Using Zotero at HSU

Zotero is a free program designed to help you collect and manage references identified during your research and to cite these references within papers and other manuscripts as you compose. It also allows you to attach notes, PDFs of documents, images and other files to each reference. It is available as a plug-in for the Firefox browser or as a standalone program with plug-ins for the Google Chrome, Safari and Firefox browers. For a quick overview see the Zotero Tour screencast.

Guides and Tutorials Installing Zotero and Word Processor Plugins Zotero Setup Managing References Collecting References Adding Attachments, Links and Snapshots to References Writing with Zotero

Accessing Zotero from Multiple Locations Backing up Zotero Collaborating using Zotero Groups Zotero Essentials (on two pages)

Guides and Tutorials

Within this guide there are specific links to Zotero help pages as well as additional guidance Tips for installing and using Zotero.

• Zotero Quick Start Guide video (Zotero)
• Screencast Tutorials video (Zotero)
• Zotero Tutorial video (California State University, Pomona)
• Zotero (Emory University. Pitts Theological Library)
• Zotero (Georgia State University Library)
• Zotero (University of Michigan Library)
• Zotero: A Guide for Librarians, Researchers and Educators (Pucket) 2011 (ref PN 171 F56 P83 2011)

Installing Zotero and Word Processor Plugins

As a first step you will need to download and install Zotero and associated plugins. This takes less than 5 minutes.

1. Download and install either Zotero for Firefox or Zotero Standalone from Zotero. With Zotero Standalone you will also need to download browser connectors for Google Chrome, Safari or Firefox. With Zotero for Firefox the Zotero icon will appear in the lower left corner of the browser after restarting Firefox. Just click this icon to open Zotero.
2. Download and install the word processor plugin for MS Word or OpenOffice. Zotero does not have plugins for other word processors, e.g., Macintosh Papers, but you can use the Quick Copy option discussed below to add references to these other word processors. (Tip: In MS Word for Windows 2007 and above the "Zotero Bibliographic Management" plugin will appear under the "Add-Ins" tab after installation.)
   
   

Zotero Setup

Below are Zotero setups you should consider. Open Zotero and click the Action Menu (gear icon) on the main Zotero toolbar.

• Syncing -- Select Preferences > Sync >. This creates a mirror image of 1) your "reference library" on Zotero's remote cloud server and 2) your attached files on a different Zotero server. Syncing allows you to work from any computer where you can install Zotero, including campus computer labs. There are two separate steps in syncing. (See Zotero Syncing for additional information.)


1. Zotero Sync Server -- This creates a mirror image of your "reference library" that includes citation information, notes, tags and links. To sync this information first Register with Zotero if you have not already done so. After your account is established you can enter your user name and password on the sync preferences page. There are no limits on the number of references that can synced. (Tip: after registering you will be sent a confirming email to which you will need to respond. If you don't find it check your spam folder.)
   
   
   


2. File Syncing -- This creates a mirror image on a remote cloud server of files that you attach to your references--PDFs of articles, web page snapshots, images and similar files. While you can store an unlimited number of attachments on your own computer without syncing there are storage limits on the number of files that you can sync remotely for free. There are currently two options for file syncing if you wish to implement this:
• Zotero Server -- this is the default option. Zotero will sync and store up to 300 MB of attachments for free. This is approximately 300 PDF files at 1 MB each. Other attachments may take less space. See Zotero File Storage for storage fees above 300 MB. (Tip: you can check your storage quota status by logging into your Zotero account and navigating to Settings > Storage. You will be sent email when your storage exceeds 300 MB.)
• WebDAV Server -- HSU provides a network folder with WebDAV capability for remote file storage. Storage capacity varies depending on whether you are student, staff or faculty. Some remote cloud servers also support the WebDAV standard for file syncing. Both CloudMe (3 GB of free storage space) and Box.net (5 GB of free storage space) have been successfully used locally.
  
