The Future of Research Communications and e-Scholarship

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Effects of gender on nigral gene expression and parkinson disease.

Author: Cantuti-Castelvetri, Ippolita Keller-McGandy, Christine Bouzou, Bérengère Asteris, Georgios Clark, Timothy W Frosch, Matthew P Standaert, David G To identify gene expression patterns in human dopamine (DA) neurons in the substantia nigra pars compacta (SNc) of male and female control and Parkinson disease (PD) patients, we harvested DA neurons from frozen SNc from 16 subjects … Read more

AlzPharm: integration of neurodegeneration data using RDF.

Author: Lam, Hugo Y K Marenco, Luis Clark, Tim Gao, Yong Kinoshita, June Shepherd, Gordon Miller, Perry Wu, Elizabeth Wong, Gwendolyn T Liu, Nian Crasto, Chiquito Morse, Thomas Stephens, Susie Cheung, Kei-Hoi BACKGROUND: Neuroscientists often need to access a wide range of data sets distributed over the Internet. These data sets, however, are typically neither … Read more

Globally distributed object identification for biological knowledgebases.

Authors: Clark, Tim Martin, Sean Liefeld, Ted The World-Wide Web provides a globally distributed communication framework that is essential for almost all scientific collaboration, including bioinformatics. However, several limits and inadequacies have become apparent, one of which is the inability to programmatically identify locally named objects that may be widely distributed over the network. This … Read more

Computational knowledge integration in biopharmaceutical research.

Authors: Ficenec, David Osborne, Mark Pradines, Joel Richards, Dan Felciano, Ramon Cho, Raymond J Chen, Richard O Liefeld, Ted Owen, James Ruttenberg, Alan Reich, Christian Horvath, Joseph Clark, Tim An initiative to increase biopharmaceutical research productivity by capturing, sharing and computationally integrating proprietary scientific discoveries with public knowledge is described. This initiative involves both organisational … Read more


Authors: Kinoshita, June Clark, Tim The Alzheimer Research Forum Web site ( ) is an independent research project to develop an online community resource to manage scientific knowledge, information, and data about Alzheimer disease (AD). Its goals are to promote rapid communication, research efficiency, and collaborative, multidisciplinary interactions. Introducing new knowledge management approaches to … Read more

Open semantic annotation of scientific publications using DOMEO

Authors: Ciccarese, Paolo Ocana, Marco Clark, Tim Background Our group has developed a useful shared software framework for performing, versioning, sharing and viewing Web annotations of a number of kinds, using an open representation model. Methods The Domeo Annotation Tool was developed in tandem with this open model, the Annotation Ontology (AO). Development of both … Read more

Micropublications: a Semantic Model for Claims, Evidence, Arguments and Annotations in Biomedical Communications

Authors:Clark, Tim Ciccarese, Paolo Carole Goble The Micropublications semantic model for scientific claims, evidence, argumentation and annotation in biomedical publications, is presented here. This model is intended to complement the more narrowly focused “nanopublication” model. It is designed to support several key requirements for exchange and value-addition of semantic metadata across the biomedical publications ecosystem. … Read more