Browsing by Author "Clark, Tim"

Now showing items 1-15 of 15

    • AlzPharm: integration of neurodegeneration data using RDF 

      Lam, Hugo YK; Marenco, Luis; Kinoshita, June; Shepherd, Gordon; Miller, Perry; Wu, Elizabeth; Wong, Gwendolyn T; Liu, Nian; Crasto, Chiquito; Morse, Thomas; Stephens, Susie; Cheung, Kei-Hoi; Clark, Timothy William; Gao, Yong (BioMed Central, 2007)
      Background: Neuroscientists often need to access a wide range of data sets distributed over the Internet. These data sets, however, are typically neither integrated nor interoperable, resulting in a barrier to answering ...

    • Computational Knowledge Integration in Biopharmaceutical Research 

      Ficenec, David; Osborne, Mark; Pradines, Joel; Richards, Dan; Felciano, Ramon; Cho, Raymond; Chen, Richard; Liefeld, Ted; Owen, James; Ruttenberg, Alan; Reich, Christian; Clark, Timothy William (2003)
      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 ...

    • The FAIR Guiding Principles for scientific data management and stewardship 

      Wilkinson, Mark D.; Dumontier, Michel; Aalbersberg, IJsbrand Jan; Appleton, Gabrielle; Axton, Myles; Baak, Arie; Blomberg, Niklas; Boiten, Jan-Willem; da Silva Santos, Luiz Bonino; Bourne, Philip E.; Bouwman, Jildau; Brookes, Anthony J.; Clark, Tim; Crosas, Mercè; Dillo, Ingrid; Dumon, Olivier; Edmunds, Scott; Evelo, Chris T.; Finkers, Richard; Gonzalez-Beltran, Alejandra; Gray, Alasdair J.G.; Groth, Paul; Goble, Carole; Grethe, Jeffrey S.; Heringa, Jaap; ’t Hoen, Peter A.C; Hooft, Rob; Kuhn, Tobias; Kok, Ruben; Kok, Joost; Lusher, Scott J.; Martone, Maryann E.; Mons, Albert; Packer, Abel L.; Persson, Bengt; Rocca-Serra, Philippe; Roos, Marco; van Schaik, Rene; Sansone, Susanna-Assunta; Schultes, Erik; Sengstag, Thierry; Slater, Ted; Strawn, George; Swertz, Morris A.; Thompson, Mark; van der Lei, Johan; van Mulligen, Erik; Velterop, Jan; Waagmeester, Andra; Wittenburg, Peter; Wolstencroft, Katherine; Zhao, Jun; Mons, Barend (Nature Publishing Group, 2016)
      There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to ...

    • Globally Distributed Object Identification for Biological Knowledge Bases 

      Clark, Timothy William; Martin, Sean; Liefeld, Ted (Henry Stewart Publications, 2004)
      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, ...

    • Huntingtin Modulates Transcription, Occupies Gene Promoters In Vivo, and Binds Directly to DNA in a Polyglutamine-Dependent Manner 

      Benn, C. L.; Sun, T.; Sadri-Vakili, Ghazaleh; McFarland, K. N.; DiRocco, D. P.; Yohrling, G. J.; Clark, Timothy William; Bouzou, B.; Cha, J.-H. J. (Society for Neuroscience, 2008)
      Transcriptional dysregulation is a central pathogenic mechanism in Huntington's disease, a fatal neurodegenerative disorder associated with polyglutamine (polyQ) expansion in the huntingtin (Htt) protein. In this study, ...

    • A Hybrid Human and Machine Resource Curation Pipeline for the Neuroscience Information Framework 

      Bandrowski, A. E.; Cachat, J.; Müller, H. M.; Sternberg, P. W.; Marenco, L.; Astakhov, V.; Grethe, J. S.; Martone, M. E.; Li, Y.; Ciccarese, Paolo Nunzio; Clark, Timothy William; Wang, R. (Oxford University Press, 2012)
      The breadth of information resources available to researchers on the Internet continues to expand, particularly in light of recently implemented data-sharing policies required by funding agencies. However, the nature of ...