  

  To set up a WebDAV server for Zotero file syncing:

  
  
  


1. Establish an account on a remote "cloud" server that supports WebDAV or use your existing HSU network folder.
2. Create a "zotero" folder on the server. (Be sure zotero is all lower case)
3. Within Zotero change "Sync attachment files in my library using ..." from "Zotero" to "WebDAV".
4. Enter the WebDAV server URL:
   
   HSU network folder-- https://users.humboldt.edu/folders/your HSU username
   CloudMe -- https://webdav.cloudme.com/your username/xios/Documents (assuming you put the "zotero" folder in the Documents folder)
   Box.net -- https://www.box.net/dav
   
5. Enter your account username and password.
6. Test the connection by clicking "Verify Server" and then click "OK"
• Styles -- Select Preferences > Export > and then choose your default citation style, e.g., APA, from the "Default Output Format" drop-down menu. This will be the default style when you use the Quick Copy option for adding references to a paper you are composing. If you don't see the citation style you need go to Preferences > Cite > Styles and click on Get additional styles... to add the style you need from the hundreds of available styles.
• Find It @ HSU -- Select Preferences > Advanced > and in the resolver box type <http://sfx.calstate.edu:9003/humboldt>. Anytime you want to locate a book, journal article, or other item available at the HSU Library, just click the "Locate" button in the right panel of Zotero.
• Proxies -- Select Preferences > Proxies >. For off-campus access to licensed databases the HSU Library uses a proxy server to validate authorized users. In Zotero you should be able to make complete use of the proxies feature without making any preference changes. By default, the first time you use a licensed database from off-campus Zotero will ask if you want to store the HSU Library proxy address. Subsequently Zotero should route you through the proxy automatically. (See Zotero Proxies for additional information.)
  
  If a URL address stored in Zotero is not allowing you to access a reference or its full text in a HSU Library database try appending the HSU Library proxy address -- http://ezproxy.humboldt.edu/login?url= -- to the front to the URL address, e.g., http://ezproxy.humboldt.edu/login?url=http://www.bioone.org/doi/pdf/10.3170/2008-7-18530.
• Enable PDF indexing (Optional) -- Select Preferences > Search > and click "Check for Installers". Zotero will download and install a small plugin. This will make the fulltext of all PDF files you attach fully searchable in the search box on the Zotero toolbar and enable the Retrieve Metadata for PDF feature.
• Automatically Attach Associated PDFs (Optional) -- Select Preferences > General > and check "Automatically attach associated PDFs and other files with saving items ". The default has this option unchecked. PDFs and other associated files will be automatically downloaded and attached to a reference you are capturing if you check this. The other option is to leave unchecked and selectively attach files as described below.
• Automatically Tag Items with Keywords and Subject Headings (Optional) -- Select Preferences > General > . The default configuration has this checked. As you save references from databases and catalogs Zotero will extract "tags" from subject indexing fields. You will have to evaluate whether you want to have these tags automatically extracted. For further information see tags below.

Managing References

Zotero is organized into three adjustable panels, similar to an iTunes interface, that displays "collections" you have established, references in each collection and details about each reference.

• Left panel -- organizes your references into 1) a master "My Library" collection containing all your references and 2) any collections and sub-collections that you create. Use the "New Collection " icon to make a new collection. (For additional information see Zotero Collections.)
  
