• The Zotero window contains your entire research collection, including:
  
• bibliographic references,
• whole documents and files,
• your notes,
  
• and other items like images and snapshots of web pages.
  
  
• Zotero runs in your Firefox web browser, which must be open in order for you to access your research collection. You do not have to be online, however, to use Zotero; features such as notes and search will work perfectly well offline, although obviously you will not be able to view some online items in your collection or to acquire other online materials.
  
  
• To open your Zotero window, click the Zotero icon in the bottom right corner of your browser window.
  

Fig. 1:  Open Zotero by clicking the logo at the bottom right of Firefox.

This brings up a pane with all of your citations, collections, and notes.

• Close Zotero by clicking on the X icon in the upper right of the Zotero window or by clicking on the logo again. You can open or close the Zotero window at any time from within Firefox. The Zotero window does not have to be open for you to do “quick saves” of material you want to add to your research collection.
• To resize your Zotero window, click and drag the bar at the top of the window.  If you have trouble resizing the window, make sure that the tag selector () is turned off.

The Three Columns of the Zotero Window Interface

My Library

The left column contains several icons that allow you to perform important actions.  Select: to add a new collection Tag Selector: to manage your tags (see below) Actions: to import/export collections, change Zotero preferences, and view information about Zotero (including version and credits) to select your Zotero library, which holds every item you have added to select a collection (a subset of your library); can be further divided into sub-collections

--> ACTIVITY 2: CREATING A NEW COLLECTION

You can create as many collections as you like to store & manage your projects. An item can be stored in multiple collections.  Every item resides in My Library, which is like a master collection.

To create a collection:

1. Hit the new collection icon () in the left panel and enter a title, such as "Rice history."
   
2. You should see a folder with your title appear in the left pane; it will be highlighted.  We'll be putting stuff there in a moment.
   
3. You can create subcollections by right clicking on a collection and choosing "New Subcollection"
   

Middle Column: Folder View--Items in a Collection

Right column: Item-level view & Note-taking Window

How Zotero Works

One of Zotero's most convenient features is its ability to sense when you are looking at an item (or items) on a web page. For instance, if you are looking at the record for a book on an online library catalog, Zotero’s book icon will appear in Firefox’s location bar (at the top of the browser window, where the current web address, or URL, appears), like so:

Simply click on the book icon and Zotero will save all of the citation information about that book into your library and whatever collection is currently selected. (The Zotero window does not have to be open for this to work.)  If the item is an article, the article icon () will appear.

Zotero senses information through site translators, which interact with web-based information sources. Zotero's translators should work with most library catalogs, some popular websites such as Amazon and the New York Times, and many databases, including EBSCOhost, InfoTrac, JSTOR, OCLC FirstSearch, ProQuest, and Google Scholar. Just look for the icon in the location/address bar. (For more information or for some sites to try out, see the Compatible Sites list at http://www.zotero.org/translators/.) The Zotero team will be adding support for additional sites over time, which will be automatically added to your Zotero installation.

Automatically Saving Items

To save an item:

1. Select the folder you want to save the reference to (Zotero will default to the folder that you were last using)
   
2. Click on the icon (book, article, etc) in the address bar to automatically download it.
   
3. Voila!  Check to make sure that the reference and associated files (such as a PDF of article) were downloaded properly and make sure that all of the informationwas captured properly.  If files are associated with the item, a plus sign will appear to the left of the item title.

1. Type http://www.jstor.org/ into your web browser. 
   
2. In the search box, enter buckyball "rice university."
3. Select one of the articles in the results list.
4. Note how a page icon appears in the address bar.  Click on the icon to download the record.
   
5. Inspect the record.  If it isn't already saved in the folder that you just created, move it there.
6. With many resources--including JSTOR--Zotero also allows you to download the accompanying PDF.  To enable this feature, click on the Actions Menu (the gear icon in Zotero, ) select Preferences from the pull-down menu, and check "Automatically attach associated PDFs...."   Now we should be able to get the PDFs associated with a record.  Test this by downloading another article.

Saving Groups of Items

Zotero makes saving groups of items easy.  If you are looking at a group of items (e.g., a list of search results from Google Scholar), a folder will appear. You can download all of the results or select which to download.

To save groups of items:
1. If you are on a results list in a compatible database or catalog, a folder icon () will appear in your address bar. Click on this folder.
2. A box will pop up with a list of all of the records on this page. Check the items you would like to import into your library.
3. After you click OK, your items will appear in your library.

-->ACTIVITY 4: DOWNLOADING MULTIPLE ITEMS

1. Return to the results of your buckyball search
   

2. See that yellow folder icon that appears in the address bar at the top of the web page?  Click it.  This will allow you to download multiple bibliographic records at one time.
   

