● Introduction: Encounter with Mendeley and parting of ways

The author's blog, “Tweets from Building No. 5” vividly describes his excitement at encountering Mendeley and how he used the software.

I believe it was in the spring of 2010. When I first encountered Mendeley, the free reference (citation) management software, I was blown away by it and spent day after day immersed in its world. Before I knew it, however, I had stopped using it. The reason is that after getting carried away and continuing to register PDF files of academic papers in Mendeley, one day I ran into the 1 GB limit of the free version and got a message saying I could no longer continue using it for free. Naturally I could have changed to the paid version of the program. No matter how reasonable the price, however, I could not muster the courage to select the paid version before making up my mind to continue using the software. So I ended up letting the matter slide. Because I had written on my blog about the excitement I felt when I encountered this software,1 and many people read the blog articles after that, I started getting inquiries like, “I've heard about the free service/software Mendeley. Could you please explain what it is about?” But these were recent, after I myself had pretty much graduated from Mendeley.

Actually there was one more reason why I had left Mendeley behind, and that was the sudden emergence around that time of so many free cloud services. One of the major features of Mendeley is that it lets you store in the cloud the PDF files of papers in your collection, which you can then access from multiple computers, whether running a Windows, Mac, or Linux OS, and even from iOS (iPad/iPhone) or Android tablets or smartphones, for example. In my case, even more than the reference management functions, what really attracted me about Mendeley was the cloud function, enabling access from anywhere at any time to the PDF files stored in your own archives. I left Mendeley behind because, even though it meant losing the excellent references organization ability, the appearance of so many new cloud services (even free ones regularly offered 2 to 5 GB of space and some as much as 50 GB for free), shooting up like mushrooms after the rain, did away with any feeling of inconvenience. Given these alternatives, the limit of 1 GB (nominally the personal area is 500 MB and the rest is for sharing) on Mendeley archives under the free plan is far too small to hold document PDF files, which continue to increase day by day.

● Why are scientists so particular about reference management?

The top page of Google Scholar, a service for searching scholarly literature, has the phrase, “Stand on the shoulders of giants.” Scientific knowledge continues to grow at a rapid pace as it is passed on in uninterrupted succession from earlier times. “Standing on the shoulders of giants” means that, while your own research results may be only a modest contribution to overall knowledge, by building on the contributions that others have made you can reach even higher than the vast corpus of knowledge that humankind has compiled up to now (giants). The other side of this is that, no matter how wonderful our own research results may be, they were possible only because of all the research work that went before. The worth of your own research achievements can only be known by checking them against the important related accomplishments of the past. This is why so much importance tends to be given to references in scientific research papers, and why such stringent reviews are made as to whether a paper properly acknowledges the importance of individual research results based on appropriate review of past accomplishments.

Each academic journal prescribes a carefully decided format for references, and follows the tradition of strictly checking whether references are cited in accord with the rules. A person submitting a paper therefore must search for suitable works to cite, must cite them in the correct format, and must create a list of cited works without format errors. In the process of writing a scholarly paper, the steps of citing works and creating a list of references are therefore one of the most stress-inducing. There is also a “myth” that no matter how painstakingly these steps are carried out, inevitably mistakes will creep into the final result. Back when data search services were not as generally available as today with the Internet and all, if a mistake crept into a list of references it could have major repercussions, in some cases resulting in not being able to trace back from the list to the original source.

That is why researchers in most fields, starting with their graduation research or right after entering graduate school, tend to put a great deal of effort into collecting and managing papers closely related to their own research and creating reference lists, and why there is a long history of attempts to make this work even a little more efficient, as reference management techniques have been developed starting with the use of index cards half a century ago. With the availability of personal computers, some people turned to editors, word processors, or general-purpose database software to manage references; but then for a long time EndNote was one of the standard software tools, being designed specifically for managing references and citations. While EndNote was without doubt functionally advanced, the high price put it beyond the reach of most young researchers, who were unable to pay for it out of their own pocket. Then along came Mendeley, like a blazing comet. This reference management software was free, came with advanced functions, and was fun to use.

