A Corpus of OWL DL Ontologies. - Nicolas Matentzoglu; Samantha Bail; Bijan Parsia (Description Logics, 2013)

OWL Reasoner Evaluation (ORE) Workshop 2013 Results: Short Report. - Rafael S. Gonçalves 001; Samantha Bail; Ernesto Jiménez-Ruiz; Nicolas Matentzoglu; Bijan Parsia; Birte Glimm; Yevgeny Kazakov (ORE, 2013)

The Empirical Robustness of Description Logic Classification. - Rafael S. Gonçalves 001; Nicolas Matentzoglu; Bijan Parsia; Uli Sattler (ISWC (Posters & Demos), 2013)

A Snapshot of the OWL Web. - Nicolas Matentzoglu; Samantha Bail; Bijan Parsia (ISWC (1), 2013)

Computable Declarative Representation of Clinical Assessment Scales in EHRs. - Mercedes Argüello Casteleiro; Nicolas Matentzoglu; Bijan Parsia; Sebastian Brandt 001 (CBMS, 2014)

An Empirical Investigation of Difficulty of Subsets of Description Logic Ontologies. - Nicolas Matentzoglu; Bijan Parsia; Uli Sattler (Description Logics, 2014)

A Family History Knowledge Base in OWL 2. - Robert Stevens 001; Nicolas Matentzoglu; Uli Sattler; Margaret Stevens (ORE, 2014)

OWL/ZIP: Distributing Large and Modular Ontologies. - Nicolas Matentzoglu; Bijan Parsia (OWLED, 2014)

The OWL Full/DL Gap in the Field. - Nicolas Matentzoglu; Bijan Parsia (OWLED, 2014)

The Manchester OWL Repository: System Description. - Nicolas Matentzoglu; Daniel Tang; Bijan Parsia; Uli Sattler (ISWC (Posters & Demos), 2014)

Empirical Investigation of Subsumption Test Hardness in Description Logic Classification. - Nicolas Matentzoglu; Uli Sattler; Bijan Parsia (Description Logics, 2015)

Verifying Reasoner Correctness - A Justication Based Method. - Michael Lee; Nicolas Matentzoglu; Uli Sattler; Bijan Parsia (ORE, 2015)

A Survey of Current, Stand-alone OWL Reasoners. - Nicolas Matentzoglu; Jared Leo; Valentino Hudhra; Uli Sattler; Bijan Parsia (ORE, 2015)

A Multi-reasoner, Justification-Based Approach to Reasoner Correctness. - Michael Lee; Nicolas Matentzoglu; Bijan Parsia; Uli Sattler (ISWC (2), 2015)

Making Entailment Set Changes Explicit Improves the Understanding of Consequences of Ontology Authoring Actions. - Nicolas Matentzoglu; Markel Vigo; Caroline Jay; Robert Stevens 001 (EKAW, 2016)

Understanding Author Intentions: Test Driven Knowledge Graph Construction. - Jeff Z. Pan; Nicolas Matentzoglu; Caroline Jay; Markel Vigo; Yuting Zhao (RW, 2016)

The OWL Reasoner Evaluation (ORE) 2015 Resources. - Bijan Parsia; Nicolas Matentzoglu; Rafael S. Gonçalves 001; Birte Glimm; Andreas Steigmiller (ISWC (2), 2016)

Module-based classification of OWL ontologies. - Nicolas Matentzoglu (2016)

The OWL Reasoner Evaluation (ORE) 2015 Competition Report. - Bijan Parsia; Nicolas Matentzoglu; Rafael S. Gonçalves 001; Birte Glimm; Andreas Steigmiller (J. Autom. Reason., 2017)

Reconciling Ontology Definitions using the Ontology Pattern Reconciliation Workbench and the DOSDP Framework. - Nicolas Matentzoglu; David Osumi-Sutherland (ICBO, 2018)

