Storing the Wisdom: Chemical Concepts and Chemoinformatics
Abstract
:1. Introduction
2. Concepts
3. Concepts in Information Science
4. Concepts in Chemistry
- Two-dimensional patterns of molecular structure
- Two-dimensional patterns of bonding
- Three-dimensional patterns of structure
- Types of reaction
- Properties of a substance or substructure
5. Representations of Chemical Concepts
6. Concepts in Chemical Information Systems
- Basic concepts
- Substance
- Reaction
- Property
- Organising concepts
- Chemical structure
- Periodicity
- Detailed concepts
- Two-dimensional patterns of structure
- Two-dimensional patterns of bonding
- Three-dimensional patterns of structure
- Reaction types
- Property concepts
6.1. Basic Concepts
6.2. Organising Concepts
6.3. Detailed Concepts
6.3.1. Two-Dimensional Patterns of Structure
6.3.2. Two-Dimensional Patterns of Bonding
6.3.3. Three-Dimensional Patterns of Structure
6.3.4. Reaction Types
6.3.5. Property Concepts
7. Conclusions
Acknowledgments
Conflicts of Interest
References
- Weitz, M. Theories of Concepts: A History of the Major Philosophical Tradition; Routledge: London, UK, 1988. [Google Scholar]
- Margolis, E.; Laurence, S. Concepts. In The Stanford Encyclopedia of Philosophy, Spring 2014 ed.; Zalta, E.N., Ed.; Available online: http://plato.stanford.edu/archives/spr2014/entries/concepts (accessed on 17 September 2015).
- Hjørland, B. Concept theory. J. Am. Soc. Inf. Sci. Technol. 2009, 60, 1519–1536. [Google Scholar] [CrossRef]
- Margolis, E.; Laurence, S. The ontology of concepts-abstract objects or mental representations? Noûs 2007, 41, 561–593. [Google Scholar] [CrossRef]
- Van Loocke, P. The Nature of Concepts: Evolution, Structure and Representation; Routledge: London, UK, 1999. [Google Scholar]
- Peacocke, C. A Study of Concepts; MIT Press: Cambridge, MA, USA, 1992. [Google Scholar]
- Zalta, E. Fregean senses, modes of presentation, and concepts. Philos. Perspect. 2001, 15, 335–359. [Google Scholar] [CrossRef]
- Hale, B. Abstract Objects; Blackwell: Oxford, UK, 1987. [Google Scholar]
- Ney, A. Metaphysics: An Introduction; Routledge: Abingdon, UK, 2014. [Google Scholar]
- Parsons, C. Mathematical Thought and Its Objects; Cambridge University Press: Cambridge, UK, 2008. [Google Scholar]
- Zhang, Y.; Salaba, A. Implementing FRBR in Libraries; Neal-Schuman: New York, NY, USA, 2009. [Google Scholar]
- Maxwell, R.L. Maxwell’s Handbook for RDA; Facet: London, UK, 2014. [Google Scholar]
- Broughton, V. Essential Classification, 2nd ed.; Facet: London, UK, 2015. [Google Scholar]
- Foskett, A.C. The Subject Approach to Information, 5th ed.; Facet: London, UK, 1996. [Google Scholar]
- Lancaster, F.W. Indexing and Abstracting in Theory and Practice, 3rd ed.; Facet: London, UK, 2003. [Google Scholar]
- Marradi, A. The concept of concept: Concepts and terms. Knowl. Org. 2012, 39, 29–54. [Google Scholar]
- Szostak, R. Complex concepts into basic concepts. J. Am. Soc. Inf. Sci. Technol. 2011, 62, 2247–2265. [Google Scholar] [CrossRef]
- Friedman, A.; Thellefsen, M. Concept theory and semiotics in knowledge organization. J. Doc. 2011, 67, 644–674. [Google Scholar] [CrossRef]
- Smiraglia, R.P.; van den Heuvel, C. Classifications and concepts: Towards an elementary theory of knowledge interaction. J. Doc. 2013, 69, 360–383. [Google Scholar] [CrossRef]
- Knight, D. Ideas in Chemistry: A History of the Science; Athlone Press: London, UK, 1992. [Google Scholar]
- Rouvray, D.H. Concepts in Chemistry: A Contemporary Challenge; Research Studies Press: Taunton, UK, 1997. [Google Scholar]
- Taber, K. Chemical Misconceptions: Prevention, Diagnosis and Cure-Theoretical Background; Royal Society of Chemistry: Cambridge, UK, 2002; Volume 1. [Google Scholar]
