The Future of Research Communications and e-Scholarship

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Toward interoperable bioscience data.

Authors: Sansone, Susanna-Assunta Philippe Rocca-Serra Field, Dawn Maguire, Eamonn Taylor, Chris Hofmann, Oliver Fang, Hong Neumann, Steffen Tong, Weida Amaral-Zettler, Linda Begley, Kimberly Booth, Tim Bougueleret, Lydie Gully Burns Chapman, Brad Clark, Tim Coleman, Lee-Ann Copeland, Jay Das, Sudeshna de Daruvar, Antoine de Matos, Paula Dix, Ian Scott Edmunds Evelo, Chris T Forster, Mark J … Read more

eXframe: reusable framework for storage, analysis and visualization of genomics experiments.

Authors: Sinha, Amit U Merrill, Emily Armstrong, Scott A Clark, Tim W Das, Sudeshna BACKGROUND: Genome-wide experiments are routinely conducted to measure gene expression, DNA-protein interactions and epigenetic status. Structured metadata for these experiments is imperative for a complete understanding of experimental conditions, to enable consistent data processing and to allow retrieval, comparison, and integration … Read more

The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside.

Authors: Luciano, Joanne S Andersson, Bosse Batchelor, Colin Bodenreider, Olivier Clark, Tim Denney, Christine K Domarew, Christopher Gambet, Thomas Harland, Lee Jentzsch, Anja Kashyap, Vipul Kos, Peter Kozlovsky, Julia Lebo, Timothy Marshall, M Scott McCusker, James P McGuinness, Deborah L Ogbuji, Chimezie Pichler, Elgar Powers, Robert L Prud'hommeaux, Eric Samwald, Matthias Schriml, Lynn Tonellato, Peter … Read more

The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside.

BACKGROUND: Translational medicine requires the integration of knowledge using heterogeneous data from health care to the life sciences. Here, we describe a collaborative effort to produce a prototype Translational Medicine Knowledge Base (TMKB) capable of answering questions relating to clinical practice and pharmaceutical drug discovery. RESULTS: We developed the Translational Medicine Ontology (TMO) as a … Read more

Building Biomedical Web Communities Using a Semantically Aware Content Management System.

Authors: Das, Sudeshna Lisa Girard Green, Tom Weitzman, Louis Lewis-Bowen, Alister Clark, Tim Web-based biomedical communities are becoming an increasingly popular vehicle for sharing information amongst researchers and are fast gaining an online presence. However, information organization and exchange in such communities is usually unstructured, rendering interoperability between communities difficult. Furthermore, specialized software to create … Read more

The SWAN Biomedical Discourse Ontology.

Authors: Ciccarese, Paolo Wu, Elizabeth Wong, Gwen Ocana, Marco Kinoshita, June Ruttenberg, Alan Clark, Tim Developing cures for highly complex diseases, such as neurodegenerative disorders, requires extensive interdisciplinary collaboration and exchange of biomedical information in context. Our ability to exchange such information across sub-specialties today is limited by the current scientific knowledge ecosystem's inability to … Read more

Advancing translational research with the Semantic Web.

Authors: Ruttenberg, Alan Clark, Tim Bug, William Samwald, Matthias Bodenreider, Olivier Chen, Helen Doherty, Donald Forsberg, Kerstin Gao, Yong Kashyap, Vipul Kinoshita, June Luciano, Joanne Marshall, M Scott Ogbuji, Chimezie Rees, Jonathan Stephens, Susie Wong, Gwendolyn T Wu, Elizabeth Zaccagnini, Davide Hongsermeier, Tonya Neumann, Eric Ivan Herman Cheung, Kei-Hoi BACKGROUND: A fundamental goal of the … Read more

Alzforum and SWAN: the present and future of scientific web communities.

Authors: Clark, Tim Kinoshita, June Scientists drove the early development of the World Wide Web, primarily as a means for rapid communication, document sharing and data access. They have been far slower to adopt the web as a medium for building research communities. Yet, web-based communities hold great potential for accelerating the pace of scientific … Read more