May 15th, 2013 by Joeran [Docear]Docear4Word 1.1 is available for download and it offers two new features that will improve your work with references in Microsoft Word a lot. Actually, we added two new elements to the “Add References” dialog.
The first one is a “Docear->Docear4Word” button. It’s intended for adding several references at once when you have multiple BibTeX keys in our clipboard. And here is how it works: Most references managers (e.g. JabRef and Docear) allow you to select several reference entries from the database and copy their BibTeX keys to the clipboard. That means you have a string like “Cohen05,ritchie2008,Eto12″ in your clipboard. Now, when you press the ”Docear->Docear4Word” button, Docear4Word will automatically get that string from the clipboard, identify the BibTeX keys and select the references belonging to the keys. This will make inserting several references at once much easier.
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May 7th, 2013 by Joeran [Docear]Docear’s PDF Inspector had a little bug: titles from PDFs were only extracted over the first two lines. That means when you had a PDF whose title expanded over three or more lines, only a part of the title was extracted. This bug is fixed in the current version 1.01.
Just for those who don’t know what Docear’s PDF Inspector is: Docear’s PDF Inspector is a JAVA library that extracts titles from a PDF file not from the PDF’s metadata but from its full-text. More precisely, Docear’s PDF Inspector extracts the full-text of the first page of a PDF and looks for the largest text in the upper third of that page. This text is returned as title. Of course, this does not always deliver the correct title (e.g. sometimes the journal name is formatted in a larger font size than an article’s title) but in about 70% you will get the correct title.
Download Docear’s PDF Inspector 1.01
April 15th, 2013 by Joeran [Docear]Docear4Word 1.02 is available for download. It fixes one bug that occurred when adding several references at once. For instance, when you inserted three references [1-3], added another three references [4-6] and then added all six references again you would expect to get [1-6] but instead you got a list like [1,2,5,3,6,4].
Just for those who don’t know what Docear4Word is: Docear4Word is an add-on for Microsoft Word (2003 and later) that allows you to insert references and bibliographies from BibTeX files to MS-Word documents. The great thing is that you don’t need to care about formatting. You can choose from 1,700+ citation styles (APA, MLA, Turabian, Harvard, IEEE, ACM, …).
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April 5th, 2013 by Joeran [Docear]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 Greece, Italy, Portugal, or Spain, 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
You should have a profound knowledge of the programming language JAVA. Knowledge in statistics, machine learning, other programming languages (especially C/++ or Python) and/or MySQL, neo4j, Hibernate, Jersey, REST Web Services, Tomcat, and Apache is a plus, but not a requirement. Of course, we would appreciate if you spoke German but it would be no problem if you only spoke English. We would prefer, if you apply for a long internship (12 weeks) but you can also apply for a shorter internship. If you are interested in combining your internship with writing a Bachelor thesis, please let us know in advance (this would be highly welcome). You can start at any date you want in summer or autumn 2013.
Important: If you don’t want to program but have profound knowledge in statistics you are also very welcome to apply. In this case you will support us evaluating how good our current recommender system is, and you will help us generating ideas for improvements. Please indicate in your application clearly that you are not interested in software development but in statistics.
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March 27th, 2013 by Joeran [Docear]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:
- #678 Adobe Acrobat Professional is included in PDF Viewer recognition on MacOS
- #782 Function to remove line breaks in annotations
- #784 More default file types to be imported
Read more…
March 21st, 2013 by Joeran [Docear]A few month ago we announced to develop an add-on allowing researchers to collaborate on the same data. Well, we haven’t finished this completely yet but the first step is done. In the past few month we developed an online viewer that allows you to view your backuped mind maps in your web browser. Right now the viewer is only capable of displaying very small mind maps but it’s our highest priority to improve the performance so you can also view larger mind maps. In addition, the online viewer displays only the basic elements such as nodes and edges. Other features such as attributes are not yet displayed but, again, we are working on it . Of course, this is just the beginning. As a next step Docear Online will allow you to edit your mind maps online. The following step will enable you to work simultaneously with different researchers on the same data either in your browser or with your desktop version of Docear.
To have a look at the preview version of Docear Online, go to https://my.docear.org and log in with your Docear user name and password. You will be able to view all those mind maps that have been created with the desktop version of Docear and that have been backuped with it. Simply select your mind map in the upper-right corner in the menu. To activate the backup function start Docear Desktop and open Tools->Preferences->Online Services->Manage Docear Service Settings.
