Oregano

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