Enhanced publication

Enhanced publications or enhanced ebooks are a form of electronic publishing for the dissemination and sharing of research outcomes, whose first formal definition can be tracked back to 2009.[1] As many forms of digital publications, they typically feature a unique identifier (possibly a persistent identifier) and descriptive metadata information. Unlike traditional digital publications (e.g. PDF article), enhanced publications are often tailored to serve specific scientific domains and are generally constituted by a set of interconnected parts corresponding to research assets of several kinds (e.g. datasets, videos, images, stylesheets, services, workflows, databases, presentations) and to textual descriptions of the research (e.g. papers, chapters, sections, tables). The nature and format of such parts and of the relationships between them, depends on the application domain and may largely vary from case to case.

The main motivations behind enhanced publications are to be found in the limitations of traditional scientific literature to describe the whole context and outcome of a research activity. Their goal is to move "beyond the simple PDF" (FORCE11 initiative[2]) and support scientists with advanced ICT tools for sharing their research more comprehensively, without losing the narrative spirit of "the publication" as dissemination means. This trend is confirmed by the several enhanced publication systems devised in the literature, offering to research communities one or more of the following functionalities: Packaging of related research assets; Web 2.0 reading capabilities; Interlinking research outputs; Re-production and assessment of scientific experiments.

Packaging of related research assets

The first enhancement introduced to move beyond the mare digitization of the publication and investigate new avenues in the digital scholarly communication was likely accompanying a digital publication (e.g. PDF file) with supplementary material. In such scenarios, scientists can share packages consisting of publication and supplementary material in an attempt to better deliver hypothesis and results of the research presented in the publication.

Enhanced Publication system References
Journals with supplementary material policies Elsevier Supplementary Data policies,[3] SAGE Journals: Author Guide to Supplementary Files[4]
Modular Article Kircz, Joost G. (2002)[5]
LORE Gerber, A., & Hunter, J. (2010)[6]

Web 2.0 reading capabilities

This category of approaches focuses on enhanced publication data models whose parts, metadata and relationships are defined with the purpose of improving the end-user experience when visualizing and discovering research materials. These approaches are the natural extension of the traditional publication, oriented to reading, and typically integrate all tools made available by the web infrastructure and its data sources.[7] Specifically, they explore the possibilities of:

  1. structuring narrative text into interconnected sub-parts;
  2. re-using the universe of web resources to enrich the text;
  3. including dynamic forms of content within the text.
Enhanced Publication system References
D4Science Live documents Candela, L., Castelli, D., Pagano P., & Simi, M. (2005)[8]
SciVee Fink & Bourne (2007)[9]
PLOS Neglected Tropical Diseases Shotton, Portwin, Klyne, & Miles (2009)[10]
The Veteran Tapes Project van den Heuvel, van Horik, Sanders, Scagliola, & Witkamp (2010)[11]
Utopia Documents Attwood, T. K., Kell, D. B., McDermott, P., Marsh, J., Pettifer, S. R., & Thorne, D. (2010)[12]
Rich Internet Publications Breure, Voorbij, & Hoogerwerf (2011)[13]
SOLE Pham, Malik, Foster, Di Lauro, & Montella (2012)[14]
Elsevier's Article of the Future Aalbersberg, I. J., Heeman, F., Koers, H., & Zudilova-Seinstra, E. (2012)[15]
Bookshelf Hoeppner (2013)[16]

Interlinking research outputs

Scientific communities, organizations, and funding agencies supports initiatives, standards and best practices for publishing and citing datasets and publications on the web.[17][18] Examples are DataCite,[19] EPIC[20] and CrossRef,[21] which establish common best practices to assign metadata information and persistent identifiers to datasets and publications. Data publishing and citation practices are advocated by research communities that believe that datasets should be discoverable and reusable in order to improve the scientific activity.[22][23] On this respect, several enhanced publication information systems were built to offer the possibility to enrich a publication with links to relevant research data, possibly deposited in data repositories or discipline specific databases. The existence of links between literature and data support the discovery of used and produced scientific data, strengthen data citation, facilitate data re-use, and reward the precious work underlying data management procedures.

