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2017 | OriginalPaper | Buchkapitel

Integrative Data Management for Reproducibility of Microscopy Experiments

verfasst von : Sheeba Samuel

Erschienen in: The Semantic Web

Verlag: Springer International Publishing

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Abstract

Reproducibility is a fundamental factor in every domain of science since it allows scientists to trust data and results. The scientific community is interested in the results of experiments which are reproducible, reusable and understandable. In this paper, we present our work towards reproducibility of scientific experiments taking into account the use case of microscopy. We aim to analyze the components that are vital for reproducibility and to develop an integrative data management platform for scientific experiments. In this article, we show the use of Semantic Web technologies to conserve an experiment environment and its workflow. This allows scientists to ask queries related to an experiment and compare results. We present our approach for scientists to represent, search and share their experimental data and results to the scientific community for better data interoperability and reuse. Our overall goal is to extend data management and Semantic Web technologies to enable reproducibility.

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Literatur
1.
Zurück zum Zitat 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. Nat. Methods 9(3), 245–253 (2012)CrossRef 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. Nat. Methods 9(3), 245–253 (2012)CrossRef
2.
Zurück zum Zitat Callahan, S.P., Freire, J., Santos, E., Scheidegger, C.E., Silva, C.T., Vo, H.T.: VisTrails: visualization meets data management. In: Proceedings of the 2006 ACM SIGMOD International Conference on Management of Data, SIGMOD 2006, pp. 745–747. ACM, New York, NY, USA (2006). http://doi.acm.org/10.1145/1142473.1142574 Callahan, S.P., Freire, J., Santos, E., Scheidegger, C.E., Silva, C.T., Vo, H.T.: VisTrails: visualization meets data management. In: Proceedings of the 2006 ACM SIGMOD International Conference on Management of Data, SIGMOD 2006, pp. 745–747. ACM, New York, NY, USA (2006). http://​doi.​acm.​org/​10.​1145/​1142473.​1142574
4.
Zurück zum Zitat Compton, M., Corsar, D., Taylor, K.: Sensor data provenance: SSNO and PROV-O together at last. Terra Cognita and Semantic Sensor Networks, pp. 67–82 (2014) Compton, M., Corsar, D., Taylor, K.: Sensor data provenance: SSNO and PROV-O together at last. Terra Cognita and Semantic Sensor Networks, pp. 67–82 (2014)
5.
Zurück zum Zitat Curcin, V., Ghanem, M.: Scientific workflow systems - can one size fit all? In: 2008 Cairo International Biomedical Engineering Conference, pp. 1–9 (2008) Curcin, V., Ghanem, M.: Scientific workflow systems - can one size fit all? In: 2008 Cairo International Biomedical Engineering Conference, pp. 1–9 (2008)
6.
Zurück zum Zitat Demchenko, Y., Zhao, Z., Grosso, P., Wibisono, A., de Laat, C.: Addressing big data challenges for scientific data infrastructure. In: Proceedings of the 4th IEEE International Conference on Cloud Computing Technology and Science, pp. 614–617 (2012) Demchenko, Y., Zhao, Z., Grosso, P., Wibisono, A., de Laat, C.: Addressing big data challenges for scientific data infrastructure. In: Proceedings of the 4th IEEE International Conference on Cloud Computing Technology and Science, pp. 614–617 (2012)
8.
Zurück zum Zitat Kume, S., Masuya, H., Kataoka, Y., Kobayashi, N.: Development of an ontology for an integrated image analysis platform to enable global sharing of microscopy imaging data. In: Proceedings of the ISWC 2016 Posters & Demonstrations Track co-located with 15th International Semantic Web Conference (ISWC 2016), Kobe, Japan, October 19, 2016 (2016). http://ceur-ws.org/Vol-1690/paper93.pdf Kume, S., Masuya, H., Kataoka, Y., Kobayashi, N.: Development of an ontology for an integrated image analysis platform to enable global sharing of microscopy imaging data. In: Proceedings of the ISWC 2016 Posters & Demonstrations Track co-located with 15th International Semantic Web Conference (ISWC 2016), Kobe, Japan, October 19, 2016 (2016). http://​ceur-ws.​org/​Vol-1690/​paper93.​pdf