MIRO: guidelines for minimum information for the reporting of an ontology. - Nicolas Matentzoglu; James Malone; Chris Mungall; Robert Stevens 001 (J. Biomed. Semant., 2018)

OWL Reasoning: Subsumption Test Hardness and Modularity. - Nicolas Matentzoglu; Bijan Parsia; Uli Sattler (J. Autom. Reason., 2018)

Inference Inspector: Improving the verification of ontology authoring actions. - Nicolas Matentzoglu; Markel Vigo; Caroline Jay; Robert Stevens 001 (J. Web Semant., 2018)

Log data generated by Protege in three settings: the laboratory, the tutorial and the remote study. - Markel Vigo; Nicolas Matentzoglu; Caroline Jay; Robert Stevens 001 (Zenodo, 2018)

Medical Action Ontology (MAxO). - Leigh C. Carmody; Xingmin Aaron Zhang; Nicole A. Vasilevsky; Christopher J. Mungall; Nicolas Matentzoglu; Peter N. Robinson (ICBO, 2019)

Where Does an Ontology Start? - Henriette Harmse; Mélanie Courtot; Warren Read; Nicolas Matentzoglu; David Osumi-Sutherland; Simon Jupp (ICBO, 2019)

Ontology-Based Generation of Medical, Multi-term MCQs. - Jared Leo; Ghader Kurdi; Nicolas Matentzoglu; Bijan Parsia; Ulrike Sattler; Sophie Forge; Gina Donato; Will Dowling (Int. J. Artif. Intell. Educ., 2019)

Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery. - Jean-Philippe F. Gourdine; Matthew H. Brush; Nicole A. Vasilevsky; Kent A. Shefchek; Sebastian Köhler 001; Nicolas Matentzoglu; Monica C. Munoz-Torres; Julie A. McMurry; Xingmin Aaron Zhang; Peter N. Robinson; Melissa A. Haendel (Database J. Biol. Databases Curation, 2019)

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. - Sebastian Köhler 001; Leigh Carmody; Nicole A. Vasilevsky; Julius O. B. Jacobsen; Daniel Danis; Jean-Philippe F. Gourdine; Michael A. Gargano; Nomi L. Harris; Nicolas Matentzoglu; Julie A. McMurry; David Osumi-Sutherland; Valentina Cipriani; et al. (Nucleic Acids Res., 2019)

Measuring expert performance at manually classifying domain entities under upper ontology classes. - Robert Stevens 001; Phillip Lord; James Malone; Nicolas Matentzoglu (J. Web Semant., 2019)

Comparing ontology authoring workflows with Protégé: In the laboratory, in the tutorial and in the 'wild'. - Markel Vigo; Nicolas Matentzoglu; Caroline Jay; Robert Stevens 001 (J. Web Semant., 2019)

Mondo Disease Ontology: Harmonizing Disease Concepts Across the World (short paper). - Nicole A. Vasilevsky; Shahim Essaid; Nicolas Matentzoglu; Nomi L. Harris; Melissa A. Haendel; Peter N. Robinson; Christopher J. Mungall (ICBO/ODLS, 2020)

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. - Kent A. Shefchek; Nomi L. Harris; Michael A. Gargano; Nicolas Matentzoglu; Deepak R. Unni; Matthew H. Brush; Dan Keith; Tom Conlin; Nicole A. Vasilevsky; Xingmin Aaron Zhang; James P. Balhoff; Larry Babb; et al. (Nucleic Acids Res., 2020)

A systematic survey of temporal requirements of bio-health ontologies. - Jared Leo; Nicolas Matentzoglu; Uli Sattler; Bijan Parsia (Semantic Web, 2020)

A Semantic Model Leveraging Pattern-based Ontology Terms to Bridge Environmental Exposures and Health Outcomes. - Lauren E. Chan; Nicole A. Vasilevsky; Anne E. Thessen; Nicolas Matentzoglu; William D. Duncan; Christopher J. Mungall; Melissa A. Haendel (ICBO, 2021)

