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).

Detailed Comparison

Operating Systems & Languages

Obviously, a reference manager must be available for your favorite operating system but it’s also important that a reference manager is available for as many operating systems as possible, in general. For instance, when you want to cooperate with another researcher, cooperation will be much easier when your collaborator is using the same reference manager as you are. Therefore, the more operating systems a reference manager is available for, the higher the chance that potential collaborators will be able to use your favorite reference manager. In addition, if you are planning a career in academia, you might be required by your employer to use a certain operating system. If your reference manager isn’t available for that system you will most likely spend quite a bit of time migrating to another one. To prevent that hassle, choose a reference manager that supports as many platforms as possible.

Windows, Linux, and Mac OS X are supported by Zotero, Mendeley, and Docear. A web version is offered only by Zotero and Mendeley. However, Docear offers a prototype web version that – for some data – gives you a version history, i.e. you can restore previous versions of your data without time restrictions. Also a mobile version is only offered by Zotero and Mendeley (Zotero does not offer a mobile version itself but there are good third party applications).

A multilingual version may be important for non-English speakers. Mendeley’s website and software are available in English only. Docear offers an English-only website, English and German support, and the software itself is mostly available in different languages. Zotero offers a multilingual user-interface and most help pages on Zotero’s website are also translated into different languages.

Information Management Approach

Eventually, reference management is all about structuring and finding information, and there are various approaches in which to do this. For instance, with tables you sort references by author name or title; with folders or social tags you structure and browse your references; and a search function helps to find reference when e.g. your folder structure isn’t meaningful enough. There is no best approach to manage your information. All approaches have their pros and cons. However, you should be aware of the different approaches and ideally you should try them out before deciding which reference manager is most suitable for you.

A three (or four) section user-interface is what most reference managers offer, and so do Zotero and Mendeley. Mendeley’s main component is a table showing all your documents (below screenshot, middle). The second component (left) lets you create categories to which you add your documents. In the third section, notes and annotations for your documents are displayed. You can create one global note per document and Mendeley also shows annotations you created directly in your PDF files with Mendeley’s internal PDF editor.

Zotero’s user-interface is quite similar to Mendeley, yet you can create several global notes but won’t be able to see the annotations you made directly in PDF files. In addition, PDFs are shown directly in your browser  (Zotero is a FireFox plug-in but there is also a stand-alone version) and your notes will also show up in the main table. If you install the add-on ‘Zotfile’, Zotero can also import PDF annotations, which should give you basically the same features as Mendeley.

Docear also offers a classic three section user-interface showing your references in a table and sorted by categories, allowing you to create one global note per document. Docear’s three section user-interface is not as comfortable and neat as the one of Mendeley and Zotero. However, the three-section user-interface isn’t Docear’s primary approach to manage information …

Docear’s primary approach to manage information is a single section user-interface. This approach shows all your categories, documents, and annotations in a single window. The downside of this approach is that it’s not as intuitive as the classic approach of Mendeley and Zotero, and takes some time to master. The advantages are manifold. First of all, a single section user-interface allows you to browse multiple documents of multiple categories at the same time. Second, you can see multiple annotations of multiple documents at the same time. Third, you can move single annotations to any category you like (instead of entire documents including all their annotations). Fourth, you can create sub-categories within a PDF to better organize your annotations. These four advantages allow a significantly more comprehensive management of your PDFs, and annotations in particular, than with the classic approach. To learn more about the single-section user interface read here….

Social tags are a great means of organizing references, in addition to the primary organization concept. Both Zotero and Mendeley offer a function to add social tags to references. Zotero also offers a list in which all your tags are listed, so you can easily select them (though, a tag-cloud is missing). We couldn’t find such a list in Mendeley which seems to make the tagging function significantly less useful than the one of Zotero. Docear doesn’t offer social tags but “attributes”.

Zotero’s social tag list

Attributes are key-value pairs that can be added to documents. Instead of adding one-dimensional tags (e.g. “reference management”), you can add two-dimensional tags (e.g. “application:reference_management” or “application:pdf_viewer” or “number_of_study_participants:15”). Overall, attributes are more difficult to use but also more powerful than social tags (read more). Mendeley and Zotero don’t offer attributes .

A standard search function is offered by all three tools. Overall, Docear and Zotero probably have the most powerful search functions. Among others, operators like “smaller/larger than”, and regular expressions are supported, and you can save search queries for later re-use.

Docear additionally offers a filtering function which leaves all matches in their original folder structure and does not list them in a plain table. In combination with the attributes, it’s possible to search/filter e.g. for those papers which you classified as reporting about a study with 15 participants (or more than 50 participants, or 20 to 120 participants, …).

Costs, Openness, Freedom and Sustainability

It’s needless to say that a reference manager offered at no cost is better than one that does cost money (given they offer the same features). Fortunately, Zotero, Mendeley, and Docear are all free to use. If you want to use Zotero’s and Mendeley’s premium services you will be charged, but we don’t see that as a disadvantage because there are no other reference managers that would offer comparable premium features for free.

In terms of openness and freedom, Zotero and Docear win over Mendeley. Both are open source and don’t require you to store your data in the cloud. Zotero offers a documented API while Docear also has an API but it’s not yet documented (which makes it basically useless for the standard user) and has only few features. Docear’s data format could be considered a little bit more open than that of Zotero. Docear stores its data in text files (BibTeX and XML) which can be read by any text editor and understood by anyone with some basic computer knowledge. Also annotations are stored directly in PDF files and can be accessed with any standard PDF reader. To read and understand Zotero’s SQLite database, significantly more knowledge is required. Both Docear and Zotero offer various export formats and users can create add-ons to extend the functionality of Docear or Zotero respectively. Since Zotero’s user base is larger than Docear’s, there are more, and also more interesting add-ons for Zotero than for Docear.

In contrast, Mendeley is a proprietary softwarerequiring a registration, and it forces you to store your data on their servers, which may lead to problems in the long run. Although Mendeley offers a well-documented API, not all data is accessible through that API (e.g. annotations), and accessing Mendeley’s SQLite database has the same restrictions as accessing Zotero’s data (a significant amount of database knowledge is required). Most importantly, Mendeley has a vendor-lock if you use Mendeley’s internal PDF viewer to create annotations in PDF files. In contrast to Docear, Mendeley is storing annotations in their SQLite database and not directly in the PDFs. This means, when you want to send a PDF, including annotations, to a friend, or when you want switch from Mendeley to another reference manager, you need to export your PDFs with the annotations. However, the export has several shortcomings.

  1. There is no bulk export for PDFs. To export multiple PDFs, you need to open each PDF separately, and select “File -> Export PDF with annotations…” and go through the saving dialog. If you have hundreds of PDFs to export, the export process will take hours.
  2. Highlighted text is not exported in the PDF standard format. Although the exported highlight is visible in a standard PDF viewer, you won’t be able to delete or modify it (see picture below).
  3. Comments (i.e. sticky notes), are exported in the PDF standard format. However, Mendeley adds some weird icons for each comment and you can’t delete these icons (see picture below).
  4. On the last page of an exported PDF, Mendeley lists all the comments you made. The problem is that even if you delete the original comment with in a standard PDF editor, the list remains as it is. This might become a privacy problem if you make some not-so-nice comments and want to change them later to being able to send the PDF to a colleague.

