textToKnowledgeGraph: Generation of Molecular Interaction Knowledge Graphs Using Large Language Models for Exploration in Cytoscape

James, F.; Churas, C.; Pratt, D.; Luna, A.

doi:10.1101/2025.07.17.664328

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bioRxiv · 10.1101/2025.07.17.664328

textToKnowledgeGraph: Generation of Molecular Interaction Knowledge Graphs Using Large Language Models for Exploration in Cytoscape

James, F.·Churas, C.·Pratt, D.·Luna, A.

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Abstract

MotivationKnowledge graphs (KGs) are powerful tools for structuring and analyzing biological information due to their ability to represent data and improve queries across heterogeneous datasets. However, constructing KGs from unstructured literature remains challenging due to the cost and expertise required for manual curation. Prior works have explored text-mining techniques to automate this process, but have limitations that impact their ability to capture complex relationships fully. Traditional text-mining methods struggle with understanding context across sentences. Additionally, these methods lack expert-level background knowledge, making it difficult to infer relationships that require awareness of concepts indirectly described in the text. Large Language Models (LLMs) present an opportunity to overcome these challenges. LLMs are trained on diverse literature, equipping them with contextual knowledge that enables more accurate extraction of information. ResultsWe present textToKnowledgeGraph, an artificial intelligence tool using LLMs to extract interactions from individual publications directly in Biological Expression Language (BEL). BEL was chosen for its compact and detailed representation of biological relationships, allowing for structured and computationally accessible encoding. This work makes several contributions. 1. Development of the open-source Python textToKnowledgeGraph package (pypi.org/project/texttoknowledgegraph) for BEL extraction from scientific articles, usable from the command line and within other projects, 2. An interactive application within Cytoscape Web to simplify extraction and exploration, 3. A dataset of extractions that have been both computationally and manually reviewed to support future fine-tuning efforts. Availabilityhttps://github.com/ndexbio/llm-text-to-knowledge-graph

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James, F., Churas, C., Pratt, D., Luna, A.. 2025-07-21. textToKnowledgeGraph: Generation of Molecular Interaction Knowledge Graphs Using Large Language Models for Exploration in Cytoscape. https://doi.org/10.1101/2025.07.17.664328

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