Alan Ruttenberg

58 papers A* 1B 2C 3Journal 25Unranked 24

Year	Rank	Type	Title / Venue / Authors
2025	—	`conf`	History in the Basic Formal Ontology. ICBO Werner Ceusters, Alan Ruttenberg
2025	C	`conf`	Towards Representing Change in the BFO. FOIS Werner Ceusters, Alan Ruttenberg
2024	J	`jnl`	MRIO: the Magnetic Resonance Imaging Acquisition and Analysis Ontology. Neuroinformatics Alexander Bartnik, Lucas M. Serra, Mackenzie T. Smith, William D. Duncan, Lauren Wishnie, Alan Ruttenberg, Michael G. Dwyer, Alexander D. Diehl
2022	J	`jnl`	BFO: Basic Formal Ontology. Appl. Ontology J. Neil Otte, John Beverley, Alan Ruttenberg
2022	—	`conf`	Development of an Image Data Set Class: Its Role in Biomedical Imaging and Neuroimaging Research. ICBO Alexander Bartnik, Lucas M. Serra, Mackenzie T. Smith, William D. Duncan, Alan Ruttenberg, Michael G. Dwyer, Alexander D. Diehl
2021	J	`jnl`	OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies. Database J. Biol. Databases Curation 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, Melissa A. Haendel, Suzanna E. Lewis, Darren A. Natale, David Osumi-Sutherland, Alan Ruttenberg, Lynn M. Schriml, Barry Smith, Christian J. Stoeckert Jr., Nicole A. Vasilevsky, Ramona L. Walls, Jie Zheng, Christopher J. Mungall, Bjoern Peters
2020	J	`jnl`	Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology. J. Biomed. Semant. William D. Duncan, Thankam Thyvalikakath, Melissa A. Haendel, Carlo Torniai, Pedro Hernández, Mei Song, Amit Acharya, Daniel J. Caplan, Titus Schleyer, Alan Ruttenberg
2017	J	`jnl`	Developing the Quantitative Histopathology Image Ontology (QHIO): A case study using the hot spot detection problem. J. Biomed. Informatics Metin N. Gurcan, John Tomaszewski, James A. Overton, Scott Doyle, Alan Ruttenberg, Barry Smith
2017	J	`jnl`	Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration. Nucleic Acids Res. Edison Ong, Zuoshuang Xiang, Bin Zhao, Yue Liu, Yu Lin, Jie Zheng, Chris Mungall, Mélanie Courtot, Alan Ruttenberg, Yongqun He
2017	J	`jnl`	Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. Nucleic Acids Res. 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, Hongzhan Huang, Jia Ren, Karen Ross, Alan Ruttenberg, Veronica Shamovsky, Barry Smith, Qinghua Wang, Jian Zhang, Abdelrahman Elsayed, Cathy H. Wu
2017	—	`conf`	Semantics-oriented data science and computational life sciences: Innovative application of semantic technologies in microRNA and lncRNA research. ICCABS Jingshan Huang, Dejing Dou, Ming Tan, Glen M. Borchert, Karen Eilbeck, Alan Ruttenberg, Ping Yang
2016	J	`jnl`	OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data. J. Biomed. Semant. Jingshan Huang, Fernando Gutierrez, Harrison J. Strachan, Dejing Dou, Weili Huang, Barry Smith, Judith A. Blake, Karen Eilbeck, Darren A. Natale, Yu Lin, Bin Wu, Nisansa de Silva, Xiaowei Wang, Zixing Liu, Glen M. Borchert, Ming Tan, Alan Ruttenberg
2016	C	`conf`	Semi-Automatic Mapping of WordNet to Basic Formal Ontology. GWC Selja Seppälä, Amanda Hicks, Alan Ruttenberg
2016	J	`jnl`	The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. J. Biomed. Semant. 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, Melissa A. Haendel, Judith A. Blake, Christopher J. Mungall
2016	C	`conf`	The Functions of Definitions in Ontologies. FOIS Selja Seppälä, Alan Ruttenberg, Barry Smith
2016	—	`conf`	The ImmPort Antibody Ontology. ICBO/BioCreative William D. Duncan, Travis Allen, Jonathan P. Bona, Olivia Helfer, Barry Smith, Alan Ruttenberg, Alexander D. Diehl
2016	J	`jnl`	The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology. J. Biomed. Semant. Jingshan Huang, Karen Eilbeck, Barry Smith, Judith A. Blake, Dejing Dou, Weili Huang, Darren A. Natale, Alan Ruttenberg, Jun Huan, Michael T. Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison J. Strachan, Yongqun He, Shaojie Zhang, Xiaowei Wang, Zixing Liu, Glen M. Borchert, Ming Tan
