Graph Schema
Edges
Edge types and their schema in OptimusKG.
OptimusKG encodes 27 edge types connecting the node types across molecular, clinical, anatomical, and environmental domains.
| Label | Relation(s) | Count |
|---|---|---|
DIS-GEN | ASSOCIATED_WITH | 9,734,774 |
ANA-GEN | EXPRESSION_PRESENT, EXPRESSION_ABSENT | 8,787,955 |
DRG-DRG | SYNERGISTIC_INTERACTION, PARENT | 1,345,376 |
PHE-GEN | ASSOCIATED_WITH | 793,279 |
GEN-GEN | INTERACTS_WITH | 327,924 |
DIS-PHE | PHENOTYPE_PRESENT | 157,144 |
BPO-GEN | INTERACTS_WITH | 158,410 |
DRG-DIS | INDICATION, CONTRAINDICATION, OFF_LABEL_USE | 70,380 |
MFN-GEN | INTERACTS_WITH | 90,933 |
DRG-PHE | ADVERSE_DRUG_REACTION, ASSOCIATED_WITH, CONTRAINDICATION, INDICATION, OFF_LABEL_USE | 13,758 |
PWY-GEN | INTERACTS_WITH | 46,977 |
BPO-BPO | IS_A | 44,494 |
DIS-DIS | PARENT | 47,892 |
CCO-GEN | INTERACTS_WITH | 105,309 |
DRG-GEN | ACTIVATOR, AGONIST, ALLOSTERIC_ANTAGONIST, ANTAGONIST, ANTISENSE_INHIBITOR, BINDING_AGENT, BLOCKER, CARRIER, CROSS_LINKING_AGENT, DEGRADER, DISRUPTING_AGENT, ENZYME, EXOGENOUS_GENE, EXOGENOUS_PROTEIN, HYDROLYTIC_ENZYME, INHIBITOR, INVERSE_AGONIST, MODULATOR, NEGATIVE_ALLOSTERIC_MODULATOR, NEGATIVE_MODULATOR, OPENER, OTHER, PARTIAL_AGONIST, POSITIVE_ALLOSTERIC_MODULATOR, POSITIVE_MODULATOR, PROTEOLYTIC_ENZYME, RELEASING_AGENT, RNAI_INHIBITOR, STABILISER, SUBSTRATE, TARGET, TRANSPORTER, VACCINE_ANTIGEN | 36,611 |
PHE-PHE | PARENT | 26,121 |
MFN-MFN | IS_A | 12,587 |
PWY-PWY | PARENT | 2,819 |
EXP-GEN | INTERACTS_WITH | 2,989 |
EXP-DIS | LINKED_TO | 2,391 |
EXP-EXP | PARENT | 2,443 |
EXP-BPO | INTERACTS_WITH | 2,260 |
ANA-ANA | PARENT | 17,082 |
CCO-CCO | IS_A | 4,639 |
EXP-MFN | INTERACTS_WITH | 47 |
EXP-CCO | INTERACTS_WITH | 13 |
DRG-BPO | INDICATION | 62 |
All edges share the same base schema in the unified edges.parquet and largest_connected_component_edges.parquet tables:
fromStringSource node identifier in CURIE format
toStringTarget node identifier in CURIE format
labelStringEdge type label (e.g. DIS-GEN)
relationStringRelation type (e.g. ASSOCIATED_WITH)
undirectedBooleanTrue if the edge has no intrinsic directionality
propertiesStringJSON-encoded edge-specific properties. Expanded to a native Struct in per-type parquet files.
In the stratified per-type parquet files (edges/<label>.parquet), properties is expanded into native typed columns as a Polars Struct.
One edge per node pair
OptimusKG guarantees at most one edge per (from, to, label) triple. This
keeps traversal simple: a path query never has to decide which of several
parallel edges to follow, and degree statistics are well defined.
When several sources describe the same node pair with different relation types,
the relation column is resolved deterministically: the relation with the
lowest RELATION_PRIORITY wins, ties are broken alphabetically. Resolution is
order-independent and reproducible across runs.
Collapsing is not lossy. Every edge also carries:
properties.relation_assertions— the complete list of{source, relation}statements contributed by each upstream database.properties.relation_conflict—truewhen those assertions include mutually exclusive relations.
