AlanSRuttenbergMD

PubMed

• 10 citations
  Developing the Quantitative Histopathology Image Ontology (QHIO)
  Metin N. Gurcan, John E. Tomaszewski, James A. Overton, Scott Doyle, Alan Ruttenberg, Barry Smith> ;Journal of Biomedical Informatics. 2017 Feb 1
• 54 citations
  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....> ;Nucleic Acids Research. 2017 Jan 4
• 69 citations
  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, Christopher J. Mungall, Mélanie Courtot, Alan Ruttenberg, Yongqun He> ;Nucleic Acids Research. 2017 Jan 4
• 139 citations
  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, ...> ;Journal of Biomedical Semantics. 2016 Jul 4
• 10 citations
  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, Nisan...> ;Journal of Biomedical Semantics. 2016 May 10
• 6 citations
  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...> ;Journal of Biomedical Semantics. 2016 May 4
• 119 citations
  The Ontology for Biomedical Investigations
  Anita Bandrowski, Ryan R. Brinkman, Mathias Brochhausen, Matthew H. Brush, Bill Bug, Marcus C. Chibucos, Kevin Clancy, Mélanie Courtot, Dirk Derom, Michel Dumontier, L...> ;Plos One. 2016 Apr 29
• 2 citations
  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...> ;International Journal of Data Mining and Bioinformatics. 2016 Jan 1
• 14 citations
  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 ...> ;Bioinformatics. 2015 Apr 15
• 200 citations
  Finding Our Way through Phenotypes.
  Andrew R. Deans, Suzanna E. Lewis, Eva Huala, Salvatore S. Anzaldo, Michael Ashburner, James P. Balhoff, David C. Blackburn, Judith A. Blake, J. Gordon Burleigh, Bruno...> ;Plos Biology. 2015 Jan 6
• Correction: Toll-Like Receptor Signaling in Vertebrates: Testing the Integration of Protein, Complex, and Pathway Data in the Protein Ontology Framework.
  Arighi C, Shamovsky V, Masci AM, Ruttenberg A, Smith B, Natale DA, Wu C, D'Eustachio P> ;PLoS ONE. 2015-01-01
• Toll-like receptor signaling in vertebrates: testing the integration of protein, complex, and pathway data in the protein ontology framework.
  Arighi C, Shamovsky V, Masci AM, Ruttenberg A, Smith B, Natale DA, Wu C, D'Eustachio P> ;PLoS ONE. 2015-01-01
• 6 citations
  The logic of surveillance guidelines: an analysis of vaccine adverse event reports from an ontological perspective.
  Mélanie Courtot, Alan Ruttenberg> ;Plos One. 2014 Mar 25
• 17 citations
  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 Sz...> ;Journal of Biomedical Semantics. 2013 Dec 6
• 20 citations
  A strategy for building neuroanatomy ontologies
  David Osumi-Sutherland, Simon Reeve, Christopher J. Mungall, Alan Ruttenberg, Gregory S.X.E. Jefferis, J. Douglas Armstrong, Fabian Neuhaus> ;Bioinformatics. 2012 May 1
• 13 citations
  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, Alan Ruttenberg, Peter D'Eustachio, Barry Smith, Judith A. Blake, Cathy H. Wu> ;BMC Bioinformatics. 2011 Sep 19
• 7 citations
  Ontology and the future of dental research informatics.
  Barry Smith, Alan Ruttenberg, Michael Glick> ;Journal of the American Dental Association. 2010 Oct 1
• 169 citations
  Modeling biomedical experimental processes with OBI
  Ryan R. Brinkman, Mélanie Courtot, Dirk Derom, Jennifer Fostel, Yongqun He, Phillip Lord, James Malone, Helen Parkinson, Bjoern Peters, Alan Ruttenberg, Susanna-Assunt...> ;Journal of Biomedical Semantics. 2010 Jun 22
• 107 citations
  OntoFox: web-based support for ontology reuse.
  Zuoshuang Xiang, Mélanie Courtot, Alan Ruttenberg, Yongqun He> ;BMC Research Notes. 2010 Jun 22
• 2 citations
  Semantic SenseLab: Implementing the vision of the Semantic Web in neuroscience
  Matthias Samwald, Alan Ruttenberg, Ernest Lim, Luis N. Marenco, Perry L. Miller, Gordon M. Shepherd, Kei-Hoi Cheung> ;Artificial Intelligence in Medicine. 2010 Jan 1
• 36 citations
  Life sciences on the Semantic Web: the Neurocommons and beyond
  Alan Ruttenberg, Jonathan Rees, Matthias Samwald, M. Scott Marshall> ;Briefings in Bioinformatics. 2009 Mar 12
• 1093 citations
  The OBO Foundry : coordinated evolution of ontologies to support biomedical data integration
  , , , , , , , , , , , , , , , , > ;Nature Biotechnology. 2007 Nov 1
• 161 citations
  Advancing translational research with the Semantic Web
  Alan Ruttenberg, Timothy Clark, William J. Bug, Matthias Samwald, Olivier Bodenreider, Helen H. Chen, Donald Doherty, Kerstin Forsberg, Yong Gao, Vipul Kashyap, June K...> ;BMC Bioinformatics. 2007 May 9
• 14 citations
  Edge-count probabilities for the identification of local protein communities and their organization.
  Victor Farutin, Keith E. Robison, Eric S. Lightcap, Alan Ruttenberg, Stanley Letovsky, Joel Pradines> ;Proteins. 2005 Dec 21
• 10 citations
  Detection of Activity Centers in Cellular Pathways Using Transcript Profiling
  , , , , , , , , , , , , , , , > ;Journal of Biopharmaceutical Statistics. 2004 Dec 29
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