Our reference management software Docear has not been actively developed for a few years, and recently, the add-on to fetch metadata from Google Scholar stopped working. Fortunately, one of our users (Li Yang) adjusted Docear’s Google Scholar Parser, and now everything works as usual. However, we have not yet integrated Read more…
Update 2018-07-31: We updated the Dropbox Link Google Scholar recently changed its layout, and as a consequence, Docear couldn’t fetch metadata anymore from Google Scholar for PDF files. Fortunately, one of our users (“Silberzwiebel”) adjusted Docear’s Google Scholar Parser, and now everything works as usual. However, we have not yet integrated Read more…
Currently, all of Docear’s online services are down, including the recommender system. This means, you cannot register, log-in to download backups, or receive recommendations. As we have no time right now for the development of Docear, we are afraid that we won’t be able to fix this problem anytime soon. Read more…
After releasing the Beta some weeks ago, we made some minor adjustments, and consider the current version 1.2 as stable. There are two major improvements and two bad news: Various improvements in the PDF Metadata retrieval function for Google Scholar. If you had some problems in the previous Docear versions with retrieving metadata Read more…
Docear 1.2 Beta is now available and has two major improvements: A new add-on to import any kind of highlighted text from PDFs This new add-on is a true milestone in the Docear development. Until now, you could only import highlighted text from PDF editors that copied the highlighted text Read more…
One reason why we originally started the development of Docear was our interest in how people are creating mind-maps and how the information contained in mind-maps could be used for building recommender systems and other user-modeling applications. As a result, we developed Docear’s research-paper recommender system, and if you are interested in how Read more…
More than half a year ago, we started a call for donation to pay a freelancer who wanted to develop an add-on for LibreOffice and OpenOffice, comparable to Docear4Word. Originally, we estimated that it would take about 2 months before the work was completed, or at least a decent demo version was ready to released. Well, that estimate wasn’t quite precise – the developer hasn’t finished even an alpha version yet. In addition, we are still missing a significant amount of donations to fully pay the developer ($1,000 are missing).
The question arises, how to proceed? We see the following options:
1. Just wait
The freelancer is still working on the add-on. So, most likely he will finish the add-on some day – maybe in 2 months, maybe in 6 months, maybe in a year. However, I have to point out that my satisfaction with the current progress and outcomes are not overwhelming. Personally, I have some doubts that the final add-on will meet the quality expectations I have, and that probably most Docear users have. However, I suggest you get an idea of the add-on yourself. The freelancer sent me a demo version that you can try out. To do so, download the add-on, store it on your hard drive, and open the downloaded file with LibreOffice or OpenOffice. This should open an installation dialog, and you need to confirm all messages in the dialog. After the installation, you should restart Libre/OpenOffice. If you are using OpenOffice, you will have a Docear entry in the menu and in the tool bar (see screenshot below). If you are using LibreOffice, you will only have an entry in the menu.
In the past few weeks, several users reported that Docear could not retrieve metadata more from Google Scholar any more. It took as a while, but now we found and fixed the problem – hopefully. We need your help to test if the fixed version really works well for all of Read more…
Compared to several other reference managers, Docear lacks a feature to directly import references from the Web. For instance, if you visit the detail page of a research article on a publisher’s website, you might wish to directly import the bibliographic data of that article to Docear. Many publishers offer export options for reference managers such as Endnote, RefWorks, or Zotero. So, how do you do it with Docear?
Fortunately, Docear uses the BibTeX format to store references. BibTeX is a de-facto standard for references that is supported by almost any publisher and any reference manager. So, read on to learn how to import bibliographic data from web-pages in two steps!
As you may know, Docear features a recommender system for academic literature. To find out which papers you might be interested in, the recommender system parses your mind maps and compares them to our digital library with currently about 1.8 million academic articles. While this is helpful and might point you to papers relevant for your general research goals, you will sometimes have to find information on a specific topic and hence search directly.
