Article

Beyond Identifier Matching: An Empirical Characterization of Failure Modes in Biomedical Knowledge Graph Integration

2026-05-28

Abstract excerpt

<h4>Objective</h4> Biomedical knowledge graphs (KGs) such as PrimeKG, Hetionet, UMLS, and PharmGKB are increasingly used as the substrate for downstream machine-learning, retrieval-augmented generation, drug-repurposing, and electronic health record (EHR) augmentation pipelines. The dominant assumption in published work is that integrating two or more such KGs is a tractable engineering step solved by identifier...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: b782a965-77e9-507e-ae8b-3c1183edc1be
DOI: 10.64898/2026.05.26.26354182

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Beyond Identifier Matching: An Empirical Characterization of Failure Modes in Biomedical Knowledge Graph IntegrationDOI 10.64898/2026.05.26.26354182Read

<i>MetaHarmonizer</i> : robust biomedical metadata harmonization and a contamination control for inflated LLM performance on public benchmarksSemantic proximity Read

Assembly and reasoning over semantic mappings at scale for biomedical data integrationSemantic proximity Read

IID-KG: An ontology-aligned literature-derived knowledge graph for infectious and immune-mediated diseasesSemantic proximity Read

A Framework for Automated Construction of Heterogeneous Large-Scale Biomedical Knowledge GraphsSemantic proximity Read

A Large-Scale Pharmacogenomic Knowledge Graph for Drug-Gene-Variant-Disease DiscoverySemantic proximity Read

The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical DataSemantic proximity Read

Drug repurposing for rare diseases via a gene-bridged heterogeneous knowledge graph and graph attention networkSemantic proximity Read

BioKG Explorer: Interactive Visual Analytics for Biomedical Knowledge Graph Exploration over PrimeKGSemantic proximity Read

Towards understanding the disease landscape of clinical trials in Germany: Ontology and embedding-based pipelines versus Large Language Models for ICD-10 HarmonizationSemantic proximity Read

Matching disease and phenotype ontologies in the ontology alignment evaluation initiative.Semantic proximity Read

BioKG Explorer: Interactive Visual Analytics for Biomedical Knowledge Graph Exploration over PrimeKGSemantic proximity Read