Login Register Cart 0
Generic placeholder image

Combinatorial Chemistry & High Throughput Screening

Editor-in-Chief

ISSN (Print): 1386-2073
ISSN (Online): 1875-5402

Back
Journal Home About Journal Editorial Board Journal Insight Current Issue Volumes/Issues
Subscribe
Opinion Article

Semiotic Thoughts on Biological Sequence Representations

Author(s): Guillermo Restrepo*

Volume 25, Issue 3, 2022

Published on: 05 July, 2021

Page: [349 - 353] Pages: 3

DOI: 10.2174/1386207324666210705112232

Price: $65

Abstract

The deluge of biological sequences ranging from those of proteins, DNA and RNA to genomes has motivated to devise models to represent them, which are further used to contrast those sequences. Here we present a brief bibliometric description of the research area devoted to the representation of biological sequences and highlight the semiotic elements of this process. Finally, we argue that this research area must learn from the evolution of mathematical chemistry and try to avoid its pitfalls.

Keywords: Biological sequences, representations, mathematical chemistry, semiotics, bibliometrics, sociology of science.

« Previous Next »
Graphical Abstract

[1]
TextAnalysisOnline. Available from:, http://textanalysisonline.com/spacy-word-lemmatize Accessed December 8, 2020.
[2]
WordClouds.com. Available from: https://www.wordclouds.com/ Accessed December 8, 2020..
[3]
Randić, M.; Zupan, J.; Balaban, A.T.; Vikić-Topić, D.; Plavsić, D. Graphical representation of proteins. Chem. Rev., 2011, 111(2), 790-862.
[http://dx.doi.org/10.1021/cr800198j] [PMID: 20939561]
[4]
Randić, M.; Novič, M.; Plavšić, D. Milestones in graphical bioinformatics. Int. J. Comput. Chem, 2013, 113, 2413-2446.
[5]
Peirce, C.S. The Essential Peirce; 1998, 2 .
[6]
Short, T.L. Peirce’s Theory of Signs; Cambridge University Press: New York, 2007.
[http://dx.doi.org/10.1017/CBO9780511498350]
[7]
Restrepo, G.; Jost, J. A formal setting for the evolution of chemical knowledge., MPI-MiS preprint, 2020. Available from:. https://www.mis.mpg.de/publications/preprints/2020/prepr2020-77.html
[8]
Todeschini, R.; Consonni, V. Molecular descriptors for chemoinformatics; Wiley: Weinheim, 2009.
[http://dx.doi.org/10.1002/9783527628766]
[9]
Randić, M. Novel molecular descriptor for structure-property studies. Chem. Phys. Lett., 1993, 211, 478-483.
[http://dx.doi.org/10.1016/0009-2614(93)87094-J]
[10]
Randić, M. Molecular bonding profiles. J. Math. Chem., 1996, 19, 375-392.
[http://dx.doi.org/10.1007/BF01166727]
[11]
Borges, J.L. Jorge Luis Borges, Collected Fictions; Penguin Books: New York, 1998.
[12]
Restrepo, G.; Willett, P. A bibliometric profile of MATCH communicationsin mathematical and in computer chemistry. MATCH Commun. Math. Comput. Chem, 2017, 77, 235-242.
[13]
Restrepo, G.; Willett, P. The Journal of Mathematical Chemistry: A bibliometric profile. J. Math. Chem., 2017, 55, 1589-1596.
[http://dx.doi.org/10.1007/s10910-017-0747-7]
[14]
Restrepo, G.; Schummer, J. Philosophical aspects of mathematical chemistry. MATCH Commun. Math. Comput. Chem., 2014, 72, 589-599.
[15]
Chen, W.; Lin, H.; Chou, K-C. Pseudo nucleotide composition or PseKNC: An effective formulation for analyzing genomic sequences. Mol. Biosyst., 2015, 11(10), 2620-2634.
[http://dx.doi.org/10.1039/C5MB00155B] [PMID: 26099739]
[16]
Restrepo, G. Mathematical chemistry, a new discipline.Essays in the philosophy of chemistry; Scerri, E; Fisher, G., Ed.; Oxford University Press: New York, 2016, pp. 332-351.
[http://dx.doi.org/10.1093/oso/9780190494599.003.0023]
[17]
Schummer, J. Why mathematical chemistry cannot copy mathematical physics and how to avoid the imminent epistemological pitfalls. Hyle, 2012, 18(1), 71-89..

Rights & Permissions Print Cite
Article Metrics
23
1
© 2024 Bentham Science Publishers | Privacy Policy