This matters because some disagreements are biologically real rather than
noise. An INDICATION and a CONTRAINDICATION between the same drug and
disease are semantically distinct statements that may both be valid under
different contexts (dose, population, comorbidity, or line of therapy). Rather
than discarding one, OptimusKG surfaces the representative relation and keeps
both assertions addressable:
import polars as pl
edges = pl.read_parquet("edges/drug_disease.parquet")
# Edges where sources genuinely disagree.
conflicting = edges.filter(pl.col("properties").struct.field("relation_conflict"))
# Recover the original per-source statements.
conflicting.select(
"from",
"to",
"relation",
pl.col("properties").struct.field("relation_assertions"),
)In the current release, 3,826 source-specific assertions are retained that a priority-only collapse would have dropped, including 339 drug–disease pairs asserted as both an indication and a contraindication, and 191 drug–phenotype pairs where an entire source statement (33 of them contraindications) was previously discarded along with its provenance.
For clinical or safety-sensitive analyses, read relation_assertions rather
than relation alone, and treat relation_conflict = true edges as requiring
source-level review.
Anatomy-Anatomy
fromStringSource node ID (CURIE format)
toStringTarget node ID (CURIE format)
labelStringEdge type label (ANA-ANA)
relationStringRelation type
undirectedBooleanFalse
propertiesStructEdge-specific properties
sourcesStructProvenance of this edge
directList[String]Datasets that directly contributed this relationship
indirectList[String]Datasets that referenced this relationship
Anatomy-Gene
fromStringSource node ID (CURIE format)
toStringTarget node ID (CURIE format)
labelStringEdge type label (ANA-GEN)
relationStringRelation type
undirectedBooleanTrue
propertiesStructEdge-specific properties
expression_rankInt32Bgee expression rank score (lower = higher expression)
call_qualityStringExpression call quality (gold/silver)
sourcesStructProvenance of this edge
directList[String]Datasets that directly contributed this relationship
indirectList[String]Datasets that referenced this relationship
Biological Process-Biological Process
fromStringSource node ID (CURIE format)
toStringTarget node ID (CURIE format)
labelStringEdge type label (BPO-BPO)
relationStringRelation type
undirectedBooleanFalse
propertiesStructEdge-specific properties
sourcesStructProvenance of this edge
directList[String]Datasets that directly contributed this relationship
indirectList[String]Datasets that referenced this relationship
Biological Process-Gene
fromStringSource node ID (CURIE format)
toStringTarget node ID (CURIE format)
labelStringEdge type label (BPO-GEN)
relationStringRelation type
undirectedBooleanTrue
propertiesStructEdge-specific properties
evidenceList[String]GO evidence codes (e.g. IDA, IMP, TAS)
gene_productList[String]Gene product IDs annotated to this term
eco_idsList[String]Evidence & Conclusion Ontology (ECO) IDs
sourcesStructProvenance of this edge
directList[String]Datasets that directly contributed this relationship
indirectList[String]Datasets that referenced this relationship
Cellular Component-Cellular Component
fromStringSource node ID (CURIE format)
toStringTarget node ID (CURIE format)
labelStringEdge type label (CCO-CCO)
relationStringRelation type
undirectedBooleanFalse
propertiesStructEdge-specific properties
sourcesStructProvenance of this edge
directList[String]Datasets that directly contributed this relationship
indirectList[String]Datasets that referenced this relationship
Cellular Component-Gene
fromStringSource node ID (CURIE format)
toStringTarget node ID (CURIE format)
labelStringEdge type label (CCO-GEN)
relationStringRelation type
undirectedBooleanTrue
propertiesStructEdge-specific properties
evidenceList[String]GO evidence codes (e.g. IDA, IMP, TAS)
gene_productList[String]Gene product IDs annotated to this term
eco_idsList[String]Evidence & Conclusion Ontology (ECO) IDs
sourcesStructProvenance of this edge
directList[String]Datasets that directly contributed this relationship
indirectList[String]Datasets that referenced this relationship
Disease-Disease
fromStringSource node ID (CURIE format)
toStringTarget node ID (CURIE format)
labelStringEdge type label (DIS-DIS)
relationStringRelation type
undirectedBooleanFalse
propertiesStructEdge-specific properties
sourcesStructProvenance of this edge
directList[String]Datasets that directly contributed this relationship
indirectList[String]Datasets that referenced this relationship
Disease-Gene
fromStringSource node ID (CURIE format)
toStringTarget node ID (CURIE format)
labelStringEdge type label (DIS-GEN)
relationStringRelation type
undirectedBooleanTrue
propertiesStructEdge-specific properties
evidence_scoreFloat64Aggregated association evidence score
evidence_countInt64Number of evidence items supporting the association
evidence_indexFloat64Combined evidence index (Open Targets)
disease_specificity_indexFloat64DSI, specificity of the gene to this disease
disease_pleiotropy_indexFloat64DPI, number of disease classes the gene is associated with
disgenet_scoreFloat64DisGeNET gene–disease association score
year_initialStringYear of the earliest supporting publication
year_finalStringYear of the most recent supporting publication
number_of_pmidsInt16Number of supporting PubMed publications
number_of_snpsInt16Number of supporting SNPs (GWAS evidence)
sourcesStructProvenance of this edge
directList[String]Datasets that directly contributed this relationship
indirectList[String]Datasets that referenced this relationship
Disease-Phenotype
fromStringSource node ID (CURIE format)
toStringTarget node ID (CURIE format)
labelStringEdge type label (DIS-PHE)
relationStringRelation type
undirectedBooleanTrue
propertiesStructEdge-specific properties
aspectList[String]HPO annotation aspect (P=phenotypic, I=inheritance, etc.)
