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Automating Data Extraction from Scientific Literature and General PDF Files Using Large Language Models and KNIME: An Application in Toxicology

Authors: José T. Moreira-Filho, Dhruv Ranganath, Ricardo S. Tieghi, Robert Patton, Vicki Sutherland, Charles Schmitt, Andrew A. Rooney, Vickie Walker, Jennifer Fostel, Trey Saddler, David Reif, Kamel Mansouri, and Nicole Kleinstreuer

DOI: https://doi.org/10.22427/NTP-DATA-502-002-002-000-1

Publication

Abstract

The increasing volume of scientific publications and reports presents a challenge in accessing and utilizing data due to their unstructured nature. Toxicology, in particular, depends on structured data for study evaluation, weight-of-evidence chemical assessments, and validation of new approach methodologies (NAMs). Manual data extraction is labor-intensive and fails to meet the demand for structured information. This work presents an automated data extraction workflow using large language models (LLMs) within the KNIME platform. The workflow integrates document parsing tools with LLMs to extract variables from scientific publications and general PDF files. Two execution modes are available: text mode and image mode. Text mode applies tools for extracting text and tables, while image mode uses multimodal LLMs to process non-linear layouts and graphical content. The workflow achieves 81.14% accuracy in text mode for scientific publications and up to 98.54% in image mode for general PDF files. The KNIME platform ensures accessibility through a user-friendly interface, allowing non-experts to use advanced data extraction methods. This automated approach facilitates toxicological research by improving the retrieval of structured data. By democratizing access to LLM-powered workflows, this approach paves the way for significant advancements in knowledge synthesis to support biomedical research.

Supplementary Material

Supporting Information

Scientific Publications

General PDFs