Current viewDisease Schema

Entity Relationship Diagram

Interactive diagram showing all disease-related tables and their relationships. Lines show data connections between systems.

Direct relationship

Indirect (bridged) relationship

All Major Relationship Reference

Relationship overview across MONDO, HPO, OMIM, Orphanet, HGNC, G2P, UBERON, MeSH, PubMed, ClinicalTrials, and Disease Ontology. Includes direct links and indirect (bridged) paths.

Relationship	Type	Source Table(s)	Data Origin	Path	Details
`mondo_relationships (MONDO hierarchy)`	direct	mondo_relationships	Ontology file (MONDO OWL import)	MONDO → MONDO	Hierarchical disease ontology edges (e.g., is_a).
`mondo_omim_mappings`	direct	mondo_omim_mappings	Ontology file (MONDO xrefs) + OMIM ID matching	MONDO → OMIM	Cross-ontology disease mappings.
`mondo_mesh_mappings`	direct	mondo_mesh_mappings	Ontology file (MONDO xrefs to MeSH)	MONDO → MeSH	Links diseases to literature indexing descriptors.
`mondo_disease_ontology_mappings`	direct	mondo_disease_ontology_mappings	Ontology file (MONDO xrefs to DO)	MONDO → Disease Ontology	Crosswalk between MONDO and DO terms.
`orphanet_mondo_mappings`	direct	orphanet_mondo_mappings	Orphanet source files/API + MONDO crosswalk	MONDO ↔ Orphanet	Rare disease mapping between MONDO and Orphanet.
`medgen_mondo_mappings`	direct	medgen_mondo_mappings	MedGen/UMLS data import + MONDO crosswalk	MONDO ↔ MedGen	Concept-level mapping used for descriptions and cross references.
`disease_has_location`	direct	mondo_uberon_mappings	Ontology file (MONDO anatomy axioms)	MONDO → UBERON	Direct MONDO anatomy location relation.
`disease_has_inflammation_site`	direct	mondo_uberon_mappings	Ontology file (MONDO anatomy axioms)	MONDO → UBERON	Direct MONDO inflammation-site relation.
`disease_arises_from_structure`	direct	mondo_uberon_mappings	Ontology file (MONDO anatomy axioms)	MONDO → UBERON	Direct MONDO relation for structure of origin.
`disease_has_basis_in_dysfunction_of`	direct	mondo_uberon_mappings	Ontology file (MONDO anatomy axioms)	MONDO → UBERON	Direct MONDO dysfunction basis relation.
`via_mondo_hpo_uberon`	bridge	mondo_uberon_mappings (+ omim_hpo_mappings/orphanet_hpo_mappings + hpo_uberon_mappings)	Derived (join-based bridge across imported mapping tables)	MONDO → (OMIM\|Orphanet) → HPO → UBERON	Loose bridge tier; broad inferred phenotype bridge coverage.
`via_mondo_hpo_uberon_medium`	bridge	mondo_uberon_mappings (+ omim_hpo_mappings/orphanet_hpo_mappings + hpo_uberon_mappings)	Derived (join + evidence/frequency filters)	MONDO → (OMIM\|Orphanet) → HPO → UBERON	Qualifier not NOT, phenotypic aspect, and evidence/frequency support.
