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Checklist Agent

The Checklist Agent evaluates scientific papers against established checklists such as STREAMS, STORMS, and ARRIVE. It helps ensure that papers conform to relevant reporting guidelines and best practices.

Features

  • Automatic selection of appropriate checklists based on paper content
  • Detailed evaluation of papers against each checklist item
  • Support for PubMed IDs and DOIs for paper retrieval
  • Provides PASS/FAIL/OTHER evaluations with explanations for each checklist item
  • Returns results as a structured markdown table

Usage

Python API

from aurelian.agents.checklist import checklist_agent, get_config

# Initialize dependencies
deps = get_config()

# Evaluate a paper against a specific checklist
result = await checklist_agent.run(
    "Evaluate https://journals.asm.org/doi/10.1128/mra.01361-19 using STREAMS",
    deps=deps
)

# Get the evaluation results
print(result.data)

Command Line Interface

aurelian checklist "Evaluate https://journals.asm.org/doi/10.1128/mra.01361-19 using STREAMS"

Gradio Interface

from aurelian.agents.checklist import chat

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

Tools

The Checklist Agent provides the following tools:

retrieve_text_from_pmid

Retrieves the full text or abstract of a paper using its PubMed ID.

retrieve_text_from_doi

Retrieves the full text or abstract of a paper using its DOI.

fetch_checklist

Retrieves a specific checklist by ID (e.g., STREAMS, STORMS, ARRIVE).

Available Checklists

The agent supports various checklists for different types of scientific papers:

  • STREAMS: Standards for Reporting Engineered Mammalian Systems
  • STORMS: STrengthening the Reporting Of Molecular Simulations
  • ARRIVE: Animal Research: Reporting of In Vivo Experiments

Examples

Example 1: Evaluating a paper using STREAMS

Evaluate https://journals.asm.org/doi/10.1128/mra.01361-19 using STREAMS

Example 2: Evaluating a paper with automatic checklist selection

Check the paper 'Exploration of the Biosynthetic Potential of the Populus Microbiome' https://journals.asm.org/doi/10.1128/msystems.00045-18