Building evidence-based knowledge graphs from full-text literature for disease-specific biomedical reasoning

• URL: http://arxiv.org/abs/2603.28325v2
• Date: Tue, 31 Mar 2026 05:35:12 GMT
• Title: Building evidence-based knowledge graphs from full-text literature for disease-specific biomedical reasoning
• Abstract summary: We present EvidenceNet, a framework for building disease-specific knowledge graphs from full-text biomedical literature.<n>EvidenceNet uses a large language model (LLM)-assisted pipeline to extract experimentally grounded findings as structured evidence nodes, normalize biomedical entities, score evidence quality, and connect evidence records through typed semantic relations.<n> Technical validation shows high component fidelity, including 98.3% field-level extraction accuracy, 100.0% high-confidence entity-link accuracy, 87.5% fusion integrity, and 90.0% semantic relation-type accuracy.
• Score: 5.198797072162084
• License: http://creativecommons.org/licenses/by-nc-sa/4.0/
• Abstract: Biomedical knowledge resources often either preserve evidence as unstructured text or compress it into flat triples that omit study design, provenance, and quantitative support. Here we present EvidenceNet, a framework and dataset for building disease-specific knowledge graphs from full-text biomedical literature. EvidenceNet uses a large language model (LLM)-assisted pipeline to extract experimentally grounded findings as structured evidence nodes, normalize biomedical entities, score evidence quality, and connect evidence records through typed semantic relations. We release two resources: EvidenceNet-HCC with 7,872 evidence records, 10,328 graph nodes, and 49,756 edges, and EvidenceNet-CRC with 6,622 records, 8,795 nodes, and 39,361 edges. Technical validation shows high component fidelity, including 98.3% field-level extraction accuracy, 100.0% high-confidence entity-link accuracy, 87.5% fusion integrity, and 90.0% semantic relation-type accuracy. In downstream evaluation, EvidenceNet improves internal and external retrieval-augmented question answering and retains structural signal for future link prediction and target prioritization. These results establish EvidenceNet as a disease-specific resource for evidence-aware biomedical reasoning and hypothesis generation.

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