Pharmkg

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

Query the PharmKG knowledge graph (180k entities, 39 relation types, >1M triples). Use whenever the user asks about biomedical relationships among genes, drugs/chemicals, and diseases — e.g. drug–gene interactions, drug–disease associations, gene–disease links, or drug–drug relationships derived from literature and curated databases.From its SKILL.md

Install

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

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

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SKILL.md

2.0 KB, 486 tokens by cl100k_base, as published. Nobody here has run it

PharmKG Query Skill

Search PharmKG triples by entity name. Matching is case-insensitive; exact match is tried first via a prebuilt index, with substring fallback.

Input Example	Matches On
`aspirin`	exact on Entity1_name or Entity2_name
`BRCA1`	exact / substring on entity names
`Alzheimer Disease`	substring on entity names

Entity & Relation Types

Entities (~188 k): Drug/Chemical (DrugBank, ChEMBL), Gene/Protein (Entrez, UniProt), Disease (DO, MeSH).

Relations (39 types): chemical–gene (inhibition, activation, binding …), chemical–disease (treatment, marker, risk factor), gene–disease (association, marker), chemical–chemical (similarity, interaction), and others.

API

Function	Input	Returns
`load_pharmkg(path)`	CSV path	`list[dict]` of triples
`_build_index(triples)`	triple list	`dict[str, list]` (entity→triples)
`search(triples, entity, index=)`	entity string	`list[dict]`
`search_batch(triples, entities, index=)`	list of strings	`dict[str, list]`
`summarize(hits, entity)`	hits + label	compact text
`to_json(hits)`	hits	JSON string

Usage

See if __name__ == "__main__" block in 55_PharmKG.py for runnable examples covering: single entity search, batch search, summarize, and JSON output.

Data

Source: raw_PharmKG-180k.csv (comma-separated)
Columns: Entity1_name, relationship_type, Entity2_name
Scale: ~188 k entities, 39 relation types, >1 M triples
Path: DATA_PATH variable in 55_PharmKG.py
Paper: Zheng et al., Briefings in Bioinformatics 22(4), 2021. DOI: 10.1093/bib/bbaa344

What ships with it: 5 files

12.7 KB alongside SKILL.md, 4 of them executable

example.pyruns5.8 KB
__init__.pyruns134 B
pharmkg_skill.pyruns4.3 KB
README.md1.7 KB
retrieve.pyruns832 B