The main idea behind Docear is that you annotate everything you consider [...]]]> Today, on February 15th, 2012 we released the first public version of Docear. It’s a Beta version and still has some bugs and missing features but overall it will give you a thorough impression of what we consider an academic literature suite should be.

The main idea behind Docear is that you annotate everything you consider important in a PDF. That means, you highlight text, write comments, or create bookmarks in the PDF. To create bookmarks and comments, you can use almost any PDF reader (highlighting text is a bit more complicated). These PDF annotations are then imported by Docear to a mind map. In this mind map you can organize all your annotations into categories, create further nodes and add more text. With the integrated reference manager, bibliographic data can be added to each of the PDF annotations (and all other nodes in the mind map). Subsequently, you can create a new mind map, drag e.g. a research paper, copy your annotations to the draft and if you need more information you just click on the PDF annotation and the PDF will open on the page the annotation was made. Watch this video to get a better idea of what Docear can do (watch it in full-screen mode).

Here is again an overview of the major changes between Docear and its predecessor SciPlore MindMapping.

Freeplane instead of FreeMind

The old SciPlore MindMapping was based on FreeMind, a good and popular but not very well maintained mind mapping software. The new Docear is based on Freeplane, a really exceptional piece of software. Freeplane has many more features compared to FreeMind (e.g. Free floating nodes, displaying images), is faster, more stable and above all: Freeplane has a great plugin system that allows us offering Docear as a plugin for Freeplane. That means, if a new version of Freeplane is released you can just install it and Docear will work with the new version. You do not need to wait until we have adjusted Docear to the new Freeplane version. Also, the Freeplane development team is highly responsive to user feedback. If you have ideas for new features regarding the mind mapping functionality, the Freeplane team will be happy to hear them.

Integrated Reference Manager

Docear has it’s own BibTeX compatible reference manager. Or better said: we fully integrated one of the best available reference managers, namely JabRef. That means you can directly create references in Docear, add them to nodes (even if they don’t have a link to a PDF), edit references in the mind map and they will automatically be changed in the BibTeX file, and you have all the wonderful standard features that JabRef offers. Of course, you can still install JabRef in parallel and work as you are used with SciPlore MindMapping.

Compatibility with other reference Managers

You don’t have to use our integrated reference manager. You can still use any other BibTeX compatible reference manager as well and also our support for Mendeley now is improved. It is no problem to use Mendeley for managing your PDFs (and extract metadata) and use Mendeley’s BibTeX file in Docear.

Workspace

Docear has a “workspace”. We believe this workspace makes Docear much easier to understand for new users. In the workspace you have several mind maps. For instance, one that lists only your new PDF files. Another one is for managing all your annotations, another one for your own publications. Of course you can still create new mind maps for each of your assignments, papers or books you are currently writing. There is also another advantage of having a workspace. All links in mind maps are set relative to the workspace. That means you can move your mind maps within the workspace and all links to PDF files will still work. It also allows you to use your data on several computers with different operating systems.

MS Word plugin

The probably biggest advantage other reference managers such as Zotero and Mendeley have over Docear is their good integration with Microsoft Word and OpenOffice. For SciPlore MindMapping we recommended using BibTeX4Word but BibTeX4Word is not very user friendly (neither the installation, nor the use in MS Word, nor installing new citation styles). We are working on a Docear4Word Add-On and hope to have it ready in a few weeks.

Download Docear 1.0 Beta 1

And for those of you who are into details: Here are the exact changes since the release of the private Alpha 1

Features:

• #215 compare files in nodes to bibtex-files only on filename
• #163 Use file type specific icons for linked files
• #302 mind maps and folders can be created in Library
• #316 Trash and Temp mind maps added to library
• #91 keyboard commands in jabref
• #230 auto recognition for BibTeX type
• #232 copy multiple reference keys at once
• #286 Open pdf files with foxit reader in WINE
• #224 offer Mac OS version
• #223 create windows installer
• #207 monitoring options as separate settings

Feature enhancements:

• #287 Mendeley Information Text
• #285 New Workspace Structure
• #325 Profile name is shown instead of “My Workspace”
• #282 close all mindmaps before changing the workspace
• #256 open link with foxit shows the wrong page
• #297 Default PDF Opener
• #250 (un)show workspace/property panel should not completely remove it
• #235 bibtex key is not generated automatically
• #324 Installer creates desktop icon (optional)
• #300 All file and folder names lowercase
• #304 consequent labeling of workspace features
• #352 no icon in workspace for .doc

Bugfixes:

