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A Framework for Citing Nanopublications

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Digital Libraries for Open Knowledge (TPDL 2019)

Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 11799))

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Abstract

In this paper we discuss the role of the Nanopublication (nanopub) model for scholarly publications with particular focus on the citation of nanopubs.

To this end, we contribute to the state-of-the-art in data citation by proposing: the nanocitation framework that defines the main steps to create a text snippet and a machine-readable citation given a single nanopub; an ad-hoc metadata schema for encoding nanopub citations; and, an open-source and publicly available citation system.

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Notes

  1. 1.

    https://www.drugbank.ca/.

  2. 2.

    http://www.disgenet.org.

  3. 3.

    https://www.globalbioticinteractions.org/.

  4. 4.

    http://emto-nanopub.referata.com/wiki/EMTO_Nanopub.

  5. 5.

    https://mith.umd.edu/research/enhancing-music-notation-addressability/.

  6. 6.

    https://dm2e.eu/open-humanities-awards-early-modern-european-peace-treaties-online-final-update/.

  7. 7.

    http://nanopub.org/.

  8. 8.

    https://www.wikipathways.org.

  9. 9.

    https://www.nextprot.org.

  10. 10.

    https://orcid.org/.

  11. 11.

    https://www.proteinatlas.org/.

  12. 12.

    https://www.ncbi.nlm.nih.gov/.

  13. 13.

    http://linkedlifedata.com.

  14. 14.

    https://www.ncbi.nlm.nih.gov.

  15. 15.

    https://spring.io/.

  16. 16.

    https://www.thymeleaf.org/.

References

  1. Out of Cite, Out of Mind: The Current State of Practice, Policy, and Technology for the Citation of Data, vol. 12. CODATA-ICSTI Task Group on Data Citation Standards and Practices, September 2013

    Google Scholar 

  2. DataCite Metadata Schema Documentation for the Publication and Citation of Research Data, Version 4.0. Technical Report, DataCite Metadata Working Group (2016)

    Google Scholar 

  3. Alawini, A., Davidson, S.B., Silvello, G., Tannen, V., Wu, Y.: Data citation: a new provenance challenge. IEEE Data Eng. Bull. 41(1), 27–38 (2018)

    Google Scholar 

  4. Altman, M., King, G.: A proposed standard for the scholarly citation of quantitative data. D-Lib Mag. 13(3/4) (2007)

    Google Scholar 

  5. Borgman, C.L.: Big Data, Little Data, No Data. MIT Press, Cambridge (2015)

    Book  Google Scholar 

  6. Buneman, P., Davidson, S.B., Frew, J.: Why data citation is a computational problem. Commun. ACM (CACM) 59(9), 50–57 (2016)

    Article  Google Scholar 

  7. Candela, L., Castelli, D., Manghi, P., Tani, A.: Data journals: a survey. J. Assoc. Inf. Sci. Technol. 66(9), 1747–1762 (2015)

    Article  Google Scholar 

  8. Carroll, J., Bizer, C., Hayes, P., Stickler, P.: Semantic web publishing using named graphs. In: Proceedings of the ISWC 2004 Workshop on Trust, Security, and Reputation on the Semantic Web. CEUR Workshop Proceedings, vol. 127. CEUR-WS.org (2004)

    Google Scholar 

  9. Davidson, S.B., Buneman, P., Deutch, D., Milo, T., Silvello, G.: Data citation: a computational challenge. In: Proceedings of the 36th ACM Symposium on Principles of Database Systems, PODS 2017, pp. 1–4. ACM Press (2017)

    Google Scholar 

  10. FORCE-11: Data Citation Synthesis Group: Joint Declaration of Data Citation Principles. FORCE11, San Diego, CA, USA (2014)

    Google Scholar 

  11. Gibson, A.P., van Dam, J.C.J., Schultes, E., Roos, M., Mons, B.: Towards computational evaluation of evidence for scientific assertions with nanopublications. In: Proceedings of the 5th International Workshop on Semantic Web Applications and Tools for Life Sciences (2012)

    Google Scholar 

  12. Golden, P., Shaw, R.: Period assertion as nanopublication: the PeriodO period gazetteer. In: Proceedings of the 24th International Conference on World Wide Web, WWW 2015 Companion, pp. 1013–1018. ACM Press (2015)

    Google Scholar 

  13. Green, T.: We need publishing standards for datasets and data tables. Technical report. OECD Publishing (2010)

    Google Scholar 

  14. Groth, P., Gibson, A., Velterop, J.: The anatomy of a nanopublication. Inf. Serv. Use 30(1–2), 51–56 (2010)

    Article  Google Scholar 

  15. Heath, T., Bizer, C.: Linked Data: Evolving the Web into a Global Data Space. Synthesis Lectures on the Semantic Web: Theory and Technology. Morgan & Claypool Publishers, San Rafael (2011)

