James P. Balhoff

The paper presents tools to validate and simplify ontology term hierarchies for better usability in biomedical research.

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

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

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.

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

The paper introduces a Gold Standard corpus for ontology-based phenotype annotation and evaluates a tool's performance against human annotations.

This study evaluates how varying levels of annotation granularity affect semantic similarity metrics in phenotype profiles, finding that coarse annotations may suffice for detecting significant similarity.

The paper describes the Monarch Initiative, a platform that integrates multimodal data across species to enhance genotype-phenotype analysis and precision medicine.

The paper describes the Phenoscape Knowledgebase, an ontology-driven database that integrates phenotype annotations from model organisms and evolutionary literature to enable computational analysis across species.