3. You should now see a list of the articles listed on the results page.  Select a few, then hit OK.

4. The bibliographic information (or "metadata") about those three articles should now be visible in Zotero, at the bottom of the web page. Review each record to confirm its accuracy by clicking on it in the middle pane and viewing the detailed information in the right hand pane.  

Saving to a Collection

If you are currently working in a specific collection (that is, a collection folder is highlighted in the left column), the references will be copied to that location as well as your overall library.

A Word of Caution: As already noted, Zotero is not always able to capture all of the bibliographic information associated with a work properly.  For instance, I've noticed that records for items in Amazon typically lack publication place.  Check the bibliographic record after you've downloaded it, since you may need to add a few details manually.

Note: You can now download citations into Zotero through Fondren's Open URL Resolver, which allows you to go from a bibliographic record in a database straight to the full text.  For instance, if you are searching for "baboon stress sapolsky" in Scopus (http://www.scopus.com/scopus/home.url ), you'll see an icon that says "Full Text Rice" underneath each bibliographic record.  Click that link.  If the full text is available, you should see the Zotero icon for article in the address bar.  If not, or if you just want to grab the citation, select Get more full-text options for your citation from the top of the screen.  At the bottom of the page, you should see Export Citation to Zotero.  Click that link. A page should load with information about the article.  Click the Zotero icon in the address bar to capture the bibliographic record.

When you open Word, you should now see this row of icons () in your Microsoft Word toolbar. These four buttons allow you to manage references in your Microsoft Word documents.

If you do not see them, try checking the “Templates and Add-ins” window. Select “Tools” from the dropdown menu at the top of your screen, pull down to “Templates and Add-ins,” and make sure that the box for Zotero.dot is checked. You may need to lower the security settings for macros as well.

When you would like to cite something from your collection,

• Click the first button, “Zotero Insert Citation” ().
  
• If this is the first citation you have added to the document, the Document Preferences window will open. Chose the bibliographic format you would like to use from the list and click OK.

Once you have chosen a format, the “Add Citation” window will pop up. Sort through your collection in this window and select the item you would like to cite. You can add the specific page number in the text box at the bottom of the window.

• When you click “OK,” you should now see a properly formatted citation in your document.
• To generate a bibliography from all the items you have referenced, click the “Zotero Insert Bibliography” button ()
• The third button, “Zotero Refresh” () updates your references to reflect any changes in your Zotero collection.  () will open the Document Preferences window again, allowing you to change your bibliographic style on the fly.

Most researchers don’t just read and gather sources; they take notes about them. We’ve all got little scribbles in the margins of books, on post-its, and on notepads (real and virtual). Zotero makes it easy to keep all those annotations, jots, and notes all in one place--better yet, it makes them all searchable. With the recent addition of the ‘grab a chunk of text off the screen’ capability, that process has become even easier.

As a scholarly workbench, Zotero reflects a basic understanding of the researcher as a both a reader and a writer.  Rather than having to switch back and forth between a Word document and your Web browser, you can take your notes directly in Zotero, whether a stand-alone note or a note associated with a particular source.

Adding a stand-alone note

Five icons appear at the top of the middle column in the Zotero pane. The yellow square with a plus sign is the “standalone note” icon. Click this button to create a new note and then type your note. 

1. Hit the add note button () to make a note. Just as with citations, you can place the note into as many collections as you like.
   
2. Compose your note in the notetaking pane on the right, or click "Edit in a separate window" to open up a new window for notes.  You can resize this window by clicking and dragging the corner.
3. Type away.  Your note will be saved automatically. 
   
4. Your note becomes part of your library/collection and is searchable.
5. To make your note easier to find, you can add tags or relationships (links to other items in Zotero). 

Hint: the first few words of your note will become the title that shows up in your collection, so you may want to use something distinct and memorable so that you can more easily find that note later.  For instance, if you want your notes to be sequential, begin the first one with "1," the second with "2," etc.  If you want to group your notes, you can create a sub-collection just for stand-alone notes.

-->ACTIVITY 13:  ADDING NOTES ABOUT AN ITEM

You can also take notes about individual items, so that the note or note series is associated with the item (e.g. a book or article). To add a note about an item:

1. Add a source to your library or find an existing record.
   
2. Either right-click on the title (ctrl-click on a Mac) in the middle column, choosing “add note” from the pop-up menu, or click on the note tab in the right column and select “Add.
3. Type your note.   As with stand-alone notes, you can click on "Edit note in a separate window" to do just that.  The notes are saved as you type.
   