evidence_typeList[String]Evidence type codes (e.g. IEA, PCS, TAS)
frequencyList[String]Phenotype frequency annotations
onsetList[String]Age of onset annotations
modifiersList[String]Clinical modifier annotations
sexesList[String]Sex-specific annotations
qualifier_notBooleanTrue if phenotype is explicitly absent
bio_curationList[String]Biocuration provenance entries
referencesList[String]Supporting publication or database references
sourcesStructProvenance of this edge
directList[String]Datasets that directly contributed this relationship
indirectList[String]Datasets that referenced this relationship
relation_assertionsList[Struct]Every source-specific relation asserted for this node pair. OptimusKG stores one edge per node pair, so this list preserves the original assertions when sources disagree.
sourceStringDataset that asserted this relation
relationStringRelation asserted by that dataset
relation_conflictBooleanTrue when relation_assertions contains mutually exclusive relations (e.g. INDICATION and CONTRAINDICATION), meaning the sources genuinely disagree.
Drug-Biological Process
fromStringSource node ID (CURIE format)
toStringTarget node ID (CURIE format)
labelStringEdge type label (DRG-BPO)
relationStringRelation type
undirectedBooleanTrue
propertiesStructEdge-specific properties
highest_clinical_trial_phaseFloat64Highest clinical trial phase for this indication
reference_idsList[String]Supporting reference identifiers
sourcesStructProvenance of this edge
directList[String]Datasets that directly contributed this relationship
indirectList[String]Datasets that referenced this relationship
Drug-Disease
fromStringSource node ID (CURIE format)
toStringTarget node ID (CURIE format)
labelStringEdge type label (DRG-DIS)
relationStringRelation type
undirectedBooleanTrue
propertiesStructEdge-specific properties
highest_clinical_trial_phaseFloat64Highest clinical trial phase for this indication
structure_idStringDrugCentral structure ID
drug_disease_idStringDrugCentral drug–disease identifier
reference_idsList[String]Supporting reference identifiers
sourcesStructProvenance of this edge
directList[String]Datasets that directly contributed this relationship
indirectList[String]Datasets that referenced this relationship
relation_assertionsList[Struct]Every source-specific relation asserted for this node pair. OptimusKG stores one edge per node pair, so this list preserves the original assertions when sources disagree.
sourceStringDataset that asserted this relation
relationStringRelation asserted by that dataset
relation_conflictBooleanTrue when relation_assertions contains mutually exclusive relations (e.g. INDICATION and CONTRAINDICATION), meaning the sources genuinely disagree.
Drug-Drug
fromStringSource node ID (CURIE format)
toStringTarget node ID (CURIE format)
labelStringEdge type label (DRG-DRG)
relationStringRelation type
undirectedBooleanFalse
propertiesStructEdge-specific properties
interaction_descriptionStringDescription of the drug–drug interaction
sourcesStructProvenance of this edge
directList[String]Datasets that directly contributed this relationship
indirectList[String]Datasets that referenced this relationship
relation_assertionsList[Struct]Every source-specific relation asserted for this node pair. OptimusKG stores one edge per node pair, so this list preserves the original assertions when sources disagree.
sourceStringDataset that asserted this relation
relationStringRelation asserted by that dataset
relation_conflictBooleanTrue when relation_assertions contains mutually exclusive relations (e.g. INDICATION and CONTRAINDICATION), meaning the sources genuinely disagree.
