A Brief History of Bioinformatics Told by Data Visualization
Bioinformatics is an interdisciplinary research field that aims to analyze biological data through computational approaches. In the last years, the evolution of technological resources has provided a tidal wave of biological data. Consequently, an unprece
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1 LBS - Laboratory of Bioinformatics and Systems, Department of Computer Science,
Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil [email protected] 2 LLP - Laboratory of Programming Languages, Department of Computer Science, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
Abstract. Bioinformatics is an interdisciplinary research field that aims to analyze biological data through computational approaches. In the last years, the evolution of technological resources has provided a tidal wave of biological data. Consequently, an unprecedented amount of studies using bioinformatics approaches have been released, increasing peer-reviewed published papers. Here, we tell a brief history of bioinformatics based on literature data analysis and visualization. We collected abstracts and other metadata from papers published from 1998 to 2019 in four leading bioinformatics journals: (i) Oxford Bioinformatics; (ii) BMC Bioinformatics; (iii) Briefings in Bioinformatics; and (iv) PLoS Computational Biology. Our results show an increase in publication number and international collaborations. We also observed an increase in publications by Chinese authors. Latin America continues to have a low percentage of global scientific bioinformatics production. However, Brazil excels in this region, being responsible for almost half of Latin America papers published. Our results also point out the recent trend of using Python as the programming language for bioinformatics applications, followed by Perl, Java, and R. We hope these data visualizations can provide insights to understand the recent changes and evolution in the bioinformatics field. The developed interactive visualizations are available at http://bioinfo.dcc.ufmg.br/his tory/. Keywords: Bioinformatics · Computational biology · Data visualization
1 Introduction Bioinformatics is an interdisciplinary research field whose principle is using models and algorithms to analyze biological data and solve biologically related problems [1]. Bioinformatics’ roots are in the early 1960s when computers, used for military purposes, became available for universities and research institutes. At that time, researchers began to use computers to try answering fundamental questions in life sciences [2]. Margaret Dayhoff was a pioneer in bioinformatics studies at that time. She proposed the use of mathematical approaches for analyzing amino acid frequencies and mutation © Springer Nature Switzerland AG 2020 J. C. Setubal and W. M. Silva (Eds.): BSB 2020, LNBI 12558, pp. 235–246, 2020. https://doi.org/10.1007/978-3-030-65775-8_22
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probabilities in biological sequences. Since the late 1950s, experimental approaches have allowed the sequencing of small protein structures, such as insulin [3]. This culminated in the creation of the first database of amino acid sequences and structures, the so-called “Atlas of Protein Sequence and Structure” [4]. Dayhoff and collaborators also proposed computational methods for sequence comparisons to d
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