    • Micropublications: a semantic model for claims, evidence, arguments and annotations in biomedical communications 

      Clark, Tim; Ciccarese, Paolo N; Goble, Carole A (BioMed Central, 2014)
      Background: Scientific publications are documentary representations of defeasible arguments, supported by data and repeatable methods. They are the essential mediating artifacts in the ecosystem of scientific communications. ...

    • An Open Annotation Ontology for Science on Web 3.0 

      Ciccarese, Paolo Nunzio; Ocana, Marco; Garcia Castro, Leyla Jael; Das, Sudeshna; Clark, Timothy William (BioMed Central, 2011)
      Background: There is currently a gap between the rich and expressive collection of published biomedical ontologies, and the natural language expression of biomedical papers consumed on a daily basis by scientific researchers. ...

    • Open Semantic Annotation Of Scientific Publications Using DOMEO 

      Ciccarese, Paolo Nunzio; Ocana, Marco; Clark, Timothy William (BioMed Central, 2012)
      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 ...

    • Pain Research Forum: application of scientific social media frameworks in neuroscience 

      Das, Sudeshna; McCaffrey, Patricia G.; Talkington, Megan W. T.; Andrews, Neil A.; Corlosquet, Stéphane; Ivinson, Adrian J.; Clark, Tim (Frontiers Media S.A., 2014)
      Background: Social media has the potential to accelerate the pace of biomedical research through online collaboration, discussions, and faster sharing of information. Focused web-based scientific social collaboratories ...

    • PAV ontology: provenance, authoring and versioning 

      Ciccarese, Paolo; Soiland-Reyes, Stian; Belhajjame, Khalid; Gray, Alasdair JG; Goble, Carole; Clark, Tim (BioMed Central, 2013)
      Background: Provenance is a critical ingredient for establishing trust of published scientific content. This is true whether we are considering a data set, a computational workflow, a peer-reviewed publication or a simple ...

    • Semantic Web repositories for genomics data using the eXframe platform 

      Merrill, Emily; Corlosquet, Stéphane; Ciccarese, Paolo; Clark, Tim; Das, Sudeshna (BioMed Central, 2014)
      Background: With the advent of inexpensive assay technologies, there has been an unprecedented growth in genomics data as well as the number of databases in which it is stored. In these databases, sample annotation using ...

    • The SWAN biomedical discourse ontology 

      Ciccarese, Paolo Nunzio; Wu, Elizabeth; Wong, Gwen; Ocana, Marco; Kinoshita, June; Ruttenberg, Alan; Clark, Timothy William (Elsevier BV, 2008)
      SWAN (Semantic Web Application in Neuromedicine) is a project to construct a semantically-organized, community-curated, distributed knowledge base of Theory, Evidence, and Discussion in biomedicine. Unlike Wikipedia and ...

    • SWAN: A Distributed Knowledge Infrastructure for Alzheimer Disease Research 

      Gao, Yong; Kinoshita, June; Wu, Elizabeth; Miller, Eric; Lee, Ryan; Seaborne, Andy; Cayzer, Steve; Clark, Timothy William (Elsevier, 2006)
      SWAN – a Semantic Web Application in Neuromedicine – is a project to develop an effective, integrated scientific knowledge infrastructure for the Alzheimer disease (AD) research community, using the energy and self-organization ...

    • The Translational Medicine Ontology and Knowledge Base: Driving Personalized Medicine By Bridging The Gap Between Bench And Bedside 

      Luciano, Joanne S; Andersson, Bosse; Batchelor, Colin; Bodenreider, Olivier; Denney, Christine K; Domarew, Christopher; Gambet, Thomas; Harland, Lee; Jentzsch, Anja; Kashyap, Vipul; Kos, Peter; Kozlovsky, Julia; Lebo, Timothy; Marshall, Scott M; McCusker, James P; McGuinness, Deborah L; Ogbuji, Chimezie; Pichler, Elgar; Samwald, Matthias; Schriml, Lynn; Whetzel, Patricia L; Stephens, Susie; Dumontier, Michel; Clark, Timothy William; Prud'hommeaux, Eric; Tonellato, Peter J; Zhao, Jun (BioMed Central, 2011)
      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 ...