Abstract
Recent chemical applications of Formal Concept Analysis are reviewed, showing that molecular structure and activity of substances may be related through association rules, which is exemplified for mutagenicity and hepatotoxicity cases. Nuclear chemistry and nuclear medicine cases are explored, where attributes of radionuclides are related. A study of biotechnology application to uranium bioremediation is conducted and some Gram-positive bacteria are found as better uranium uptakers.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Bartel H-G, Bruggemann R (1998) Application of formal concept analysis to structure-activity relationships. Fresenius J Anal Chem 361:23–38
Bäuerlein E (2003) Biomineralization of unicellular organisms: an unusual membrane biochemistry for the production of inorganic nano- and microstructures. Angew Chem Int Ed Engl 42:614–641
Bemis GW, Murcko MA (1996) The properties of known drugs. 1. Molecular Frameworks. J Med Chem 39:2887–2893
Berardi M, Appice A, Loglisci C, Leo P (2006) Supporting visual exploration of discovered association rules through multi-dimensional scaling. In: Esposito F, Râs ZW, Malerba D, Semeraro G (eds) Foundations of intelligent systems, 16th International Symposium, ISMIS 2006, vol 4203, Lecture notes in computer science. Springer, Berlin
Carpineto C, Romano G (2004) Concept data analysis: theory and applications. Wiley, Hoboken, NJ, 07030, USA, pp 1–220
Carrió I, González P, Estorch M, Canessa J, Mitjavila M, Massardo T (2003) Medicina nuclear. Aplicaciones clínicas. Masson. S.A, Barcelona
Chen M, Vijay V, Shi Q, Liu Z, Jang H, Tong W (2011) FDA-approved drug labeling for the study of drug-induced liver injury. Drug Discov Today 16:697–703
Clark RD, Wolohan PR, Hodgkin EE, Kelly JH, Sussman NL (2004) Modelling in vitro hepatotoxicity using molecular interaction fields and SIMCA. J Mol Graph Model 22:487–497
Dambach D, Andrews B, Moulin F (2005) New technologies and screening strategies for hepatotoxicity: use of in vitro models. Toxicol Pathol 33:17–26
Ekins S, Williams AJ, Xu JJ (2010) A predictive ligand-based Bayesian model for human drug-induced liver injury. Drug Metab Dispos 38(12):2302–2308
Franke R, Gruska A, Giuliani A, Benigni R (2001) Prediction of rodent carcinogenicity of aromatic amines: a quantitative structure-activity relationships model. Carcinogenesis 22(9):1561–1571
Ganter B, Wille R (1998) Formal concept analysis: mathematical foundations. Springer, Berlin
Gardiner EJ, Gillet VJ (2015) Perspectives on knowledge discovery algorithms recently introduced in chemoinformatics: rough set theory, association rule mining, emerging patterns, and formal concept analysis. J Chem Inf Model 55(9):1781–1803
Greene N, Fisk L, Naven RT, Note RR, Patel ML, Pelletier DJ (2010) Developing structure-activity relationships for the prediction of hepatotoxicity. Chem Res Toxicol 19(23):1215–1222
Gupta R, Saxena RK, Mohapatra H, Ahuja P (2002) Microbial variables for bioremediation of heavy metals from industrial effluents. In: Singh VP, Stapleton JR (eds) Biotransformations: bioremediation and technology for health and environmental protection, vol 36, Progress in industrial microbiology. Elsevier, Amsterdam, pp 189–230
Hammaini A, González F, Ballester A, Blázques ML, Muñoz JA (2007) Biosorption of heavy metals by activated sludge and their desorption characteristics. J Environ Manage 84:419–426
Herzog H, Tellmann L, Scholten B, Cohenen HH, Qaim SM (2008) PET imaging problems with the non-standard positron emitters Yttrium-86 and Iodine-124. Q J Nucl Med Mol Imaging 52(2):159–165
Horikoshi T, Nakajima A, Sakaguchi T (1981) Studies on the accumulation of heavy metal elements in biological systems. Eur J Appl Microbiol 12(2):90–96
