The eNanoMapper database for nanomaterial safety information

Beilstein Journal of Nanotechnology

Volumn 6, Issue 1, 2015, Pages 1609-1634

  Jeliazkova, Nina ^a   Chomenidis, Charalampos ^b   Doganis, Philip ^b   Fadeel, Bengt ^c   Grafström, Roland ^c   Hardy, Barry ^d   Hastings, Janna ^e   Hegi, Markus ^d   Jeliazkov, Vedrin ^a   Kochev, Nikolay ^a,f   Kohonen, Pekka ^c   Munteanu, Cristian R ^g,h   Sarimveis, Haralambos ^b   Smeets, Bart ^g   Sopasakis, Pantelis ^b,i   Tsiliki, Georgia ^b   Vorgrimmler, David ^j   Willighagen, Egon ^g  

^a IDEACONSULT LTD   (Bulgaria)

^b NATIONAL TECHNICAL UNIVERSITY OF ATHENS   (Greece)

^c KAROLINSKA INSTITUTE   (Sweden)

^d Douglas Connect GmbH   (Switzerland)

^e EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Italy)

^f UNIVERSITY OF PLOVDIV   (Bulgaria)

^g MAASTRICHT UNIVERSITY   (Netherlands)

^h UNIVERSITY OF A CORUÑA   (Spain)

ⁱ IMT SCHOOL FOR ADVANCED STUDIES LUCCA   (Italy)

^j In Silico Toxicology   (Switzerland)

more..

Author keywords

Database; EU NanoSafety Cluster; Nanoinformatics; Nanomaterials ontology; Nanomaterials; ; NanoQSAR; Safety testing

Indexed keywords

APPLICATION PROGRAMMING INTERFACES (API); ARTIFICIAL INTELLIGENCE; DATABASE SYSTEMS; GRAPHICAL USER INTERFACES; INFORMATION MANAGEMENT; INTERFACE STATES; LEARNING ALGORITHMS; LEARNING SYSTEMS; MOLECULAR GRAPHICS; NANOSTRUCTURED MATERIALS; OPEN SOURCE SOFTWARE; SAFETY TESTING; SPREADSHEETS; WEB SERVICES;

COMPUTATIONAL INFRASTRUCTURE; ENGINEERED NANOMATERIALS; NANOINFORMATICS; NANOQSAR; NANOSAFETY; OPEN-SOURCE COMPONENTS; QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIP; REPRESENTATIONAL STATE TRANSFER;

DIGITAL STORAGE;

EID: 84947938601     PISSN: None     EISSN: 21904286     Source Type: Journal    
DOI: 10.3762/bjnano.6.165     Document Type: Article

References (71)

