Docear 1.0.3 Beta: rate recommendation, new web interface, bug fixes, …

Update: February 18, 2014: No bugs were reported, as such we declare Docear 1.03 with its recommender system as stable. It can be downloaded on the normal download page.


With Docear 1.0.3 beta we have improved PDF handling, the recommender system, provided some help for new users and enhanced the way how you can access your mind maps online.

PDF Handling

We fixed several minor bugs with regard to PDF handling. In previous versions of Docear, nested PDF bookmarks were imported twice when you drag & dropped a PDF file to the mind map. Renaming PDF files from within Docear changed the file links in your mind maps but did not change them in your BibTeX file. Both issues are fixed now. To rename a PDF file from within Docear you just have to right-click it in Docear’s workspace panel on the left hand side and it is important that the mind maps you have linked the file in, are opened. We know, this is still not ideal, and will improve this in future versions of Docear.

Rate Your Recommendations

You already know about our recommender system for academic literature. If you want to help us improving it, you can now rate how good a specific set of recommendations reflects your personal field of interest. Btw. it would be nice if you do not rate a set of recommendations negatively only because it contains some recommendations you received previously. Currently, we have no mechanism to detect duplicate recommendations.

rate a literature recommendation set

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Docear 2013 in review and our plans for 2014

It’s almost a bit late to review 2013 but better late than never. 2013 doubtlessly was the most active and most successful year for Docear, so far. First and foremost, we finally released Docear 1.0, after releasing many Beta and Release Candidates. Of course, Docear 1.0 is far from being perfect, but we are really proud of it and we think it’s an awesome piece of software to manage references, PDFs, and much more. But there were many noteworthy events more, some of which we took pictures of:

We presented several research papers at the JCDL in Chicago, TPDL on Malta, and RecSys/RepSys in Hong Kong. It is always a pleasure to attend such conferences. Not only because they take place at really nice locations, but because you meet really interesting people (for instance Kris Jack from Mendeley, a really enthusiastic and smart guy who develops Mendeley’s recommender system, or Joseph A. Konstan, who is a true pioneer in the field of recommender systems).

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TPDL on Malta

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JCDL in Chicago

2013 hong kong

RecSys in Hong Kong

Almost every year, our mentor Prof. Andreas Nürnberger is inviting his team members to a sailing turn, and so he did 2013. For several days we were sailing the Baltic Sea, learned a lot about team work and had a lot of fun.

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Sailing turn with our mentor Prof. Nürnberger, the Docear team, and some PhD students of his working group

We had the honour to supervise an excellent student team at HTW Berlin thanks to Prof. Weber-Wulff. The students did a great job in developing the Docear Web prototype. It’s a pity that the prototype has not yet found its way into our live system, but we have not had the time to give the prototype the last bug fixes and features it needs. However, this is very high on our todo list.

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Four of the five students at HTW Berlin who developed a prototype of “Docear Web”

Docear is primarily located in Magdeburg, Germany, which is close to Berlin. Therefore, we didn’t think twice when Researchgate hosted the 10th “Recommender Stammtisch” (regulars’ table) in Berlin. There, we could listened to an enlightening talk of Andreas Lommatzsch, and an entertaining introduction of Researchgate’s CEO Ijad Madisch.

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Comprehensive Comparison of Reference Managers: Mendeley vs. Zotero vs. Docear

Which one is the best reference management software? That’s a question any student or researcher should think about quite carefully, because choosing the best reference manager may save lots of time and increase the quality of your work significantly. So, which reference manager is best? Zotero? Mendeley? Docear? …? The answer is: “It depends”, because different people have different needs. Actually, there is no such thing as the ‘best’ reference manager but only the reference manager that is best for you (even though some developers seem to believe that their tool is the only truly perfect one).

In this Blog-post, we compare Zotero, Mendeley, and Docear and we hope that the comparison helps you to decide which of the reference managers is best for you. Of course, there are many other reference managers. Hopefully, we can include them in the comparison some day, but for now we only have time to compare the three. We really tried to do a fair comparison, based on a list of criteria that we consider important for reference management software. Of course, the criteria are subjectively selected, as are all criteria by all reviewers, and you might not agree with all of them. However, even if you disagree with our evaluation, you might find at least some new and interesting aspects as to evaluate reference management tools. You are very welcome to share your constructive criticism in the comments, as well as links to other reviews. In addition, it should be obvious that we – the developers of Docear – are somewhat biased. However, this comparison is most certainly more objective than those that Mendeley and other reference managers did ;-).

Please note that we only compared about 50 high-level features and used a simple rating scheme in the summary table. Of course, a more comprehensive list of features and a more sophisticated rating scheme would have been nice, but this would have been too time consuming. So, consider this review as a rough guideline. If you feel that one of the mentioned features is particularly important to you, install the tools yourself, compare the features, and share your insights in the comments! Most importantly, please let us know when something we wrote is not correct. All reviewed reference tools offer lots of functions, and it might be that we missed one during our review.

