| name | oregano-query |
| description | Query the OREGANO knowledge graph for computational drug repurposing. Use whenever the user asks about drug–target–disease–gene–pathway relationships, compound cross-references, drug repurposing hypotheses, or wants to explore neighbors of any biomedical entity in a knowledge graph that includes natural compounds.
|
OREGANO Query Skill
Search the OREGANO knowledge graph (88,937 nodes, 824,231 links) by any entity. Auto-resolves input to OREGANO node IDs via cross-reference tables.
| Input Pattern | Detected As | Match Logic |
|---|
OREGANO internal ID (e.g. 1234) | OREGANO node ID | exact in triplet index |
DB00331 / DrugBank ID | external xref | exact in COMPOUND.tsv |
| UniProt / KEGG / MeSH / UMLS ID | external xref | exact across all metadata TSVs |
metformin, BRCA1, free text | entity name | substring on name columns |
API
| Function | Input | Returns |
|---|
search(query) | single entity string | dict: {query, resolved_ids, metadata, triplets} |
search_batch(queries) | list of entity strings | dict[str, search_result] |
summarize(result) | search result dict | compact LLM-readable text |
to_json(result) | search result dict | JSON-serializable dict |
get_stats() | — | graph-level counts (triplets, nodes, predicates, entity types) |
Graph Schema
11 node types: Compound (90,868), Gene (35,794), Target (22,096), Disease (18,333), Phenotype (11,605), Side Effect (6,060), Indication (2,714), Pathway (2,129), Effect (171), Activity (78).
19 relation types (predicates): e.g. has_target, has_indication, has_side_effect, interacts_with, involved_in_pathway, associated_with, has_phenotype, etc. Run get_stats() to list all predicates with counts.
Usage
See if __name__ == "__main__" block in 21_OREGANO.py for runnable examples covering: free-text drug name search, DrugBank ID lookup, batch search, JSON pipeline output, and graph statistics.
Data
- Source: Zenodo DOI 10.5281/zenodo.10103842 (CC-BY 4.0)
- Version: v2.1 (published 2023-11-10)
- Core file:
OREGANO_V2.1.tsv — tab-delimited triplets (Subject, Predicate, Object)
- Metadata files:
COMPOUND.tsv, TARGET.tsv, GENES.tsv, DISEASES.tsv, PHENOTYPES.tsv, PATHWAYS.tsv, INDICATION.tsv, SIDE_EFFECT.tsv, ACTIVITY.tsv, EFFECT.tsv
- Path:
DATA_DIR variable in 21_OREGANO.py
Citation
Boudin, M., Diallo, G., Drancé, M. & Mougin, F. The OREGANO knowledge graph for computational drug repurposing. Sci Data 10, 871 (2023). https://doi.org/10.1038/s41597-023-02757-0