1. Maynard, A. D., Aitken, R. J., Butz, T., Colvin, V., Donaldson, K., Oberdörster, G., Philbert, M. A., Ryan, J., Seaton, A., Stone, V., Tinkle, S. S., Tran, L., Walker, N. J., Warheit, D. B. Nature 2006, 444, 267-269. doi:10.1038/444267a
2. European Commission. Types and uses of nanomaterials, including safety aspects; 2012.
3. Cárdenas, W. H. Z., Mamani, J. B., Sibov, T. T., Caous, C. A., Amaro, E., Jr., Gamarra, L. F. Int. J. Nanomed. 2012, 7, 2699-2712. doi:10.2147/IJN.S30074
4. Kelder, T., van Iersel, M. P., Hanspers, K., Kutmon, M., Conklin, B. R., Evelo, C. T., Pico, A. R. Nucleic Acids Res. 2012, 40, D1301-D1307. doi:10.1093/nar/gkr1074
5. Mills, K. C., Murry, D., Guzan, K. A., Ostraat, M. L. J. Nanopart. Res. 2014, 16, No. 2219. doi:10.1007/s11051-013-2219-8
6. Miller, A. L., Hoover, M. D., Mitchell, D. M., Stapleton, B. P. J. Occup. Environ. Hyg. 2007, 4, D131-D134. doi:10.1080/15459620701683947
7. Gaheen, S., Hinkal, G. W., Morris, S. A., Lijowski, M., Heiskanen, M., Klemm, J. D. Comput. Sci. Discovery 2013, 6, 014010. doi:10.1088/1749-4699/6/1/014010
8. Marquardt, C., Kühnel, D., Richter, V., Krug, H. F., Mathes, B., Steinbach, C., Nau, K. J. Phys.: Conf. Ser. 2013, 429, 012060. doi:10.1088/1742-6596/429/1/012060
9. Kong, L., Tuomela, S., Hahne, L., Ahlfors, H., Yli-Harja, O., Fadeel, B., Lahesmaa, R., Autio, R. PLoS One 2013, 8, e68414. doi:10.1371/journal.pone.0068414
10. Jeliazkova, N., Doganis, P., Fadeel, B., Grafstrom, R., Hastings, J., Jeliazkov, V., Kohonen, P., Munteanu, C. R., Sarimveis, H., Smeets, B., Tsiliki, G., Vorgrimmler, D., Willighagen, E. The first eNanoMapper prototype: A substance database to support safe-by-design. In 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), IEEE: Piscataway, NJ, United States of America, 2014; pp 1-9. doi:10.1109/bibm.2014.6999367
11. Mustad, A. P., Smeets, B., Jeliazkova, N., Jeliazkov, V., Willighagen, E. Summary of the Spring 2014 NSC Database Survey; 2014. doi:10.6084/m9.figshare.1195888
12. Panneerselvam, S., Choi, S. Int. J. Mol. Sci. 2014, 15, 7158-7182. doi:10.3390/ijms15057158
13. Lynch, I. Compendium of Projects in the European NanoSafety Cluster. European NanoSafety Cluster; 2014; pp 250 ff.
14. Jeliazkova, N., Jeliazkov, V. J. Cheminf. 2011, 3, 18. doi:10.1186/1758-2946-3-18
15. Sansone, S.-A., Rocca-Serra, P., Field, D., Maguire, E., Taylor, C., Hofmann, O., Fang, H., Neumann, S., Tong, W., Amaral-Zettler, L., Begley, K., Booth, T., Bougueleret, L., Burns, G., Chapman, B., Clark, T., Coleman, L.-A., Copeland, J., Das, S., de Daruvar, A., de Matos, P., Dix, I., Edmunds, S., Evelo, C. T., Forster, M. J., Gaudet, P., Gilbert, J., Goble, C., Griffin, J. L., Jacob, D., Kleinjans, J., Harland, L., Haug, K., Hermjakob, H., Ho Sui, S. J., Laederach, A., Liang, S., Marshall, S., McGrath, A., Merrill, E., Reilly, D., Roux, M., Shamu, C. E., Shang, C. A., Steinbeck, C., Trefethen, A., Williams-Jones, B., Wolstencroft, K., Xenarios, I., Hide, W. Nat. Genet. 2012, 44, 121-126. doi:10.1038/ng.1054
