Reliable Granular References to Changing Linked Data

  • Tobias Kuhn
  • Egon Willighagen
  • Chris Evelo
  • Núria Queralt-Rosinach
  • Emilio Centeno
  • Laura I. Furlong
Conference paper
First Online:
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10587)

Abstract

Nanopublications are a concept to represent Linked Data in a granular and provenance-aware manner, which has been successfully applied to a number of scientific datasets. We demonstrated in previous work how we can establish reliable and verifiable identifiers for nanopublications and sets thereof. Further adoption of these techniques, however, was probably hindered by the fact that nanopublications can lead to an explosion in the number of triples due to auxiliary information about the structure of each nanopublication and repetitive provenance and metadata. We demonstrate here that this significant overhead disappears once we take the version history of nanopublication datasets into account, calculate incremental updates, and allow users to deal with the specific subsets they need. We show that the total size and overhead of evolving scientific datasets is reduced, and typical subsets that researchers use for their analyses can be referenced and retrieved efficiently with optimized precision, persistence, and reliability.

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Notes

Acknowledgments

We would like to thank Javier D. Fernández for valuable input and discussions on RDF versioning. L.I. Furlong and E. Centeno received support from ISCIII-FEDER (PI13/00082, CP10/00524, CPII16/00026), the EU H2020 Programme 2014-2020 under grant agreements no. 634143 (MedBioinformatics) and no. 676559 (Elixir-Excelerate).