• #204 JabRef extract metadata via MrDlib
• #216 Create new Directory in projects folder does not work
• #194 pdf monitoring does not work after changing the link types of the mindmap
• #173 Converting old splmm maps
• #209 monitoring does not work at all
• #213 updating_references_for_map
• #219 dialog is shown twice
• #191 interrupted exception
• #154 update reference in current mind map – repaint error
• #245 timeout on connection to mrdlib
• #257 pdf links in mendeley bibtex are not recognized correctly
• #229 bibtex data from mendeley is not recognized
• #254 workspace panel is gone
• #225 keyboard input in reference window takes place in mind map window
• #214 notes from pdfs (monitoring) are out of order
• #236 multiple pdf files for one bibtex entry do not work
• #255 no auto-adding of reference on missing bibtex key
• #276 FolderMonitoring does not work properly
• #244 drag&drop of files does not work any more
• #196 mindmap version should be checked whenever the mindmap is touched
• #105 spaces in dialogs
• #201 When choosing the BibTeX file –> filter for “*.bib” in JFileChooser
• #220 converter does not recognize old splmm mind maps if opened twice
• #183 starting freeplane with empty bibtex database
• #246 dragging a pdf out of the workspace into nautilus does not work
• #261 NullPointerException while updating SPLMM-Mindmap
• #262 NullPointer on createNewMindmap for Incoming Map
• #278 NullPointerException if no bibtex file was opened
• #260 NullPointerException after Changign LinkTypes
• #258 concurrent modification exception after cancelling link type update
• #172 Error after Link was removed from a node with annotationmodel
• #289 PDF can not be dragged or dropped into the mindmap
• #308 Remove/Delete file from workspace did not work
• #331 NullPointerException after renaming a pdf on the literature repository
• #292 Attributes were sometimes shown though they should be hidden
• #328 Updating mindmap attributes does not work
• #248 Shortcut “F1″ calls freeplaneTutorial.mm instead of docear-welcome.mm
• #330 welcome map does not exist after changing the workspace
• #237 hyperlink to mm file does not work after moving a branch to a new map
• #334 icon for file in workspace changes after renaming action
• #327 “File not found Message” for LinkNodes linked to no longer existing files
• #358 first start: closing workspace selection dialog crashes software
• #270 Disable all prohibited Actions in JabrefFrame.fillMenu
• #235 bibtex key is not generated automatically
• #338 adjust about dialog
• #337 Docear Icon in Installer
• #344 Reference Preferences
• #343 PNG instead of PGN is imported
• #317 Error on duplicate/conflicted BibTeX data
• #341 “Copy” did not work in the workspace window

Originally, we planned  to develop our own Docear4Word but we just didn’t have the time because [...]]]> Up to now we recommended using BibTeX4Word to cite your papers in Microsoft Word. However, the installation of BibTeX4Word is complex and its use is not that user friendly (the Word add-ons from Zotero and Mendeley are much more intuitive).

Originally, we planned  to develop our own Docear4Word but we just didn’t have the time because we want to focus on Docear itself. Therefore we wrote a detailed specification of what we want to have developed. If you think you could help us (for money or even free), or if you have ideas of what is missing in the specification, please let us know.

Beta 16 is about to be released (Preview for Blog readers available now)

The last Beta was released in March, quite a while ago. We were really busy with preparing the relaunch of SciPlore MindMapping as Docear. However, we also had time to finish Beta 16 with two [...]]]> There is lots of great news.

Beta 16 is about to be released (Preview for Blog readers available now)

The last Beta was released in March, quite a while ago. We were really busy with preparing the relaunch of SciPlore MindMapping as Docear. However, we also had time to finish Beta 16 with two really nice new features and lots of improvements and bug fixes. This will be the last version of SciPlore MindMapping. The next release will be a Beta version of the all-new Docear. Before releasing Beta 16, we would like to ask you – our Blog readers – to test it. If you should find bugs during the next two days, we will fix them before releasing Beta 16 officially. All bugs discovered after that deadline will be fixed in the first Docear Beta scheduled for September.

Here is the change log:

• New: Bookmarks and comments in PDFs are renamed when the linking node in a mind map is renamed
• New: PDF can now be opened on the page where the bookmark is (only Acrobat)
• Improved: Recommendations are now also based on selection in incoming window
• Improved: Recommendations can be deactivated
• Improved: Smart Update is default update mechanism now, instead of Thorough Update
• Improved: Import Highlighted text is selected by default
• Improved: Zotero and Mendeley BibTeX file support should work now more reliably, also under Linux
• Improved: Layout of recommendations changed
• Fixed: Under some circumstances CPU load of the software was 100% even if nothing was done Fixed: Null pointer exception when last opened mind map was closed
• Fixed: Some users could not open PDF links out of a mind map
• Fixed: Mind Maps were destroyed in some cases when the user was using a proxy server
• Fixed: Exception under MacOS when monitoring folder was updated
• Fixed: Monitoring did not work for some users

Download Beta 16 Preview here, and report problems as soon as possible in our new forum for bug reports. Also, feel free to tell us your ideas for new features we can integrate in Docear

Cooperation with Freeplane

This weekend, the entire Docear team went to Munich to meet Dimitry Polivaev and Volker Börchers from the Freeplane team. As announced earlier, it was clear that Docear and Freeplane wanted to cooperate but it wasn’t sure in which way. This weekend we met to figure out the details and I have to say that I really enjoyed the meeting. Dimitry and Volker are two amazing software developers who created a really great piece of software that is just perfect for our purposes. In addition, it was a real pleasure to meet with them and discuss our ideas for the future of Freeplane and Docear.

Working together with the Freeplane team

The outcome in short: Docear will be developed as a independent Add-On for Freeplane. That means you will be able to download the complete package (Freeplane+Docear) from our website but you can also install Freeplane updates whenever you like (until now, you had to wait for us, integrating a new version of FreeMind to our own code). Also, the Docear team will closely work together with the Freeplane team to assure that developments of Freeplane will not contradict the interests of our users. And, the Docear team will also engage in the development of basic Freeplane features such as an enhanced search function. We also will use a common repository for our code.