Reclassification of Infectious Disease in the Mondo Disease Ontology. - Nicole A. Vasilevsky; Sabrina Toro; Nicolas Matentzoglu; Dazhi Jiao; Melissa A. Haendel; Peter N. Robinson; Christopher J. Mungall (ICBO, 2021)

OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies. - Rebecca C. Jackson; Nicolas Matentzoglu; James A. Overton; Randi Vita; James P. Balhoff; Pier Luigi Buttigieg; Seth Carbon; Mélanie Courtot; Alexander D. Diehl; Damion M. Dooley; William D. Duncan; Nomi L. Harris; et al. (Database J. Biol. Databases Curation, 2021)

The Human Phenotype Ontology in 2021. - Sebastian Köhler 001; Michael A. Gargano; Nicolas Matentzoglu; Leigh Carmody; David Lewis-Smith; Nicole A. Vasilevsky; Daniel Danis; Ganna Balagura; Gareth Baynam; Amy M. Brower; Tiffany J. Callahan; Christopher G. Chute; et al. (Nucleic Acids Res., 2021)

KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response. - Justin T. Reese; Deepak R. Unni; Tiffany J. Callahan; Luca Cappelletti; Vida Ravanmehr; Seth Carbon; Kent A. Shefchek; Benjamin M. Good; James P. Balhoff; Tommaso Fontana; Hannah Blau; Nicolas Matentzoglu; et al. (Patterns, 2021)

A comparative study of methods for a priori prediction of MCQ difficulty. - Ghader Kurdi; Jared Leo; Nicolas Matentzoglu; Bijan Parsia; Uli Sattler; Sophie Forge; Gina Donato; Will Dowling (Semantic Web, 2021)

Adapting the Harmonized Data Quality Framework for Ontology Quality Assessment. - Tiffany J. Callahan; William A. Baumgartner Jr.; Nicolas A. Matentzoglu; Nicole A. Vasilevsky; Lawrence E. Hunter; Michael G. Kahn (Zenodo, 2021)

Ubergraph: Integrating OBO Ontologies into a Unified Semantic Graph. - James P. Balhoff; Ugur Bayindir; Anita R. Caron; Nicolas Matentzoglu; David Osumi-Sutherland; Christopher J. Mungall (ICBO, 2022)

Building an Application Ontology and Knowledge Graph for Rare Disease Patient-Level Data. - Emily Hartley; Daniel Olson; Ian Braun; Nicolas Matentzoglu; James A. Overton; Ramona L. Walls (ICBO, 2022)

COB: A Core Ontology for Biology and Biomedicine. - James A. Overton; Rebecca C. Jackson; Nicolas Matentzoglu; William D. Duncan; Randi Vita; Nomi L. Harris; Christopher J. Mungall; Bjoern Peters (ICBO, 2022)

OBO Academy: Training Materials for Bioontologists. - James A. Overton; Rebecca C. Jackson; Sabrina Toro; Shawn Zheng Kai Tan; Bradley Varner; David Osumi-Sutherland; Nicolas Matentzoglu; Nicole A. Vasilevsky (ICBO, 2022)

Classifying Animal Breeds with the Vertebrate Breed Ontology (VBO). - Sabrina Toro; Nicolas Matentzoglu; Kathleen R. Mullen; Nicole A. Vasilevsky; Halie Rando; Melissa A. Haendel; Christopher J. Mungall; Zhi-Liang Hu; Gregoire Leroy; Imke Tammen; Frank W. Nicholas (ICBO, 2022)

A simple standard for ontological mappings 2022: updates of data model and outlook. - Nicolas Matentzoglu; Joe E. Flack; John B. Graybeal; Nomi L. Harris; Harshad B. Hegde; Charles Tapley Hoyt; Hyeongsik Kim 001; Sabrina Toro; Nicole A. Vasilevsky; Christopher J. Mungall (OM@ISWC, 2022)

