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REPRODUCE-ME: Ontology-Based Data Access for Reproducibility of Microscopy Experiments

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The Semantic Web: ESWC 2017 Satellite Events (ESWC 2017)

Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 10577))

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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.

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Notes

  1. 1.

    http://www.receptorlight.uni-jena.de/.

  2. 2.

    http://ontop.inf.unibz.it/.

  3. 3.

    http://fusion.cs.uni-jena.de/fusion/repr/.

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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.

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Authors and Affiliations

  1. Heinz-Nixdorf Chair for Distributed Information Systems, Friedrich-Schiller University, Jena, Germany

    Sheeba Samuel & Birgitta König-Ries

Authors
  1. Sheeba Samuel
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  2. Birgitta König-Ries
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Corresponding author

Correspondence to Sheeba Samuel .

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Editors and Affiliations

  1. Linköping University, Linköping, Sweden

    Eva Blomqvist

  2. Aalborg University, Aalborg, Denmark

    Katja Hose

  3. University of Mannheim, Mannheim, Germany

    Heiko Paulheim

  4. Poznan University of Technology, Poznan, Poland

    Agnieszka Ławrynowicz

  5. University of Sheffield, Sheffield, United Kingdom

    Fabio Ciravegna

  6. Linköping University, Linköping, Sweden

    Olaf Hartig

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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

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  • DOI: https://doi.org/10.1007/978-3-319-70407-4_4

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-70406-7

  • Online ISBN: 978-3-319-70407-4

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