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NetMe 2.0: a web-based platform for extracting and modeling knowledge from biomedical literature as a labeled graph.

Antonio Di Maria1, Lorenzo Bellomo2, Fabrizio Billeci3

  • 1Department of Clinical and Experimental Medicine, University of Catania, Catania, 95125, Italy.

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Scientists can now build accurate biomedical networks from literature using NetMe 2.0. This platform extracts entities and relations, creating knowledge graphs and generating explanations for easier understanding.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Biomedical Informatics

Background:

  • The exponential growth of biomedical literature presents a significant challenge for researchers seeking to stay current with scientific advancements.
  • Network analysis is a vital computational tool in life sciences, but constructing accurate and comprehensive biomedical networks from literature remains difficult.

Purpose of the Study:

  • To introduce NetMe 2.0, a web-based platform designed to automate the construction of biomedical knowledge graphs (BKG) from diverse text sources.
  • To enhance the utility of BKGs through an innovative Retrieval Augmented Generation (Graph-RAG) module for generating explanatory sentences.

Main Methods:

  • NetMe 2.0 automatically extracts biomedical entities and their relationships from user-provided texts (PubMed Central articles, free text, PDFs).
  • Extracted information is modeled into a BioMedical Knowledge Graph (BKG).
  • A Graph-RAG module processes the BKG to generate coherent sentences explaining the modeled relationships.

Main Results:

  • NetMe 2.0 successfully infers comprehensive and reliable biological networks.
  • The platform demonstrates significant Precision-Recall metrics when compared to existing state-of-the-art methods.
  • The Graph-RAG module effectively distills well-formed sentences explaining the BKG content.

Conclusions:

  • NetMe 2.0 offers a robust solution for overcoming the challenges of building biomedical networks from extensive literature.
  • The platform facilitates a deeper understanding of complex biological relationships through automated knowledge graph construction and explanation generation.
  • NetMe 2.0 is available at https://netme.click/.