Drug-Gene
fromStringSource node ID (CURIE format)
toStringTarget node ID (CURIE format)
labelStringEdge type label (DRG-GEN)
relationStringRelation type
undirectedBooleanFalse
propertiesStructEdge-specific properties
mechanisms_of_actionList[String]Mechanism of action descriptions
source_idsList[String]Source-specific interaction identifiers
source_urlsList[String]URLs to source evidence records
sourcesStructProvenance of this edge
directList[String]Datasets that directly contributed this relationship
indirectList[String]Datasets that referenced this relationship
relation_assertionsList[Struct]Every source-specific relation asserted for this node pair. OptimusKG stores one edge per node pair, so this list preserves the original assertions when sources disagree.
sourceStringDataset that asserted this relation
relationStringRelation asserted by that dataset
relation_conflictBooleanTrue when relation_assertions contains mutually exclusive relations (e.g. INDICATION and CONTRAINDICATION), meaning the sources genuinely disagree.
Drug-Phenotype
fromStringSource node ID (CURIE format)
toStringTarget node ID (CURIE format)
labelStringEdge type label (DRG-PHE)
relationStringRelation type
undirectedBooleanTrue
propertiesStructEdge-specific properties
highest_clinical_trial_phaseFloat64Highest clinical trial phase
structure_idStringDrugCentral structure ID
drug_disease_idStringDrugCentral drug–disease identifier
reference_idsList[String]Supporting reference identifiers
sourcesStructProvenance of this edge
directList[String]Datasets that directly contributed this relationship
indirectList[String]Datasets that referenced this relationship
relation_assertionsList[Struct]Every source-specific relation asserted for this node pair. OptimusKG stores one edge per node pair, so this list preserves the original assertions when sources disagree.
sourceStringDataset that asserted this relation
relationStringRelation asserted by that dataset
relation_conflictBooleanTrue when relation_assertions contains mutually exclusive relations (e.g. INDICATION and CONTRAINDICATION), meaning the sources genuinely disagree.
Exposure-Biological Process
fromStringSource node ID (CURIE format)
toStringTarget node ID (CURIE format)
labelStringEdge type label (EXP-BPO)
relationStringRelation type
undirectedBooleanTrue
propertiesStructEdge-specific properties
evidence_countUInt32Number of evidence entries
number_of_receptorsInt64Number of receptor/study participants
receptorsList[String]Receptor identifiers (e.g. cell line, organism)
receptor_notesList[String]Free-text notes on receptors
smoking_statusesList[String]Smoking status of study subjects
sexesList[String]Sex of study subjects
racesList[String]Race/ethnicity of study subjects
methodsList[String]Measurement methods used
mediumsList[String]Biological mediums measured (e.g. blood, urine)
detection_limitList[String]Lower limit of detection values
detection_limit_uomList[String]Units of detection limit values
detection_frequencyList[String]Detection frequency values
age_entriesUInt32Number of age-stratified entries
age_range_valuesList[String]Age range values for subjects
age_mean_valuesList[String]Mean age values
age_median_valuesList[String]Median age values
age_point_valuesList[String]Point age values
age_open_range_valuesList[String]Open-ended age range values
study_countriesList[String]Countries where studies were conducted
states_or_provincesList[String]States or provinces of study
city_town_region_areasList[String]City/town/region of study
outcome_relationshipsList[String]Observed outcome relationships
exposure_event_notesList[String]Notes on the exposure event
exposure_outcome_notesList[String]Notes on the exposure outcome
referencesList[String]Supporting literature references
associated_study_titlesList[String]Titles of associated studies
enrollment_start_yearsList[String]Study enrollment start years
enrollment_end_yearsList[String]Study enrollment end years
study_factorsList[String]Study design factors
assay_notesList[String]Notes on the assay used
sourcesStructProvenance of this edge
directList[String]Datasets that directly contributed this relationship
indirectList[String]Datasets that referenced this relationship
Exposure-Cellular Component
fromStringSource node ID (CURIE format)
toStringTarget node ID (CURIE format)
labelStringEdge type label (EXP-CCO)
relationStringRelation type
undirectedBooleanTrue
propertiesStructEdge-specific properties
evidence_countUInt32Number of evidence entries
number_of_receptorsInt64Number of receptor/study participants
