AHKR, University of Bergen


Creating your own electronic library

Over the last few years there have appeared several programs for academic pursuits, not just word processing or note juggling, but aids to help us find, organize and write references for our papers. I have been slightly put off by such programs as they all seem to focus only on medical science and chemistry, giving the impression that the humanities are of no interest to them and thus they to us.

However, when you dig into them and weed out all the "PubMed" stuff, there are actually programs out there that can be used for our purposes. I have been looking into a few to see what they can do for someone interested in the human or social sciences, a kind of review over what is there on the market, partly for Mac and PC, partly for Mac only.

What these programs should do, is to aid us in three stages of our projects:
  • They should help us look up references and sources in electronic catalogues and databases, and store the results we find into a private bibliography we build on our topic.
  • They should help us organize and work with our references, be they for a master's thesis or a research project. That includes keeping track of and letting us read electronic articles (e-journals), on the web or in PDFs we have downloaded to our computer.
  • They should let us insert and automatically format references from our bibliography in a paper or article that we write, in Word or another word processor, in a format of our choosing.
We can do all of this "manually" using our web browser, word processor and so on. How far do these special academic programs give us something extra beyond what we can do in our regular ones? And which of these reference programs are best?

I have focused on six such programs, and the conclusion is unfortunately not quite straigthforward: Some programs are better at the first part of the process, searching & reading; others are better at the last, the writing part. Some are fairly good in both.

The contenders are:
  • EndNote is the "mother of all reference programs", the touchstone all others measure up against. It exists for both PC and Mac, and costs $250 (but many universities keep site licences). It may, however, seem a bit outmoded in that it is more a bibliography and library program that is not so helpful when it comes to finding and accessing online texts.
  • Papers is at the opposite end, it is a new small program aimed directly at e-journals and keeping track of your PDFs, but is of less use in the production phase when you want to get your references into Word. Papers exists Mac and Windows at €59 (students €39), and has an iOS (iPad/iPhone) version for $10.
  • Sente is a compromise between the two ambitions, it aims at the full process from searching catalogues to a finished paper in Word. It has many functions, and is free for Mac and iOS, for syncing you can get a account in the "cloud" for $60. It is only for Mac/iOS.
  • BookEnds is another "all-round" program for the complete process, but a bit better on book titles than on-line articles. It is a powerful program, and again only for Macs. It sells at $50 (students $70). There is also a free mini-version, Reference Miner, which allows you to search, but not store the finds into a bibliography.
  • Zotero is not a program, but an extension to Firefox (free, PC and Mac). It is thus a bit different from the others, but fairly straightforward to use and covers the complete process from searching to paper.
  • Mendeley is a quite new program for PC and Mac, free while it is in development, and tries like Zotero to cover the complete process.
Windows users also have some other options that I have not tested extensively (see a separate note for them), but this is already a wide selection. Many of the programs also look remarkably similar at first glance, but a number of differences appear with use. We will look at them in more detail, but let us start with the verdict:  
- For smaller papers, up to the master's level with a few dozen references, Zotero seems to be a good choice: It is excellent in the search phase, easy to co-ordinate between different computers, and has a straightforward adaptation to Word.
- If you want to quickly read up on a topic, then Papers is very charming. It is easy to use, does not have have very many options, but really lets you create an "electronic library" where you can read the texts and not just a list of titles.
- In a larger project, Sente may be the program that best covers all three stages of a researcher's work and gives you most flexibility. While other programs may shine in some aspects but are less useful in others, Sente is fairly good at all its tasks.

Let us, however, look at each task in turn.

A: Searching for literature on the Internet

If you are attached to a university that has a reasonable collection of electronic journals or fulltext databases like JStor, then it is likely that you have access to more, perhaps considerably more, literature online than on paper, even in Middle Eastern or Islamic studies. In order to search and read these e-journals, or just check our university library's book catalogue for what they have on their shelves, we can use our normal web browsers like Explorer or Safari. For the reference programs to be useful beyond the browsers, they must do something more: they collect and store the bibliographic information (name of author, title, journal, page numbers etc., the "metadata") of the item and store it in a "bibliography" on our own computer. Then we can later consult, organize and pull out the references we need for the paper we should end up writing.

