Noctua FAQs

Question 1

Who is the target audience for Noctua?

Accepted Answer

Noctua is primarily designed for developers, bioinformaticians, and AI agents (such as LLMs like Claude Code) who need programmatic control over GO-CAM models for tasks like gene ontology curation, knowledge graph construction, and AI-driven scientific inference.

Question 2

What is Noctua?

Accepted Answer

Noctua is an MCP (Model Context Protocol) server designed to enable AI agents and LLMs to programmatically edit, create, and query GO-CAM (Gene Ontology Causal Activity Model) models through a standardized interface, leveraging the Barista API.

Question 3

What GO-CAM operations can Noctua perform?

Accepted Answer

Noctua provides comprehensive tools for GO-CAM model editing, including adding/removing individuals, facts, and evidence. It also facilitates the creation of standardized model patterns like basic pathways and causal chains, and allows for retrieval and summarization of full GO-CAM models.

Question 4

How does Noctua ensure secure interaction with the Barista API?

Accepted Answer

Noctua securely handles Barista API tokens by allowing configuration via environment variables (e.g., BARISTA_TOKEN) and providing a dedicated `configure_token` tool for runtime setup, ensuring that sensitive credentials are not exposed or echoed in outputs.

Question 5

What is the Model Context Protocol (MCP) and why is it important for Noctua?

Accepted Answer

MCP is a standard protocol that defines how tools and resources are exposed to Large Language Models (LLMs) and agent clients. Noctua implements FastMCP to offer a unified, machine-readable interface, making it easy for AI agents to discover, understand, and interact with its GO-CAM editing capabilities consistently.

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