Dgidb

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

Query the DGIdb (Drug-Gene Interaction Database) for drug-gene interactions, gene druggability categories, and drug target information. Use whenever the user asks about drug targets, druggable genes, gene-drug interactions, or wants to look up any entity (gene name, drug name, druggability category) in DGIdb.From its SKILL.md

Install

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

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

2.3 KB, 575 tokens by cl100k_base, as published. Nobody here has run it

DGIdb Query Skill

Search DGIdb records by any entity. Auto-detects type by naming convention:

Input Pattern	Detected As	Example
ALL-CAPS ≤15 chars	Gene	`EGFR`, `BRAF`, `TP53`
Known category keyword	Druggability category	`clinically actionable`, `kinase`
Anything else	Drug	`imatinib`, `erlotinib`

Supported category keywords: clinically actionable, drug resistance, druggable genome, tumor suppressor, transcription factor, kinase, g protein coupled receptor, hormone activity, ion channel, protease, dna repair.

API

Function	Input	Returns
`search(entity)`	single entity string	`list[dict]`
`search_batch(entities)`	list of entity strings	`dict[str, list[dict]]`
`summarize(results, entity)`	result list + label	compact text for LLM
`to_json(results)`	result list	`list[dict]` (passthrough)

Key Fields

Gene result: name, long_name, categories, interaction_count, interactions[] (each with drug, drug_concept_id, score, types, directionality, attributes, pmids, sources).

Drug result: name, concept_id, approval_ratings, interaction_count, interactions[] (each with gene, gene_long_name, score, types, directionality, attributes, pmids, sources).

Category result: category, gene_count, genes[] (each with name, long_name).

Usage

See if __name__ == "__main__" block in 16_DGIdb.py for runnable examples covering: single gene, single drug, category, batch (mixed types), and JSON output.

Data Source

Database: DGIdb v5.0 — Drug-Gene Interaction Database
Endpoint: https://dgidb.org/api/graphql (GraphQL, no API key)
Coverage: 40+ source databases, ~100 k drug-gene interactions
Paper: Freshour et al., Nucleic Acids Res. 2024; 52(D1):D1227-D1235. DOI: 10.1093/nar/gkac1046

What ships with it: 5 files

19.8 KB alongside SKILL.md, 4 of them executable

dgidb_skill.pyruns5.7 KB
example.pyruns12.3 KB
__init__.pyruns126 B
README.md936 B
retrieve.pyruns762 B