Originally we planned on working together on Saturday and Sunday, but the meeting went so well that we discussed all the points on our agenda on Saturday already. This meant, we had plenty of time left to visit Munich and its pubs

The Freeplane and Docear teams having a beer in "Löwenbräu". From left to right: Dimitry (Freeplane), Stefan (Docear), Volker (Freeplane), Christoph (Docear Volunteer), Marcel (Docear), Joeran (Docear)

Docear team receives funding for one year (100,000€)

During the last years only a few hours a month could be spend on the development of SciPlore MindMapping because we had lots of other work to do. This has changed since July 1, 2011. We (that is Stefan Langer, Marcel Genzmehr, and I – Joeran Beel) got a scholarship from the German Federal Ministry of Economics and Technology for one year, worth 100,000€ (~143,000 US$), to work full-time on the development of Docear. Our goal is, to develop Docear into an academic literature suite helping you in all aspects of literature management, i.e. literature search, literature organization and literature creation. I would like to stress, that we are extremely happy to have this scholarship as there are no strings attached. It’s not a loan we would have to pay back, and it’s not an investment from some investors expecting a huge return on investment. It’s almost like winning in a lottery because we can just focus on developing a great product during the next year and we will have enough money to pay our rent and food. After the year, we hope we will be able to continue the development of Docear in a similar way as Zotero is doing it, with research grants and funding from non-commercial organizations.

We plan to release Docear’s first public Beta and new website in September 2011. However, feel free to use already now our new forum for bug reports, general questions and submit your ideas to our idea tracker. More information will come soon .

Hilah is a fan of SciPlore and for her research she wants to perform a user study (interviews) with some users of SciPlore MindMapping to understand how academics are using SciPlore MindMapping. The [...]]]> We – that is the SciPlore team and Hilah Geer (Head librarian at the Oslo School of Management) – need your help!

Hilah is a fan of SciPlore and for her research she wants to perform a user study (interviews) with some users of SciPlore MindMapping to understand how academics are using SciPlore MindMapping. The results will help us to understand how you are using the software and how we can improve it. Therefore, please, if you are an active academic user of Sciplore MindMapping, help us understanding how you work with SciPlore MindMapping. Participate in the 30minutes interviews and read on what Hilah has to tell you about the interviews:

Introductory Letter:

I am a seasoned academic librarian doing research in the field of Science & Technology Studies (STS).  And I need your help. I have chosen SciPlore as my research object because of its brilliant combination of functionalities for academics.  However, according to STS theory, it is not brilliant functionality that changes society; functionality cannot even really be brilliant on its own.  It is brilliant use of functionality that counts.

I think the people at SciPlore would agree.  Perhaps their secret is that they are not really concerned with creating software at all.  They are concerned with facilitating your brilliant uses for evolving functionalities.  That means that for me to understand SciPlore I need to understand how you are using it.  Data on downloads and clicks, luckily enough for us humans, is not enough.

Academic institutions allow researchers enormous freedom in managing their personal libraries. Okay, perhaps there is a little neglect mixed in with the freedom, but either way you have undoubtedly fostered a rich information ecology on your personal computer.  And you use SciPlore, which offers practical and logical functionality for managing and wrestling with ideas and texts in a digital environment.  Much of this meaningful work is hidden, black boxed, while you work independently at your personal computer. It would be a great privilege for me and I believe of benefit for SciPlore to be able to conduct telephone interviews with active SciPlore users.  Look under the proverbial hood so to speak.  Who knows, it may even help you clarify some things for yourself.

Hilah Geer

Details about the study

About me:

I am been a librarian since the early 90s.  I have worked at MIT, Harvard Business School, and a consulting firm in Berkeley, California among other places.  Most recently I have moved to Norway and am the head librarian at the Oslo School of Management.  I am exploring the field of Science & Technology Studies as a means of getting a better grasp on the role technology plays in my work.  I would very much appreciate your help!

About the interviews:

Who will be interviewed: Anyone who is working in an academic/research environment who uses SciPlore to any extent with any regularity is valuable to my research.  I will be interviewing as many of you as possible.

How will they be conducted: I personally will be conducting all of the interviews.  They will be done either on Skype or via telephone.  They will take 30 minutes.  I will be more than willing to go more in depth if the interviewee is interested.  Otherwise, I will protect your time and stick to 30 minutes.

What will they include:  first I will want to gather standardized information:  demographics, field of study, institution(s), hardware, software, and networked resources.  Then I will have a series of questions to steer a discussion of how you use SciPlore and why.

When: The main interview period will be between May 2. and June 24 (There is a degree of flexibility as regards dates).  I will be available for interviews on weekends but weekdays are preferable.

Conditions: Of course the results of the interviews will be made entirely anonymous.  Upon arrangement of the interviews you will be given a signed terms of agreement that you can choose to alter if you wish.  All processed anonymous data will be shared with SciPlore, unless requested otherwise.

 

Send an email to survey@sciplore.org to arrange an interview or ask a question about them. And Thanks!

My colleague and I performed several tests with Google Scholar and found out that it is really easy to fool Google Scholar. [...]]]> Are you using Google Scholar? For finding scientific literature? For obtaining citation counts and publication lists of researchers? Have you ever thought about how trustworthy the information is you get on Google Scholar?

