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Zotero is free bibliographic software that allows you to easily collect, annotate, and cite bibliographic data. It runs as a plugin for the excellent Firefox browser, which means that you have the web at your fingertips as kyou manage information, and also that it can run on any operating system that Firefox can run on (that is, all of them). It is also open-source, which means that anyone can improve it and develop for it. It is a great alternative to more expensive software, and also has a number of advantages over its more wealthy brethren.

This is a guide to using Zotero effectively in biblical studies, though using Zotero effectively in biblical studies is usually similar to using Zotero effectively in other fields. I will add a couple of remarks along the way, however, especially for those of us in theological fields.

Step 1: Installing Zotero

Your first step in using Zotero is getting everything installed. If you are not already running Firefox (an excellent open-source web-browser), then shame on you. Install that by following the easy steps here.

Installing Zotero

Open up Firefox and browse to the Zotero site (here). Click on “try out 2.0 beta.” It might seem at first that 1.0 is the better option, but there are SO many new features with 2.0 that it’s really the way to go. I use Zotero daily and have had no major issues with 2.0. The rest of the guide will assume that you are running that version.

Once you click, Firefox will do the rest—download, install, and ask you to restart. Restart Firfox and you are ready to go.

The Zotero website is also a great place for guides and videos, so browse around a bit.

Step 2: Move Your Zotero Directory

The VERY FIRST thing you need to do with your new Zotero setup is change the location where it stores all its data. By default Zotero puts all the information you want it to remember in the same place where all your Firefox settings are stored. This is terrible. It’s like storing your valuables in something that looks exactly like a trash can—someone will eventually forget it’s not a trashcan and throw it away. You’ll either upgrade Firefox, or Windows, or something, and then it will be gone (and backup software may not know to back up this directory). So let’s move it. (Note: if you already have data in your Zotero directory, back it up first using Zotero’s export command. When you move your directory in Zotero it will seem like your data is gone, but it isn’t. It’s still in the old directory. Either move it manually or import the data you just exported).

Create a New Folder. Open up your file browser and go to a directory where you keep important data. Something like “My Documents” in Windows—you know, where you save documents. Hopefully it is also a directory that gets backed-up by your backup software. In that directory create a new (empty) directory called “Zotero.” (For an always-on backup solution that super-secures your data, you may want to put Zotero in a Dropbox directory; see “Securing Zotero” below).

zotero window
data directory

Tell Zotero what to do. Now in Firefox you will now notice an icon in the bottom right corner that says “Zotero” (labeled “1″ in the picture to the right). Click on that to get your Zotero window up. Then look for a gear icon (“2″ in the picture), which you should click, and select “Preferences.” We’re going straight to the “advanced” tab (“1″ in the second picture), then clicking the “Custom” option (2), and then clicking “choose” (3). Select the directory you created and click ”

Step 3: Get Some Data

Alrighty, now that we know our data isn’t going anywhere, let’s get some actual data. You can add books and articles and what not manually, but that is SO 2008. One of the great things about Zotero is that it sits in your web browser, so you can use the web to get data for you. A number of popular sites (Amazon, Google books, etc) support Zotero data. Chances are your school library does as well. Let’s start with Amazon, though. Go here. Now look at the address bar. There should be a little folder icon there. If you click on that, it will bring up all the books on the current page, from which you can select which to add to Zotero. Now go here. Just one book this time, and the Zotero icon in the address bar is now a book. Click on it and it will add the bibliographic data to your database.

A lot of blogs also support Zotero, including this one. See the icon in the address bar when you go to nerdlets.org? That means you can add blog entries straight into your Zotero database.

zotero bar

Play around for a bit. Try Google books. Or the library of congress. Or your favorite library site. Also notice the various icons in the middle section of your Zotero interface. These all allow you to add a variety of things to Zotero, from webpage snapshots, to manual data for books that are not on your preferred website, to files on your computer.

Step 4: Using Zotero with your Word Processor

Install Word Processor Plugins. Now that you have some data you probably want to use it. Zotero has a number of plugins that integrate with your favorite word processor. You can find out more about those here, and the install page is here. Make sure you scroll down for the 2.0 plugins; the 1.0 plugins will not work. The plugins install just like Zotero itself, as browser add-ins. The plugins update automatically, and automatically install all the needed files into your word-processor. Easy. There is one for Microsoft Word (here) and for OpenOffice (here).