- Atkins, P. Chemistry: A Very Short Introduction; Oxford University Press: Oxford, UK, 2015. [Google Scholar]
- Rice, J.E. Organic Chemistry Concepts and Applications for Medicinal Chemistry; Academic Press: San Diego, CA, USA, 2014. [Google Scholar]
- Chalmers, A. What is This Thing Called Science? 4th ed.; Open University Press: Buckingham, UK, 2013. [Google Scholar]
- Needham, P. Chemical substances and intensive properties. Ann. N. Y. Acad. Sci. 2003, 988, 99–113. [Google Scholar] [CrossRef] [PubMed]
- Rouvray, D.H. Are the concepts of chemistry all fuzzy? In Concepts in Chemistry: A Contemporary Challenge; Research Studies Press: Taunton, UK, 1997; pp. 1–15. [Google Scholar]
- Scerri, E.R. The Periodic Table: Its Story and Significance; Oxford University Press: Oxford, UK, 2007. [Google Scholar]
- Marchese, F.T. Periodicity, visualization and design. Found. Chem. 2013, 15, 31–55. [Google Scholar] [CrossRef]
- Babaev, E.V.; Hefferlin, R. The concepts of periodicity and hyperperiodicity: From atoms to molecules. In Concepts in Chemistry: A Contemporary Challenge; Rouvray, D.H., Ed.; Research Studies Press: Taunton, UK, 1997; pp. 41–100. [Google Scholar]
- Hjørland, B. The periodic table and the philosophy of classification. Knowl. Org. 2011, 38, 9–21. [Google Scholar]
- Scerri, E. Trouble in the periodic table. Educ. Chem. 2012, 13–17. Available online: http://www.rsc.org/images/Scerri%20Trouble%20PT_EiC_January2012_tcm18-212413.pdf (accessed on 19 November 2015). [Google Scholar]
- Villaveces, J.L.; Daza, E.E. The concept of chemical structure. In Concepts in Chemistry: A Contemporary Challenge; Rouvray, D.H., Ed.; Research Studies Press: Taunton, UK, 1997; pp. 101–132. [Google Scholar]
- Goodwin, W. How do structural formulas embody the theory of organic chemistry? Br. J. Philos. Sci. 2010, 61, 621–633. [Google Scholar] [CrossRef]
- Lewis, G.N. Valence and the Structure of Atoms and Molecules; The Chemical Catalog Company: New York, NY, USA, 1923. [Google Scholar]
- Crum Brown, A. On chemical constitution and its relation to physical and physiological properties. Philos. Mag. 1869, 37, 395–400. [Google Scholar]
- Chemical Society. Aromaticity: An International Symposium; full proceedings; Chemical Society: London, UK, 1967. [Google Scholar]
- Badger, G.M. Aromatic Character and Aromaticity; Cambridge University Press: Cambridge, UK, 1969. [Google Scholar]
- Randic, M. Aromaticity and conjugation. J. Am. Chem. Soc. 1977, 99, 444–450. [Google Scholar] [CrossRef]
- Garratt, P.J. Aromaticity; Wiley: New York, NY, UK, 1986. [Google Scholar]
- King, R.B. Aromaticity from planar organic molecules to polyhedral inorganic species. In Concepts in Chemistry: A Contemporary Challenge; Rouvray, D.H., Ed.; Research Studies Press: Taunton, UK, 1997; pp. 152–203. [Google Scholar]
- Krygowski, T.M.; Cyranski, M.K. Aromaticity in Heterocyclic Compounds; Springer: Berlin, Germany, 2009. [Google Scholar]
- Olis, W.D. Introduction. In Aromaticity: An International Symposium; Chemical Society: London, UK, 1967; pp. 1–3. [Google Scholar]
- Sayle, R.A. So you think you understand tautomerism? J. Comput. Aided Mol. Des. 2010, 24, 485–496. [Google Scholar] [CrossRef] [PubMed]
- Gilat, G. The concept of structural chirality. In Concepts in Chemistry: A Contemporary Challenge; Rouvray, D.H., Ed.; Research Studies Press: Taunton, UK, 1997; pp. 325–351. [Google Scholar]
- Bawden, D. Classification of chemical reactions: Potential, possibilities and continuing relevance. J. Chem. Inf. Comput. Sci. 1991, 31, 212–216. [Google Scholar] [CrossRef]
- Kraut, J.; Eiblmaier, J.; Grethe, G.; Löw, P.; Matuszczyk, H.; Saller, H. Algorithm for reaction classification. J. Chem. Inf. Model. 2013, 53, 2884–2895. [Google Scholar] [CrossRef] [PubMed]