My colleague and I performed several tests with Google Scholar and found out that it is really easy to fool Google Scholar. You can easily increase citation counts of articles and therefore increase the article’s rankings. You can easily add invisible keywords to articles and make the article appear relevant for searches it actually isn’t. You can also create complete non-sensical articles with the paper generator SciGen and make Google Scholar index them. And you can place any kind of advertisement in manipulated articles and make users of Google Scholar downloading them.
Of course, our results do not mean that you cannot trust Google Scholar at all or shouldn’t use it at all. Despite our results I am using Google Scholar frequently – imho it’s still the best academic search engine on the market. However, as with all other search engines you should be aware that there might be spam and manipulated information and you should really be carefully using citation counts from Google Scholar. Maybe there are no, or little, manipulations right now. But the more citation counts from Google Scholar are used for performance evaluations, the higher the incentive for researchers to manipulate them (and, as said, it’s really easy).

What I am interested in now is: What’s you opinion on this subject? Have you every found something on Google Scholar that was suspicious? Please let me know.

If you are interested in more information read the full article, titled “Academic Search Engine Spam and Google Scholar’s Resilience Against it”, here.

Update 2010/12/31:

We got a few questions when we did the experiments on Google Scholar (unfortunately we didn’t state that in the paper). The answer: Between early 2009 and mid of 2009. We first submitted the paper to WWW2010 in November 2009 but it was rejected. Well, and then it took… many many month (and edits) before the Journal of Electronic Publishing finally accepted and published the paper .

Update 2011/01/02:

There is another really interesting article about spamming Google Scholar: Cyril Labbe created a fake researcher called Ike Antkare and made him one of the most cited authors of all time (according to Google Scholar). Read the article here.

Download Beta 10 here.

I am currently in Toronto presenting our new paper titled “On the Robustness of Google Scholar against Spam” at Hypertext 2010. The paper is about some experiments we did on Google Scholar to find out how reliable their citation data etc. is. The paper [...]]]> Update: The final article is published. Please read here.

I am currently in Toronto presenting our new paper titled “On the Robustness of Google Scholar against Spam” at Hypertext 2010. The paper is about some experiments we did on Google Scholar to find out how reliable their citation data etc. is. The paper soon will be downloadable on our publication page but for now i will post a pre-print version of that paper here in the blog:

Abstract

In this research-in-progress paper we present the current results of several experiments in which we analyzed whether spamming Google Scholar is possible. Our results show, it is possible: We ‘improved’ the ranking of articles by manipulating their citation counts and we made articles appear in searchers for keywords the articles did not originally contained by placing invisible text in modified versions of the article.

1.    Introduction

Researchers should have an interest in having their articles indexed by Google Scholar and other academic search engines such as CiteSeer(X). The inclusion of their articles in the index improves the ability to make their articles available to the academic community. In addition, authors should not only be concerned about the fact that their articles are indexed, but also where they are displayed in the result list. As with all ranked search results, articles displayed in top positions are more likely to be read.

In recent studies we researched the ranking algorithm of Google Scholar [1-3] and gave advice to researchers on how to optimize their scholarly literature for Google Scholar [4]. However, there are provisos in the academic community against what we called “Academic Search Engine Optimization” [4]. There is the concern that some researchers might use the knowledge about ranking algorithms to ‘over optimize’ their papers in order to push their articles’ rankings in non-legitimate ways.

We conducted some experiments to find out how robust Google Scholar is against spamming. The experiments are not all completed yet but those that are completed show interesting results which are presented in this paper.

2.    Related Work

Most web search engines rank web pages based on two factors, namely the web page content and the amount and quality of links that point to the web page. Accordingly, spammers try to manipulate one or both of these factors to improve the ranking of their web sites for a specific set of keywords. This practice is commonly known as ‘link spam’ and ‘content spam’.

Link spammers have different options to create fraudulent links. They can create dummy web sites which link to the website they want to push (link farms), exchange links with other webmasters, buy links on third party web pages, and post links to their websites, for instance, in blogs. To detect link spam, much research has been performed, among others [5-12].

Content spammers try to make their website appear more relevant for a certain keyword search than it is. This can be accomplished by taking content of other websites and combining different (stolen) texts as ‘new content’, or by stuffing many keywords in a web page’s meta tags[1], title, ALT-tags of images, the body text, creating doorway pages, and placing invisible text on a web page. Invisible text usually means text in the same color as the background or text in layers which are behind the normal text or which are invisible. Again, much research has been performed to identify content spam, among others [13-15].

Although spammers are continuously adjusting their methods and developing new techniques (e.g. scraper sites, page hijacking, social media spam, Wikipedia spam, and gadget spam), overall, search engines are capable to fight web spam quite well.

No studies are available, to our knowledge, on the existence of spam in academic search engines or whether it can be recognized and prevented.

3.    Methodology

We modified already published academic articles by adding references and (invisible) text. These modified articles were then uploaded as PDF to the Web to see whether Google Scholar was indexing them. Currently, not all experiments are completed. The current results are presented in the following. A more detailed analysis and explanation of the methodology shall be provided in another paper as soon as all experiments are completed.

4.    Results

Google Scholar did index the PDFs with invisible text and grouped these PDFs with the original article. That means, a researcher could add invisible keywords to his article after its publication and upload this PDF to the web. This way a researcher could make the article appear for keyword searches the article originally was not relevant for.

Moreover, Google Scholar did count references that were added to a modified version of an already published article. Citation counts and rankings of the cited articles increased. That means, authors could add additional references in their articles after official publication. If these altered articles were uploaded to the Web, Google would index them. This way, researchers could increase citation counts and rankings of the additionally cited articles. They could also arouse more attention to their articles because the cited authors might investigate who has cited them. It is to assume that researchers could also modify articles from other authors and add references to their own articles. This way, scholars could create the impression that their articles were cited by an authority in their field and increase citation counts as well.

