Egon Willighagen

The paper enhances AOP networks by annotating Key Events with Gene Ontology terms, improving transcriptomics-based assessment of KE perturbation in pesticide-induced hepatotoxicity.

PlantMetWiki integrates plant metabolic pathway data across species to enable cross-species analysis and hypothesis generation.

ArrayAnalysis provides an interactive web and desktop platform for analyzing microarray and RNA-seq data, offering tools for preprocessing, differential expression, and visualization to support both novice and expert users.

The paper describes the development and evaluation of an agentic framework using LLMs to explore molecular interaction maps through user-driven prototyping and testing.

The paper describes a standardized approach to represent Inherited Metabolic Disorders in WikiPathways, highlights limitations in machine-readable disease information, and introduces methods for data curation and analysis using SPARQL queries.

This paper presents a framework integrating metabolic pathway knowledge with patient data to aid in diagnosing inherited metabolic disorders through visualization of biomarker interactions.

The paper introduces molecular AOPs to link KEs from AOP-Wiki to biological pathways in WikiPathways, enabling transcriptomics data analysis for KE activation identification.

The paper presents a computational framework for analyzing SARS-CoV-2-host interactions to identify drug targets and model disease mechanisms.

The paper introduces the Bioregistry, an open metaregistry that integrates and expands existing biomedical entity registries to improve interoperability and data reuse.

The paper semantifies and harmonizes biological pathway diagrams from WikiPathways to enable semantic querying and integration with linked data.

The paper introduces the LOTUS initiative, which curates and shares 750,000+ structure-organism pairs via Wikidata to improve data interoperability and knowledge management in natural products research.

This paper provides a dataset linking rare monogenic diseases to their causative genes, revealing the timeline of discoveries and their relation to methodological and database advancements.

The paper describes a protocol for enhancing Wikidata with structured knowledge using Shape Expressions, demonstrating its application to SARS-CoV-2 and other coronaviruses.

The paper presents a computational workflow to assess FAIRness of datasets in life sciences using two real use cases and proposes a FAIR balloon plot for visualization.

The paper describes Wikidata as a FAIR knowledge graph for life sciences, showcasing its breadth, tools for integration, and use cases in biomedical analysis.

This paper introduces an interoperability layer to convert OpenAPI specifications to bio.tools annotations for FAIR web services.

This paper reviews systems biology approaches to assess nanoparticle hazards, highlighting their value in understanding NP effects on biological systems.