Similarity in Chemical Reaction Networks: Categories, Concepts and Closures

Similarity studies are important for chemistry and their applications range from the periodic table to the screening of large databases in the searching for new drugs. In this later case, it is assumed that similarity in molecular structure is related to similarity in reactivity. However, we state t...

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Autores:
Tipo de recurso:
Fecha de publicación:
2015
Institución:
Universidad del Rosario
Repositorio:
Repositorio EdocUR - U. Rosario
Idioma:
eng
OAI Identifier:
oai:repository.urosario.edu.co:10336/23852
Acceso en línea:
https://doi.org/10.1016/B978-1-68108-053-6.50002-8
https://repository.urosario.edu.co/handle/10336/23852
Palabra clave:
Chemical elements
Chemical reactions
Circuit theory
Directed graphs
Formal concept analysis
Graph theory
Molecular structure
Topology
Binary compounds
Category theory
Chemical classification
Chemical networks
Closure
Closure operators
Directed hypergraphs
Order theory
Periodic table
Reaction network
Similarity
Chemical analysis
Binary compounds
Category theory
Chemical classification
Chemical networks
Closure
Closure operators
Directed hypergraphs
Formal concept analysis
Graph theory
Network theory
Order theory
Periodic table
Reaction networks
Similarity
Topology
Rights
License
Abierto (Texto Completo)
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spelling 94c92f82-c9e4-46fd-943b-1fddb085aed5-1055fe31e-934b-492c-b322-0b9246214cd3-1700430fb-2375-4527-9406-e23af4725470-1be17b3dc-e893-4662-81ff-19d33587b136-12020-05-26T00:06:03Z2020-05-26T00:06:03Z2015Similarity studies are important for chemistry and their applications range from the periodic table to the screening of large databases in the searching for new drugs. In this later case, it is assumed that similarity in molecular structure is related to similarity in reactivity. However, we state that structural formulas can be regarded as abstract representations emerging from the analysis of large amounts of data upon chemical reactivity. Hence, chemical formulas such as organic functions are not direct pictures of the atomic constitution of matter, but signs used to represent similarity in the reactivity of a class of substances. Therefore, reactivity, rather than molecular structure, becomes the fundamental feature of chemical substances. As reactivity is important, chemical identity is given by the relations substances establish with each other, giving place to a network of chemical reactions. We explore similarity in the network rather than in molecular structure. By characterising each substance in terms of the related ones, we show how Category Theory helps in this description. Afterwards, we study the similarity among substances using topological spaces, which leads us to concepts such as closure and neighbourhood, which formalise the intuition of things lying somewhere near around. The second focus of the chapter is the exploration of the potential of closure operators, and of topological closures in particular, as more general descriptors of chemical similarity. As we introduce the formalism, we develop a worked example, concerning the analysis of similarity among chemical elements regarding their ability to combine into binary compounds. The results show that several of the trends of chemical elements are found through the current approach. © 2015 Bentham Science Publishers Ltd Published by Elsevier Inc. All rights reserved.application/pdfhttps://doi.org/10.1016/B978-1-68108-053-6.50002-8https://repository.urosario.edu.co/handle/10336/23852engElsevier Inc.5424Advances in Mathematical Chemistry and ApplicationsVol. 2Advances in Mathematical Chemistry and Applications, Vol.2,(2015); pp. 24-54https://www.scopus.com/inward/record.uri?eid=2-s2.0-84966930053&doi=10.1016%2fB978-1-68108-053-6.50002-8&partnerID=40&md5=e901fb514d64eb38c9e5e1b1b23f7ebcAbierto (Texto Completo)http://purl.org/coar/access_right/c_abf2instname:Universidad del Rosarioreponame:Repositorio Institucional EdocURChemical elementsChemical reactionsCircuit theoryDirected graphsFormal concept analysisGraph theoryMolecular structureTopologyBinary compoundsCategory theoryChemical classificationChemical networksClosureClosure operatorsDirected hypergraphsOrder theoryPeriodic tableReaction networkSimilarityChemical analysisBinary compoundsCategory theoryChemical classificationChemical networksClosureClosure operatorsDirected hypergraphsFormal concept analysisGraph theoryNetwork theoryOrder theoryPeriodic tableReaction networksSimilarityTopologySimilarity in Chemical Reaction Networks: Categories, Concepts and ClosuresbookPartParte de librohttp://purl.org/coar/version/c_970fb48d4fbd8a85http://purl.org/coar/resource_type/c_3248Bernal A.Llanos E.Leal W.Restrepo G.10336/23852oai:repository.urosario.edu.co:10336/238522022-05-02 07:37:18.388343https://repository.urosario.edu.coRepositorio institucional EdocURedocur@urosario.edu.co
dc.title.spa.fl_str_mv Similarity in Chemical Reaction Networks: Categories, Concepts and Closures
title Similarity in Chemical Reaction Networks: Categories, Concepts and Closures
spellingShingle Similarity in Chemical Reaction Networks: Categories, Concepts and Closures
Chemical elements
Chemical reactions
Circuit theory
Directed graphs
Formal concept analysis
Graph theory
Molecular structure
Topology
Binary compounds
Category theory
Chemical classification
Chemical networks
Closure
Closure operators
Directed hypergraphs
Order theory
Periodic table
Reaction network
Similarity
Chemical analysis
Binary compounds