Read more…
March 12th, 2013 by Joeran [Docear]We are experiencing a very high server load due to several reasons (many people are using our services, we are doing some extensive research analyses, etc.). Therefore we decided to deactivate the metadata retrieval and recommendations for a while, hopefully only a few days. We will let you know as soon as the services are available again.
UPDATE (April 15th): Service is online again!
February 18th, 2013 by Joeran [Docear]Today we released Docear4Word 1.01. The add-on for Microsoft Word allows you to manage your Docear references (and any other references stored as BibTeX) directly within Microsoft Word. Version 1.01 includes the following changes. Download it here!
- Added warning message if a BibTex file is considered corrupt, rather than just ignoring it. (#740, #692)
- BibTex load now also supports CP1252 codepage.
- Unexpected exceptions now logged to the log file. (#740)
- Added workaround for missing BibTex keys. We create a new one of the form “_Unknown_XX” where XX increase with each missing key within the file.
- DEV: Added MLA.csl sample file.
- Fixed bug where the ID was being used instead of the Name.
- Made toolbar dropdown wider.
- Added warning message and instruction when no BibTex database is configured. (#740)
- Parser now copes with no tags present.
- Removed paragraph formatting from within Field code as it influence formatting in the main document.
- JSON is now stored within the Field with space separators and LineFeeds since it could influence formatting in the main document. (#729)
- Updated Citeproc.js to v1.0.426 which fixed these issues:
- Incorrect trimming of punctuation. (#743)
- “Tri-graph” styles not working. (#694)
- Failure to load some styles containing comments.
- BibTex Lexer now supports unix line endings. (#692)
- Issue tag is now supported (#743)
- Fixed bug with Issue and Number casing.
Read more…
February 4th, 2013 by Joeran [Docear]A while ago we released Docear with automatic metadata extraction. Several users asked us if this functionality was also available as stand-alone tool. Therefore, we decided to create a little tool which we name “Docear’s PDF Inspector”. Docear’s PDF Inspector extracts titles from PDF files not from the PDF’s metadata but from its full-text. More precisely, Docear’s PDF Inspector extracts the full-text of the first page of a PDF and looks for the largest text in the upper third of that page. This text is returned as title. Of course, this does not always deliver the correct title (e.g. sometimes the journal name is formatted in a larger font size than an article’s title) but in about 70% you will get the correct one. The main features of Docear’s PDF Inspector are
- Extracts titles from PDF files with good accuracy (~70%) and excellent run-time (few milliseconds per PDF in batch mode)
- Usable as library (other tools can easily integrate Docear’s PDF Extractor to extract titles from PDFs.
- Usable as stand-alone command-line application (returns a PDFs’ title on the command line)
- Usable in batch mode (stores the extracted titles into a CSV file)
- Reads all PDF versions (other tools such as SciPlore Xtract or ParsCit are using PDFBox for processing the PDFs. However, PDFBox sometimes has problems extracting text from PDFs not being 100% compliant to the PDF standard – Docear’s PDF Inspector is more tolerant)
- Written entirely in JAVA 1.6. Hence, Docear’s PDF Inspector runs on any major operating system, including Windows, Linux, and Mac OS, without any other tools required (besides the JAVA run time environment, of course)
- Completely independent of further tools – you only need Docear’s PDF Inspector, that’s it (e.g. SciPlore Xtract requires pdftohtml to be installed)
- Released under the GNU General Public License (GPL) 2 or later, which means it is completely free to use and its source code can be downloaded and modified by anyone.
Read more…
January 25th, 2013 by Joeran [Docear]Just a quick notice: Since a while Docear can automatically retrieve bibliographic information for PDF files. So far, only 15 requests per day per users were possible. We increased this limit to 50. If you have not yet tried this feature, do it, it saves a lot of time!
January 19th, 2013 by Joeran [Docear]As a Docear user you probably did some research before you decided to use Docear and maybe you stumbled upon the reference manager Mendeley. Mendeley definitely has some nice features and made it to one of the top reference management tools in the past few years (besides the fact that they don’t use mind maps for literature management, the main reason I wouldn’t use Mendeley is the fact that they store the annotations you make in PDFs in a proprietary format — this locks you in to Mendeley and makes it really hard/impossible to switch to another tool). Two days ago Techcrunch reported that the well known publisher Elsevier takes an interest in buying Mendeley for presumably 100.000.000 US$. That’s right: 100 Million US$. Considering that Mendeley is supposed to have 2 Million users that would be 50$ per user (and I don’t know if the 2 Million users are really active users). As far as I remember, the shareholders of Facebook payed about 100 Dollars per user when Facebook shares were first available at the stock market. Not bad .
