Article

Integrating Semantic Retrieval, LLM-based Refinement, and Structured Expert Curation for Scalable AOP Gene Mapping

2026-06-30

Abstract excerpt

Toxicogenomics can support regulatory toxicology, but its use is limited by the difficulty of translating molecular responses into mechanistic, decision-relevant interpretations. Adverse Outcome Pathways (AOPs) provide a framework for this translation, yet omics applications require scalable mapping of Key Events (KEs) to molecular features. Here, we present an AI-assisted, multi-step workflow for KE-to-gene mappi...

Topics

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

Identifiers and source

Literature Corpus work: 27b46d68-1f36-51d5-b104-6d2b97d1ba94
DOI: 10.64898/2026.06.25.734475

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Integrating Semantic Retrieval, LLM-based Refinement, and Structured Expert Curation for Scalable AOP Gene MappingDOI 10.64898/2026.06.25.734475Read

Ontology-driven association rule mining for biomedical entity relationships: integrating hierarchical knowledge to improve gene-disease discovery.Semantic proximity Read

Molecular annotation of AOPs guides the development of the next generation mechanistic chemical safety assessment and new approach methodsSemantic proximity Read

A CTD-Pfizer collaboration: manual curation of 88,000 scientific articles text mined for drug-disease and drug-phenotype interactions.Semantic proximity Read

AOPGraphExplorer 2.0: An Interactive Graph-Based Platform for Multi-Domain Mechanistic Annotation and Exploration of Adverse Outcome PathwaysSemantic proximity Read

Chemical-Induced Phenotypes at CTD Help Inform the Predisease State and Construct Adverse Outcome Pathways.Semantic proximity Read

Semantic characterization of adverse outcome pathways.Semantic proximity Read

Safetyome and specialized panels for over 3,000 phenotypes: a systematic and translational approach using human genetics and pharmacology.Semantic proximity Read

Interpreting Omics Data Analysis with Large Language Models for Disease Target and Drug DiscoverySemantic proximity Read

Applying knowledge-driven mechanistic inference to toxicogenomicsSemantic proximity Read

Application of Large Language Models for Annotating Genes into Reactome PathwaysSemantic proximity Read

The Comparative Toxicogenomics Database's 10th year anniversary: update 2015.Semantic proximity Read

RD-OMICS: An Integrative Multi-Omics Data Inventory in Rare DiseasesSemantic proximity Read