It has to be noted that Mendeley’s export factor has improved in the past months. A while ago Mendeley couldn’t export highlighted text at all, and comments were only exported in a weird format that was basically not usable at all. Hence, there seems to be a good chance that some day Mendeley will provide a truly decent export. Until then, we would suggest that you not use Mendeley’s annotation function (or use another reference manager if you want to annotate PDFs).

Another important aspect for choosing a reference manager is its long-term sustainability, at least if you are planning a career in academia. By long-term sustainability we mean the probability that a reference manager is continuously developed over time in the way you would want it to be developed. In this regard, Zotero, Mendeley, and Docear are quite different.

Zotero is owned by the George Mason University; it’s entire source code is open source; and there is a great community behind Zotero. It’s very unlikely that Zotero’s development would stop in the coming years and even if it did, others could adopt the source code and continue the development. In addition, it’s unlikely that Zotero would do something you wouldn’t want them to do, e.g. selling your data, strongly increasing prices for the premium services, etc. Zotero is a true non-profit project and the major stakeholders don’t have to worry about generating enormous profits etc.

Docear is also open source but its financial backup is less strong than that of Zotero. Hence, chances that Docear exists in ten years are lower than chances that Zotero exists in ten years. However, even if there weren’t any more financial support for our team, chances are that we would continue the development in our spare time or others adopt our source code. In addition, some of our team members are pursuing an academic career. As such, there is a good chance that in a few years, Docear will have a sustainability similar to Zotero.

A while ago, Mendeley was acquired by Elsevier for an estimated 69-100 Million Dollars. That’s good, on the one hand: You can be pretty sure that Mendeley’s development is important to Elsevier, and most likely Elsevier will further invest of the development. On the other hand, Elsevier is not known for its charity and certainly wants something in return for their investment. Nobody really knows what Elsevier expects from its investment. And nobody knows what Elsevier would do if their expectations are not met. Would they sell Mendeley? Would they bury it? Would they try to increase revenues by any means? Therefore, compared to Zotero, the future of Mendeley is more uncertain. If you are interested in more details, there are two interesting Blog posts, including excellent comments, about the sustainability of Mendeley and Zotero: 1. “Zotero Versus” by Sean Takats, the director of Zotero, and 2. “The Mendeley Dilemma”.

Reference Management

Zotero, Mendeley, and Docear all offer the basic features for managing references, that is creating and editing references, choosing a publication type (article, book, thesis, …), showing and sorting the entries in a table, etc.

Docear additionally offers some enhanced formatting capabilities. For instance, you can format the text, add icons, change colors of the categories, and add visual links between papers. Mendeley and Zotero don’t have such functions.

web-importer may be useful when you want to import data from external sources, e.g. Google Scholar, or other digital libraries. Both, Zotero and Mendeley have such importers. Since we are not intensively using Mendeley and Zotero, we cannot tell which one is better (please share your experiences in the comments). Docear has no web-importer.

Text Processing Software Integration

Zotero, Mendeley, and Docear all offer add-ons for Microsoft Word (Docear only for Windows). For LibreOffice and OpenOffice, Zotero and Mendeley offer add-ons, and Docear plans to develop such an add-on. All add-ons are based on the citation style language which means with either add-on you have access to the same citation styles. The interfaces and functions of the add-ons slightly differ. Mendeley’s interface is the simplest, without any settings. For instance, you cannot specify page numbers for your citations. Docear and Zotero offer more options such as adding page numbers or suppressing author names. Docear’s add-on has the disadvantage that you cannot add references in footnotes.

If you are using LaTeX, Docear probably is more suitable for you than Mendeley or Zotero. Docear stores its reference data as BibTeX by default and hence can directly be used with LaTeX. Mendeley and Zotero may export their data to BibTeX. Mendeley does this automatically and updates the BibTeX file every time you change some data in Mendeley. Unfortunately, Mendeley has some serious bugs and only few features regarding the BibTeX export. For instance, there are often duplicate entries, sometimes with the same BibTeX key. Furthermore, it is not possible to specify the pattern of how BibTeX keys are created. As far as we know, Zotero has no such bugs but don’t give you too many options for the export. Another issue is that Zotero does not automatically update the BibTeX file, when you change your data (though, there are external add-ons doing this).

PDF Management

Nowadays, researchers often work with digital copies of books and research articles, i.e. PDFs. Most modern reference managers offer features to support PDF management, for instance with automatic metadata extraction or automatic file renaming.

A watch folder function monitors a certain folder on your hard drive for new PDFs. Once a new PDF is stored in that folder, it will be listed in your reference management software automatically. If you work a lot with PDFs, such a function is really useful. Both Mendeley and Docear offer such a feature, Zotero does not by default (with the add-on Zotfile you can add such functions).

Metadata extraction from PDF files saves you from manually typing all the bibliographic data manually. Again, if you work a lot with PDFs such a feature massively reduces your work-load. All three reference managers offer such a feature but Mendeley’s metadata extraction is best. Mendeley automatically extracts metadata for all your PDFs with quite decent precision. With Zotero and Docear you must explicitly select a PDF and choose to retrieve the metadata. Precision also seems to be slightly lower (just a gut feeling, no hard evidence).

(Automatic) PDF renaming is best with Mendeley. Once the bibliographic data for a PDF is available you can specify a pattern that Mendeley renames the file to (e.g. Author_year.pdf). Zotero automatically renamed PDFs only when you import them through the Web Importer. Otherwise, you need to do a right click on a PDF to start the renaming. You can also not specify the pattern how the PDF shall be renamed but Zotero always renames it like “Author – Year – Title.pdf”. However, the add-on Zotfile offers many options more for renaming PDF files in Zotero. In Docear, you can rename PDF files manually (to any name you want), but the new file name won’t be updated in your reference database (you would have to do this manually or with a ‘search and replace’ command).

Mendeley and Docear allow you to select a personal PDF storage location wherever you want (e.g. c:\my data\pdfs\). In Zotero, all PDFs are stored in a cryptic and hidden directory (e.g. C:\Users\<username>\AppData\Roaming\Mozilla\Firefox\Profiles\6xv833gw.default\zotero\storage\MAFR7WED\), by default. You can change that path but it’s only possible to specify one directory. It’s also worth noticing that Zotero always creates a copy when you ‘drag and drop’ a file into Zotero and does not link the file. Again, the add-on Zotfile compensate this shortcoming.

Full-text search for your PDFs is offered by Mendeley and Zotero but not by Docear.

Viewing PDFs is possible with all three reference managers. Mendeley offers an internal PDF viewer that can display PDFs, copy text, and rotate pages. That’s basically it. There is no print function, you cannot create snapshots, change the page layout, add text or images to the PDF, and so on and so forth. Another major disadvantage is that Mendeley’s PDF viewer uses the Mendeley window exclusively. This means that you cannot open a PDF in Mendeley and work at the same time at your reference data. Both Zotero and Docear open PDFs in an external viewer when you click on a PDF link in the reference manager. This has the advantage that you can work with the reference data and PDF at the same time. More important, there are plenty of free PDF viewer that offers lots of features such as printing, different page layouts, snapshots, etc.

