Ontology development for biological systems: immunology. - Alexander D. Diehl; Jamie A. Lee; Richard H. Scheuermann; Judith A. Blake (Bioinform., 2007)

An improved ontological representation of dendritic cells as a paradigm for all cell types. - Anna Maria Masci; Cecilia N. Arighi; Alexander D. Diehl; Anne E. Lieberman; Chris Mungall; Richard H. Scheuermann; Barry Smith 001; Lindsay G. Cowell (BMC Bioinform., 2009)

Protein-Centric Connection of Biomedical Knowledge: Protein Ontology (PRO) Research and Annotation Tools. - Cecilia N. Arighi; Darren A. Natale; Judith A. Blake; Carol J. Bult; Michael Caudy; Alexander D. Diehl; Harold J. Drabkin; Peter D'Eustachio; Alexei V. Evsikov; Hongzhan Huang; Natalia V. Roberts; Alan Ruttenberg; et al. (ICBO, 2011)

Gene Ontology Signatures for Immune Cell-Types Inferred by Gene Expression Analysis. - Terrence F. Meehan; Christopher J. Mungall; Judith A. Blake; Alexander D. Diehl (ICBO, 2011)

Revising the Cell Ontology. - Terrence F. Meehan; Christopher J. Mungall; Alexander D. Diehl (ICBO, 2011)

Modularization for the Cell Ontology. - Christopher J. Mungall; Melissa A. Haendel; Amelia Ireland; Shahid Manzoor; Terry Meehan; David Osumi-Sutherland; Carlo Torniai; Alexander D. Diehl (ICBO, 2011)

Cell Line Ontology: Redesigning the Cell Line Knowledgebase to Aid Integrative Translational Informatics. - Sirarat Sarntivijai; Zuoshuang Xiang; Terrence F. Meehan; Alexander D. Diehl; Uma Vempati; Stephan C. Schürer; Chao Pang; James Malone; Helen E. Parkinson; Brian D. Athey; Yongqun He (ICBO, 2011)

How the Gene Ontology Evolves. - Sabina Leonelli; Alexander D. Diehl; Karen R. Christie; Midori A. Harris; Jane Lomax (BMC Bioinform., 2011)

Logical Development of the Cell Ontology. - Terrence F. Meehan; Anna Maria Masci; Amina Abdulla; Lindsay G. Cowell; Judith A. Blake; Christopher J. Mungall; Alexander D. Diehl (BMC Bioinform., 2011)

Hematopoietic cell types: Prototype for a revised cell ontology. - Alexander D. Diehl; Alison Deckhut Augustine; Judith A. Blake; Lindsay G. Cowell; Elizabeth S. Gold; Timothy A. Gondré-Lewis; Anna Maria Masci; Terrence F. Meehan; Penelope A. Morel; Anastasia Nijnik; Bjoern Peters; Bali Pulendran; et al. (J. Biomed. Informatics, 2011)

Alignment of Cultured Cell Modeling Across OBO Foundry Ontologies: Key Outcomes, Insights. - Matthew H. Brush; Jie Zheng 001; Yongqun He; Sirarat Sarntivijai; Bjoern Peters; Alexander D. Diehl; Christian J. Stoeckert Jr.; Melissa A. Haendel (ICBO, 2013)

Measuring Cognitive Functions: Hurdles in the Development of the NeuroPsychological Testing Ontology. - Alexander P. Cox; Mark Jensen; Alan Ruttenberg; Kinga Szigeti; Alexander D. Diehl (ICBO, 2013)

Representing Disease Courses: An Application of the Neurological Disease Ontology to Multiple Sclerosis Typology. - Mark Jensen; Alexander P. Cox; Barry Smith 001; Alexander D. Diehl (ICBO, 2013)

The Ocular Disease Ontology. - Patrick Ray; Alexander D. Diehl (ICBO, 2013)