receptorsList[String]Receptor identifiers (e.g. cell line, organism)
receptor_notesList[String]Free-text notes on receptors
smoking_statusesList[String]Smoking status of study subjects
sexesList[String]Sex of study subjects
racesList[String]Race/ethnicity of study subjects
methodsList[String]Measurement methods used
mediumsList[String]Biological mediums measured (e.g. blood, urine)
detection_limitList[String]Lower limit of detection values
detection_limit_uomList[String]Units of detection limit values
detection_frequencyList[String]Detection frequency values
age_entriesUInt32Number of age-stratified entries
age_range_valuesList[String]Age range values for subjects
age_mean_valuesList[String]Mean age values
age_median_valuesList[String]Median age values
age_point_valuesList[String]Point age values
age_open_range_valuesList[String]Open-ended age range values
study_countriesList[String]Countries where studies were conducted
states_or_provincesList[String]States or provinces of study
city_town_region_areasList[String]City/town/region of study
outcome_relationshipsList[String]Observed outcome relationships
exposure_event_notesList[String]Notes on the exposure event
exposure_outcome_notesList[String]Notes on the exposure outcome
referencesList[String]Supporting literature references
associated_study_titlesList[String]Titles of associated studies
enrollment_start_yearsList[String]Study enrollment start years
enrollment_end_yearsList[String]Study enrollment end years
study_factorsList[String]Study design factors
assay_notesList[String]Notes on the assay used
sourcesStructProvenance of this edge
directList[String]Datasets that directly contributed this relationship
indirectList[String]Datasets that referenced this relationship
Exposure-Disease
fromStringSource node ID (CURIE format)
toStringTarget node ID (CURIE format)
labelStringEdge type label (EXP-DIS)
relationStringRelation type
undirectedBooleanFalse
propertiesStructEdge-specific properties
evidence_countUInt32Number of evidence entries
number_of_receptorsInt64Number of receptor/study participants
receptorsList[String]Receptor identifiers (e.g. cell line, organism)
receptor_notesList[String]Free-text notes on receptors
smoking_statusesList[String]Smoking status of study subjects
sexesList[String]Sex of study subjects
racesList[String]Race/ethnicity of study subjects
methodsList[String]Measurement methods used
mediumsList[String]Biological mediums measured (e.g. blood, urine)
detection_limitList[String]Lower limit of detection values
detection_limit_uomList[String]Units of detection limit values
detection_frequencyList[String]Detection frequency values
age_entriesUInt32Number of age-stratified entries
age_range_valuesList[String]Age range values for subjects
age_mean_valuesList[String]Mean age values
age_median_valuesList[String]Median age values
age_point_valuesList[String]Point age values
age_open_range_valuesList[String]Open-ended age range values
study_countriesList[String]Countries where studies were conducted
states_or_provincesList[String]States or provinces of study
city_town_region_areasList[String]City/town/region of study
outcome_relationshipsList[String]Observed outcome relationships
exposure_event_notesList[String]Notes on the exposure event
exposure_outcome_notesList[String]Notes on the exposure outcome
referencesList[String]Supporting literature references
associated_study_titlesList[String]Titles of associated studies
enrollment_start_yearsList[String]Study enrollment start years
enrollment_end_yearsList[String]Study enrollment end years
study_factorsList[String]Study design factors
assay_notesList[String]Notes on the assay used
sourcesStructProvenance of this edge
directList[String]Datasets that directly contributed this relationship
indirectList[String]Datasets that referenced this relationship
Exposure-Exposure
fromStringSource node ID (CURIE format)
toStringTarget node ID (CURIE format)
labelStringEdge type label (EXP-EXP)
relationStringRelation type
undirectedBooleanFalse
propertiesStructEdge-specific properties
evidence_countUInt32Number of evidence entries
number_of_receptorsInt64Number of receptor/study participants
receptorsList[String]Receptor identifiers (e.g. cell line, organism)
receptor_notesList[String]Free-text notes on receptors
smoking_statusesList[String]Smoking status of study subjects
sexesList[String]Sex of study subjects
racesList[String]Race/ethnicity of study subjects
methodsList[String]Measurement methods used
mediumsList[String]Biological mediums measured (e.g. blood, urine)
