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GO-CAM Agent

The GO-CAM Agent assists with creating, editing, and understanding Gene Ontology Causal Activity Models (GO-CAMs). It provides tools for working with GO terms, genes, and modeling biological pathways using the GO-CAM framework.

Features

  • Search for GO terms and gene products
  • Create and edit GO-CAM models
  • Explain GO-CAM concepts and best practices
  • Visualize biological processes and molecular functions
  • Convert between different GO-CAM representations

Usage

Python API

from aurelian.agents.gocam import gocam_agent, get_config

# Initialize dependencies
deps = get_config()

# Query about GO-CAM
result = await gocam_agent.run(
    "How do I represent a phosphorylation process in GO-CAM?",
    deps=deps
)

# Get the response
print(result.data)

Command Line Interface

aurelian gocam "How do I represent a phosphorylation process in GO-CAM?"

Gradio Interface

from aurelian.agents.gocam import chat

# Launch Gradio interface
interface = chat()
interface.launch()

Tools

The GO-CAM Agent provides the following tools:

search_go_terms

Searches the Gene Ontology for terms matching a query string.

search_genes

Searches for genes by name, symbol, or description.

create_gocam_model

Creates a new GO-CAM model with specified components.

visualize_gocam

Generates a visualization of a GO-CAM model.

Examples

Example 1: Creating a simple GO-CAM model

Create a GO-CAM model for TP53 regulating apoptosis

Example 2: Finding relevant GO terms

What GO terms are related to DNA repair?

Example 3: Explaining GO-CAM concepts

Explain how to represent a protein kinase activity in GO-CAM