Enhanced Publication system References
SCOPE Cheung, Hunter, Lashtabeg, & Drennan (2008)[24]
CENS ORE Aggregations Pepe, Mayernik, Borgman and Van de Sompel (2009) [25]
europePMC McEntyre et al. (2011)[26]
WormBase Yook et al. (2012)[27]
DANS Enhanced Publication Project Farace, Frantzen, Stock, Sesink, & Rabina (2012)[28]
BioTea Garcia et al. (2013)[29]
OpenAIRE multi-disciplinary Enhanced Publications Hoogerwerf et al. (2013)[30]

Re-production and assessment of scientific experiments

Scientists should be equipped with the facilities necessary to repeat or reproduce somebody else's experiment. In enhanced publications with executable parts, narrative parts are accompanied by executable workflows with the purpose of reproducing and repeating experiments.

Enhanced Publication system References
Scientific Model Packages Hunter (2006a),[31] Hunter (2006b),[32] Hunter & Cheung (2007)[33]
MyExperiment (Research Objects) De Roure et al. (2009),;[34] Bechhofer, Soure, Gamble, Goble, & Buchan (2010)[35]
IODA Siciarek and Wiszniewski (2011)[36]
Paper Mâché Brammer, Crosby, Matthews, & Williams (2011)[37]
Collage Authoring Environment Nowakowski et al. (2011)[38]
SciCrunch's RRIDs Jeffrey et al. (2014)[39]
SHARE Van Gorp & Mazanek (2011)[40]

