The first eNanoMapper prototype: A substance database to support safe-by-design

Proceedings - 2014 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2014

Volumn , Issue , 2014, Pages 1-9

  Jeliazkova, Nina ^a   Doganis, Philip ^b   Fadeel, Bengt ^c   Grafstrom, Roland ^c,d   Hastings, Janna ^e   Jeliazkov, Vedrin ^a   Kohonen, Pekka ^c   Munteanu, Cristian R ^f   Sarimveis, Haralambos ^b   Smeets, Bart ^f   Tsiliki, Georgia ^b   Vorgrimmler, David ^g   Willighagen, Egon ^f  

^a IDEACONSULT LTD   (Bulgaria)

^b NATIONAL TECHNICAL UNIVERSITY OF ATHENS   (Greece)

^c KAROLINSKA INSTITUTE   (Sweden)

^d VTT TECHNICAL RESEARCH CENTRE OF FINLAND   (Finland)

^e EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^f MAASTRICHT UNIVERSITY   (Netherlands)

^g In Silico Toxicology   (Switzerland)

Author keywords

database; nanomaterials; NanoSafety Cluster; safety

Indexed keywords

EID: 84922824394     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBM.2014.6999367     Document Type: Conference Paper

References (42)

1. A. D. Maynard, "Don't define nanomaterials." Nature, vol. 475, no. 7354, p. 31, Jul. 2011.
2. H. Stamm, "Risk factors: Nanomaterials should be defined." Nature, vol. 476, no. 7361, p. 399, Aug. 2011.
3. S. Mann, "Life as a nanoscale phenomenon." Angewandte Chemie (International ed. in English), vol. 47, no. 29, pp. 5306-20, Jan. 2008.
4. E. Roduner, "Size matters: why nanomaterials are different." Chemical Society reviews, vol. 35, no. 7, pp. 583-92, Jul. 2006.
5. R. Landsiedel, L. Ma-Hock, A. Kroll et al., "Testing met al-oxide nanomaterials for human safety," Advanced materials (Deerfield Beach, Fla.), vol. 22, no. 24, pp. 2601-27, Jun. 2010.
6. A. E. Porter, M. Gass, K. Muller, J. N. Skepper, P. A. Midgley, and M. Welland, "Direct imaging of single-walled carbon nanotubes in cells." Nature nanotechnology, vol. 2, no. 11, pp. 713-7, Nov. 2007.
7. D. B. Warheit, "Debunking some misconceptions about nanotoxicology." Nano letters, vol. 10, no. 12, pp. 4777-82, Dec. 2010.
8. A. Nel, T. Xia, L. Mädler, and N. Li, "Toxic potential of materials at the nanolevel." Science (New York, N.Y.), vol. 311, no. 5761, pp. 622-7, Feb. 2006.
9. K. Donaldson, C. A. Poland, and R. P. F. Schins, "Possible genotoxic mechanisms of nanoparticles: criteria for improved test strategies." Nanotoxicology, vol. 4, no. December, pp. 414-20, Dec. 2010.
10. B. Fadeel, "Clear and present danger Engineered nanoparticles and the immune system." Swiss medical weekly, vol. 142, p. w13609, Jan. 2012.
11. A. E. Nel, L. Mädler, D. Velegol et al., "Understanding biophysicochemical interactions at the nano-bio interface." Nature materials, vol. 8, no. 7, pp. 543-57, Jul. 2009.
12. X. Fan, E. K. Lobenhofer, M. Chen et al., "Consistency of predictive signature genes and classifiers generated using different microarray platforms." The pharmacogenomics journal, vol. 10, no. 4, pp. 247-57, Aug. 2010.
13. S. Wijnhoven and M. Bakker, "Development of an inventory for consumer products containing nanomaterials," Centre for Substances and Integrated Risk Assessment, Tech. Rep., 2010. [Online]. Available: http: //ec.europa.eu/environment/chemicals/nanotech/pdf/study inventory.pdf
14. Woodrow Wilson database, "Consumer Products An inventory of nanotechnology-based consumer products currently on the market." 2011. [Online]. Available: http://www.nanotechproject.org/inventories/ consumer/
15. E. Bleeker, "Interpretation and implications of the European Commission Recommendation on the definition of nanomaterial," RIVM, Tech. Rep., 2012. [Online]. Available: http://www.rivm.nl/ dsresource?objectid=rivmp:181801&type=org&disposition=inline
16. P. Kohonen, R. Ceder, I. Smit et al., "Cancer Biology, Toxicology and Alternative Methods Development Go Hand-in-Hand." Basic & clinical pharmacology & toxicology, vol. 115, no. 1, pp. 50-8, Jul. 2014.
17. Y. Wang, T. Suzek, J. Zhang et al., "PubChem BioAssay: 2014 update." Nucleic acids research, vol. 42, no. Database issue, pp. D1075-82, Jan. 2014.
18. A. P. Bento, A. Gaulton, A. Hersey et al., "The ChEMBL bioactivity database: an update." Nucleic acids research, vol. 42, no. Database issue, pp. D1083-90, Jan. 2014.
19. G. Rustici, N. Kolesnikov, M. Brandizi et al., "ArrayExpress update-trends in database growth and links to data analysis tools." Nucleic acids research, vol. 41, no. Database issue, pp. D987-90, Jan. 2013.
