A common request from graduate students who are writing their thesis or dissertation is for instructions on how to use EndNote and Cite While You Write to create a "journal-style" bibliography - one where each chapter of the document has its own bibliography rather than the document as a whole having one big one at the end. There are different ways to accomplish this that depend on whether you are using the full EndNote software or EndNote Web.
The full EndNote software can leverage the document structure tools within Microsoft Word itself to accomplish this.
The first thing to do is to make sure that you have created a new Section for each segment of your document that you wish to have its own bibliography. You do this by placing the cursor where you wish the current section to end, then from the Layout tab select the Breaks dropdown and select the Section break type that matches your preference.
The second required element is simply to be using a citation style in Cite While You Write that uses these section breaks. If the one you've already selected is set to do so and you've already inserted the citations into your paper, the above step should have resulted in the new bibliographies automatically. If you're unsure, it's an easy thing to check in EndNote itself.
If you're using EndNote 20 or later, click in the Tools menu and then go to Output Styles and click on Open Style Manager. If you're using EndNote X9 or earlier, you start in the Edit menu instead of Tools.
From there, find the style that you're interested in using and double click (or click once to select it and then click the Edit button). In the window this opens, browse into the Sections area.
From there you can select the option that matches how you wish to have Cite While You Write manage the document sections. That is, you can have one bibliography at the end, a new bibliography for each section (with or without continuous numbering throughout the document), or both.
Unfortunately, the free web-based version of EndNote cannot support multiple bibliographies, even if the citation style selected in Cite While You Write is configured to do so. As such, we need to use a work-around of one form or another. All of which simply require that you save each "section" of your final document as its own Word file while you're working and simply use Cite While You Write normally within each document.
Most of this process from here on will assume that you've completed your writing and are simply preparing the final document.
You will want to make sure that all documents have used the same citation style in Cite While You Write so that everything is consistent and that the bibliographies are complete. Additionally, they should be titled such that alphabetical ordering has them in the correct sequence - the methods we'll be using to combine them later default to file name order.
Now that you have your collection of separate files for your various chapters, there are two main methods to combine them: using Word itself or Adobe Acrobat. Both programs have methods of building a new file from a series of existing ones.
It is strongly advised that you save a backup copy of all of your files at this point. We are about to make one-way transformations that cannot be undone, so having a backup is important.
In each document, in the EndNote tab there is a drop-down menu for Convert Citations and Bibliography. Click into that and then on Convert to Plain Text and save the new document separately so that you do not overwrite the old version. This command strips out all of the internal "hooks" in the document that EndNote and Cite While You Write use to edit your document automatically.
Once that is done for all sections, open a new blank document and click into the Insert menu. One option available is for Object with a sub-option of Text From File.
The window this opens allows you to select all of the files to be combined into a single Word Document. In my testing, this appears to be a one-time event so editing the base documents does not edit the final one so this step will need to be repeated if you do make any edits to the base documents. You may find that you need to add page breaks between your sections, but because we're still within a Word context you can still use automated page numbering.
Because we stripped out all of the EndNote "hooks" in the previous step, you cannot edit the imported text using Cite While You Write. If we had not done so, you could still edit the citations here, but any editing "event" that triggers CWYW to update the citations and bibliography will simply create an updated, full-document bibliography at the end of the file and will not update any internal bibliographies. It's simpler and less likely to cause problems if you strip out that functionality ahead of time.
You will likely want to edit the page numbering of every file in turn so that they begin on the page following the end of the previous file. You can do this in Word by clicking into the Header/Footer to bring up the appropriate menu. From there select the Page Number option and click on Format Page Numbers. In the window that brings up, simply select the Start At radio button and enter the appropriate page to begin the current document.
In Adobe Acrobat (either on its own or via the Adobe Creative Cloud package), you can combine discrete Word documents into a single file. Under the Tools menu there is a Combine Files option. Simply drag the files you wish to combine into the designated space in the order you wish them to appear and click on Combine. This option will automatically start each document on a new page, but won't renumber them, which is why we needed to do that step earlier. Additionally, since Acrobat doesn't have any equivalent functionality to Cite While You Write further edits can't be made using EndNote directly.
If you wish to also have a bibliography at the end of your document, it's relatively straightforward do create one in one of two ways.
The first option requires you to have done some organizational work ahead of time or to do so now. The EndNote Web interface itself can generate a bibliography for you based on a "Group" of references. If you've already been organizing the references you're using for this project into a single Group you're all set, otherwise you'll have to build that Group now.
Once that's done, you can click into the Format --> Bibliography section of your account. In the three drop-down menus, select the name of the Group that your references are in, the citation style you've used for your paper, and RTF format (the other options are a Text file which wouldn't be able to include things like italicized text and HTML which would likely work, but Rich Text is more likely to copy and paste into Word cleanly).
Clicking Save should process the references and save a .rtf file in your usual downloads location. You will want to open that file in Word and edit it to use the same formatting style as the rest of your document (typeface, font size, margins, etc.). From there you can either include it in the "combining" steps above or if working in Word you can simply copy and paste the text at the end of the document.
The other option for creating a comprehensive bibliography is a bit messy. We'll just be opening each file comprising your documents various sections, copying the contents, and then pasting everything into a single Word file. If you had already written your paper before coming to this guide, you likely already have a suitable file saved somewhere. Once you've got all of your content in this one file, click on Update Citations and Bibliography button in the EndNote menu of Word and it should build the single bibliography at the end of your document. Save a backup and go through the Convert To Plain Text steps mentioned in the "Instructions for Microsoft Word" section above to get a version of the bibliography that you can copy and paste freely without worrying about CWYW making further edits. At that point you can add it to your paper using the methods described above.
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