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Research Ideas and Outcomes : Software Description
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Daisuke Tsugama
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Corresponding author: Daisuke Tsugama (tsugamedaisaku@gmail.com)
Received: 14 Sep 2018 | Published: 26 Sep 2018
© 2018 Daisuke Tsugama
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation: Tsugama D (2018) Cafebr - Citation Amender/Formatter for Biological Research. Research Ideas and Outcomes 4: e29773. https://doi.org/10.3897/rio.4.e29773
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Abstract
Background
A reference list is an essential part of a manuscript for an academic article. It is often necessary to reformat (i.e., change orders of pieces of article information such as authors, article title, publication year, and journal where the article was published) of a preformatted reference list when a manuscript is declined by one journal and submitted to another. EndNote, Zotero and Mendeley are examples of sophisticated reference management programs that help generate a reference list with less errors. However, their multifunctionality seems to have complicated the process of generating a reference list: they require many selection steps to obtain a final output, and also require to manually edit a file outside the execuiton program even to make small changes in the output.
New information
The author developed a program, Cafebr (Citation Amender/Formatter for Biological Research), to more simply generate a reference list for an article of biological research. It is written in HTML/JavaScript, and as such works on a web browser on any platform. On Cafebr, articles for a final reference list can be either given by a user or collected from PubMed. Pieces of article information are then extracted according to the format of these articles or to the delimiters designated by a user. Preset formats for output are currently only four, but all of them can be directly edited on the user interface, allowing to change output formats quickly and flexibly. All of the functions of Cafebr is available on its website (either http://stdtgm.itigo.jp/cafebr/cafebr.html (main) or http://studtsugama.s1006.xrea.com/cafebr/cafebr.xhtm (backup)) with aids of a CGI program. A stand-alone version of Cafebr is available at these websites or Zenodo (10.5281/zenodo.1404887).
Keywords
Biology, HTML, JavaScript, Matching and replacement of characters, PubMed, Reference management software
Introduction
A reference list is an essential part of a manuscript for an academic article. Different journals require different formats for a reference list. Due to this situation, it is often necessary to reformat a preformatted reference list if a manuscript is declined by a journal for publication and submitted to another. It is error-prone and takes time to manually format a reference list. To quickly generate a reference list with less errors, reference management software packages have been developed. EndNote, which was developed by Clarivate Analytics (previously Thomson Reuters), is an example of such packages. It allows users to search for articles of interest, to deposit them in a database, and to output information about selected articles in a style chosen from more than 2000 preset styles (https://endnote.com/product-details). However, it is a commercial, non-free program, and incompatible with Linux operating systems. Zotero (developed by Center for History and New Media at George Mason University in 2006; https://www.zotero.org) and Mendeley (developed by Mendeley Ltd., which was purchased by Elsevier; https://www.mendeley.com) are examples of free reference management programs that can implement the functions similar to those of EndNote, and can run on Windows, Mac OS X, and Linux. All of these programs have many functions and user-friendly interfaces, and have still been improving. However, such multifunctionality seems to have been counteracting with simplicity: It requires many selection steps (i.e., cursor movements and clicks) to obtain a final output; even making small changes in the output requires users to look into and edit a file outside a main execution file. To simplify the process of generating a reference list for biological research, the author developed a new program, Cafebr (Citation Amender/Formatter for Biological Research).
Project description
Cafebr - Citation Amender/Formatter for Biological Research
Cafebr was developed to more simply generate a reference list. It uses only PubMed (managed by The United States National Library of Medicine (NLM) at the National Institutes of Health (NIH), https://www.ncbi.nlm.nih.gov/pubmed) as a search engine to find articles of interest, and thus primarily for biological research. However, once a list (or database) of articles is provided, Cafebr can work on it regardless of whether the articles are those of biological research or not.
Cafebr was originally written in Perl, and most of the functions were copied to a GUI version written in HTML/JavaScript. This GUI version, as an HTML file, works on a web browser on any platform. To obtain an output reference list simply and flexibly, Cafebr focuses its functions on finding and replacing certain patterns of words rather than on managing (i.e., storing and displaying) articles.
To find articles, Cafebr can search the MEDLINE database with PubMed search engine (managed by The United States National Library of Medicine (NLM) at the National Institutes of Health (NIH), https://www.ncbi.nlm.nih.gov/pubmed), which covers articles with a wide variety of biology fields and is therefore most commonly used for biological research. Cafebr then extracts pieces of informaiton on articles from search results, and displays them in a table for selecting articles for further processing (Fig.
The extracted pieces of information or fields are formatted to generate a final reference list. Currently only four preset formats are available. However, all of them can be directly edited on the user interface, allowing to change output formats quickly and flexibly (Fig.