2016	J	`jnl`	The development of non-coding RNA ontology. Int. J. Data Min. Bioinform. Jingshan Huang, Karen Eilbeck, Barry Smith, Judith A. Blake, Dejing Dou, Weili Huang, Darren A. Natale, Alan Ruttenberg, Jun Huan, Michael T. Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison J. Strachan, Nisansa de Silva, Mohan Vamsi Kasukurthi, Vikash Kumar Jha, Yongqun He, Shaojie Zhang, Xiaowei Wang, Zixing Liu, Glen M. Borchert, Ming Tan
2015	—	`conf`	A domain ontology for the Non-Coding RNA field. BIBM Jingshan Huang, Karen Eilbeck, Judith A. Blake, Dejing Dou, Darren A. Natale, Alan Ruttenberg, Barry Smith, Michael T. Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Yongqun He, Shaojie Zhang, Xiaowei Wang, He Zhang, Zixing Liu, Ming Tan
2015	—	`conf`	A semantic approach for knowledge capture of MIcroRNA-Target gene interactions. BIBM Jingshan Huang, Fernando Gutierrez, Dejing Dou, Judith A. Blake, Karen Eilbeck, Darren A. Natale, Barry Smith, Yu Lin, Xiaowei Wang, Zixing Liu, Ming Tan, Alan Ruttenberg
2015	—	`conf`	Ontology-driven patient history questionnaires. ICBO Jonathan P. Bona, Gunther Kohn, Alan Ruttenberg
2015	J	`jnl`	flowCL: ontology-based cell population labelling in flow cytometry. Bioinform. 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
2014	—	`conf`	An Ontological Representation and Analysis of Patient-reported and Clinical Outcomes for Multiple Sclerosis. ICBO Mark Jensen, Alexander P. Cox, Patrick Ray, Barbara E. Teter, Bianca Weinstock-Guttman, Alan Ruttenberg, Alexander D. Diehl
2014	J	`jnl`	Protein Ontology: a controlled structured network of protein entities. Nucleic Acids Res. 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, Jia Ren, Natalia V. Roberts, Karen Ross, Alan Ruttenberg, Veronica Shamovsky, Barry Smith, Meher Shruti Yerramalla, Jian Zhang, Aisha AlJanahi, Irem Çelen, Cynthia Gan, Mengxi Lv, Emily Schuster-Lezell, Cathy H. Wu
2014	—	`conf`	Representing Modification Sites in PRO. ICBO Jonathan P. Bona, Alan Ruttenberg, Jenny Rouleau
2013	—	`conf`	Diagnostic criteria and clinical guidelines standardization to automate case classification. ICBO Mélanie Courtot, Jie Zheng, Christian J. Stoeckert Jr., Ryan Remy Brinkman, Alan Ruttenberg
2013	—	`conf`	Measuring Cognitive Functions: Hurdles in the Development of the NeuroPsychological Testing Ontology. ICBO Alexander P. Cox, Mark Jensen, Alan Ruttenberg, Kinga Szigeti, Alexander D. Diehl
2013	—	`ed.`	Proceedings of the ICBO2013 Workshops: International Workshop on Vaccine and Drug Ontology Studies (VDOS 2013), International Workshop on Definitions in Ontologies (DO 2013), part of the Semantic Trilogy 2013 , Montreal, Quebec, Canada, July 6th - 12th 2013. VDOS+DO@ICBO Cui Tao, Yongqun He, Luca Toldo, Sivaram Arabandi, Selja Seppälä, Alan Ruttenberg
2013	—	`conf`	Representing Intracoronal Tooth Restorations in the Ontology for Oral Health and Disease. ICBO William D. Duncan, Titus Schleyer, Alan Ruttenberg
2013	—	`conf`	Survey on Defining Practices in Ontologies: Report Summary. VDOS+DO@ICBO Selja Seppälä, Alan Ruttenberg
2013	J	`jnl`	The neurological disease ontology. J. Biomed. Semant. Mark Jensen, Alexander P. Cox, Naveed Chaudhry, Marcus Ng, Donat Sule, William D. Duncan, Patrick Ray, Bianca Weinstock-Guttman, Barry Smith, Alan Ruttenberg, Kinga Szigeti, Alexander D. Diehl
2012	J	`jnl`	A strategy for building neuroanatomy ontologies. Bioinform. David Osumi-Sutherland, Simon Reeve, Christopher J. Mungall, Fabian Neuhaus, Alan Ruttenberg, Gregory S. X. E. Jefferis, J. Douglas Armstrong
2012	J	`jnl`	A strategy for building neuroanatomy ontologies. Bioinform. David Osumi-Sutherland, Simon Reeve, Christopher J. Mungall, Fabian Neuhaus, Alan Ruttenberg, Gregory S. X. E. Jefferis, J. Douglas Armstrong
2012	—	`conf`	Adverse events following immunization: reporting standardization, automatic case classification and signal detection. ICBO Mélanie Courtot, Ryan Remy Brinkman, Alan Ruttenberg
2012	—	`ed.`	Proceedings of the 2nd International Conference on Biomedical Ontology, Buffalo, NY, USA, July 26-30, 2011 ICBO Olivier Bodenreider, Maryann E. Martone, Alan Ruttenberg
2011	—	`conf`	Building the OBO Foundry - One Policy at a Time. ICBO Mélanie Courtot, Chris Mungall, Ryan Remy Brinkman, Alan Ruttenberg
