Abstract
Scientific information communicated in scholarly literature remains largely inaccessible to machines. The global scientific knowledge base is little more than a collection of (digital) documents. The main reason is in the fact that the document is the principal form of communication and—since underlying data, software and other materials mostly remain unpublished—the fact that the scholarly article is, essentially, the only form used to communicate scientific information. Based on a use case in life sciences, we argue that virtual research environments and semantic technologies are transforming the capability of research infrastructures to systematically acquire and curate machine readable scientific information communicated in scholarly literature.
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Notes
- 1.
Open Research Knowledge Graph: http://orkg.org (Accessed: October 16, 2018).
- 2.
https://rdflib.readthedocs.io/ (Accessed: October 16, 2018).
References
Aamodt, A., Nygård, M.: Different roles and mutual dependencies of data, information, and knowledge - an AI perspective on their integration. Data Knowl. Eng. 16(3), 191–222 (1995)
Allan, R.: Virtual Research Environments: From Portals to Science Gateways. Chandos Publishing, Oxford (2009)
Aryani, A., Wang, J.: Research graph: building a distributed graph of scholarly works using research data switchboard. In: Open Repositories Conference (2017)
Atkinson, M., Filgueira, R., Spinuso, A., Trani, L.: Download considered harmful (2018). Manuscript in preparation
Auer, S.: Towards an open research knowledge graph, January 2018
Auer, S. Kovtun, V., Prinz, M., Kasprzik, A., Stocker, M., Vidal, M.E.: Towards a Knowledge Graph for Science. In: Proceedings of the 8th International Conference on Web Intelligence, Mining and Semantics, WIMS 2018, pp. 1:1–1:6. ACM, New York (2018)
Barwise, J., Perry, J.: Situations and attitudes. J. Philos. 78(11), 668–691 (1981)
Bechhofer, S., Roure, D.D., Gamble, M., Goble, C., Buchan, I.: Research objects: towards exchange and reuse of digital knowledge. In: Nature Precedings, July 2010
Bornmann, L., Mutz, R.: Growth rates of modern science: a bibliometric analysis based on the number of publications and cited references. J. Assoc. Inf. Sci. Technol. 66(11), 2215–2222 (2015)
Burton, A.: The Scholix framework for interoperability in data-literature information exchange. D-Lib Mag. 23(1/2) (2017)
Candela, L., Castelli, D., Pagano, P.: D4Science: an e-infrastructure for supporting virtual research environments. In: Agosti, M., Esposito, F., Thanos, C. (eds) Proceedings of the 5th Italian Research Conference on Digital Libraries (IRCDL 2009), Padova January 2009
Candela, L., Castelli, D., Pagano, P.: Virtual research environments: an overview and a research agenda. Data Sci. J. 12 GRDI75-GRDI81 (2013)
Capadisli, S., Guy, A., Verborgh, R., Lange, C., Auer, S., Berners-Lee, T.: Decentralised authoring, annotations and notifications for a read-write web with dokieli. In: Cabot, J., De Virgilio, R., Torlone, R. (eds.) ICWE 2017. LNCS, vol. 10360, pp. 469–481. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-60131-1_33
Chen, X., Dallmeier-Tiessen, S., Dani, A., Dasler, R., Fernández, J.D., Fokianos, P., Herterich, P., Šimko, T.: CERN analysis preservation: a novel digital library service to enable reusable and reproducible research. In: Fuhr, N., Kovács, L., Risse, T., Nejdl, W. (eds.) Research and Advanced Technology for Digital Libraries. pp, pp. 347–356. Springer International Publishing, Cham (2016)
Ciccarese, P., Ocana, M., Castro, L.J.G., Das, S., Clark, T.: An open annotation ontology for science on web 3.0. J. Biomed. Semant. 2(2), S4 (2011)
de Sompel, H.V., Payette, S., Erickson, J., Lagoze, C., Warner, S.: Rethinking scholarly communication. D-Lib Mag. 10(9), (2004)
de Waard, A., Breure, L., Kircz, J.G., van Oostendorp, H.: Modeling rhetoric in scientific publications. In Proceedings of the International Conference on Multidisciplinary Information Sciences and Technologies (InSciT 2006) (2006)
de Waard, A., Shum, S.M., Carusi, A., Park, J., Samwald, M., Sándor, Á.: Hypotheses, evidence and relationships: the HypER approach for representing scientific knowledge claims. In: Clark, T., Luciano, J.S., Marshall, M.S., Prud’hommeaux, E.., Stephens, S. (eds), Proceedings of the Workshop on Semantic Web Applications in Scientific Discourse (SWASD 2009), vol. 523, Washington October 2009. CEUR
Devlin, K.: Logic and Information. Cambridge University Press, Cambridge (1991)
