Drugrepobank

Skill BioTender-max/awesome-bio-agent-skills/skills/drugclaw/drugrepobank

Query the DrugRepoBank drug repurposing evidence database. Use whenever the user asks about repurposing candidates, drug–disease–target repurposing evidence, or wants to look up any entity (drug name, DrugBank ID, ChEMBL ID, PubChem CID, TTD target ID, UniProt ID, disease name) in DrugRepoBank.From its SKILL.md

Install

npx -y skills add BioTender-max/awesome-bio-agent-skills --skill drugrepobank

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

One thing to look at

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SKILL.md

2.6 KB, 689 tokens by cl100k_base, as published. Nobody here has run it

DrugRepoBank Query Skill

Search four linked tables (Drug, Target, DrugTargetInteraction, Literature) for repurposing evidence. Auto-detects entity type by prefix:

Input Pattern	Detected As	Example
`DB00945`	DrugBank ID	exact on `DrugBank_ID` / `DrugID`
`T47101`	TTD Target ID	exact on `TargetID`
`FGFR1_HUMAN`	UniProt ID	exact on `UniprotID`
`CHEMBL2103749`	ChEMBL ID	exact on `ChEMBL ID` in Drug table
`16129704` (digits)	PubChem CID	exact on `PubChem_Compound_ID` / `PubChemID`
anything else	free text	substring on drug Name, TargetName, Disease, NewDisease

API

Function	Input	Returns
`load_all()`	—	`dict` with keys `drug`, `dti`, `lit`, `target` (lists of row-dicts)
`search(tables, entity)`	tables dict + single entity string	`dict` with keys `entity`, `entity_type`, `drug`, `target`, `dti`, `literature`
`search_batch(tables, entities)`	tables dict + list of entity strings	`dict[str, search_result]`
`summarize(result)`	single `search()` result	compact one-line LLM-readable text
`to_json(result)`	single `search()` result	JSON string (trimmed heavy fields)

Usage

See if __name__ == "__main__" block in 42_DrugRepoBank.py for runnable examples covering: drug name, DrugBank ID, TTD target ID, UniProt ID, ChEMBL ID, disease free-text, batch search, and JSON output.

Data

Four CSV tables in DATA_DIR:

File	Key Columns	Description
`Drug.csv`	DrugBank_ID, Name, Drug Groups, PubChem_Compound_ID, ChEMBL ID, SMILES	Drug identifiers & structures
`DrugTargetInteraction.csv`	UniprotID, PubchemID, TargetID, DrugID, Highest_status, MOA	Drug–target links with mechanism of action
`Literature.csv`	DrugName, DrugID, Target, Disease, NewDisease, Evidence, Insilico, Invitro, Invivo, Clinicaltrial, PMID	Repurposing evidence & literature references
`Targets.csv`	TargetID, UniprotID, TargetName, TargetGeneName, TargetType, Function	Target annotations & pathway memberships

Path: DATA_DIR variable in 42_DrugRepoBank.py
(resources_metadata/drug_repurposing/DrugRepoBank)
Source: https://awi.cuhk.edu.cn/DrugRepoBank/php/index.php
Paper: Huang et al., Database 2024, baae051. DOI:10.1093/database/baae051

What ships with it: 5 files

19.2 KB alongside SKILL.md, 4 of them executable

drugrepobank_skill.pyruns5.2 KB
example.pyruns11.5 KB
__init__.pyruns154 B
README.md1.5 KB
retrieve.pyruns811 B