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Mendeley is (mainly) a proprietary social network to share basic citation data and research papers. see also

Are there any free and open source substitutes for this service?

A technical possibility: users could collect BibTeX data and a hash and share this information. It would be very useful to have such a free service because every journal provides the citation data in a different format. That includes false field entries, broken files and hidden download buttons on the website.

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Jonas Stein
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    You might find some options here: http://en.wikipedia.org/wiki/Comparison_of_reference_management_software –  Nov 12 '12 at 19:44
  • Nice link. http://en.wikipedia.org/wiki/Connotea could be a solution. –  Nov 13 '12 at 01:36
  • Related (but not a duplicate): http://academia.stackexchange.com/q/854/1033 – gerrit Nov 20 '12 at 15:41
  • related: http://academia.stackexchange.com/questions/36/suitable-citation-management-softaware – matth Nov 27 '12 at 12:23
  • The opening sentence could be controversial, as much as it is secondary to the context. Maybe you could rephrase it. – Kris Nov 28 '12 at 06:18
  • The question, as stated, is erroneous and meaningless, because it doesn't make a distinction between a client and a server. Mendeley makes a client which is proprietary, but the content available via API is under a CC-BY license, so anyone can built a open source client. – William Gunn Nov 04 '14 at 18:57
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    @WilliamGunn your employer can call it what it wants, but the client software is closed, the server software is closed and the data is only open in the loosest sense of the word. If you want the data to be considered open, provide a nightly push of the entire database that can be downloaded without an API. – StrongBad Nov 05 '14 at 10:01
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    I guess I'm confused as to what the question is about. Is the question about open source software that can manage references, or is it about something that does exactly what Mendeley does, but is 100% open source as opposed to only partially composed of open source components, or is it about the catalog, which if you want a nightly dump of 17 TB, be my guest, but available via nightly dump isn't in the definition of open data. – William Gunn Nov 05 '14 at 20:39
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    @WilliamGunn to be fair I don't know what open data really means, so I asked over at OpenData.SE. – StrongBad Nov 06 '14 at 11:07
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    Jonas, do you only need the software to be open source software? Or do you also need the data to be open data (freely reusable license, such as CC-BY-SA or CC0)? By data I mean everything that is shared between users, presumably citations and "social" information. – nic Nov 06 '14 at 11:22
  • @nic, Yes, I do not need social information at all, but the data and the client should be open/free as you described. – Jonas Stein Mar 08 '19 at 20:28

8 Answers8

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The only alternative that comes to my mind is Zotero:

  • It is open-source,
  • it comes as a standalone application or as a web-based version with Firefox, Chrome and Safari connectors,
  • it integrates with Word or OpenOffice,
  • it syncs with the Zotero server,
  • it has BibTeX export,
  • and more.

The Zotero standalone client is cross-platform and open-source (AGPL licence), and it can be run on its own or synchronized with the web version. The web service is free to use up to a fixed storage quota, with paid storage available, and there is an open-source implementation of the dataserver available if you want to roll your own. The local client stores its data in SQLite format so in principle your data is not locked in, but the database is relatively hard to trawl externally; however, since the client is open source there are relatively few future-proofing concerns.

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matth
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    Is it truly free? I think that the client only is; the server is proprietary. – Federico Poloni Nov 27 '12 at 12:27
  • That is true, but Zotero can be used without the server. Your data will never be locked, you can always export it. – matth Nov 27 '12 at 12:30
  • It can be used partially without the server. Only a subset of its functions will still work. – Federico Poloni Nov 27 '12 at 12:31
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    What functions don't work without the server? Except syncing to the server, of course? – matth Nov 27 '12 at 12:34
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    Well, syncing data among different clients. :) There is really no technical reason why this couldn't be done on a completely FOSS stack. It is only a commercial choice. I don't blame them, that is their business, but it is a fact that Zotero is not 100% open, despite their claims. – Federico Poloni Nov 27 '12 at 18:03
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    You can run a WebDAV server, no sweat: https://github.com/fishburn/phpZoteroWebDAV – Tony Boyles Aug 02 '13 at 15:44
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    @FedericoPoloni I think you are misinterpreting the "free" in free software: Zotero is still developed and distributed under AGPL. That does not mean that the developers may not charge for their server services. Furthermore, there is the possibility to run your own WebDAV server as Tony pointed out. – non-numeric_argument Nov 20 '13 at 10:03
  • @non-numeric_argument my claim above is that some of the functionality in Zotero depends on closed-source, commercial server code, and there are functions (such as syncing your files between a desktop and a laptop) that you can obtain only after payment. We may discuss whether this means "free" or not. If I understand correctly, the program that Tony pointed out is an open-source, third-party, non-official replacement for the server code. The only fact that this project exists should support the statement that Zotero is not "free" enough, at least in someone's opinion. – Federico Poloni Nov 20 '13 at 19:34
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    @FedericoPoloni First, Zotero itself provides some sourcecode for running a dataserver. Second, the Freemium storage and syncing service by Zotero Server resembles Mendeley very much. The other reommended open source software BibDesk has no server or sync functionality whatsoever and I do not know of any open source software which is an original desktop reference manager which comes with that funtionality (of course, there are open source web-based reference manager). – non-numeric_argument Nov 22 '13 at 14:01
  • @non-numeric_argument thanks for the pointer, I did not know of the existence of this dataserver repository. I haven't checked its functionalities but it seems interesting. On the other point, I agree with you, as far as I know there are no (other) open-source desktop reference managers with that functionality. – Federico Poloni Nov 22 '13 at 14:19
  • See also unofficial info on running the server. – Beni Cherniavsky-Paskin May 13 '14 at 22:10
  • Zotero is unstable and I had many headaches when trying to integrate in Microsoft Word. – Cape Code Dec 19 '16 at 10:22
  • zotero organizes my pdfs? – a06e May 31 '17 at 18:31
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    +1 for Zotero as an alternative to Mendeley. It is open source and allows you to take control on how you want to manage your files. In addition, Zotero now supports migrations from Mendeley. Be aware that starting Mendeley v1.19, Mendeley has started encrypting their database making it difficult to migrate away and ensures you're locked into using Mendely. https://www.zotero.org/support/kb/mendeley_import – Zythyr Jun 18 '18 at 06:15
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Docear