detection_limitList[String]Lower limit of detection values
detection_limit_uomList[String]Units of detection limit values
detection_frequencyList[String]Detection frequency values
age_entriesUInt32Number of age-stratified entries
age_range_valuesList[String]Age range values for subjects
age_mean_valuesList[String]Mean age values
age_median_valuesList[String]Median age values
age_point_valuesList[String]Point age values
age_open_range_valuesList[String]Open-ended age range values
study_countriesList[String]Countries where studies were conducted
states_or_provincesList[String]States or provinces of study
city_town_region_areasList[String]City/town/region of study
outcome_relationshipsList[String]Observed outcome relationships
exposure_event_notesList[String]Notes on the exposure event
exposure_outcome_notesList[String]Notes on the exposure outcome
referencesList[String]Supporting literature references
associated_study_titlesList[String]Titles of associated studies
enrollment_start_yearsList[String]Study enrollment start years
enrollment_end_yearsList[String]Study enrollment end years
study_factorsList[String]Study design factors
assay_notesList[String]Notes on the assay used
sourcesStructProvenance of this edge
directList[String]Datasets that directly contributed this relationship
indirectList[String]Datasets that referenced this relationship
Exposure-Gene
fromStringSource node ID (CURIE format)
toStringTarget node ID (CURIE format)
labelStringEdge type label (EXP-GEN)
relationStringRelation type
undirectedBooleanFalse
propertiesStructEdge-specific properties
evidence_countUInt32Number of evidence entries
number_of_receptorsInt64Number of receptor/study participants
receptorsList[String]Receptor identifiers (e.g. cell line, organism)
receptor_notesList[String]Free-text notes on receptors
smoking_statusesList[String]Smoking status of study subjects
sexesList[String]Sex of study subjects
racesList[String]Race/ethnicity of study subjects
methodsList[String]Measurement methods used
mediumsList[String]Biological mediums measured (e.g. blood, urine)
detection_limitList[String]Lower limit of detection values
detection_limit_uomList[String]Units of detection limit values
detection_frequencyList[String]Detection frequency values
age_entriesUInt32Number of age-stratified entries
age_range_valuesList[String]Age range values for subjects
age_mean_valuesList[String]Mean age values
age_median_valuesList[String]Median age values
age_point_valuesList[String]Point age values
age_open_range_valuesList[String]Open-ended age range values
study_countriesList[String]Countries where studies were conducted
states_or_provincesList[String]States or provinces of study
city_town_region_areasList[String]City/town/region of study
outcome_relationshipsList[String]Observed outcome relationships
exposure_event_notesList[String]Notes on the exposure event
exposure_outcome_notesList[String]Notes on the exposure outcome
referencesList[String]Supporting literature references
associated_study_titlesList[String]Titles of associated studies
enrollment_start_yearsList[String]Study enrollment start years
enrollment_end_yearsList[String]Study enrollment end years
study_factorsList[String]Study design factors
assay_notesList[String]Notes on the assay used
sourcesStructProvenance of this edge
directList[String]Datasets that directly contributed this relationship
indirectList[String]Datasets that referenced this relationship
Exposure-Molecular Function
fromStringSource node ID (CURIE format)
toStringTarget node ID (CURIE format)
labelStringEdge type label (EXP-MFN)
relationStringRelation type
undirectedBooleanTrue
propertiesStructEdge-specific properties
evidence_countUInt32Number of evidence entries
number_of_receptorsInt64Number of receptor/study participants
receptorsList[String]Receptor identifiers (e.g. cell line, organism)
receptor_notesList[String]Free-text notes on receptors
smoking_statusesList[String]Smoking status of study subjects
sexesList[String]Sex of study subjects
racesList[String]Race/ethnicity of study subjects
methodsList[String]Measurement methods used
mediumsList[String]Biological mediums measured (e.g. blood, urine)
detection_limitList[String]Lower limit of detection values
detection_limit_uomList[String]Units of detection limit values
detection_frequencyList[String]Detection frequency values
age_entriesUInt32Number of age-stratified entries
age_range_valuesList[String]Age range values for subjects
age_mean_valuesList[String]Mean age values
age_median_valuesList[String]Median age values
age_point_valuesList[String]Point age values
