MassGeneral Institute for Neurodegenerative Disease

Translating today's discoveries into tomorrow's cures

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Publications

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Clark T, Goble C. The World-Wide Web. In: Dubitzky W, Wolkenhauer O, Cho K-H, Yokota H (Eds.), Encyclopedia of Systems Biology. Heidelberg, DE: Springer; 2013
Clark T, Ciccarese P, Goble C. Micropublications: a Semantic Model for Claims, Evidence, Arguments and Annotations in Biomedical Communications [Internet]. Journal of Biomedical Semantics Submitted;Available from: http://arxiv.org/abs/1305.3506
Clark T, Ciccarese P, Attwood T, de Waard A, Pettifer S. A Round-Trip to the Annotation Store: Open, Transferable Semantic Annotation of Biomedical Publications. In: Beyond the PDF, San Diego, 19-21 Jan 2011. 2011
Clark T, Martin S, Liefeld T. Globally Distributed Object Identification for Biological Knowledgebases. Brief Bioinform 2004;5(1):59-70.
Clark T, Kinoshita J. Alzforum and SWAN: The Present and Future of Scientific Web Communities. Brief Bioinform 2007;8(3):163-71.
Clark T. Knowledge Integration in Biomedicine: Technology and Community. Brief Bioinform 2007;
Clark T. Collaborative and distributed biomedical applications. In: Dubitzky W, Wolkenhauer O, Cho K-H, Yokota H (Eds.), Encyclopedia of Systems Biology. Heidelberg, DE: Springer; 2013
Ciccarese P, Soiland-Reyes S, Clark T. Web Annotation as a First Class Object. IEEE Internet Computing In Press;
Ciccarese P, Wu E, Wong G, Ocana M, Kinoshita J, Ruttenberg A, Clark T. The SWAN Biomedical Discourse Ontology. J Biomed Inform 2008;41(5):739-51.
Ciccarese P, Ocana M, Das S, Clark T. AO: An Open Annotation Ontology for Science on the Web. In: Bio-Ontologies 2010, July 9-10 2010, Boston MA. 2010
Ciccarese P, Ocana M, Castro LJael Garci, Das S, Clark T. An Open Annotation Ontology for Science on Web 3.0. J Biomed Semantics 2011;2 Suppl 2:S4.
Ciccarese P, Peroni S. The Collections Ontology: creating and handling collections in OWL 2 DL frameworks [Internet]. Semantic Web Journal In Press;Available from: http://www.semantic-web-journal.net/system/files/swj506.pdf
Ciccarese P, Wu E, Clark T. An Overview of the SWAN 1.0 Discourse Ontology [Internet]. In: Workshop on Health Care and Life Sciences Data Integration for the Semantic Web, WWW2007. 16th International World Wide Web Conference. Banff, Canada: 2007Available from: http://www2007.org/workshops/paper_145.pdf
Ciccarese P, Shotton D, Peroni S, Clark T. CiTO + SWAN: The Web Semantics of Bibliographic Records, Citations, Evidence and Discourse Relationships. [Internet]. Semantic Web Journal 2012;Available from: http://www.semantic-web-journal.net/system/files/swj175_1.pdf
Ciccarese P, Ocana M, Clark T. DOMEO: a web-based tool for semantic annotation of online documents. In: Bio-Ontologies 2011, July 15-16, Vienna Austria. 2011
Ciccarese P, Ocana M, Clark T. Open semantic annotation of scientific publications using DOMEO. J Biomed Semantics 2012;3 Suppl 1:S1.
Cases M, Furlong LI, Albanell J, Altman RB, Bellazzi R, Boyer S, Brand A, Brookes AJ, Brunak S, Clark TW, Gea J, Ghazal P, Graf N, Guigó R, Klein TE, López-Bigas N, Maojo V, Mons B, Musen M, Oliveira JL, Rowe A, Ruch P, Shabo A, Shortliffe EH, Valencia A, van der Lei J, Mayer MA, Sanz F. Improving data and knowledge management to better integrate health care and research. J Intern Med 2013;274(4):321-8.
Carusi A, Clark T, M Marshall S. Web Semantics in Action: Web 3.0 in e-Science. In: 5th IEEE International Conference on e-Science. Oxford, UK: 2009
Cantuti-Castelvetri I, Keller-McGandy C, Bouzou B, Asteris G, Clark T, Frosch MP, Standaert DG. Effects of Gender on Nigral Gene Expression and Parkinson Disease. Neurobiol Dis 2007;26(3):606-14.
B
Bourne P, Clark T, Dale R, de Waard A, Herman I, Hovy E, Shotton D. The Future of Research Communication and e-Scholarship. Dagstuhl reports 2011;1(8)
Bourne P, Clark T, Dale R, de Waard A, Herman I, Hovy E, Shotton D. Improving Future Research Communication and e-Scholarship: A Summary of Findings. Informatik-Spektrum 2012;35(1):56-57.
Bandrowski AE, Cachat J, Li Y, Müller HM, Sternberg PW, Ciccarese P, Clark T, Marenco L, Wang R, Astakhov V, Grethe JS, Martone ME. A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework. Database (Oxford) 2012;2012:bas005.

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