We can do three things with the references we found: We can just store the reference, the name of the author and book etc., and then go away and pick up the book on our library's bookshelf. Or we can read the article online, directly in Explorer or Safari, if it is available electronically. Or we can download and store the article as a PDF file on our hard disk, so we can leisurley read it later (or print it out) when we are off-line. The programs should help us in all of this and in a simple way link the reference to the online text, so that we can later read the article just by clicking on its title in our bibliography, while the program at the same time has all the data we need to refer to the article in our paper.

In the first task, searching for possible sources on the Net, a program can use two different procedures. One is searching in the program's own set-up: You are presented with an open form where you write what you are looking for (author, keyword, subject) and what library or database to look for it in. Then the program contacts that catalogue, transmits the question, and presents the answers ("hits") for you in a list. From this, you can select those titles that look interesting and store ("import") the bibliographic data, the reference, to your local bibliography. That is the way that EndNote and Papers work.

Endnote Search

List searches in EndNote: at the bottom the Search form, above the results returned from the library.

The other way is to use the web page that each library or database provides. Then you search in Google or JStor in the same way you would in Explorer or Safari. But when you have done the search and got a list of titles in your browser window, the program lets you select a few of them, and then extracts the bibliographic information from the entry and stores to your bibliography. This is how Zotero and Mendeley work. Sente and BookEnds have both options, you search in "list mode" in some catalogues and in "web mode" in others.

Web, sente

Web search in Sente: In front of each title there is a small red dot, click on it to fetch the data into your bibliography.

The program must in both cases cooperate with the catalogue at the other end to identify each piece of information so it goes in its right place. They are therefore limited to the catalogues that they "understand". So, we must first evaluate what kind of catalogues and databases are useful for us humanists and social scientists. If you look at the demos and how the programs present themselves, you would think that PubMed and chemistry and acetotes are all that exist. Happily, that is not the case. But which of the sources useful for us can each of these programs actually get information from?

As for books, the most complete catalogue around is without doubt WorldCat. It is also covered in almost all programs, only Papers lack it (in EndNote you may be asked for a password you do not have, your university library may or may not provide it). Other important libraries for us are the School of Oriental and African Studies in London, Northwestern University (the Africana library), the Halle-Tübingen unified catalogue and the Bibliothèque de France. Coverage here is a bit more sketchy, only EndNote and Zotero has all of those.

In searching for electronic journal articles, Google Scholar is the most important source for information today. All programs except EndNote cover this. The same is true for JStor. However, as these databases do not have subject or keyword searches, looking for articles on a more general topic will often lead to quite unwieldy results with several thousand hits. For such survey searches, more structured databases are often better suited. In our field of Middle Eastern studies, Index Islamicus is probably the most central such structured source, but it is not well covered by our programs, only Zotero is able to extract bibliographic data from the Index (depending, of course, on your campus library subscribing to it). You can also find useful information on our type of subjects, although far from complete and dependent on your topic, in such bases as Historical Abstracts, ProQuest, HighWire, Project Muse  and Web of Knowledge. Only the last two, which also have wide coverage of the natural sciences, are universally supported, for the others, Sente and Zotero are better than the other four programs. The same applies for those journal sites that let you search online content (here represented by IJMES and Die Welt des Islams); Sente, Zotero, and in part Mendeley stand above the others.  

Sources available in different programs

EndNote Sente BookEnds Papers Zotero Mendeley
WorldCat L W W


Northwestern L L

Halle L

Library of Congress L L,W W
U of Chicago L L L
B de France L

--Journal databases --
Google Scholar
W W (list)
Muse L L,W L
[bug] W

Index Islamicus

Historical Abstracts


Web of Knowledge L W L L W W

Publishers: IJMES



Die Welt des Islams



L: Searches in list format; W: Web searches; (W): Only picks up from individual item pages, not lists.

The picture presented by the table is quite clear, Zotero is by far the most versatile when it comes to the number of relevant sources to search, with Sente the closest second. EndNote, however, has an impressive collection of "connections", you can search over 4,000 libraries across the world. Sente and BookEnds are a bit more modest with 300 and 200 libraries respectively. EndNote is however weak on journal databases, while Papers cannot search in any library catalogue, it is for our purposes only useful for searches in Google Scholar and JStor, the most complete but also the least structured sources.