4. Click the "X" in the right corner to close the note.

Deleting a Note Clicking on the minus sign that appears next to a note in the right column will delete it, as will right-clicking on the note icon in the middle column and then selecting “Delete Selected Item from Library”.

Because new research often incorporates pre-existing work, Zotero makes it easy for you to copy quotable material from a web-based source into your notes, thus saving you from having to transcribe text. 

1. Highlight the text of a web page.
   
2. Right-click (ctrl-click on the Mac) to open a pop-up menu, and select “Create Zotero Note from Selection” (Figures 4 and 5).
   
3. An item level record will automatically be created for the source with which the chunk of text is associated, so you can keep track of where the quotation is from. Note, though, that the Zotero translator does not appear to work with this approach, so you will only capture the title of the page, the URL, and the date of the download.

Tagging allows you to categorize items (and thus find them more easily) by attaching your own descriptive words (or tags) to them. Once you've tagged items, you can sift through your collections based on your own descriptions.

1. To add a tag to an item, simply select an item in the center pane, then select the tags tab in the right column and hit the button.
   
2. Type your tag (it can be more than one word) and hit enter.  For instance, you may wish to add "nanotechnology" or "Rice history" to selected resources.
   
3. Once you have added the tag, you will see it has also been added to the tag selector box in the left column. You will need to hit "Add" for each tag that you wish to add.
4. Zotero will autocomplete tags based on tags already created.  You may notice that some tags have already been created--Zotero automatically downloads any keywords associated with an item.
   
   

Located in the left-hand corner of the Zotero pane, the tag selector adds an additional layer of information management to complement the collection and search systems.

1. Clicking on the tag selector icon () turns it on and off.
   
2. By clicking on any of the tags, you can filter the items within your Library, collections and saved searches by as many or as few tags as you like.
   
3. You can toggle the tag selector in and out of view by clicking the the show/hide tag selector button ( ).The tag selector updates its inventory from tags you place on individual items in your Library.
   
   
   Tag Selector Box
   
   
4. The tag selector defaults to showing all the tags on items in the current folder. When you click on a given tag, the center pane updates to display only the items with that tag. You can select multiple tags to further focus the results in the center pane or click on a tag again to deselect it.
   
5. To quickly find a tag in the list, type part of its name in the Filter box; selected tags not matching what you type remain selected, allowing you to quickly find and select multiple items. Click the “Deselect all” button to return the center pane to displaying all the items in the selected folder.

6. You can add tag to other items by dragging them onto tag in tag selector box.

7. From the tag selector box you can also control the tags globally. By right-clicking on a tag (or Control-clicking on the Mac), you can choose to rename a tag across all items or delete it from all of the records it is attached to.
   

You can also assign tags to multiple items at once by dragging items from the items pane onto tags in the tag selector. This is where the “Display all tags” checkbox comes in handy: while the tag selector normally only shows you tags on items in the current view, clicking “Display all tags” causes tags not assigned to currently visible items to appear in gray. You can then drag items onto one of the gray tags to assign it to those items. 

Note that some items that you save will come with tags already attached. If Zotero detects classification information or other metadata as part of a catalog record, it will, in some cases, extract that information as a tag. For example, OPAC (Online Public Access Catalog) record subject headings become Zotero tags. You can manage these automatic tags in the same way that you manage the tags you add manually.

Note also that the tag selector box takes up a lot of room.  If you find that you can't drag your Zotero window down to reduce its height, click the tag selector to de-select it.

XII. Importing Items

Importing PDFs

Zotero makes it easy to create bibliographic records for PDFs of articles that you've downloaded. Drag the PDF file into the center pane of the Zotero interface. Right click (or control click on a Mac) on the file, then select "Retrieve Metadata for PDF."  Zotero will then search Google Scholar for the article and automatically download the metadata if it makes a match.  Note that this process isn't always successful--sometimes Zotero doesn't find the article in Google Scholar, and sometimes the bibliographic information is incomplete.  Still, it beats having to type in all of the information yourself.

Importing from other bibliographic software

To import a file from a program such as EndNote or from a database that uses the RIS bibliographic format:

1. Export your citations from the other program and save as a RIS file. For instance, in Newsbank you should:

1. Mark all of the results that you want to save
2. Click "Saved Articles" in the left sidebar.
3. Select the articles to export.
   
4. Choose "Export Articles" 
   
5. A file called "Export" will then be downloaded to wherever your downloads typically appear (e.g., the desktop).
   

2. Open your Zotero Window
3. Click on the Actions icon () menu and select Import. A dialog box will appear.
4. Locate your saved file (it will probably have the RIS extension) and click on open to bring it into Zotero.

