Enhanced publication

Enhanced publications or enhanced ebooks are a form of electronic publishing for the dissemination and sharing of research outcomes, which first formal definition can be tracked back to 2009. [1] As many forms of digital publications, they typically feature a unique identifier Persistent identification ) and descriptive metadata information. Unlike traditional digital publications (eg PDF article), enhanced publications are often tailored to serve specific scientific domains and are generally constituted by a set of interconnected parts (eg datasets, videos, images, stylesheets, services, workflows , Databases, Presentations) and to textual descriptions of the research (eg papers, chapters, sections, tables). The nature and format of such parts and of the relationships between them, depends on the application domain and may vary widely 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 paper is a compilation of a series of research papers on the subject of research and development. Web 2.0 reading capabilities; Interlinking research outputs; Re-production and assessment of scientific experiments.

Packaging of related research assets

The first enhancement to move beyond the mare digitization of the publication and investigate new avenues in the digital scholarly communication was likely accompanying a digital publication (eg PDF file) with supplementary material. In such scenarios, scientists can share the results of the 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 methods focuses on enhancing the quality and quality of the materials used. 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, TK, Kell, DB, McDermott, P. Marsh, J. Pettifer, SR, & Thorne, D. (2010) [12]
Rich Internet Publications Breure, Voorbij, & Hoogerwerf (2011) [13]
SOLE Pham, Malik, Foster, Di Lauro, and Montella (2012) [14]
Elsevier’s Article of the Future Aalbersberg IJ Heeman, F., Koers, H., & Zudilova-Seinstra, E. (2012) [15]
Bookshelf Hoeppner (2013) [16]

Interlinking research outputs

Scientific communities, organizations, and funding agencies 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 provide common metadata information and persistent identifiers to datasets and publications. Data publishing and citation practices are advocated by research communities that believe that data should be discoverable and reusable in order to improve the scientific activity. [22] [23] On this respect, And the discipline specific databases. (2). The existence of links between literature and data support, and the reliability of the data.

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]
IN 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 Mash 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. Jump up^ Vernooy-Gerritsen, Marjan (2009). Emerging standards for enhanced publications and repository technology: survey on technology . Amsterdam University Press.
  2. Jump up^ “FORCE11 initiative” .
  3. Jump up^ “Elsevier Supplementary Data policies” .
  4. Jump up^ “SAGE Journals: Author Guide to Supplementary Files” .
  5. Jump up^ 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. Jump up^ Gerber, A .; Hunter, J. (2010). “Authoring, editing and visualizing compound objects for literary scholarship” . Journal of digital information. 11 (1). ISSN  1368-7506 .
  7. Jump up^ Jankowski, NW; 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. Jump up^ 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. ISBN  978-3-540-30850-8 . Doi :10.1007 / 11599517_2 .
  9. Jump up^ Fink, J. Lynn; Bourne, Philip E. (2007). “Reinventing scholarly communication for the electronic age” . CTWatch Quarterly . 3 (3).
  10. Jump up^ 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. PMC  2663789  . PMID  19381256 . Doi : 10.1371 / journal.pcbi.1000361 .
  11. Jump up^ van den Heuvel, H .; Van Horik, R .; Scagliola, SI; Sanders, EP; 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 January 27,2014 .
  12. Jump up^ Attwood, TK ; Kell, DB ; McDermott, P .; Marsh, J .; Pettifer, SR ; Thorne, D. (2010). “Utopia documents: Linking scholarly literature with research data” . Bioinformatics . 26 (18): 1568-1574. PMC  2935404  . PMID  20823323 . Doi : 10.1093 / bioinformatics / btq383 .
  13. Jump up^ Breure, L .; Voorbij, H .; Hoogerwerf, M. (2011). “Rich Internet Publications:” Show What You Tell ” ” . Journal of Digital Information . 12 (1).
  14. Jump up^ 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. ISBN  978-3-642-34221-9 . Doi : 10.1007 / 978-3-642-34222-6_16 .
  15. Jump up^ Zudilova-Seinstra, E .; Koers, H .; Heeman, F .; Aalbersberg, IJ (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. Jump up^ Hoeppner, MA (2012). “NCBI Bookshelf: Books and papers in life sciences and health care” . Nucleic Acids Research . 41 : D1251. PMC  3531209  . PMID  23203889 . Doi : 10.1093 / nar / gks1279 .
  17. Jump up^ 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. Jump up^ 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. Jump up^ “DataCite” . Retrieved January 27, 2014 .
  20. Jump up^ “EPIC – European Persist Identifier Consortium” . Retrieved January 28, 2014 .
  21. Jump up^ “CrossRef” . Retrieved January 27, 2014 .
  22. Jump up^ 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 Centers”. International Journal of Digital Curation . 7 : 107-113. Doi : 10.2218 / ijdc.v7i1.218 .
  23. Jump up^ Parsons, MA; Fox, PA (2013). “Is Data Publication the Right Metaphor?”. Data Science Journal . 12 : WDS32. Doi : 10.2481 / dsj.wds-042 .
  24. Jump up^ 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. Jump up^ Pepe, A .; Mayernik, M .; Borgman, CL; Van de Sompel, H. (2009). “Technology to Represent Scientific Practice: Data, Life Cycles, and Value Chains” .
  26. Jump up^ McEntyre, JR; Ananiadou, S .; Andrews, S .; Black, WJ; 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, SJ; 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 for life sciences” . Nucleic Acids Research . 39(Database issue): D58-D65. PMC  3013671  . PMID  21062818 . Doi :10.1093 / nar / gkq1063 .
  27. Jump up^ Yook, K .; Harris, TW; Bieri, T .; Cabunoc, A .; Chan, J .; Chen, WJ; 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, EM; Ann Tuli, M .; Van Auken, K .; Wang, D. (2011). “Worm Base 2012: More genomes, more data, new website” . Nucleic Acids Research . 40 : D735. PMC  3245152  . PMID  22067452 . Doi : 10.1093 / nar / gkr954 .
  28. Jump up^ Farace, DJ; Frantzen, J .; Stock, C .; Sesink, L .; Rabina, DL (2012). “Linking full-text gray literature to underlying research and post-publication data: An Enhanced Publications Project 2011-2012” (PDF) . The Gray journal . 8 (3): 181-189.
  29. Jump up^ 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. Jump up^ Hoogerwerf, M. (2009). “Durable enhanced publications” (PDF) . Proceedings of African Digital Scholarship & Curation . Retrieved January 27, 2014 .
  31. Jump up^ Hunter, Jane (2006). Scientific Models: A User-oriented Approach to the Integration of Scientific Data and Digital Libraries . VALA2006. pp. 1-16. Retrieved January 27, 2014 .
  32. Jump up^ 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. Jump up^ Hunter, J .; Cheung, K. (2007). “Provenance Explorer-a graphical interface for constructing scientific publications from provenance trails”. International Journal on Digital Libraries . 7 : 99-107. Doi : 10.1007 / s00799-007-0018-5 .
  34. Jump up^ De Roure, D .; Goble, C .; Stevens, R. (2009). “The design and realization 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. Jump up^ Bechhofer, S .; Bechhofer, S .; From 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. Jump up^ 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. Jump up^ Brammer, GR; Crosby, RW; Matthews, SJ; Williams, TL (2011). “Paper Mash: Creating Dynamic Reproducible Science”. Procedia Computer Science . 4 : 658-667. Doi : 10.1016 / j.procs.2011.04.069 .
  38. Jump up^ 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. Jump up^ 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. Jump up^ 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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