Publications by authors named "James Balhoff"

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Mondo: Integrating Disease Terminology Across Communities.
Nicole A Vasilevsky, Sabrina Toro, Nicolas Matentzoglu, Joseph E Flack, Kathleen R Mullen, James P Balhoff

Genetics· October 2025

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A general strategy for generating expert-guided, simplified views of ontologies.
Anita R Caron, Aleix Puig-Barbe, Ellen M Quardokus, James P Balhoff, Jasmine Belfiore

bioRxiv· August 2025

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The Cell Ontology in the age of single-cell omics.
Shawn Zheng Kai Tan, Aleix Puig-Barbe, Damien Goutte-Gattat, Caroline Eastwood, Brian Aevermann, James P Balhoff

ArXiv· June 2025

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The Vertebrate Breed Ontology: Toward Effective Breed Data Standardization.
Kathleen R Mullen, Imke Tammen, Nicolas A Matentzoglu, Marius Mather, James P Balhoff

J Vet Intern Med· May 2025

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The Unified Phenotype Ontology : a framework for cross-species integrative phenomics.
Nicolas Matentzoglu, Susan M Bello, Ray Stefancsik, Sarah M Alghamdi, Anna V Anagnostopoulos, James P Balhoff

Genetics· March 2025

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The Vertebrate Breed Ontology: Towards effective breed data standardization.
Kathleen R Mullen, Imke Tammen, Nicolas A Matentzoglu, Marius Mather, James P Balhoff

ArXiv· January 2025

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The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics.
Nicolas Matentzoglu, Susan M Bello, Ray Stefancsik, Sarah M Alghamdi, Anna V Anagnostopoulos, James P Balhoff

bioRxiv· September 2024

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Computable species descriptions and nanopublications: applying ontology-based technologies to dung beetles (Coleoptera, Scarabaeinae).
Giulio Montanaro, James P Balhoff, Jennifer C Girón, Max Söderholm, Sergei Tarasov

Biodivers Data J· June 2024

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The Human Phenotype Ontology in 2024: phenotypes around the world.
Michael A Gargano, Nicolas Matentzoglu, Ben Coleman, Eunice B Addo-Lartey, Anna V Anagnostopoulos, James P Balhoff

Nucleic Acids Res· January 2024

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The Ontology of Biological Attributes (OBA)-computational traits for the life sciences.
Ray Stefancsik, James P Balhoff, Meghan A Balk, Robyn L Ball, Susan M Bello

Mamm Genome· September 2023

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The Gene Ontology knowledgebase in 2023.

Genetics· May 2023

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The Ontology of Biological Attributes (OBA) - Computational Traits for the Life Sciences.
Ray Stefancsik, James P Balhoff, Meghan A Balk, Robyn Ball, Susan M Bello

bioRxiv· January 2023

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Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge From Anatomy Ontologies.
Diego S Porto, Wasila M Dahdul, Hilmar Lapp, James P Balhoff, Todd J Vision

Syst Biol· October 2022

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Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies.
Nicolas Matentzoglu, Damien Goutte-Gattat, Shawn Zheng Kai Tan, James P Balhoff, Seth Carbon

Database (Oxford)· October 2022

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A Simple Standard for Sharing Ontological Mappings (SSSOM).
Nicolas Matentzoglu, James P Balhoff, Susan M Bello, Chris Bizon, Matthew Brush

Database (Oxford)· May 2022

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Reactome and the Gene Ontology: digital convergence of data resources.
Benjamin M Good, Kimberly Van Auken, David P Hill, Huaiyu Mi, Seth Carbon, James P Balhoff

Bioinformatics· October 2021

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OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies.
Rebecca Jackson, Nicolas Matentzoglu, James A Overton, Randi Vita, James P Balhoff

Database (Oxford)· October 2021

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Application of MCAT questions as a testing tool and evaluation metric for knowledge graph-based reasoning systems.
Karamarie Fecho, James Balhoff, Chris Bizon, William E Byrd, Sui Hang

Clin Transl Sci· September 2021

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KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response.
Justin T Reese, Deepak Unni, Tiffany J Callahan, Luca Cappelletti, Vida Ravanmehr, James P Balhoff

Patterns (N Y)· January 2021

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Visualization Environment for Federated Knowledge Graphs: Development of an Interactive Biomedical Query Language and Web Application Interface.
Steven Cox, Stanley C Ahalt, James Balhoff, Chris Bizon, Karamarie Fecho

JMIR Med Inform· November 2020

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Transforming the study of organisms: Phenomic data models and knowledge bases.
Anne E Thessen, Ramona L Walls, Lars Vogt, Jessica Singer, Robert Warren, James P Balhoff

PLoS Comput Biol· November 2020

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A Logical Model of Homology for Comparative Biology.
Paula M Mabee, James P Balhoff, Wasila M Dahdul, Hilmar Lapp, Christopher J Mungall

Syst Biol· March 2020

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The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.
Kent A Shefchek, Nomi L Harris, Michael Gargano, Nicolas Matentzoglu, Deepak Unni, James P Balhoff

Nucleic Acids Res· January 2020

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ROBOKOP KG and KGB: Integrated Knowledge Graphs from Federated Sources.
Chris Bizon, Steven Cox, James Balhoff, Yaphet Kebede, Patrick Wang

J Chem Inf Model· December 2019

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Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems.
Paul D Thomas, David P Hill, Huaiyu Mi, David Osumi-Sutherland, Kimberly Van Auken, James P Balhoff

Nat Genet· October 2019

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