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Zudilova-Seinstra-Elsevier-data and the article of the future-nfdp13
Zudilova-Seinstra-Elsevier-data and the article of the future-nfdp13
Zudilova-Seinstra-Elsevier-data and the article of the future-nfdp13
Zudilova-Seinstra-Elsevier-data and the article of the future-nfdp13
Zudilova-Seinstra-Elsevier-data and the article of the future-nfdp13
Zudilova-Seinstra-Elsevier-data and the article of the future-nfdp13
Zudilova-Seinstra-Elsevier-data and the article of the future-nfdp13
Zudilova-Seinstra-Elsevier-data and the article of the future-nfdp13
Zudilova-Seinstra-Elsevier-data and the article of the future-nfdp13
Zudilova-Seinstra-Elsevier-data and the article of the future-nfdp13
Zudilova-Seinstra-Elsevier-data and the article of the future-nfdp13
Zudilova-Seinstra-Elsevier-data and the article of the future-nfdp13
Zudilova-Seinstra-Elsevier-data and the article of the future-nfdp13
Zudilova-Seinstra-Elsevier-data and the article of the future-nfdp13
Zudilova-Seinstra-Elsevier-data and the article of the future-nfdp13
Zudilova-Seinstra-Elsevier-data and the article of the future-nfdp13
Zudilova-Seinstra-Elsevier-data and the article of the future-nfdp13
Zudilova-Seinstra-Elsevier-data and the article of the future-nfdp13
Zudilova-Seinstra-Elsevier-data and the article of the future-nfdp13
Zudilova-Seinstra-Elsevier-data and the article of the future-nfdp13
Zudilova-Seinstra-Elsevier-data and the article of the future-nfdp13
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Zudilova-Seinstra-Elsevier-data and the article of the future-nfdp13

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Presentation by Elena Zudilova-Seinstra on Elsevier's work on data and the article of the future and open data given at the Now and Future of Data Publishing Symposium, 22 May 2013, Oxford, UK

Presentation by Elena Zudilova-Seinstra on Elsevier's work on data and the article of the future and open data given at the Now and Future of Data Publishing Symposium, 22 May 2013, Oxford, UK

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  • So the key message is that it’s all about adaptation. The way that research is performed has changed considerably over the last 20 or 100 years, moving from a print-based endeavour to an electronic endeavour. That means that researchers who want to disseminate their work have different needs, since it is no longer just about text and images – but also raw data, computer code, multimedia files, etc.At the same time, from a reader’s perspective, there are more and more articles, and it can be a real challenge to keep up with the literature. So it is ever more crucial find relevant article and developer deep insights.
  • At the same time, the scientific article has remained the same over the past centuries. It has moved from print to PDF which has a lot of advantages in terms of delivery and discoverability but the format is still very much the same as centuries ago – geared for one style of reading, inadequate support for electronic material and disconnected from the rest of the world. A format that does not capture the full richness of modern-day research output and does not take full advantage of modern technologies to offer an optimal user experience.
  • GoalsIncrease archiving and sharing of research dataIncrease the value and use of shared data (with metadata)Foster and assist with the credit and impact assessment of research data for the researcher, the institution, and the funding bodiesIncrease the sustainability of data repositoriesPrinciplesOpen data – all data remain open and availableCollaborative – with institutions, the research community, funding bodiesTransparent business model – if we make money, some goes back to fund the repositories
  • Transcript

