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Updated: Sep 10, 2025

Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems
Published on: June 13, 2025
Bridging the Scientific Knowledge Gap and Reproducibility: A Survey of Provenance, Assertion and Evidence Ontologies
Tek Raj Chhetri1, Yaroslav O Halchenko2, Dorota Jarecka1
1McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
Abstract:
The rapid growth of scientific publications and evolving experimental paradigms create significant challenges in staying up-to-date with current advances. Assertions are often unstructured and have limited provenance, which hinders reproducibility. Ontologies and knowledge graphs (KGs) offer structured solutions by capturing assertions, evidence, and provenance to support reproducibility. This paper reviews 23 ontologies - 13 focused on assertions and evidence and 10 on provenance - providing an overview of the current landscape while highlighting key challenges and opportunities for improvement.
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