The neurological disease ontology. - Mark Jensen; Alexander P. Cox; Naveed Chaudhry; Marcus Ng; Donat Sule; William D. Duncan; Patrick Ray; Bianca Weinstock-Guttman; Barry Smith 001; Alan Ruttenberg; Kinga Szigeti; Alexander D. Diehl (J. Biomed. Semant., 2013)

Ontology based molecular signatures for immune cell types via gene expression analysis. - Terrence F. Meehan; Nicole A. Vasilevsky; Christopher J. Mungall; David S. Dougall; Melissa A. Haendel; Judith A. Blake; Alexander D. Diehl (BMC Bioinform., 2013)

Applications of OBI 'assay'. - Mark Jensen; Alexander P. Cox; Jonathan P. Bona; William D. Duncan; Patrick L. Ray; Alexander D. Diehl (ICBO, 2014)

An Ontological Representation and Analysis of Patient-reported and Clinical Outcomes for Multiple Sclerosis. - Mark Jensen; Alexander P. Cox; Patrick Ray; Barbara E. Teter; Bianca Weinstock-Guttman; Alan Ruttenberg; Alexander D. Diehl (ICBO, 2014)

The Ontological Treatment of Sight and Blindness. - Patrick Ray; Alexander P. Cox; Mark Jensen; Alexander D. Diehl (ICBO, 2014)

CLO: The cell line ontology. - Sirarat Sarntivijai; Yu Lin; Zuoshuang Xiang; Terrence F. Meehan; Alexander D. Diehl; Uma D. Vempati; Stephan C. Schürer; Chao Pang; James Malone; Helen E. Parkinson; Yue Liu; Terue Takatsuki; et al. (J. Biomed. Semant., 2014)

Protein Ontology: a controlled structured network of protein entities. - Darren A. Natale; Cecilia N. Arighi; Judith A. Blake; Carol J. Bult; Karen R. Christie; Julie Cowart; Peter D'Eustachio; Alexander D. Diehl; Harold J. Drabkin; Olivia Helfer; Hongzhan Huang; Anna Maria Masci; et al. (Nucleic Acids Res., 2014)

A promoter-level mammalian expression atlas. - Fantom Consortium; RIKEN PMII; RIKEN CLST (DGT); Alistair R. R. Forrest; Hideya Kawaji; Michael Rehli; J. Kenneth Baillie; Michiel J. L. de Hoon; Vanja Haberle; Timo Lassmann; Ivan V. Kulakovskiy; Marina Lizio; et al. (Nat., 2014)

flowCL: ontology-based cell population labelling in flow cytometry. - Mélanie Courtot; Justin Meskas; Alexander D. Diehl; Radina Droumeva; Raphael Gottardo; Adrin Jalali; Mohammad Jafar Taghiyar; Holden T. Maecker; J. Philip McCoy; Alan Ruttenberg; Richard H. Scheuermann; Ryan Remy Brinkman (Bioinform., 2015)

The ImmPort Antibody Ontology. - William D. Duncan; Travis Allen; Jonathan P. Bona; Olivia Helfer; Barry Smith 001; Alan Ruttenberg; Alexander D. Diehl (ICBO/BioCreative, 2016)

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. - Alexander D. Diehl; Terrence F. Meehan; Yvonne M. Bradford; Matthew H. Brush; Wasila M. Dahdul; David S. Dougall; Yongqun He; David Osumi-Sutherland; Alan Ruttenberg; Sirarat Sarntivijai; Ceri E. Van Slyke; Nicole A. Vasilevsky; et al. (J. Biomed. Semant., 2016)

Representing vision and blindness. - Patrick L. Ray; Alexander P. Cox; Mark Jensen; Travis Allen; William D. Duncan; Alexander D. Diehl (J. Biomed. Semant., 2016)

Towards an Ontology for Representing Malignant Neoplasms. - William D. Duncan; Carmelo Gaudioso; Alexander D. Diehl (ICBO, 2017)

Integrating an Ontology for RDOC with Existing Biomedical Ontologies. - Mark Jensen; Alexander D. Diehl (ICBO, 2017)

