BODHI

Biomedical Ontology & Diagnostic Hypergraph Infrastructure

BODHI is a suite of open medical knowledge graphs built for clinical AI. It encodes structured clinical relationships — conditions, symptoms, drugs, lab tests, and their interactions — into Neo4j graph databases, with export pipelines for downstream ML and application use.

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Networks

Network	Focus	Nodes	Relationships
bodhi-s	Condition ↔ Symptom ↔ Speciality	4,855	13,204
bodhi-m	Concept ↔ Drug ↔ LabInvestigation	4,469	3,566

Both graphs share the same Neo4j instance (default database) and are distinguished by their node labels.

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bodhi-s — Condition-Symptom Network

Maps conditions to their presenting symptoms, clinical specialities, and inter-condition influences.

Stats

Metric	Count
Condition nodes	779
Symptom nodes (variants)	4,037
Symptom root concepts (distinct SNOMED IDs)	590
Speciality nodes	39
Total relationships	13,204
Symptom → Condition edges (PRESENT_IN)	10,352
Condition → Speciality edges (TREATED_BY)	1,558
Condition → Condition edges (IS_INFLUENCED_BY)	1,020
Condition → Condition edges (RELATED_TO)	221
Condition → Condition edges (HAS_PREREQUISITE)	53

Condition types: Disorder 607 · Misc 84 · FamilyHistory 49 · Lifestyle 21 · Procedure 16 · Allergy 1 · Symptom 1

Avg symptoms per condition: 13.3

Condition triage: OPD Managed 367 (47%) · Worrisome 223 (29%) · Emergency 189 (24%)

Symptom triage: OPD Managed 2,244 (56%) · Worrisome 1,540 (38%) · Emergency 252 (6%)

Most symptomatic conditions: Sickle cell anaemia (54) · Psoriasis (46) · Cerebrovascular accident (45) · Gonorrhea (44) · Multiple sclerosis (42)

Most cross-cutting symptoms: Fever (145 conditions) · Fatigue (126) · Headache (110) · Vomit (94) · Malaise (81)

Top specialities by condition volume: Internal Medicine (292) · General Physician (205) · Orthopedic (139) · Neurologist (83) · General Surgeon (81)

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Schema

Node: Condition

A diagnosable medical condition, disorder, or clinical entity.

Property	Type	Values	Description
snomed_id	string	SNOMED CT ID	Globally unique clinical identifier
name	string	—	Clinical name of the condition
concept_type	enum	Disorder Misc FamilyHistory Lifestyle Procedure Allergy Symptom	Classification of the concept
triage_level	enum	opd_managed worrisome emergency	Clinical urgency
type_condition	enum	acute chronic acute_that_may_turn_chronic chronic_with_acute_aggravation lifestyle medical_history Event Injury	Temporal nature of condition
overall_likelihood	enum	rare low medium high very_high	Population prevalence signal
likelihood_male	float	0.0–1.0	Relative likelihood in males
likelihood_female	float	0.0–1.0	Relative likelihood in females
likelihood_age_0_1	float	0.0–1.0	Relative likelihood in age 0–1
likelihood_age_1_5	float	0.0–1.0	Relative likelihood in age 1–5
likelihood_age_6_12	float	0.0–1.0	Relative likelihood in age 6–12
likelihood_age_13_18	float	0.0–1.0	Relative likelihood in age 13–18
likelihood_age_19_30	float	0.0–1.0	Relative likelihood in age 19–30
likelihood_age_30_45	float	0.0–1.0	Relative likelihood in age 30–45
likelihood_age_45_60	float	0.0–1.0	Relative likelihood in age 45–60
likelihood_age_60_plus	float	0.0–1.0	Relative likelihood in age 60+

Node: Symptom

A clinical symptom or refinement thereof. Symptoms are structured with parent-child refinements (e.g. "Headache > Throbbing headache > Throbbing headache on right side").