    • 1. Integrating research data in the Article of the Future Dr. Elena Zudilova-Seinstra, Content Innovation Manager, Journal & Content Technology, STM Journals
    • 2. Outline • Data and Scientific Article • The Article of the Future platform for data integration • Ongoing data-linking initiatives at Elsevier STM Journals • Elsevier “Research Data Services” • Summary
    • 3. Research communication is changing… • Different kinds of modern research output: • articles, data, multimedia, code, ... • More research output: • Need for efficient selection of relevant information and data • Be able to explore, build deep insight efficiently From “print science” to “digital science”
    • 4. … and the scientific article needs to adapt “The Article of the Future” is a project to improve the scientific article so that it allows researchers to optimally communicate scientific research in all (digital) dimensions Article format (PDF) is still very much print-based: • “Ink on paper” • No support for data, multimedia, computer code • Limits validation and reproducibility • Geared towards one style of reading: top-left to bottom-right • Stand-alone - disconnected from relevant, related scientific information
    • 5. Article of the Future: Approach & timeline ◦ Deeply involve researchers through interviews, workshops, forums, surveys, etc. Over 800 people provided feedback. ◦ Focus on domain-specific enhancements – one size does not fit all ◦ Value- adding content and tools that are integrated with the article – no “bells and whistles” ◦ Main focus is on HTML ◦ Novel article display format ◦ Continuous enhancements: The Article of the Future is a framework rather than an end-point solution. Timeline & status ◦ 2009: started with Cell Press ◦ 2011: 13 prototype articles on articleofthefuture.com ◦ 2012: roll-out on ScienceDirect ◦ Ongoing: further enhancements
    • 6. Article of the Future | Presentation The three-pane format Center pane: “Traditional” full- text view, designed for optimal online reading experience Right pane: Additional content & tools. Shown here: reference browser Left pane: efficient navigation & browsing
    • 7. Article of the Future: Presentation, Content, Context 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 – discipline-specific interactive content, executable computer code, multimedia files, and data sets. ◦ Context: Connecting the online article to trustworthy scientific resources to present valuable additional information in the context of the article
    • 8. • Author-provided models (PDB, PSE, MOL/MOL2 format) • Fully 3D – enlarge in canvas • Real-time user interaction • Supports all major browsers and mobile devices (without additional plug-ins) • Huge files: 100s of MBs • Display modes: “ribbon” and “balls & sticks” • 9 participating journals • Molecular biology, food research, biochemistry http://dx.doi.org/10.1016/j.jmb.2012.11.040 http://dx.doi.org/10.1016/j.str.2012.10.007 Article of the Future: Content Interactive Viewer for 3D Molecular Models http://www.elsevier.com/3DMolecularModels
    • 9. Article of the Future: Content Interactive phylogenetic tree viewer http://www.elsevier.com/phylogenetictrees • Explore phylogenetic trees: zoom, search, collapse/expand, change layout, etc. • Integrated into the article • Tree data provided by the authors • Newick and NeXML file formats are supported • 12 participating journals • Phylogenetics, genomics, theoretical biology, etc. • Validation tool http://dx.doi.org/10.1016/j.ympev.2012.08.015 http://dx.doi.org/10.1016/j.ygcen.2012.07.023
    • 10. Article of the Future: Content Collage Executable Paper • Collage authoring tool lets authors capture their “numerical experiment”: data, code, and their relationship • Readers can re-compute results from the paper • Explore and study methodology by changing parameters • All code and data elements are available for download • Pilot with CS journals http://www.elsevier.com/executablepaper http://www.sciencedirect.com/science/article/pii/S0097849313000484 http://www.sciencedirect.com/science/article/pii/S0097849313000472
    • 11. Connecting with Data Repositories • Supplementary material is not always a good solution • Many poor solutions in use: data on PCs, university websites, personal homepages, ... • Data repositories: ◦ Some scientists prefer independent data repositories ◦ Domain-specific coordination ◦ Centralized information “hubs” • “Raw data should be freely accessible to researchers” • Collaboration between Publishers and Data Repositories: ◦ Ensure long-term availability of useful content and context ◦ Coordinate submission process / deposit mechanism
    • 12. DB linking partners of the Elsevier STM Journals ModelDB RunMyCode http://www.elsevier.com/databaselinking EMAGE NIF Dryad
    • 13. Online Linking Schemes ScienceDirect can support different linking arrangements: ◦ Article-level: associate an article with a data set • Example: a data set that underlies the analysis in an article • Could be author-deposited or curated ◦ Entity-level: link entities in articles to relevant data • Examples: taxons, chemicals, proteins, ... • Could be manual tagging: accurate, non-ambiguous, but additional work for the author • Could be text-mining: retrospective, automatic, but less accurate (ambiguities) • Could be embedded applications: enable researchers to interactive explore data while reading the article
    • 14. Article of the Future: Context Data-linking via a DB banner • Link to relevant datasets available in the external (curated) data repository • 10+ active banner linking schemes • In close collaboration with data repositories • Links can be added retrospectively
    • 15. Article of the Future: Context Data-linking based on tagged entities • For entities (concepts) mentioned in an article – proteins, genes, standards planets, cities, etc. • Available for 20+ data repositories • Unique identifiers provided by the authors http://www.elsevier.com/databaselinking 5
    • 16. Article of the Future: Context Application-based linking (e.g., with Protein Data Bank) • Explore protein structures relevant to the article – zoom, rotate, change display settings, etc. • 3D structure data integrated from Protein Data Bank • Unique protein codes provided by the authors • 60+ journals • Biology, biochemistry, neuroscience, food research, etc. • In collaboration with Protein Data Bank http://dx.doi.org/10.1016/j.jmb.2010.05.030
    • 17. Article of the Future: Context Application-based linking with NCBI GenBank • View and analyze sequence data of genes and genomes mentioned in articles • Flip the strands, zoom in/out, zoom to a sequence, go to a specific position to define a track of interest within the sequence, "drag" to another location in the sequence • Unique NCBI accession codes provided by the author • 50+ journals • Genetics, toxicology, neuroscience, etc. • In collaboration with NCBI http://dx.doi.org/10.1016/j.gene.2011.03.004
    • 18. Data articles: Genomics Data Journal Genomics Data is an open access journal that publishes high quality and standardized reports on all aspects of genome-scale analysis • Limited only to nucleic acids analysis • Microarray and Next-Generation Sequencing data • All organisms Journal info: http://www.elsevier.com/locate/gdata Submission: http://ees.elsevier.com/gdata https://basespace.illumina.com/apps/ 144144/Genomics-Data (from BaseSpace)
    • 19. Research Data Services New Division within Elsevier • Goals: explore role of Elsevier in helping: ◦ Archive and share research data ◦ Increase the value and use of data (with metadata) ◦ Credit and impact assessment of research data ◦ Sustainability of data repositories • Principles: ◦ Open data – and open software ◦ Collaborative – work with existing repositories ◦ Transparent and flexible business model http://researchdata.elsevier.com/
    • 20. 2013: Running pilots to explore data preservation Data preservation pilot with Carnegie Mellon: • Tablet app replacing paper lab notebook • Record all aspects during experiment Data preservation pilot with Columbia/NASA: • Enriching and storing NASA’s data on lunar sample (moon rocks) • Develop process to train data curators: what skills are needed? Data integration pilot with Duke: • Scale up image repository including disclosure/annotation services • Build integrated solution to visualize and share medical imaging data The 2013 International Data Rescue Award in the Geosciences Organised by IEDA and Elsevier Research Data Services
    • 21. Summary • Integration of Data and Articles brings value to researchers • The Article of the Future provides a new platform for improved online presentation, rich content, and valuable context from data repositories (and other resources) • Applications provide tools to directly integrate data and articles • Elsevier is working together with a great number of data repositories to establish article/entity-based linking and building applications together • “Research Data Services” is a new research group exploring how Elsevier can help researchers share and annotate data Thank you! e.zudilova-seinstra@elsevier.com

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