MIND Informatics develops and applies integrative computational methods in biomedical and brain research, working with leading clinicians and researchers to understand and cure neurological disorders.

Publications

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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.
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
Cases M, Furlong LI, Albanell J, Altman RB, Bellazzi R, Boyer S, Brand A, Brookes AJ, Brunak S, Clark T, 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.
Ciccarese P, Soiland-Reyes S, Belhajjame K, Gray AJG, Goble C, Clark T. PAV ontology: Provenance, Authoring and Versioning [Internet]. Journal of Biomedical Semantics 2013;4(37)Available from: http://www.jbiomedsem.com/content/4/1/37
Ciccarese P, Soiland-Reyes S, Clark T. Web Annotation as a First Class Object. Internet Computing, IEEE 2013;
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, 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, 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 2013;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.
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
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;
Comeau DC, Doğan RI, Ciccarese P, Cohen KB, Krallinger M, Leitner F, Lu Z, Peng Y, Rinaldi F, Torii M, Valencia A, Verspoor K, Wiegers TC, Wu CH, Wilbur WJ. BioC: A Minimalist Approach to Interoperability for Biomedical Text Processing. Database 2013;

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