Quick Start

This guide walks you through launching ARK CLI and having your first conversation with a biomedical knowledge graph.

Prerequisites

• ARK CLI installed (Installation)
• ANTHROPIC_API_KEY set in your .env file

Launch ARK CLI

pnpm cli

The terminal UI will start and display the available knowledge graphs as separate agents, each with its own color indicator.

Select a Knowledge Graph

ARK CLI ships with three bundled knowledge graphs. For this guide, we'll use PrimeKG, a precision medicine knowledge graph covering diseases, drugs, genes, and more.

Select the PrimeKG agent from the list to start a conversation.

Ask Your First Question

Once you've selected a graph, type a question in natural language:

What genes are associated with Alzheimer's disease?

The AI agent will:

1. Search for "Alzheimer's disease" in the graph nodes using findNodesByName
2. Find the matching disease node and retrieve its neighbors with getNeighborsByNodeId
3. Filter for gene/protein-type connections
4. Fetch details on the relevant genes with getNodeDetails
5. Return a summary of associated genes with citations

Understanding the Output

As the agent works, you'll see its reasoning process in the terminal. The agent shows which tools it's calling and what results it finds. This transparency helps you understand how it's traversing the knowledge graph.

Tool call results are rendered as structured blocks in the terminal. For example, the getNodeDetails tool displays node name, type, ID, knowledge graph name, and a formatted list of properties.

Follow-Up Questions

The agent maintains conversation context. You can ask follow-ups without repeating context:

Which of those genes are also involved in Parkinson's disease?

The agent uses the previous conversation history and makes new graph queries to find the overlap between gene sets.

Try Other Graphs

Each knowledge graph has its own agent. Switch between them to explore different domains:

• PrimeKG: Precision medicine, drug-disease-gene relationships
• AfriMedKG: Pan-African medical knowledge
• OptimusKG: Modern multimodal biomedical KG

See Bundled Knowledge Graphs for details on each graph.

Next Steps