Kazy SK, D’Souza SFD, Pinaki S (2009) Uranium and thorium sequestration by a Pseudomonas sp.: mechanism and chemical characterization. J Hazard Mater 163:65–72
Lattice Miner (2015) http://sourceforge.net/projects/lattice-miner/. Accessed 25 Apr 2015
Leach AR, Guillet V (2007) An introduction to chemoinformatics. Kluwer, Dordrecht, The Netherlands. doi:10.1007/978-1-4020-6291-9
Lenca P, Meyer P, Vaillant B, Lallich S (2008) On selecting interestingness measures for association rules: user oriented description and multiple criteria decision aid. Eur J Oper Res 184(2):610–628
Lounkine E, Auer J, Bajorath J (2008) Formal concept analysis for the identification of molecular fragment combinations specific for active and highly potent compounds. J Med Chem 51(17):5342–5348
Low Y, Uehara T, Minowa Y, Yamada H, Ohno Y, Urushidani T, Sedykh A, Muratov E, Kuz’min V, Fourches D, Zhu D, Rusyn I, Tropsha A (2011) Predicting drug-induced hepatotoxicity using QSAR and toxicogenomics approaches. Chem Res Toxicol 24(8):1251–1262
McNicholas PD, Murphy TB, O’Regan M (2008) Standardising the lift of an association rule. Comput Stat Data Anal 52:4712–4721
Nakajima A, Sakaguchi T (1986) Selective accumulation of heavy metals by microorganisms. Appl Microbiol Biot 24:59–64
Nakajima A, Tsuruta T (2002) Competitive biosorption of thorium and uranium by actinomycetes. J Nucl Sci Technol 39(Suppl 3):528–531
Nakajima A, Tsuruta T (2004) Competitive biosorption of thorium and uranium by Micrococcus luteus. J Radioanal Nucl Chem 260(1):13–18
Njoku DB (2014) Drug-induced hepatotoxicity: metabolic, genetic and immunological basis. Int J Mol Sci 15:6990–7003
Noyes R (1995) Nuclear wastes cleanup technology and opportunities. Noyes, Park Ridge, NJ
Osborne JW (2010) Improving your data transformations: applying the Box-Cox transformation. Practical assessment. Res Eval 15(12):1–9
Ozer JS, Chetty R, Kenna G, Palandra J, Zhang Y, Lanevschi A, Koppiker N, Souberbielle BE, Ramaiah SK (2010) Enhancing the utility of alanine aminotransferase as a reference standard biomarker for drug-induced liver injury. Regul Toxicol Pharmacol 56:237–246
Pagani M, Stone-Elander S, Larsson SA (1997) Alternative positron emission tomography with non-conventional positron emitters: effects of their physical properties on image quality and potential clinical applications. Eur J Nucl Med 24(10):1301–1327
Plasse M, Niang N, Saporta G, Villeminot A, Leblond L (2007) Combined use of association rules mining and clustering methods to find relevant links between binary rare attributes in a large data set. Comput Stat Data Anal 52(1):596–613
Priss U (2008) FcaStone-FCA file format and interoperability software. In: Croitoru M, Jaschkë R, Rudolph S (eds). Conceptual structures and the web. Proceedings of the third conceptual structures and tool interoperability workshop, pp 33–43
Quintero NY, Restrepo G, Cohen IM (2013a) Chemotopological study of positron emitters ra-dionuclides used in PET diagnostic imaging: physical, physico-chemical, dosimetric, quantum and nuclear properties. J Radioanal Nucl Chem 295(2):823–833
Quintero NY, Restrepo G, Cohen IM (2013b) Relating β + radionuclides’ properties by order theory. J Radioanal Nucl Chem 298(3):1937–1946
Raaphorst RM, Windhorst AD, Elsinga PH, Colabufo NA, Lammertsma AA, Luurtsema G (2015) Radiopharmaceuticals for assessing ABC transporters at the blood-brain barrier. Clin Pharmacol Ther 97(4):362–371
Reitz T, Merroun ML, Rossberg A, Selenska-Pobell S (2010) Interactions of Sulfolobus acidocaldarius with uranium. Radiochim Acta 98:249–257
