Alan Ruttenberg

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 19

Top Topics

Domain Ontology

Magnetic Resonance Imaging

Semantic Search

Top Venues

J. Biomed. Semant.

Nucleic Acids Res.

Publications

Alexander Bartnik, Lucas M. Serra, Mackenzie T. Smith, William D. Duncan, Lauren Wishnie, Alan Ruttenberg, Michael G. Dwyer, Alexander D. Diehl
MRIO: the Magnetic Resonance Imaging Acquisition and Analysis Ontology. Neuroinformatics 22 (3) (2024)
J. Neil Otte, John Beverley, Alan Ruttenberg
BFO: Basic Formal Ontology. Appl. Ontology 17 (1) (2022)
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
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies. Database J. Biol. Databases Curation 2021 (2021)
William D. Duncan, Thankam Thyvalikakath, Melissa A. Haendel, Carlo Torniai, Pedro Hernández, Mei Song, Amit Acharya, Daniel J. Caplan, Titus Schleyer, Alan Ruttenberg
Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology. J. Biomed. Semant. 11 (1) (2020)
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
Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. Nucleic Acids Res. 45 (Database-Issue) (2017)
Metin N. Gurcan, John Tomaszewski, James A. Overton, Scott Doyle, Alan Ruttenberg, Barry Smith
Developing the Quantitative Histopathology Image Ontology (QHIO): A case study using the hot spot detection problem. J. Biomed. Informatics 66 (2017)
Jingshan Huang, Dejing Dou, Ming Tan, Glen M. Borchert, Karen Eilbeck, Alan Ruttenberg, Ping Yang
Semantics-oriented data science and computational life sciences: Innovative application of semantic technologies in microRNA and lncRNA research. ICCABS (2017)
Edison Ong, Zuoshuang Xiang, Bin Zhao, Yue Liu, Yu Lin, Jie Zheng, Chris Mungall, Mélanie Courtot, Alan Ruttenberg, Yongqun He
Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration. Nucleic Acids Res. 45 (Database-Issue) (2017)
Selja Seppälä, Amanda Hicks, Alan Ruttenberg
Semi-Automatic Mapping of WordNet to Basic Formal Ontology. GWC (2016)
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
The development of non-coding RNA ontology. Int. J. Data Min. Bioinform. 15 (3) (2016)
William D. Duncan, Travis Allen, Jonathan P. Bona, Olivia Helfer, Barry Smith, Alan Ruttenberg, Alexander D. Diehl
The ImmPort Antibody Ontology. ICBO/BioCreative (2016)
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
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. J. Biomed. Semant. 7 (2016)
Selja Seppälä, Alan Ruttenberg, Barry Smith
The Functions of Definitions in Ontologies. FOIS (2016)
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
The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology. J. Biomed. Semant. 7 (2016)
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
OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data. J. Biomed. Semant. 7 (2016)
Jonathan P. Bona, Gunther Kohn, Alan Ruttenberg
Ontology-driven patient history questionnaires. ICBO (2015)
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
A domain ontology for the Non-Coding RNA field. BIBM (2015)
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
A semantic approach for knowledge capture of MIcroRNA-Target gene interactions. BIBM (2015)
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
flowCL: ontology-based cell population labelling in flow cytometry. Bioinform. 31 (8) (2015)
Mark Jensen, Alexander P. Cox, Patrick Ray, Barbara E. Teter, Bianca Weinstock-Guttman, Alan Ruttenberg, Alexander D. Diehl
An Ontological Representation and Analysis of Patient-reported and Clinical Outcomes for Multiple Sclerosis. ICBO (2014)
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
Protein Ontology: a controlled structured network of protein entities. Nucleic Acids Res. 42 (Database-Issue) (2014)
Jonathan P. Bona, Alan Ruttenberg, Jenny Rouleau
Representing Modification Sites in PRO. ICBO (2014)
Mélanie Courtot, Jie Zheng, Christian J. Stoeckert Jr., Ryan Remy Brinkman, Alan Ruttenberg
Diagnostic criteria and clinical guidelines standardization to automate case classification. ICBO (2013)
Selja Seppälä, Alan Ruttenberg
Survey on Defining Practices in Ontologies: Report Summary. VDOS+DO@ICBO (2013)
William D. Duncan, Titus Schleyer, Alan Ruttenberg
Representing Intracoronal Tooth Restorations in the Ontology for Oral Health and Disease. ICBO (2013)
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
The neurological disease ontology. J. Biomed. Semant. 4 (2013)