Please note that the developers of all three tools constantly improve their tools and add new features. Therefore, the table might be not perfectly up-to-date. In addition, it’s difficult to rate a particular functionality with only one out of three possible ratings (yes; no; partly). Therefore, we highly suggest to read the detailed review, which explains the rationale behind the ratings.

The  table above provides an overview of how Zotero, Mendeley, and Docear support you in various tasks, how open and free they are, etc. Details on the features and ratings are provided in the following sections. As already mentioned, if you notice a mistake in the evaluation (e.g. missed a key feature), please let us know in the comments.

Overview

If you don’t want to read a lot, just jump to the summary

We believe that a reference manager should offer more features than simple reference management. It should support you in (1) finding literature, (2) organizing and annotating literature, (3) drafting your papers, theses, books, assignments, etc., (4) managing your references (of course), and (5) writing your papers, theses, etc. Additionally, many – but not all – students and researchers might be interested in (6) socializing and collaboration, (7) note, task, and general information management, and (8) file management. Finally, we think it is important that a reference manager (9) is available for the major operating systems, (10) has an information management approach you like (tables, social tags, search, …), and (11) is open, free, and sustainable (see also What makes a bad reference manager).

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Docear 1.02 Beta: Serious PDF Bug Fix; added a donation button

We discovered a serious bug in Docear that relates to the PDF management. In some situations, it could happen that when you edited a PDF, the annotation IDs were not recognized correctly, and a conflict was shown. We fixed this bug and publish Docear 1.02 as a beta version today. Right now, the Beta version download is only available in our forum. We would appreciate if you could test the new version. If there are no more serious bugs found, we will publish it as stable version without any further notifications.

We also added a “Please Donate” note to the workspace panel. It leads you to our donation page and you are sincerely invited to make use of that page :-). If you have already donated, if you just don’t want to donate, or if you need every pixel in the workspace, do a right-click on that note and you will be able to hide it. In addition, we also changed the welcome page that opens after you have installed Docear.

New “Please donate” note in Docear

New “Welcome” page 

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Docear 1.01 with some minor improvements and bug fixes

A few days ago we released the experimental version of Docear and wrote about it in our experimental release forum (you can subscribe to that forum if you want to be informed about new experimental releases). Today we declare Docear 1.01 as stable and from now on it’s available on our primary download page. Changes are rather minor. 

Enhancements include

  • A slightly modified dialog for selecting your PDF viewer (some links were updated)
  • The labeling of the file monitoring settings are now more uniform
  • The colors for “Move …” in the “Nodes” ribbon were changed from green to blue. There’s quite a funny story behind it. One of our team members recently told me that the arrows for moving nodes would point to the wrong direction. I told him that they were absolutely correct and we had quite a discussion. Then we realized that the team member is (red-green) color blind and couldn’t recognize the green arrows properly. Well, now the arrows are blue (see screenshot) and all people should be able to recognize them correctly 🙂

In addition, we did some bug fixes.

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Searching and filtering via 2-dimensional tags (i.e. attributes): One of Docear’s most powerful features

One of Docear’s most unique feature is its “single-section” user-interface, which allows a highly effective organization of your PDFs, references, and notes. When you want to look-up some information you browse through your data, and usually you should be able to find what you are looking for quite fast. However, sometimes browsing your data is not ideal and you want to search over the papers’ full-text or meta data (title, author, …), or you want to use (social) tags to classify your papers.

Unfortunately, there is one problem about tags: they are one-dimensional. Imagine, you wanted to do a literature survey about recommender systems, and you have dozens of papers about this topic. Some of the papers’ authors evaluated their recommender system with user studies, some with offline experiments, and some with online experiments. The user studies were conducted with with different amounts of participants e.g. one study was conducted with 20 participants, one with 43, and one with 68. With social tags it would be difficult to represent this information. Of course, you could easily add the tag “recommender system” to each of your papers, but how about reflecting the evaluation type? Would you want to create different tags for each evaluation type, i.e. evaluation_user-study, evaluation_offline, evaluation_online? You might do this, but in situations with more than three options this approach would become confusing. You definitely run into a problem when you want to store the amount of study participants via social tags. This simply wouldn’t be possible except maybe you would create tags like no_of_participants_1-10, no_of_participants_11-50, etc.

What you would want to have are “2-dimensional” tags, i.e. one dimension for adding e.g. the tag “evaluation_type” to a paper and one dimension for specifying which evaluation type it is (e.g. “offline evaluation”). In Docear, there are two-dimensional tags, i.e. attribute-value pairs, and these attributes give you much more power than social tags. Here is, how it works:

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