Quantitative analysis of the scientific literature is a frequent task in bibliometrics. Several large online resources collect and disseminate bibliographic information, paving the way for broad... Show moreQuantitative analysis of the scientific literature is a frequent task in bibliometrics. Several large online resources collect and disseminate bibliographic information, paving the way for broad analyses and statistics. The Europe PubMed Central (PMC) and its Web Services is one of these resources, providing a rich platform to retrieve information and metadata on scientific publications. However, a complete bibliometric analysis that involves gathering information and deriving statistics on an author, topic, or country is laborious when consuming Web Services on the command-line or using low level automation. In contrast, scientific workflow managers can integrate different types of software tools to automate multi-step processes. The Taverna workflow engine is a popular open-source scientific workflow manager, giving easy access to availableWeb Services. In this tutorial, we demonstrate how to design scientific workflows for bibliometric analyses in Taverna by integrating Europe PubMed Central Web Services and statistical analysis tools. To our knowledge, this is also the first time scientific workflow managers have been used to perform bibliometric analyses using these Web Services. Show less
Guler, A.T.; Waaijer, C.J.F.; Mohammed, Y.; Palmblad, M. 2016
Quantitative analysis of the scientific literature is a frequent task in bibliometrics. Several large online resources collect and disseminate bibliographic information, paving the way for broad... Show moreQuantitative analysis of the scientific literature is a frequent task in bibliometrics. Several large online resources collect and disseminate bibliographic information, paving the way for broad analyses and statistics. The Europe PubMed Central (PMC) and its Web Services is one of these resources, providing a rich platform to retrieve information and metadata on scientific publications. However, a complete bibliometric analysis that involves gathering information and deriving statistics on an author, topic, or country is laborious when consuming Web Services on the command-line or using low level automation. In contrast, scientific workflow managers can integrate different types of software tools to automate multi-step processes. The Taverna workflow engine is a popular open-source scientific workflow manager, giving easy access to available Web Services. In this tutorial, we demonstrate how to design scientific workflows for bibliometric analyses in Taverna by integrating Europe PubMed Central Web Services and statistical analysis tools. To our knowledge, this is also the first time scientific workflow managers have been used to perform bibliometric analyses using these Web Services. (C) 2016 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Show less
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... Show moreScientific 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. Show less
Holl, S.; Zimmermann, O.; Palmblad, M.; Mohammed, Y.; Hofmann-Apitius, M. 2014
A large part of modern biology is dedicated to the functional annotation and interpretation of genetic information and its influence on the subject__s phenotype. Proteomics describes the state of... Show moreA large part of modern biology is dedicated to the functional annotation and interpretation of genetic information and its influence on the subject__s phenotype. Proteomics describes the state of the system from the perspective of expression, structure, localization, interaction and function of the proteins. It is a complex field which requires a combination of various disciplines such as cellular biology and biochemistry for sample preparation, analytical chemistry for sample measurement and bioinformatics for the processing of data. Different chapters of this thesis illustrate various aspects of the proteomics pipeline and emphasize the importance and connection between them. Therefore the information in this dissertation can be divided into three major parts depicting these aspects of a proteomics experiment. First, sample preparation for proteomics has been addressed through two studies aimed at decreasing sample complexity and increasing proteome coverage. The second part is dedicated mostly to the technical step of the mass spectrometry measurement and the analysis of obtained spectra. The final part describes example- and proof-of-principle applications. Show less