age_open_range_valuesList[String]Open-ended age range values
study_countriesList[String]Countries where studies were conducted
states_or_provincesList[String]States or provinces of study
city_town_region_areasList[String]City/town/region of study
outcome_relationshipsList[String]Observed outcome relationships
exposure_event_notesList[String]Notes on the exposure event
exposure_outcome_notesList[String]Notes on the exposure outcome
referencesList[String]Supporting literature references
associated_study_titlesList[String]Titles of associated studies
enrollment_start_yearsList[String]Study enrollment start years
enrollment_end_yearsList[String]Study enrollment end years
study_factorsList[String]Study design factors
assay_notesList[String]Notes on the assay used
sourcesStructProvenance of this edge
directList[String]Datasets that directly contributed this relationship
indirectList[String]Datasets that referenced this relationship
Gene-Gene
fromStringSource node ID (CURIE format)
toStringTarget node ID (CURIE format)
labelStringEdge type label (GEN-GEN)
relationStringRelation type
undirectedBooleanTrue
propertiesStructEdge-specific properties
sourcesStructProvenance of this edge
directList[String]Datasets that directly contributed this relationship
indirectList[String]Datasets that referenced this relationship
Molecular Function-Gene
fromStringSource node ID (CURIE format)
toStringTarget node ID (CURIE format)
labelStringEdge type label (MFN-GEN)
relationStringRelation type
undirectedBooleanTrue
propertiesStructEdge-specific properties
evidenceList[String]GO evidence codes (e.g. IDA, IMP, TAS)
gene_productList[String]Gene product IDs annotated to this term
eco_idsList[String]Evidence & Conclusion Ontology (ECO) IDs
sourcesStructProvenance of this edge
directList[String]Datasets that directly contributed this relationship
indirectList[String]Datasets that referenced this relationship
Molecular Function-Molecular Function
fromStringSource node ID (CURIE format)
toStringTarget node ID (CURIE format)
labelStringEdge type label (MFN-MFN)
relationStringRelation type
undirectedBooleanFalse
propertiesStructEdge-specific properties
sourcesStructProvenance of this edge
directList[String]Datasets that directly contributed this relationship
indirectList[String]Datasets that referenced this relationship
Pathway-Gene
fromStringSource node ID (CURIE format)
toStringTarget node ID (CURIE format)
labelStringEdge type label (PWY-GEN)
relationStringRelation type
undirectedBooleanTrue
propertiesStructEdge-specific properties
sourcesStructProvenance of this edge
directList[String]Datasets that directly contributed this relationship
indirectList[String]Datasets that referenced this relationship
Pathway-Pathway
fromStringSource node ID (CURIE format)
toStringTarget node ID (CURIE format)
labelStringEdge type label (PWY-PWY)
relationStringRelation type
undirectedBooleanFalse
propertiesStructEdge-specific properties
sourcesStructProvenance of this edge
directList[String]Datasets that directly contributed this relationship
indirectList[String]Datasets that referenced this relationship
Phenotype-Gene
fromStringSource node ID (CURIE format)
toStringTarget node ID (CURIE format)
labelStringEdge type label (PHE-GEN)
relationStringRelation type
undirectedBooleanFalse
propertiesStructEdge-specific properties
evidence_scoreFloat64Aggregated association evidence score
evidence_countInt64Number of evidence items supporting the association
evidence_indexFloat64Combined evidence index (Open Targets)
disease_specificity_indexFloat64DSI, specificity of the gene to this disease
disease_pleiotropy_indexFloat64DPI, number of disease classes the gene is associated with
disgenet_scoreFloat64DisGeNET gene–disease association score
year_initialStringYear of the earliest supporting publication
year_finalStringYear of the most recent supporting publication
number_of_pmidsInt16Number of supporting PubMed publications
number_of_snpsInt16Number of supporting SNPs (GWAS evidence)
sourcesStructProvenance of this edge
directList[String]Datasets that directly contributed this relationship
indirectList[String]Datasets that referenced this relationship
Phenotype-Phenotype
fromStringSource node ID (CURIE format)
toStringTarget node ID (CURIE format)
labelStringEdge type label (PHE-PHE)
relationStringRelation type
undirectedBooleanFalse
propertiesStructEdge-specific properties
sourcesStructProvenance of this edge
directList[String]Datasets that directly contributed this relationship
indirectList[String]Datasets that referenced this relationship