- Warr, W.A. A short review of chemical reaction database systems, computer-aided synthesis design, reaction prediction and synthetic feasibility. Mol. Inform. 2014, 33, 469–476. [Google Scholar] [CrossRef]
- Güner, O.F.; Bowen, J.P. Setting the record straight: The origin of the pharmacophore concept. J. Chem. Inf. Model. 2014, 54, 1269–1283. [Google Scholar] [CrossRef] [PubMed]
- Cook, A.; Johnson, P.A.; Law, J.; Mirzazadeh, M.; Ravitz, O.; Simon, A. Computer-aided synthesis design: 40 years on. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2012, 2, 79–107. [Google Scholar] [CrossRef]
- Bøgevig, A.; Federsel, H.-J.; Huerta, F.; Hutchings, M.G.; Kraut, H.; Langer, T.; Löw, P.; Oppawsky, C.; Rein, T.; Saller, H. Route design in the 21st century: The ICSYNTH software tool as an idea generator for synthesis prediction. Org. Process Dev. 2015, 19, 357–368. [Google Scholar] [CrossRef]
- Goodwin, W. Scientific understanding and synthetic design. Br. J. Philos. Sci. 2009, 60, 271–301. [Google Scholar] [CrossRef]
- Mitchell, M. Complexity: A Guided Tour; Oxford University Press: New York, NY, USA, 2009. [Google Scholar]
- Bawden, D.; Robinson, L. “Waiting for Carnot”: Information and complexity. J. Assoc. Inf. Sci. Technol. 2015, 66, 2177–2186. [Google Scholar] [CrossRef]
- Bonchev, D.; Seitz, W.A. The concept of complexity in chemistry. In Concepts in Chemistry: A Contemporary Challenge; Rouvray, D.H., Ed.; Research Studies Press: Taunton, UK, 1997; pp. 353–381. [Google Scholar]
- Krivovichev, S.V. Which inorganic structures are the most complex? Angew. Chem. Int. Ed. 2014, 53, 654–661. [Google Scholar] [CrossRef] [PubMed]
- Vincent, A. Molecular Symmetry and Group Theory, 2nd ed.; Wiley: Chichester, UK, 2013. [Google Scholar]
- Rouvray, D.H. The changing role of the symbol in the evolution of chemical notation. Endeavour 1977, 1, 23–31. [Google Scholar] [CrossRef]
- Lewis, G.N. The atom and the molecule. J. Am. Chem. Soc. 1916, 38, 762–785. [Google Scholar] [CrossRef]
- Crum Brown, A. On the theory of isomeric compounds. Trans. R. Soc. Edinb. 1864, 23, 707–719. [Google Scholar] [CrossRef]
- Ritter, C. An early history of Alexander Crum Brown’s graphical formulas. In Tools and Modes of Representation in the Laboratory Sciences; Klein, U., Ed.; Kluwer: Dordrecht, The Netherlands, 2001; pp. 35–46. [Google Scholar]
- Goodwin, W. Explanation in organic chemistry. Ann. N. Y. Acad. Sci. 2003, 988, 141–153. [Google Scholar] [CrossRef] [PubMed]
- Goodwin, W. Sustaining a controversy: The non-classical ion debate. Br. J. Philos. Sci. 2013, 64, 787–816. [Google Scholar] [CrossRef]
- Meadows, J. The Victorian Scientist: The Growth of a Profession; The British Library: London, UK, 2004. [Google Scholar]
- Willett, P. From chemical documentation to chemoinformatics: 50 years of chemical information science. J. Inf. Sci. 2008, 34, 477–500. [Google Scholar] [CrossRef]
- Lynch, M.F.; Harrison, J.M.; Town, W.G.; Ash, J.E. Computer Handling of Chemical Structure Information; MacDonald: London, UK, 1971. [Google Scholar]
- Bottle, R.T. The Use of Chemical Literature, 2nd ed. revised; Butterworths: London, UK, 1971. [Google Scholar]
- Ash, J.E.; Hyde, E. Chemical Information Systems; Ellis Horwood: Chichester, UK, 1975. [Google Scholar]
- Ash, J.; Chubb, P.; Ward, S.; Welford, S.; Willett, P. Communication, Storage and Retrieval of Chemical Information; Ellis Horwood: Chichester, UK, 1985. [Google Scholar]
- Ash, J.E.; Warr, W.A.; Willett, P. Chemical Structure Systems; Ellis Horwood: Chichester, UK, 1991. [Google Scholar]
- Leach, A.R.; Gillet, V.J. An Introduction to Chemoinformatics, 2nd ed.; Springer: Dordrecht, UK, 2007. [Google Scholar]