  The lower part of this panel displays subject tags that have been assigned to each reference, either manually by you or automatically as you capture references. These tags are useful for categorizing your references. By default the tag selector shows tags for references displayed in the middle panel. Check "Display all Tags in This Library" to display tags for all your references in Zotero. Using the tag selector you can:
  • Click on a tag to filter to only matching references. You can repeat this process to continue refining your results, e.g. first click on the "bleaching" tag, and then with the resulting list of references click on the "reefs" tag to further refine matching references.
  • Use the search box to find matching tags.
  • Globally delete or rename a tag by right-clicking (ctrl-clicking on the Mac) on it.
  • Add a tag to a reference by dragging and dropping the reference on top of a tag.
  • Use the multi-colored icon to disable all tags created by automatic download.
• Middle panel -- As you highlight a collection in the left panel the middle panel displays all references assigned to that collection. "My Library" by default displays all the references you have added to Zotero. In the middle panel you can:
  • Drag and drop one or more references in a displayed collection to a different collection in the left panel.
  • Use the small table icon to choose what fields to display, e.g. creator, title, etc.
  • Click the top of each field column to sort your references by that field. (Tip: Using "Date Added" as the active sort field allows you to easily find the most recently added references.
  • Highlight all collections that contain the same reference by holding down the “Option” key on Macs or the “Control” key on Windows.
• Right panel -- displays information on each reference displayed in the middle panel.
  • Locate button -- click the "Locate" button to find out if the HSU Library has access to a journal article or book reference if you have setup this feature above.
  • Info tab -- contains detailed bibliographic information on each reference. The fields will vary by item type.
  • Notes tab -- you can add personal notes about a reference; cut and paste text excerpts; add book reviews, etc. There is no limit on how many notes you can add. On the main Zotero toolbar you can also use the "New Note" icon to add a note to a reference. (For additional information see Zotero Notes.) Zotero also includes other specialized note taking options:
    • Attach notes to snapshots of web pages --. When viewing the snapshot of a web page you will see in the upper left corner of the web page an "annotation bar" for creating "sticky notes" of text you highlight. (For further information see Archive the Web.)
    • Create notes from highlighted web page text-- Highlight quotable text from a web page that you want, right-click (ctrl-click on the Mac) to open a pop-up menu, and select “Create Zotero Item and Note from Selection”. This will create a new reference in your Zotero library with the selected text as an attached note.
  • Tags tab -- these are subject keywords that 1) you create by clicking the "add" button in this tab or 2) subject keywords that are automatically downloaded from indexing fields in databases. Tags are useful for categorizing your references. They are fully searchable and also display in the left panel. (For further information see Zotero Tags.) (Tip: See setup above for turning off the automatic download feature.)
  • Related tab -- you can associate other references with the reference you are viewing. (For further information see Zotero Related.)

There are several options for adding references to Zotero. All references you add go into My Library and also into the collection that you highlight in Zotero's left panel. (Tip: Remember you must be using the Firefox browser to collect references if you are using Zotero for Firefox.)

• References from Databases and Library Catalogs -- When displaying a list of references in a database or library catalog (e.g., the HSU Library Catalog, Google Scholar and other library databases), look for an icon to the left of the star in the URL address box-- a yellow folder when there are multiple references on a page; or a sheet of paper or book icon when there is a single reference on the page. Clicking on this icon allows you to add one or more references to Zotero. (Note: In the Safari browser the icons are to the left of the address bar.) There are also Android and iPhone apps for smart phones.
  
  
  
  
  
  

  If you don't see one of the above icons Zotero is not "sensing" the references in the database you are using which means the database is probably not on the list of Compatible Sites.

  If you don't see the above icons in a database you can do one of the following to get references into Zotero:

  • Manually enter the reference information as described below.
  • Find a fulltext PDF of the reference and use the PDF technique described below.
  • Copy, paste and search an ISBN, DOI, or PMID unique number.
    
  • Export one or more references from the database in a compatible format and import them into Zotero.

  It is important that you review each reference as it is added to Zotero since having complete and correct bibliographic information is critical as you write with Zotero. Zotero translators developed for each database may not map all bibliographic information into the correct fields. You should check that the proper "Item Type" format is being used and that bibliographic information is present in key fields. Editing can often be done by cutting and pasting pertinent information into the correct fields. (Tip: If the reference is mapped to the wrong "Item Type"format, e.g. "Journal Article" rather than "Book Section", just click on "Item Type" and select the most appropriate format.)

  
• Web Pages -- You can capture bibliographic information on a web page and a snapshot of the page by doing either of the following:
  1. Using the "Create New Item from Current Page" icon on the main Zotero toolbar.
  2. Grabbing the web page icon at the far left of the URL address box and dragging and dropping it into the Zotero middle panel.
     
