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Phenopacket Agent

The Phenopacket Agent provides a natural language interface for working with GA4GH Phenopackets, a standard format for sharing disease and phenotype information for genomic medicine. It helps users create, analyze, and interpret phenopackets for rare disease diagnosis and research.

Features

  • Create and validate phenopackets from natural language descriptions
  • Search and analyze phenopacket databases
  • Extract phenotypes, diseases, and genetic variants from clinical descriptions
  • Convert between phenopacket formats
  • Assist with rare disease diagnosis
  • Generate human-readable summaries of phenopackets

Usage

Python API

from aurelian.agents.phenopackets import phenopackets_agent, get_config

# Initialize dependencies
deps = get_config()

# Query phenopacket information
result = await phenopackets_agent.run(
    "Create a phenopacket for a patient with Marfan syndrome",
    deps=deps
)

# Get the response
print(result.data)

Command Line Interface

aurelian phenopackets "Create a phenopacket for a patient with Marfan syndrome"

Gradio Interface

from aurelian.agents.phenopackets import chat

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

Tools

The Phenopacket Agent provides the following tools:

create_phenopacket

Creates a new phenopacket from a description of phenotypes, diseases, and variants.

validate_phenopacket

Validates a phenopacket against the schema.

search_phenopackets

Searches a phenopacket database for matching cases.

summarize_phenopacket

Generates a human-readable summary of a phenopacket.

Examples

Example 1: Creating a phenopacket

Create a phenopacket for a 5-year-old male with osteogenesis imperfecta

Example 2: Searching for similar cases

Find phenopackets with similar phenotypes to: HP:0000347, HP:0001382, HP:0011304

Example 3: Analyzing a phenopacket

Summarize the clinical information in this phenopacket:

{
  "id": "example-patient",
  "subject": {
    "id": "patient1",
    "timeAtLastEncounter": {
      "age": {
        "iso8601duration": "P5Y"
      }
    },
    "sex": "MALE"
  },
  "phenotypicFeatures": [
    {
      "type": {
        "id": "HP:0000347",
        "label": "Micrognathia"
      }
    },
    {
      "type": {
        "id": "HP:0001382",
        "label": "Joint hypermobility"
      }
    }
  ]
}