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Format your citations in the correct style. Now Zotero will work with your word processor, adding data into footnotes as needed, and all in the proper format. Speaking of proper format, you may want to add bibliographic styles not included by default. For theology or church history you’ll probably want to use what Zotero calls “Chicago Manual of Style (Full Note with Bibliography),” which is included by default. For biblical studies you’ll probably want the SBL style, which is not installed by default, but fear not! Because Zotero is open source anyone can create their own style, and a number of users have done just that. Most likely your preferred style is out there somewhere. Let’s install the SBL Style as an example. Go to Zotero preferences and click on the “Styles” tab. Then click on “Get additional styles…” This will take you to a webpage with a whole list of styles; just click “install” to add it to Zotero. The SBL style guide is in that list, or you can install that by clicking here.

Back in the preferences dialog click on the “Export” tab. Select the style you prefer in the “Default Output Format” box.

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Cite, my friend, cite! Now open up your favorite word processor. I’m using OpenOffice, but the process is the same for Word. You should notice a new toolbar. If you don’t see it, go to “View” and “Toolbars” and look for one that says Zotero. Once you find it, hover over each button to see what they do.

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Let’s assume you want to add a citation that is SBL compliant. Create a footnote. Now add a citation (“1″ in the picture). If this is the first Zotero citation you have added a window will pop up asking about how you want to format this document. Make sure SBL is selected and click OK. You will notice that a field has been added to your footnote (2), and a new dialog window has popped up (3). Now search for a citation you want to add, either by browsing through folders or by using the search dialog (4). Select your citation (5), and add page numbers (6). You can also choose “Multiple Citations” if necessary (7). When you’re done click OK (8).

Once you are done with your document you can automatically generate a bibliography (3rd button). You can edit citations with the second button. Have fun!

Step 5: Helpful Hints and Best Practices

Zotero is pretty powerful software, but you have probably already encountered some problems. Here are a few tips on how to use Zotero effectively.

  1. Use folders sparingly, use tags generously. Folders are a great way of organizing information, provided you don’t have too many and the hierarchy doesn’t go too deep. I create folders for each major topic that I am studying. Every paper I write or class I teach gets a folder. This allows me to have a kind of record of research. But if you get to specific this can get unwieldy. Instead, use tags for the specifics. Tags are search-able and non-hierarchical. You can add as many as you want and it won’t junk up your database.
  2. Every paper your write gets its own folder. Again, this allows you to retain a record of research. Anything you cite in a paper goes in that folder.
  3. Stick to a standardized naming scheme for authors and publishers. One of the major problems with Zotero is that it does not store author and publisher names in a hierarchy. So if you add Calvin’s Institutes under “Calvin, J.” and then later one of his commentaries under “Calvin, John,” Zotero will think it is two different authors, which will mess up your bibliography. Rather than making lots of piddly changes down the road, stick to a standardized naming scheme now. Make it work with whatever bibliographic style you are using. For authors I stick to last name and 1-2 initials. For publishers I always exclude the words “Publishing” or “Press” unless its a university (“Oxford University Press”). If the book contains a number of articles, I always have a separate entry for the book as a whole, then “copies” of that entry for various articles. Find a system that works for you and stick with it.
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  5. Always type out quotes you want to use in Zotero first, then copy and paste into your article. I like to do research “on the fly”; that is, I like to research as I write, and write as I research. This means that my papers are always in process. It also could mean that my research is less easily reusable. In order to find that quote I need to find that paper in which I typed it out. To avoid this, type out all quotes as notes in Zotero. Right click on the book from which the quote is taken and select “Add note.” On the top line type two or so words that identify the topic of the quotes (think: “how will I search for this in two years”) and the page number. Then type out the quote (Zotero has a handy “quote” style), then any comments you might have. Notes like this will always be associated with their respective books, no matter where you drag and drop that book, and notes can be tagged like anything else.

Step 7: Syncing Zotero

The latest version of Zotero allows you to sync multiple databases, and also sync online. To set that up, follow the directions here. That will allow you to sync your data. To sync files—like all those PDFs you have saved—things get more complicated, but all is explained in the aforementioned link.

Please remember, though, that SYNC does not mean BACKUP. Sync means that everything you do is synced between multiple computers. If you do something idiotic, your idiocy will then be replicated 10 fold. A mirror doesn’t make your face any less dirty. You still need a backup, so keep reading.