16. Thomas, D. G., Gaheen, S., Harper, S. L., Fritts, M., Klaessig, F., Hahn-Dantona, E., Paik, D., Pan, S., Stafford, G. A., Freund, E. T., Klemm, J. D., Baker, N. A. BMC Biotechnol. 2013, 13, 2. doi:10.1186/1472-6750-13-2
17. Roebben, G., Rasmussen, K., Kestens, V., Linsinger, T. P. J., Rauscher, H., Emons, H., Stamm, H. J. Nanopart. Res. 2013, 15, 1455. doi:10.1007/s11051-013-1455-2
18. Series on the Safety of Manufactured Nanomaterials No. 27. List of manufactured nanomaterials and list of endpoints for phase one of the sponsorship programme for the testing of manufactured nanomaterials: revision, 2010.
19. Rumble, J., Freiman, S., Teague, C. The description of nanomaterials: A multi-disiciplinary uniform description system. In 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), IEEE: Piscataway, NJ, United States of America, 2014; pp 34-39. doi:10.1109/BIBM.2014.6999372
20. CODATA-VAMAS Working Group on the Description of Nanomaterials, Uniform Description System for Materials on the Nanoscale, 2015.
21. Abeyruwan, S., Vempati, U. D., Küçük-McGinty, H., Visser, U., Koleti, A., Mir, A., Sakurai, K., Chung, C., Bittker, J. A., Clemons, P. A., Brudz, S., Siripala, A., Morales, A. J., Romacker, M., Twomey, D., Bureeva, S., Lemmon, V., Schürer, S. C. J. Biomed. Semantics 2014, 5 (Suppl. 1), S5. doi:10.1186/2041-1480-5-S1-S5
22. Hastings, J., Jeliazkova, N., Owen, G., Tsiliki, G., Munteanu, C. R., Steinbeck, C., Willighagen, E. J. Biomed. Semantics 2015, 6, 10. doi:10.1186/s13326-015-0005-5
23. Hardy, B., Douglas, N., Helma, C., Rautenberg, M., Jeliazkova, N., Jeliazkov, V., Nikolova, I., Benigni, R., Tcheremenskaia, O., Kramer, S., Girschick, T., Buchwald, F., Wicker, J., Karwath, A., Gütlein, M., Maunz, A., Sarimveis, H., Melagraki, G., Afantitis, A., Sopasakis, P., Gallagher, D., Poroikov, V., Filimonov, D., Zakharov, A., Lagunin, A., Gloriozova, T., Novikov, S., Skvortsova, N., Druzhilovsky, D., Chawla, S., Ghosh, I., Ray, S., Patel, H., Escher, S. J., Cheminf. 2010, 2, 7. doi:10.1186/1758-2946-2-7
24. Kohonen, P., Benfenati, E., Bower, D., Ceder, R., Crump, M., Cross, K., Grafström, R. C., Healy, L., Helma, C., Jeliazkova, N., Jeliazkov, V., Maggioni, S., Miller, S., Myatt, G., Rautenberg, M., Stacey, G., Willighagen, E., Wiseman, J., Hardy, B. Mol. Inf. 2013, 32, 47-63. doi:10.1002/minf.201200114
25. European Commission. Towards the replacement of in vivo repeated dose systemic toxicity testing; 2013; Vol. 3.
26. Thangasamy, I. OpenAM; Packt Publishing Ltd.: Birmingham, U.K., 2011; pp 276 ff.
27. Willighagen, E. NanoWiki (release 1), 2015. doi:10.6084/m9.figshare.1330208
28. Walkey, C. D., Olsen, J. B., Song, F., Liu, R., Guo, H., Olsen, D. W. H., Cohen, Y., Emili, A., Chan, W. C. W. ACS Nano 2014, 8, 2439-2455. doi:10.1021/nn406018q
29. Vinken, M. Toxicology 2013, 312, 158-165. doi:10.1016/j.tox.2013.08.011
