| name | drkg-query |
| description | Query the DRKG (Drug Repurposing Knowledge Graph). Use whenever the user asks about drug–gene, drug–disease, gene–disease, or other biomedical entity relationships in a knowledge-graph context, drug repurposing candidates, COVID-19 drug repurposing, or wants to explore neighbours of any biomedical entity (compound, gene, disease, pathway, side effect, etc.) in DRKG.
|
DRKG Query Skill
Search the Drug Repurposing Knowledge Graph (97 238 entities, 5 874 261
triplets, 107 relation types) by any entity. Auto-detects entity type by
input pattern and returns all KG neighbours.
Entity Format
Entities in DRKG are typed strings: Type::ID.
| Entity Type | Example | Count |
|---|
| Compound | Compound::DB00945 | 24 313 |
| Gene | Gene::1956 | 39 220 |
| Disease | Disease::DOID:162 | 5 103 |
| Anatomy | Anatomy::UBERON:0001474 | 400 |
| Biological Process | Biological Process::GO:0006915 | 11 381 |
| Cellular Component | Cellular Component::GO:0005634 | 1 391 |
| Molecular Function | Molecular Function::GO:0005515 | 2 884 |
| Pathway | Pathway::PC7_8078 | 1 822 |
| Pharmacologic Class | Pharmacologic Class::N0000175605 | 345 |
| Side Effect | Side Effect::C0000737 | 5 701 |
| Symptom | Symptom::D009325 | 415 |
| Atc | Atc::N02BE01 | 4 048 |
| Tax | Tax::9606 | 215 |
Relations are typed strings: Source::RelType::HeadType:TailType, e.g.
DRUGBANK::target::Compound:Gene, Hetionet::CtD::Compound:Disease.
Input Auto-Detection
| Input Pattern | Detected As | Match Logic |
|---|
Compound::DB00945 | full DRKG entity | exact match |
DB\d{5,} | DrugBank ID | prepend Compound:: |
DOID:\d+ / MESH:D\d+ | Disease ID | prepend Disease:: |
GO:\d+ | GO term | try BP / MF / CC |
pure digits (1956) | Entrez Gene ID | prepend Gene:: |
| anything else | free text | case-insensitive substring across all entities |
API
| Function | Input | Returns |
|---|
search(query, limit=200) | single entity string | dict with resolved, as_head, as_tail |
search_batch(queries, limit=200) | list of entity strings | dict[query → result] |
get_sources(entity) | resolved DRKG entity | source attribution string |
get_relation_info(relation) | relation string | glossary dict |
entity_types() | — | list of 13 entity type names |
summarize(result) | search result dict | compact LLM-readable text |
to_json(result) | search result dict | JSON-serialisable dict |
Usage
See if __name__ == "__main__" block in 25_DRKG.py for runnable examples:
single-entity search (full ID, bare ID, free text), batch search, relation
glossary lookup, and JSON output.
Data Sources
DRKG integrates six databases plus COVID-19 literature:
| Source | Triplets | Coverage |
|---|
| DrugBank | 1 424 790 | drug–drug, drug–gene, drug–disease, ATC |
| Hetionet | 2 250 197 | gene–gene, anatomy, pathways, side effects |
| GNBR | 335 369 | gene–gene, compound–gene, disease–gene |
| STRING | 1 496 708 | protein–protein interactions |
| IntAct | 256 151 | protein–protein interactions |
| DGIdb | 26 290 | drug–gene interactions |
| Bibliography | 84 756 | COVID-19 related |
Data Files
Located at DATA_DIR in 25_DRKG.py:
| File | Description |
|---|
drkg.tsv | 5 874 261 triplets (head, relation, tail) |
relation_glossary.tsv | relation type glossary with source info |
entity2src.tsv | entity → original data-source mapping |
Citation
Ioannidis et al. "DRKG - Drug Repurposing Knowledge Graph for Covid-19", 2020.
https://github.com/gnn4dr/DRKG
