Nicolas Matentzoglu

Phenologs at knowledge-graph scale: a mouse-to-slime-mold catalog of candidate genes for thousands of human diseases

The paper identifies 61,243 phenologs between human diseases and model organism phenotypes, using a hypergeometric method to rank candidate genes and validate their predictive power.

AI semantics for biomedical data integration

This paper describes an AI semantics workflow using LLM agents to integrate multimodal biomedical data through ontologies and knowledge graphs.

Every Cure Knowledge Graph: A Unified Biomedical Knowledge Graph for Drug Repurposing

The paper introduces EC-KG, a unified biomedical knowledge graph for drug repurposing that integrates multiple existing knowledge graphs to enhance coverage and uncover novel mechanistic pathways.

Towards a standard benchmark for phenotype-driven variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework

PhEval provides a standardized framework to benchmark phenotype-driven variant and gene prioritisation algorithms using real-world patient data and controlled test corpora.

The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics

The paper introduces uPheno, a framework for cross-species phenomics integration by harmonizing phenotype data across species and ontologies.

The Ontology of Biological Attributes (OBA) - Computational Traits for the Life Sciences

This paper introduces OBA, a formalized ontology for biological attributes to facilitate data integration across phenotypic, genetic, and environmental data.

Brain Data Standards - A method for building data-driven cell-type ontologies

The paper introduces a data-driven method to extend cell ontologies for multi-modal single-cell omics data, focusing on the Primary Motor Cortex in humans, mice, and marmosets.

Unifying the Identification of Biomedical Entities with the Bioregistry

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

The Xenopus Phenotype Ontology: bridging model organism phenotype data to human health and development.

The paper introduces the Xenopus Phenotype Ontology (XPO) to standardize phenotype data from Xenopus experiments and link them to human health and development.

OBO Foundry in 2021: Operationalizing Open Data Principles to Evaluate Ontologies

The paper describes how the OBO Foundry formalized its principles into operational rules and implemented automated checks to evaluate ontology compliance, improving interoperability and quality.

The Planarian Anatomy Ontology: A resource to connect data within and across experimental platforms

The paper constructs a planarian anatomy ontology to standardize nomenclature and enable cross-platform data integration and curation.

KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response

KG-COVID-19 creates customizable knowledge graphs for COVID-19 response by integrating siloed biomedical data into structured formats for various research applications.