The interplay between QSAR/QSPR studies and partial order ranking and formal concept analyses

International Journal of Molecular Sciences

Volumn 10, Issue 4, 2009, Pages 1628-1657

  Carlsen, Lars ^a,b  

^a Awareness Center Roskilde   (Denmark)

^b Department of General and Applied Chemistry   (Kazakhstan)

Author keywords

Environmental impacts; Human health impact; Partial order ranking, hasse diagrams, posets, formal concept analysis; QSAR; QSPR; Risk assessment; Rocket fuel

Indexed keywords

1,1 DIMETHYLHYDRAZINE; FUEL;

ACUTE TOXICITY; ANALYTIC METHOD; ANALYTICAL PARAMETERS; BIOACCUMULATION; BIOREMEDIATION; CHEMICAL ANALYSIS; ECOTOXICOLOGY; ENVIRONMENTAL IMPACT; FORMAL CONCEPT ANALYSIS; HUMAN; PARTIAL ORDER RANKING; POLLUTANT; QUANTITATIVE STRUCTURE ACTIVITY RELATION; QUANTITATIVE STRUCTURE PROPERTY RELATION; REVIEW;

ENVIRONMENTAL IMPACTS; HUMAN HEALTH IMPACT; PARTIAL ORDER RANKING, HASSE DIAGRAMS, POSETS, FORMAL CONCEPT ANALYSIS; QSAR; QSPR; RISK ASSESSMENT; ROCKET FUEL;

ANIMALS; BIODEGRADATION, ENVIRONMENTAL; DAPHNIA; DIMETHYLHYDRAZINES; ECOTOXICOLOGY; ENVIRONMENTAL POLLUTANTS; HALF-LIFE; HUMANS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; RISK ASSESSMENT; SOIL; WATER;

EID: 67149084293     PISSN: None     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms10041628     Document Type: Review

References (70)