Property	Type	Values	Description
uuid	string	UUID	Unique compound symptom identifier
snomed_id	string	SNOMED CT ID	SNOMED identifier for the symptom
root_snomed_id	string	SNOMED CT ID	Parent/root symptom SNOMED ID
root_snomed_name	string	—	Parent symptom name
name	string	—	Full compound symptom name
triage_level	enum	opd_managed worrisome emergency	Clinical urgency of this symptom
relation1_type	enum	characteristic severity location laterality onset duration_since duration_lasts temporal_pattern pain_type radiating aggravated relieved	Type of the first refinement axis
child1_name	string	—	Value of the first refinement
grouping1_selection_type	enum	s m	Single (s) or multi-select (m) for axis 1
relation2_type	enum	(same as relation1_type)	Type of the second refinement axis
child2_name	string	—	Value of the second refinement
grouping2_selection_type	enum	s m	Single or multi-select for axis 2
relation3_type	enum	(same as relation1_type)	Type of the third refinement axis
child3_name	string	—	Value of the third refinement
grouping3_selection_type	enum	s m	Single or multi-select for axis 3

Node: Speciality

A medical speciality or care discipline.

Property	Type	Description
id	string	Internal speciality identifier
name	string	Speciality name e.g. Cardiologist

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Relationships

(Symptom)-[:PRESENT_IN]->(Condition)

Links a symptom to a condition it presents in. Encodes bidirectional likelihood.

Property	Values	Description
likelihood_symptom_given_condition	zero rare low medium high very_high	How commonly this symptom appears when the condition is present — P(symptom | condition)
likelihood_condition_given_symptom	zero rare low medium high very_high	How predictive this symptom is of the condition — P(condition | symptom)

(Condition)-[:TREATED_BY]->(Speciality)

Indicates which speciality manages a condition.

Property	Values	Description
weight	rare low medium high very_high	Strength of the referral association

(Condition)-[:IS_INFLUENCED_BY]->(Condition)

Condition A is clinically influenced by the presence of condition B (e.g. Diabetes IS_INFLUENCED_BY Obesity).

Property	Values	Description
relation_strength	zero rare low medium high very_high	Magnitude of influence
relation_polarity	positive negative	Positive = B increases risk of A; Negative = B decreases risk of A

(Condition)-[:HAS_PREREQUISITE]->(Condition)

Condition A requires condition B to be present (e.g. Diabetic nephropathy HAS_PREREQUISITE Diabetes mellitus).

Property	Values	Description
relation_strength	medium high very_high	How mandatory the prerequisite is
relation_polarity	positive negative	Direction of dependency

(Symptom/Condition)-[:RELATED_TO]->(Symptom/Condition)

Ontological relatedness — used for symptom deduplication and SNOMED hierarchy linkage.

Property	Values	Description
relation_type	same similar snomed_parent refinement_same_to_root refinement_same_to_refinement refinement_similar_to_root refinement_similar_to_refinement	Nature of the ontological relationship

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bodhi-m — Concept-Drug-Lab Investigation Network

Maps clinical concepts (conditions/disorders) to their treatments (generic drugs) and monitoring parameters (lab tests / vitals), organised in a three-level clinical hierarchy.

Stats

Metric	Count
Concept nodes	2,471
Drug nodes	1,186
LabInvestigation nodes	812
Total relationships	3,566
Concept → Concept edges (CHILD_OF)	1,768
Concept → Drug edges (TREATED_BY)	908
LabInvestigation → Concept edges (IMPACTS)	808
Concept → LabInvestigation edges (MONITORED_BY)	82

Concept hierarchy: System 14 → Group 250 → Granular 1,942 (+ 265 unmapped)

Hierarchy coverage: 1,540 / 1,942 granular linked to group · 228 / 250 groups linked to system

Top drug therapeutic classes: GI (197) · Cardiac (182) · Derma (157) · Neuro/CNS (153) · Vitamins & Minerals (148) · Respiratory (111)

Most treated conditions: Hypertension (59 drugs) · Diabetes mellitus (33) · Acid Peptic Disease (28) · Fungal infection (21) · Heart failure (21)

Most monitored conditions: Dyslipidemia (4 vitals) · Diabetes mellitus (4) · Hypothyroidism (3) · Iron deficiency (3) · Hyperglycemia (3)

LabInvestigation health domains: Immunological (276) · Renal (120) · Hematological (82) · Endocrine (65) · Gastrointestinal (60)

LabInvestigation LOINC coverage: 812 of 1,973 vitals have LOINC IDs — only LOINC-mapped vitals are included for open interoperability.

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Schema

Node: Concept

A clinical concept — condition, disorder, finding, procedure, or lifestyle factor — organised in a three-level hierarchy: System → Group → Granular.

