Repodb

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

Query the RepoDB drug repurposing database. Use whenever the user asks about drug-disease associations, drug repurposing candidates, or wants to look up any entity (drug name, indication, DrugBank ID, UMLS CUI, NCT ID) in RepoDB.From its SKILL.md

Install

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

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

1.4 KB, 335 tokens by cl100k_base, as published. Nobody here has run it

RepoDB Query Skill

Search RepoDB records by any entity. Auto-detects type by prefix:

Input Pattern	Detected As	Match Logic
`DB00584`	DrugBank ID	exact on `drugbank_id`
`C0020538`	UMLS CUI	exact on `ind_id`
`NCT00001234`	Trial ID	exact on `NCT`
anything else	free text	substring on `drug_name` OR `ind_name`

API

Function	Input	Returns
`load_repodb(path)`	CSV path	DataFrame
`search(df, entity)`	single entity string	DataFrame
`search_batch(df, entities)`	list of entity strings	dict[str, DataFrame]
`summarize(hits, entity)`	DataFrame + label	compact text
`to_json(hits)`	DataFrame	list[dict]

Usage

See if __name__ == "__main__" block in repodb_query.py for runnable examples covering: drug name, DrugBank ID, UMLS CUI, indication name, batch search, and JSON output.

Data

Source: full.csv (comma or tab separated, auto-detected)
Columns: drug_name, drugbank_id, ind_name, ind_id, NCT, status, phase, DetailedStatus
Path: DATA_PATH variable in repodb_query.py

What ships with it: 5 files

12.4 KB alongside SKILL.md, 4 of them executable

example.pyruns3.9 KB
__init__.pyruns130 B
README.md1.2 KB
repodb_skill.pyruns6.4 KB
retrieve.pyruns806 B