Pharmkg Query

Community

QSong-github

pharmkg-query

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.

Overview

Publisher	QSong-github
Repository	`DrugClaw`
Skill name	`pharmkg-query`
Stars	118
Forks	3
Bundled files	4
Links	Skill source Repository Homepage

Markdown instructions
A SKILL.md file the model loads on demand, so it only costs tokens when a request actually matches.
Works with any LLM
AI skills are plain Markdown, not provider-specific code, so this works with GPT, Claude, Gemini, Grok, or a local model.
4 bundled files
Scripts, templates, and references the model can read while it works. Files are read-only and never executed.
Open source
Published by QSong-github on GitHub. Read the source before you install it.

Installation

Install the Pharmkg Query AI skill in TypingMind to use it with any LLM, or drop it into another agent that reads SKILL.md.

Install in TypingMind

TypingMind installs a skill straight from its GitHub folder — it reads SKILL.md, bundles the resource files, and stores the result locally.

Open the app and go to Plugins → Skills.
Choose "Install from GitHub".
Paste the skill folder URL below and confirm.
https://github.com/QSong-github/DrugClaw/tree/main/skills/drug_knowledgebase/pharmkg
Enable the skill in any chat where you want it available.

Plugins → Skills → Add skill → From GitHub URL, then paste the folder URL and press Continue.

Install in another agent

Any agent that reads the Agent Skills format can use this skill — copy the folder into that agent's skills directory.

Claude Code — .claude/skills

git clone --depth 1 https://github.com/QSong-github/DrugClaw.git /tmp/DrugClaw
mkdir -p .claude/skills
cp -r /tmp/DrugClaw/skills/drug_knowledgebase/pharmkg .claude/skills/pharmkg-query

Restart Claude Code after copying so it picks up the new skill.

Use it in TypingMind

Enable Pharmkg Query in any TypingMind chat and the model takes it from there. Its name and description sit in the system prompt, and the moment a request matches, the model loads the full instructions itself — you never invoke it by hand, and it costs no tokens until it is actually used.

The model loads Pharmkg Query on its own as soon as a request matches it.

Works with any AI model

AI skills are plain Markdown instructions rather than provider-specific code, so Pharmkg Query is not tied to the model it was written for. Install it once in TypingMind and use it with GPT-5, Claude, Gemini, Grok, DeepSeek, Mistral, Llama, or a local model you run yourself — all on your own API keys.

Loaded only when it is needed
The system prompt carries just the name and description. The instructions are fetched on the first matching request, so an idle skill costs nothing.
Switch models mid-chat
Because the skill is instructions rather than code, changing model does not break it — the next model reads the same SKILL.md.

Skill instructions

This is the SKILL.md content the model loads. Read it before installing — a skill is instructions your model will follow.

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

Bundled files

The model reads these on demand while the skill is loaded. They are exposed as readable files and are never executed.

Frequently asked questions

What does the Pharmkg Query AI skill do?

Why use Pharmkg Query on TypingMind?

Because you install it once and use it with any model. Pharmkg Query is plain Markdown rather than provider-specific code, so the same skill runs on GPT-5, Claude, Gemini, Grok, or a local model — and you can switch model mid-chat without it breaking. TypingMind runs on your own API keys, so you pay providers directly instead of a per-seat subscription, and your skills and chats stay in your own storage.

How do I install Pharmkg Query in TypingMind?

Open Plugins → Skills → Install from GitHub in TypingMind and paste https://github.com/QSong-github/DrugClaw/tree/main/skills/drug_knowledgebase/pharmkg. TypingMind reads its SKILL.md and bundles its files and installs it as a skill you can enable per chat.

Which AI models can use Pharmkg Query?

Any model you connect in TypingMind. AI skills are plain Markdown instructions rather than provider-specific code, so GPT, Claude, Gemini, Grok, and local models can all load this skill when a request matches it.

How many AI models can I use with Pharmkg Query?

As many as you like. As long as a model supports skills, you can use Pharmkg Query with it — GPT, Claude, Gemini, Grok, DeepSeek, Mistral, Llama and more — all on TypingMind with your own API keys.

Is the Pharmkg Query AI skill free?

It is published on GitHub by QSong-github. Check the repository for licensing terms. You only pay your own AI provider for the tokens you use.

What are AI skills?

An AI skill is a reusable instruction bundle that teaches an AI model how to do one specific task. It follows the open Agent Skills format: a SKILL.md file with a name and description, plus any scripts, templates or reference files the model may need. The model reads the instructions only when your request matches the skill, so an installed skill costs nothing until it is used.

How are AI skills different from plugins or MCP servers?

A plugin or MCP server gives a model new tools to call — code that runs somewhere and returns a result. An AI skill gives the model knowledge and process instead: how to approach a task, which steps to follow, what good output looks like. Skills are plain Markdown, so they need no server, no API key and no runtime, and they work with any model.

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Overview

Installation

Install in TypingMind

Install in another agent

Use it in TypingMind

Works with any AI model

Skill instructions

PharmKG Query Skill

Entity & Relation Types

API

Usage

Data

Bundled files

Frequently asked questions

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