What do you think? Is Mendeley worth 100 Million Dollar? Is it a smart move from Elsevier to buy Mendeley? And what are the consequences for Mendeley’s users since Elsevier is known for a very harsh publishing policy which lead to a boycott of Elsevier and lots of criticism by many academics).
Read more…
January 19th, 2013 by Joeran [Docear]Docear4Word is an add-on that allows managing your Docear references in Microsoft Word. It uses the citation style language (CSL), an open XML-based language to describe the formatting of citations and bibliographies. Not only Docear is using CSL but also other reference managers such as Zotero (who initiated the development of CSL) and Mendeley and they are all contributing their styles – this is why there are more than 2,000 citation styles you can use with Docear4Word, and the other reference managers. However, sometimes the citation style you need is not in the citation style repository and up to now it was quite challenging to create a new style (or edit an existing one).
During the past months, the Columbia University Libraries, Alfred P. Sloan Foundation, and Mendeley developed a WYSIWYG editor for citation styles (What You See Is What You Get). This editor makes it easier than ever to edit existing styles and create new ones. So, if you are missing a citation style for a journal or conference you are submitting a paper to, well… create it and send a big thank you to the three organizations making this possible! .
Read more…
January 15th, 2013 by Joeran [Docear]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 BibTeX keys automatically when database is saved
Bug fixes include:
#724 NPE occured after starting Docear
#714 error occured when using XMP metadata import
#722 Metadata retrieval “crashes” for non-registered users
#720 fixed errors on opening / deleting mind maps in Docear
#716 Incoming mind map did not have monitoring attributes under certain circumstances
#721 Error in Update Notifier
#723 “Copy reference keys…” menu entry was full of bugs
#668 Hyperlinks to open folders did not always work
#625 double check PDF-XCV compatibility settings
You might wonder why there are so few new features. Well, that’s for three reasons: First, we are working really hard on an online version of Docear with our students. We hope to have a simple viewer for your mind maps ready in a few weeks. Second, we are doing a lot of research on the recommendations of Docear and write papers for conferences (SIGIR 2013, and JCDL 2013). Third, hey, it was Christmas and New Year and we deserve a little break, don’t you think?  .
December 6th, 2012 by Joeran [Docear]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
Read more…
November 21st, 2012 by Joeran [Docear]Beta 7 is out and has one major new feature: (semi-)automatic extraction of bibliographic metadata from PDF files. That means, when creating a new reference, you don’t have to type everything manually but bibliographic information such as title, author, year, journal, etc. is all provided to you automatically. Here is how it works:
Do a right click on a node with a PDF and select as shown in the picture
October 29th, 2012 by Joeran [Docear]Last year in July we met the core developers of the mind mapping software Freeplane in Munich (Docear’s mind mapping component is based on Freeplane). At that meeting we decided that Freeplane and Docear would closely cooperate. Now, more than a year later it was time to meet again and discuss the next big steps in the development of Freeplane and Docear. So we met this weekend in Magdeburg, Docear’s “headquarter”. And while last year six people attended the meeting, this year we were nine participants (three from Docear, three from Freeplane and three students from HTW Berlin) plus one Freeplane developer attending via video. In the following I would like to provide a brief overview of the discussed topics and results.
 The Freeplane and Docear team in Docear’s office in Magdeburg (Germany) Read more…
October 22nd, 2012 by Joeran [Docear]It’s a while ago that we started crawling the Web for academic PDFs to index them and use them for Docear’s research paper recommender system. Meanwhile, we have collected quite a few PDFs. Unfortunately, in a foreseeable future, our servers’ disks will be full and the load of our servers is too high already (that’s why you sometimes won’t get recommendations in Docear – our servers simply are too busy).