B: Creating and reading your own electronic library

When we have found the references we are to use, we thus want to work with them in various ways. Most programs allow you to make personal notes to the references, and to sort them in "groups" or mark them in different ways. The big ones, Sente and BookEnds give you many options in how to structure your references while you work, the others are less expansive.

Your bibliography will of course include references to both books and articles, and of the latter some will be available on paper and others on-screen. How many of each will depend on your university library, but a quick survey I made on my own campus showed that perhaps one out of three articles written on my topic was available on-screen, a surprisingly good result for a field such as Islamic studies.

So, we would want to create an "electronic library" of those articles we can access online. We can of course read them in Safari or Explorer by looking up each title in JStor or wherever, or read the downloaded PDF in Acrobat, but how easy is it for the programs to link the item in their bibliography to its electronic text?

Papers, Sente, BookEnds and Zotero are most useful here, in falling order. The most straightforward program is without a doubt Papers. When I search for "waqf Syria" in e.g. JStor, Papers presents me with a list of the references found there. If I click on a title, the article appears immediately on-screen under its own tab. If I quit Papers and re-open it later, the search result is still there, as are the articles I opened in their respective tabs. I do not have to import the references into my bibliography if I do not want to keep them. But if I do, I can also click on "PDF" and it is downloaded and linked to the item in my list, so I can later read it when I am off-line. In Papers, there is otherwise almost no difference between keeping and reading online content by locally stored PDFs or on the remote database.


Papers: To the left the list of references, to the right the article under its own tab.

You can also in Sente and BookEnds link references to online full-text or downloaded PDFs, but it is a bit more cumbersome. Sente will also remember the search results, but depends more on your downloading stuff you want to read as PDFs, and you have most often to go through several operations before this PDF is linked to the bibliography item (it depends a bit on the PDF as well as the source reference). BookEnds can only read online articles from one source, Google Scholar (which also inlcludes JStor articles and other third-party databases). You may in some cases be able to download a PDF to a bibliography item, but the result is sparser than in the other two programs. Both here in Sente and BookEnds as well as in Zotero, the solution is often to download the PDF separately, then import this into the program as a new item, and then link this item to the original reference. But when you have done this, you can in the same manner unite the online text/PDF and bibliographic data in your electronic library.

Sente search
Sente: The reference list above, the  PDF below, item info to the right, and structure on the left.

The same is partly true for old PDFs you may have lying around your hard disk or acquire in other ways. All five programs (EndNote apart) have the possibility to "import" these and link to references in your bibliography. How easy this is depends, again, on the PDF. Some are automatically linked to the reference because they have a hidden "ID code". For others, the program lets you copy some words from the PDF (the article's title, e.g.) and searches Google Scholar for a match. If the article is registered there, its bibliographic information is imported and linked to the PDF. This works well in Papers, Sente and BookEnds. In Zotero, you have to go through two steps; look up the reference and import to your library, and then link the PDF to this new reference "manually" by drag-and-drop; a few more clicks for each PDF, but doable if you only have a small number of them to handle.

BookEnds: Setup deceptively similar to that of Sente.

Since Zotero is not a separate program but an integrated part of Firefox, it looks a bit different from the others. Clicking on the "Z" icon in Firefox brings up the Zotero database where you will find your reference library. Clicking on an item there will take you to the website where you found the reference, and you can read the full text there. If the reference is linked to a local PDF on your hard drive, you will be sent to Acrobat and can read the PDF in a separate window.

The Zotero panel at the bottom of a Firefox window. Online articles display in the regular Firefox window, PDFs in Acrobat.

Zotero makes it easy to coordinate your bibliography if you work on several computers (campus / home). The reference library is by default linked to an account you set up on their web server and is immediately synchronized there. If you go to another PC with Firefox and Zotero installed, you can just log into your account and your library is available as you left it. (All users get 100MB free, if you want more room, you have to pay.) Sente and BookEnds can also synchronize libraries on several Macs. Mendeley is primarily a web site, you get an account of 500 MB for free, and can log onto your library from any web browser, of from the separate Mendeley Desktop application.

C: Writing footnotes without having to write them.

The last part of our work is to write out what we have found, be it in a master's thesis or a professional article. This part was probably what actually inspired the creation of such reference programs that we discuss; natural scientists submitted the same manuscript to many different journals in turn, and each journal required the author to rewrite the references and bibliographies according to the specific rules of that journal. Thus EndNote was created to take care of this reformatting for the authors.

