ADReCS-query
ResearchQuery the ADReCS (Adverse Drug Reaction Classification System) v3.3 database. Use whenever the user asks about adverse drug reactions, drug safety profiles, ADR classification, ADR severity/frequency, or wants to look up any entity (drug name, BADD Drug ID, DrugBank ID, ATC code, CAS RN, PubChem CID, KEGG ID, ADR term, ADReCS ID, MedDRA code, MeSH ID) in ADReCS.
How to use this skill
Bring this guide into your coding agent with a prompt tailored to the tool you use.
- Open your project in Codex.
- Copy and paste the prompt below.
- Review files and risks before approving any action.
Inspect the Agent Skill at https://github.com/BioTender-max/awesome-bio-agent-skills/blob/HEAD/skills/drugclaw/adrecs/SKILL.md and all supporting files. Report provenance, permissions, scripts, dependencies, and security risks. Propose an exact installation into .agents/skills/adrecs-query, but wait for my approval before writing files or running scripts.
Copying this prompt does not install or run the skill. Review third-party files before use.
ADReCS Query Skill
Search ADReCS v3.3 records by any entity. Auto-detects type by prefix:
| Input Pattern | Detected As | Example |
|---|---|---|
BADD_D00142 | BADD Drug ID | exact on drug_id column |
DB00945 | DrugBank ID | resolved via Drug_information |
A02BC01 | ATC code | resolved via Drug_information |
50-78-2 | CAS RN | resolved via Drug_information |
CID2244 or bare digits | PubChem CID | resolved via Drug_information |
D00109 (5-digit) | KEGG ID | resolved via Drug_information |
08.06.02.001 | ADReCS ID | substring on ADReCS_ID column |
10003781 (8-digit) | MedDRA code | resolved via ADR_ontology |
D###### (6+ digit) | MeSH ID | resolved via ADR_ontology |
| anything else | free text | substring on drug_name OR ADR_term |
API
| Function | Input | Returns |
|---|---|---|
load_drug_adr(path) | txt path | DataFrame (Drug–ADR pairs) |
load_drug_info(path) | xlsx path | DataFrame (drug metadata) |
load_adr_ontology(path) | xlsx path | DataFrame (ADR hierarchy) |
search(entity) | single entity string | DataFrame of matching Drug–ADR rows |
search_batch(entities) | list of entity strings | dict[str, DataFrame] |
summarize(hits, entity) | DataFrame + label | compact LLM-readable text |
to_json(hits) | DataFrame | list[dict] |
Usage
See if __name__ == "__main__" block in 62_ADReCS.py for runnable examples covering: drug name lookup, BADD Drug ID, DrugBank ID, ADR term, ADReCS ID prefix, batch search, and JSON output.
Data
- Source: ADReCS v3.3 — https://www.bio-add.org/ADReCS/
- Primary file:
Drug_ADR_v3.3.txt(drug–ADR association pairs) - Drug metadata:
Drug_information_v3.3.xlsx(name, synonyms, DrugBank/KEGG/PubChem/ATC/CAS cross-refs) - ADR hierarchy:
ADR_ontology_v3.3.xlsx(ADReCS ID, ADR term, MedDRA code, MeSH ID, 4-level classification) - Path:
DATA_DIRvariable in62_ADReCS.py
Citation
Cai MC et al. (2015) ADReCS: an ontology database for aiding standardization and hierarchical classification of adverse drug reaction terms. Nucleic Acids Research 43(D1):D907–D913.