Abstract
It has always been the aim of every scientist to make their work reproducible so that the scientific community can verify and trust the experiment results. With more complex in vivo and in vitro studies, achieving reproducibility has become more challenging over the last decades. In this work, we focus on integrative data management for reproducibility aspects related to execution environment conservation taking into account the use case of microscopy experiments. We use Semantic Web technologies to describe the experiment and its execution environment. We have developed an ontology, REPRODUCE-ME (Reproduce Microscopy Experiments) by extending the existing vocabulary PROV-O. Scientists can use this ontology to make semantic queries related to reproducibility of experiments on the microscopic data. To ensure efficient execution of these queries, we rely on ontology-based data access to source data stored in a relational DBMS.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Allan, C., Burel, J.M., Moore, J., Blackburn, C., Linkert, M., Loynton, S., MacDonald, D., Moore, W.J., Neves, C., Patterson, A., et al.: OMERO: flexible, model-driven data management for experimental biology. Nature Methods 9(3), 245–253 (2012)
Compton, M., Corsar, D., Taylor, K.: Sensor data provenance: SSNO and PROV-O together at last. In: Terra Cognita and Semantic Sensor, Networks, pp. 67–82 (2014)
Jupp, S., Malone, J., Burdett, T., Heriche, J.K., Williams, E., Ellenberg, J., Parkinson, H., Rustici, G.: The cellular microscopy phenotype ontology. J. Biomed. Semant. 7(1), 28 (2016). http://dx.doi.org/10.1186/s13326-016-0074-0
Lebo, T., Sahoo, S., McGuinness, D., Belhajjame, K., Cheney, J., Corsar, D., Garijo, D., Soiland-Reyes, S., Zednik, S., Zhao, J.: PROV-O: the PROV ontology. W3C Recommendation 30 (2013)
Samuel, S.: Integrative data management for reproducibility of microscopy experiments. In: Blomqvist, E., Maynard, D., Gangemi, A., Hoekstra, R., Hitzler, P., Hartig, O. (eds.) ESWC 2017. LNCS, vol. 10250, pp. 246–255. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-58451-5_19
Samuel, S., Taubert, F., Walther, D., König-Ries, B., Bücker, H.M.: Towards reproducibility of microscopy experiments. D-Lib Magaz. 23(1/2) (2017)
Soldatova, L.N., King, R.D.: An ontology of scientific experiments. J. R. Soc. Interface 3(11), 795–803 (2006)
Acknowledgements
This research is supported by the “Deutsche Forschungsgemeinschaft” (DFG) in Project Z2 of the CRC/TRR 166 “High-end light microscopy elucidates membrane receptor function - ReceptorLight”. Birgitta König-Ries was on sabbatical at DFG FZT 118 iDiv while working on this paper. We thank Christoph Biskup and Kathrin Groeneveld from University Hospital Jena, Germany, for providing the requirements to develop the proposed approach and validating the system and our colleagues Martin Bücker, Frank Taubert und Daniel Walther for their feedback.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer International Publishing AG
About this paper
Cite this paper
Samuel, S., König-Ries, B. (2017). REPRODUCE-ME: Ontology-Based Data Access for Reproducibility of Microscopy Experiments. In: Blomqvist, E., Hose, K., Paulheim, H., Ławrynowicz, A., Ciravegna, F., Hartig, O. (eds) The Semantic Web: ESWC 2017 Satellite Events. ESWC 2017. Lecture Notes in Computer Science(), vol 10577. Springer, Cham. https://doi.org/10.1007/978-3-319-70407-4_4
Download citation
DOI: https://doi.org/10.1007/978-3-319-70407-4_4
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-70406-7
Online ISBN: 978-3-319-70407-4
eBook Packages: Computer ScienceComputer Science (R0)