Display options
Cite
Jeliazkova N, Chomenidis C, Doganis P, et al. The eNanoMapper database for nanomaterial safety information. Beilstein J Nanotechnol. 2015;6:1609-34doi: 10.3762/bjnano.6.165.
Jeliazkova, N., Chomenidis, C., Doganis, P., Fadeel, B., Grafström, R., Hardy, B., Hastings, J., Hegi, M., Jeliazkov, V., Kochev, N., Kohonen, P., Munteanu, C. R., Sarimveis, H., Smeets, B., Sopasakis, P., Tsiliki, G., Vorgrimmler, D., & Willighagen, E. (2015). The eNanoMapper database for nanomaterial safety information. Beilstein journal of nanotechnology, 61609-34. https://doi.org/10.3762/bjnano.6.165
Jeliazkova, Nina, et al. "The eNanoMapper database for nanomaterial safety information." Beilstein journal of nanotechnology vol. 6 (2015): 1609-34. doi: https://doi.org/10.3762/bjnano.6.165
Jeliazkova N, Chomenidis C, Doganis P, Fadeel B, Grafström R, Hardy B, Hastings J, Hegi M, Jeliazkov V, Kochev N, Kohonen P, Munteanu CR, Sarimveis H, Smeets B, Sopasakis P, Tsiliki G, Vorgrimmler D, Willighagen E. The eNanoMapper database for nanomaterial safety information. Beilstein J Nanotechnol. 2015 Jul 27;6:1609-34. doi: 10.3762/bjnano.6.165. eCollection 2015. PMID: 26425413; PMCID: PMC4578352.
Copy Download .nbib Format: NLM
Share it on

Beilstein J Nanotechnol. 2015 Jul 27;6:1609-34. doi: 10.3762/bjnano.6.165. eCollection 2015.

The eNanoMapper database for nanomaterial safety information.

Beilstein journal of nanotechnology

Nina Jeliazkova, Charalampos Chomenidis, Philip Doganis, Bengt Fadeel, Roland Grafström, Barry Hardy, Janna Hastings, Markus Hegi, Vedrin Jeliazkov, Nikolay Kochev, Pekka Kohonen, Cristian R Munteanu, Haralambos Sarimveis, Bart Smeets, Pantelis Sopasakis, Georgia Tsiliki, David Vorgrimmler, Egon Willighagen

Affiliations

  1. Ideaconsult Ltd., Sofia, Bulgaria.
  2. National Technical University of Athens, School of Chemical Engineering, Athens, Greece.
  3. Karolinska Institutet, Stockholm, Sweden.
  4. Douglas Connect GmbH, Zeiningen, Switzerland.
  5. European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom.
  6. Ideaconsult Ltd., Sofia, Bulgaria ; Department of Analytical Chemistry and Computer Chemistry, University of Plovdiv, Plovdiv, Bulgaria.
  7. Department of Bioinformatics, NUTRIM, Maastricht University, Maastricht, The Netherlands ; Computer Science Faculty, University of A Coruna, A Coruña, Spain.
  8. Department of Bioinformatics, NUTRIM, Maastricht University, Maastricht, The Netherlands.
  9. National Technical University of Athens, School of Chemical Engineering, Athens, Greece ; IMT Institute for Advanced Studies Lucca, Lucca, Italy.
  10. in silico toxicology Gmbh (IST), Basel, Switzerland.

PMID: 26425413 PMCID: PMC4578352 DOI: 10.3762/bjnano.6.165

Abstract

BACKGROUND: The NanoSafety Cluster, a cluster of projects funded by the European Commision, identified the need for a computational infrastructure for toxicological data management of engineered nanomaterials (ENMs). Ontologies, open standards, and interoperable designs were envisioned to empower a harmonized approach to European research in nanotechnology. This setting provides a number of opportunities and challenges in the representation of nanomaterials data and the integration of ENM information originating from diverse systems. Within this cluster, eNanoMapper works towards supporting the collaborative safety assessment for ENMs by creating a modular and extensible infrastructure for data sharing, data analysis, and building computational toxicology models for ENMs.