Step 8: Securing your Life’s Work

I now use Zotero as my bibliographic database, as a document library for all my PDFs, as a web bookmarking database, a recipe book, an interview manager, and a job-search tool. If it fails, I’m sunk. You need to back up your Zotero database. How do you do that?

Zotero is just a collection of files. Place your Zotero directory somewhere that gets backed up every day, like your My Documents folder (see above for how to do this). Better yet, use Dropbox. Dropbox is an application that you can install that creates a folder, and then automatically backs-up and syncs any data you put into it. Dropbox is free, works on any OS, and provides you with 2gb of storage. You can install it by going here. Once you have your dropbox folder up and running, move your Zotero folder into it.

You should also have a local backup. That is, every night your computer should back up all important data onto a separate hard disk. By an external harddrive (newegg.com) and backup your data to it daily (using something like the free version of syncback.

Conclusion

When your research is searchable, re-usable, and secure, life is good.

 
Image representing Google as depicted in Crunc...
Image via CrunchBase

OCR is the technology used to turn an image of text into plain (editable, search-able) text. If you’re like me (i.e., a nerd) you probably have a pile of scanned journal articles and books and such meticulously sorted on your hard drive (PDFs for example). You can read them and print them, but you can’t search them or edit them. Wouldn’t it be nice if you could?

Well, there are a number of free options on the web, but they all have their problems. Google has some of the best OCR technology out there–they recently acquired CAPTCHA to make it even better–and they have apparently been rolling this out into Google Docs. The Google Docs version is not as wonderful as you might like, but it works on high-res documents. Read about how to turn your images into text here.

Update: I was not able to get this to work with PDFs, surprisingly. The web-app only accepts PNG, JPEG, or GIF images right now. That is unfortunate, and I assume will be “corrected” in the future. Has anyone tried this on an image yet?

 

PDFAs a follow-up to my previous post, here is an excellent review of some more great PDF conversion and manipulation tools.

Also I am happy to report that I have had good success converting PDF images to plain text with OCR terminal, so give it a try!

 

PDF

Paper isn’t going away, of course, but having all your documents on such an antiquated medium is often less than ideal. There is at least one major disadvantage to paper: searching is much more difficult. That’s just one of the reasons PDFs are so popular! Anybody can open a PDF file for free, search it for the information they need, and store it for later browsing without any significant impact on harddrive space.

Not all PDFs are Created Equal

But perhaps you don’t know that there are two kinds of PDFs. The best kind of PDF is the kind generated by computer software from a text file. These PDFs are searchable because the text is preserved.

But many PDFs are generated from images rather than text. If you create a PDF by scanning a document in a photocopier or image scanner then the result is usually an image-based PDF, rather than a text-based PDF. This means that your PDF will not be searchable because you computer does not have access to the underlying text, even though you can read it just fine.

Searching any PDF with OCR

So how can you overcome this difficulty? By using Optical Recognition (OCR) software. OCR tools look at the image and try to convert it to plain text, which can then be searched, copy-and-pasted, and indexed just like any other document (I worked with several such software systems during my undergraduate degree).

There are several good free OCR tools available for converting PDF documents to plain text. The best out there is that used by Google, which powers its Google Books services. The problem here is that you don’t have direct access to their software. You need to go fishing and wait for Google to bite. You can find instructions for doing that here.

If you want more control over your software, and you probably do, check out this list of handy PDF tools, many of which are OCR converters. There is also a lot of great software on this list.

Finally a new service, PDF-to-word, currently in invite-only Beta, accurately converts PDF images to MS Word documents. You might have to just bookmark this one since it’s not yet available to the public, but you might find an invite code online, such as here.

Conclusions

One remaining limitation of all this is that the OCR software listed above is optimized for English. Problems often occur with German and French, and don’t even bother trying it on Greek or Hebrew. Nevertheless the advantages for English scanned images are worth investing some time experimenting with one of these systems, especially if you have a lot of scanned PDF documents.

 

Digitalization is the way of the future, and with the recent deal between authors and Google books, that future may in fact be bright for all parties.

In the course of my dissertation work I often have to track down primary sources, and when those sources are particularly rare it becomes difficult. Or it used to be difficult. Now I Google it.

Exhibit A: This morning I needed to track down some homilies of Hebrews by Chrysostom. Being a dedicated Greek Geek, I wanted the “original,” which means I need Patrologia Graeca volume 63. Where am I going to get it? Google Books of course–they have the entire series digitalized and downloadable for your convenience. This is what sites like Google Books and archive.org are made for—primary sources in the open domain.

