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Expert Knowledge & Machine Understanding: Bridging Reactome's Ontology with LLM Semantic Embeddings

arXiv · AI, language, vision and robotics · article · Aug 28, 2026 · UTC

Biological knowledgebases like Reactome provide high-quality pathways that include biological elements' relationships and textual descriptions (metadata). The quality of such pathways is granted by manual curation, that presents, however, significant scalability challenges. Lately, numerous NLP tools have been proposed to cope with this issue, leveraging textual information to automatically expand biological knowledgebases. However, little exploration has been done so far to assess whether relationships among textual descriptions mirror higher order biological relationships. This study explore

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