Cells in experimental life sciences - challenges and solution to the rapid evolution of knowledge. - Sirarat Sarntivijai; Alexander D. Diehl; Yongqun He (BMC Bioinform., 2017)

Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. - Darren A. Natale; Cecilia N. Arighi; Judith A. Blake; Jonathan P. Bona; Chuming Chen; Sheng-Chih Chen; Karen R. Christie; Julie Cowart; Peter D'Eustachio; Alexander D. Diehl; Harold J. Drabkin; William D. Duncan; et al. (Nucleic Acids Res., 2017)

The Implementation of the Precision Oncology Data Repository in the Veterans Affairs Healthcare System. - Danne C. Elbers; Frank Meng; Scott Doyle; Sylvester Sakilay; Sung Feng-Chi; Brett R. Johnson; Robert B. Hall; Nathanael Fillmore; Daniel Chen; Alexander D. Diehl; Samuel Ajjarapu; Karen E. Pierce-Murray; et al. (AMIA, 2018)

Early steps of an Ontology for Magnetic Resonance Imaging: MRIO. - Lucas M. Serra; Michael G. Dwyer; William D. Duncan; Alexander D. Diehl (ICBO, 2019)

Tripartite Term Enrichment Analysis of Multiple Sclerosis Patient Reported Outcomes. - Mackenzie T. Smith; Lauren M. Wishnie; William D. Duncan; Mark Jensen; Alexander D. Diehl (ICBO, 2019)

Representation of Protein Aggregates in an Ontological Framework. - Lauren Wishnie; Alexander P. Cox; Alexander D. Diehl (ICBO, 2019)

OSCI: standardized stem cell ontology representation and use cases for stem cell investigation. - Yongqun He; William D. Duncan; Daniel J. Cooper; Jens Hansen; Ravi Iyengar; Edison Ong; Kendal Walker; Omar Tibi; Sam Smith; Lucas M. Serra; Jie Zheng 001; Sirarat Sarntivijai; et al. (BMC Bioinform., 2019)

Reporting and connecting cell type names and gating definitions through ontologies. - James A. Overton; Randi Vita; Patrick Dunn; Julie G. Burel; Syed Ahmad Chan Bukhari; Kei-Hoi Cheung; Steven H. Kleinstein; Alexander D. Diehl; Bjoern Peters (BMC Bioinform., 2019)

Cells in ExperimentaL Life Sciences (CELLS-2018): capturing the knowledge of normal and diseased cells with ontologies. - Sirarat Sarntivijai; Yongqun He; Alexander D. Diehl (BMC Bioinform., 2019)

An ontology for representing hematologic malignancies: the cancer cell ontology. - Lucas M. Serra; William D. Duncan; Alexander D. Diehl (BMC Bioinform., 2019)

Foundations for a Realism-Based Ontology of Protein Aggregates. - Lauren Wishnie; Alexander P. Cox; Alexander D. Diehl; Werner Ceusters (ICBO/ODLS, 2020)

Recent Refinements of the NeuroPsychological Testing Ontology. - Alexander P. Cox; Kiernan L. Johnson; Lauren Wishnie; Aaron S. Kemp; Jonathan P. Bona; Alexander D. Diehl (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 Gene Ontology resource: enriching a GOld mine. - Seth Carbon; Eric Douglass; Benjamin M. Good; Deepak R. Unni; Nomi L. Harris; Christopher J. Mungall; Siddartha Basu; Rex L. Chisholm; Robert J. Dodson; Eric Hartline; Petra Fey; Paul D. Thomas; et al. (Nucleic Acids Res., 2021)

Development of an Image Data Set Class: Its Role in Biomedical Imaging and Neuroimaging Research. - Alexander Bartnik; Lucas M. Serra; Mackenzie T. Smith; William D. Duncan; Alan Ruttenberg; Michael G. Dwyer; Alexander D. Diehl (ICBO, 2022)