References

  1. ↑ Vernooy-Gerritsen, Marjan (2009). Emerging standards for enhanced publications and repository technology: survey on technology. Amsterdam University Press.
  2. ↑ "FORCE11 initiative".
  3. ↑ "Elsevier Supplementary Data policies".
  4. ↑ "SAGE Journals: Author Guide to Supplementary Files".
  5. ↑ Kircz, Joost G. (2002). "New practices for electronic publishing 2: New forms of the scientific paper". Learned Publishing (Association of Learned and Professional Society Publishers) 15 (1): 27–32. doi:10.1087/095315102753303652.
  6. ↑ Gerber, A.; Hunter, J. (2010). "Authoring, editing and visualizing compound objects for literary scholarship". Journal of digital information 11 (1). ISSN 1368-7506.
  7. ↑ Jankowski, N. W.; Scharnhorst, A.; Tatum, C.; Tatum, Z. (2013). "Enhancing scholarly publications: Developing hybrid monographs in the humanities and social sciences". Scholarly and Research Communication 4 (1).
  8. ↑ Candela, L.; Castelli, D.; Pagano, P.; Simi, M. (2005). "From Heterogeneous Information Spaces to Virtual Documents". Digital Libraries: Implementing Strategies and Sharing Experiences. Lecture Notes in Computer Science 3815. p. 11. doi:10.1007/11599517_2. ISBN 978-3-540-30850-8.
  9. ↑ Fink, J. Lynn; Bourne, Philip E. (2007). "Reinventing scholarly communication for the electronic age". CTWatch Quarterly 3 (3).
  10. ↑ Shotton, D.; Portwin, K.; Klyne, G.; Miles, A. (2009). Bourne, Philip E, ed. "Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article". PLoS Computational Biology 5 (4): e1000361. doi:10.1371/journal.pcbi.1000361. PMC: 2663789. PMID 19381256.
  11. ↑ van den Heuvel, H.; van Horik, R.; Scagliola, S. I.; Sanders, E. P.; Witkamp, P. (2010). "The VeteranTapes: Research Corpus, Fragment Processing Tool, and Enhanced Publications for the e-Humanities". Proceedings of LREC. 7th International Conference on Language Resources and Evaluation (LREC). pp. 2687–2692. Retrieved 27 January 2014.
  12. ↑ Attwood, T. K.; Kell, D. B.; McDermott, P.; Marsh, J.; Pettifer, S. R.; Thorne, D. (2010). "Utopia documents: Linking scholarly literature with research data". Bioinformatics 26 (18): i568–i574. doi:10.1093/bioinformatics/btq383. PMC: 2935404. PMID 20823323.
  13. ↑ Breure, L.; Voorbij, H.; Hoogerwerf, M. (2011). "Rich Internet Publications: "Show What You Tell"". Journal of Digital Information 12 (1).
  14. ↑ Pham, Q.; Malik, T.; Foster, I.; Lauro, R.; Montella, R. (2012). "SOLE: Linking Research Papers with Science Objects". Provenance and Annotation of Data and Processes. Lecture Notes in Computer Science 7525. p. 203. doi:10.1007/978-3-642-34222-6_16. ISBN 978-3-642-34221-9.
  15. ↑ Zudilova-Seinstra, E.; Koers, H.; Heeman, F.; Aalbersberg, I. J. (2012). "Elsevier's Article of the Future enhancing the user experience and integrating data through applications". Insights: the UKSG journal 25: 33–43. doi:10.1629/2048-7754.25.1.33.
  16. ↑ Hoeppner, M. A. (2012). "NCBI Bookshelf: Books and documents in life sciences and health care". Nucleic Acids Research 41: D1251. doi:10.1093/nar/gks1279. PMC: 3531209. PMID 23203889.
  17. ↑ Reilly, A.; Schallier, W.; Schrimpf, S.; Smit, E.; Wilkinson, M. (2013). "Report on integration of data and publications". Scholarly and Research Communication 4 (1).
  18. ↑ Mooney, H.; Newton, M. (2012). "The Anatomy of a Data Citation: Discovery, Reuse, and Credit". Journal of Librarianship and Scholarly Communication 1. doi:10.7710/2162-3309.1035.
  19. ↑ "DataCite". Retrieved 27 January 2014.
  20. ↑ "EPIC - European Persistent Identifier Consortium". Retrieved 28 January 2014.
  21. ↑ "CrossRef". Retrieved 27 January 2014.
  22. ↑ Callaghan, S.; Donegan, S.; Pepler, S.; Thorley, M.; Cunningham, N.; Kirsch, P.; Ault, L.; Bell, P.; Bowie, R.; Leadbetter, A.; Lowry, R.; Moncoiffé, G.; Harrison, K.; Smith-Haddon, B.; Weatherby, A.; Wright, D. (2012). "Making Data a First Class Scientific Output: Data Citation and Publication by NERC's Environmental Data Centres". International Journal of Digital Curation 7: 107–113. doi:10.2218/ijdc.v7i1.218.
  23. ↑ Parsons, M. A.; Fox, P. A. (2013). "Is Data Publication the Right Metaphor?". Data Science Journal 12: WDS32. doi:10.2481/dsj.wds-042.
  24. ↑ Cheung, K.; Hunter, J.; Lashtabeg, A.; Drennan, J. (2008). "SCOPE: A Scientific Compound Object Publishing and Editing System". International Journal of Digital Curation 3 (2): 4–18. doi:10.2218/ijdc.v3i2.55.