1. Voigt, K.; Brüggemann, R.; Pudenz, S. Chemical databases evaluated by order theoretical tools. Anal. Bioanal.Chem., 2004, 380, 467-474.
2. Voigt, K.; Brüggemann, R.; Pudenz, S. A multi-criteria evaluation of environmental databases using the Hasse Diagram Technique (ProRank) software. Environ. Modell. Softw. 2006b, 21, 1587-1597.
3. Voigt, K.; Brüggemann R.; Pudenz S. Information quality of environmental and chemical databases exemplified by high production volume chemicals and pharmaceuticals. Online Inf. Rev. 2006, 30, 8-23.
4. Carlsen, L.; Kenesova, O.A.; Batyrbekova, S.E. A preliminary assessment of the potential environmental and human health impact of unsymmetrical dimethylhydrazine as a result of space activities. Chemosphere 2007, 67, 1108-1116.
5. Carlsen, L.; Kenessov, B.N.; Batyrbekova, S.Ye. A QSAR/QSTR study on the environmental health impact by the rocket fuel heptyl and its transformation products. Environ. Health Insights 2008, 1, 11-20. Available online: http://la-press.com/article.php?article-id=913, Accessed February 2009.
6. Carlsen, L.; Kenessov, B.N.; Batyrbekova, S.Ye. A QSAR/QSTR study on the human health impact of the rocket fuel 1,1-dimethyl hydrazine and its transformation products. Multicriteria hazard ranking based on partial order methodologies. Environ. Toxicol. Pharmacol. 2009, 27, 415-423.
7. Ivanciuc, T.; Ivanciuc, O.; Klein, D.J. Posetic Quantitative Superstructure/Activity Relationships (QSSARs) for Chlorobenzenes. J. Chem. Inf. Model. 2005, 45, 870-879.
8. Klein, D.J.; Ivanciuc, T.; Ryzhov, A.; Ivanciuc, O. Combinatorics of Reaction-Network Posets. Comb. Chem. High Throughput Scr. 2008, 11, 723-733.
9. Verdonck, F.A.M.; Boeije, G.; Vandenberghe, V.; Comber, M.; de Wolf, W.; Feijtel, T.; Holt, M.;Koch, K.; Lecloux, A.; Siebel-Sauer, A.; Vanrolleghem, P.A. A rule-based screening environmental risk assessment tool derived from EUSES. Chemosphere 2005, 58, 1169-1176.
10. Sørensen, P.B.; Brüggemann, R.; Carlsen, L.; Mogensen, B.B.; Kreuger, J.; Pudenz, S. Analysis of monitoring data of pesticide residues in surface waters using partial order ranking theory, Environ. Toxicol. Chem. 2003, 22, 661-670.
11. Carlsen, L. Giving molecules an identity. On the interplay between QSARs and Partial Order Ranking. Molecules 2004, 9, 1010-1018. Available online http://www.mdpi.org/molecules/-papers/91201010.pdf. Accessed February 2009.
12. Carlsen, L. A QSAR Approach to physico-chemical data for organophosphates with special focus on known and potential nerve agents. Internet Electron. J. Mol. Des. 2005, 4, 355-366. Available online http://biochempress.com/Files/IECMD-2004/IECMD-2004-001.pdf, Accessed February 2009.
13. Carlsen, L. Partial order ranking of organophosphates with special emphasis on nerve agents, MATCH-Commun. Math. Comput. Chem. 2005, 54, 519-534.
14. Carlsen, L. Interpolation schemes in QSAR. In Partial Order in Environmental Sciences and Chemistry, Brüggemann, R., Carlsen, L., Eds.; Springer, Berlin, 2006; pp. 163-180.
15. Carlsen, L. A combined QSAR and partial order ranking approach to risk assessment. SAR QSAR Environ. Res. 2006, 17, 133-146.
16. Carlsen, L. Hierarchical partial order ranking. Environ. Pollut. 2008, 155, 247-253.
17. Burmeister, P. Formal concept analysis with ConImp: Introduction to the basic features. Available online http://www.mathematik.tu-darmstadt.de/ ∼burmeister/ConImpIntro.pdf, Accessed February 2009.
18. Formal Concept Analysis: Foundations and Applications, Ganter, B.; Stumme, G.; Wille, R., Eds.; Springer: Berlin, Germany, 2005.
19. Johnson, M.H.; Maggiora, G.M. Concepts and Applications of Molecular Similarity; Wiley, New York, USA, 1990.
20. Crum-Brown, A.; Frazer, T. On the connection between chemical constitution and physiological action. Part I. On the physiological action of the ammonium bases, derived from Strychia, Brucia, Thebaia, Codeia, Morphia and Nicotia. Trans. Royal Soc. Edinburgh 1868/1869, 25, 257-274.
21. Meyer, H. Zur Theorie der Alkoholnarkose, welche Eigenschaft die Anästhetica bedingt ihre narkotische Wirkung. Arch. Exp. Pathol. Pharmakol. 1899, 42, 109-118.
22. Overton, C.E. Studien über die Narkose. Zugleich ein Beitrag zur Allgemeine Pharmakologie. Gustav Fischer Verlag: Jena, Germany, 1901.
23. Ferguson, J. The use of chemical potentials as indicators for toxicity. Proc. Royal Soc. B 1939, 127, 387.
24. Hansch, C.; Leo, A. Exploring QSAR. Fundamentals and Applications in Chemistry and Biology; ACS: Washington DC, USA, 1995.
