Skip to main content

Modelling Aquatic Toxicity with Advanced Computational Techniques: Procedures to Standardize Data and Compare Models

  • Conference paper
Knowledge Exploration in Life Science Informatics (KELSI 2004)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 3303))

Abstract

Predictive chemical models, commonly called quantitative structure-activity relationships (QSAR), are facing a period of changes and challenges. There is a transition from classical models to new models, more sophisticated. Meanwhile, there is an increased interest in regulators on QSAR in fields as toxicity assessment. This requires more standardisation, even though the research is very dynamic and no common opinion exists on many issues. The present article is a contribution to the discussion on how to standardize data and compare models, with a special attention to advanced QSAR methods, identifying the problems and targets in the field.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Walker, J.D. (ed.): QSARs for Pollution Prevention, Toxicity Screening, Risk Assessment, and Web Applications. Society of Environmental Toxicology and Chemistry (SETAC), Pensacola FL, USA (2003)

    Google Scholar 

  2. Gini, G.C., Katritzky, A.R. (eds.): Predictive Toxicology of Chemicals: Experiences and Impact of AI Tools. AAAI 1999 Spring Symposium Series. AAAI Press, Menlo Park (1999)

    Google Scholar 

  3. Benfenati, E., Piclin, N., Roncaglioni, A., Varì, M.R.: Factors Influencing Predictive Models for Toxicology. SAR and QSAR in environmental research 12, 593–603 (2001)

    Article  Google Scholar 

  4. Russom, C.L., Bradbury, S.P., Broderius, S.J., Hammermeister, D.E., Drummond, R.A.: Predicting modes of action from chemical structure: Acute toxicity in the Fathead Minnow (Pimephales Promelas). Environmental Tox. and Chem. 16, 948–957 (1997)

    Google Scholar 

  5. http://airlab.elet.polimi.it/imagetox/

  6. http://www.openmolgrid.org/

  7. http://www.demetra-tox.net/

  8. http://www.epa.gov/ecotox/

  9. Benfenati, E., Pelagatti, S., Grasso, P., Gini, G.: COMET: the approach of a project in evaluating toxicity. In: Gini, G.C., Katritzky, A.R. (eds.) Predictive Toxicology of Chemicals: Experiences and Impact of AI Tools. AAAI 1999 Spring Symposium Series, pp. 40–43. AAAI Press, Menlo Park (1999)

    Google Scholar 

  10. Rudén, C., Hansson, S.O.: How accurate are the European Union.s classifications of chemical substances. Toxicology Letters 44, 159–172 (2003)

    Article  Google Scholar 

  11. Roncaglioni, A., Benfenati, E., Boriani, E., Clook, M.: A protocol to select high quality datasets of ecotoxicity values for pesticides. Journal of Environ. Science and Health, Part B 39, 641–652 (2004)

    Article  Google Scholar 

  12. Hermens, J.L.M.: Quantitative structure-activity relationships for predicting fish toxicity. In: Karcher, W., Devillers, J. (eds.) Practical Applications of Quantitative structure-activity relationships (QSAR) in Environmental Chemistry and Toxicology, pp. 263–280. Kluwer Academic Publishers, Dordrecht (1990)

    Google Scholar 

  13. Benfenati, E., Gini, G., Piclin, N., Roncaglioni, A., Varì, M.R.: Predicting LogP of pesticides using different software. Chemosphere 53, 1155–1164 (2003)

    Article  Google Scholar 

  14. Roncaglioni, A.: Comparison of chemical descriptors calculated in four laboratories. In: The Second IMAGETOX Seminars, Descriptors, analysis tools and industrial applications in modeling toxicity of compounds, Tartu, Estonia, June 2-4 (2003)

    Google Scholar 

  15. Smiesko, M., Benfenati, E.: Alerts on preparing datasets for QSAR studies in toxicity predictions. In: The 14 Annual Meeting, SETAC Europe, Prague, Czech Republic (April 18-22, 2004)

    Google Scholar 

  16. Roncaglioni, A., Fratev, F., Benfenati, E., Gustafsson, J.-Å.: Studies on oestrogen receptor: species and subtypes differences. In: The 11th International Workshop on Quantitative Structure-Activity Relationships in the Human Health and Environmental Sciences (QSAR 2004), Liverpool, England, (May 9-13, 2004)

