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Biblio Agent

The Biblio Agent helps organize and search bibliographic data and citations. It provides tools for searching a bibliography database, retrieving scientific publications, and accessing web content.

Features

  • Search a bibliography database for relevant entries
  • Retrieve publication content using PubMed IDs
  • Search the web for additional information
  • Retrieve web page content for detailed analysis
  • Format results with bioregistry links and markdown tables

Usage

Python API

from aurelian.agents.biblio import biblio_agent, get_config

# Initialize dependencies
deps = get_config()

# Search for publications about a specific topic
result = await biblio_agent.run(
    "What patients have liver disease?",
    deps=deps
)

# Get the search results
print(result.data)

Command Line Interface

aurelian biblio "What patients have liver disease?"

Gradio Interface

from aurelian.agents.biblio import chat

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

Tools

The Biblio Agent provides the following tools:

search_bibliography

Performs a retrieval search over the biblio database. The query can be any text, such as the name of a disease, phenotype, gene, etc.

lookup_pmid

Retrieves the full text or abstract of a publication using its PubMed ID (format: "PMID:nnnnnnn").

search_web

Searches the web using a text query and returns matching web pages with summaries.

retrieve_web_page

Fetches the contents of a specific web page.

Examples

Example 1: Searching for publications about a specific disease

What patients have liver disease?

Example 2: Searching for publications involving specific genes

What biblio involve genes from metabolic pathways?

Example 3: Analyzing genotype-phenotype relationships

How does the type of variant affect phenotype in peroxisomal disorders?

Example 4: Examining publications on a specific condition

Examine biblio for skeletal dysplasias, check them against publications