Reitz T, Rossberg A, Barkleit A, Selenska-Pobell S, Merroun ML (2014) Decrease of U (VI) immobilization capability of the facultative anaerobic strain Paenibacillus sp. JG-TB8 under anoxic conditions due to strongly reduced phosphatase activity. PLoS One 9(8):1–13
Restrepo G, Mesa H, Llanos EJ, Villaveces JL (2004) Topological study of the periodic system. JChem Inf Comput Sci 44(1):68–75
Restrepo G, Mesa H (2011) Chemotopology: beyond neighbourhoods. Curr Comput Aided Drug Des 7(2):90–97
Restrepo G, Basak S, Mills D (2011) Comparison of QSARs and characterization of structural basis of bioactivity using partial order theory and formal concept analysis: a case study with mutagenicity. Curr Comput Aided Drug Des 7(2):109–121
Restrepo G, Harré R (2015) Mereology of quantitative structure-activity relationships models. HYLE Int J Phil Chem 21:19–38
Rincón-Villamizar E, Restrepo G (2014) Rules relating hepatotoxicity with structural attributes of drugs. Toxicol Environ Chem 96(4):594–613
Sanche R, Lonergan KF (2006) Variable reduction for predictive modeling with modeling clustering. Casualty Actuarial Society Forum, pp 89–100
Singh N, Gadi R (2012) Bioremediation of Ni (II) and Cu (II) from wastewater by the nonliving biomass of Brevundimonas vesicularis. J Environ Chem Ecotoxicol 4(8):137–142
Smith JT (2011) Nuclear accidents. In: Hester RE, Harrison RM (eds) Nuclear power and environment, vol 32, Issues in environmental science and technology. Royal Society of Chemistry, London
Stephens LJ (1998) Theory and problems of beginning statistics, Schaum’s outline series. McGraw-Hill, Mexico
Suk KT, Kim DJ (2012) Drug-induced liver injury: present and future. Clin Mol Hepatol 18(3):249–257
Todeschini R, Consonni V (2009) Molecular descriptors for chemoinformatics. Wiley-VCH, Weinheim
Tsuruta T (2007) Removal and recovery of uranium using microorganisms isolated from North American uranium deposits. Am J Environ Sci 3(2):60–66
van Hullebusch E, Lens PNL, Tabak HH (2005) Developments in bioremediation of soils and sediments polluted with metals and radionuclides. 3. Influence of chemical speciation and bioavailability on contaminants immobilization/mobilization bio-processes. Rev Environ Sci Biotechnol 4:185–212
Yevtushenko SA (2000) System of data analysis “Concept Explorer”. Proceedings of the 7th national conference on Artificial Intelligence KII, Russia, pp 127–134
Yi Z, Lian B (2012) Adsorption of U (VI) by Bacillus mucilaginosus. J Radioanal Nucl Chem 293(1):321–329
Yi Z, Yao J (2012) Kinetic and equilibrium study of uranium (VI) adsorption by Bacillus licheniformis. J Radioanal Nucl Chem 293(3):907–914
Ziessmann H, O’Malley J, Thrall JH (2007) Medicina nuclear: Los requisitos en radiología. Elsevier, España
Acknowledgements
N. Y. Quintero thanks Colciencias (Colombia) for the Ph.D. grant to conduct the current study. She also thanks Professors A. Nakajima and T. Reitz for their valuable comments regarding U bioremediation. G. Restrepo thanks the Alexander von Humboldt Foundation/Stiftung and the Universidad de Pamplona for the support to conduct this research.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer International Publishing AG
About this chapter
Cite this chapter
Quintero, N.Y., Restrepo, G. (2017). Formal Concept Analysis Applications in Chemistry: From Radionuclides and Molecular Structure to Toxicity and Diagnosis. In: Fattore, M., Bruggemann, R. (eds) Partial Order Concepts in Applied Sciences. Springer, Cham. https://doi.org/10.1007/978-3-319-45421-4_14
Download citation
DOI: https://doi.org/10.1007/978-3-319-45421-4_14
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-45419-1
Online ISBN: 978-3-319-45421-4
eBook Packages: Earth and Environmental ScienceEarth and Environmental Science (R0)