  25. ↑ Pepe, A.; Mayernik, M.; Borgman, C. L.; van de Sompel, H. (2009). "Technology to Represent Scientific Practice: Data, Life Cycles, and Value Chains".
  26. ↑ McEntyre, J. R.; Ananiadou, S.; Andrews, S.; Black, W. J.; Boulderstone, R.; Buttery, P.; Chaplin, D.; Chevuru, S.; Cobley, N.; Coleman, L. -A.; Davey, P.; Gupta, B.; Haji-Gholam, L.; Hawkins, C.; Horne, A.; Hubbard, S. J.; Kim, J. -H.; Lewin, I.; Lyte, V.; MacIntyre, R.; Mansoor, S.; Mason, L.; McNaught, J.; Newbold, E.; Nobata, C.; Ong, E.; Pillai, S.; Rebholz-Schuhmann, D.; Rosie, H.; Rowbotham, R. (2010). "UKPMC: A full text article resource for the life sciences". Nucleic Acids Research 39 (Database issue): D58–D65. doi:10.1093/nar/gkq1063. PMC: 3013671. PMID 21062818.
  27. ↑ Yook, K.; Harris, T. W.; Bieri, T.; Cabunoc, A.; Chan, J.; Chen, W. J.; Davis, P.; de la Cruz, N.; Duong, A.; Fang, R.; Ganesan, U.; Grove, C.; Howe, K.; Kadam, S.; Kishore, R.; Lee, R.; Li, Y.; Muller, H. -M.; Nakamura, C.; Nash, B.; Ozersky, P.; Paulini, M.; Raciti, D.; Rangarajan, A.; Schindelman, G.; Shi, X.; Schwarz, E. M.; Ann Tuli, M.; Van Auken, K.; Wang, D. (2011). "Worm Base 2012: More genomes, more data, new website". Nucleic Acids Research 40: D735. doi:10.1093/nar/gkr954.
  28. ↑ Farace, D. J.; Frantzen, J.; Stock, C.; Sesink, L.; Rabina, D. L. (2012). "Linking full-text grey literature to underlying research and post-publication data: An Enhanced Publications Project 2011-2012" (PDF). The Grey journal 8 (3): 181–189.
  29. ↑ Garcia Castro, L.; McLaughlin, C.; Garcia, A. (2013). "Biotea: RDFizing Pub Med Central in support for the paper as an interface to the Web of Data". Journal of Biomedical Semantics 4: S5. doi:10.1186/2041-1480-4-S1-S5.
  30. ↑ Hoogerwerf, M. (2009). "Durable enhanced publications" (PDF). Proceedings of African Digital Scholarship & Curation. Retrieved 27 January 2014.
  31. ↑ Hunter, Jane (2006). Scientific Models: A User-oriented Approach to the Integration of Scientific Data and Digital Libraries. VALA2006. pp. 1–16. Retrieved 27 January 2014.
  32. ↑ Hunter, J. (2006). "Scientific Publication Packages – A Selective Approach to the Communication and Archival of Scientific Output". International Journal of Digital Curation 1: 33–52. doi:10.2218/ijdc.v1i1.4.
  33. ↑ Hunter, J.; Cheung, K. (2007). "Provenance Explorer-a graphical interface for constructing scientific publication packages from provenance trails". International Journal on Digital Libraries 7: 99–107. doi:10.1007/s00799-007-0018-5.
  34. ↑ De Roure, D.; Goble, C.; Stevens, R. (2009). "The design and realisation of the myExperiment Virtual Research Environment for social sharing of workflows". Future Generation Computer Systems 25 (5): 561–567. doi:10.1016/j.future.2008.06.010.
  35. ↑ Bechhofer, S.; Bechhofer, S.; De Roure, D.; Gamble, M.; Goble, C.; Buchan, I. (2010). "Research Objects: Towards Exchange and Reuse of Digital Knowledge". Nature Precedings. doi:10.1038/npre.2010.4626.1.
  36. ↑ Siciarek, J.; Wiszniewski, B. (2011). "IODA - an Interactive Open Document Architecture". Procedia Computer Science 4: 668–677. doi:10.1016/j.procs.2011.04.070.
  37. ↑ Brammer, G. R.; Crosby, R. W.; Matthews, S. J.; Williams, T. L. (2011). "Paper Mâché: Creating Dynamic Reproducible Science". Procedia Computer Science 4: 658–667. doi:10.1016/j.procs.2011.04.069.
  38. ↑ Nowakowski, P.; Ciepiela, E.; Harężlak, D.; Kocot, J.; Kasztelnik, M.; Bartyński, T.; Meizner, J.; Dyk, G.; Malawski, M. (2011). "The Collage Authoring Environment". Procedia Computer Science 4: 608–617. doi:10.1016/j.procs.2011.04.064.
  39. ↑ Jeffrey, Grethe; Anita, Bandrowski; Davis, Banks; Christopher, Condit; Amarnath, Gupta; Stephen, Larson; Yueling, Li; Ibrahim, Ozyurt; Andrea, Stagg; Patricia, Whetzel; Luis, Marenco; Perry, Miller; Rixin, Wang; Gordon, Shepherd; Maryann, Martone (2014). "SciCrunch: A cooperative and collaborative data and resource discovery platform for scientific communities". Frontiers in Neuroinformatics 8. doi:10.3389/conf.fninf.2014.18.00069.
  40. ↑ Van Gorp, P.; Mazanek, S. (2011). "SHARE: A web portal for creating and sharing executable research papers". Procedia Computer Science 4: 589–597. doi:10.1016/j.procs.2011.04.062.
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