Ontology Builder¶
Build ontology graphs from structured OBO files (deterministic) or from any document using LLM extraction.
Subcommands¶
| Command | Mode | What it does |
|---|---|---|
ontology status |
— | Show available OBO files and export status |
ontology export |
Structured | Parse OBO files → JSONL |
ontology build |
Structured | Parse OBO files → Neo4j |
ontology extract |
LLM | Extract ontology from any document |
Supported Ontologies (OBO)¶
| Ontology | ID | Node Label | Size |
|---|---|---|---|
| MONDO | mondo |
Disease | ~49 MB |
| Disease Ontology | disease_ontology |
Disease | ~7 MB |
| EFO | efo |
Disease | ~84 MB |
| Gene Ontology | gene_ontology |
GeneOntologyTerm | ~31 MB |
Quick Start¶
# 1. Download ontology files
bioingest download gene_ontology disease_ontology mondo efo
# 2. Check what's available
bioingest ontology status
# 3. Build the graph
bioingest ontology build --uri bolt://localhost:7687 --user neo4j --password secret
What Gets Created¶
Nodes¶
(:Disease:Entity {id, name, definition, synonyms, xrefs, source})(:GeneOntologyTerm:Entity {id, name, definition, ...})(:OntologyVersion {version_id, timestamp, node_count, sources})
Relationships¶
(:Disease)-[:IS_A]->(:Disease)— hierarchy(:Disease)-[:XREF]->(:Disease)— cross-references (MONDO ↔ DOID ↔ EFO)(:GeneOntologyTerm)-[:PART_OF]->(:GeneOntologyTerm)— structure
Cross-Referencing¶
When multiple ontologies are parsed together, cross-references are automatically resolved:
graph LR
M[MONDO:0000002<br/>cardiovascular disease] -->|XREF| D[DOID:1287<br/>cardiovascular system disease]
M -->|XREF| E[EFO:0000319<br/>cardiovascular disease]
D -->|XREF| MSee OBO Parsing and LLM Extraction for details.