- Currano, J.N.; Roth, D.L. Chemical Information for Chemists: A Primer; RSC Publishing: Cambridge, UK, 2014. [Google Scholar]
- Buntrock, R.E. Beilstein and Gmelin: Classical chemical information for people who hate classics. Database 1992, 15, 104–106. [Google Scholar]
- Lawson, A.J.; Swienty-Busch, J.; Géoul, T.; Evans, D. The making of Reaxys-towards unobstructed access to relevant chemical information. In The Future of the History of Chemical Information, American Chemical Society Symposium Series; McEwan, L.R., Buntrock, R.E., Eds.; Oxford University Press: New York, NY, USA, 2014; Volume 1164, Chapter 8; pp. 127–148. [Google Scholar]
- Loukine, E.; Stumpfe, D.; Bajorath, J. Molecular formal concept analysis for compound selectivity profiling in biologically annotated databases. J. Chem. Inf. Model. 2009, 49, 1359–1368. [Google Scholar] [CrossRef] [PubMed]
- Gardiner, E.J.; Gillet, V.J. 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. 2015, 55, 1781–1803. [Google Scholar] [CrossRef] [PubMed]
- Fugmann, R.; Nickelsen, H.; Nickelsen, I.; Winter, J.H. TOSAR-a system for the structural formula-like representation of concept connections in chemical publications. J. Chem. Inf. Comput. Sci. 1975, 15, 52–55. [Google Scholar] [CrossRef] [PubMed]
- Van der Vet, P.E.; Mars, N.J.I. Structured system of concepts for storing, retrieving, and manipulating chemical information. J. Chem. Inf. Comput. Sci. 1993, 33, 564–568. [Google Scholar] [CrossRef]
- Hicks, M.G. Similarity and the Beilstein information system: Searching for concepts with current facts. J. Chem. Inf. Comput. Sci. 1992, 32, 631–638. [Google Scholar] [CrossRef]
- Bawden, D. Chemical reaction information. In Chemical Structure Systems; Ash, J.E., Warr, W.A., Willett, P., Eds.; Ellis Horwood: Chichester, UK, 1991; pp. 57–87. [Google Scholar]
- Currano, J.N. Reaction searching. In Chemical Information for Chemists: A Primer; Currano, J.N., Roth, D.L., Eds.; RSC Publishing: Cambridge, UK, 2014; pp. 224–254. [Google Scholar]
- Ash, J.E.; Warr, W.A. Databanks. In Chemical Structure Systems; Ash, J.E., Warr, W.A., Willett, P., Eds.; Ellis Horwood: Chichester, UK, 1991; pp. 154–191. [Google Scholar]
- Allen, F.H. The Cambridge Structural Database: A quarter of a million crystal structures and rising. Acta Crystallogr. Sec. B Struct. Sci. 2002, 58, 380–388. [Google Scholar] [CrossRef]
- Wagner, A.B. Physical properties and spectra. In Chemical Information for Chemists: A Primer; Currano, J.N., Roth, D.L., Eds.; RSC Publishing: Cambridge, UK, 2014; pp. 146–183. [Google Scholar]
- Groom, C.R.; Allen, F.H. The Cambridge Structural Database in retrospect and prospect. Angew. Chem. Int. Ed. 2014, 53, 662–671. [Google Scholar] [CrossRef] [PubMed]
- Bruno, I.J.; Groom, C.R. A crystallographic perspective on sharing data and knowledge. J. Comput. Aided Mol. De. 2014, 28, 1015–1022. [Google Scholar] [CrossRef] [PubMed]
- Currano, J.N. Searching by structure and substructure. In Chemical Information for Chemists: A Primer; Currano, J.N., Roth, D.L., Eds.; RSC Publishing: Cambridge, UK, 2014; pp. 107–145. [Google Scholar]
- Bender, A.; Glen, R.C. Molecular similarity: A key technique in molecular informatics. Org. Biomol. Chem. 2004, 2, 3204–3218. [Google Scholar] [CrossRef] [PubMed]
- Willett, P. Similarity-based virtual screening using 2D fingerprints. Drug Discov. Today 2006, 11, 1046–1053. [Google Scholar] [CrossRef] [PubMed]
- Stumpfe, D.; Bajorath, J. Similarity searching. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2011, 1, 260–282. [Google Scholar] [CrossRef]
- Lewis, R.A.; Wood, D. Modern 2D QSAR for drug discovery. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2014, 4, 505–522. [Google Scholar] [CrossRef]
