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Innovation & Supplementary Material

Innovation & Supplementary Material. Eleonora Presani – Elsevier e.presani@elsevier.com. Overview. Data & the Scientific Article Supplementary Material Connecting with Data Repositories Online Linking Schemes Article-level & Entity-level Linking Examples Applications

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Innovation & Supplementary Material

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  1. Innovation & Supplementary Material EleonoraPresani – Elsevier e.presani@elsevier.com

  2. Overview • Data & the Scientific Article • Supplementary Material • Connecting with Data Repositories • Online Linking Schemes • Article-level & Entity-level Linking • Examples • Applications • SciVerse Applications • Applications and Data • The Article of the Future

  3. Supplementary Material • Authors can upload Supplementary Material with their paper • Pro’s • Coupling of data and article • Peer review • Citation mechanism • Preservation (byte-wise) • Con’s • Limited data type support • Compatibility (format support) • Limited capacity • Data not centrally stored

  4. Connecting with Data Repositories • Supplementary material is not a perfect solution • Many poor solutions in use: data on PCs, university websites, personal homepages, ... • Data repositories: the community’s answer? • Scientists prefer independent data repositories above publishers • Domain-specific coordination • Centralized information “hubs” • “Raw data should be freelyaccessible to researchers” “... believe that, as a general principle, data sets, raw data outputs of research, and sets or subsets of that data should wherever possible be made freely accessible to other scholars ...”(Statement from STM & ALPSP, June 2006)

  5. DB Linking Option 1: Entity Linking • For entities (concepts) mentioned inan article – proteins, genes, standardsplanets, cities, etc. etc. • Author-tagged in manuscript http://dx.doi.org/10.1016/j.coldregions.2012.03.009

  6. Option 2: Image-based (article) linking • For links between article as a whole and related data sets • No author involvement required on Elsevier side • Links managed by data repository http://dx.doi.org/10.1016/j.gca.2008.08.005

  7. HEPData Linking (Mike Whalley)

  8. SciVerse Applications • Scientific literature: a node that could more efficientlyconnect resources • Mass of data available to researchers outside the formalliterature is huge and growing • Many disconnected nodes - minimal interoperability, even when connections exist • This is inefficient - task switching between multiple interfaces, hard to find resources... • An open platform for publishing can “un-silo” data and literature • Smart apps can facilitate interoperability, bring relevant data into context with papers • Integrated user experience, save researchers from searching in multiple data sources while reading the literature • Introduces researchers to new tools and resources they may never have found otherwise

  9. SciVerse Applications Features & Benefits • Use information from SciVerse and the web • Support for rich user interfaces • Integrated directly into the online article • Simple to build using Content and Framework APIs • Open standards (Apache Shindig, Open Social)

  10. SciVerse Applications & Data • SciVerse Applications enable the community to create the publishing platform they need by building their own applications. • Benefits for data repositories • Increase visibility, discoverability, and usage(ScienceDirect: ~600M page views/year) • Provide context: connect data with the formal literature, avoid misinterpretations and incorrect usage • Enable researchers to interactive explore data

  11. Applications example: NCBI Genome Viewer • Scans the article and builds list of sequences based on NCBI accession numbers tagged in the article • View/analyze sequence data from genes in the article using NCBI Sequence Viewer • See specific information about each strand; zoom in/out; export data Screenshots of journal article on ScienceDirect (http://dx.doi.org/10.1016/j.ygeno.2007.07.010)

  12. Applications example: PANGAEA • Document identifier sent to PANGAEA data repository for earth sciences • PANGAEA returns map plotted with locations where cited data was collected • Push-pins open with details of dataset and direct link to data on PANGAEA.de Screenshots of journal article on ScienceDirect (http://dx.doi.org/10.1016/S0377-8398(01)00044-5)

  13. NED/SIMBAD Linking

  14. MOCK-UP Example: PDGLive linking

  15. Putting all together: Article of the Future Three components of the Article of the Future concept: • Presentation: Offering an optimal online browsing and reading experience • Content: Support authors to share a wider range of research output – data, computer code, multimedia files, etc. • Context: Connecting the online article to trustworthy scientific resources to present valuable additional informationin the context of the article • http://www.articleofthefuture.com/

  16. Examples of features of interest for HEP • Supplementary Material • ROOT Files support • Inline SourceCode • DataBase linking • HEPData • PDG • Applications • MatLab viewer • Interactive Plots • ROOT Viewer

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