Using Zotero for notes, transcription, and writing papers

For the purposes of the seminar, and, hopefully for all your future research and writing, you are expected to:

1) acquire a USB flash drive of  2 or more gigabytes

2) PC users are to install the version of  the Firefox Browser on the USB drive.  I  recommend installing the full menu of Portableapps applications and creating an autorun.inf file that automatically starts the sequence of note taking programs when you insert the USB drive into your computer.  How to create the inf file will be addressed separately in seminar.  Once the portableapps menu and firefox have been installed, go to the options menu in firefox and make  about:blank your default home page

MAC users are to download and install the MAC version of the most recent Firefox Browser.

3) with the installed Firefox browser on the flash drive, go to and install the Zotero note taking program for your operating system (PC, MAC, Linux, etc.).  You may have to download the Zotero xpi file (right click on the download button and save the xpi file to a 'software' directory on your flash drive.  If you have to download the xpi file to install Zotero, do so by finding the file with your browser and double clicking on the xpi file.

4) once Zotero has been installed in your Fire Fox Browser (the name should appear in the lower right corner of your Firefox browser screen),  click on Zotero and go the gear symbol on the row of choices.  Go to Preferences and then to Advanced.  Select Custom and go to the root of your flash drive.  Make a new folder labeled with zotero, your initials, and 'wih' which stands for the seminar, What is History?.   My folder, for example, is labeled zotero_ecp_usb98, because I wanted to make the file unique and distinct from other zotero files on other usb drives and my Zotero files encompass more than the WIH seminar.   Note that in labeling files and folders on the USB drive or the hard drive of the computer, never use spaces.  Always use underscores. except in designating sequential files where hyphens are used.  This eases cross platform communication problems and programming for retrieval.  After making the new folder, click o.k.  You will then have to restart Firefox.  From that point on, all of your zotero files will be located in the new folder you created on your flash drive.  Note that you can use spaces and other symbols in creating the virtual folders in Zotero and in the file descriptions of Zotero.  It is only in folders and file names created on the drives associated with the PC that spaces and special characters must be avoided.

Note:  from this point on, instructions for installing software are for PC users only.  There should be similar MAC based software that can be used in the same manner as is discussed below, but students who use a MAC should consult with the instructor to determine what works best.

5) go to through the portableapps menu, download and install KOMPOZER.  At the menu go to options then to 'get more apps ...'.  Download and install KOMPOZER following the instructions under options again, for installing software or simply install from the downloaded executable in the software folder..

6) go to the IRFAN web site and download/install both the IRFAN software and the plug ins.  I would recommend downloading both the software and the plugins to your software directory and then install both from the directory, being sure to install the software on your flash drive.

You are now ready to begin taking notes, composing papers, and transcribing documents

The key to successful use of Zotero is to read through the help sections on the web site and to organize your note taking, writing, and transcription within the foldered environment of Zotero (the far left column of Zotero).   There you create folders and sub folders that are maintained in the ZOTERO sql database.  Always be sure to back up those files either by periodically exporting  all files to another location, or copying the whole of your zotero directory to another drive/location.

There are three elements to the Zotero window:

  1. the left hand column where you create virtual folders/collections and virtual sub folders/sub collections. The contents of these folders/collections when highlighted are displayed in the middle column

  2. the middle column where you import files from the web, create your own files, and label/index your files.

  3. the right hand column which indicates the location of the highlighted file in the middle column and where you keep/compose notes relating to the highlighted file.

Across the top of the Zotero window are the function buttons with which you create your folders/collections, download files from the web, reference files on your flash and hard drives, and otherwise create and manage your notes.

As an example of how Zotero might be used for note taking, transcription, editing and composition, we use the John White Webster murder trial (1850).   This trial in Boston appeared as a daily record transmitted by telegraph to newspapers all over the country.  There is one official transcript (Bemis) and several unofficial ones, two of which were provided by the newspapers who had reporters present, and one by a promoter of a new approach to trial transcripts which he called "phonographic" (Stone). These have been converted to searchable pdfs and comprise the printed primary sources. The official transcript is also available on line, searchable, from Google Books.  In addition there are the defendants and defense attorney's notes that have survived and have been imaged for transcription, editing, and interpretation at the web site.  The secondary writings of historians include two books that also have been  converted to searchable pdfs (for personal educational purposes and uses only).  