Property	Type	Values	Description
snomed_id	string	SNOMED CT ID	Primary unique identifier (open standard)
name	string	—	Clinical name
display_name	string	—	Consumer-friendly name e.g. High Blood Pressure
level_concept	enum	system group granular	Position in the clinical hierarchy
type_concept	enum	Disorder Finding Procedure Lifestyle Allergy Situation	Clinical category
type_information	enum	SelfHistory FamilyHistory	Whether this pertains to the patient themselves or family history
active	string	1	Whether this concept is active in the knowledge base

Hierarchy levels:

• system — broad health domain e.g. Cardiovascular health, Endocrine health (14 nodes)
• group — clinical cluster e.g. Diabetes mellitus, Coronary Artery Disease (250 nodes)
• granular — specific diagnosable entity e.g. Diabetes mellitus type II (1,942 nodes)

Node: Drug

A generic drug formulation. Combination drugs are stored as a single node.

Property	Type	Description
hash	string	MD5 hash of the generic name — unique deduplication key
name	string	Generic drug name e.g. metformin, atorvastatin + aspirin
therapeutic_class	string	Comma-separated therapeutic class(es) e.g. Anti Diabetic, Cardiovascular

Node: LabInvestigation

A lab test or clinical measurement, identified by LOINC standard code.

Property	Type	Values	Description
loinc_id	string	LOINC ID	Globally unique lab test identifier (open standard)
name	string	—	Standard test name
display_name	string	—	Display/friendly name
system_map	string	—	Health domain e.g. Renal health, Endocrine health
timespan_problem	enum	stat less_than_24_hr week_1 month_1 month_3 month_6 year_1 lifetime	How long this lab investigation result stays clinically relevant for a related condition
impact_problem	enum	zero low medium high	Clinical significance of this lab investigation in disease management

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Relationships

(Concept)-[:CHILD_OF]->(Concept)

Encodes the three-level clinical hierarchy. Granular concepts point to their parent Group; Group concepts point to their parent System.

No properties.

(LabInvestigation)-[:IMPACTS]->(Concept)

A lab investigation broadly belongs to and impacts a health domain concept (always a system-level concept). Represents the primary health system this test monitors.

No properties.

(Concept)-[:TREATED_BY]->(Drug)

A clinical concept is treated by a generic drug. Encodes gender exclusivity signals for prescribing guidance.

Property	Values	Description
therapeutic_class	string	The drug class relevant for this specific indication
exclusivity	zero low high	How specific this drug is to this condition vs. used broadly
exclusivity_male	low high	Prescribing exclusivity signal for males
exclusivity_female	low high	Prescribing exclusivity signal for females

(Concept)-[:MONITORED_BY]->(LabInvestigation)

A condition is monitored or diagnostically associated with a specific lab test. Encodes the deduction power and directional threshold.

Property	Values	Description
polarity	above below equal	Which direction relative to the threshold is clinically significant
category_threshold	normal borderline_low borderline_high high abnormal critically_high	The result range that triggers this association
vital_expiry_value	stat week_1 month_1 month_3 month_6 year_1	How frequently this test should be re-ordered for this condition
exclusivity	low high	Deduction power — how strongly an abnormal result predicts this condition

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Repository Structure

BODHI/
├── bodhi-s/
│   └── neo4j/              # Ingest pipeline for condition-symptom graph
│       ├── ingest.py
│       ├── config.py
│       ├── schema.py
│       ├── db.py
│       └── loaders/
├── bodhi-m/
│   └── neo4j/              # Ingest pipeline for concept-drug-lab investigation graph
│       ├── ingest.py
│       ├── config.py
│       ├── schema.py
│       ├── db.py
│       └── loaders/
└── knowledge-bases/        # Source CSV files used for ingestion

Running the Ingest

# Set up environment
cd bodhi-m/neo4j        # or bodhi-s/neo4j
python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt

# Run ingestion (--wipe clears existing data first)
python3 ingest.py --wipe

Requires a running Neo4j instance. Default connection: bolt://localhost:7687. Configure via .env:

NEO4J_URI=bolt://localhost:7687
NEO4J_USER=neo4j
NEO4J_PASSWORD=your_password
KB_DIR=../../knowledge-bases

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Standards Used

Standard	Used for
SNOMED CT	Condition and concept identifiers
LOINC	Lab investigation identifiers

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License

Knowledge graph structure and code: Apache 2.0

Source clinical knowledge bases are proprietary to Eka Care.