- Maggiora, G.; Vogt, M.; Stumpfe, D.; Bajorath, J. Molecular similarity in medicinal chemistry. J. Med. Chem. 2014, 57, 3186–3204. [Google Scholar] [CrossRef] [PubMed]
- Willett, P. The calculation of molecular structural similarity: Principles and practice. Mol. Inform. 2014, 33, 403–413. [Google Scholar] [CrossRef]
- Charton, B. Searching the literature for concepts. J. Chem. Inf. Comput. Scie. 1977, 17, 45–46. [Google Scholar] [CrossRef]
- Twiss-Brooks, A. Searching using text: Beyond web search engines. In Chemical Information for Chemists: A Primer; Currano, J.N., Roth, D.L., Eds.; RSC Publishing: Cambridge, UK, 2014; pp. 93–108. [Google Scholar]
- Smith, E.G. The Wiswesser Line-Formula Chemical Notation; McGraw-Hill: New York, NY, USA, 1968. [Google Scholar]
- Blower, P.E.; Myatt, G.J.; Petras, M.W. Exploring functional group transformations on CASREACT. J. Chem. Inf. Comput. Sci. 1997, 37, 54–58. [Google Scholar] [CrossRef]
- Loftus, F. Computer-aided synthesis design. In Chemical Structure Systems; Ash, J.E., Warr, W.A., Willett, P., Eds.; Ellis Horwood: Chichester, UK, 1991; pp. 222–262. [Google Scholar]
- Batchelor, C. Chemistry ontologies. In The Future of the History of Chemical Information; American Chemical Society Symposium Series; McEwan, L.R., Buntrock, R.E., Eds.; Oxford University Press: New York, NY, USA, 2014; Volume 1164, Chapter 13; pp. 219–235. [Google Scholar]
- Barnard, J.M. Structure representation and searching. In Chemical Structure Systems; Ash, J.E., Warr, W.A., Willett, P., Eds.; Ellis Horwood: Chichester, UK, 1991; pp. 9–56. [Google Scholar]
- Warr, W.A. Tautomerism in chemical information management systems. J. Comput. Aided Mol. Des. 2010, 24, 497–520. [Google Scholar] [CrossRef] [PubMed]
- Fujita, S. The stereoisogram approach for remedying discontents of stereochemical terminology. Tetrahedron Asymmetry 2014, 25, 1612–1623. [Google Scholar] [CrossRef]
- Mills, J.E.; Baughman, B. REACCS in the chemical development environment. 3. Graphically nonequivalent representation of molecules and reactions. J. Chem. Inf. Comput. Sci. 1990, 30, 431–435. [Google Scholar] [CrossRef]
- Gakh, A.A.; Burmett, M.N.; Trepalin, S.V.; Yarkov, A.V. Modular Chemical Descriptor Language (MCDL): Stereochemical modules. J. Cheminform. 2011. [Google Scholar] [CrossRef] [PubMed]
- Jiang, L.; Rizzo, R.C. Pharmacophore-based similarity scoring for DOCK. J. Phys. Chem. B 2015, 119, 1083–1102. [Google Scholar] [CrossRef] [PubMed]
- Pickett, S.D.; Luttmann, C.; Guerin, V.; Laoui, A.; James, E. DIVSEL and COMPLIB-strategies for the design and comparison of combinatorial libraries using pharmacophoric descriptors. J. Chem. Inf. Comput. Sci. 1998, 38, 144–150. [Google Scholar] [CrossRef] [PubMed]
- Todd, M.H. Computer-aided organic synthesis. Chem. Soc. Rev. 2005, 34, 247–266. [Google Scholar] [CrossRef] [PubMed]
- Walker, M.A. Public chemical databases and the Semantic Web. In The Future of the History of Chemical Information; American Chemical Society Symposium Series; McEwan, L.R., Buntrock, R.E., Eds.; Oxford University Press: New York, NY, 2014; Volume 1164, Chapter 12; pp. 197–217. [Google Scholar]
© 2015 by the author; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license ( http://creativecommons.org/licenses/by/4.0/).
Share and Cite
Bawden, D. Storing the Wisdom: Chemical Concepts and Chemoinformatics. Informatics 2015, 2, 50-67. https://doi.org/10.3390/informatics2040050
Bawden D. Storing the Wisdom: Chemical Concepts and Chemoinformatics. Informatics. 2015; 2(4):50-67. https://doi.org/10.3390/informatics2040050
Chicago/Turabian StyleBawden, David. 2015. "Storing the Wisdom: Chemical Concepts and Chemoinformatics" Informatics 2, no. 4: 50-67. https://doi.org/10.3390/informatics2040050