5.    Discussion

Our study on the robustness of Google Scholar delivers surprising results: It seems that Google Scholar is far easier to spam than the classic Google Search for web pages. Apparently, Google Scholar applies no or only very rudimentary mechanisms to detect and prevent spam. With comparatively little effort we could manipulate articles’ citation counts and hence their rankings and make Google Scholar indexing invisible text.

6.    Outlook

This poster is work-in-progress. We are currently conducting more experiments. For instance, we created nonsensical text with the random paper generator SciGen to see if this text, when published on the Web, is indexed by Google Scholar. We are also analyzing whether we can make one article appear as several search results to spam result sets and whether PDFs containing advertisement is indexed by Google Scholar.

We would like to note that the intention of this paper was not to expose Google Scholar. The intention was to stimulate a discussion about academic search engine optimization. We chose Google Scholar as the subject of our study because Google Scholar probably is the best and largest academic search engine, indexing PDFs from the Web. Currently, we are developing our own academic search engine SciPlore (www.sciplore.org), however as yet, SciPlore has not any precautions against spam either.

References

[1]   Jöran Beel and Bela Gipp. Google Scholar’s Ranking Algorithm: The Impact of Citation Counts (An Empirical Study). In André Flory and Martine Collard, editors, Proceedings of the 3rd IEEE International Conference on Research Challenges in Information Science (RCIS’09), pages 439–446, Fez (Morocco), April 2009. IEEE. doi: 10.1109/RCIS.2009.5089308. ISBN 978-1-4244-2865-6. Available on http://www.sciplore.org.

[2]   Jöran Beel and Bela Gipp. Google Scholar’s Ranking Algorithm: An Introductory Overview. In Birger Larsen and Jacqueline Leta, editors, Proceedings of the 12th International Conference on Scientometrics and Informetrics (ISSI’09), volume 1, pages 230–241, Rio de Janeiro (Brazil), July 2009. International Society for Scientometrics and Informetrics. ISSN 2175-1935. Available on http://www.sciplore.org.

[3]   Jöran Beel and Bela Gipp. Google Scholar’s Ranking Algorithm: The Impact of Articles’ Age (An Empirical Study). In Shahram Latifi, editor, Proceedings of the 6th International Conference on Information Technology: New Generations (ITNG’09), pages 160–164, Las Vegas (USA), April 2009. IEEE. doi: 10.1109/ITNG.2009.317. ISBN 978-1424437702. Available on http://www.sciplore.org.

[4]   Jöran Beel, Bela Gipp, and Erik Wilde. Academic Search Engine Optimization (ASEO): Optimizing Scholarly Literature for Google Scholar and Co. Journal of Scholarly Publishing, 41 (2): 176–190, January 2010. doi: 10.3138/jsp.41.2.176. University of Toronto Press. Available on http://www.sciplore.org.

[5]   Z. Gyöngyi and H. Garcia-Molina. Link spam alliances. In Proceedings of the 31st international conference on Very large data bases, page 528. VLDB Endowment, 2005.

[6]   AA Benczur, K Csalogány, T Sarlós, and M Uher. SpamRank – Fully Automatic Link Spam Detection. In Adversarial Information Retrieval on the Web (AiRWEB’05), 2005.

[7]   I. Drost and T. Scheffer. Thwarting the nigritude ultramarine: Learning to identify link spam. Lecture Notes in Computer Science, 3720: 96, 2005.

[8]   D. Fetterly, M. Manasse, and M. Najork. Spam, damn spam, and statistics: Using statistical analysis to locate spam web pages. pages 1–6, 2004.

[9]   A. Benczúr, K. Csalogány, and T. Sarlós. Link-based similarity search to fight web spam. Adversarial Information Retrieval on the Web (AIRWEB), Seattle, Washington, USA, 2006.

[10] H. Saito, M. Toyoda, M. Kitsuregawa, and K. Aihara. A large-scale study of link spam detection by graph algorithms. In Proceedings of the 3rd international workshop on Adversarial information retrieval on the web, page 48. ACM, 2007.

[11] B. Wu and K. Chellapilla. Extracting link spam using biased random walks from spam seed sets. In Proceedings of the 3rd international workshop on Adversarial information retrieval on the web, page 44. ACM, 2007.

[12] Q. Gan and T. Suel. Improving web spam classifiers using link structure. In Proceedings of the 3rd international workshop on Adversarial information retrieval on the web, page 20. ACM, 2007.

[13] T. Urvoy, T. Lavergne, and P. Filoche. Tracking web spam with hidden style similarity. In AIRWeb 2006, 2006.

[14] I.S. Nathenson. Internet infoglut and invisible ink: Spamdexing search engines with meta tags. Harv. J. Law & Tec, 12: 43–683, 1998.

[15] C. Castillo, D. Donato, A. Gionis, V. Murdock, and F. Silvestri. Know your neighbors: Web spam detection using the web topology. In Proceedings of the 30th annual international ACM SIGIR conference on Research and development in information retrieval, page 430. ACM, 2007.

