Workshop Papers

 Nr      Authors  Title      Topics (from list below)
Tim Clark, Paolo Ciccarese, Terri Attwood, Anita de Waard and Steve Pettifer A Round-Trip to the Annotation Store: Open, Transferable Semantic Annotation of Biomedical Publications  1.1, 2.2, 2.4
 2 Cameron Neylon, Martin Fenner Blogging beyond the PDF or Copy by Reference 1.1-1.4, 2.1, 2.4, 3, 5
 3   Paul Groth Total Impact: Aggregating alternative measures of impact  5, 1.3
 4         Juliana Freire    
Towards Provenance-Rich Publications (presentation)

 1.1, 1.2, 3, 5
 5 Anita de Waard    
From Claim to Fact: A Small Use Case in Scientific Fact Making, Using the Bourne Corpus
 2.2, 5
Jill Mesirov    
Accessible Reproducible Research  1.1, 1.2, 3        
 7 Peter Sefton Bringing the web to the researcher 1.1, 1.2, 1.3, 1.4, 2, 3
 8       Rik Belew
Analogical publishing  1.3, 2.5, 3, 5
 9       Gully APC Burns
Structured nanopublications pertaining to the drugome: A Knowledge Engineering from Experimental Design (KEfED) model  1.2, 3
 10 Paul Thompson, Anita de Waard, Maria Liakata, Raheel Nawaz and Sophia Ananiadou
Comparing scientific discourse annotation schemes for enhanced knowledge extraction  2.2, 2.3, 2.4
 11 Eduard Hovy
   2.4, 2.2, 2.3, 4
 12 David Argue, Karl Clark, Andrew Petzold, Stephen Ekker Beyond the Dead Sea PDFs - A Next-Generation Paper Format
 13     Peter Murray-Rust
Quixote and GreenChainReaction    
1.1, 1.2, 2.2, 2.3, 2.4, 3
 14     Michael J. Kurtz The Recent Experience of Astrophysics in Scholarly Communication  2.5, 3, 4. 
 15   Barend Mons    
Is the (enriched) paper computer-reasonable?  
 16     Daniel Mietchen, Konrad Förstner and Mark Hahnel
Integrating wikis with scientific workflows
1.1-1.4, 2.1, 3, 5
 17 D. Rebholz-Schuhmann, S. Kavaliauskas, P. Pezik  PaperMaker:  Validation of biomedical scientific publications 1.1 
 18         D. Rebholz-Schuhmann, I. Lewin, S. Kafkas, C. Li In the CALBC project the project partners solve the problem of integrating different kinds of annotations in a large-scale corpus.  The integrated annotations comply with any XML document format. 2.1 
 19     D. Rebholz-Schuhmann, I. Harrow, W. Filsell, C. Grabmueller, S. Kavaliauskas, S. Croset  In the SESL project the members of the Pistoia Alliance and selected publishing companies work towards an infrastructure to broker data from biomedical resources in combination with the scientific literature. The project is based on Semantic Web technology. 2.4, 2.5, 5 

 20    Jodi Schneider Supporting Active Reading, Just-in-Time Reading, and Reading Avoidance (Use Cases) 3
 21 David Shotton and Silvio Peroni  Semantic annotation of publication entities    
Paper at
Topics 2.1, 2.2, 2.4, 3
 22 Alex Garnett  Using PKP Platforms to Teach a New Dog Old Tricks  1.1,1.2,
2.4, 3
 23 Maryann Martone, Anita Bandrowski, Jeffrey Grethe, Amarnath Gupta Intelligent Handling of Resources for Human and Machines – It’s not too early to start…

1.4, 2.2, 2.4, 2.5
 24 Yolanda Gil Shared Provenance Representations: The W3C Provenance Group
 2.4, 3, 5
 25 Yolanda Gil Shared Provenance Representations: Cross-Organization Reproducibility with Semantic Workflow
 26 John Kunze, Rachael Hu, Trisha Cruse, Catherine Mitchell, Stephen Abrams, Kirk Hastings, Lisa Schiff Baby steps to data publication

 1.1, 1.3
 27  Jeff Beck    
Structured documents: Why we want them, When we want them, and How we get them when we want them.
 28  Carl Leubsdorf, Jr. Annotum: an open-source journal authoring and publishing platform based on WordPress  1.1-1.4, 2.5, 3
 29  S. Pettifer and T. K. Attwood.. Utopia Documents : Linking scientific data and literature  1.1-1.4, 2.5, 3

Topic codes:

1. Tools
1.1 Authoring tools
1.2 Research workflow tools
1.3 Document management tools
1.4 Rendering tools

2. Annotation and new formats.

2.1 New formats for scientific papers (please provide use case for each new format, see 3.)
2.2  Models of annotation: what parts of the document are marked up, when (in the authoring/publishing process) and why?
2.3 Text mining and computational linguistics: how can we find these parts automatically?
2.4 Annotation standards and ontologies: how do we call the pieces we find?
2.5 Systems for combining and rendering annotated documents.

3. Use cases and examples.

4. Business and/or Intellectual Property rights.

5. Attribution/Evaluation/Archiving.
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