Computational knowledge integration in biopharmaceutical research. - David Ficenec; Mark Osborne; Joël R. Pradines; Daniel R. Richards; Ramon M. Felciano; Raymond J. Cho; Richard O. Chen; Ted Liefeld; James Owen; Alan Ruttenberg; Christian G. Reich; Joseph Horvath; et al. (Briefings Bioinform., 2003)

Experience Using OWL DL for the Exchange of Biological Pathway Information. - Alan Ruttenberg; Jonathan Rees; Joanne Luciano (OWLED, 2005)

What BioPAX Communicates and how to extend OWL to help it. - Alan Ruttenberg; Jonathan Rees; Jeremy Zucker (OWLED, 2006)

Hey! You Got Imperative in My Declarative, or A Mashup Made in Heaven: Making OWL friendlier with Javascript. - Alan Ruttenberg (OWLED, 2007)

Connectedness Profiles in Protein Networks for the Analysis of Gene Expression Data. - Joël R. Pradines; Vlado Dancík; Alan Ruttenberg; Victor Farutin (RECOMB, 2007)

Advancing translational research with the Semantic Web. - Alan Ruttenberg; Tim Clark; William J. Bug; Matthias Samwald; Olivier Bodenreider; Helen Chen; Donald Doherty; Kerstin Forsberg; Yong Gao; Vipul Kashyap; June Kinoshita; Joanne Luciano; et al. (BMC Bioinform., 2007)

Simplifying Access to Large-Scale Health Care and Life Sciences Datasets. - Holger Stenzhorn; Kavitha Srinivas; Matthias Samwald; Alan Ruttenberg (ESWC, 2008)

The OWL of Biomedical Investigations. - Mélanie Courtot; William J. Bug; Frank Gibson; Allyson L. Lister; James Malone; Daniel Schober; Ryan Remy Brinkman; Alan Ruttenberg (OWLED, 2008)

Report on semantic web for health care and life sciences workshop. - Huajun Chen; Kei-Hoi Cheung; Michel Dumontier; Eric Prud'hommeaux; Alan Ruttenberg; Susie Stephens; Yimin Wang (WWW, 2008)

The SWAN biomedical discourse ontology. - Paolo Ciccarese; Elizabeth Wu; Gwendolyn T. Wong; Marco Ocana; June Kinoshita; Alan Ruttenberg; Tim Clark (J. Biomed. Informatics, 2008)

Life sciences on the Semantic Web: the Neurocommons and beyond. - Alan Ruttenberg; Jonathan Rees; Matthias Samwald; M. Scott Marshall (Briefings Bioinform., 2009)

Semantic SenseLab: Implementing the vision of the Semantic Web in neuroscience. - Matthias Samwald; Huajun Chen; Alan Ruttenberg; Ernest Lim; Luis N. Marenco; Perry L. Miller; Gordon M. Shepherd; Kei-Hoi Cheung (Artif. Intell. Medicine, 2010)

Modeling biomedical experimental processes with OBI. - Ryan Remy Brinkman; Mélanie Courtot; Dirk Derom; Jennifer Fostel; Yongqun He; Phillip W. Lord; James Malone; Helen E. Parkinson; Björn Peters; Philippe Rocca-Serra; Alan Ruttenberg; Susanna-Assunta Sansone; et al. (J. Biomed. Semant., 2010)

Towards a Body Fluids Ontology: A Unified Application Ontology for Basic and Translational Science. - Jiye Ai; Mauricio Barcellos Almeida; André Queiroz de Andrade; Alan Ruttenberg; David Tai Wai Wong; Barry Smith 001 (ICBO, 2011)

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)

Reporting Adverse Events: Basis for a Common Representation. - Mélanie Courtot; Ryan Remy Brinkman; Alan Ruttenberg (ICBO, 2011)

Building the OBO Foundry - One Policy at a Time. - Mélanie Courtot; Chris Mungall; Ryan Remy Brinkman; Alan Ruttenberg (ICBO, 2011)

owl_cpp, a C++ Library for Working with OWL Ontologies. - Mikhail K. Levin; Alan Ruttenberg; Anna Maria Masci; Lindsay G. Cowell (ICBO, 2011)

Connecting Ontologies for the Representation of Biological Pathways. - Anna Maria Masci; Mikhail K. Levin; Alan Ruttenberg; Lindsay G. Cowell (ICBO, 2011)

Ontobee: A Linked Data Server and Browser for Ontology Terms. - Zuoshuang Xiang; Chris Mungall; Alan Ruttenberg; Yongqun He (ICBO, 2011)

MIREOT: The minimum information to reference an external ontology term. - Mélanie Courtot; Frank Gibson; Allyson L. Lister; James Malone; Daniel Schober; Ryan Remy Brinkman; Alan Ruttenberg (Appl. Ontology, 2011)

Overcoming the ontology enrichment bottleneck with Quick Term Templates. - Philippe Rocca-Serra; Alan Ruttenberg; Martin J. O'Connor; Patricia L. Whetzel; Daniel Schober; Jay Greenbaum; Mélanie Courtot; Ryan Remy Brinkman; Susanna-Assunta Sansone; Richard H. Scheuermann; Bjoern Peters (Appl. Ontology, 2011)