The printed primary and secondary sources are assumed to be on the flash drive in separate folders.  Links to them in Zotero are made to them in folders/collections created for that purpose. After creatiing a folder/collection in the left column and highlighting it, At the plus sign (green) button in zotero, use the link to ... function to create working links to the printed primary and secondary sources on your flash drive.

Begin using the Zotero 'system' by testing how to initiate composition.   Create a folder/collection in the left hand column of Zotero for the transcription/editing assignment.  Go to your home page (it should be blank if you used about:blank as your home page). Consider this your 'white board' for composition. Copy the page to you new folder/collection using the camera icon at the top of the window iin zotero.  Label the downloaded page with something like "transcription assignment" and click on the page.  It will still be blank.   Use the show file tab in the right column of Zotero.  When the window appears, right click on 'blank.html'  and use the open with function to open the file with KOMPOZER or Open Office Writer Portable.  You may have to browse the files on your flash drive to find the software the first time (found in the portableapps directory on your flash drive).

Edit the page, placing in it any information useful for the oversight of the transcription assignment (the assignment from the schedule can be scraped/copied and placed on the page). Save the file and return to Zotero's menu.  You have successfully created your first composition in Zotero and saved it to a folder managed by Zotero.

Transcription assignments:

1) find your transcription assignments on the seminar schedule.  For the purposes of demonstration see: and the following page.

2) the pages are transcribed  using [] to indicate anything that is not on the original page, including expansion of contractions, footnotes, etc. The transcript can be viewed without a user name and password, but to edit any pages you will need to log in with a user name and password obtained from the instructor,  or using the email option on the site to request one.

3) create a folder on the root of your flash drive labeled with your last name, initials, and the abbreviation 'trans'.  For example: papenfuse_e_transcription was used with this example.   Save each page you transcribe to that folder by placing your cursor in the window where your transcription appears, right click, select this frame and save frame as, saving the frame to the directory you have just created, labeling the files as they are labeled in the frame (for this example: the first transcribed file is labeled webster-0700).  Save all your transcription this way.   Use the green plus sign button in Zotero to link to these files.  You may then edit the files you saved following the instructions above for composition (Use the go to file tab in the right hand column of Zotero, right click on the file and begin editing).  Any further editing/transcription work done for this page can be scraped from your local file and copied on to the new 'live' file at, or, if you prefer, any changes or corrections can be made on the live file, saving it back to the local file over the previous version.

Using this letter as an example of how to further take notes, you might find the author intriguing.  Check all the searchable secondary and primary sources provided to see if James Roosevelt is mentioned. You will discover that Judge Sullivan in his book on the Webster trial accepts the letter as genuine and quotes it in full.  Having downloaded the transcription to a local file, you can take the text from the pdf of Sullivan and add it to your notes for that page in the far right column of Zotero (assuming you have highlighted the transcription).  Note that not all pdfs have searchable and thus copyable text.  In those cases you will need to take your notes on the zotero note pad provided or on an html of your own creation using the white board approach outlined above.You might also want to use the web to see what could be found about James Roosevelt and possibly challenge the authenticity of the letter.  There is a Wikipedia article about the James Roosevelt who was the father of FDR.   At this point in your note taking the questions mostly center on the authenticity of the letter and how it is/ought to be employed by the historian.

Image acquisition/editing and incorporation into compositions

Most anything you will want to download, edit, annotate and incorporate into your editing and writing in the way of images (gifs, jpgs, tifs, etc.) can be accomplished on the PC with IRFAN, a free software package.  Let's assume that you want to illustrate the James Roosevelt letter with an image of Roosevelt.  First download the Wikipedia article about him to your Zotero folder using the camera button.   Bring the file into the browser from your locally captured file or stay with the Wikipedia version. Right click on the photograph of  Roosevelt and save it in your folder as a zotero image.  Access the file from Zotero that you just saved. You can then locate the file using show file, right click and edit it with IRFAN, adding text, correcting color, etc.  In the current version of, you will not be able to insert the image into your edited text on line, but you can into the text when you download it to zotero.  Copy the image into memory.  Locate the local file of your transcribed page, open it in Open Office Writer Portable,  and use the ctl V key combination, or the insert function to place the image where you want it with any bracketed annotation you might want to provide.

Note that IRFAN is versatile and can convert images from and to almost any format including the creation of pdfs, the most universal way of communicating documents via email.