Image view of v63 of Patrologia Graeca

Image view of v63 of Patrologia Graeca

Here are some screenshots for you. The first is the standard scan, downloadable as a pdf. The second is Google’s attempt at a little OCR, which obviously is struggling with both the Greek and the Latin. This is to be expected. I did a little natural language processing way-back-when; a lot of OCR software will “guess” the letters based not only on shape, but on the software’s (limited) understanding of the language, which for Greek and Hebrews is probably NULL. Still, I was impressed, and this is a harbinger of great things to come.

OCR view of v63 of Patrologia Graeca

OCR view of v63 of Patrologia Graeca

So what primary sources have you been trying to track down? How do you use research tools like these? Post in the comments!

 

In addition to a whole host of great features, you can use Zotero to annotate Web pages that you have saved as snapshots.

Now you can annotate you favorite web pages

Now you can annotate you favorite web pages

Zotero allows you to take a snapshot of any web page for later viewing. If I then view that snapshot (all the files for which are stored on your hard drive, and therefore are in principle modifiable), a little toolbar pops up. The options are primitive, but helpful. I can highlight text or add little sticky-style notes to the page. The toolbar pops up for stored PDFs as well, but the functionality does not seem to work here yet–just web pages for now. Perhaps later releases will add PDF support.

You can download Zotero Sync preview here. Though this is the version I recommend, be  careful, it is still pre-Beta. If you want the stable release, go here.

If you have not yet set up Zotero, follow this guide.

Update: Apparently this functionality has been available for awhile now, and I just failed to notice. Ooops. This post has been modified to take that into account.

 

The folks over at BibleWorks have announced the release of the eighth iteration of their software product. The announcement includes an extensive list of upgrades and new features. Read the whole announcement. Here are some highlights:

New Features

The biggest advances appear to be in the area of searching and analysis (rather than text handling or diagramming, though there are a few additions here as well). They have added a new phrase matching tool, as well as some other search improvements:

Over lunch in mid-2007, we asked ourselves, “How could we find all verses which are similar to each other?” Out of this discussion came the Phrase Matching Tool and Related Verses Tool. The new Phrase Matching Tool takes your current verse and finds all verses containing similar phrases. The new Related Verses Tool finds all verses using some of the same words from the current verse.

They are also adding in an “External Resource Manager” that lats you organize and collect your massive storehouse of documents, PDFs, and images into Bibleworks’s main interface. Personally I use Zotero for this, but some might like this feature.

New Databases

Two additional modern grammars are now available in the suite: Waltke/O’Connor for Hebrew and Wallace for Greek. The complete Early Church Fathers is also available (only the Apostolic Fathers are available in BW 7).More importantly, Bibleworks will finally include the Greek Text of the OT Pseudepigrapha (BW 7 included the Apocrypha, but not the Pseudepigrapha), which is a much needed addition. The Targum of the Psalms will also be added, though only in English.

Thoughts

There are a couple of features that would motivate me to upgrade from BibleWorks 7, and only one of them appears to be included: the OT Pseudopigrapha. I would really like to see Bibleworks include a robust semantic diagramming module (Logos has one). And I wish BDAG was bundled with the rest of the suite (though that is Chicago’s fault). BibleWorks also needs to seriously improve it’s map functionality (the map module is excessively sluggish on my computer, and my computer is rarely excessively sluggish). The most serious need in my opinion is full-fledged Unicode support. They claimed this would be available in Bibleworks 7, and while oen can certainly export text in Unicode, it is not native built it. ASCII is dead as a doornail. There should be no ASCII text visible in BibleWorks, especially since it attempts to handle so many languages.

I am optimistic, but need a couple of more features explained before I am ready to purchase. Stay tuned for updates!

Purchase

Bibleworks 8 can be purchased by visiting the Bibleworks site. Special upgrade prices are available for those with Bibleworks 6 or Bibleworks 7. Bibleworks will not ship out until mid-December, however, so you still have some time.

 

The following is a set of links that will be useful for those trying to set up Zotero on their computers. (Not sure what Zotero is or why you would want it? Check out their site, and don’t miss the demo video).