The Representation of Protein Complexes in the Protein Ontology (PRO). - Carol J. Bult; Harold J. Drabkin; Alexei V. Evsikov; Darren A. Natale; Cecilia N. Arighi; Natalia V. Roberts; Alan Ruttenberg; Peter D'Eustachio; Barry Smith 001; Judith A. Blake; Cathy H. Wu (BMC Bioinform., 2011)

Adverse events following immunization: reporting standardization, automatic case classification and signal detection. - Mélanie Courtot; Ryan Remy Brinkman; Alan Ruttenberg (ICBO, 2012)

A strategy for building neuroanatomy ontologies. - David Osumi-Sutherland; Simon Reeve; Christopher J. Mungall; Fabian Neuhaus; Alan Ruttenberg; Gregory S. X. E. Jefferis; J. Douglas Armstrong (Bioinform., 2012)

Diagnostic criteria and clinical guidelines standardization to automate case classification. - Mélanie Courtot; Jie Zheng 001; Christian J. Stoeckert Jr.; Ryan Remy Brinkman; Alan Ruttenberg (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 Intracoronal Tooth Restorations in the Ontology for Oral Health and Disease. - William D. Duncan; Titus Schleyer; Alan Ruttenberg (ICBO, 2013)

Survey on Defining Practices in Ontologies: Report Summary. - Selja Seppälä; Alan Ruttenberg (VDOS+DO@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)

Representing Modification Sites in PRO. - Jonathan P. Bona; Alan Ruttenberg; Jenny Rouleau (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)

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 domain ontology for the Non-Coding RNA field. - Jingshan Huang; Karen Eilbeck; Judith A. Blake; Dejing Dou; Darren A. Natale; Alan Ruttenberg; Barry Smith 001; Michael T. Zimmermann; Guoqian Jiang; Yu Lin; Bin Wu 008; Yongqun He; et al. (BIBM, 2015)

A semantic approach for knowledge capture of MIcroRNA-Target gene interactions. - Jingshan Huang; Fernando Gutierrez; Dejing Dou; Judith A. Blake; Karen Eilbeck; Darren A. Natale; Barry Smith 001; Yu Lin; Xiaowei Wang; Zixing Liu; Ming Tan; Alan Ruttenberg (BIBM, 2015)

Ontology-driven patient history questionnaires. - Jonathan P. Bona; Gunther Kohn; Alan Ruttenberg (ICBO, 2015)

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 Functions of Definitions in Ontologies. - Selja Seppälä; Alan Ruttenberg; Barry Smith 001 (FOIS, 2016)

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)

Semi-Automatic Mapping of WordNet to Basic Formal Ontology. - Selja Seppälä; Amanda Hicks; Alan Ruttenberg (GWC, 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)

The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology. - Jingshan Huang; Karen Eilbeck; Barry Smith 001; Judith A. Blake; Dejing Dou; Weili Huang; Darren A. Natale; Alan Ruttenberg; Jun Huan; Michael T. Zimmermann; Guoqian Jiang; Yu Lin; et al. (J. Biomed. Semant., 2016)

OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data. - Jingshan Huang; Fernando Gutierrez; Harrison J. Strachan; Dejing Dou; Weili Huang; Barry Smith 001; Judith A. Blake; Karen Eilbeck; Darren A. Natale; Yu Lin; Bin Wu 008; Nisansa de Silva; et al. (J. Biomed. Semant., 2016)

The development of non-coding RNA ontology. - Jingshan Huang; Karen Eilbeck; Barry Smith 001; Judith A. Blake; Dejing Dou; Weili Huang; Darren A. Natale; Alan Ruttenberg; Jun Huan; Michael T. Zimmermann; Guoqian Jiang; Yu Lin; et al. (Int. J. Data Min. Bioinform., 2016)

Semantics-oriented data science and computational life sciences: Innovative application of semantic technologies in microRNA and lncRNA research. - Jingshan Huang; Dejing Dou; Ming Tan; Glen M. Borchert; Karen Eilbeck; Alan Ruttenberg; Ping Yang (ICCABS, 2017)

Developing the Quantitative Histopathology Image Ontology (QHIO): A case study using the hot spot detection problem. - Metin N. Gurcan; John Tomaszewski 001; James A. Overton; Scott Doyle; Alan Ruttenberg; Barry Smith 001 (J. Biomed. Informatics, 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)

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration. - Edison Ong; Zuoshuang Xiang; Bin Zhao; Yue Liu; Yu Lin; Jie Zheng 001; Chris Mungall; Mélanie Courtot; Alan Ruttenberg; Yongqun He (Nucleic Acids Res., 2017)

Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology. - William D. Duncan; Thankam Thyvalikakath; Melissa A. Haendel; Carlo Torniai; Pedro Hernández; Mei Song; Amit Acharya; Daniel J. Caplan; Titus Schleyer; Alan Ruttenberg (J. Biomed. Semant., 2020)

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)

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)

BFO: Basic Formal Ontology. - J. Neil Otte; John Beverley; Alan Ruttenberg (Appl. Ontology, 2022)

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)