30. Godwin, H., Nameth, C., Avery, D., Bergeson, L. L., Bernard, D., Beryt, E., Boyes, W., Brown, S., Clippinger, A. J., Cohen, Y., Doa, M., Hendren, C. O., Holden, P., Houck, K., Kane, A. B., Klaessig, F., Kodas, T., Landsiedel, R., Lynch, I., Malloy, T., Miller, M. B., Muller, J., Oberdorster, G., Petersen, E. J., Pleus, R. C., Sayre, P., Stone, V., Sullivan, K. M., Tentschert, J., Wallis, P., Nel, A. E. ACS Nano 2015, 9, 3409-3417. doi:10.1021/acsnano.5b00941
31. Lynch, I., Weiss, C., Valsami-Jones, E. Nano Today 2014, 9, 266-270. doi:10.1016/j.nantod.2014.05.001
32. Klimisch, H.-J., Andreae, M., Tillmann, U. Regul. Toxicol. Pharmacol. 1997, 25, 1-5. doi:10.1006/rtph.1996.1076
33. ECHA. Evaluation of available information. Guidance on information requirements and chemical safety assessment; 2011; pp 16 ff.
34. Jahnke, L., Asher, A., Keralis, S. D. C. The Problem of Data; Council on Library and Information Resources, 2012.
35. ECHA Dissemination site, Multi-Walled Carbon Nanotubes (MWCNT), synthetic graphite in tubular shape. http://apps.echa.europa.eu/registered/data/dossiers/DISS-b281d1a0-c 6d8-5dcf-e044-00144f67d031/AGGR-64114fd2-a71c-46aa-ad6a-b519f e96dbc1_DISS-b281d1a0-c6d8-5dcf-e044-00144f67d031.html#AGGR- 64114fd2-a71c-46aa-ad6a-b519fe96dbc1 (accessed June 6, 2015).
36. Jaworska, J., Nikolova-Jeliazkova, N. SAR QSAR Environ. Res. 2007, 18, 195-207. doi:10.1080/10629360701306050
37. Jeliazkova, N., Kochev, N. Mol. Inf. 2011, 30, 707-720. doi:10.1002/minf.201100028
38. Nikolova, N., Jaworska, J. QSAR Comb. Sci. 2004, 22, 1006-1026. doi:10.1002/qsar.200330831
39. Willett, P., Barnard, J., Downs, G. J. Chem. Inf. Model. 1998, 38, 983-996. doi:10.1021/ci9800211
40. Maggiora, G., Vogt, M., Stumpfe, D., Bajorath, J. J. Med. Chem. 2014, 57, 3186-3204. doi:10.1021/jm401411z
41. Arts, J. H. E., Hadi, M., Irfan, M.-A., Keene, A. M., Kreiling, R., Lyon, D., Maier, M., Michel, K., Petry, T., Sauer, U. G., Warheit, D., Wiench, K., Wohlleben, W., Landsiedel, R. Regul. Toxicol. Pharmacol. 2015, 71, S1-S27. doi:10.1016/j.yrtph.2015.03.007
42. Gajewicz, A., Cronin, M. T. D., Rasulev, B., Leszczynski, J., Puzyn, T. Nanotechnology 2015, 26, 015701. doi:10.1088/0957-4484/26/1/015701
43. D3: A JavaScript visualization library for HTML and SVG; 2015, https://github.com/mbostock/d3/.
44. ambit.js, Release 0.0.2; E. Willighagen, 2015. doi:10.5281/zenodo.16517
45. Rorabacher, D. A. Anal. Chem. 1991, 63, 139-146. doi:10.1021/ac00002a010
46. Angiulli, F., Pizzuti, C. Fast Outlier Detection in High Dimensional Spaces. In Principles of Data Mining and Knowledge Discovery; Elomaa, T., Mannila, H., Toivonen, H., Eds., Lecture Notes in Computer Science, Vol. 2431; Springer: Berlin, Germany, 2002; pp 15-27.
47. Hautamaki, V., Karkkainen, I., Franti, P. Outlier Detection Using k-Nearest Neighbour Graph. In Proceedings of the 17th International Conference on Pattern Recognition (ICPR'04), IEEE Computer Society: Washington, DC, USA, 2004; pp 430-433.
48. Hsu, C.-W., Chang, C.-C., Lin, C.-J. A Practical Guide to Support Vector Classification. http://www.csie.ntu.edu.tw/~cjlin/papers/guide/guide.pdf (accessed March 15, 2015).
49. Arora, M., Bhambhu, L. Int. J. Adv. Res. Comput. Sci. Software Eng. 2014, 4, 271.
50. Guazzelli, A., Zeller, M., Lin, W.-C., Williams, G. The R Journal 2009, 1, 60-65.
