUP
lacks_part REL_GROUP
manifestation_of REL_GROUP
located_in REL_GROUP
occurs_in REL_GROUP
physically_interacts_with REL_GROUP
precedes REL_GROUP
predisposes REL_GROUP
prevents REL_GROUP
produces REL_GROUP
regulates REL_GROUP
related_to REL_GROUP
same_as REL_GROUP
subclass_of REL_GROUP
superclass_of REL_GROUP
temporally_related_to REL_GROUP
transcribed_from REL_GROUP
translates_to REL_GROUP
treats REL_GROUP