Fathalla, S., Vahdati, S., Auer, S., Lange, C.: Towards a knowledge graph representing research findings by semantifying survey articles. In: Kamps, J., Tsakonas, G., Manolopoulos, Y., Iliadis, L., Karydis, I. (eds.) Research and Advanced Technology for Digital Libraries. pp, pp. 315–327. Springer International Publishing, Cham (2017). https://doi.org/10.1007/978-3-319-67008-9_25
Floridi, L.: The Philosophy of Information. Oxford University Press, Oxford (2011)
García-Castro, L.J., Giraldo, O.X., García-Castro, A.: Using annotations to model discourse: an extension to the annotation ontology. In García-Castro, A. Lange, C., van Harmelen, F., Good, B. (eds), Proceedings of the 2nd Workshop on Semantic Publishing, vol. 903, pp. 13–22, Hersonissos, May 2012. CEUR
Groth, P., Gibson, A., Velterop, J.: The anatomy of a nanopublication. Inf. Serv. Use 30(1–2), 51–56 (2010)
Haddad, S.: Iron-regulatory proteins secure iron availability in cardiomyocytes to prevent heart failure. Eur. Heart J. 38(5), 362–372 (2017)
Hanson, K.L., DiLauro, T., Donoghue, M.: The RMap project: capturing and preserving associations amongst multi-part distributed publications. In: Proceedings of the 15th ACM/IEEE-CS Joint Conference on Digital Libraries, JCDL 2015, pp. 281–282. ACM, New York (2015)
Hentze, M.W., Muckenthaler, M.U., Galy, B., Camaschella, C.: Two to tango: regulation of mammalian iron metabolism. Cell 142(1), 24–38 (2010)
Jinha, A.E.: Article 50 million: an estimate of the number of scholarly articles in existence. Learn. Publishing 23(3), 258–263 (2010)
Jones, E., Oliphant, T., Peterson, P. et al.: SciPy: Open source scientific tools for Python (2001)
Kluyver, T.: Jupyter notebooks–a publishing format for reproducible computational workflows. In: Loizides, F., Schmidt, B. (eds), Positioning and Power in Academic Publishing: Players, Agents and Agendas, pp. 87–90. IOS Press (2016)
Manola, F., Miller, E., McBride, B.: RDF Primer. W3C Recommendation 10(1–107), 6 (2004)
Mons, B., Velterop, J.: Nano-publication in the e-science era. In: Workshop on Semantic Web Applications in Scientific Discourse (SWASD 2009), Washington (2009)
Priem, J.: Beyond the paper. Nature 495(7442), 437–440 (2013)
Schneider, C.A., Rasband, W.S., Eliceiri, K.W.: NIH Image to imageJ: 25 years of image analysis. Nat. Methods 9(7), 671–675 (2012)
Smith, B., et al.: The OBO foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol. 25(11), 1251–1255 (2007)
Star, S.L.: The ethnography of infrastructure. Am. Behav. Sci. 43(3), 377–391 (1999)
Stocker, M.: Advancing the software systems of environmental knowledge infrastructures. In: Chabbi, A., Loescher, H.W. (eds.) Terrestrial Ecosystem Research Infrastructures: Challenges and Opportunities, pp. 399–423. CRC Press, Taylor & Francis Group (2017)
Stocker, M.: From data to machine readable information aggregated in research objects. D-Lib Mag. 23(1/2) (2017)
Stocker, M.: Jupyter notebook for DILS 2018 paper on research infrastructures that curate scientific information. Figshare, July 2018
Stocker, M., Baranizadeh, E., Portin, H., Komppula, M., Rönkkö, M., Hamed, A., Virtanen, A., Lehtinen, K., Laaksonen, A., Kolehmainen, M.: Representing situational knowledge acquired from sensor data for atmospheric phenomena. Environ. Model. Softw. 58, 27–47 (2014)
Stocker, M., et al.: Representing situational knowledge for disease outbreaks in agriculture. J. Agric. Inf. 7(2), 29–39 (2016)
Stocker, M., Paasonen, P., Fiebig, M., Zaidan, M.A., Hardisty, A.: Curating scientific information in knowledge infrastructures. Data Sci. J. 17 (2018). https://doi.org/10.5334/dsj-2018-021
Stocker, M., Rönkkö, M., Kolehmainen, M.: Situational knowledge representation for traffic observed by a pavement vibration sensor network. IEEE Trans. Intell. Transp. Syst. 15(4), 1441–1450 (2014)
White, K.E., Robbins, C., Khan, B., Freyman, C.: Science and engineering publication output trends: 2014 shows rise of developing country output while developed countries dominate highly cited publications. Technical Report NSF 18–300, National Science Foundation, October 2017
Wilkinson, M.D., et al.. The FAIR guiding principles for scientific data management and stewardship. Scientific Data, 3 March 2016
Acknowledgements
We thank the TIB Leibniz Information Centre for Science and Technology for supporting this project and our colleagues and the participants of the project’s workshop series for their contributions.
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Stocker, M., Prinz, M., Rostami, F., Kempf, T. (2019). Towards Research Infrastructures that Curate Scientific Information: A Use Case in Life Sciences. In: Auer, S., Vidal, ME. (eds) Data Integration in the Life Sciences. DILS 2018. Lecture Notes in Computer Science(), vol 11371. Springer, Cham. https://doi.org/10.1007/978-3-030-06016-9_6
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