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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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, Ocana M, Clark T. Open semantic annotation of scientific publications using DOMEO. J Biomed Semantics 2012;3 Suppl 1:S1.
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
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Das S, McCaffrey PG, Talkington MWT, Andrews NA, Corlosquet S, Ivinson AJ, Clark T. Pain Research Forum: application of scientific social media frameworks in neuroscience. Front Neuroinform 2014;8:21.
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
Das S, Rogan M, Kawadler H, Corlosquet S, Brin S, Clark T. PD Online: a case study in scientific collaboration on the Web [Internet]. In: Workshop on the Future of the Web for Collaborative Science, 19th International World Wide Web Conference. Raleigh, North Carolina USA: 2010Available from: http://imageweb.zoo.ox.ac.uk/pub/2010/Proceedings/FWCS2010/02/Paper2.pdf
Das S, Rogan M, Kawadler H, Corlosquet S, Brin S, Clark T. PD Online: a case study in scientific collaboration on the Web. In: Workshop on the Future of the Web for Collaborative Science, 19th International World Wide Web Conference, Raleigh, North Carolina USA - April 26-30, 2010. 2010
Corlosquet S, R D, Clark T, Polleres A, Decker S. Produce and Consume Linked Data with Drupal! [Internet]. In: 8th International Semantic Web Conference (ISWC 2009); October 25-29, 2009, Washington DC. 2009Available from: http://openspring.net/sites/openspring.net/files/corl-etal-2009iswc.pdf
Corlosquet S, Delbru R, Clark T, Polleres A, Decker S. Produce and Consume Linked Data with Drupal [Internet]. In: 8th International Semantic Web Conference (ISWC 2009). Washington DC: 2009Available from: http://openspring.net/sites/openspring.net/files/corl-etal-2009iswc.pdf
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Das S, Goetz M, Girard L, Clark T. Scientific Publications on Web 3.0 [Internet]. In: 13th International Conference on Electronic Publishing (ELPUB 2009). Milan, Italy: 2009Available from: http://elpub.scix.net/cgi-bin/works/Show?149_elpub2009
Lam HYK, Marenco L, Clark T, Gao Y, Kinoshita J, Shepherd G, Miller P, Wu E, Wong GT, Liu N, Crasto C, Morse T, Stephens S, Cheung K-H. Semantic Web Meets e-Neuroscience: An RDF Use Case. Semantic Web - ASWC 2006: First Asian Semantic Web Conference 2006;:158-170.
Merrill E, Corlosquet S, Ciccarese P, Clark T, Das S. Semantic Web repositories for genomics data using the eXframe platform [Internet]. Journal of Biomedical Semantics 2014;5(Supplement 1)Available from: http://www.jbiomedsem.com/content/5/S1/S3
Groza T, Handschuh S, Clark T, Shum SB. A Short Survey of Scientific Discourse Representation Models [Internet]. In: Workshop on Semantic Web Applications in Scientific Discourse, 8th International Conference on Semantic Web (ISWC 2009), Oct 25-29 2009, Washington DC. 2009Available from: http://www.w3.org/wiki/images/c/c8/HCLS$$ISWC2009$$Workshop$Groza.pdf
Groza T, Handschuh S, Clark T, Shum SBuckingham, de Waard A. A Short Survey of Scientific Discourse Representation Models [Internet]. In: Workshop on Semantic Web Applications in Scientific Discourse, 8th International Conference on Semantic Web (ISWC 2009). Washington DC: 2009Available from: http://www.w3.org/wiki/images/c/c8/HCLS$$ISWC2009$$Workshop$Groza.pdf
Gao Y, Kinoshita J, Wu E, Miller E, Lee R, Seaborne A, Cayzer S, Clark T. SWAN: A Distributed Knowledge Infrastructure for Alzheimer Disease Research. Journal of Web Semantics 2006;4(3):222-228.
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.
Passant A, Ciccarese P, Breslin J, Clark T. SWAN/SIOC: Aligning Scientific Discourse Representation and Social Semantics [Internet]. In: Workshop on Semantic Web Applications in Scientific Discourse, 8th International Conference on Semantic Web (ISWC 2009), Oct 25-29 2009, Washington DC. 2009Available from: http://www.johnbreslin.org/files/publications/20091026_swas2009.pdf
Passant A, Ciccarese P, Breslin JG, Clark T. SWAN/SIOC: Aligning Scientific Discourse Representation and Social Semantics [Internet]. In: Workshop on Semantic Web Applications in Scientific Discourse, 8th International Conference on Semantic Web (ISWC 2009). Washington DC: 2009Available from: http://www.johnbreslin.org/files/publications/20091026_swas2009.pdf
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Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns G, Chapman B, Clark T, Coleman L-A, Copeland J, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S, Evelo CT, Forster MJ, Gaudet P, Gilbert J, Goble C, Griffin JL, Jacob D, Kleinjans J, Harland L, Haug K, Hermjakob H, Sui SJHo, Laederach A, Liang S, Marshall S, McGrath A, Merrill E, Reilly D, Roux M, Shamu CE, Shang CA, Steinbeck C, Trefethen A, Williams-Jones B, Wolstencroft K, Xenarios I, Hide W. Toward interoperable bioscience data. Nat Genet 2012;44(2):121-6.
Luciano JS, Andersson B, Batchelor C, Bodenreider O, Clark T, Denney CK, Domarew C, Gambet T, Harland L, Jentzsch A, Kashyap V, Kos P, Kozlovsky J, Lebo T, Marshall SM, McCusker JP, McGuinness DL, Ogbuji C, Pichler E, Powers RL, Prud'hommeaux E, Samwald M, Schriml L, Tonellato PJ, Whetzel PL, Zhao J, Stephens S, Dumontier M. The Translational Medicine Ontology and Knowledge Base: Driving personalized medicine by bridging the gap between bench and bedside. J Biomed Semantics 2011;2 Suppl 2:S1.
Luciano JS, Andersson D, Batchelor C, Bodenreider O, Clark T, Denney C, Domarew C, Gambet T, Jentzsch A, Kashyap V, Kos P, Kozlovsky J, Marshall MS, McCusker JP, McGuinness DL, Lebo T, Ogbuji C, Pichler E, Powers RL, Prud’hommeaux E, Samwald M, Schriml L, Tonellato PJ, Whetzelm PL, Zhao J, Stephens S, Dumontier M. The Translational Medicine Ontology and Knowledge Base: Using Semantic Web Technology in Personalized Medicine for Data Integration. In: AMIA Summit on Translational Bioinformatics, March 7-9, 2011, San Francisco CA, USA. 2011
Dumontier M, Anderson B, Batchelor C, Domarew C, Jentsch A, Luciano J, Pichler E, Prud’hommeaux E, Whetzel P, Bodenreider O, Clark T, Harland L, Kashyap V, Kos P, Kozlovsky J, McGurk J, Ogbuji C, Samwald M, Schriml L, Tonatello P, Zhao J, Stephens S. Translational Medicine Ontology: Driving personalized medicine by bridging the gap from bedside to bench. In: Bio-Ontologies 2010, July 9-10 2010, Boston MA. 2010

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