Creating annotations directly in PDFs and integrating them in your reference manager is – in our opinion – the most effective way of managing PDFs and their content. Both Mendeley and Docear generally offer such a function. Mendeley’s integrated PDF viewer can highlight text and create comments, and shows comments also in the main window aside the reference table. What you cannot do with Mendeley is to create bookmarks, underline or cross-out text, select the highlight color, or access highlighted text directly in Mendeley’s main window. With Docear, you create annotations in your external PDF viewer. There are several free PDF viewers that can highlight text (in various colors), create comments, and bookmarks. Docear then imports all three type of the annotations and allows to organize them in Docear. As in Mendeley, a click on an annotation opens the PDF at the corresponding page. For Windows users, we think that “Docear + external PDF” viewer is superior to “Mendeley + Internal PDF Viewer” in all respects. However, for Mac and Linux users, no really perfect (free) PDF viewers are available. Therefore, Linux users should ideally use e.g. PDF XChange Viewer with Wine. If they don’t want that, Mendeley might be the superior alternative, though, there is one serious disadvantage more of Mendeley that will be covered in the next paragraph. Zotero cannot import PDF annotations to organize them in Zotero. With the add-on Zotfile you may import annotations but some important features such as “jump to page” are missing.

We consider it crucial that you use a PDF editor that complies to the PDF standard. Otherwise, you can’t send PDFs (including annotations) to colleagues, or read and edit the annotations in other PDF software tools. For instance, it will be very difficult, if not to say impossible, to ever change your reference manager (see lock-in effect). Mendeley’s PDF viewer does not comply to the PDF standard and does not provide a decent export for your PDFs. Mendeley’s PDF viewer also doesn’t show comments you made with other PDF viewers in your PDFs. Since Docear and Zotero use external PDF viewers, these usually store all their information in the PDF standard format. 

File Management

With Zotero, Mendeley, and Docear you can drag & drop files of any type (images, spreadsheets, …) to the software and create references for them. Docear offers some more advanced file management features which eases your daily work with non-PDF files.

Docear may watch folders for any file type and not only for new PDFs. This means that whenever you store new images, text documents, spreadsheets, etc. in your watch-folders, Docear imports them. Which file types eventually are imported can be specified by the user.

A simple file browser (screenshot, left part) allows browsing your files and to create shortcuts in your mind maps to these files and folders.

The file browser also allows simple file operations such as  moving, copying, deleting, and renaming files. However, these functions are not yet fully usable because e.g. the path of a moved PDF won’t be changed in the mind maps.

Screenshot of Docear’s file manager (icons are illustrated)

Social Network & Collaboration

Mendeley offers a social network. You may create a personal homepage showing your publications and other information, and you may connect to other researchers and receive their updates (new publications, etc.). In addition, you may embed your publication list on external web pages. Zotero and Docear offer no social network, though Zotero users may embed their publication list on external web pages through Zotero’s API. However, this requires some programming knowledge and Mendeley’s function is more comfortable. If you are interested in academic networks, you may also look at Researchgate or Academia.edu, which are pure academic networks with more feature than Mendeley but without offering a reference manager.

Profile page at Mendeley

An Integrated synchronization function is offered by both Mendeley and Zotero. This function allows you to synchronize your data between different devices, e.g. your home and work computer – out of the box. Such a function is very comfortable but it’s not free, after you use more than 300MB (Zotero) or 2 GB (Mendeley) storage. If you need more storage, Mendeley charges you $5 a month for 5GB ($55/y), $10 a month for 10GB ($110/y), and $15 for unlimited storage ($165/y). Zotero charges you roughly around the same. Docear has no integrated synchronization feature, but it’s being planned.

If you want to synchronize your data with 3rd party tools such as Dropbox or OwnCloud, Docear is probably more suitable than Mendeley and Zotero, though not perfect. Docear stores its data in text files (BibTeX and XML) or directly in PDFs. This means, you can easily store all your files in Docear and synchronize them e.g. with Dropbox or SVN. Mendeley and Zotero store their data in local SQLite database. It’s possible to synchronize these databases but it’s not that comfortable.

Mendeley and Zotero offer some integrated functions to collaborate. For instance, you can share your documents with colleagues and edit together on the bibliographic data. There are some significant differences between Zotero and Mendeley. With Mendeley, you need to subscribe to a pricy team plan, if you want to collaborate with more than three colleagues. For instance, if you want to collaborate with five people and you are an educational or non-profit organization you pay $49 every month. If you are a profit-organization, and you want to collaborate with e.g. 25 colleagues, you pay $299 every month ($~3.200 a year). With Zotero you only need to pay for a storage package (see above) and have unlimited collaborators for free. The same is true for private groups and shared library space. With Mendeley, you need a team plan to use more than 1 private group or more than 100 MB shared library space. In Zotero, these features are included in the normal storage prices.

Collaborating via 3rd party tools is not possible with Mendeley and Zotero because there is no easy way to keep SQLite databases in sync when different users change the data at the same time. With Docear, synchronization is partly possible. For instance, you could use SVN to collaborate on BibTeX files and mind-maps, and merge changes automatically. However, this is sometimes error-prone and installing SVN is not as simple as installing e.g. Dropbox.

Docear offers (partial) backup & versioning which is free of charge, and entirely optional. Whenever you change data in your mind maps, Docear creates a restore point on its server for that mind map. This means that when you accidently delete some data in your mind-maps, you can easily restore it. To some extent, Mendeley and Zotero’s synchronization tool may also be used as backup but as soon as you delete or change data and synchronization takes place, your data is gone.

Literature Search & Discovery

A recommender system for research papers is offered by Mendeley and Docear. All papers that Docear recommends are available for free in full-text, though sometimes the linked URLs are dead. Mendeley offers two recommender systems. The first one, “Mendeley Suggest”, is only offered for premium users. The second one, “Related Papers”, is free and allows you to select a folder in Mendeley that contains a list of papers. Mendeley then calculates a list of related papers. Both recommender systems cannot filter for freely downloadable papers. This means, you might get promising recommendations, but you often will have to look where you eventually find the full-text.

docear recommendation mockup

Docear’s recommender system for research papers

Screenshot of Mendeley Suggest (Source: Kris Jack)

Explicitly searching the paper catalog is only possible with Mendeley. You can directly search the catalog from within the desktop software and download the search results, if they are available in full-text. Based on our experience, it seems that only a small fraction of Mendeley’s search results can be downloaded (perhaps one in 20 or 30 results). Unlike the recommender system, you can filter search results for freely downloadable papers (see also the comments below this post).

Mendeley’s search interface (in this example, no result can be downloaded in full-text)

While Docear’s catalog is rather small (2 Million full-text articles), Mendeley’s catalog is significantly larger. As such, one potentially might expect more relevant recommendations and search results from Mendeley than from Docear. However, as stated, the recommendations cannot be filtered for freely downloadable papers. In our opinion, this reduces the usefulness of Mendeley’s recommender system and catalog size.

