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...
- 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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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 |
_version_ |
1814167531049451520 |