`via_mondo_hpo_uberon_strict`	bridge	mondo_uberon_mappings (+ omim_hpo_mappings/orphanet_hpo_mappings + hpo_uberon_mappings)	Derived (join + strict evidence constraints)	MONDO → (OMIM\|Orphanet) → HPO → UBERON	Strong bridge: qualifier not NOT, aspect=P, evidence PCS/TAS, frequency present.
`hpo_relationships (HPO hierarchy)`	direct	hpo_relationships	Ontology file (HPO OWL import)	HPO → HPO	Parent/child phenotype hierarchy.
`omim_hpo_mappings`	direct	omim_hpo_mappings	Data file (HPOA annotations from OMIM)	OMIM → HPO	Disease-phenotype associations with evidence, frequency, qualifier, aspect.
`orphanet_hpo_mappings`	direct	orphanet_hpo_mappings	Data file/API (HPOA/Orphanet phenotype annotations)	Orphanet → HPO	Rare disease phenotype associations.
`hpo_uberon_mappings`	direct	hpo_uberon_mappings	Ontology file (HPO OWL restrictions referencing UBERON)	HPO → UBERON	Phenotype-to-anatomy links extracted from HPO OWL references.
`omim_uberon_mappings`	bridge	omim_hpo_mappings + hpo_uberon_mappings	Derived (bridge table from OMIM-HPO and HPO-UBERON)	OMIM → HPO → UBERON	Derived bridge from OMIM phenotypes to anatomy.
`g2p_hpo_mapping`	direct	g2p_hpo_mapping	Data file/API (G2P import)	G2P → HPO	Phenotypes linked to curated gene-disease entries.
`g2p_mondo_mapping`	direct	g2p_mondo_mapping	Data file/API (G2P import + MONDO normalization)	G2P → MONDO	G2P disease terms normalized to MONDO.
`g2p_omim_mapping`	direct	g2p_omim_mapping	Data file/API (G2P import + OMIM normalization)	G2P → OMIM	G2P links to OMIM disease identifiers.
`hgnc_omim_mappings`	direct	hgnc_omim_mappings	Data file/API (HGNC import)	HGNC → OMIM	Gene-level cross-reference to OMIM.
`hgnc_pubmed_mappings`	direct	hgnc_pubmed_mappings	Data file/API (HGNC import)	HGNC → PubMed	Gene-associated literature links.
`hgnc_g2p_xref`	direct	hgnc_g2p_xref	Cross-reference table (HGNC ↔ G2P linking)	HGNC ↔ G2P	Cross-reference between HGNC genes and G2P entries.
`mesh_pubmed_mappings`	direct	mesh_pubmed_mappings	PubMed metadata + MeSH indexing import	MeSH → PubMed	Descriptor-level indexing of PubMed articles.
`clinical_trial_mesh_terms`	direct	clinical_trial_mesh_terms	ClinicalTrials.gov API payload normalization	ClinicalTrial → MeSH	Clinical trials linked to MeSH descriptors.
`clinical_trial_mondo_mapping`	bridge	clinical_trial_mesh_terms + mondo_mesh_mappings	Derived (bridge from trial-MeSH and MONDO-MeSH)	ClinicalTrial → MeSH → MONDO	Trial-to-disease mapping inferred from MeSH overlap.
`pubmed_mondo_mapping`	direct	pubmed_mondo_mapping	Direct mapping pipeline (with provenance in source_pipeline)	PubMed → MONDO	Article-to-disease mapping with direct-link flag (`is_direct_mapping`) and pipeline provenance.
`pubmed_clinical_trial_mapping`	direct	pubmed_clinical_trial_mapping	Text extraction / parsing from publications	PubMed ↔ ClinicalTrial	Links PMIDs to NCT IDs when trial IDs are found in literature.