What should be the minimum requirements for making FAIR ontology alignments? - Cássia Trojahn; Nicolas Matentzoglu (OM@ISWC, 2022)

A Simple Standard for Sharing Ontological Mappings (SSSOM). - Nicolas Matentzoglu; James P. Balhoff; Susan M. Bello; Chris Bizon; Matthew H. Brush; Tiffany J. Callahan; Christopher G. Chute; William D. Duncan; Chris T. A. Evelo; Davera Gabriel; John B. Graybeal; Alasdair J. G. Gray; et al. (Database J. Biol. Databases Curation, 2022)

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; Anita R. Caron; William D. Duncan; Joe E. Flack; Melissa A. Haendel; Nomi L. Harris; William R. Hogan; Charles Tapley Hoyt; et al. (Database J. Biol. Databases Curation, 2022)

The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development. - Malcolm E. Fisher; Erik Segerdell; Nicolas Matentzoglu; Mardi J. Nenni; Joshua D. Fortriede; Stanley Chu; Troy J. Pells; David Osumi-Sutherland; Praneet Chaturvedi; Christina James-Zorn; Nivitha Sundararaj; Vaneet S. Lotay; et al. (BMC Bioinform., 2022)

Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies. - Nicolas Matentzoglu; Damien Goutte-Gattat; Shawn Zheng Kai Tan; James P. Balhoff; Seth Carbon; Anita R. Caron; William D. Duncan; Joe E. Flack; Melissa A. Haendel; Nomi L. Harris; William R. Hogan; Charles Tapley Hoyt; et al. (CoRR, 2022)

Ontologizing Health Systems Data at Scale: Making Translational Discovery a Reality. - Tiffany J. Callahan; Adrianne L. Stefanski; Jordan M. Wyrwa; Chenjie Zeng; Anna Ostropolets; Juan M. Banda; William A. Baumgartner Jr.; Richard D. Boyce; Elena Casiraghi; Ben D. Coleman; Janine H. Collins; Sara J. Deakyne Davies; et al. (CoRR, 2022)

Adapting the Harmonized Data Quality Framework for Ontology Quality Assessment. - Tiffany J. Callahan; William A. Baumgartner Jr.; Nicolas A. Matentzoglu; Nicole A. Vasilevsky; Lawrence E. Hunter; Michael G. Kahn (Zenodo, 2022)

A simple standard for ontological mappings 2023: updates on data model, collaborations and tooling. - Nicolas Matentzoglu; Ian Braun; Anita R. Caron; Damien Goutte-Gattat; Benjamin M. Gyori; Nomi L. Harris; Emily Hartley; Harshad B. Hegde; Sven Hertling; Charles Tapley Hoyt; Hyeongsik Kim 001; Huanyu Li 001; et al. (OM@ISWC, 2023)

KG-Hub - Building and Exchanging Biological Knowledge Graphs. - J. Harry Caufield; Tim E. Putman; Kevin Schaper; Deepak R. Unni; Harshad Hegde; Tiffany J. Callahan; Luca Cappelletti; Sierra A. T. Moxon; Vida Ravanmehr; Seth Carbon; Lauren E. Chan; Katherina Cortes; et al. (CoRR, 2023)

An Open-Source Knowledge Graph Ecosystem for the Life Sciences. - Tiffany J. Callahan; Ignacio J. Tripodi; Adrianne L. Stefanski; Luca Cappelletti; Sanya Bathla Taneja; Jordan M. Wyrwa; Elena Casiraghi; Nicolas A. Matentzoglu; Justin T. Reese; Jonathan C. Silverstein; Charles Tapley Hoyt; Richard D. Boyce; et al. (CoRR, 2023)