    Google Scholar 

  17. Arciniegas, F., Bennett, K., Breneman, C., Embrechts, M.: Molecular database mining using self-organizing maps for the design of novel pharmaceuticals. In: Dagli, C.H. (ed.) Intelligent Engineering Systems through Artificial Neural Networks: Smart Engineering System Design, vol. 10, pp. 477–482. ASME Press, Washington (2000)

    Google Scholar 

  18. Allen, D.M.: The relationship between variable selection and data augmentation and a method for prediction. Technometrics 16, 125–127 (1974)

    Article  MATH  MathSciNet  Google Scholar 

  19. Clark, R.D.: Boosted leave-many-out cross-validation: the effect of training and test set diversity on PLS statistics. J. Comp.-Aided Mol. Des. 17, 265–275 (2003)

    Article  Google Scholar 

  20. Golbraikh, A., Tropsha, A.: Beware of q2! Journal of Molecular Graphics and Modelling 20, 269–276 (2002)

    Google Scholar 

  21. Hawkins, D.M.: The problem of overfitting. J. Chem. Inf. Comput. Sci. 44, 1–12 (2004)

    MathSciNet  Google Scholar 

  22. http://www.epa.gov/oppt/newchems/21ecosar.htm

  23. Renners, I., Grauel, A., Ludwig, L.A., Benfenati, E., Pelegatti, S., Robert, D., Carbó-Dorca, R., Girones, X.: Modeling toxicity with molecular descriptors and similarity measures via B-spline networks. In: Proceedings of the 8th International Conference on Information Processing and Management of Uncertainty in Knowledge-Based Systems, IPMU 2000, Madrid, Spain, July 3-7, vol. II, pp. 1021–1026 (2000)

    Google Scholar 

  24. Katritzky, A.R., Lobanov, V.S., Karelson, M.: CODESSA: Comprehensive Descriptors for Structural and Statistical Analysis, version 2.2.1. Reference Manual. University of Florida, Gainesville, Florida, U.S.A (1994)

    Google Scholar 

  25. Roncaglioni, A., Colombo, A., Maran, U., Karelson, M., Benfenati, E.: Prediction of acute aquatic Toxicity to Fish Comparing Different QSAR Approaches. In: 41st Congress of the European Societies of Toxicology, Florence, Italy, (September 28 - October 1, 2003)

    Google Scholar 

  26. Lemke, F., Benfenati, E., Gini, G., Netzeva, T., Cronin, M., Aynur, A.O., Schüürmann, G.: GMDH Models for fathead minnow toxicity using ab initio or AM1 descriptors. In: The 11th International Workshop on Quantitative Structure-Activity Relationships in the Human Health and Environmental Sciences (QSAR 2004), Liverpool, England, May 9-13 (2004)

    Google Scholar 

  27. Toropov, A.A., Benfenati, E.: QSAR modelling of aldehyde toxicity by means of optimization of correlation weights of nearest neighbourings code. J. Mol. Struct (THEOCHEM) 676, 165–169 (2004)

    Article  Google Scholar 

  28. Smiesko, M., Benfenati, E.: Predictive models for aquatic toxicity of aldehydes designed for various model chemistries. J. Chem. Inf. Comput. Sci. 44, 976–984 (2004)

    Google Scholar 

  29. König, C., Gini, G., Marian, C., Benfenati, E.: Multi-class classifier from a combination experts: towards distributed computation real-problem classifiers. International Journal of Pattern Recognition and Artificial Intelligence (in press)

    Google Scholar 

  30. Benfenati, E., Gini, G., König, C., Craciun, M.: Prediction of Aquatic Toxicity with combined Neural Networks. The 14 Annual Meeting, SETAC Europe, Prague, Czech Republic, (April 18-22, 2004)

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2004 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Benfenati, E. (2004). Modelling Aquatic Toxicity with Advanced Computational Techniques: Procedures to Standardize Data and Compare Models. In: López, J.A., Benfenati, E., Dubitzky, W. (eds) Knowledge Exploration in Life Science Informatics. KELSI 2004. Lecture Notes in Computer Science(), vol 3303. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30478-4_20

Download citation

  • DOI: https://doi.org/10.1007/978-3-540-30478-4_20

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-23927-7

  • Online ISBN: 978-3-540-30478-4

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics