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How to Write a PhD Thesis (Part I): Literature Management

To write a good PhD thesis it is key to keep track of related work in your field. That includes that you know all the relevant studies, results, facts, ideas and so on in your field. Keep in mind, by the end of your literature review you will have read or at least skipped through hundreds of books and papers. You must be a genius to remember every interesting fact and idea you have read in a paper without any tools. Before the computer-age, academics could only rely on index cards, (post it) notes, highlighting pens, indices, etc. With computers, and especially mind mapping software, new possibilities evolved.

In this part of the tutorial we explain how to search for literature with academic search engines. Then we show how you create summaries of your PDFs with bookmarks and keep on overview of all important information in our mind map. By the end, your mind map will contain literally all information that you have considered to be important. Whenever you want to know something, you can look it up in your mind map, and read in more detail about it by clicking on the link to the PDF.

Searching for (Electronic) Literature

A prerequisite for a good PhD thesis is to know what others have done in your field of research. But how to find this related work? Due to computers and the internet, searching for literature has changed dramatically over the last years. Instead of using catalogues in libraries, students can use full text search offered by academic search engines and databases such as Google Scholar, SciPlore and ACM Digital Library. In addition, academic search engines usually offer sophisticated ranking algorithms which help in finding the most relevant documents [10-12].
Dozens of academic search engines exist. Some are focusing on specific disciplines such as computer science and some are trying to cover several or even all disciplines. For the field of computer science, popular academic databases are Springerlink, ACM Digital Library and IEEE Xplore as well as ScienceDirect and to sometimes Emerald Insight (Wikipedia provides you with an extensive list of available resources). All these databases require a subscription to access their content. If you are lucky, your university has an agreement with these databases so you can access all their articles for free. Ask your supervisor or in your library which databases you have access to. Free alternatives are CiteSeer and SciPlore which provide you free access to many academic articles. Google Scholar is a special case: Often you can download the linked content for free but not always.

In this tutorial we will focus solely on the management of electronic literature.
Storing Files in Folder Structures

Most academic search engines and databases offer to download scholarly literature in PDF format. The probably simplest way to store (and retrieve) these PDFs is a reasonable structured folder system. Each PDF can be stored in one folder which is labeled with an appropriate descriptor. It is usually helpful to give a meaningful filename to the PDF such as the article’s title. In case that one document fits into two or more categories, most operating systems allow creating a shortcut or alias for a file (see picure). Some feel this approach as being too structured and prefer tagging.
Possibility: Save PDFs for your PhD in different folders

Possibility: Save PDFs for your PhD in different folders


Tagging

Tagging allows assigning multiple keywords (tags) to a file independently of where the file is stored. Based on these tags, users can retrieve the files from their hard drive. Popular tagging tools for the desktop are Tag2Find, iTag, and Punakea. There are also services allowing to tag and store academic articles online such as Connotea, CiteULike or Bibsonomy.

However, for the approach we present in this tutorial we will focus on desktop tools and, more importantly, neither folder structures nor tags are important for the approach we present. Of course, a good folder structure never harms but you do not really need it.
Starting to Search and Storing Files in One flat Folder

In the beginning of your PhD you should just search for the most relevant keywords in academic search engines and store whatever paper you get on your hard drive. If you wanted to do a PhD about academic search engines, it might make sense to start doing some research about Google Scholar, one of the leading academic search engines. Let’s assume you have found a hand full of interesting PDFs and stored them in c:\myliterature\ (don’t spend too much time with judging the relevance of a PDF. If the title or abstract sound interesting, store it).
Your first PDFs for writing a PhD thesis

Your first PDFs for writing a PhD thesis
Memorizing a PDF’s important information
What you really need to know as a researcher is: Where have I read which information? For your thesis it is worthless to know something but not where the information is from. Eventually you will have to reference the origin (ideally with page number). As a first stept, PDF readers are perfect to keep track of a PDF’s most important information. You need a PDF reader that can create bookmarks and ideally highlight passages and create annotations. If you have access to Adobe Acrobat that’s great (the free Acrobat Reader is not sufficient). Otherwise we would recommend the free version of Foxit Reader.

Now, whenever you read an interesting PDF you create a bookmark for every statement that might be interesting for your PhD thesis. We would also suggest highlighting the interesting text directly in the document. Have a look at the picture.
Marking important information for your PhD thesis

Highlighting important information for your PhD thesis

This is the PDF of an article titled “Academic Search Engine Optimization (ASEO): Optimizing Scholarly Literature for Google Scholar and Co.”. It is about how to get your papers indexed and well ranked by academic search engines such as Google Scholar. If you write your PhD about academic search engines it might be interesting to keep in mind that this paper is the very first paper about academic search engine optimization. And also the definition of “academic search engine optimization” might be relevant later for your PhD thesis. Therefore you create a bookmark for each of this information (see the picture).

It is up to you how detailed you make the bookmark structure. In the very beginning it might be appropriate to create just one bookmark that briefly describes the paper (e.g. “first paper about academic search engine optimization”). If you need more information you could come back to this paper later. It is easy to get lost with all the information you read. So, for the beginning, really, create bookmarks only for the very important information. When finishing reading the first PDF you proceed with the other PDFs in the same way.
Managing information from various PDFs
In the long run, it is not very helpful to have the information only in the PDFs. Here is where mind mapping joins the game. Mind maps were ‘invented’ by Tony Buzan in the 1970s [13]. A mind map is a diagram with a central topic and subtopics branching from it, like a tree (see the picture for an example). Usually a node in a mind map contains only one or two important keywords. Due to its visual structure a mind map is more effective for learning for many people. In this tutorial we use the mind mapping tool SciPlore MindMapping as it is especially designed for students and researchers. Please download and install it.
Example of a Mind Map

Example of a Mind Map

When you never did mind mapping before, the concept might appear strange to you in the beginning. And actually, mind mapping is not for everyone the best solution. But please, invest 30 minutes and we guarantee that the chance you will love it is really high.
Monitor all new PDFs in your Mind Map

We want to keep track of all the information you have read in one single place. Open SciPlore MindMapping and create a new mind map which you will use to manage your literature (press Ctrl+N). By clicking on the already existing node called New Mindmap this node is selected and can be renamed by either pressing F2 or just typing the new name, for instance My Literature.

One of SciPlore MindMapping’s special features is monitoring a folder for new files. We use this feature to list all our PDF in the mind map. The aim is that whenever you find a new PDF on the Internet, you store it on your hard drive, and immediately it will be displayed in your mind map.

Create a new child node by pressing the Insert key on your keyboard or selecting Insert | New Child Node from the menu. Call this node Incoming Literature. Now, right-click on that node, select Add PDF Monitoring Directory and choose your literature directory (e.g. c:\myliterature\). Now, all PDF files (plus DOC(X), TXT, RTF, ODT and XLS(X)) that are stored in the defined folder are displayed in your mind map’s Incoming Literature node. Other files are ignored. And the best – also the PDF bookmarks are imported. The following picture illustrates this.
Monitoring a folder for new PDFs that are important for your thesis


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