Initial Setup

  1. Firefox Web Browser. Zotero runs as a plugin within this excellent browser.
  2. The Zotero Plugin. There are two options here. Pick one of the following:
    • Zotero 2.0 Beta (recommended). This is the latest release. It is Beta software, which means you may experience bugs. But I have been using this release for sometime and have not experienced any problems. There are several advantages of this release: online syncing (though see below), rich-text editor, more functionality. Create an account online to store your Zotero database here.
    • Zotero Version 1.0. This is the “safe” option, but you loose some functionality, and I have not had any problems with the “cutting-edge” version above. This version will be upgraded soon, so whichever option you pick will be fine in the long term.

Learning Zotero

  1. Demo Video
  2. Tour of Features
  3. Quick Start Guide
  4. Dan Cohen’s Blog often has good Zotero-related news
  5. As does my blog.

Extending Zotero

  1. Plugins for Microsoft Word or OpenOffice
    • If you chose the Beta version, go here and follow the instructions.
    • This now runs as a browser plugin, which installs the Word Processor integration utility automatically. Smooth and easy.

    • If you downloaded the regular 1.0 version, go here and follow the instructions.
  2. Customized Bibliography Styles. Zotero comes with a wide variety of default styles, including Chicago. But if there is a specific style that you need, check out this link to see if it is available. Researchers in Biblical Studies might be particularly interested in the SBL Style. Just click and Zotero will install everything for you.

Securing Zotero

  1. Use the Sync Preview release (above). It will securely back up and sync all your information and notes online, which can be accessed here. It does not backup stored files or PDFs, however; only text.
  2. If you are computer savvy, you can set up a WebDAV server to store and sync your entire Zotero database. This is like option (1) but also stores PDFs and other files. Check out this forum for suggestions.
  3. Use Dropbox. This is the best possible solution. Install Dropbox and then open your Zotero preferences dialog. Go to the Advanced tab, then place your Zotero database in a custom location: your “My Dropbox” folder. Now anytime a change is made the Dropbox software will upload it in real-time. You can also use this to sync your Zotero database accross multiple computers, and it includes all your files (movies, PDFs, images, etc). Your data is encrypted on Dropbox’s servers, so you don’t have to worry about security concerns.
  • Update: I should mention one issue I have had with the Dropbox solution. Dropbox cannot save open files, which means it will not upload or download your Zotero database until you close Firefox. If you are syncing your Zotero database across two computers, be aware of this limitation. Make sure you close Firefox on both computers, and that Dropbox has finished syncing all the data, before you switch workstations. Dropbox does save conflicting copies of files, so your data should ultimately be safe, but it may be a lot of work to recover it.

Update: This post was modified from the original on Sept. 17 2009 to bring it in line with the current status of the Zotero project.

 

One handy OpenOffice extension out there is Sun’s PDF Import Extension. Their description:

The PDF Import Extension allows modifying existing PDF files for which the original source files do not exist anymore. PDF documents are imported in Draw and Impress to preserve the layout and to allow basic editing. It is the perfect solution for changing dates, numbers or small portions of text.

There is another and even more important feature in this plugin, however. Most people don’t follow my advice and download OpenOffice, which means that I often have to export my files into PDFs. I do this for Impress presentations for my classes, for example. Some students, however, do use OpenOffice. Why should they be punished for their progressive attitude and superior brain power? Shouldn’t they get the originals? Well now they can:

The PDF Import extension will also enable the PDF export into a hybrid PDF file, which is a PDF with the embedded source file as ODF. Hybrid PDF files will be opened in StarOffice as an ODF file without any layout differences, while users without StarOffice can open the PDF part of the hybrid file.

It works perfectly, in my experience. It works so well, in fact, I wish I could just save my documents as Hybrid PDFs.

You can download the plugin here. You will need OpenOffice 3.0 for this to work.

 

There are a variety of method of diagramming available to the student of the Bible, but very few tools to actually assist in creating such diagrams. Well BibleArc does just thought, providing scholars and preachers alike with an easy way to begin constructing their own diagrams. You can view my hastily created diagram to the left to get a taste.

The website includes instructions, a brief description of what all the symbols mean, and a plethora of videos and tutorials. You can diagram in a variety of English translations, or in Greek (complete with parsings). Improvements to the user interface (which is still a little cumbersome), as well as a repository of user-created diagrams, are apparently on the way. You can save diagrams to their site (with a user name and password), or export them as PDF documents.

Read more here

If you’re interest in the theory behind thought-flow diagrams, or with other types of diagrams (each with their own advantages and disadvantages), Cotterell’s Linguistics and Biblical Interpretation is an excellent starter resource.

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