[1] Meta tags usually are not used by spammers any more since most search engines ignore meta tags due to spam issues

Meanwhile, we have finished the work on a second paper on this topic and it is really surprising that Google Scholar, in my opinion the best web based academic search engine, seems to do nothing to prevent spam. For instance, we managed to make Google Scholar indexing several fake papers we created with SciGen and hence increase rankings and citations counts of our papers that were cited by these fake articles. More information will follow soon…

If you want to reference the paper please use the following bibliographic data:

Jöran Beel and Bela Gipp. On the Robustness of Google Scholar Against Spam.In Proceedings of the 21th ACM Conference on Hyptertext and Hypermedia. ACM, June 2010.

Search engine optimization (SEO) has a golden age in this internet era, but to use it in academic research, it sounds quite strange for me. After reading this publication (pdf) [...]]]> In January we published our article about Academic Search Engine Optimization (ASEO). As expected, feedback varied strongly. Here are some of the opinions on ASEO:

Search engine optimization (SEO) has a golden age in this internet era, but to use it in academic research, it sounds quite strange for me. After reading this publication (pdf) focusing on this issue, my opinion changed.

[...] on first impressions it sounds like the stupidest idea I’ve ever heard.

ASEO sounds good to me. I think it’s a good idea.

Good Article..

As you have probably guessed from the above criticisms, I thought that the article was a piece of crap.

In my opinion, being interested in how (academic) search engines function and how scientific papers are indexed and, of course, responding to these… well… circumstances of the scientific citing business is just natural.

Check out the following Blogs to read more about it (some in German and Dutch)

http://scienceroll.com/2010/01/28/academic-search-engine-optimization-in-google-scholar/

http://blog.webometrics.org.uk/2010/03/academic-search-engine-optimization-an-inevitable-evil/

http://vokabelaustausch.wordpress.com/2010/02/15/academic-search-engine-optimization/

http://www.scienceblogs.de/frischer-wind/2010/03/wie-sinnvoll-ist-die-optimierung-wissenschaftlicher-artikel-fur-google-scholar-co.php

http://www.insyde.nl/weblog/aseo-academic-search-engine-optimization/item435/

For all people who want to have their own opinion… have a look at the original article and tell us what you think.

1. BibTeX files created with Mendeley can now be used with SciPlore MindMapping

2. A PDF’s title is extracted from BibTeX files and displayed in the mindmap Download the software here http://www.sciplore.org/software/sciplore_mindmapping/

How to write a PhD thesis? This is not a trivial task. Related literature needs to be found, notes need to be taken and finally the thesis has to be [...]]]> Translations: Chinese (thanks to Chen Feng) | Portuguese (thanks to Marcelo Cruz dos Santos) | Russian (thanks to Sergey Loy) | send us your translation

How to write a PhD thesis? This is not a trivial task. Related literature needs to be found, notes need to be taken and finally the thesis has to be drafted and written including the creation of the bibliography. Dozens of books exist about how to do a literature survey and how to write a PhD and scholarly literature in general (e.g. [1-9]). However, software tools that might help in doing a literature survey or writing a thesis are hardly covered by these books, if at all. This is surprising as many software tools exist facilitating the daily work of a PhD student.

In this tutorial we present a new method to reviewing scholarly literature and drafting a PhD thesis with mind mapping software, PDF readers and reference managers. This tutorial focuses on PhD students. However, Bachelor and Master students can use the here presented methods as well to plan and write their thesis. What makes this tutorial special is the fact that everything – PDF files, the content of PDFs (bookmarks) and references are integrated with mind mapping and word processing software.

To make the tutorial better understandable we provide many examples for which we assume that you want to write a PhD thesis about academic search engines.

Please note that

• All tools presented in this tutorial are free and open source (except Microsoft Word)
• All tools presented in this tutorial are based on Java and run on Windows, Linux and MacOS (again, except Microsoft Word)
• All tools used in this tutorial may be substituted:
  • SciPlore Mindmapping may be substituted with FreeMind, MindManager, XMIND and most other mind mapping tools allowing to link PDF files
  • Foxit Reader may be substituted with Adobe Acrobat
  • JabRef may be substituted with any other reference manager supporting BibTeX (e.g. BibDesk, Referencer and Mendeley)
  • Microsoft Word may be substituted with OpenOffice or LaTeX or any other word processor that BibTeX support/plugins exist for

You will spend the next couple of years doing your PhD (or months if you are doing a Master or Bachelor). We highly recommend to read this and other tutorials to find out the way that is best for you to manage your literature and references and write your PhD. Spending a few hours now will save you days if not even weeks later. This tutorial will be updated from time to time to consider the latest features of the tools presented here. Last update of this tutorial: March 2011

Before starting, we present some user feedback that we got by email for our software and this tutorial. We hope it motivates you to read the complete tutorial .

You have read my mind. You have put into practice what I could envisage yet not even come close to develop.

You are helping to tackle the biggest obstacle to my research

I really like SciPlore’s approach. Connecting papers through a mindmap is genious!

I’m in the middle of my PhD and was becoming overwhelmed with the amount of information I need to manage. Nothing else was really cutting it for me and I stumbled on Sciplore.

Great software! Trying to get my adviser and all the graduate students in our lab to start using SciPlore. Keep up the efforts!

I very much enjoyed using Sciplore and was very impressed by its performance and options.

Congratulations on a great time saver and program to make PDF Bookmarks useful.

I’d like to thank you for the great work you’re doing.

I love your product

Great software, thanks!

Your tool is great

Thank you very much for the excellent software. SciPlore has helped me organise my notes and research while undertaking my Masters degree.

