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Authors

Helge Knüttel


Institution

University Library of Regensburg, Germany


Abstract

Introduction

Medical librarians/information specialists providing mediated, systematic searches are dealing a lot with text data when developing search strategies, handling search results and documenting the search process. Dedicated software such as reference managers as wells as general word processors are usually employed in these tasks. Yet, a lot of manual work remains and many functions wanted are not or not well supported by these programs. Classic command line tools do not seem to be well known by many expert searchers nowadays but could be candidates for easier, semi-automated workflows. These tools are freely available or even already installed on many computers.

Methods

A number of typical tasks in systematic searching was identified where additional software support was wanted and a solution seemed feasible with limited resources. These tasks and the need arose from the author’s own practice and communication with colleagues. Commands to be entered at the command line were developed that work on simple text files containing text data such as query strings, database accession numbers, search results and search strategies exported form search interfaces.

Results

Simple command line tools were built in order to help in constructing query strings, checking search results for export errors, post-processing search result for easier import, comparing search results, updating searches and documenting searches. The list of use cases and the tools developed will be available for free reuse and further development on GitHub.

Discussion Command line tools such as the bash shell and the GNU Core Utilities are descendants of a decades-long tradition of Unix-like operating systems. The philosophy of these tools is to have simple programs that „should do one thing well” and then combine these programs to accomplish a specific task [1]. Already a limited set of commands and their combination provided a number of practical tools for the expert searcher that helped to identify and avoid errors, to save time and to achieve tasks that would have been impossible otherwise. On the other side, there is some investment in learning to work with the command line. The tools provided might help as a starter. Besides these practical considerations, there also is a matter of philosophy. Currently, the work of the expert searcher/information specialist often seems to be tied closely to a range of GUI-based software products that shape the way one works and thinks. Getting some basic understanding of command line tools may save from many of the repetitive tasks that computers were built for and concentrate on the things that (currently) only people can do. Generally, this will enhance ones skill set and may introduce a new way of thinking about software. Which may make you happier and more confident and set you on a path that will lead to new ideas (more automation, new analyses).


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