Based on our knowledge about recommender systems and some user requests, we decided to implement a direct search feature on our digital library. I am very grateful to Keystone, who supported me in visiting Dr. Georgia Kapitsaki at the University of Cyprus (UCY) in Nicosia for a full month to work on this idea. Dr. Kapitsaki’s has already supported us in our work on Docear’s recommender system in July 2013. Her knowledge about the inner mechanics and her ideas on the the search engine were essential for the implementation and the research part of the project.
How to use it
You can access the search feature from Docear’s ribbon bar (“Search and Filter > Documents > Online search”) or by double-clicking the “Online search” entry in Docear’s workspace panel. Since both the recommender system and the personalized search engine make use of your mind maps. you need to enable the recommendation service in Docear.
After opening the search page, you will see
- a text box for your search query,
- a “Search” button, and
- several buttons below the text box reflecting search terms you might be interested in. If Docear does not have enough data to decide about your interests, this part remains empty.
In the past years, Docear evolved to a powerful software for managing literature and references. However, we have to admit that Docear is still not as user friendly as we would like it to be. This is mainly caused by the workspace concept which is not very intuitive. We are aware of this problem and we would like to fix it. Therefore, we spent the last weeks with a lot of brainstorming and discussions, and we came up with a new concept. We believe it to be more intuitive, and more similar to the concepts you know from other reference managers. In the following, we would like to introduce our ideas for the new workspace concept and some other changes and we ask you for your feedback. Please let us know in the comments if you like our ideas, and how we could make the concept even better.
This is how the new workspace panel would look like after you freshly installed Docear and sorted a few PDFs including annotations (click the image to enlarge it).
There are four main categories in the workspace panel (left).
Docear 1.1 Beta Released: New PDF Metadata Extraction, Better Zotero and Mendeley BibTeX support, and Bug Fixes
If you have tested the Preview of Docear 1.1 you may already know about some of Docear’s new features. With your feedback and the mind maps, log files and BibTeX files you shared with us, these features have matured. We are proud to introduce the first (and hopefully only) Beta release of Docear 1.1.
The new key features of Docear 1.1
Improved metadata retrieval
Thanks to your donations, our student Christoph greatly enhanced Docear’s PDF metadata retrieval. For us, it works really great, and with Docear 1.1 Beta the last bugs have been fixed. Btw. if you like what Christoph did, and if you are using LibreOffice, or OpenOffice, please also read our call for donation to develop an add-on for these two text processing tools.
Improved support for Zotero / Mendeley BibTeX files
Thanks to all the generous donors, our student Christoph could work on an improved PDF metadata retrieval for Docear, and today it’s time to present the first preview. The new Docear 1.1 (preview) is able to extract the title of a PDF and fetch appropriate metadata from Google Scholar. Whenever you select a PDF in your mind-map and chose “Create or Update reference”, the following new dialog appears.
The dialog shows the file name of your PDF file, and the extracted title. In the background, the extracted title is sent to Google Scholar and metadata for the first three search results are shown in the dialog. If the title was extracted incorrectly, you can manually correct it. You may also chose to use the PDF’s file name for the search. For instance, when you named your PDF already according to the title, select the radio button with the file name, and the file name is sent as search query to Google Scholar (you may also manually correct the file name before it’s sent to Google Scholar). Of course, all other options you already know are still available, such as creating a blank entry, or importing the XMP data of PDFs. Btw. Docear remembers your choice, i.e. when you select to create a blank entry, the option will be pre-selected when open that dialog the next time. It might happen, that your IP will be blocked by Google Scholar when you use the service too frequently. If this happens, a captcha should appear, and after solving it, you should be able to proceed. We did not yet test this thoroughly. Please let us know your experiences.
The precision of our metadata tool depends on two factors, A) the precision of the title extraction and B) the coverage of Google Scholar. According to a recent experiment, title extraction of our tool is around 70%. However, the final result very much depends on the format of your research articles. In my research field (i.e. recommender systems), I would say that our tool extracts the title correctly for about 90% of the articles in my personal library. In addition, almost all articles that are relevant for my research are indexed by Google Scholar (i would estimate, more than 90%). This means, for around 80% of my PDFs the correct metadata is retrieved fully automatically. Given that I provide the title manually, for even more than 90% the metadata may be retrieved. Please let us know your experience (and your research field). (more…)
Call for donation was successful: 1800 Euros donated to improve Docear’s PDF metadata retrieval function
One month ago, we started a call for donation and asked our users for money so we could pay our student Christoph to improve Docear’s PDF metadata retrieval. We asked for 1800 Euros (~2500 US$) and today we achieved our goal. We would like to thank all donors who Read more…
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.