All our programs take on this heritage, and cooperate with the word processors where we write our papers, mainly Microsoft Word. The typical procedure is that when we want to refer to a source in our paper, we select the relevant title in or from the reference program, which then sends the title to Word correctly formatted in the journal system we have chosen. It also creates a full bibliography of cited literature at the end of the paper and allows us later, with a simple menu choice, to change the reference format if we are to submit the paper to a different journal.

This not only saves us typing, but also gives us the confidence that the data is correctly entered without any of our typos or other errors. But we also then leave the control over the appearance of the reference to the program. In our kind of work, the journals are probably not as strict as the naturalists, but we still have our traditions, so it is of some importance how the programs format the references in our paper and how they work together with our word processor. 

The most commonly used word processor is of course Microsoft Word, and this shows in our programs. Papers has a minimal export to Word 2008 option, but with few alternatives. All the others add an extra "citation" menu to Word (Sente only in Word 2004, Mendeley did not work for me). In this menu you choose "Add citation", which lets you find the reference in the reference program, and also manipulate the references in different ways. Some insert fully formatted citations, others use temporary codes that are formatted after your choice at the end. This last procedure can also be used in word processors the program does not support directly (each program supports some word processors apart from Word, thus Nisus with BookEnds, Pages with EndNote, and so on).

The same similarity goes for the variation and control over reference formats. All four support hundreds of different formats for all kinds of strange journals (from 250 in BookEnds to 1,000 in Sente, 1,500 in Zotero and 3,500 in EndNote), most so similar that you will have great problems telling them apart. All four also allow you to fiddle with the formats and create your own, even if that does require some patience and is in some cases not far from real programming. (Sente, Zotero and Mendeley can share a format setup).

In sum: Which program is best?

There are two programs I cannot really find serious faults with. One is free, simple, but probably best adapted to smaller projects with less than a couple of hundred references: Zotero.

The other, Sente, does require some effort to master fully, but is the most flexible allround program. It is only slightly less extensive in searching than Zotero; it is OK, although not as straightforward as Papers in handling full text and PDFs, and its integration with word processors is also OK. And it is probably the best at organizing references in your research work.

I am also a firm believer in Papers, which really shows how valuable such academic programs can be in your research. I will still go to this whenever I need to quickly read up on the available online literature for a specific question. For many, however, its integration with different word processors may not be as flexible as they may want.

BookEnds is a solid product with many powerful functions in handling references, although you may have to dig a bit into the menus to find them. It is superior to Sente in many ways, and not far behind in others. But it is still a bit weaker at working with online text for our purposes, which gives Sente a small advantage overall. However, if online text is of less importance to you, BookEnds can give EndNote a run for its money at half the price.

Many will probably fall back to the most established solution, EndNote, which is also thoroughly solid after many years of development; I have a database of 12,000 titles that EndNote handles with ease. But it is not aimed at the broader tasks including reading full text as the other programs, and it is also less versatile than both BookEnds and Sente in manipulating the data in its library. It is more a pure bibliography program aimed at the tasks that were important a decade ago than a fully rounded reference program. And for individuals it costs twice as much as any of the other programs here.

Of the others, Mendely is not yet fully functional in its present form, and Zotero is better on this level of free programs. There are also many other web-based "reference sites" for Mac and PC, but (with one exception, RefWorks) they lack the functions we have been looking at in the dedicated reference programs, and none are very relevant in our field.

The PC folk have several other programs to choose from, but few that cover the full range of tasks discussed, thus the Windows version of Papers is probably a good choice for those who want such a range. Zotero may still seem to be the best option for smaller projects, but PC users who want to try out more powerful reference programs (and in particular those who master German) can try out the free versions of the Swiss Citavi, the German Bibliographix, and perhaps also the slightly more expensive Biblioscape.

Knut S. Vikør
July 2010
Price and availability information updated February 2014

>> More details on the programs discussed.


Research Group in Middle Eastern and African Studies, AHKR
  Phone + 47 55 58 26 47, fax + 47 55 58 98 91, e-mail:
Postal address: AHKR, University of Bergen. PO Box 7800 Bergen, Norway
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