Haven't tried it yet but https://www.docear.org/ seems to stand out as one of the leading open-source alternative to mendeley.

Docear is basically a marriage of JabRef and Freeplane. It uses JabRef as a backend for its reference management and Freeplane to organize references, annotations you make in the pdf, and any other information (including images, links and crossreferences) in a mind-map.

As the original author of this answer pointed out it is indeed open-source—licensed under the GNU General Public License.

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Martin Van der Linden
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    Isse on JabRef for crafting a new mindmap solution for JabRef: https://github.com/koppor/jabref/issues/433 – koppor Jan 21 '21 at 22:02
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I have tried any number of reference management programs (from EndNote to Mendeley and back), and have come to the conclusion that the most important criterion is that the reference manager directly, natively writes in .bib, or some other text-based, open-source format.

This has several advantages:

  • no proprietary or otherwise lock-in
  • future-proof
  • fast and robust
  • if all else fails, you can always fix it "by hand" in a text editor
  • works well with LaTeX, no "lost in BibTeX-Export" problems
  • works nicely with versioning software (such as git), which requires text files for meaningful diffs.
  • especially with git, you have maximum peace of mind about just what exactly is happening with your library.

This leaves a pretty small number of editors:

maxheld
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I really liked Mendeley's potential but got frustrated with both their pricing model (maybe I just never learned how to use the software correctly) and it consistently butchering imported BibTeX entries.

I've been a pretty happy BibDesk user for a long time, it is true open source software, but unfortunately it has not been ported outside of the OS X environment, so this is only a qualified answer.

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    BibDesk, indeed, is an excellent tool. It doesn't offer a built in syncing feature across computers, but this can be achieved in other ways such as Dropbox or git. I highly recommend BibDesk! – crsh Nov 30 '12 at 12:41
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We have developed an open source solution, downloadable from GitHub at https://github.com/scientilla/scientilla, that allows users to collaboratively share and refine their scientific bibliographic metadata.

The system relies on a "peer-to-peer" and "open-data" approach as well as on a "clone-and-refine" algorithm. It can import data from external web services.

The more the system is used, the more the information that flows on the network become clean.

Moreover, using Scientilla, any user can obtain the whole metadata shared through the network.

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Antonio De Luca
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4

Finally I found I, librarian on http://i-librarian.net/ which is a kind of mixture between Filestorage-Server, JabRef and a personal open source Mendeley server.

Interested users may try the demo account on the website.

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Jonas Stein
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In creating such a system, the cost of the software and the expense of running the server(s) to host the data is microscopic compared to the expense of the army of knowledgeable people checking out references, cleaning up the barely legal (and semantically often complete nonsense) BibTeX entries offered by some journals, knit them up from scratch where not even the above is available.

Better create your central database, share it with your research group. Have everybody chip in by adding references to interesting papers found while browsing, whatever they cite in their publications/theses, and perhaps keep another file with publications generated locally (comes handy when asked for "publications of the group last year" or so). Publish guidelines, enforce them, perhaps occasionally organize a refer-thon to clean up entries and fill out missing details. If you ask everybody who reads a paper/document to add a short (3-5 lines) summary/abstract (they'll have to write one anyway for "state of the art"), a URL or other pointer where to find the document, you create an (at least locally) very valuable resource.

If it grows enough, or as a side product of the work, publish it on the webpage of the group. Might even ask for contributions from outside while you are at it.

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No, there isn't anything that is an exact copy of Mendeley, the server, the clients, the API, and the content, but all composed of 100% open source software.

For the record, Mendeley does contain some open source and the API is freely available, so if you wanted to build an application of service to the scholarly community, you'd probably be better off building your own open source client but leveraging the messy and difficult bits that we've already solved and make available via API, such as the metadata extraction and impact tracking bits.

William Gunn
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