MapperGPT: Large Language Models for Linking and Mapping Entities. - Nicolas Matentzoglu; J. Harry Caufield; Harshad B. Hegde; Justin T. Reese; Sierra A. T. Moxon; Hyeongsik Kim 001; Nomi L. Harris; Melissa A. Haendel; Christopher J. Mungall (CoRR, 2023)

Ontologizing health systems data at scale: making translational discovery a reality. - Tiffany J. Callahan; Adrianne L. Stefanski; Jordan M. Wyrwa; Chenjie Zeng; Anna Ostropolets; Juan M. Banda; William A. Baumgartner Jr.; Richard D. Boyce; Elena Casiraghi; Ben D. Coleman; Janine H. Collins; Sara J. Deakyne Davies; et al. (npj Digit. Medicine, 2023)

COVoc and COVTriage: novel resources to support literature triage. - Déborah Caucheteur; Zoë May Pendlington; Paola Roncaglia; Julien Gobeill; Luc Mottin; Nicolas Matentzoglu; Donat Agosti; David Osumi-Sutherland; Helen E. Parkinson; Patrick Ruch (Bioinform., 2023)

The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond. - Lauren E. Chan; Anne E. Thessen; William D. Duncan; Nicolas Matentzoglu; Charles Schmitt; Cynthia J. Grondin; Nicole A. Vasilevsky; Julie A. McMurry; Peter N. Robinson; Christopher J. Mungall; Melissa A. Haendel (J. Biomed. Semant., 2023)

Standardising Biological Trait Representation with the Ontology of Biological Attributes (OBA). - Arwa Ibrahim; Raymund Stefancsik; Vinicius de Souza; Anita R. Caron; Nicolas Matentzoglu; James A. McLaughlin; Zoë May Pendlington (ICBO, 2024)

FAIR 2.0: Extending the FAIR Guiding Principles to Address Semantic Interoperability. - Lars Vogt; Philip Strömert; Nicolas Matentzoglu; Naouel Karam; Marcel Konrad; Manuel Prinz; Roman Baum (CoRR, 2024)

The Vertebrate Breed Ontology: Towards Effective Breed Data Standardization. - Kathleen R. Mullen; Imke Tammen; Nicolas A. Matentzoglu; Marius Mather; Christopher J. Mungall; Melissa A. Haendel; Frank W. Nicholas; Sabrina Toro; Vertebrate Breed Ontology Consortium (CoRR, 2024)

Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning. - J. Harry Caufield; Harshad Hegde; Vincent Emonet; Nomi L. Harris; Marcin P. Joachimiak; Nicolas Matentzoglu; Hyeongsik Kim 001; Sierra A. T. Moxon; Justin T. Reese; Melissa A. Haendel; Peter N. Robinson; Christopher J. Mungall (Bioinform., 2024)

A change language for ontologies and knowledge graphs. - Harshad Hegde; Jennifer Vendetti; Damien Goutte-Gattat; J. Harry Caufield; John B. Graybeal; Nomi L. Harris; Naouel Karam; Christian Kindermann; Nicolas Matentzoglu; James A. Overton; Mark A. Musen; Christopher J. Mungall (Database J. Biol. Databases Curation, 2025)

The Cell Ontology in the age of single-cell omics. - Shawn Zheng Kai Tan; Aleix Puig-Barbe; Damien Goutte-Gattat; Caroline Eastwood; Brian D. Aevermann; Alida Avola; James P. Balhoff; Ismail Ugur Bayindir; Jasmine Belfiore; Anita R. Caron; David S. Fischer; Nancy George; et al. (CoRR, 2025)

Towards a standard benchmark for phenotype-driven variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework. - Yasemin Bridges; Vinicius de Souza; Katherina G. Cortes; Melissa A. Haendel; Nomi L. Harris; Daniel R. Korn; Nikolaos M. Marinakis; Nicolas Matentzoglu; James A. McLaughlin; Christopher J. Mungall; Aaron Odell; David Osumi-Sutherland; et al. (BMC Bioinform., 2025)