    Google Scholar 

  16. Hey, T., Tansley, S., Tolle, K. (eds.): The Fourth Paradigm: Data-Intensive Scientific Discovery. Microsoft Research, Redmond (2009)

    Google Scholar 

  17. Klyne, G., Carroll, J.J.: Resource description framework (RDF): concepts and abstract syntax. Technical report W3C (2004)

    Google Scholar 

  18. Kuhn, T.: nanopub-java: a Java library for nanopublications. In: Proceedings of the 5th Workshop on Linked Science 2015 co-located with (ISWC 2015). CEUR Workshop Proceedings, vol. 1572, pp. 19–25. CEUR-WS.org (2015)

    Google Scholar 

  19. Kuhn, T., et al.: Decentralized provenance-aware publishing with nanopublications. PeerJ Comput. Sci. 2, e78 (2016)

    Article  Google Scholar 

  20. Kuhn, T., et al.: Nanopublications: a growing resource of provenance-centric scientific linked data. In: 14th IEEE International Conference on e-Science, pp. 83–92. IEEE Computer Society (2018)

    Google Scholar 

  21. Kuhn, T., Willighagen, E., Evelo, C., Queralt-Rosinach, N., Centeno, E., Furlong, L.I.: Reliable granular references to changing linked data. In: d’Amato, C., et al. (eds.) ISWC 2017. LNCS, vol. 10587, pp. 436–451. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-68288-4_26

    Chapter  Google Scholar 

  22. Mons, B., et al.: The value of data. Nat. Genetics 43(4), 281–283 (2011)

    Article  Google Scholar 

  23. Piñero, J., et al.: DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants. Nucleic Acids Res. 45(D1), D833–D839 (2017)

    Article  Google Scholar 

  24. Queralt-Rosinach, N., Piñero, J., Bravo, À., Sanz, F., Furlong, L.: DisGeNET-RDF: harnessing the innovative power of the semantic web to explore the genetic basis of diseases. Bioinformatics 32(14), 2236–2238 (2016)

    Article  Google Scholar 

  25. Rauber, A., Ari, A., van Uytvanck, D., Pröll, S.: Identification of reproducible subsets for data citation, sharing and re-use. Bull. IEEE Techn. Comm. Digit. Libr. Spec. Issue Data Cit. 12(1), 6–15 (2016)

    Google Scholar 

  26. Silvello, G.: Learning to cite framework: how to automatically construct citations for hierarchical data. J. Assoc. Inf. Sci. Technol. (JASIST) 68(6), 1505–1524 (2017)

    Article  Google Scholar 

  27. Silvello, G.: Theory and practice of data citation. J. Assoc. Inf. Sci. Technol. (JASIST) 69(1), 6–20 (2018)

    Article  Google Scholar 

  28. Starr, J., Gastl, A.: isCitedBy: a metadata scheme for DataCite. D-Lib Mag. 17(1/2) (2011)

    Google Scholar 

  29. Wu, Y., Alawini, A., Davidson, S.B., Silvello, G.: Data citation: giving credit where credit is due. In: Proceedings of the 2018 International Conference on Management of Data, SIGMOD Conference 2018, pp. 99–114. ACM Press (2018)

    Google Scholar 

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Acknowledgments

The work was partially funded by the “Computational Data Citation” (CDC) STARS-StG project of the University of Padua. The work was also partially funded by the EXAMODE (contract n. 825292) part of the H2020-ICT-2018-2 call of the European Commission.

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Authors and Affiliations

  1. Department of Information Engineering, University of Padua, Padua, Italy

    Erika Fabris & Gianmaria Silvello

  2. Department of Computer Science, VU University Amsterdam, Amsterdam, The Netherlands

    Tobias Kuhn

Authors
  1. Erika Fabris
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  2. Tobias Kuhn
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  3. Gianmaria Silvello
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Corresponding author

Correspondence to Erika Fabris .

Editor information

Editors and Affiliations

  1. University of La Rochelle, La Rochelle, France

    Antoine Doucet

  2. VU University Amsterdam, Amsterdam, The Netherlands

    Antoine Isaac

  3. Linnaeus University, Växjö, Sweden

    Koraljka Golub

  4. OsloMet – Oslo Metropolitan University, Oslo, Norway

    Trond Aalberg

  5. Kyoto University, Kyoto, Japan

    Adam Jatowt

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Fabris, E., Kuhn, T., Silvello, G. (2019). A Framework for Citing Nanopublications. In: Doucet, A., Isaac, A., Golub, K., Aalberg, T., Jatowt, A. (eds) Digital Libraries for Open Knowledge. TPDL 2019. Lecture Notes in Computer Science(), vol 11799. Springer, Cham. https://doi.org/10.1007/978-3-030-30760-8_6

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  • DOI: https://doi.org/10.1007/978-3-030-30760-8_6

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  • Online ISBN: 978-3-030-30760-8

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