I was greatly surprised to find SciPlore, and it seemed to be exactly what I needed for my work

Just wanted to say that SciPlore is a wonderful program. I use it to organize my thoughts and my research. Can’t wait to see what’s coming!

Thanks for making SciPlore!

This tutorial is divided into three parts. the first part covers how to manage literature. The second part covers how to draft a PhD thesis. The final part covers how to write a PhD thesis and how to manage references.

But now, let’s start…

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

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

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.

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

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

That means, as of now the important information are not only in the PDFs but all together 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 later at any time). 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.

Giving Structure to your Mind Map and Literature (and hence to the PhD thesis)

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. But there is one big advantage (and there will be more): In contrast to a folder structure you have not only sorted your PDFs but the PDFs’ contents by having direct access to the bookmarks in the mind map. Despite this, creating, deleting, renaming, copying and moving nodes in a mind map is much faster than doing this with folders in a file structure.

Deepening the Literature Review

Basically, you can go on as you did before. You find new PDFs, read them, create bookmarks, and sort them in 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. Then you can just click on the node “Differences between ASEO and classic SEO” in the mind map.

Add more bookmarks if a PDF is relevant for the thesis

The PDF will open on the right position and you can read on that topic and, if you like, create more bookmarks (in the current version, only the front page of the PDF is opened when clicking on the bookmark in the mind map). The new bookmarks can be easily imported by a right click and on the node and selecting Import Bookmarks.

Import new PDF bookmarks to the mind map to complement the PhD literature review

After a while you will have a huge mind map with all the information that is important for your PhD thesis. You can use the search function (STGR+F) to find special nodes and (un) fold to get a better overview by selecting a node and pressing Space.

Making Notes

Another feature that makes mind maps superior to simple file systems is the possibility to add notes. To each node you can add any kind of text as a note and this note is shown in a separate window and as hover effect (see illustration).

Making additional notes in the mind map

How to Write a PhD Thesis (Part II): Structuring and Drafting the PhD Thesis

This is the second part of our tutorial about how to write a PhD thesis. In this part we cover how to structure and draft your thesis.

Typical structure of a PhD thesis in a mind map

There is lots of good literature on how to exactly to structure your PhD so we will not cover this in detail here. However, either in your literature mind map or in a new mind map you start with a basic structure such as in the picture. You can then start drafting your thesis directly in the mind map. Create one node for each heading and one sub-node for each sentence. You might wonder why not doing this directly in a word processor. Simply, because it is much easier to move mind map nodes than sentences and paragraphs in a word document. Moreover, you have all the important information in your mind map already. And, in a mind map it will be much easier for you to restructure the thesis (we guarantee that you will have to restructure your thesis several times before you are really happy with the structure).

You can also put all the administrational data in our mind map, as you see in the picture in the left half. For instance, deadlines of your PhD, important contacts and so on.

The following shows how a final mind map for a PhD thesis could look like (nodes with a circle are folded and contain more nodes). You will notice that the related work section is very similar to your literature mind map. However, it is not the same. Most likely you will not use all the literature you have read. Accordingly, your literature mind map will probably contain much more information than your final related work section in your mind map / thesis. For finally structuring your thesis these information are not important. Therefore, we suggest using two mind maps: one for your literature in general and one for your PhD.

The complete draft of a PhD thesis in a mind map (nodes with a circle contain more sub nodes)

Keep in mind that your mind map for the thesis does not only include PDF links but you can write complete sentences. Again, have a look at the picture to get an idea how your final mind map should look like.

Now, read in the third part how to finally write a phd thesis.

How to Write a PhD Thesis (Part III): Writing the PhD Thesis up and Managing References

This is the third part of our tutorial series about how to write a PhD thesis. In this part we finally explain how write up a PhD thesis and how to manage references.

How to Write the PhD Thesis

There is not much to say about eventually writing up your phd thesis. Basically, all you need to do is taking some word processing software of your choice and start writing everything up that is already in your mind map (see Part II of the tutorial). You could argue that this is inefficient because why should you type everything twice, once in your mind map and then again in your word processing software. And you are right. Therefore, we are working on a function that lets you export a mind map perfectly to MS-Word and OpenOffice. However, this will not happen in the next few months or so. And it has also advantages to do the part of the work twice. You will find much more errors and enhance the text much more if you are forced to write your thesis after you have structured it in great detail in the mind map than as if you had started directly in the text document.

In theory, you could write your thesis within a few days if you had a really, really good mind map. In practice, it probably will take you a few weeks because when finally writing the thesis up you will realize some issues you want to do some more work on.

Maintaining References

There is one important part we have left out so far: The management of bibliographic data and creation of reference lists. This is probably the most annoying part in writing a PhD thesis. It is not unusual that a thesis is referencing a hundred or even more publications. Imagine you have to create for 200 publications the bibliography list as shown in the right part of the picture. And imagine, you did this and then your supervisor tells you that you have to use a different style and you have to do it all over again. Or you have numbered your references manually (see left part of the pictures) and for whatever reason you have to insert another reference at the beginning of your thesis and therefore renumber all references in your phd thesis.

Example of a reference list in a PhD thesis and its use in the full text

Fortunately, this can all be done automatically (more or less).

Reference Management Software

Download and install JabRef. With JabRef you can maintain a database of all bibliographic data of the publications you want to reference. Eventually, your BibTeX database file will look like this.

Managing Bibliographies for a PhD thesis with JabRef

A brief step-by-step tutorial how to create your first BibTeX database and create new entries is available here and the complete manual here.