Notes, Task & Information Management

Docear integrates a mind-mapping application, namely Freeplane, which is one of the best mind-mapping tools available. Freeplane offers some simple task management features that allow you to create tasks with a reminder. You can add progress icons to your tasks, and connect tasks with other entries in your mind map. It’s also easy to create notes and manage other information such as the conferences you want to attend, the journals you want to publish in, or the ideas you have. You can even link your information to OpenStreetMaps locations to, for instance, quickly find the location where a conference takes place. Neither the task management, nor the note taking is particularly feature-rich, but it’s far better than nothing.

Zotero also allows creating stand-alone notes in their table view. As with Docear, notes can be formatted with rich text. Overall, the note-taking features of Zotero are significantly less powerful than those of Docear. Mendeley has no such features.

Document Drafting & Outlining

Drafting your own papers, assignments, books, theses, etc. is possible with Docear only. In Docear, you can create new mind maps and outline your paper. Your draft may include LaTeX formulas, HTML code and other formatting, screenshots, notes, and many features more.

Particularly useful is the option to copy PDFs, annotations and references to your draft. This way, you can draft your entire paper, and when you want to look up some information you may click on an annotation and the PDF opens at the page where you made the annotation. This process gives a new dimension to managing your literature. Usually you sort your literature based on your general research categories. In Docear, you may additionally sort your literature and annotations for a particular paper you are planning to write.

Docear allows exporting the draft in many formats such as Microsoft Word or HTML. However, the export has some limitations and hence manual labor is required to transform a draft into the final document.


Now, which reference manager is the best one (for you)? The chart above shows the strengths and weaknesses of the three reference managers, and hopefully helps you to understand the main differences between Zotero, Mendeley, and Docear. The chart below shows the tasks a reference manager should support you in, and how good Zotero, Mendeley and Docear are actually doing it. If a reference manager offers good features to support a particular task, the reference manager’s logo is displayed. If it only offers some features, the logo is displayed less intensive. If a reference manager has hardly any features to support a task, its logo is not shown.

Overall, when you want a reference manager that is available for as many platforms as possible, you should look at Mendeley and Zotero, because Docear has neither a decent web nor mobile version. If openness and sustainability is important to you, focus on Docear and Zotero, but not on Mendeley because Mendeley is not open source, and there is the risk of a lock-in effect. If you want a simple user interface that is intuitive but not very powerful, Zotero or Mendeley are the reference managers to go for. If you want a really powerful user-interface and are willing to invest some time, check out Docear – you will either hate or love its approach (probably latter one :-)). Or, to say it in the words of a user we recently talked with:

“If you are not computer savvy, and just need a simple tool for your assignment, then Zotero or Mendeley is the tool for you, but if you work on scientific papers on a regular basis, or write your thesis, you should invest a few hours to learn the more powerful, but therefore also more complex approach, of Docear”.

If literature search and discovery is important to you, look at Mendeley (Premium) and Docear. If you are working a lot with PDFs, you must choose between: a) Mendeley with its great PDF metadata extraction and file renaming, but a PDF viewer that offers only very few features and uses a proprietary format for PDF annotations b) Docear, which allows you to select from various standard PDF readers, and provides more sophisticated options for sorting and browsing PDFs and their annotations and c) Zotero that offers good pdf management capabilities, if you are investigating which add-ons are available and which ones are best. With respect to simple reference management, it probably doesn’t matter which reference manager you choose (if you are only interested in reference management, you might also be quite happy with JabRef). If you want to draft papers with your reference manager, and use our references and annotations in the drafts, Docear should be the reference manager of your choice. When it comes to writing your papers, theses, etc. all three reference managers have their weaknesses. If you are using Microsoft Word (Windows) or LaTeX, you should probably favor Docear. Docear offers the advantage that – with some limitations – you can export your drafts as e.g. MS-Word document which may ease your writing process significantly. In addition, Docear has a good add-on for MS-Word to format your references (Docear4Word). If you are using MS-Word on Mac, or LibreOffice or OpenOffice, you would probably favor Zotero, because Zotero offers add-ons for all major word processing software and the add-ons have more features than Mendeley’s. When it comes to social networking and embedding publication lists, Mendeley is the reference manager to choose (or look at Researchgate and Academia.edu). When it comes to collaboration, you should look at Mendeley and Zotero if you want to collaborate with others who are using Zotero/Mendeley; but keep in mind that Mendeley’s team plans are quite pricy. If you want to collaborate with colleagues who use a different reference manager than you, or if you don’t want to spend money for collaboration, or if you don’t want to store your data in the cloud, look at Docear. Finally, if you want an all-in-one solution that also allows basic file management and note, task & general information management, go for Docear.

Please, let us know what you think and share your ideas and thoughts in the comments! Tell us what you like most about Zotero, about Mendeley, about Docear, about …, and let us know what you like least!

You might also be interested in:
What makes a bad reference manager?
Which one is the best reference management software?
On the popularity of reference managers, and their rise and fall

Joeran Beel

Please visit https://isg.beel.org/people/joeran-beel/ for more details about me.


Paolo · 22nd May 2024 at 08:03

ready for Zotero 7?

Grant Robertson · 25th October 2017 at 20:16

Zotero 5.x allows one to store an unlimited amount of DATA on the Zotero servers. The only thing that consumes “storage space” is file attachments. (I am not sure if web page snapshots count as data or files.) Therefore, if one keeps their files in a separate location – and only links to those files from within Zotero – then one will be able to store an unlimited number of bibliographic entries.

Claire Gronow · 3rd May 2017 at 05:27

I’ve been using Mendeley and there’s a lot of things I like about it, but I am now going to change to endnote because Mendeley becomes incredibly slow once you get over about 30-40 references in a paper/chapter. It can take 1-2 minutes just to insert a citation. When I try to edit citations, it freezes. I’ve been trying to get a response from Mendeley support for months now – the best they can do is suggest reinstalling (doesn’t work). So, sadly, goodbye to Mendeley.

Xiaodong Qi · 11th September 2016 at 22:36

I understand that no software is perfect or can do everything you need. My question is simply can any of them work in parallel with each other and other reference management software?

My experience on Zotero is that it will mess up with bibtex file and pdf files (renames and so on), and its design philosophy is to be different from others. Docear is better, but its builtin interface doesn’t allow me to use the latest version of JabRef and Freeplane and its menu bar is limited so that it’s hard for me to use the latest extract bibtex info from partial info via the latest JabRef. Mendeley, I am not sure. It seems Mendeley has its only standards as well and manage PDFs based on folders rather than projects (more precise observation will be appreciated). However, Mendeley seems to have a better social sharing feature than Docear, and should Docear support people to use Mendeley in parallel with Docear itself?

Any thoughts on the contribution of Docear along this line?

    Emiliano Heyns · 4th October 2016 at 00:30

    Not sure what is meant by “will mess up with BibTeX renames”, but Bib(La)TeX export is as good as it gets for non-native-BibTeX managers through Better BibTeX.

    And while you are of course welcome to your opinion, Zotero’s design philosophy is not to be different from others (if you think I’m mistaken on this issue, feel free to provide a reference to where one of the Zotero devs makes this claim). Its design is spartan — sure. This is a relatively small team putting out a comprehensive product, and the team evidently focuses on features, not looks, but that’s a long stretch from saying the design philosophy is to be different for difference sake.