51. Pechter, R. ACM SIGKDD Explorations Newsletter 2009, 11, 19-25. doi:10.1145/1656274.1656279
52. Tcheremenskaia, O., Benigni, R., Nikolova, I., Jeliazkova, N., Escher, S. E., Batke, M., Baier, T., Poroikov, V., Lagunin, A., Rautenberg, M., Hardy, B. J. Biomed. Semantics 2012, 3 (Suppl. 1), No. S7. doi:10.1186/2041-1480-3-S1-S7
53. Hall, M., Frank, E., Holmes, G., Pfahringer, B., Reutemann, P., Witten, I. H. ACM SIGKDD Explorations Newsletter 2009, 11, 10-18. doi:10.1145/1656274.1656278
54. R Core Team. R: A language and environment for statistical computing; R Foundation for Statistical Computing: Vienna, Austria, 2012.
55. Ooms, J. arXiv 2014, No. 1406.4806.
56. Smith, D. R is hot. http://www.revolutionanalytics.com/whitepaper/r-hot (accessed March 31, 2015).
57. Kim, J., Wang, G., Bae, S. T. Int. J. Semantic Comput. 2014, 08, 99-117. doi:10.1142/S1793351X14500056
58. Chang, C.-C., Lin, C.-J. ACM Trans. Intell. Syst. Technol. 2011, 2, No. 27. doi:10.1145/1961189.1961199
59. Sarimveis, H., Alexandridis, A., Bafas, G. Neurocomputing 2003, 51, 501-505. doi:10.1016/S0925-2312(03)00342-4
60. Steinbeck, C., Hoppe, C., Kuhn, S., Floris, M., Guha, R., Willighagen, E. L. Curr. Pharm. Des. 2006, 12, 2111-2120. doi:10.2174/138161206777585274
61. Stewart, J. J. P. J. Comput.-Aided Mol. Des. 1990, 4, 1-103. doi:10.1007/BF00128336
62. Netzeva, T. I., Worth, A., Aldenberg, T., Benigni, R., Cronin, M. T. D., Gramatica, P., Jaworska, J. S., Kahn, S., Klopman, G., Marchant, C. A., Myatt, G., Nikolova-Jeliazkova, N., Patlewicz, G. Y., Perkins, R., Roberts, D., Schultz, T., Stanton, D. W., van de Sandt, J. J. M., Tong, W., Veith, G., Yang, C. ATLA, Altern. Lab. Anim. 2005, 33, 155-173.
63. Jaworska, J., Nikolova-Jeliazkova, N., Aldenberg, T. ATLA, Altern. Lab. Anim. 2005, 33, 445-459.
64. O'Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., Hutchison, G. R. J. Cheminf. 2011, 3, 33. doi:10.1186/1758-2946-3-33
65. Gajewicz, A., Schaeublin, N., Rasulev, B., Hussain, S., Leszczynska, D., Puzyn, T., Leszczynski, J. Nanotoxicology 2015, 9, 313-325. doi:10.3109/17435390.2014.930195
66. Schneider, C. A., Rasband, W. S., Eliceiri, K. W. Nat. Methods 2012, 9, 671-675. doi:10.1038/nmeth.2089
67. Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. Nucleic Acids Res. 2012, 40, D109-D114. doi:10.1093/nar/gkr988
68. Kim, D., Joung, J.-G., Sohn, K.-A., Shin, H., Park, Y. R., Ritchie, M. D., Kim, J. H. J. Am. Med. Inf. Assoc. 2015, 22, 109-120.
69. Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., Harris, M. A., Hill, D. P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J. C., Richardson, J. E., Ringwald, M., Rubin, G. M., Sherlock, G. Nat. Genet. 2000, 25, 25-29. doi:10.1038/75556
70. Jeliazkova, N. Expert Opin. Drug Metab. Toxicol. 2012, 8, 791-801. doi:10.1517/17425255.2012.685158
71. Fielding, R. T., Taylor, R. N. Principled Design of the Modern Web Architecture. In Proceedings of the 22Nd International Conference on Software Engineering, ACM: New York, NY, U.S.A., 2000; pp 407-416.