Writing an article is a quite complex job. Over the course of studies it is necessary to collect, read and review a large body of literature and information in various formats. Software tools can assist with this work.

Writing an article

 PDF reader

PDF readers are good to keep track of a PDF’s most important information. It is nice to have a PDF reader that can create bookmarks, highlight passages and create annotations. Some of them are PDF XChange Viewer, Adobe Acrobat Reader and Foxit Reader.

Highlighting important information

Managing Information from Multiple PDFs

A mind map is a diagram with a central topic and subtopics branching from it like a tree. Usually a node in a mind map contains only one or two important keywords. Due to its visual structure, many people consider mind maps very effective tools. They promote freeform thinking and enable quick organization of ideas and complex information.

Mind mapping tools – Docear, FreeMind, MindManager, XMIND.

Most mind mapping tools allow to link PDF files.

Links to sites with lists of mind-mapping software:

https://en.wikipedia.org/wiki/List_of_concept-_and_mind-mapping_software

http://www.peterrussell.com/MindMaps/MMSoft.php

https://www.dmoz.org/Reference/Knowledge_Management/Knowledge_Creation/Mind_Mapping/Software/

Docear

Docear is a solution to literature management, i.e. it helps to organize, create and discover academic literature.

Docear

With Docear, documents and annotations (comments, bookmarks, and highlighted text from PDFs) can be sorted into categories. One of Docear’s special features is monitoring a folder for new files (Details & Features). All the information you annotated in your PDFs are accessible and manageable in a mind map. You have direct access to all the bookmarks in all the PDFs via your mind map. You can find new PDFs, read them, create bookmarks, and categorized them within your mind map. Docear combines several tools in a single application (pdf management, reference management, mind mapping). You can add text, pictures or formula, insert icons, link to other files and webpages, highlight nodes (Docear’s User Manual).

Reference management software

Keeping track of the literature you encounter can be facilitated by using a reference manager. An efficient reference management workflow simplifies the academic writing process.

Reference management software is software for scholars and authors to use for recording and utilising bibliographic citations. Citations, after recording, can be used in generating bibliographies (lists of references).

These software packages normally include a database to enter and store bibliographic references, also they can have a system for generating selective lists of articles in the different formats. Contemporary reference management packages can usually be integrated with word processors to produce a reference list in the appropriate format as an article is written, reducing that a cited source is not included in the reference list. They will also have a facility for importing the details of publications from bibliographic databases.

Besides from managing references, most reference management software also enables users to search references from online libraries.

Reference managers – JabRef, KbibTeX, Zotero, BibDesk, Referencer and Mendeley.

Links to sites which compare different reference management software:

https://en.wikipedia.org/wiki/Comparison_of_reference_management_software

https://www.library.wisc.edu/services/citation-managers/comparison-chart/

http://guides.library.utoronto.ca/c.php?g=250610&p=1671260

http://blogs.plos.org/mfenner/reference-manager-overview/

JabRef

JabRef by default is integrated into the Docear suite, to manage reference data. JabRef allows you to maintain a database of bibliographic data in BibTex format (The word ‘BibTeX’ stands for a tool and a file format which are used to describe and process lists of references, mostly in conjunction with LaTeX documents.). You need to create a BibTex entry for each paper you want to cite. To integrate your BibTeX data with your mind map you need to link the corresponding PDF to the BibTeX entry. Docear supports BibTeX.

Zotero

Zotero is free and open-source reference management software to manage bibliographic data and related research materials (such as PDF files).

Zotero

Features:

web browser integration; online syncing; generation of in-text citations; footnotes and bibliographies; integration with the word processors - Microsoft Word, LibreOffice, OpenOffice.org Writer and NeoOffice.

Zotero shows an icon when a resource (book, article, thesis) is being viewed on many websites. Clicking this icon saves the full reference information to the Zotero library. Zotero can also save a copy of the webpage, or, in the case of academic articles, a copy of the full text PDF. Users can then add notes, tags, attachments, and their own metadata.

Selections of the local reference library data can later be exported as formatted bibliographies. Furthermore, all entries including bibliographic information and user-created rich-text memos of the selected articles can be summarized into an HTML report.

Citation formatting:

It is possible to generate citations and bibliographies through word processor plugins, or directly in Zotero, using Citation Style Language styles.

Zotero can import and export citations from/to many formats, including Wikipedia Citation Templates, BibTeX, BibLateX, RefWorks, MODS, CoinS, Citation Style Language/JSON, refer/BibIX, RIS, TEI, several flavours of RDF, Evernote, EndNote.

How to use Zotero and Docear at the same time? 

If you want to use Zotero together with Docear you need to export a BibTeX file, each time you change or add an entry in Zotero. This process can be done automatically with the Zotero plugins “Better Bib(La)TeX” and “Zotero Autoexport“. You also can export the BibTeX file manually by following these steps (you have to do it each time you make changes in Zotero):

1. Export Zotero’s references to a BibTeX file. Save the BibTeX file in a location that will be part of your Docear project home.

2. Select your Zotero BibTeX file in Docear (right mouse click on “References”).

3. After selecting the BibTeX file, you need to tell Docear where Zotero saves your PDF files.

   a. Open the “Change location” dialog in Docear (right mouse click on “Literature Repository”)
   b. Select the folder in which your PDFs are.