    As to working in parallel, do you mean whether you can use different tools at separate occasions, all acting on one database? Then no — the structure of the Zotero/Docear/Mendeley databases are not semantically equivalent, so some loss is always incurred when translating between them.

Hadeda Bird · 19th July 2016 at 18:00

Only thing that will make me change from Zotero is if you guys get a plug in to insert citations in Scrivener.

    Emiliano Heyns · 4th October 2016 at 00:20

    That’s not up to Docear — L&L have no interest in building the integration points to make it possible, otherwise Zotero (through one of my plugins) would have gotten there ages ago.

Robin · 13th September 2015 at 19:50

There are a lot of nitty gritty issues that this overview does not cover. I have been using Zotero which is open, free, has a nice clean interface, and connects to LibreOffice and my web browser. So far so good. But what happens when I try to cite a review? Zotero does not support a review type! Unbelievable. No matter how good the rest of the software is, if it can’t store and format all required citation types for the style I am using, it is useless.

So, what citation limitations do the competition have?

Steve Powell · 10th September 2015 at 14:31

Just to point out – it seems the new android version of foxit reader for android does just what we want – it copies highlighted text into the highlight bubble! At last!

Tony · 9th August 2015 at 17:22

Have been using Papers 3. Wonky. Patent meta data is poor. Tried sente 3. Doesn’t pull in patent meta data. I have many many US and global PDF patents that I would like to organize. Any one know what software is best for patents? Or is there something I can add, plug in? Any help is appreciated.

Samuel Bronson · 29th January 2015 at 21:48

Um, you could just use BibTeX as usual, couldn’t you? That is, after all, how Docear stores its database…

Yifan Huang · 23rd January 2015 at 21:44

Hello, I think Docear is great, but why not provide a support for LibreOffice. As you know, some researchers are accustomed to Linux and LibreOffice, therefore they would be appreciated if they can get LibreOffice add-on from Docear. Best wishes.

Narayan · 23rd January 2015 at 09:21


I am weighing the three reference managers for a non-academic use.
The compiled knowledge is for my own use, and also to impart it to my children.

So my sources are websites (e.g. blogs) and physical books; apart from pdfs and non-pdf files.

What is important for me is the ability to-
(a) extract content from these sources, and
(b) handling of content with diverging/contradictory assertions.

For need#1: How do I point to a certain page number, paragraph number and line number of a physical book that does not have any virtual entity (e.g. a pdf file) to represent it? How do I point to a website content? (Apart from the URL, I also need to pinpoint the specific statement/figure on the web page.)

For need#2: IINW, a mind map cannot handle conflicts/contradictions in the content. A concept map can.
(In a collaborative knowledge discovery scenario, even argument maps could be used to robustly debate the merits and demerits of an issue. But since Docear is meant for one individual, argumentation is ruled out.)

Given this, is there any way to create a concept map with the content compiled with Docear?

Thanks in advance!

Bhikshuni · 12th January 2015 at 04:49

Another issue you guys (all guys it seems) have failed to address is user privacy and support of e-stazi culture.

After reading the post above from qiqqa dude, I saw the qiqqa.com and was so impressed I was all ready to sign up until I started reading the user qiqqa “Terms and Conditions.”

I then checked into this issue on qiqqa forums and discovered that they are using Amazon Cloud servers!

You might as well be a department of the NSA & CIA, qiqqa!


Back to Mendeley and Docear and SPSS for this “might have been” customer. The demand of personal risk for software data integration is TOO HIGH! I am a private academic, not a Stazi-state wannabee!

Let me know when qiqqa gets a gold seal of approval from EFF like Drop Box got, on user encryption, privacy, and subpeona disclosures, and I might consider coming back again.

Qiqqa connection to Amazon makes me too uncomfortable to even install the free version for running offline!

If Aaron Schwartz was still alive (RIP), he would NO DOUBT concur with my choice!

Philip · 2nd December 2014 at 00:27

Docdear is completely unfathomable

Jeroen Bosman · 4th October 2014 at 14:29

@MrGunn Yes it is hard to keep these things up to date. Yet I only see 20 reds for Menedeley. Shouldn’t take more than 20 mins to look at those and state which ones should be blue. I would certainly invest those 20 minutes for my favourite tool.

mrgunn (@mrgunn) · 11th September 2014 at 01:20

A twitter discussion today brought me back to this post.

I know what a pain it is to try to keep these things up-to-date, as we made such a chart ourselves at one point, but as of this date, many things about the chart are wrong where it comes to Mendeley. If it were just one or two things, I’d point them out, but there are quite a few, and we just don’t have the time to get into a back-and-forth over exactly what is required to get a checkmark in any given category.

Thanks for putting in the effort to try to synthesize what’s going on in the rapidly changing reference management space these days.

    Joeran [Docear] · 11th September 2014 at 11:49

    Hello Mr Gunn,

    thank you for your feedback. You are absolutely right, Mendeley is constantly improving (as are Zotero and Docear). I also understand that you don’t have the time to give updates here in the Blog whenever Mendeley adds a new feature. However, I still believe the comparison to give a rough overview of the tools pros and cons.

    Of course, if someone (e.g. a passionate user?) wants to post a comment about some major updates that where made in Mendeley, he or she is highly welcome to do so.

    Eventually, I can only recommend to everyone to try out all three tools because this will give a much better impression than any review could ever give.

Martin Kucej · 5th September 2014 at 23:24

Please, don’t get discouraged by the opinion of Mr. Adam Smith on I, Librarian. I, Librarian is definitely not a limited application. It is a feature-rich PDF manager that can import PDFs and references from many sources directly or indirectly through RIS, or Bibtex files. Also, I, Librarian supports scientific collaboration the right way. It is true that the software does not have citation features (coming soon). However, there is a whole lot of scientists that never use any citation features. Citation formating is a specific (and rather grotesque) problem in academic publishing.

Pat · 31st August 2014 at 17:31

Although you mention this in passing, I think you need to emphasize one critical difference between these tools: with Mendeley it is difficult to add page numbers to citations – for dissertations and most journals, page numbers are required.

    Joeran [Docear] · 1st September 2014 at 08:04

    Yes that’s correct, the missing page-numbers feature is big disadvantage of Mendeley’s add-on. On the other hand, e.g. Docear does not allow adding references to footnotes, which is also quite a serious disadvantage, and I am not sure if Zotero’s add-on has not also some disadvantages.

Sean · 16th August 2014 at 21:56

It seems that Docear has some important features that Zotero lacks but Zotero has some important features that Docear lacks. Why was Docear developed instead of just adding the missing features to Zotero since it’s an open-source project after all?

    Joeran [Docear] · 18th August 2014 at 07:54

    Docear consists basically of the mind-mapping tool Freeplane + the reference manager JabRef + some new functionality regarding PDF management. It would have not been possible to use Zotero instead of JabRef because of Zotero’s architecture and programming language. However, developing an entire mind-mapping component for Zotero from scratch would have been impossible (for us).

Seif · 9th July 2014 at 11:23

Nice comparison. I was using Mendeley but then I switched to Qiqqa. Do you guys know of a similar fair comparison between Qiqqa and the rest of the programs?

