Alpha 2.0
Login Register
» Articles » PMID: 27122644

Scientific Workflows for Bibliometrics

Overview
Journal Scientometrics
Publisher Springer
Date 2016 Apr 29
PMID 27122644
Citations 93
Authors
Arzu Tugce Guler
Cathelijn J F Waaijer
Magnus Palmblad
Affiliations
Soon will be listed here.
Abstract

Scientific workflows organize the assembly of specialized software into an overall data flow and are particularly well suited for multi-step analyses using different types of software tools. They are also favorable in terms of reusability, as previously designed workflows could be made publicly available through the myExperiment community and then used in other workflows. We here illustrate how scientific workflows and the Taverna workbench in particular can be used in bibliometrics. We discuss the specific capabilities of Taverna that makes this software a powerful tool in this field, such as automated data import via Web services, data extraction from XML by XPaths, and statistical analysis and visualization with R. The support of the latter is particularly relevant, as it allows integration of a number of recently developed R packages specifically for bibliometrics. Examples are used to illustrate the possibilities of Taverna in the fields of bibliometrics and scientometrics.

Citing Articles

Trends in Research on Hypertrophic Cardiomyopathy and Mitochondria From 2003 to 2023: A Bibliometric Analysis.

Yang L, Zhang H, Zhu Z, Wang J, Liu X, Lu L Health Sci Rep. 2025; 8(3):e70314.

PMID: 40041771 PMC: 11872595. DOI: 10.1002/hsr2.70314.

Global landscape of hepatic organoid research: A bibliometric and visual study.

Li T, Bo R, Yan J, Johnson N, Liao M, Li Y World J Hepatol. 2025; 17(2):95624.

PMID: 40027550 PMC: 11866153. DOI: 10.4254/wjh.v17.i2.95624.

Global Research Trends and Focus on the Link Between Heart Failure and NLRP3 Inflammasome: A Bibliometric Analysis From 2010 to 2024.

Lian Y, Zhang H, Xing W, Li S, Lai X, Jia S J Multidiscip Healthc. 2025; 18:697-710.

PMID: 39949850 PMC: 11822290. DOI: 10.2147/JMDH.S505356.

Visualization of the relationship between metabolism and lung diseases from the perspective of bibliometric analysis: research trends and future prospects.

Wang M, Mo X, Yi M, Lu H Front Med (Lausanne). 2024; 11:1443926.

PMID: 39664315 PMC: 11631585. DOI: 10.3389/fmed.2024.1443926.

Research trends and hotspots of the applications of single-cell RNA sequencing in cardiovascular diseases: a bibliometric and visualized study.

Yu Y, Ye J, Wang R, Wang J, Wang J, Xu Q Ann Med Surg (Lond). 2024; 86(12):7164-7177.

PMID: 39649887 PMC: 11623828. DOI: 10.1097/MS9.0000000000002681.

References
1.
Waaijer C, Palmblad M . Bibliometric mapping: eight decades of analytical chemistry, with special focus on the use of mass spectrometry. Anal Chem. 2015; 87(9):4588-96. DOI: 10.1021/ac5040314. View
2.
de Bruin J, Deelder A, Palmblad M . Scientific workflow management in proteomics. Mol Cell Proteomics. 2012; 11(7):M111.010595. PMC: 3394934. DOI: 10.1074/mcp.M111.010595. View
3.
Goecks J, Nekrutenko A, Taylor J . Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010; 11(8):R86. PMC: 2945788. DOI: 10.1186/gb-2010-11-8-r86. View
4.
Wolstencroft K, Haines R, Fellows D, Williams A, Withers D, Owen S . The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud. Nucleic Acids Res. 2013; 41(Web Server issue):W557-61. PMC: 3692062. DOI: 10.1093/nar/gkt328. View
5.
Goble C, Bhagat J, Aleksejevs S, Cruickshank D, Michaelides D, Newman D . myExperiment: a repository and social network for the sharing of bioinformatics workflows. Nucleic Acids Res. 2010; 38(Web Server issue):W677-82. PMC: 2896080. DOI: 10.1093/nar/gkq429. View