  (Tip: Zotero only pulls in information available on the web page, e.g., if the author is not listed, you will have to enter the author(s) manually in the right panel.)
• PDFs --There are several options for adding PDFs to Zotero:
  
  
  1. If you are viewing a PDF on a web site you can drag and drop it into Zotero's middle panel by grabbing the icon at the far left of the URL address box. (Tip: the PDF icon in the address bar may vary depending on the site. If the site will not drag and drop the PDF into Zotero you will need to save the PDF as a file on your computer and use option 2 below.)
     
     
     
     
  2. If you already have PDF files stored on your computer of articles or other publications you have collected you can open a directory window on your computer; select one or more files; and then drag and drop them into Zotero's middle panel. You will need to have both your Zotero window and your directory window open.
     
     
  
  
  3. Using the "New Item" icon on the main Zotero toolbar you can choose the "Store Copy of File..." option and select the PDF file you want to add.
  
  

  After adding a PDF file using any of these methods you can try to create a complete bibliographic reference for the file by right-clicking (ctrl-click on the Mac) on the PDF in the middle panel and choosing "Retrieve Metadata for PDF". Zotero will search Google Scholar and other sources to find a matching reference and retrieve the appropriate bibiographic information. If Google Scholar does not find matching bibliographic information you will need to either find and capture the matching reference in another database or manually create a reference. In either case you can then drag and drop the PDF file on top of the reference you create. (Note: To use the "Retrieve Metadata for PDF" feature you must first enable full text indexing of PDFs.) (See Zotero Retrieve PDF Metadata for additional information.)

• Unique Identifier – You can add a reference to Zotero if you have an unique number for the reference--ISBN (for books), DOI (for articles) or PMID (for articles). Use the "Add Item by Identifier" icon on the main Zotero toolbar. Zotero will search the web and automatically add the reference.
  
• Reference Import – You can import references stored in other reference managers, e.g., EndNote. In the other reference manager choose the RIS format for exporting references. In Zotero click the Action Menu icon and choose "Import..."
• Manual Input -- Use the "New Item" icon on the main Zotero toolbar to manually enter a new reference. Choose from over 30 item formats.

Adding Attachments, Links and Snapshots to References

You can attach PDFs, snapshots of web pages, images and other similar files to references stored in Zotero. As discussed in File Syncing above you can store an unlimited number of attachments on your computer but there are storage limits on the number of files that you can sync remotely. (For further information see Adding Files to your Zotero Library.) (Tip: You can just link to these files which does not consume storage space but does run the danger of "link rot.")

You can use one of the following three options to add attachments and links:

• Drag and drop web pages and PDFs on top of a reference in the middle panel as discussed above.
• Click on the "New Child Attachment" icon on the main Zotero toolbar. You will be presented with four options:
  • Attach Snapshot of Current Page -- this could be a PDF,web page or image. (Tip: If a PDF opens in new window you will need to open Zotero in that new window and repeat this attachment command.)
  • Attach Link to Current Page
  • Attach Stored Copy of File... -- e.g., this could be a PDF of an article that you already have stored on your computer.
  • Attach Link to File...
• Right-click (ctrl-click on the Mac) on a reference in the middle panel and choose "Add Attachment". You will be presented with the same four options.

Writing with Zotero

As you compose papers there are several options for creating in-text citations, footnotes, endnotes and bibliographies from your Zotero library of references.

• MS Word and OpenOffice Plugins -- These word processor plugins provide the most robust option for creating in-text citations, footnotes, endnotes, and bibliographies. (For further information see Using the Zotero Word Processor Plugins.)



