Alan Ruttenberg

According to our database, Alan Ruttenberg authored at least 53 papers between 2003 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

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, July, 2024

2022

BFO: Basic Formal Ontology.

J. Neil Otte, John Beverley, Alan Ruttenberg

Appl. Ontology, 2022

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

Proceedings of the International Conference on Biomedical Ontology 2022 (ICBO), Ann Arbor, Michigan, USA, September 25, 2022

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, 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

Database J. Biol. Databases Curation, 2021

2020

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

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, Chris Mungall, Mélanie Courtot, Alan Ruttenberg, Yongqun He

Nucleic Acids Res., 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, Hongzhan Huang, Jia Ren, Karen Ross, Alan Ruttenberg, Veronica Shamovsky, Barry Smith, Qinghua Wang, Jian Zhang, Abdelrahman Elsayed, Cathy H. Wu

Nucleic Acids Res., 2017

Developing the Quantitative Histopathology Image Ontology (QHIO): A case study using the hot spot detection problem.

Metin N. Gurcan, John Tomaszewski, James A. Overton, Scott Doyle, Alan Ruttenberg, Barry Smith

J. Biomed. Informatics, 2017

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

Proceedings of the 7th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2017

2016

The development of non-coding RNA ontology.

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

Int. J. Data Min. Bioinform., 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, 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

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, 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

J. Biomed. Semant., 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, Melissa A. Haendel, Judith A. Blake, Christopher J. Mungall

J. Biomed. Semant., 2016

Semi-Automatic Mapping of WordNet to Basic Formal Ontology.

Selja Seppälä, Amanda Hicks, Alan Ruttenberg

Proceedings of the 8th Global WordNet Conference, 2016

The ImmPort Antibody Ontology.

William D. Duncan, Travis Allen, Jonathan P. Bona, Olivia Helfer, Barry Smith, Alan Ruttenberg, Alexander D. Diehl

Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

The Functions of Definitions in Ontologies.

Selja Seppälä, Alan Ruttenberg, Barry Smith

Proceedings of the Formal Ontology in Information Systems, 2016

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

Ontology-driven patient history questionnaires.

Jonathan P. Bona, Gunther Kohn, Alan Ruttenberg

Proceedings of the International Conference on Biomedical Ontology, 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, Yu Lin, Xiaowei Wang, Zixing Liu, Ming Tan, Alan Ruttenberg

Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015

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, Michael T. Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Yongqun He, Shaojie Zhang, Xiaowei Wang, He Zhang, Zixing Liu, Ming Tan

Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015

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, 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

Nucleic Acids Res., 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

Proceedings of the 5th International Conference on Biomedical Ontology, 2014

Representing Modification Sites in PRO.

Jonathan P. Bona, Alan Ruttenberg, Jenny Rouleau

Proceedings of the 5th International Conference on Biomedical Ontology, 2014

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, Alan Ruttenberg, Kinga Szigeti, Alexander D. Diehl

J. Biomed. Semant., 2013

Survey on Defining Practices in Ontologies: Report Summary.

Selja Seppälä, Alan Ruttenberg

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, 2013

Representing Intracoronal Tooth Restorations in the Ontology for Oral Health and Disease.

William D. Duncan, Titus Schleyer, Alan Ruttenberg

Proceedings of the 4th International Conference on Biomedical Ontology, 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

Proceedings of the 4th International Conference on Biomedical Ontology, 2013

Diagnostic criteria and clinical guidelines standardization to automate case classification.

Mélanie Courtot, Jie Zheng, Christian J. Stoeckert Jr., Ryan Remy Brinkman, Alan Ruttenberg

Proceedings of the 4th International Conference on Biomedical Ontology, 2013

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

Adverse events following immunization: reporting standardization, automatic case classification and signal detection.

Mélanie Courtot, Ryan Remy Brinkman, Alan Ruttenberg

Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), 2012

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, Judith A. Blake, Cathy H. Wu

BMC Bioinform., 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

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

Ontobee: A Linked Data Server and Browser for Ontology Terms.

Zuoshuang Xiang, Chris Mungall, Alan Ruttenberg, Yongqun He

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

Connecting Ontologies for the Representation of Biological Pathways.

Anna Maria Masci, Mikhail K. Levin, Alan Ruttenberg, Lindsay G. Cowell

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

<i>owl_cpp</i>, a C++ Library for Working with OWL Ontologies.

Mikhail K. Levin, Alan Ruttenberg, Anna Maria Masci, Lindsay G. Cowell

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

Building the OBO Foundry - One Policy at a Time.

Mélanie Courtot, Chris Mungall, Ryan Remy Brinkman, Alan Ruttenberg

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

Reporting Adverse Events: Basis for a Common Representation.

Mélanie Courtot, Ryan Remy Brinkman, Alan Ruttenberg

Proceedings of the 2nd International Conference on Biomedical Ontology, 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, Barry Smith, Jian Zhang, Cathy H. Wu

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

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

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

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, Larisa N. Soldatova, Christian J. Stoeckert Jr., Jessica A. Turner, Jie Zheng, et al.

J. Biomed. Semant., 2010

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

2009

Life sciences on the Semantic Web: the Neurocommons and beyond.

Alan Ruttenberg, Jonathan Rees, Matthias Samwald, M. Scott Marshall

Briefings Bioinform., 2009

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

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

Proceedings of the 17th International Conference on World Wide Web, 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

Proceedings of the Fifth OWLED Workshop on OWL: Experiences and Directions, 2008

Simplifying Access to Large-Scale Health Care and Life Sciences Datasets.

Holger Stenzhorn, Kavitha Srinivas, Matthias Samwald, Alan Ruttenberg

Proceedings of the Semantic Web: Research and Applications, 2008

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, 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

BMC Bioinform., 2007

Connectedness Profiles in Protein Networks for the Analysis of Gene Expression Data.

Joël R. Pradines, Vlado Dancík, Alan Ruttenberg, Victor Farutin

Proceedings of the Research in Computational Molecular Biology, 2007

Hey! You Got Imperative in My Declarative, or A Mashup Made in Heaven: Making OWL friendlier with Javascript.

Alan Ruttenberg

Proceedings of the OWLED 2007 Workshop on OWL: Experiences and Directions, 2007

2006

What BioPAX Communicates and how to extend OWL to help it.

Alan Ruttenberg, Jonathan Rees, Jeremy Zucker

Proceedings of the OWLED*06 Workshop on OWL: Experiences and Directions, 2006

2005

Experience Using OWL DL for the Exchange of Biological Pathway Information.

Alan Ruttenberg, Jonathan Rees, Joanne Luciano

Proceedings of the OWLED*05 Workshop on OWL: Experiences and Directions, 2005

2003

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, Tim Clark

Briefings Bioinform., 2003