References

  1. 1.
    Auer, S., Herre, H.: A versioning and evolution framework for RDF knowledge bases. In: Virbitskaite, I., Voronkov, A. (eds.) PSI 2006. LNCS, vol. 4378, pp. 55–69. Springer, Heidelberg (2007). doi: 10.1007/978-3-540-70881-0_8 CrossRefGoogle Scholar
  2. 2.
    Banda, J.M., Kuhn, T., Shah, N.H., Dumontier, M.: Provenance-centered dataset of drug-drug interactions. In: Arenas, M., et al. (eds.) ISWC 2015. LNCS, vol. 9367, pp. 293–300. Springer, Cham (2015). doi: 10.1007/978-3-319-25010-6_18 CrossRefGoogle Scholar
  3. 3.
    Belleau, F., Nolin, M.-A., Tourigny, N., Rigault, P., Morissette, J.: Bio2RDF: towards a mashup to build bioinformatics knowledge systems. J. Biomed. Inf. 41(5), 706–716 (2008)CrossRefGoogle Scholar
  4. 4.
    Bohler, A., Wu, G., Kutmon, M., Pradhana, L.A., Coort, S.L., Hanspers, K., Haw, R., Pico, A.R., Evelo, C.T.: Reactome from a WikiPathways perspective. PLoS Comput. Biol. 12(5), e1004941 (2016)CrossRefGoogle Scholar
  5. 5.
    Chard, K., D’Arcy, M., Heavner, B., Foster, I., Kesselman, C., Madduri, R., Rodriguez, A., Soiland-Reyes, S., Goble, C., Clark, K., et al.: I’ll take that to go: Big data bags and minimal identifiers for exchange of large, complex datasets. In: IEEE International Conference on Big Data, pages 319–328. IEEE (2016)Google Scholar
  6. 6.
    Chichester, C., Karch, O., Gaudet, P., Lane, L., Mons, B., Bairoch, A.: Converting nextprot into linked data and nanopublications. Semant. Web 6(2), 147–153 (2015)Google Scholar
  7. 7.
    Cohen, J.P., Lo, H.Z.: Academic torrents: A community-maintained distributed repository. In: Proceedings of XSEDE 2014, p. 2. ACM (2014)Google Scholar
  8. 8.
    Fabregat, A., et al.: The reactome pathway knowledgebase. Nucleic Acids Res. 44(D1), D481–D487 (2016)CrossRefGoogle Scholar
  9. 9.
    Fernández, J.D. Polleres, A., Umbrich, J.: Towards efficient archiving of dynamic linked open data. In: DIACRON@ESWC, pp. 34–49 (2015)Google Scholar
  10. 10.
    Frommhold, M., Piris, R.N., Arndt, N., Tramp, S., Petersen, N., Martin, M.: Towards versioning of arbitrary RDF data. In: Proceedings of the 12th International Conference on Semantic Systems, pp. 33–40. ACM (2016)Google Scholar
  11. 11.
    Graube, M. Hensel, S., Urbas, L.: R43ples: revisions for triples. In Proceedings of the 1st Workshop on Linked Data Quality. Citeseer (2014)Google Scholar
  12. 12.
    Groth, P., Gibson, A., Velterop, J.: The anatomy of a nanopublication. Inf. Serv. Use 30(1–2), 51–56 (2010)CrossRefGoogle Scholar
  13. 13.
    Käfer, T., Abdelrahman, A., Umbrich, J., O’Byrne, P., Hogan, A.: Observing linked data dynamics. In: Cimiano, P., Corcho, O., Presutti, V., Hollink, L., Rudolph, S. (eds.) ESWC 2013. LNCS, vol. 7882, pp. 213–227. Springer, Heidelberg (2013). doi: 10.1007/978-3-642-38288-8_15 CrossRefGoogle Scholar
  14. 14.
    Kuhn, T.: Nanopub-java: a java library for nanopublications. In: Proceedings of the 5th Workshop on Linked Science (LISC 2015) (2015)Google Scholar
  15. 15.
    Kuhn, T., Barbano, P.E., Nagy, M.L., Krauthammer, M.: Broadening the scope of nanopublications. In: Cimiano, P., Corcho, O., Presutti, V., Hollink, L., Rudolph, S. (eds.) ESWC 2013. LNCS, vol. 7882, pp. 487–501. Springer, Heidelberg (2013). doi: 10.1007/978-3-642-38288-8_33 CrossRefGoogle Scholar
  16. 16.
    Kuhn, T., Chichester, C., Krauthammer, M., Dumontier, M.: Publishing Without publishers: a decentralized approach to dissemination, retrieval, and archiving of data. In: Arenas, M., et al. (eds.) ISWC 2015. LNCS, vol. 9366, pp. 656–672. Springer, Cham (2015). doi: 10.1007/978-3-319-25007-6_38 CrossRefGoogle Scholar
  17. 17.
    Kuhn, T., Chichester, C., Krauthammer, M., Queralt-Rosinach, N., Verborgh, R., Giannakopoulos, G., Ngomo, A.-C.N., Viglianti, R., Dumontier, M.: Decentralized provenance-aware publishing with nanopublications. PeerJ Comput. Sci. 2, e78 (2016)CrossRefGoogle Scholar
  18. 18.
    Kuhn, T., Dumontier, M.: Trusty URIs: verifiable, immutable, and permanent digital artifacts for linked data. In: Presutti, V., d’Amato, C., Gandon, F., d’Aquin, M., Staab, S., Tordai, A. (eds.) ESWC 2014. LNCS, vol. 8465, pp. 395–410. Springer, Cham (2014). doi: 10.1007/978-3-319-07443-6_27 CrossRefGoogle Scholar
  19. 19.
    Kuhn, T., Dumontier, M.: Making digital artifacts on the web verifiable and reliable. IEEE Trans. Knowl. Data Eng. 27(9), 2390–2400 (2015)CrossRefGoogle Scholar
  20. 20.
    Kutmon, M., et al.: WikiPathways: capturing the full diversity of pathway knowledge. Nucleic Acids Res. 44(D1), D488–D494 (2016)CrossRefGoogle Scholar
  21. 21.
    Meinhardt, P., Knuth, M., Sack, H.: TailR: a platform for preserving history on the web of data. In: Proceedings of the 11th International Conference on Semantic Systems, pp. 57–64. ACM (2015)Google Scholar