Since our budget is tight and we don’t want to spend too much time for server administration neither, we are asking for your help: Do you have a server that you could spare? What we need is the following
Read more…
October 18th, 2012 by Joeran [Docear]There is amazing news – Docear cooperates with the HTW Berlin (Berlin’s university of applied sciences for technology and economy). We will supervise the Master’s projects of five students (Alexander, Florian, Julius, Michael, and Paul). Other than at most other universities, the student’s goal is not to do some theoretical work but gaining some real-world development experience– by joining Docear’s development team. That means, we roughly double our development power and we are not talking about a few weeks internship. We are talking about the next eight months working almost half-time, so there should really be some noteworthy results. We still have to discuss what exactly “The Five” will be doing but since all of them prefer web development and design, it will be definitely something web-based. Right now we are considering a simple web-version of Docear and a synchronization add-on to sync your files between different computers and the Web. Ideally, the add-on additionally allows you to work collaboratively on the same data with other Docear users.
Read more…
September 28th, 2012 by Joeran [Docear]To optimize Docear’s research paper recommender system I was looking for an extensive stop word list – a list of words that is ignored for the analysis of your mind maps and research papers (for instance ‘the’, ‘and’, ‘or’, …). It’s easy to find some lists for some languages but I couldn’t find one extensive list for several languages. So I created one based on the stop lists from
- http://dev.mysql.com/doc/refman/5.5/en/fulltext-stopwords.html
- http://jmlr.csail.mit.edu/papers/volume5/lewis04a/a11-smart-stop-list/english.stop
- http://members.unine.ch/jacques.savoy/clef/
- http://norm.al/2009/04/14/list-of-english-stop-words/
- http://snowball.tartarus.org/algorithms/english/stop.txt
- http://solariz.de/649/deutsche-stopwords.htm
- http://www.lextek.com/manuals/onix/
- http://www.ranks.nl/resources/stopwords.html
- http://www.textfixer.com/resources/common-english-words.php
- http://www.translatum.gr/forum/index.php?topic=2476.0
In case anyone else needs such a stop word list: Here it is, 6513 stop words for English, French, German, Catalan, Czech, Danish, Dutch, Finish, Norwegian, Polish, Portuguese, Rumanian, Spanish, Swedish, and Turkish. I believe that some words have an encoding problem. If you discover an error, please let me know and I will correct it. Also, I wouldn’t be surprised to learn that a stop word from one language is an important word in another language. If you discover some words in the list that should not be ignored by our research paper recommender system… please let us know
Read more…
September 21st, 2012 by Joeran [Docear]As you may know, Docear offers literature recommendations and as you may know further, it’s part of my PhD to find out how to make these recommendations as good as possible. To accomplish this I need to know what a ‘good’ recommendation is. So far we have been using Click Through Rates (CTR) to evaluate different recommendation algorithms. CTR is a common performance measure in online advertisement. For instance, if a recommendation is shown 1000 times and clicked 12 times, then the CTR is 1,2% (12/1000). That means if an algorithm A has a CTR of 1% and algorithm B has a CTR of 2%, B is better.
Recently, we submitted a paper to a conference. The paper summarized the results of some evaluations we did with different recommendation algorithms. The paper was rejected. Among others, a reviewer criticized the CTR as a too simple evaluation metric. We should rather use metrics that are common in information retrieval such as Mean Absolute Error (MAE), Mean Squared Error (MSE), Root Mean Squared Error (RMSE), or Precision (i.e. Mean Average Precision, MAE).
The funny thing is, CTR, MAE, MSE, RMSE and Precision are basically all the same, at least in a binary classification problem (recommendation relevant / clicked vs. recommendation irrelevant / not clicked). The table shows an example. Assume, you show ten recommendations to users (Rec1…Rec10). Then is the ‘Estimate’ for each recommendation ’1′, i.e. it’s clicked by a user. The ‘Actual‘ value describes if a user actually clicked on a recommendation (’1) or not (’0′). The ‘Error’ is either 0 (if the recommendation actually was clicked) or 1 (if it was not clicked). The mean absolute error (MAE) is simply the sum of all errors (6 in the example) devided by the number of total recommendations (10 in the example). Since we have only zeros and ones, it makes no difference if they are squared or not. Consequently, the mean squared error (MSE) is identical to MAE. In addition, precision and mean average precision (MAP) is identical to CTR; precision (and CTR) is exactly 1-MAE (or 1-MSE), and also RMSE perfectly correlates with the other values because it’s simply the root square of MSE (or MAE).
 In a binary evaluation (relevant / not relevant) in information retrieval, there is no difference in the significance between Click Through Rate (CTR), Mean Absolute Error (MAE), Mean Squared Error (MSE), Root Mean Squared Error (RMSE), and Precision. Read more…
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