Alan Ruttenberg

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. Bioinformatics 28(9): 1262-1269 (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. Bioinformatics 28(15): 2091 (2012)

Mélanie Courtot, Ryan R. Brinkman, Alan Ruttenberg: Adverse events following immunization: reporting standardization, automatic case classification and signal detection. ICBO 2012

Olivier Bodenreider, Maryann E. Martone, Alan Ruttenberg (Eds.): Proceedings of the 2nd International Conference on Biomedical Ontology, Buffalo, NY, USA, July 26-30, 2011. CEUR Workshop Proceedings 833, CEUR-WS.org 2012

Philippe Rocca-Serra, Alan Ruttenberg, Martin J. O'Connor, Patricia L. Whetzel, Daniel Schober, Jay Greenbaum, Mélanie Courtot, Ryan R. Brinkman, Susanna-Assunta Sansone, Richard H. Scheuermann, Bjoern Peters: Overcoming the ontology enrichment bottleneck with Quick Term Templates. Applied Ontology 6(1): 13-22 (2011)

Mélanie Courtot, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan R. Brinkman, Alan Ruttenberg: MIREOT: The minimum information to reference an external ontology term. Applied Ontology 6(1): 23-33 (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 Bioinformatics 12: 371 (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

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

Mélanie Courtot, Ryan R. Brinkman, Alan Ruttenberg: Reporting Adverse Events: Basis for a Common Representation. ICBO 2011

Mélanie Courtot, Chris Mungall, Ryan R. Brinkman, Alan Ruttenberg: Building the OBO Foundry - One Policy at a Time. ICBO 2011

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

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

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

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. Artificial Intelligence in Medicine 48(1): 21-28 (2010)

Alan Ruttenberg, Jonathan Rees, Matthias Samwald, M. Scott Marshall: Life sciences on the Semantic Web: the Neurocommons and beyond. Briefings in Bioinformatics 10(2): 193-204 (2009)

Catherine Dolbear, Alan Ruttenberg, Ulrike Sattler (Eds.): 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

Paolo Ciccarese, Elizabeth Wu, Gwendolyn T. Wong, Marco Ocana, June Kinoshita, Alan Ruttenberg, Tim Clark: The SWAN biomedical discourse ontology. Journal of Biomedical Informatics 41(5): 739-751 (2008)

Holger Stenzhorn, Kavitha Srinivas, Matthias Samwald, Alan Ruttenberg: Simplifying Access to Large-Scale Health Care and Life Sciences Datasets. ESWC 2008: 864-868

Mélanie Courtot, William J. Bug, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan R. Brinkman, Alan Ruttenberg: The OWL of Biomedical Investigations. OWLED 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: 1273-1274

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 Bioinformatics 8(S-3) (2007)

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

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

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 Reich, Joseph Horvath, Tim Clark: Computational knowledge integration in biopharmaceutical research. Briefings in Bioinformatics 4(3): 260-278 (2003)