2011	—	`conf`	Connecting Ontologies for the Representation of Biological Pathways. ICBO Anna Maria Masci, Mikhail K. Levin, Alan Ruttenberg, Lindsay G. Cowell
2011	J	`jnl`	MIREOT: The minimum information to reference an external ontology term. Appl. Ontology Mélanie Courtot, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan Remy Brinkman, Alan Ruttenberg
2011	—	`conf`	Ontobee: A Linked Data Server and Browser for Ontology Terms. ICBO Zuoshuang Xiang, Chris Mungall, Alan Ruttenberg, Yongqun He
2011	J	`jnl`	Overcoming the ontology enrichment bottleneck with Quick Term Templates. Appl. Ontology 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
2011	—	`conf`	Protein-Centric Connection of Biomedical Knowledge: Protein Ontology (PRO) Research and Annotation Tools. ICBO 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, Barry Smith, Jian Zhang, Cathy H. Wu
2011	—	`conf`	Reporting Adverse Events: Basis for a Common Representation. ICBO Mélanie Courtot, Ryan Remy Brinkman, Alan Ruttenberg
2011	J	`jnl`	The Representation of Protein Complexes in the Protein Ontology (PRO). BMC Bioinform. 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, Judith A. Blake, Cathy H. Wu
2011	—	`conf`	Towards a Body Fluids Ontology: A Unified Application Ontology for Basic and Translational Science. ICBO Jiye Ai, Mauricio Barcellos Almeida, André Queiroz de Andrade, Alan Ruttenberg, David Tai Wai Wong, Barry Smith
2010	J	`jnl`	Modeling biomedical experimental processes with OBI. J. Biomed. Semant. 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, Larisa N. Soldatova, Christian J. Stoeckert Jr., Jessica A. Turner, Jie Zheng, et al.
2010	J	`jnl`	Semantic SenseLab: Implementing the vision of the Semantic Web in neuroscience. Artif. Intell. Medicine Matthias Samwald, Huajun Chen, Alan Ruttenberg, Ernest Lim, Luis N. Marenco, Perry L. Miller, Gordon M. Shepherd, Kei-Hoi Cheung
2009	J	`jnl`	Life sciences on the Semantic Web: the Neurocommons and beyond. Briefings Bioinform. Alan Ruttenberg, Jonathan Rees, Matthias Samwald, M. Scott Marshall
2009	—	`ed.`	Proceedings of the Fifth OWLED Workshop on OWL: Experiences and Directions, collocated with the 7th International Semantic Web Conference (ISWC-2008), Karlsruhe, Germany, October 26-27, 2008 OWLED Catherine Dolbear, Alan Ruttenberg, Ulrike Sattler
2008	A*	`conf`	Report on semantic web for health care and life sciences workshop. WWW Huajun Chen, Kei-Hoi Cheung, Michel Dumontier, Eric Prud'hommeaux, Alan Ruttenberg, Susie Stephens, Yimin Wang
2008	B	`conf`	Simplifying Access to Large-Scale Health Care and Life Sciences Datasets. ESWC Holger Stenzhorn, Kavitha Srinivas, Matthias Samwald, Alan Ruttenberg
2008	—	`conf`	The OWL of Biomedical Investigations. OWLED Mélanie Courtot, William J. Bug, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan Remy Brinkman, Alan Ruttenberg
2008	J	`jnl`	The SWAN biomedical discourse ontology. J. Biomed. Informatics Paolo Ciccarese, Elizabeth Wu, Gwendolyn T. Wong, Marco Ocana, June Kinoshita, Alan Ruttenberg, Tim Clark
2007	J	`jnl`	Advancing translational research with the Semantic Web. BMC Bioinform. 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, M. Scott Marshall, Chimezie Ogbuji, Jonathan Rees, Susie Stephens, Gwendolyn T. Wong, Elizabeth Wu, Davide Zaccagnini, Tonya Hongsermeier, Eric Neumann, Ivan Herman, Kei-Hoi Cheung
2007	B	`conf`	Connectedness Profiles in Protein Networks for the Analysis of Gene Expression Data. RECOMB Joël R. Pradines, Vlado Dancík, Alan Ruttenberg, Victor Farutin
2007	—	`conf`	Hey! You Got Imperative in My Declarative, or A Mashup Made in Heaven: Making OWL friendlier with Javascript. OWLED Alan Ruttenberg
2006	—	`conf`	What BioPAX Communicates and how to extend OWL to help it. OWLED Alan Ruttenberg, Jonathan Rees, Jeremy Zucker
2005	—	`conf`	Experience Using OWL DL for the Exchange of Biological Pathway Information. OWLED Alan Ruttenberg, Jonathan Rees, Joanne Luciano
2003	J	`jnl`	Computational knowledge integration in biopharmaceutical research. Briefings Bioinform. 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, Tim Clark