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…
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…
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!
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).
Finally, after releasing the alpha and beta, today we release Docear 1.1 stable. If you have tried already one of the previous versions, there is not much news. Otherwise, read on.
Thanks to all the generous donors, our student Christoph could work on an improved PDF metadata retrieval for Docear. The new Docear 1.1 is able to extract the title of a PDF and fetch metadata from Google Scholar for that title. To do so, select a PDF in your mind-map and chose “Create or Update reference”, …
… and 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 two 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…)
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.
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.
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…)
–> Read here for the latest update <–
One of our users’ most requested feature is an add-on for LibreOffice and OpenOffice, similar to Docear4Word, which allows adding formatted references and bibliographies in Microsoft Word based on Docear’s BibTeX files. Unfortunately, we have no skills in developing add-ons for Libre or OpenOffice, which is why we were looking for a freelancer to help us. Now, finally, we found one. The freelancer is offering to develop a pendant to Docear4Word that works with LibreOffice and OpenOffice. This means, you will be able to select a reference from Docears’ BibTeX database, and the add-on will insert the in-text citation and the bibliography in your Libre/OpenOffice document. Analog to Docear4Word, you will be able to choose from more than 2,000 citation styles to format your references.
However, the freelancer is not developing the add-on for free. He asks for 2500 US$ (~1,900€), which we believe to be a fair price. Therefore, we kindly ask you to donate, so we can pay the freelancer to develop a Docear4Libre/OpenOffice. Of course, the add-on will be open-source, reading not only Docear’s BibTeX files but also BibTeX files of other BibTeX based reference managers. The freelancer already developed a simple proof-of concept (see screenshot), which uses citeproc-java to add BibTeX based references. As such, we have no doubts that the freelancer will be able to deliver the promised add-on — if we can collect enough money.
The freelancer’s is already working on the add-on and his goal is to finish it in the next two months or so. However, as long as we cannot pay him, he will not release the add-on, even if he has finished his work (and if he learns that there are no donations coming, he might decide to stop his work at any time). Therefore, if you want a Docear4Libre/OpenOffice, please donate now! Donate 1$, 5$, 10$, 50$ or 500$ — any contribution matters, and the sooner we have all the money, the sooner you can manage your BibTeX references in LibreOffice and OpenOffice.
Donate via PayPal, or, to save PayPal fees, make a SEPA bank transfer to Docear, IBAN DE18700222000020015578, BIC FDDODEMMXXX. SEPA bank transfers are free of charge within the European Union.
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We will keep you posted on the amount of donations, and any important news.
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On March 10th and March 11th we will be presenting Docear at CeBIT. CeBIT is the digital industry’s biggest and most international event and always worth a visit. We will be at HALL 9, STAND B18. Feel free to visit us and meet the Docear team in person (Stefan will be 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.
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.
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).
TPDL on Malta
JCDL in Chicago
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.
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.
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.
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.
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.
New “Please donate” note in Docear
New “Welcome” page
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.
Enhancements include
In addition, we did some bug fixes.
Like the previous years, we offer the opportunity for Bachelor students from the US, UK or Canada to do a paid internship at Docear in summer 2014 (if you are from Germany, please read here). The internship should last for 8-12 weeks with the earliest start date being May and Read more…
This weekend, I had some spare time and I wondered which was the most popular reference manager (and how Docear is doing in comparison). So, I took a list of reference managers from Wikipedia, and checked some statistics on Alexa, Google Trends, and Google Keyword Planner. Since I had the data anyway, I thought I share it with you :-). Please note that this is a quick and dirty analysis. I cannot guarantee that there is not one or two reference managers missing (i just took the list from Wikipedia), and, of course, there are many alternatives to Alexa and Google for measuring the popularity of a reference manager.
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:
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.
Some of Docear’s new icons in the ribbon bar
The last version of Docear was released three month ago and you might wonder what we were doing. Well, I can tell you we were really busy. Besides working on some research papers for conferences in Indianapolis and on Malta (read here and here), we finally implemented two major milestones for Docear. These two milestones actually were the last ones we had on our road-map for releasing the final 1.0 version of Docear. And here it is, Docear 1.0 (RC 1) with:
We have completely redesigned the dialog that appears when Docear is first started. We believe it to be much more user friendly and intuitive. We also listened to those users who criticized that our terms of service had to be accepted even when no online services were activated. Now you have the choice. You can either use Docear as a registered user and enjoy the full potential including PDF metadata retrieval, online backup, online mind map viewer, and recommendations. Or you can use Docear as a local user with no data at all being submitted to Docear and no requirement for accepting any terms of service (just use Docear as you would use any other GPL desktop software).
The 9th Beta of Docear is available for free download. It contains no new features but several bug fixes and feature improvements. One improvement includes the removal of line breaks in imported annotations. So far, when you highlighted text over several lines in a PDF, Docear imported the lines breaks of the highlighted text which sometimes caused a not so nice layout. In the new Docear you can do a right click on a node that links an annotation and select “PDF->Remove lines breaks from annotation”. Bug fixes include a fix for the bug that the Adobe Acrobat Professional PDF Viewer wasn’t recognized under MacOS. On Linux the splash screen does not hide any more the setup screen on the very first start of Docear. For a detailed list of all changes see the following change log. And keep in mind – we are always looking forward for your feedback and don’t forget to have a look at the new preview of Docear’s Online Viewer.
Feature Enhancements:
Beta 8 of Docear is available for download. There is no major new feature but a few bug fixes. In addition, we merged Docear’s source code with the latest version of Freeplane (1.2.21 beta) which includes many new features and bug fixes not listed here. Feature improvements include: #672 Create Read more…
We are glad to announce that we, again, will offer a paid internship in cooperation with the German Academic Exchange service (DAAD). If you are an undergraduate student, interested in software engineering or statistics, and coming from the US, UK or Canada, get yourself started and do an 8-12 weeks internship in summer or autumn 2013, fully paid. And if you are not applicable to apply for the internship – please tell your friends to apply! 🙂
Your project
Your research question to answer will be “How to provide (better) research paper recommendations to our users?”. As such, it will be your task to support the Docear team in researching how the interests of Docear’s users can be identified from the users’ mind maps and how these interests can be matched with interesting items to recommend. You will do literature research, create new ideas, analyze user data, and implement new recommendation approaches in JAVA. Of course, you don’t have to do all of this alone – you will be closely cooperating with the Docear team. Your work will be integrated into Docear and used by thousands of researchers around the world. If your work is outstanding, we will write a research paper with you.
Requirements