Ethieboy · 10th April 2014 at 13:12

I commend you for the amount of work you clearly put into this.

I use Goodreader to annotate my PDFs. I have decided to make Mendeley my PDF organizer. Can I store my PDFs on Google drive, annotate them with Goodreader and have Mendeley update its library so that it contains the annotated PDF?

Is this even possible with any of the other PDF organizers?


Pan Srathongjai · 3rd March 2014 at 08:21

Dear all developers of Docear,

Most features of appearances and Docear are awesome! Anyway, It will be great if you can bind it to such a plagiarism programme as well. I mean, most people who use Docear are graduate students and professionals. So, when they cite the sources, some would like to know that his or her writing not to plagiarise other ideas of authors or any research. If you all guys can add such features, I think it may benefit more and more to other people as well. 🙂



    Joeran [Docear] · 11th March 2014 at 09:09

    Thank you very much for your idea. We will discuss it in our team during the next meeting.

Mary A. Axford · 21st February 2014 at 15:12

Excellent in-depth coverage!
If you are planning to expand this in the future to other reference managers, there are three I am most interested in as a librarian trying to help students choose the best program: EndNote (http://endnote.com/?gclid=CPShlv6x3bwCFajm7Aod1UYABw), Qiqqa (http://www.qiqqa.com/), and colwiz (https://www.colwiz.com/).

Endnote is the only one that is not free, so you may not want to include it, but a lot of U.S. universities have site licenses to it, so it is heavily used here. Qiqqa was developed at Cambridge and seems to have a lot of features, as does colwiz, which was developed at Oxford. Many of colwiz features are about research management rather than reference management, though. My definition of research management is the process from idea for a publication through to publication.

Thanks for all your great work to help make the world better for researchers around the world!

Phil R · 20th February 2014 at 19:07

Thanks for the review. I regularly use Zotero, but remain interested in other open source tools like this and Docear looks good.

With respect to your comment about synchronization, and access to an “open, free” solution for zotero, I have found that the phpZoteroWebDAV 2.0 – a php-based Zotero WebDAV server and library viewer found at http://blog.holz.ca/2011/11/proudly-presenting/ works perfectly to provide for synchronization of the PDF files themselves without depending on Zotero for storage. Admittedly, it requires that one has access to a web server, or a webdav server, but it is a good solid method, and additionally provides one access to the PDF files themselves, from a friends machine, or a mobile phone or tablet in a pinch.

tedus · 10th February 2014 at 15:09

This is kind of ironic – dont you think?
In another article (https://ISG.beel.org/blog/2013/08/27/off-topic-which-one-is-the-best-reference-management-software-tool/) you mock about others making a comparison where their reference manager in conclusion is the best.
So far so good – but half a year later this list…

Taking the comments you missed some points by the competition at first 😉 – and also the colours – mainly red for Zotero and Mendeley in categories they are not build for – but docear is:
– file managment – nice to have – but kind of irrelevant as a to mention feature for reference manageres dont you think?
– Literature search and discovery: again – you like your recommander system – we got that – but you can get that with a simple web browser to. Also i would recommand a tool like recently which gives recommendations based on article databases
– note, task etc. (aka mind mapping) – guess what: this category is what docear is about – so any others may hardly point. Also i would give docear not a whole plus as the pdf (and by this note taking) solution does not work out-of-the-box on every system (guess i am a linux user)
– the above one also is for drafting etc – where docear actually has a minus compared to zotero where you have an addon to use open/libreoffice.

Dont get me wrong – this is not a rant- i like docear and use it along with zotero (and sometimes mendeley) – but i had to smile when i saw this list and remembered your old post.
At least the colour effect does the thing – maybe next time dont choose only blue and red (for example zotero also has a recommendation service in their roadmap).

Overall i would recommend the (german) literaturverwaltung Blog (https://literaturverwaltung.wordpress.com/) to anyone searching for quite good comparison to find their reference manager of choice.
Joeran probably knows this as i remember reading some articles about docear there.

Personally i would recommend Zotero for reference managment – and the combination of Zotero + Docear to everyone who wants to manage notes etc.

    Joeran [Docear] · 10th February 2014 at 23:21

    Hi Tedus,

    thanks for your feedback. Let me try to answer some of your criticisms.

    Taking the comments you missed some points by the competition at first

    Yes, that was indeed embarrassing and shouldn’t have happened :-(.

    In another article (https://ISG.beel.org/blog/2013/08/27/off-topic-which-one-is-the-best-reference-management-software-tool/) you mock about others making a comparison where their reference manager in conclusion is the best.

    I was indeed mocking about the other developers who make comparison charts that present their tools as the one-and-only perfect reference manager. I admit that my comparison might be somewhat biased but at least it does not completely conceal Docear’s weaknesses and the strengths of the competitors. So, I think that my comparison has at least some value, while those of the other developers are pretty much worthless. And I still believe that it’s impossible to write a perfect review comparing all the features of different reference managers. Hence, I still believe that one should first decide about which features a reference manager should not possess (https://ISG.beel.org/blog/2013/10/14/what-makes-a-bad-reference-manager/), then read at least two or three reviewes on the favorite candidates (reviews like this one, and/or like those linked on http://literaturverwaltung.wordpress.com/ ), and then try the most interesting candidates yourself.

    – file managment – nice to have – but kind of irrelevant as a to mention feature for reference manageres dont you think?
    – Literature search and discovery: again – you like your recommander system – we got that – but you can get that with a simple web browser to. Also i would recommand a tool like recently which gives recommendations based on article databases
    – note, task etc. (aka mind mapping) – guess what: this category is what docear is about – so any others may hardly point.

    In my opinion, file management and note taking is pretty important and one of the reasons why I wasn’t satisfied with Zotero and started to develop Docear. But that’s the thing about any review: every reviewer has his personal preferences and he will design the review according to these preferences. Because I consider note-taking important, I included it in the review, while others wouldn’t. But the good thing is, that when you know that you don’t care about note-taking etc. you can just ignore that part of the table :-).

    Also i would give docear not a whole plus as the pdf (and by this note taking) solution does not work out-of-the-box on every system (guess i am a linux user)

    Well… that’s a good point. Maybe I’ll change it, when I edit the article the next time.

    – the above one also is for drafting etc – where docear actually has a minus compared to zotero where you have an addon to use open/libreoffice.

    I gave Docear a minus for that in the category “Writing / Add Ons for text processors”

poyan · 28th January 2014 at 23:34

I was quite interested in qiqqa, but I deinstalled it rather soon again, because I don’t like to be locked in any way.
I use docear since the very beginning, and I like it, but some features are still missing. I use Mendeley for collaboration with my doctorates and with some colleagues worldwide. However the one-way-“syncing” (from Mendeley to Docear) is very annoying.
There is another probable partner for coop, it is bibsonomy: http://www.bibsonomy.org/
The functionality is similar to Mendeley, it is free, and basically they provide a plugin for jabref which offers a two-side-synchro. However – I don’t get it working. If it would – docear is based on jabref.
In my eyes workgroup-functionality and cloud-storage of literature (pdf-files) for working-groups is a primary must.