Alexander P. Cox, Mark Jensen, Alan Ruttenberg, Kinga Szigeti, Alexander D. Diehl
Measuring Cognitive Functions: Hurdles in the Development of the NeuroPsychological Testing Ontology. ICBO (2013)
David Osumi-Sutherland, Simon Reeve, Christopher J. Mungall, Fabian Neuhaus, Alan Ruttenberg, Gregory S. X. E. Jefferis, J. Douglas Armstrong
A strategy for building neuroanatomy ontologies. Bioinform. 28 (15) (2012)
David Osumi-Sutherland, Simon Reeve, Christopher J. Mungall, Fabian Neuhaus, Alan Ruttenberg, Gregory S. X. E. Jefferis, J. Douglas Armstrong
A strategy for building neuroanatomy ontologies. Bioinform. 28 (9) (2012)
Mélanie Courtot, Ryan Remy Brinkman, Alan Ruttenberg
Adverse events following immunization: reporting standardization, automatic case classification and signal detection. ICBO (2012)
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
Protein-Centric Connection of Biomedical Knowledge: Protein Ontology (PRO) Research and Annotation Tools. ICBO (2011)
Anna Maria Masci, Mikhail K. Levin, Alan Ruttenberg, Lindsay G. Cowell
Connecting Ontologies for the Representation of Biological Pathways. ICBO (2011)
Mélanie Courtot, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan Remy Brinkman, Alan Ruttenberg
MIREOT: The minimum information to reference an external ontology term. Appl. Ontology 6 (1) (2011)
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
The Representation of Protein Complexes in the Protein Ontology (PRO). BMC Bioinform. 12 (2011)
Jiye Ai, Mauricio Barcellos Almeida, André Queiroz de Andrade, Alan Ruttenberg, David Tai Wai Wong, Barry Smith
Towards a Body Fluids Ontology: A Unified Application Ontology for Basic and Translational Science. ICBO (2011)
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
Overcoming the ontology enrichment bottleneck with Quick Term Templates. Appl. Ontology 6 (1) (2011)
Mélanie Courtot, Ryan Remy Brinkman, Alan Ruttenberg
Reporting Adverse Events: Basis for a Common Representation. ICBO (2011)
Mikhail K. Levin, Alan Ruttenberg, Anna Maria Masci, Lindsay G. Cowell
, a C++ Library for Working with OWL Ontologies. ICBO (2011)
Zuoshuang Xiang, Chris Mungall, Alan Ruttenberg, Yongqun He
Ontobee: A Linked Data Server and Browser for Ontology Terms. ICBO (2011)
Mélanie Courtot, Chris Mungall, Ryan Remy Brinkman, Alan Ruttenberg
Building the OBO Foundry - One Policy at a Time. ICBO (2011)
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.
Modeling biomedical experimental processes with OBI. J. Biomed. Semant. 1 (S-1) (2010)
Matthias Samwald, Huajun Chen, Alan Ruttenberg, Ernest Lim, Luis N. Marenco, Perry L. Miller, Gordon M. Shepherd, Kei-Hoi Cheung
Semantic SenseLab: Implementing the vision of the Semantic Web in neuroscience. Artif. Intell. Medicine 48 (1) (2010)
Alan Ruttenberg, Jonathan Rees, Matthias Samwald, M. Scott Marshall
Life sciences on the Semantic Web: the Neurocommons and beyond. Briefings Bioinform. 10 (2) (2009)
Holger Stenzhorn, Kavitha Srinivas, Matthias Samwald, Alan Ruttenberg
Simplifying Access to Large-Scale Health Care and Life Sciences Datasets. ESWC (2008)
Mélanie Courtot, William J. Bug, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan Remy Brinkman, Alan Ruttenberg
The OWL of Biomedical Investigations. OWLED (2008)
Paolo Ciccarese, Elizabeth Wu, Gwendolyn T. Wong, Marco Ocana, June Kinoshita, Alan Ruttenberg, Tim Clark
The SWAN biomedical discourse ontology. J. Biomed. Informatics 41 (5) (2008)
Huajun Chen, Kei-Hoi Cheung, Michel Dumontier, Eric Prud'hommeaux, Alan Ruttenberg, Susie Stephens, Yimin Wang
Report on semantic web for health care and life sciences workshop. WWW (2008)
Alan Ruttenberg
Hey! You Got Imperative in My Declarative, or A Mashup Made in Heaven: Making OWL friendlier with Javascript. OWLED (2007)
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
Advancing translational research with the Semantic Web. BMC Bioinform. 8 (S-3) (2007)
Joël R. Pradines, Vlado Dancík, Alan Ruttenberg, Victor Farutin
Connectedness Profiles in Protein Networks for the Analysis of Gene Expression Data. RECOMB (2007)
Alan Ruttenberg, Jonathan Rees, Jeremy Zucker
What BioPAX Communicates and how to extend OWL to help it. OWLED (2006)
Alan Ruttenberg, Jonathan Rees, Joanne Luciano
Experience Using OWL DL for the Exchange of Biological Pathway Information. OWLED (2005)
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
Computational knowledge integration in biopharmaceutical research. Briefings Bioinform. 4 (3) (2003)