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2020 – today
- 2024
[j25]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): 269-283 (2024)- 2022
- [j24]J. Neil Otte, John Beverley
, Alan Ruttenberg:
BFO: Basic Formal Ontology. Appl. Ontology 17(1): 17-43 (2022) - [c29]Alexander Bartnik, Lucas M. Serra, Mackenzie T. Smith, William D. Duncan, Alan Ruttenberg, Michael G. Dwyer, Alexander D. Diehl:
Development of an Image Data Set Class: Its Role in Biomedical Imaging and Neuroimaging Research. ICBO 2022: 1-9 - 2021
- [j23]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) - 2020
- [j22]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): 8 (2020)
2010 – 2019
- 2017
- [j21]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: 129-135 (2017) - [j20]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): D339-D346 (2017) - [j19]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): D347-D352 (2017) - [c28]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: 1 - 2016
- [j18]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: 24 (2016) - [j17]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: 25 (2016) - [j16]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: 44 (2016) - [j15]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): 214-232 (2016) - [c27]Selja Seppälä, Alan Ruttenberg, Barry Smith:
The Functions of Definitions in Ontologies. FOIS 2016: 37-50 - [c26]William D. Duncan, Travis Allen, Jonathan P. Bona, Olivia Helfer, Barry Smith, Alan Ruttenberg, Alexander D. Diehl:
The ImmPort Antibody Ontology. ICBO/BioCreative 2016 - [c25]Selja Seppälä, Amanda Hicks, Alan Ruttenberg:
Semi-Automatic Mapping of WordNet to Basic Formal Ontology. GWC 2016: 373-381 - 2015
- [j14]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): 1337-1339 (2015) - [c24]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: 621-624 - [c23]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: 975-982 - [c22]Jonathan P. Bona, Gunther Kohn, Alan Ruttenberg:
Ontology-driven patient history questionnaires. ICBO 2015 - 2014
- [j13]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): 415-421 (2014) - [c21]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: 52-55 - [c20]Jonathan P. Bona, Alan Ruttenberg, Jenny Rouleau:
Representing Modification Sites in PRO. ICBO 2014: 60-63 - 2013
- [j12]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: 42 (2013) - [c19]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: 78-83 - [c18]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: 101-104 - [c17]William D. Duncan, Titus Schleyer, Alan Ruttenberg:
Representing Intracoronal Tooth Restorations in the Ontology for Oral Health and Disease. ICBO 2013: 109-112 - [c16]Selja Seppälä, Alan Ruttenberg:
Survey on Defining Practices in Ontologies: Report Summary. VDOS+DO@ICBO 2013 - [e3]Cui Tao, Yongqun He, Luca Toldo, Sivaram Arabandi, 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 - 12th 2013. CEUR Workshop Proceedings 1061, CEUR-WS.org 2013 [contents] - 2012
- [j11]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): 1262-1269 (2012) - [j10]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): 2091 (2012) - [c15]Mélanie Courtot, Ryan Remy Brinkman, Alan Ruttenberg:
Adverse events following immunization: reporting standardization, automatic case classification and signal detection. ICBO 2012 - [e2]Olivier Bodenreider, Maryann E. Martone, Alan Ruttenberg:
Proceedings of the 2nd International Conference on Biomedical Ontology, Buffalo, NY, USA, July 26-30, 2011. CEUR Workshop Proceedings 833, CEUR-WS.org 2012 [contents] - 2011
- [j9]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): 13-22 (2011) - [j8]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): 23-33 (2011) - [j7]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: 371 (2011) - [c14]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 - [c13]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 - [c12]Mélanie Courtot, Ryan Remy Brinkman, Alan Ruttenberg:
Reporting Adverse Events: Basis for a Common Representation. ICBO 2011 - [c11]Mélanie Courtot, Chris Mungall, Ryan Remy Brinkman, Alan Ruttenberg:
Building the OBO Foundry - One Policy at a Time. ICBO 2011 - [c10]Mikhail K. Levin, Alan Ruttenberg, Anna Maria Masci, Lindsay G. Cowell:
owl_cpp, a C++ Library for Working with OWL Ontologies. ICBO 2011 - [c9]Anna Maria Masci, Mikhail K. Levin, Alan Ruttenberg, Lindsay G. Cowell:
Connecting Ontologies for the Representation of Biological Pathways. ICBO 2011 - [c8]Zuoshuang Xiang, Chris Mungall, Alan Ruttenberg, Yongqun He:
Ontobee: A Linked Data Server and Browser for Ontology Terms. ICBO 2011 - 2010
- [j6]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): 21-28 (2010) - [j5]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): S7 (2010)
2000 – 2009
- 2009
- [j4]Alan Ruttenberg, Jonathan Rees, Matthias Samwald, M. Scott Marshall:
Life sciences on the Semantic Web: the Neurocommons and beyond. Briefings Bioinform. 10(2): 193-204 (2009) - [e1]Catherine Dolbear, Alan Ruttenberg, Ulrike Sattler:
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. CEUR Workshop Proceedings 432, CEUR-WS.org 2009 [contents] - 2008
- [j3]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): 739-751 (2008) - [c7]Holger Stenzhorn, Kavitha Srinivas, Matthias Samwald, Alan Ruttenberg:
Simplifying Access to Large-Scale Health Care and Life Sciences Datasets. ESWC 2008: 864-868 - [c6]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 - [c5]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: 1273-1274 - 2007
- [j2]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) - [c4]Alan Ruttenberg:
Hey! You Got Imperative in My Declarative, or A Mashup Made in Heaven: Making OWL friendlier with Javascript. OWLED 2007 - [c3]Joël R. Pradines, Vlado Dancík, Alan Ruttenberg, Victor Farutin:
Connectedness Profiles in Protein Networks for the Analysis of Gene Expression Data. RECOMB 2007: 296-310 - 2006
- [c2]Alan Ruttenberg, Jonathan Rees, Jeremy Zucker:
What BioPAX Communicates and how to extend OWL to help it. OWLED 2006 - 2005
- [c1]Alan Ruttenberg, Jonathan Rees, Joanne Luciano:
Experience Using OWL DL for the Exchange of Biological Pathway Information. OWLED 2005 - 2003
- [j1]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): 260-278 (2003)
Coauthor Index
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