Enhancing Childhood Nutrition Data with Open Biomedical Ontologies. - Jonathan P. Bona; Alexander D. Diehl; Alexander P. Cox; Aaron S. Kemp; Linda Larson-Prior (ICBO, 2022)

The Protein Conformation Ontology. - Morgan Mitchell; Lauren M. Wishnie; Alexander D. Diehl (ICBO, 2022)

Ontology Representation for Cholangiocarcinoma. - Anuwat Pengput; Alexander D. Diehl (ICBO, 2022)

Development of Axiomatization for the Cholangiocarcinoma Ontology Using Common Logic Interchange Format. - Anuwat Pengput; Alexander D. Diehl (ICBO, 2022)

A Data Structure for the Implementation of Referent Tracking Systems. - Lauren Wishnie; Alexander D. Diehl (ICBO, 2022)

GlycoEnzOnto: a GlycoEnzyme pathway and molecular function ontology. - Theodore Groth; Alexander D. Diehl; Rudiyanto Gunawan; Sriram Neelamegham (Bioinform., 2022)

Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI). - Sabrina Toro; Anna V. Anagnostopoulos; Sue Bello; Kai Lewis Blumberg; Rhiannon Cameron; Leigh Carmody; Alexander D. Diehl; Damion M. Dooley; William D. Duncan; Petra Fey; Pascale Gaudet; Nomi L. Harris; et al. (CoRR, 2023)

An Ontological Representation of Oral Dysbiosis. - Gopikrishnan Mannamparambil Chandrasekharan; Alexander D. Diehl; Nivedita Dutta; William D. Duncan (ICBO, 2024)

CellCards: Development of a Dynamic Ontology-Derived ETL Pipeline for Automatic Cell Information Extraction and Analysis. - Mary Czelusniak; Emily Tran; Fatima Oudeif; Jie Zheng 001; William D. Duncan; Alexander D. Diehl; Yongqun He (ICBO, 2024)

Initial Steps in Developing an Ontology of Dental Care-Related Fear, Anxiety, and Phobia. - William D. Duncan; Astha Singhal; Olga S. Enz; Alexander D. Diehl; Brenda Heaton; Daniel W. McNeil (ICBO, 2024)

Representing Bionic-vision Devices in the Neural Electronic Interface Ontology. - Jisoo Seo; Alexander D. Diehl; Daniel L. Rathbun; Gopikrishnan Mannamparambil Chandrasekharan; Callie L. McGrath; William D. Duncan (ICBO, 2024)

Building an Ontology of Pain. - Finn D. Wilson; Gopikrishnan Mannamparambil Chandrasekharan; Matthew Diller; Jisoo Seo; Alexander D. Diehl; William D. Duncan (ICBO, 2024)

Modelling the EGFR through the Protein Conformation Ontology. - Giacomo De Colle; Morgan Mitchell; Alexander D. Diehl (SeWeBMeDA@ESWC, 2024)

MRIO: the Magnetic Resonance Imaging Acquisition and Analysis Ontology. - Alexander Bartnik; Lucas M. Serra; Mackenzie T. Smith; William D. Duncan; Lauren Wishnie; Alan Ruttenberg; Michael G. Dwyer; Alexander D. Diehl (Neuroinformatics, 2024)

Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI). - Sabrina Toro; Anna V. Anagnostopoulos; Susan M. Bello; Kai Lewis Blumberg; Rhiannon Cameron; Leigh Carmody; Alexander D. Diehl; Damion M. Dooley; William D. Duncan; Petra Fey; Pascale Gaudet; Nomi L. Harris; et al. (J. Biomed. Semant., 2024)

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)

A fourfold pathogen reference ontology suite. - John Beverley; Shane Babcock; Carter Benson; Giacomo De Colle; Sydney Cohen; Alexander D. Diehl; Ram A. N. R. Challa; Ray Mavrovich; Joshua Billig; Anthony Huffman; Yongqun He (J. Biomed. Semant., 2025)