• Insert Citation -- Click this button to add a new in-text citation, footnote or endnote to your document.
  1. If this is the first time you have added a reference to your current document a "Document Preferences" window will open. Choose the citation style you need. If you don't see the citation style you need go to the Action Menu> Preferences > Cite > Styles and click  Get additional styles... to add the style you need from the hundreds of available styles.
  2. An "Add/Edit Citation" window will appear. Select the reference you want to cite in your document.
     • You can select multiple references by clicking the "Multiple Sources…" button and adding references to the right panel.
     • You can add page numbers as well as prefixes and suffixes using the boxes at the bottom of the window, if your citation style requires it.
  3. To preview your in-text reference, click the "Show Editor…" button. You can edit the reference in this box if necessary.
  4. Click OK. A properly formated in-text reference, footnote or endnote will appear in your document.
• Edit Citation -- Use this button to edit an in-text citation, footnote or endnote you inserted in a document.
  1. Click on the in-text reference you would like to edit.
  2. Click the "Edit Citation" button.
  3. The "Add/Edit Citation" window will appear with your in-text reference highlighted.
  4. To edit your in-text reference click the "Show Editor" button and edit it in this box.
  5. Click OK when you are done. (Warning: A reference you edit using the word processor does not change the reference in your Zotero library.)
• Insert Bibliography --Click this button to generate a bibliography from all references you have cited in your document. The bibliography will be inserted at your cursor location in the document. As you add new in-text references they will be automatically added to the bibliography.
• Edit Bibliography -- Click this button to edit the bibliography you inserted in a document.
  1. The "Edit Bibliography" window will appear containing your Zotero library on the left and the references currently in your bibliography on the right.
  2. To add a reference to your bibliography, click on the reference you would like to add and append it to the list in the right panel.
  3. To edit a reference in your bibliography, click on the reference in the right panel and edit it in the edit box.
  4. Click OK when you are done.
• Zotero Refresh -- Click this button if you made any changes to your Zotero Library since inserting a reference or generating a bibliography in a document. Any reference changes you made will be incorporated in your document.
• Zotero Set Document Preferences -- Click this button to change the citation style of the references in the document you are composing. A window will appear allowing you to change citation styles.
• Zotero Remove Codes --  Click this button to remove Zotero's codes from a Word document in case you are working with a collaborator who is using a different citation management tool or if a journal editor requires that codes be removed. (Tip: Since this action cannot be reversed is best practice is to save two copies, one with the codes and one with codes removed.)
• Quick Copy -- You can create in-text citations, footnotes, endnotes and bibliographies using a drag and drop method. The citation style format used is the default style you set above. You can change this if needed. Unfortunately, using this method there is no way to universally change the citation style once references are inserted into your document. (For further information see Creating Bibliographies .) (Tip: You will need to have windows open on your computer for both your word processor and Zotero.)
  • To create in-text citations or footnotes highlight one or more references in the middle panel of Zotero, hold down the Shift key and drag and drop them into your document.
  • To create a bibliography or "Literature Cited" highlight one or more references in the middle panel of Zotero, then drag and drop them into your text document. If you drag and drop more than one reference Zotero will automatically create an alphabetized bibliography.

  You can also use Zotero's shortcut keys to perform these same drag and drop operations. (Tip: See Action Menu > Preferences > Shortcut Keys if you want to change these shortcut keys.)

  • Ctrl+Alt+a will copy one or more highlighted references as an in-text citation or footnote to your clipboard.
  • Ctrl+Alt+c will copy one or more highlighted references as a bibliography to your clipboard.
  • Ctrl+Alt+v will paste the copied references from your clipboard into your document.
• Create a Bibliography -- You can easily create a standalone bibliography using the methodology below or the Quick Copy option above. (For further information see Creating Bibliographies.)
  1. Highlight one or more references in the Zotero middle panel.
  2. Right-click (ctrl-click on the Mac) and choose “Create Bibliography from Selected Item(s)” to open the "Create Bibliography" window.
  3. Choose the citation style you would like to use, if different than the default style you set above.
  4. Choose the option for printing or saving your bibliography.
     • Save as RTF -- for adding to a Word document
     • Save as HTML -- for adding to a web page
     • Copy to Clipboard
     • Print
  5. Click Ok

Accessing Zotero from Multiple Locations

Using the following options you can access your Zotero database from any computer or mobile device where you can install Zotero for Firefox, Zotero Standalone or one of the third party applications for mobile devices:

• Syncing-- As described in the Setup section above syncing will create a mirror image on remote servers of 1) your Zotero reference library and 2) your attached files. Install Zotero in a campus lab computer or other computer and bring in your synced reference library and attached files by going into Preferences > Sync and enter your Zotero username, password and server location of your attached files.
  