Sadid · 18th January 2014 at 02:42

Thanks for the great article,

I’m using Zotero and Docear side by side. Zotero’s web importing is great and Docear is very useful in literature process and as research assistant suite. Both can be used together, apparently with some overlaps (I’ve also use some 3rd parties such as DocFetcher, DirSyncPro, Git, OneSync/Duplicati and Dropbox in between). However I think you should pay more attention to Qiqqa. It’s very similar to Docear and have provided many features as a research suite. Personally I don’t like closed source solutions but I think Docear is not in the same camp as Zotero or Mendeley are, but Qiqqa definitely is.

adam.smith · 17th January 2014 at 08:13

You could use Docear as a frontend for pandoc (using BibLaTeX) which allows you something along those lines.

FWIW, Mendeley does not offer such a feature. Zotero natively offers RTF scan, though it’s not super versatile or reliable. For that purpose I have co-written an add-on that delivers more powerful scanning into “live” Zotero citations http://zotero-odf-scan.github.io/zotero-odf-scan/

Chris · 16th January 2014 at 21:29

I don’t like to write in Word, which happens to be very unstable on the Mac.
Some reference managers, amongst them most if not all LaTeX -based workflows that I am aware of, allow to insert temporary citations in plain text, usually using some kind of delimiter as described by {Beel #38550}.
In this hypothetical example the curly brackets are the delimiter and #38550 would be the unique identifier in the literature database for the paper written by Beel et al that I wanted to cite.
Whenever I feel like it I would instruct the reference management program to “scan” the text file and 1) convert the placeholders into proper in-text citations, like (Beel et al, 2013) and 2) generate a bibliography using the proper citation style for the journal.
The advantage is that I can write in whatever program I feel like, including Textedit, Notepad, Scrivener, etc, thus avoiding the notoriously unstable MS Word (Mac, it is much more stable under Windows) and only in the end export to Word-formating.
Is something similar possible with Docear?

Steve · 16th January 2014 at 18:35

This looks promising! I wasn’t aware of it.

I normally use LaTeX but sometimes need to add references in Word (on a Mac). Do you plan to add support for this? Any ballpark idea on when it might happen?


adam.smith · 16th January 2014 at 18:28

Mendeley is developing a fully featured Android app, they hope to get it out this year. This: https://secure.zoteroreader.com/ actually works relatively nicely as a reader on Android for Zotero and last I talked to him the dev was planning to hire someone to turn it into an app.

I, Librarian is a much more limited application, e.g. without any citation features and with very limited import.

adam.smith · 16th January 2014 at 18:17

I think you’re talking past each other. As Joeran says, you cannot collaborate on a Zotero database without using Zotero sync. As Andres says, you can use all other Zotero features (i.e. everything but groups) without syncing or even creating an account. You can also collaborate on a document without syncing, as Zotero embeds citation metadata (though using a group is a bit smoother).

andres · 16th January 2014 at 13:45

If you want to collaborate with colleagues who use a different reference manager than you, or if you don’t want to spend money for collaboration, or if you don’t want to store your data in the cloud, look at Docear.

I thought zotero can do this as well, you are not forced to share in the ‘cloud’. At least I don’t.

    Joeran [Docear] · 16th January 2014 at 13:49

    How do you share the data between colleagues? As far as I know you could share the database e.g. via dropbox but if two persons would do changes at the same time (or one person is offline and doing some changes while another one is working on the data online), there will be a conflict that is not easy to resolve. Am I wrong?

      Sadid · 18th January 2014 at 01:57

      I think via Git/GitLab or Git/Dropbox it is possible. Also both should develop source such as LaTeX. These reminds me Authorea.com (irrelevent to Zotero :D)

Joeran [Docear] · 16th January 2014 at 11:34

ok, I hope I got all the changes right 🙂

Nicolas · 16th January 2014 at 00:44

Thanks for the comparison. I have waiting for one like this for a time (I was thinking to make one by myself). It would be great to have also “I, Librarian” in the comparison since the application seems promising (http://www.bioinformatics.org/librarian/).

None of these apps have version for Android, and for the part of reviewing literature it would be great to use my tablet, but a web viewer can suffice in some extent this part.

One feature that I haven’t figured out about Docear was the note taking, that I found great!

Thanks again for the postm


Chris · 15th January 2014 at 22:58

Thanks for that informative comparison.
I have two questions:
1) You mention that there is no support for word processors on the Mac, only for Windows at the moment. What about temporary in-text placeholders that would get replaced with properly formatted citations by scanning a text file or RTF file at a later time. It seems to be similar to how a Bibtex-based workflow works but what if the output was not supposed to be a LaTeX file?
2) I am not sure what information contained in my mind maps would be shared with others and what would remain private, either by design or by accident. You mention the privacy problem yourself when talking about exporting a pdf from Mendeley but I see the same problem with Docear’s recommendation system. Some of my comments are simply not meant to be public and I would feel like I was censoring myself if I knew that they could potentially be passed on to others.

I’d appreciate some enlightenment on these two points, thanks

    Joeran [Docear] · 16th January 2014 at 09:56

    hi Chris,

    re 1) I am not sure what you mean by this? Could you explain that idea in more detail?

    re 2) First of all, Docear does not require you to store your data on our servers. This means, if you want, you can install Docear and use it as any other “normal” desktop software with all your data stored only on your computer. If you activate online services such as backup or recommendation, your mind maps will be transferred to our servers. However, we will never ever publish them. They are just stored on our servers either for backup, recommendations, or for research purposes. Of course, as with any online storage, we cannot 100% exclude that some hackers might get access to your data some day. So, in general you can be sure that nobody gets access to your comments. However, if you want to be 100% sure, just do not activate Docear’s online services.

adam.smith · 15th January 2014 at 22:10

(sorry, missed the blockquotes around “though, I am not really seeing how to use it as filter function” )
oh and wrt

I am really sorry, that I did these mistakes, but let me assure that I didn’t do them on purpose, and I will update the post (including table) soon.

I certainly didn’t think you did. I’m not very convinced about the usefulness of the tables in general — I find the in-depth discussions give people a much better sense of what the software actually does (and doesn’t) do — but as they go, I find this one of the more useful ones (though I’d certainly say the selection is biased towards Docear’s strenghts. But that’s fine: it reflects your design philosophy and priorities).

adam.smith · 15th January 2014 at 22:02

By “import”, do you mean, when I drag & drop a PDF to Zotero? I don’t find any option to rename a PDF in that scenario. Could you give me some more details how to do it? And can PDFs also be renamed after the import?

no, I mean via the web importer, which is the typical way to import items – including PDFs – into Zotero. If you add PDFs differently – e.g. by drag and drop – you need to trigger the rename by using right-click –> Rename from Parent Metadata (can be done in batch)

Could you tell me, which PDF viewers can be used in FireFox that offer some more advanced features than print, zoom, etc.?