Table Descriptions & Relationships

clinical_trials

Clinical study metadata from ClinicalTrials.gov registry.

Key Fields: id, nct_id, brief_title, study_type, overall_status, has_results

Relationships: Links to phases, conditions, interventions, MeSH terms, MONDO mappings, and trial results tables

Purpose: Normalized core trial model for analytics and ontology mapping

trial_phases

Normalized per-trial phase records (e.g., Phase 1/2, Phase 3).

Key Fields: trial_id, phase

Relationships: ClinicalTrial ↔ TrialPhase

Purpose: Supports filtering and cohorting by clinical phase

trial_conditions

Diseases and conditions studied in clinical trials.

Key Fields: trial_id, condition

Relationships: ClinicalTrial ↔ TrialCondition

Purpose: Stores condition text prior to ontology-level standardization

trial_interventions

Therapeutic interventions being tested in trials.

Key Fields: trial_id, intervention_type, intervention_name

Relationships: Belongs to ClinicalTrial

Purpose: Track drugs, devices, procedures being studied

clinical_trial_mesh_terms

MeSH indexing for clinical trials.

Key Fields: trial_id, descriptor_id, term

Relationships: ClinicalTrial ↔ MeSHTerm

Purpose: Subject classification and bridge to MONDO via MeSH mappings

clinical_trial_mondo_mapping

Normalized disease mappings between clinical trials and MONDO terms.

Key Fields: trial_id, mondo_id, mapping_method, confidence, via_mesh_descriptor_id

Relationships: ClinicalTrial ↔ MONDOTerm (optionally via MeSHTerm)

Purpose: Disease standardization for ontology-first trial analysis

trial_outcome_measures

Primary/secondary endpoints and measurement payloads from posted results.

Key Fields: trial_id, outcome_type, title, unit_of_measure, time_frame

Relationships: ClinicalTrial ↔ TrialOutcomeMeasure

Purpose: Outcome analytics across studies and interventions

trial_adverse_events

Structured adverse-event data from reported trial results.

Key Fields: trial_id, event_type, term, organ_system, event_stats

Relationships: ClinicalTrial ↔ TrialAdverseEvent

Purpose: Safety signal and tolerability analysis

trial_baseline_characteristics

Baseline participant characteristic distributions from trial results.

Key Fields: trial_id, measure_title, measure_param_type, measurements_data

Relationships: ClinicalTrial ↔ TrialBaselineCharacteristic

Purpose: Population comparability and subgroup context

trial_participant_flow

Recruitment and participant progression across trial periods.

Key Fields: trial_id, recruitment_details, periods_data, total_enrolled

Relationships: ClinicalTrial ↔ TrialParticipantFlow

Purpose: Attrition/completion analysis and study conduct tracking

Key Relationships & Integration Points

🔗

MONDO as Hub

MONDO serves as the central integration point, mapping to OMIM, MeSH, Disease Ontology, Orphanet, and MedGen.

🧬

HPO Cross-References

HPO phenotypes link across OMIM, Orphanet, G2P, and UBERON anatomy, enabling phenotype-based disease and anatomical exploration.

🔬

G2P Integration

G2P entries reference OMIM IDs (gene_mim, disease_mim) and MONDO IDs, creating gene-disease-phenotype connections.

📚

Literature Links

MeSH indexes PubMed articles, and direct PubMed↔MONDO mappings provide faster disease-specific literature retrieval. G2P entries cite supporting publications.

🧪

Clinical Trials

ClinicalTrials.gov data is normalized into trial core, ontology mappings (MeSH/MONDO), and posted results tables for translational evidence tracking.

🌐

Rare Disease Focus

Orphanet provides specialized rare disease data with epidemiology, genes, and phenotypes.

🏥

Clinical Genetics

G2P panels organize gene-disease associations by clinical specialty (DD, Cancer, Cardiac).

🔖

Multi-Ontology

System integrates 10+ databases: MONDO, HPO, OMIM, G2P, Orphanet, MedGen, MeSH, PubMed, ClinicalTrials, Disease Ontology.

Disease Database Schema

Entity Relationship Diagram

All Major Relationship Reference

Table Descriptions & Relationships

mondo_terms

mondo_relationships

mondo_omim_mappings

mondo_mesh_mappings

mondo_disease_ontology_mappings

mondo_metadata

hpo_terms

hpo_relationships

omim_hpo_mappings

orphanet_hpo_mappings

hpo_uberon_mappings

omim_terms

mondo_omim_mappings

omim_hpo_mappings

hgnc_genes

hgnc_gene_groups & hgnc_gene_group_association

hgnc_alias_symbols & hgnc_alias_symbol_association

hgnc_omim_mappings

hgnc_pubmed_mappings

hgnc_g2p_xref

g2p_entry

g2p_hpo_mapping

g2p_mondo_mapping

g2p_omim_mapping

g2p_publication

g2p_panel & g2p_entry_panel

g2p_variant_type & g2p_entry_variant_type

orphanet_diseases

orphanet_mondo_mappings

orphanet_hpo_mappings

orphanet_genes

orphanet_phenotypes

orphanet_epidemiology

medgen_concepts

medgen_mondo_mappings

uberon_terms

uberon_relationships

mondo_uberon_mappings

omim_uberon_mappings