● The impact of Mendeley

Reference management is a task people approach in individual ways, each adopting their own methods for finding, collecting, and managing references. Citation management is something that is carried out as the final step in preparing a dissertation or other research paper, putting the final touches on research activity. In the overall research work that has gone on before, it can be seen as a relatively minor part. Partly because this, progress in this area has seemed slower to come compared to word processor or presentation software; but along with the accumulation of data published on the Internet and advances in search technology, in recent years the pace of development appears to have suddenly taken off. Seizing the initiative in this area was Mendeley. According to Wikipedia, “Mendeley was founded in November 2007 and is based in London. The first public beta version was released in August 2008.” Its use began spreading in the West from around 2009, but was slower to catch on in Japan owing to the lack of a Japanese version. I myself at last became aware of its existence in the spring of 2010. Because it was free software, I downloaded it right away. I remember how, even though it was surprisingly easy to use, the results it output were the equal of those from full-fledged reference management programs, and I soon found myself caught up in it. Let me quote portions of my blog written at that time. (Some parts I have omitted or edited including changes in line breaks.)

It's amazingly simple to register a PDF file; just drag the file over to the list portion and drop it in the window. A link to the PDF file will be created in the computer. At the same time it gathers bibliographic information about the paper, apparently by accessing the Internet. So all you've done is throw a PDF file at it; the bibliographic information is created automatically. First, the abstract. Next, so-called bibliographic information. Then, surprisingly most of the time (though not in every case), it will automatically extract the list of cited references at the end of the paper. (This function for making a list of references seems to have disappeared from the current version.) Naturally you can make use of this information as data for document cataloging and searching, or when writing a paper of your own. It's enough to make you shed tears of gratitude.

To my shame, I have in fact never used the famous EndNote; but I wouldn't be surprised if Mendeley functions are at least comparable to it if not superior. Not only that, but although Mendeley Desktop has a limit of 500 MB, online synchronization across multiple computers is supported (cloud), so by sharing with others, two or more persons can read the same paper or work on it together. (Since I used the software only by myself, I haven't actually tried that function.) There is also a browser mode that makes it easy to check a list of papers from another location. It seems that things like memos or marker additions can also be shared.

Some people have called this an SNS for research paper handling. Of course, it is powerful enough for individual users like me to synchronize across multiple computers. Come to think of it, this is still beta software, so if it continues to advance it definitely has a good chance of becoming a fantastic industry standard program.

As I read over what I wrote back them, I'm almost embarrassed by the level of excitement that comes through. It does remind me, though, that I truly felt thrilled by the way it could extract bibliographic information from a PDF file just by dragging and dropping it in the window.

● On to the ReadCube era

ReadCube screen
Opening ReadCube Web Reader in a browser and reading the latest Nature papers in an extended screen (Extended PDF). The standalone software has practically the same screen.

The reason I stopped using Mendeley after that is as I explained earlier, but I have not stopped doing reference management. A powerful rival to Mendeley has since appeared, and I ended up switching to that. The rival is ReadCube, which of course is a free service. As with Mendeley, ReadCube consists of a desktop application and online Web component. The functions of the desktop program as reference management software are highly advanced like those of Mendeley, while the Web version at present is strictly a document reader. This means the user, without even needing to log on, can not only access the PDF full text files but can also (if in a LAN environment where access is possible) access with a single click the supplementary information attached to a paper, related articles, the original source of a cited paper, and other such information. It truly is a super reader. As if that were not enough, there is more big news. Starting from November 2, 2011, the academic journals of NPG, publisher of Nature among other journals, have ReadCube built in as official reader (viewer). If you are connected to a LAN with access rights, all you have to do is click on the “View in ReadCube” icon that now appears below the “Download PDF” icon next to a paper. You then find yourself in a magic world where this reader becomes your very own. You can experience for yourself how amazing this service is by viewing an open access Nature paper2 provided as a sample. Simply clicking on a link not only lets you view the Supplementary Information, Editor’s Summary, and News & Views in Nature, but you can jump to the original source from a document number in the paper or from the list of cited references in the sidebar.

If you are in a university or other institutional environment with a Web subscription to NPG research papers, you will be able to read any of the papers with this super reader. (Though this function is apparently not yet available, eventually it will be possible to connect a downloaded PDF to the Web service and read it in the same super reader style.) Combining ReadCube with your choice of cloud service, you can use ReadCube to manage PDF files of research papers stored in the cloud, while taking advantage of the advanced reader functions to jump interactively to various links via the Web from an enhanced PDF file. Experiencing this service shows just how far we have come today. Some of the functions are supposedly not yet complete, but now that NPG is on board I think it is safe to hold out high expectations for ReadCube.

References