Ontology Sources¶

MONDO¶

The Monarch Disease Ontology — a unified disease hierarchy merging terms from OMIM, Orphanet, EFO, DOID, MeSH, NCIt, and ICD. With ~47K terms and extensive cross-references, MONDO is the canonical backbone of disease_map. Every disease in bioingest resolves to a MONDO ID.

Field	Example	Description
`id`	`MONDO:0005015`	MONDO term ID
`name`	`diabetes mellitus`	Human-readable label
`namespace`	`mondo`	Always "mondo"
`definition`	`A metabolic disease...`	Textual definition
`is_a`	`MONDO:0005066`	Parent term (hierarchy)
`xref`	`DOID:9351`, `EFO:0000400`, `MESH:D003920`, `ICD10CM:E11`	Cross-references

Cross-refs provided: EFO, DOID, MeSH, ICD-10-CM, MedGen, OMIM, Orphanet, MedDRA Role in disease_map: Primary source — all rows derived from MONDO xrefs

uv run bioingest download mondo
uv run bioingest ontology build --uri bolt://localhost:7687 --user neo4j --password secret

Disease Ontology¶

Community-driven ontology of human diseases with ~12K terms. Provides hierarchical classification and cross-references to MeSH, ICD, OMIM, and NCI Thesaurus. Complements MONDO with additional synonym coverage.

Field	Example	Description
`id`	`DOID:9351`	Disease Ontology ID
`name`	`diabetes mellitus`	Label
`is_a`	`DOID:4`	Parent term
`xref`	`MESH:D003920`, `ICD10CM:E11`	Cross-references

Term count: ~12,000 Cross-refs: MeSH, ICD-10-CM, OMIM, NCI, UMLS Role in disease_map: Supplementary — disease_map.doid links here

uv run bioingest download disease_ontology

EFO (Experimental Factor Ontology)¶

EMBL-EBI ontology used by Open Targets, GWAS Catalog, and Expression Atlas to annotate experimental variables. Covers diseases, phenotypes, assays, and anatomical terms. ~53K classes.

Field	Example	Description
`id`	`EFO:0000311`	EFO term ID
`name`	`cancer`	Label
`is_a`	`EFO:0000408`	Parent
`xref`	`MONDO:0004992`, `DOID:162`, `MESH:D009369`	Cross-references

Term count: ~53,000 Cross-refs: MONDO, DOID, MeSH, NCIt, OMIM Role in disease_map: disease_map.efo_id — required for joining Open Targets associations

uv run bioingest download efo

Gene Ontology¶

Three-branch ontology (Biological Process, Molecular Function, Cellular Component) with ~45K terms. Used for functional annotation of proteins. Integrated via interpro2go mappings and QuickGO annotations.

Field	Example	Description
`id`	`GO:0006915`	GO term ID
`name`	`apoptotic process`	Label
`namespace`	`biological_process`	Branch (BP/MF/CC)
`is_a`	`GO:0012501`	Parent term

Term count: ~45,000 Cross-refs: MetaCyc, Reactome, KEGG (via relationships) Role in disease_map: Not directly in disease_map — used for protein functional annotation

uv run bioingest download gene_ontology
# Athena — after publish
SELECT id, name, namespace FROM bioingest.gene_ontology__go_basic WHERE namespace = 'biological_process' LIMIT 100;

MeSH (Medical Subject Headings)¶

NLM's controlled vocabulary for indexing PubMed articles and ClinicalTrials.gov. Hierarchical descriptors cover diseases, anatomy, chemicals, and procedures. ~30K descriptors with tree numbers enabling hierarchical queries.

Field	Example	Description
`DescriptorUI`	`D003920`	MeSH unique ID
`DescriptorName`	`Diabetes Mellitus`	Preferred term
`TreeNumber`	`C18.452.394.750`	Hierarchical classification

Term count: ~30,000 descriptors Cross-refs: Mapped to MONDO/DOID via cross-reference tables Role in disease_map: disease_map.mesh_id — bridges PubMed/ClinicalTrials to MONDO

uv run bioingest download mesh

ICD-10-CM¶

WHO International Classification of Diseases, 10th revision, Clinical Modification. Used for clinical billing and epidemiology. Provides the code system referenced in EHR data and clinical trials.

Field	Example	Description
`code`	`E11.9`	ICD-10-CM code
`description`	`Type 2 diabetes mellitus without complications`	Code description
`category`	`E11`	Parent category

Term count: ~72,000 codes Cross-refs: Mapped to MONDO via disease_map.icd10_code Role in disease_map: disease_map.icd10_code — bridges clinical codes to MONDO

uv run bioingest download icd