9.
Zurück zum Zitat Kvilekval, K., Fedorov, D., Obara, B., Singh, A., Manjunath, B.: Bisque: a platform for bioimage analysis and management. Bioinformatics 26(4), 544–552 (2010)CrossRef Kvilekval, K., Fedorov, D., Obara, B., Singh, A., Manjunath, B.: Bisque: a platform for bioimage analysis and management. Bioinformatics 26(4), 544–552 (2010)CrossRef
10.
Zurück zum Zitat 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) 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)
12.
Zurück zum Zitat McPhillips, T., Song, T., Kolisnik, T., Aulenbach, S., Belhajjame, K., Bocinsky, K., Cao, Y., Chirigati, F., Dey, S., Freire, J., et al.: YesWorkflow: a user-oriented, language-independent tool for recovering workflow information from scripts (2015). arXiv preprint arXiv:1502.02403CrossRef McPhillips, T., Song, T., Kolisnik, T., Aulenbach, S., Belhajjame, K., Bocinsky, K., Cao, Y., Chirigati, F., Dey, S., Freire, J., et al.: YesWorkflow: a user-oriented, language-independent tool for recovering workflow information from scripts (2015). arXiv preprint arXiv:​1502.​02403CrossRef
13.
Zurück zum Zitat Moreau, L.: Provenance-based reproducibility in the semantic web. Web Seman. Sci. Serv. Agents World Wide Web 9(2), 202–221 (2011)CrossRef Moreau, L.: Provenance-based reproducibility in the semantic web. Web Seman. Sci. Serv. Agents World Wide Web 9(2), 202–221 (2011)CrossRef
14.
Zurück zum Zitat Murta, L., Braganholo, V., Chirigati, F., Koop, D., Freire, J.: noWorkflow: capturing and analyzing provenance of scripts. In: Ludäscher, B., Plale, B. (eds.) IPAW 2014. LNCS, vol. 8628, pp. 71–83. Springer, Cham (2015). doi:10.1007/978-3-319-16462-5_6CrossRef Murta, L., Braganholo, V., Chirigati, F., Koop, D., Freire, J.: noWorkflow: capturing and analyzing provenance of scripts. In: Ludäscher, B., Plale, B. (eds.) IPAW 2014. LNCS, vol. 8628, pp. 71–83. Springer, Cham (2015). doi:10.​1007/​978-3-319-16462-5_​6CrossRef
16.
Zurück zum Zitat Pimentel, J.F., Dey, S., McPhillips, T., Belhajjame, K., Koop, D., Murta, L., Braganholo, V., Ludäscher, B.: Yin & yang: demonstrating complementary provenance from noWorkflow & YesWorkflow. In: Mattoso, M., Glavic, B. (eds.) IPAW 2016. LNCS, vol. 9672, pp. 161–165. Springer, Cham (2016). doi:10.1007/978-3-319-40593-3_13CrossRef Pimentel, J.F., Dey, S., McPhillips, T., Belhajjame, K., Koop, D., Murta, L., Braganholo, V., Ludäscher, B.: Yin & yang: demonstrating complementary provenance from noWorkflow & YesWorkflow. In: Mattoso, M., Glavic, B. (eds.) IPAW 2016. LNCS, vol. 9672, pp. 161–165. Springer, Cham (2016). doi:10.​1007/​978-3-319-40593-3_​13CrossRef
17.
Zurück zum Zitat Samuel, S., Taubert, F., Walther, D., König-Ries, B., Bücker, H.M.: Towards reproducibility of microscopy experiments. D-Lib Mag. 23(1/2) (2017) Samuel, S., Taubert, F., Walther, D., König-Ries, B., Bücker, H.M.: Towards reproducibility of microscopy experiments. D-Lib Mag. 23(1/2) (2017)
18.
Zurück zum Zitat Taylor, B.N., Kuyatt, C.E.: Guidelines for Evaluating and Expressing the Uncertainty of NIST Measurement Results. Tech. rep., NIST Technical Note 1297 (1994) Taylor, B.N., Kuyatt, C.E.: Guidelines for Evaluating and Expressing the Uncertainty of NIST Measurement Results. Tech. rep., NIST Technical Note 1297 (1994)
Metadaten
Titel
Integrative Data Management for Reproducibility of Microscopy Experiments
verfasst von
Sheeba Samuel
Copyright-Jahr
2017
DOI
https://doi.org/10.1007/978-3-319-58451-5_19

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