25. Bevan, D.R. QSAR and Drug Design. Available online http://www.netsci.org/ Science/-Compchem/feature12.html, Accessed February 2009.
26. 3D-QSAR in drug design. In Theory Methods and Applications, Kubinyi, H. Ed.; Kluwer/Escom: Dordrecht, The Netherlands, 1998.
27. Neural Networks in QSAR and Drug Design, Devilliers, J. Ed.; Academic Press: London, UK, 1996.
28. Kurup, A.; Garg, R.; Carini, D.J.; Hansch, C. Comparative QSAR: Angiotensin II antagonists, Chem. Rev. 2001, 101, 2727-2750.
29. Jaworska, J.; Comber, M.; Auer, C.; Leeuwen, C.J. Summary of a workshop on regulatory acceptance of (Q)SARs for human health and environmental endpoints. Env. Health Perspect. 2003, 111, 1358-1360.
30. Eriksson, L.; Jaworska, J.; Worth, A.P.; Cronin, M.T.D.; McDowell, R.M.; Gramatica, P. Methods for reliability and uncertainty assessment, and for applicability evaluations of classification- and regression-based QSARs. Env. Health Perspect. 2003, 111, 1361-1375.
31. Cronin, M.T.D.; Walker, J.D.; Jaworska, J.S.; Comber, M.H.I.; Watts, C.D.; Worth, A.P. Use of QSARs in international decisions-making frameworks to predict ecological effects and environmental fate of chemical substances. Env. Health Perspect. 2003, 111, 1376-1390.
32. Cronin, M.T.D.; Walker, J.D.; Jaworska, J.S.; Comber, M.H.I.; Watts, C.D.; Worth, A.P. Use of QSARs in international decisions-making frameworks to predict health effects of chemical substances. Env. Health Perspect. 2003, 111, 1391-1401.
33. Worth, A. QSC QSAR and Combinatorial. Science 2008, 27, 1-132.
34. EPA Estimation Program Interface (EPI) Suite. Available online http://www.epa.gov/oppt/-exposure/pubs/episuite.htm, Accessed February 2009.
35. PASS1, Prediction of Activity Spectra for Substances. Available online http://195.178.207.233/PASS/, Accessed February 2009.
36. Pharma Algorithms 1, ADME/Tox WEB. Available online http://www.pharma-algorithms.com/webboxes/, Accessed February 2009.
37. Nauryzbaev, M.K.; Batyrbekova, S.E; Tassibekov, Kh.S.; Kenesov, B.N.; Vorozheikin, A.P.; Proskuryakov, Yu.V. Ecological problems of central Asia resulting from space rocket debris. In History and Society in Central and Inner Asia, Toronto Studies in Central and Inner Asia, No. 7, Asian Institute, University of Toronto, Toronto, 2005; pp. 327-349.
38. System analysis of environmental objects in the territories of Kazakhstan, which suffered negative influence through Baikonur space port activity, Final technical Report of ISTC K451.2, Center of Physical-Chemical Methods of Analysis, al-Farabi Kazakh National University in Almaty, Kazakhstan, 2006.
39. European Commission. Regulation (EC) No 1907/2006 of the European Parliament and of the Council of 18 December 2006 concerning the Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH), establishing a European Chemicals Agency, amending Directive 1999/45/EC and repealing Council Regulation (EEC) No 793/93 and Commission Regulation (EC) No 1488/94 as well as Council Directive 76/769/EEC and Commission Directives 91/155/EEC, 93/67/EEC, 93/105/EC and 2000/21/EC. Available online http://eur- lex.europa.eu/ LexUriServ/site/en/oj/2006/l-396/l-39620061230en00010849.pdf, Article 57d,e, 2006, Assessed February 2009.
40. European Commision. Technical Guidance Document on Risk Assessment in support of Commission Directive 93/67/EEC on Risk Assessment for new notified substances Commission Regulation (EC) No 1488/94 on Risk Assessment for existing substances Directive 98/8/EC of the European Parliament and of the Council concerning the placing of biocidal products on the market Part I. EUR 20418 EN/1. 2003.European Communities, 2003.
41. Adushkin, V.V; Kozlov, C.I.; Petrov, A.V. Ecological Problems and Risks of Rocket-Space Techniques Impacts on Environment. Ankil: Moscow, Russia, 2000.
42. Carlsen, L. Formal concept analyses of the ecotoxicological and health effects of residual rocket fuel and its transformation products. 2009, in press.
43. Ivanciuc, O.; Ivanciuc, D. J. Klein. Modeling the Bioconcentration Factors and BioaccumulationFactors of Polychlorinated Biphenyls with Posetic Quantitative Super- Structure/Activity Relationships (QSSAR). Mol. Diversity 2006, 10, 133-145.
44. Partial Order in Environmental Sciences and Chemistry, Brüggemann, R., Carlsen, L., Eds.; Springer, Berlin, Germany, 2006.
45. Walker, J.D.; Carlsen, L. QSARs for Identifying and Prioritizing Substances with Persistence and Bioconcentration Potential. SAR QSAR Environ. Res. 2002, 13, 713-726.