Two things: 1. You can configure Zotero to use your system’s default PDF viewer and not open PDFs in Firefox – both on a one-off basis (right-click –> open in external viewer) and permanently using the launchNonNativeFiles hidden pref. 2. On Windows, I believe both pdfXchange and Foxit have fully featured PDF plugins, as does Adobe Acrobat (I don’t keep up how much annotation acrobat supports in the free version). I’m not sure about Mac, there’s no FF plugin with annotation capabilities for Linux (PDF annotations in Linux are a sad story anyway).

Fair enough re: 3rd party add-ons, that distinction makes sense. As a general FYI (I wouldn’t expect this to be part of a review/comparison) – the fact that all Zotero add-ons are open source and mostly (all?) GPL or GPL-compatible licensed, and because Firefox/Zotero add-ons essentially work by overlaying code over the existing code, they’re relatively easy to integrate into the main code-base. For ZotFile, specifically, I’m pretty sure Zotero’s devs would integrate large chunks of it into the Zotero code if Joscha were to stop maintaining it.

though, I am not really seeing how to use it as filter function
Maybe I’m misunderstanding filters, but the way I see them, they’re “just” saved searches that, instead of creating a separate virtual folder, let you view items in their regular folder/collection structure. Zotero does the saved-search/virtual folder part very nicely, but not the second part – so it depends on what you’re after. In any case – I think the lack of a saved search feature in Mendeley is a major oversight, I’m not sure why they’re not prioritizing that more. I think it’s absolutely crucial.

    Joeran [Docear] · 16th January 2014 at 10:22

    thanks for the clarifications, i will update the post shortly.

    Maybe I’m misunderstanding filters, but the way I see them, they’re “just” saved searches that, instead of creating a separate virtual folder, let you view items in their regular folder/collection structure. Zotero does the saved-search/virtual folder part very nicely, but not the second part – so it depends on what you’re after

    To me, a filter function is the second part that you described, i.e. in Zotero a filter function would hide all the collections that do not contain relevant documents, and in the table, only relevant documents were shown. IMHO the “save searches” part is a search feature. I will try to make it more clear in the review what I mean by filter.

adam.smith · 15th January 2014 at 16:25

A couple of notes and question:
– Zotero does automatically rename PDFs on import, even without ZotFile. That one should be blue
– You can use Zotero with any 3rd party PDF reader just like Docear, so I think the distinction you’re making there is a bit odd – by what logic does Docear offer standard PDF functions where Zotero doesn’t? (as a matter of fairness, I also find it a bit odd that you color things where Zotero relies on 3rd party tools like ZotFile red, but things where Docear relies on 3rd party tools blue…)
– Zotero offers standalone and attached rich text notes. The note taking feature may be less powerful than Docear’s – I don’t know – but I don’t think you can claim it doesn’t exist.
– I do think you give Zotero’s search features short thrift – there is limited regex support, smaller/larger does exist e.g. for dates, and most importantly, saved searches/virtual folders are possible – imho these are quite close to Filters in functionality.

    Joeran [Docear] · 15th January 2014 at 18:55

    Hi Adam,

    thank you very much, I highly appreciate your feedback (as always :-)).

    > Zotero does automatically rename PDFs on import,
    > even without ZotFile. That one should be blue

    By “import”, do you mean, when I drag & drop a PDF to Zotero? I don’t find any option to rename a PDF in that scenario. Could you give me some more details how to do it? And can PDFs also be renamed after the import?

    >You can use Zotero with any 3rd party PDF reader just like Docear,
    >so I think the distinction you’re making there is a bit odd – by
    >what logic does Docear offer standard PDF functions where Zotero doesn’t?

    You are right. With regard to PDF standard functions, Zotero and Docear should be rated equally, at least in principle. Could you tell me, which PDF viewers can be used in FireFox that offer some more advanced features than print, zoom, etc.? All PDF viewer add-ins for FireFox that I have tried were very basic, and not comparable to “normal” stand-alone PDF viewers such as PDF XChange viewer (or is there an easy way to tell Zotero to open PDFs not in Firefox but in an external viewer?)

    >(as a matter of fairness, I also find it a bit odd that you color things
    >where Zotero relies on 3rd party tools like ZotFile red, but things where
    >Docear relies on 3rd party tools blue…)

    Good point, actually I was thinking about that quite a while. My rational is the following. I gave credit to Zotero for its excellent sustainability and openness. However, these credits do not necessarily apply to e.g. Zotfile and other add-ons. For the add-ons, it’s more likely that the developers stop their work, suddenly charge money, etc. than for Zotero. Therefore, if I rated e.g. Zotero’s PDF capabilities “blue”, because there is Zotfile, readers would think “Cool, Zotero has the best sustainability and great PDF management capabilities”. However, it might well be that one day the Zotfile developer stops his work and then the user only has Zotero without Zotfile’s PDF management capabilities. Therefore, I decided to not include third party add-ons in the ratings (but to mention them).

    With respect to Docear, I don’t think that Docear relies on any 3rd party add-ons, except the external PDF viewer, and I would not really consider the PDF viewer an add-on. However, even if you did, I don’t think that in this case it would be a problem to include the external PDF viewer in the rating, because, in contrast to e.g. Zotfile, there is no reason to assume that in the future there wouldn’t be any external PDF viewers that may be used, more or less well, with Docear. In other words: you should be more concerned that we, the Docear developers, stop our work than the developers of the PDF viewers 😉

    In addition, probably every Docear user knows that he needs an external PDF viewer (and 99% probably also have already installed one before they try Docear). This means, chances that someone uses Docear without a PDF viewer, and hence misses some core features, are close to zero. Also, many users won’t need to install a new PDF viewer because they already have one. In contrast, the chances that someone only uses the default Zotero, and hence misses e.g. some important features that Zotfile would offer, are rather high. In any case, users will have to install additional add-ons what always requires time, and often is error prone.

    >Zotero offers standalone and attached rich text notes. The note taking
    >feature may be less powerful than Docear’s – I don’t know – but I don’t
    >think you can claim it doesn’t exist.

    Sorry, I missed the “standalone-notes” icon when I reviewed Zotero.

    >I do think you give Zotero’s search features short thrift – there is limited
    >regex support, smaller/larger does exist e.g. for dates, and most importantly,
    >saved searches/virtual folders are possible – imho these are quite close to
    >Filters in functionality.

    You are right, again. I only used the search field of Zotero and missed the search icon which indeed opens quite a powerful search dialog (though, I am not really seeing how to use it as filter function).

    I am really sorry, that I did these mistakes, but let me assure that I didn’t do them on purpose, and I will update the post (including table) soon.

Kris · 15th January 2014 at 13:01

Nice post. Would be great to discuss many of these points in detail if we bump into each other again. Until then, a couple of comments.

Mendeley Catalogue Search provides the functionality to show only Open Access results. You can select the Open Access option from the search filters or add “oa_journal:yes” in the query box.

Mendeley Suggest doesn’t provide such a filter but it would be nice to add one too. It’s important that Mendeley Suggest doesn’t limit itself to only recommending articles that are freely downloadable, however, but that it brings all relevant articles of interest to the attention of researchers.

    Joeran [Docear] · 15th January 2014 at 13:28

    Hi Kris, thanks for the information. I will update the Blog post soon (I will wait, if others find some more errors, and then correct them all at once).

      Laura · 21st September 2017 at 11:26

      it still isn’t changed in the post

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