RESULTS: The eNanoMapper database solution builds on the previous experience of the consortium partners in supporting diverse data through flexible data storage, open source components and web services. We have recently described the design of the eNanoMapper prototype database along with a summary of challenges in the representation of ENM data and an extensive review of existing nano-related data models, databases, and nanomaterials-related entries in chemical and toxicogenomic databases. This paper continues with a focus on the database functionality exposed through its application programming interface (API), and its use in visualisation and modelling. Considering the preferred community practice of using spreadsheet templates, we developed a configurable spreadsheet parser facilitating user friendly data preparation and data upload. We further present a web application able to retrieve the experimental data via the API and analyze it with multiple data preprocessing and machine learning algorithms.

CONCLUSION: We demonstrate how the eNanoMapper database is used to import and publish online ENM and assay data from several data sources, how the "representational state transfer" (REST) API enables building user friendly interfaces and graphical summaries of the data, and how these resources facilitate the modelling of reproducible quantitative structure-activity relationships for nanomaterials (NanoQSAR).

Keywords: EU NanoSafety Cluster; NanoQSAR; database; nanoinformatics; nanomaterials; nanomaterials ontology; safety testing

References

  1. Nat Genet. 2000 May;25(1):25-9 - PubMed
  2. Altern Lab Anim. 2005 Apr;33(2):155-73 - PubMed
  3. Altern Lab Anim. 2005 Oct;33(5):445-59 - PubMed
  4. Curr Pharm Des. 2006;12(17):2111-20 - PubMed
  5. Nature. 2006 Nov 16;444(7117):267-9 - PubMed
  6. SAR QSAR Environ Res. 2007 May-Jun;18(3-4):195-207 - PubMed
  7. J Occup Environ Hyg. 2007 Dec;4(12):D131-4 - PubMed
  8. J Cheminform. 2010 Aug 31;2(1):7 - PubMed
  9. J Cheminform. 2011 May 16;3:18 - PubMed
  10. J Comput Aided Mol Des. 1990 Mar;4(1):1-105 - PubMed
  11. J Cheminform. 2011 Oct 07;3:33 - PubMed
  12. Nucleic Acids Res. 2012 Jan;40(Database issue):D109-14 - PubMed
  13. Nucleic Acids Res. 2012 Jan;40(Database issue):D1301-7 - PubMed
  14. Arch Toxicol. 2012 Jan;86(1):13-5 - PubMed
  15. Nat Genet. 2012 Jan 27;44(2):121-6 - PubMed
  16. J Biomed Semantics. 2012 Apr 24;3 Suppl 1:S7 - PubMed
  17. Expert Opin Drug Metab Toxicol. 2012 Jul;8(7):791-801 - PubMed
  18. Int J Nanomedicine. 2012;7:2699-712 - PubMed
  19. Nat Methods. 2012 Jul;9(7):671-5 - PubMed
  20. BMC Biotechnol. 2013 Jan 14;13:2 - PubMed
  21. PLoS One. 2013 Jul 12;8(7):e68414 - PubMed
  22. Toxicology. 2013 Oct 4;312:158-65 - PubMed
  23. J Med Chem. 2014 Apr 24;57(8):3186-204 - PubMed
  24. ACS Nano. 2014 Mar 25;8(3):2439-55 - PubMed
  25. Int J Mol Sci. 2014 Apr 25;15(5):7158-82 - PubMed
  26. Nanotoxicology. 2015 May;9(3):313-25 - PubMed
  27. J Am Med Inform Assoc. 2015 Jan;22(1):109-20 - PubMed
  28. J Biomed Semantics. 2014 Jun 03;5(Suppl 1 Proceedings of the Bio-Ontologies Spec Interest G):S5 - PubMed
  29. Comput Sci Discov. 2013 Nov 21;6(1):014010 - PubMed
  30. Nanotechnology. 2015 Jan 9;26(1):015701 - PubMed
  31. ACS Nano. 2015;9(4):3409-17 - PubMed
  32. J Biomed Semantics. 2015 Mar 21;6:10 - PubMed
  33. Regul Toxicol Pharmacol. 2015 Mar 15;71(2 Suppl):S1-27 - PubMed
  34. Mol Inform. 2011 Aug;30(8):707-20 - PubMed
  35. Mol Inform. 2013 Jan;32(1):47-63 - PubMed
  36. Regul Toxicol Pharmacol. 1997 Feb;25(1):1-5 - PubMed

Publication Types