• Zotero Export/Import -- Click the Zotero Action Menu , choose "Export Library..." on the drop-down menu and save the "Zotero RDF" file on your USB drive, your network folder or other drive. You have the option of also exporting your attached files. On another computer where you have installed Zotero, click the Action Menu , choose "Import...", and import the Zotero RDF file that you saved. You can repeat this process as you move from computer to computer.
• Portable Firefox -- Use Portable Firefox to carry Zotero with you and launch it from any computer. You can copy your reference library and attached files using Zotero's Export/Import option; or you can set up syncing for both your reference library and attached files. You can install Portable Firefox and Zotero on a USB drive, portable hard drive or your network folder. (For futher information see Using Portable Firefox on a USB Drive.) (Tip: If you experience slow reponse time when using Portable Firefox see Improving Firefox Portable's Performance.)

Backing Up Zotero

On the Zotero Action menu choose Preferences > Advanced > and click the "Show Data Directory" button to find the location of the Zotero folder on your computer. From the Zotero folder copy both the "zotero.sqlite" file that contains your bibliographic information, notes and tags; and the "Storage" folder that contains your attached files. (Warning: Before you copy these files be sure that Firefox or Zotero Standalone are closed, otherwise your data may be damaged.) (For further information see Backing up and Restoring your Zotero Library.)

Collaborating Using Zotero Groups

The Groups feature in Zotero allows you to share references with other Zotero users. It is an excellent way to set up a shared library for a class project or other collaborative research project. Groups can be set up to be public or private with various levels of editing priviledges for group members. For additional information see Creating Groups.

To create a Group Library:

1. Log into your Zotero account by clicking on the "New Group" icon at the top of the left panel in Zotero. Another option is to login directly to your Zotero account, click on the "Groups" tab and then, on the resulting Zotero Groups page, click the "Create a New Group" button.
2. On the "Create a New Group" page create your public or private new group and click the "Create Group" button.
3. On the "Group Settings" page add information about your group, invite other Zotero members to join the group and set permissions for group members by using the "Group", "Members" and "Library" tabs.
   
4. Make sure you have your reference library synced with the Zotero Sync Server. This will also sync Group Libraries that you "own". If you decide to also sync your attached files in the Group Library they must be synced to the Zotero server. As the Group Library "owner" attached files added by other group members are counted against your storage quota on this Zotero server.

To manage a Group Library that you "own" login to your account at Zotero.org and click the "Groups" tab.

After creating a Group Library or accepting an invitation to join one, you will see two sections in your Zotero left panel--your "My Library" list of collections which you have created and a "Group Libraries" list of libraries to which you belong. To add references to a Group Library where you have editing priviledges: Drag an existing reference from any of your My Library collections and drop it on top of a Group Library or collection within a Group Library. To add a new reference highlight a Group Library or collection within a Group Library and use any of the Collecting References options above. References in Group Libraries are maintained independently from your My Library references. Any new references you add directly to a Group Library or any changes you make to a reference in a Group Library will not be reflected in your My Library unless you drag and drop the new or modified reference into your My Library.

If you want to share your reference library without joining a group or creating a group with only you as a member you can just login into your Zotero account, click on "Settings", and then the "Privacy" tab. Checking "Publish Entire Library" will make all items in your library viewable by anyone under the "People" tab at zotero.org. Your reference library will be publically viewable at www.zotero.org/your username/items.