Part I: Literature Management
Keeping track of related work in your field is key to writing a good thesis, especially for writing a good PhD thesis. This tasks entails knowing about the relevant studies, results, facts, and ideas in your field. Keep in mind that by the end of your literature review for your PhD thesis you will have read or at least skimmed through hundreds of papers and books. Without using tools, you must be a genius to remember every interesting fact and idea you have read. Before the computer-age, academics relied 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 use academic search engines to find relevant literature. Then we show you how to create summaries of your PDFs using bookmarks and how to keep an overview of all important information in a mind map. By the end of this part, 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 about it in more detail by clicking on the link to the PDF.
Searching for (Electronic) Literature
Knowing what others have done in your field of research is a prerequisite for any thesis. 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 library catalogs, students can use full text search offered by academic search engines and databases such as Google Scholar and ACM Digital Library. In addition, academic search engines usually offer sophisticated ranking algorithms that help in finding the most relevant documents [10-12]. Dozens of academic search engines exist. Some focus on specific disciplines such as computer science, while others try to cover several or even all academic disciplines. For computer science, popular academic databases include Springerlink, ACM Digital Library, IEEE Xplore, ScienceDirect and to some extent 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 institution has an agreement that allows you to access some or all of these databases for free. Ask your supervisor or the staff in your institution’s library about which databases you can access. Free alternatives to commercial literature databases include CiteSeer, SciPlore’s collection, which is accessible through Docear. Often, but not always, Google Scholar provides a free download link to articles in its listings. In this tutorial we will focus solely on the management of electronic literature.
Storing Documents in a Folder Structure
Most academic search engines and databases offer to download scholarly literature as PDFs. The simplest way to store (and retrieve) these PDFs is by organizing the PDFs in a reasonably structured folder system. Each PDF can be stored in one folder labeled with an appropriate descriptor. Assigning meaningful file names, such as the article’s title, to PDFs is generally helpful. If one document falls into two or more categories, most operating systems allow creating a shortcut or alias for a file (see picture). Some users consider this approach as being too structured and prefer tagging instead.
Tagging allows assigning multiple keywords (tags) to a file independent of the file’s physical storage location. Based on these tags, users can retrieve the files from their hard drive. Popular desktop tagging tools include Tag2Find, iTag, and Punakea. There are also services that allow online tagging and storage of academic articles, e.g., CiteULike or Bibsonomy. However, the approach we present in this tutorial focuses on desktop tools and, more importantly, neither folder structures, nor tags are necessary. Of course, a good folder structure never hurts, but it is not a requirement.
Storing Files in a Single Folder
Especially at the beginning of a PhD, you should use academic search engines to search for the most relevant keywords in your field and store any paper you get on your hard drive. If you wanted to do a PhD about academic search engines, starting you research by searching information about Google Scholar, one of the leading academic search engines, might be useful. Let’s assume you have found a hand full of interesting PDFs and stored them in c:\literature\ Don’t spend too much time on judging the relevance of a PDF. If the title or abstract sound interesting, store it.
Keeping Track of Important Information in PDFs
What you really need to know as a researcher is: Where have I read certain information? Information for which you forgot the origin is worthless or even harmful for your thesis, because you may inadvertently plagiarize if you present certain information without proper attribution. You will have to reference the origin of information taken from other sources, ideally with page number. As a first step, PDF readers are perfect to keep track of a PDF’s most important information. You need a PDF reader that can create bookmarks, highlight passages and create annotations. For best compatibility with Docear, we recommend the free version of PDF XChange Viewer. However, the free Foxit Reader or Adobe Acrobat Reader will do, too. Now, whenever you read an interesting PDF, you create a bookmark for every statement that might be interesting for your thesis. We would also suggest highlighting the interesting text directly in the document. Have a look at the picture.
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 thesis 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. Additionally, the definition of “academic search engine optimization” might be relevant for your thesis. Therefore you create a bookmark for each of these information (see the picture). How detailed you create your bookmark structure is up to you. In the very beginning of your literature research, creating just one bookmark that briefly describes the paper (e.g. “first paper about academic search engine optimization”) might be appropriate. If you need more information, you could return to the paper later. Getting lost in all the information you read is very easy. Therefore, we recommend to start with only creating bookmarks for very important information. When you have finished reading the first PDF, you proceed with the other PDFs in the same way.
Managing Information from Multiple PDFs
In the long run, having information annotated solely in the PDFs isn’t very helpful. At this point, mind mapping joins the game. Mind maps were ‘invented’ by Tony Buzan in the 1970s . 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, many people consider mind maps very effective learning tools. If you never used mind mapping before, the concept might appear strange to you at first. In fact, mind mapping isn’t the best solution for everybody. However, we urge you to invest 30 minutes and give mind mapping a try. We guarantee that the chance you will love mind mapping is really high.
Monitor all new PDFs in your Mind Map
Our goal is to keep track of all the information you have read in one single place. To achieve this, Open Docear and create a new mind map, which you will use to manage your literature (press Ctrl+N). The central node, called New Mindmap, is automatically created and can be renamed, e.g. to My Literature, by either clicking on it or pressing F2 and typing the new name. One of Docear’sspecial features is monitoring a folder for new files. We use this feature to automatically include all our PDF in the mind map. The goal is that whenever you find a new PDF on the Internet, you store it in this special folder, to have it displayed immediately within 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 specified 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.
That means, as of now all the information you annotated in your PDFs are accessible and manageable in a single place – your mind map.
Giving Structure to Your Mind Map and Literature
After you have read the first PDFs and created bookmarks, you should start giving some structure to the information: Create nodes for all the important categories you plan to do research in (you can change them at any time later on). Then drag & drop the bookmarks from the incoming node to the appropriate categories. If you feel that one bookmark fits to several categories, just create a copy of it. The following picture shows an example.
Now you have a good overview of what you have read. On first glance, this might seem similar to a folder structure on your hard drive and indeed it is. However, there is one big advantage (and there will be more): In contrast to a folder structure, you have not only categorized your PDFs but the PDFs’ contents and you have direct access to all the bookmarks in all the PDFs via your mind map. Furthermore, creating, deleting, renaming, copying and moving nodes in a mind map is much faster than doing the same operations with folders in a file structure.
Deepening the Literature Review
To extend and deepen your literature review, you can basically go on as you did before. You find new PDFs, read them, create bookmarks, and categorized them within your mind map. Let’s assume you want more information about a certain topic that is already in your mind map. For instance, about differences between academic and classic search engine optimization. In this case, you can just click on the node “Differences between ASEO and classic SEO” in the mind map.
The PDF will open at the corresponding position in the paper, so you can read more about that topic and, if you like, create more bookmarks. Jumping to the in-text position of bookmarks only works when using Docear in combination with PDF XChange viewer.Other PDF viewers will open the front page of the PDF when clicking on the bookmark in the mind map. This behavior is due to the handling of bookmarks by the viewers and can not be influenced by Docear. The new bookmarks can be easily imported by performing a right click on the respective node and selecting Import Bookmarks.
After a while, you will have a large mind map with all the information that is important for your thesis. You can use the search function (STGR+F) to find nodes. To get a better overview, you can fold and unfold nodes by selecting a node and pressing Space.
Another feature that makes mind maps superior to simple file systems is the possibility to add notes. You can add any kind of text as a note to any node in the mind map. The note is shown in a hovering window when passed over by the mouse or in a separate window when clicked (see illustration).