  22. 22.
    Miller, A., Juels, A., Shi, E., Parno, B., Katz, J.: Permacoin: repurposing Bitcoin work for data preservation. In: Proceedings of the IEEE Symposium on Security and Privacy (SP), pp. 475–490. IEEE (2014)Google Scholar
  23. 23.
    Mons, B., et al.: The value of data. Nat. Genet. 43(4), 281–283 (2011)CrossRefGoogle Scholar
  24. 24.
    Moreau, L., Groth, P.: Provenance: an introduction to prov. Synth. Lect. Semant. Web Theor. Technol. 3(4), 1–129 (2013)CrossRefGoogle Scholar
  25. 25.
    Nanopubs extracted from DisGeNET v2.1.0.0, incremental dataset. Nanopublication index, 9 May 2017. http://purl.org/np/RADYX-ia_TZYAw_eZD0-2oGGA7gnMxOnVj-Gh8wdJgAzI
  26. 26.
    Nanopubs extracted from DisGeNET v3.0.0.0, incremental dataset. Nanopublication index, 9 May 2017. http://purl.org/np/RAufQaKzv1pZlMhZo2eBuZtx9vuugLBJsrs4ZkvR53xzw
  27. 27.
    Nanopubs extracted from DisGeNET v4.0.0.0, incremental dataset. Nanopublication index, 9 May 2017. http://purl.org/np/RAu0PUrg-M8HxkOiYRXkTg7r9fgOIzFZNINj8q7ywNrdM
  28. 28.
    Nanopublications extracted from WikiPathways, incremental dataset, 20170510. Nanopublication index, 11 May 2017. http://purl.org/np/RAKz0OQ3Dq8dDWqF7SIY4TgYcZRX4d2TnmLUEbOwnaGmQ
  29. 29.
    Task Group on Data Citation Standards and Practices.: Out of cite, out of mind: The current state of practice, policy, and technology for the citation of data. In: Data Sci. J. 12, pp. CIDCR1-CIDCR75 (2013)Google Scholar
  30. 30.
    Piñero, J., Bravo, À., Queralt-Rosinach, N., Gutiérrez-Sacristán, A., Deu-Pons, J., Centeno, E., García-García, J., Sanz, F., Furlong, L.I.: DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants. Nucleic Acids Res. 45, D833–D839 (2016)CrossRefGoogle Scholar
  31. 31.
    Queralt-Rosinach, N., Kuhn, T., Chichester, C., Dumontier, M., Sanz, F., Furlong, L.I.: Publishing DisGeNET as nanopublications. Semant. Web 7(5), 519–528 (2016)CrossRefGoogle Scholar
  32. 32.
    Queralt-Rosinach, N., Piñero, J., Bravo, À., Sanz, F., Furlong, L.I.: DisGeNET-RDF: harnessing the innovative power of the semantic web to explore the genetic basis of diseases. Bioinformatics 32, 2236–2238 (2016)CrossRefGoogle Scholar
  33. 33.
    Rauber, A., Asmi, A., van Uytvanck, D., Pröll, S.: Identification of reproducible subsets for data citation, sharing and re-use. Bull. IEEE Tech. Comm. Digit. Libr. 12(1), 6–15 (2016)Google Scholar
  34. 34.
    Schandl, B.: Replication and versioning of partial RDF graphs. In: Aroyo, L., Antoniou, G., Hyvönen, E., ten Teije, A., Stuckenschmidt, H., Cabral, L., Tudorache, T. (eds.) ESWC 2010. LNCS, vol. 6088, pp. 31–45. Springer, Heidelberg (2010). doi: 10.1007/978-3-642-13486-9_3 CrossRefGoogle Scholar
  35. 35.
    Silvello, G.: A methodology for citing linked open data subsets. D-Lib Magazine, 21(1/2) (2015)Google Scholar
  36. 36.
    Tzitzikas, Y., Theoharis, Y., Andreou, D.: On storage policies for semantic web repositories that support versioning. In: Bechhofer, S., Hauswirth, M., Hoffmann, J., Koubarakis, M. (eds.) ESWC 2008. LNCS, vol. 5021, pp. 705–719. Springer, Heidelberg (2008). doi: 10.1007/978-3-540-68234-9_51 CrossRefGoogle Scholar
  37. 37.
    Van de Sompel, H., Sanderson, R., Nelson, M.L., Balakireva, L.L., Shankar, H., Ainsworth, S.: An HTTP-based versioning mechanism for linked data (2010). arXiv:1003.3661
  38. 38.
    Vander Sande, M., Colpaert, P., Verborgh, R., Coppens, S., Mannens, E., Van de Walle, R.: R&Wbase: git for triples. In: LDOW (2013)Google Scholar
  39. 39.
    Volkel, M., Winkler, W., Sure, Y., Kruk, S.R., Synak, M.: Semversion: A versioning system for RDF and ontologies. In: Proceedings of ESWC (2005)Google Scholar
  40. 40.
    Waagmeester, A., Kutmon, M., Riutta, A., Miller, R., Willighagen, E.L., Evelo, C.T., Pico, A.R.: Using the semantic web for rapid integration of WikiPathways with other biological online data resources. PLoS Comput. Biol. 12(6), e1004989 (2016)CrossRefGoogle Scholar
  41. 41.
    Wilkinson, M.D., Dumontier, M., et al.: The FAIR guiding principles for scientific data management and stewardship. Sci. data 3, 160018 (2016)CrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Tobias Kuhn
    • 1
  • Egon Willighagen
    • 2
  • Chris Evelo
    • 2
  • Núria Queralt-Rosinach
    • 3
  • Emilio Centeno
    • 4
  • Laura I. Furlong
    • 4
  1. 1.Department of Computer ScienceVrije Universiteit AmsterdamAmsterdamNetherlands
  2. 2.Department of Bioinformatics, NUTRIMMaastricht UniversityMaastrichtNetherlands
  3. 3.Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaUSA
  4. 4.Research Group on Integrative Biomedical Informatics (GRIB), Institut Hospital Del Mar D’Investigacions Mèdiques (IMIM)Universitat Pompeu Fabra (UPF)BarcelonaSpain

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