Category theory
Chemical classification
Chemical networks
Closure
Closure operators
Directed hypergraphs
Formal concept analysis
Graph theory
Network theory
Order theory
Periodic table
Reaction networks
Similarity
Topology
title_short Similarity in Chemical Reaction Networks: Categories, Concepts and Closures
title_full Similarity in Chemical Reaction Networks: Categories, Concepts and Closures
title_fullStr Similarity in Chemical Reaction Networks: Categories, Concepts and Closures
title_full_unstemmed Similarity in Chemical Reaction Networks: Categories, Concepts and Closures
title_sort Similarity in Chemical Reaction Networks: Categories, Concepts and Closures
dc.subject.keyword.spa.fl_str_mv Chemical elements
Chemical reactions
Circuit theory
Directed graphs
Formal concept analysis
Graph theory
Molecular structure
Topology
Binary compounds
Category theory
Chemical classification
Chemical networks
Closure
Closure operators
Directed hypergraphs
Order theory
Periodic table
Reaction network
Similarity
Chemical analysis
Binary compounds
Category theory
Chemical classification
Chemical networks
Closure
Closure operators
Directed hypergraphs
Formal concept analysis
Graph theory
Network theory
Order theory
Periodic table
Reaction networks
Similarity
Topology
topic Chemical elements
Chemical reactions
Circuit theory
Directed graphs
Formal concept analysis
Graph theory
Molecular structure
Topology
Binary compounds
Category theory
Chemical classification
Chemical networks
Closure
Closure operators
Directed hypergraphs
Order theory
Periodic table
Reaction network
Similarity
Chemical analysis
Binary compounds
Category theory
Chemical classification
Chemical networks
Closure
Closure operators
Directed hypergraphs
Formal concept analysis
Graph theory
Network theory
Order theory
Periodic table
Reaction networks
Similarity
Topology
description Similarity studies are important for chemistry and their applications range from the periodic table to the screening of large databases in the searching for new drugs. In this later case, it is assumed that similarity in molecular structure is related to similarity in reactivity. However, we state that structural formulas can be regarded as abstract representations emerging from the analysis of large amounts of data upon chemical reactivity. Hence, chemical formulas such as organic functions are not direct pictures of the atomic constitution of matter, but signs used to represent similarity in the reactivity of a class of substances. Therefore, reactivity, rather than molecular structure, becomes the fundamental feature of chemical substances. As reactivity is important, chemical identity is given by the relations substances establish with each other, giving place to a network of chemical reactions. We explore similarity in the network rather than in molecular structure. By characterising each substance in terms of the related ones, we show how Category Theory helps in this description. Afterwards, we study the similarity among substances using topological spaces, which leads us to concepts such as closure and neighbourhood, which formalise the intuition of things lying somewhere near around. The second focus of the chapter is the exploration of the potential of closure operators, and of topological closures in particular, as more general descriptors of chemical similarity. As we introduce the formalism, we develop a worked example, concerning the analysis of similarity among chemical elements regarding their ability to combine into binary compounds. The results show that several of the trends of chemical elements are found through the current approach. © 2015 Bentham Science Publishers Ltd Published by Elsevier Inc. All rights reserved.
publishDate 2015
dc.date.created.spa.fl_str_mv 2015
dc.date.accessioned.none.fl_str_mv 2020-05-26T00:06:03Z
dc.date.available.none.fl_str_mv 2020-05-26T00:06:03Z
dc.type.eng.fl_str_mv bookPart
dc.type.coarversion.fl_str_mv http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.coar.fl_str_mv http://purl.org/coar/resource_type/c_3248
dc.type.spa.spa.fl_str_mv Parte de libro
dc.identifier.doi.none.fl_str_mv https://doi.org/10.1016/B978-1-68108-053-6.50002-8
dc.identifier.uri.none.fl_str_mv https://repository.urosario.edu.co/handle/10336/23852
url https://doi.org/10.1016/B978-1-68108-053-6.50002-8
https://repository.urosario.edu.co/handle/10336/23852
dc.language.iso.spa.fl_str_mv eng
language eng
dc.relation.citationEndPage.none.fl_str_mv 54
dc.relation.citationStartPage.none.fl_str_mv 24
dc.relation.citationTitle.none.fl_str_mv Advances in Mathematical Chemistry and Applications
dc.relation.citationVolume.none.fl_str_mv Vol. 2
dc.relation.ispartof.spa.fl_str_mv Advances in Mathematical Chemistry and Applications, Vol.2,(2015); pp. 24-54
dc.relation.uri.spa.fl_str_mv https://www.scopus.com/inward/record.uri?eid=2-s2.0-84966930053&doi=10.1016%2fB978-1-68108-053-6.50002-8&partnerID=40&md5=e901fb514d64eb38c9e5e1b1b23f7ebc
dc.rights.coar.fl_str_mv http://purl.org/coar/access_right/c_abf2
dc.rights.acceso.spa.fl_str_mv Abierto (Texto Completo)
rights_invalid_str_mv Abierto (Texto Completo)
http://purl.org/coar/access_right/c_abf2
dc.format.mimetype.none.fl_str_mv application/pdf
dc.publisher.spa.fl_str_mv Elsevier Inc.
institution Universidad del Rosario
dc.source.instname.spa.fl_str_mv instname:Universidad del Rosario
dc.source.reponame.spa.fl_str_mv reponame:Repositorio Institucional EdocUR
repository.name.fl_str_mv Repositorio institucional EdocUR
repository.mail.fl_str_mv edocur@urosario.edu.co
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