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.
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).
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.
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.
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.
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.
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.
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).
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.
After reporting about the rather low donation volume a few weeks ago, donations rapidly increased during the past two weeks. In these two weeks we received more than 200 Dollars, which is half of what we got in the past two years. We don’t know whether this is caused by Read more…
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.
- 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.
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:
Today, Docear 1.0 (stable) is finally available for Windows, Mac, and Linux to download. It’s been almost two years since we released the first private Alpha of Docear and we are really proud of what we accomplished since then. Docear is better than ever, and in addition to all the enhancements we made during the past years, we completely rewrote the manual with step-by-step instructions including an overview of supported PDF viewers, we changed the homepage, we created a new video, and we made the features & details page much more comprehensive. For those who already use Docear 1.0 RC4, there are not many changes (just a few bug fixes). For new users, we would like to explain what Docear is and what makes it so special.
Docear is a unique solution to academic literature management that helps you to organize, create, and discover academic literature. The three most distinct features of Docear are:
- A single-section user-interface that differs significantly from the interfaces you know from Zotero, JabRef, Mendeley, Endnote, … and that allows a more comprehensive organization of your electronic literature (PDFs) and the annotations you created (i.e highlighted text, comments, and bookmarks).
- A ‘literature suite concept’ that allows you to draft and write your own assignments, papers, theses, books, etc. based on the annotations you previously created.
- A research paper recommender system that allows you to discover new academic literature.
Aside from Docear’s unique approach, Docear offers many features more. In particular, we would like to point out that Docear is free, open source, not evil, and Docear gives you full control over your data. Docear works with standard PDF annotations, so you can use your favorite PDF viewer. Your reference data is directly stored as BibTeX (a text-based format that can be read by almost any other reference manager). Your drafts and folders are stored in Freeplane’s XML format, again a text-based format that is easy to process and understood by several other applications. And although we offer several online services such as PDF metadata retrieval, backup space, and online viewer, we do not force you to register. You can just install Docear on your computer, without any registration, and use 99% of Docear’s functionality.
But let’s get back to Docear’s unique approach for literature management…
Today we released the 4th release candidate version of Docear. With all the changes introduced into Docear with RC3, there were still some bugs to fix which could cause some distortion in the workspace tree or even prevented users with Chinese language settings from seeing Docear’s ribbon. RC4 is something like Read more…
Today we released RC3 (Release Candidate) of Docear 1.0 (not yet on the official download page but here in the Blog only). It has one major change compared to previous Docear versions, namely we got rid of the “Incoming” mind map. In the past, most users never really got used to the idea why there was an ‘Incoming’ mind map and a ‘Literature & Annotations’ mind map. Now, there is only the ‘Literature & Annotations’ mind map but it has a special “incoming” node in which new PDFs are added. We hope that this concept is easier to understand. It also means that when you move a PDF from the incoming node to any other node in the mind map, and you create new annotations in the PDF, the new annotations are directly added to the PDF node in the mind map and there won’t be any new node in the incoming node. However, if you prefer the old concept, don’t worry. You can keep your old incoming mind map and use Docear as you were used to be.
There is a new version of Docear available for download. It’s basically the (experimental) RC1 version done right. RC2 fixes a lot of bugs that were caused by the new workspace model with multiple projects, it features a refined and polished version of the Ribbon, fixes a lot of bugs in general and supports the standard PDF viewers of MacOSX (Preview and Skim) and probably a lot of other viewers as well!
If you are still using Beta9 of Docear, a lot of things will change and improve with this new version of Docear. However converting your old maps to this new format is a one-way process (you can’t use these files with Beta9 of Docear anymore) and the process itself might take some time, depending on the size of your mind maps. Please backup your files before upgrading to Docear RC2.