So what you need to do is creating an entry for each of the papers you want to cite. This is still a lot of work but that’s how it is. To integrate your BibTeX data with your mind map (and finally MS Word, OpenOffice, …) one more step is necessary. You need to link the corresponding PDF to the BibTeX entry. This can easily be done by drag & drop the PDF from your literature directory to the BibTeX entry.

Integrating BibTeX (JabRef) with SciPlore MindMapping

SciPlore MindMapping has support for BibTeX (no other mind mapping software can do that). That means whenever a node in your mind map links a PDF (or PDF bookmark) the BibTeX key will be displayed as an attribute. To do so, just go to SciPlore MindMapping | Preferences and specify your BibTeX file. Then select SciPlore MindMapping | Update reference keys in current mind map.

Displying BibTeX keys and title in a mind map

You now see the title and BibTeX key of the linked PDF file as attribute. This way you can easily see where the information in your mind map is from. If the information is annoying you, select View | Attributes | Hide All Attributes (the attributes are still stored in your mind map, you just won’t see them any more). You might not realize this right now while reading this text but actually this feature is fantastic. It will allow you to very easily create a reference list for your PhD. Read on…

Integrating BibTeX and SciPlore MindMapping with Microsoft Word

To automatically create reference lists in MS-Word, based on BibTeX, you need a plug-in. We recommend BibTeX4Word. The installation is anything but user friendly and also requires the separate installation of MikTeX but it is definitely worth the effort. If you have installed BibTeX4Word you can simply copy and paste the BibTeX key from SciPlore MindMapping to MS Word as shown on the following picture.

Copy bibliographic data from SciPlore MindMapping to your PhD thesis in MS Word

Then you can copy the BibTeX key from SciPlore MindMapping with a right mouse click and paste it into MS-Word (click on the red +).

Creating an in-text reference in your PhD thesis

After copying the BibTeX key to your word processor you just need to click on the reference list icon and there reference list is created automatically (you can choose out of hundreds of reference styles such as APA, IEEE, ACM, Harvard, …)

Create a bibliography (reference list) for your PhD thesis automatically

That’s it, your PhD thesis is done To remind you what makes this tutorial (and the software SciPlore MindMapping) special in contrast to other software tools and tutorials is the fact that everything – PDF files, the content of PDFs (bookmarks) and references are integrated with mind mapping and word processing software. Imagine, for instance, you would not have the BibTeX keys in the mind map (or wherever else you draft your PhD with). You would have to manually make some notes where the information is from and later look the bibliographic data up in you reference manager. And without having PDF bookmarks you could hardly read in more detail about something that interests you. You might have a note somewhere (maybe even with the page number the information is from) but to look it up would take some time. With PDF bookmarks it takes 2 seconds.

If you have any questions, please contact us or post a comment here in the Blog.

References

[1] A. Fink. Conducting research literature reviews: from the Internet to paper. Sage Publications, Inc, 2009.

[2] J.L. Galvan. Writing literature reviews: A guide for students of the social and behavioral sciences. Pyrczak, 3 edition, 2005.

[3] Judith Garrard. Health sciences literature review made easy: the matrix method. JONES AND BARTLETT P, 2006.

[4] Chris Hart. Doing a Literature Review: Releasing the Social Science Research Imagination. SAGE Publications, 1998.

[5] L.A. Machi and B.T. McEvoy. The Literature Review: Six Steps to Success. Corwin Press, 2008.

[6] D. Ridley. The literature review: a step-by-step guide for students. Sage, 2008.

[7] John M. Swales. Telling a Research Story: Writing a Literature Review. University of Michigan Press/ESL, 2009.

[8] Rudi Studer, Richard V. Benjamins, and Dieter Fensel. Knowledge Engineering: Principles and Methods. Data and Knowledge Engineering, 25 (1-2): 161–197, 1998. Elsevier.

[9] Steffen Staab and Rudi Studer, editors. Handbook on Ontologies in Information Systems. Springer-Verlag, 2004.

[10] Jöran Beel and Bela Gipp. Google Scholar’s Ranking Algorithm: The Impact of Citation Counts (An Empirical Study). In André Flory and Martine Collard, editors, Proceedings of the 3rd IEEE International Conference on Research Challenges in Information Science (RCIS’09), pages 439–446, Fez (Morocco), April 2009. IEEE. doi: 10.1109/RCIS.2009.5089308. ISBN 978-1-4244-2865-6. Available on http://www.sciplore.org.

[11] Jöran Beel and Bela Gipp. Google Scholar’s Ranking Algorithm: An Introductory Overview. In Birger Larsen and Jacqueline Leta, editors, Proceedings of the 12th International Conference on Scientometrics and Informetrics (ISSI’09), volume 1, pages 230–241, Rio de Janeiro (Brazil), July 2009. International Society for Scientometrics and Informetrics. ISSN 2175-1935. Available on http://www.sciplore.org.

[12] Jöran Beel and Bela Gipp. Google Scholar’s Ranking Algorithm: The Impact of Articles’ Age (An Empirical Study). In Shahram Latifi, editor, Proceedings of the 6th International Conference on Information Technology: New Generations (ITNG’09), pages 160–164, Las Vegas (USA), April 2009. IEEE. doi: 10.1109/ITNG.2009.317. ISBN 978-1424437702. Available on http://www.sciplore.org.

[13] Toni Buzan. Making the Most of your Mind. Pan Books, 1977.