20. L. Kong, S. Tuomela, L. Hahne et al., "NanoMiner-integrative human transcriptomics data resource for nanoparticle research." PloS one, vol. 8, no. 7, p. e68414, Jan. 2013.
21. B. Hardy, N. Douglas, C. Helma et al., "Collaborative development of predictive toxicology applications," Journal of cheminformatics, vol. 2, no. 1, p. 7, 2010.
22. A. J. Williams, L. Harland, P. Groth et al., "Open PHACTS: semantic interoperability for drug discovery." Drug discovery today, Jun. 2012.
23. J. Nyström-Persson, Y. Igarashi, M. Ito et al., "Toxygates: interactive toxicity analysis on a hybrid microarray and linked data platform." Bioinformatics (Oxford, England), vol. 29, no. 23, pp. 3080-6, Dec. 2013.
24. S. Jupp, J. Malone, J. Bolleman et al., "The EBI RDF platform: linked open data for the life sciences." Bioinformatics (Oxford, England), vol. 30, no. 9, pp. 1338-9, May 2014.
25. A. D. Maynard, R. J. Aitken, T. Butz et al., "Safe handling of nanotechnology." Nature, vol. 444, no. 7117, pp. 267-9, Nov. 2006.
26. European Commission, "Types and uses of nanomaterials, including safety aspects," European Commission, Brussels, Tech. Rep., 2012.
27. W. H. Z. Cárdenas, J. B. Mamani, T. T. Sibov, C. A. Caous, E. Amaro, and L. F. Gamarra, "Particokinetics: computational analysis of the superparamagnetic iron oxide nanoparticles deposition process." International journal of nanomedicine, vol. 7, pp. 2699-712, Jan. 2012.
28. T. Kelder, M. P. van Iersel, K. Hanspers et al., "WikiPathways: building research communities on biological pathways." Nucleic acids research, vol. 40, no. Database issue, pp. D1301-7, Jan. 2012.
29. S.-A. Sansone, P. Rocca-Serra, D. Field et al., "Toward interoperable bioscience data." Nature genetics, vol. 44, no. 2, pp. 121-6, Feb. 2012.
30. D. G. Thomas, S. Gaheen, S. L. Harper et al., "ISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheetbased Format," BMC Biotechnology, vol. 13, no. 1, p. 2, 2013.
31. J. Hastings, E. Willighagen, G. Owen, N. Jeliazkova, The eNanoMapper Consortium, and C. Steinbeck, "eNanoMapper: Opportunities and challenges in using ontologies to enable data integration for nanomaterial risk assessment," in Proceedings of the ISMB Bio-Ontologies SIG meeting, Boston, USA, July 11-12 2014, 2014.
32. S. Abeyruwan, U. D. Vempati, H. Küç ük-McGinty et al., "Evolving BioAssay Ontology (BAO): modularization, integration and applications." Journal of biomedical semantics, vol. 5, no. Suppl 1 Proceedings of the Bio-Ontologies Spec Interest G, p. S5, Jan. 2014.
33. U. D. Vempati, M. J. Przydzial, C. Chung et al., "Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO)." PloS one, vol. 7, no. 11, p. e49198, Jan. 2012.
34. D. G. Thomas, R. V. Pappu, and N. A. Baker, "NanoParticle Ontology for cancer nanotechnology research." Journal of biomedical informatics, vol. 44, no. 1, pp. 59-74, Feb. 2011.
35. CODATA-VAMASWorking Group on the Description of Nanomaterials, "Uniform Description System for Materials on the Nanoscale," CODATA, Tech. Rep., 2014. [Online]. Available: http://www.codata. org/uploads/DraftUDS9Septfinal.pdf
36. N. Jeliazkova and V. Jeliazkov, "AMBIT RESTful web services: an implementation of the OpenTox application programming interface." Journal of cheminformatics, vol. 3, no. 1, p. 18, Jan. 2011.
37. P. Kohonen, E. Benfenati, D. Bower et al., "The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing," Molecular Informatics, vol. 32, no. 1, pp. 47-63, Jan. 2013.
38. C. D. Walkey, J. B. Olsen, F. Song et al., "Protein corona fingerprinting predicts the cellular interaction of gold and silver nanoparticles." ACS nano, vol. 8, no. 3, pp. 2439-55, Mar. 2014.
39. C. A. Schneider, W. S. Rasband, and K. W. Eliceiri, "NIH Image to ImageJ: 25 years of image analysis." Nature methods, vol. 9, no. 7, pp. 671-5, Jul. 2012.
40. J. Stewart, "MOPAC2012," Stewart Computational Chemistry, Colorado Springs, CO, USA, Tech. Rep., 2012. [Online]. Available: http: //openmopac.net/
41. M. Ashburner, C. A. Ball, J. A. Blake et al., "Gene ontology: tool for the unification of biology. The Gene Ontology Consortium." Nature genetics, vol. 25, no. 1, pp. 25-9, May 2000.
42. C. Munteanu, A. Magalhaes, A. Duardo-Sanchez, A. Pazos, and H. Gonzalez-Diaz, "S2SNet: A Tool for Transforming Characters and Numeric Sequences into Star Network Topological Indices in Chemoinformatics, Bioinformatics, Biomedical, and Social-Legal Sciences," Current Bioinformatics, vol. 8, no. 4, pp. 429-437, Aug. 2013.