Note: You can set up Zotero so that it will automatically download RIS files.  Go to Actions > Preferences and make sure that "Use Zotero to download RIS/Refer files" is checked.  Unfortunately, this doesn't always work; sometimes you will need to import RIS files manually, as described above.

Zotero also supports importing Zotero RDF (useful if you want to import a collection from another instance of Zotero), MODS (Metadata Object Description Schema), BibTeX, Refer/BibIX, and Unqualified Dublin Core RDF.

The best way to back up your Zotero library is to close Firefox and then copy the Zotero folder, stored in a subdirectory of your Firefox profile directory, to an external drive. The Zotero folder holds your database and all the related files (images, PDFs, webpages, etc.) and can usually be found in these locations:

On a Mac:
/Users/<username>/Library/Application Support/Firefox/Profiles/<randomstring>/zotero

On Windows 2000/XP:
C:\Documents and Settings\<username>\ApplicationData\Mozilla\Firefox\Profiles\<randomstring>\zotero

On Windows Vista:
C:\users\<User Name>AppData\Roaming\Mozilla\Firefox\Profiles\<randomstring>\zotero

By backing up this directory you will back up your entire Zotero library. If something dramatic happens (hard drive melts, computer is stolen, etc.), you can simply place your archived backup Zotero folder into your new Firefox profile. When you open Firefox, your Zotero library will be there waiting for you. As with all important data, it is a good idea to back up your Zotero library frequently.

XIV. Current Limitations and Future Plans: Zotero Sync and Beyond

• Zotero can be sluggish; if you've got a lot of data in Zotero, it can take approx. 15-30 seconds for each record to be downloaded, locking up your web browser.   I sometimes check my email while Zotero is doing its thing.
  
• Not every database and catalog format is supported--yet.
• Zotero doesn't always capture complete bibliographic information, so you need to check the data you've collected.
• A few tasks aren't intuitive, but the software is generally simple and elegant.  You can do a lot by right clicking (CTRL clicking on a Mac) on items and collections. 

The benefits of such networking and the emphasis on semantic entities like books, articles, and letters opens up new possibilities for scholarly communication. A group of historians interested in a topic lacking a chapter in the Guide to Historical Literature will be able to build a bibliography of important works in their field collaboratively, which then could be shared with students. Scholars will be able to track more easily publications of interest in their fields and hear of archival documents newly discovered or scanned by other Zotero users, based on tags, recommendations, and the holdings of personal collections. Historians from around the globe will be able to combine virtually to annotate a primary source that has just been digitized and placed online. Most intriguingly, this interaction of people, tools, and resources—what we might call an "ecology of scholarship" (which undoubtedly will include software other than Zotero)—perhaps will lead to the discovery of new knowledge by aggregating and analyzing our shared wisdom. (Cohen 2007)

Other Options for Bibliographic Software

• EndNote/ EndNoteWeb: Costs $100+.  Very powerful, but can be dauntingly complex.  Possibly better on Word integration. 
  
• Refworks: Costs aprrox. $100.  Web-based. Reputedly not as intuitive as Zotero.
  
• Connotea: Free, online, developed by Nature and aimed at scientists.  Especially good for collaboration; weak on notetaking, integration with word, automatic downloading of bibliographic information.
• CiteULike: Nice online bibliographic tool, primarily used (right now) by scientists.  No Word integration.
• See http://digitalresearchtools.pbworks.com/Citation+Management+Toolsfor more tools
  

XV. Further Information

• Zotero maintains an active forum at http://forums.zotero.org/categories/ I've found a lot of useful information by searching the forum.
  
• The Zotero team offers great support; if you run into trouble, you can go to Actions > Report Errors to report a problem and get help or email the Zotero team directly.  For instance, my database became corrupted, but I was able to repair it quickly by using the online database repair tool at http://www.zotero.org/utils/dbfix /
  
• Zotero Documentation, http://www.zotero.org/documentation/
• Zotero has developed a number of short, clear screencasts that demonstrate how to use the software: http://www.zotero.org/support/screencast_tutorials
• Daniel J. Cohen, "Zotero: Social and Semantic  Computing for Historical Scholarship." Perspectives (May 2007). http://www.historians.org/Perspectives/issues/2007/0705/0705tec2.cfm
• CiteFest: Zotero Wins citation software contest, http://citefest.pbwiki.com/
  
• Scott McLemee, "Mark of Zotero," Inside Higher Ed (Sept. 26, 2007). http://www.insidehighered.com/views/2007/09/26/mclemee
• "Managing Your Citations with Zotero," http://www.lib.umich.edu/exploratory/pdfs/Ztero.pdf