46. Ecological Structure Activity Relationship (Escosar), Available online http://www.epa.gov/oppt/-newchems/tools/21ecosar.htm, Accessed February 2009.
47. Pharma Algorithms 2, ADME Boxes 4.0, Available online http://pharma-algorithms.com/-adme-boxes.htm, Accessed February 2009.
48. Sazonovas, A. Descriptions, incl. validation of the sigle ADME Boxes and ToxBoxes modules. Personal communication from A. Sazonovas, Pharma Algorithms, 2009.
49. PASS2, List of predicted activities, Available online http://195.178.207.233/PASS/A.php,Accessed February 2009.
50. PASS3. Quality of prediction, Available online http://195.178.207.233/PASS/QA.html, AccessedFebruary 2009.
51. PASS4. Basic elements of PASS, Available online http://195.178.207.233/PASS/Pe.htmlAccessed February 2009.
52. Poroikov, V.V.;Filimonov, D.A.; Ihlenfeldt, W.-D.; Gloriozova, T.A.; Lagunin, A.A.; Borodina, Yu.V.; Stepanchikova, A.V.; Nicklaus M.C. PASS Biological activity spectrum predictions in the enhanced open NCI database browser. J. Chem. Inform. Comput. Sci. 2003, 43, 228-236.
53. PASS5. Limitations. Available online http://195.178.207.233/PASS/ Lim.html, Accessed February 2009.
54. Davey, B.A.; Priestley, H.A. Introduction to lattices and Order. Cambridge University Press: Cambridge, UK, 1990.
55. Brüggemann, R.; Halfon, E.; Welzl, G.; Voigt, K.; Steinberg, C.E.W. Applying the concept of partially ordered sets on the ranking of near-shore sediments by a battery of tests. J. Chem. Inf. Comput. Sci. 2001, 41, 918-925.
56. Halfon, E.; Reggiani, M.G. On the ranking of chemicals for environmental hazard. Environ. Sci. Technol. 1986, 20, 1173-1179.
57. Hasse, H. Über die Klassenzahl abelscher Zahlkörper. Akademie Verlag: Berlin, Germany, 1952.
58. Brüggemann, R.; Halfon, E.; Bücherl, C. Theoretical base of the program "Hasse". GSF-Bericht 20/95, Neuherberg, Germany, 1995. The software may be obtained by contacting Dr. R. Brüggemann, Institute of Freshwater Ecology and Inland Fisheries, Berlin (brg-home@web.de).
59. European Chemical Bureau DART. Decision Analysis by Ranking Techniques; Available online http://ecb.jrc.it/qsar/qsar-tools/index.php?c= DART, Accessed February 2009.
60. Brüggemann, R.; Restrepo, G.; Voigt, K. Towards a New and Advanced Partial Order Program: PyHasse in Multicriteria Ordering and Ranking: Partial Orders, Ambiguities and Applied Issues, Systems Research Institute Polish Academy of Sciences, Warsaw, pp. 11-33. The software may be obtained by contacting Dr. R. Brüggemann, Institute of Freshwater Ecology and Inland Fisheries, Berlin (brg-home@web.de).
61. Fishburn, P.C. On the family of linear extensions of a partial order. J. Combinat. Theory 1974, 17, 240-243.
62. Graham, R.L. Linear Extensions of Partial Orders and the FKG Inequality. In Ordered Sets, Rival, I., Ed.; Reidel Publishing Company: Dordrecht, The Netherlands, 1982, pp. 213-236.
63. Winkler, P.M. Average height in a partially ordered set. Discrete Math. 1982, 39, 337-341.
64. Winkler, P.M. Correlation among partial orders. Siam. J. Alg. Disc. Meth. 1983, 4, 1-7.
65. Sørensen, P.B.; Lerche, D.B.; Carlsen and L.; Brüggemann, R. Statistically approach for estimating the total set of linear orders. A possible way for analysing larger partial order sets In Order Theoretical Tools in Environmental Science and Decision Systems, Brüggemann, R., Pudenz, S., Lühr, H.-P., Eds.; Berichte des IGB, Leibniz-Institut of Freshwater Ecology and Inland Fisheries: Berlin, Heft 14, Sonderheft IV, 2001; pp. 87-97.
66. Lerche, D.; Brüggemann, R.; Sørensen, P.; Carlsen, L.; Nielsen, O.J. A comparison of partial order technique with three methods of multi-criteria analysis for ranking of chemical substances. J. Chem. Inf. Comput. Sci. 2002, 42, 1086-1098.
67. Lerche, D.; Sørensen, P.B.; Brüggemann, R. Improved estimation of ranking probabilities in partial orders using random linear extensions by approximation of the mutual ranking probability. J. Chem. Inf. Comput. Sci. 2003, 43, 1471-1480.
68. Brüggemann, R.; Lerche, D.; Sørensen, P.B.; Carlsen, L. Estimation of average ranks by a local partial order model, J. Chem. Inf. Comput. Sci. 2004, 44, 618-625.
69. Sørensen, P.B.; Mogensen, B.B.; Carlsen, L.; Thomsen M. The influence of partial order ranking from input parameter uncertainty. Definition of a robustness parameter. Chemosphere 2000, 41, 595-601.
70. th National Conference on Artificial Intelligence KII-2000, Russia, 2000; pp. 127-134.