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Research Guides

EndNote

Configuring the OpenURL Link Resolver

Find Full Text searches for full text journal articles and links PDFs to references in your EndNote library. Another way to search for full text is OpenURL searching which makes use of the library's e-journal subscriptions. Using OpenURL directly also displays a Get It For Me link so you can request articles that we don't have access to online. Please note: though OpenURL is listed as a Find Full Text source, it appears that EndNote does not make use of OpenURL as we have it implemented here. So, the OpenURL Link search which does use our OpenURL link resolver will probably find additional subscription full text. See closing comments in this note for more information.

Configuring Find Full Text

EndNote Edit (menu) + Preferences
Find Full Text in the left column

EndNote's Preferences + Find Full Text

Select the sources you want Find Full Text to use:

Web of Science
DOI
PubMed (select only if PubMed is a useful source for your research. PubMed can slow the full text search some.)
OpenURL (EndNote does not seem to use our implementation of the OpenURL Link Resolver)

‚ÄčOpenURL Path for on campus is
http://linkresolver.tamu.edu:9003/tamu

OpenURL Path for off campus is
http://ezproxy.library.tamu.edu/login?url=http://linkresolver.tamu.edu:9003/tamu

Authenticate with is
http://ezproxy.library.tamu.edu/login 

Using Find Full Text--select the records in your EndNote Library that you want to find full text for, and then click the EndNote References menu + Find Full Text, then Authenticate. Then you sign on with your NetID. You will have to close the authentication window after signing on to again access the EndNote menus. Then with the references still selected, click the EndNote References menu + Find Full Text + Find Full Text. EndNote should show in the left column that it is searching for the full text and after the search it will list how many PDFs it found and it will also attach the PDFs to the references in the library.

Using OpenURL search--using OpenURL Link search directly will probably find full text articles that Find Full Text does not. To use OpenURL Link search click a reference in the library so that it is highlighted (important first step) and then right-click it and point at URL and then click OpenURL Link. (Sometimes both OpenURL Link and Open URL may be options; for this feature to work, make sure to click the OpenURL Link option.)

A good strategy may be searching all references first with the Find Full Text search (because it can search multiple items at once and also links the pdf's), then use the OpenURL Link search for items that Find Full Text did not find, and if OpenURL Link search does not find the article, then send a Get It For Me request.

Configuring EndNote Desktop for Syncing

If you click the Sync Library icon in the EndNote Desktop toolbar (the icon appears as a circle with two arrows), it will Sync your library, or if you have not created an EndNote Online account yet, it will prompt you to create an EndNote Online account. Another way to configure EndNote is to go to the EndNote Edit menu + Preferences + Sync + click the Enable Sync button.

Journal Abbreviations

Some fields of study or citation styles require that journal title abbreviations be used in bibliographies instead of the full journal name. EndNote uses a method called the Journal Terms List to allow EndNote to use abbreviations for journal names. The Journal Terms List is a listing of journal names with up to three abbreviations per journal name. You can find more information about this in the EndNote Knowledge Base article .

A few additional things that may be helpful:

  • if a journal that you are citing is not in the journal term list you imported, you may have to add the abbreviation in the journal term list for that journal. To do that, in EndNote desktop click the Tools menu + point at Open Term Lists + click Journals Term List. (Make sure the Terms tab is selected.) Then find the journal title in the list and select it. (If the title is not yet listed, you can add it in the next step.) Then click the Edit Term button. You can (add the title if it is not yet in the list and) add the correct abbreviation in the appropriate abbreviation field. To see what of the 3 abbreviation fields your style is using, you can close the term list window and click the EndNote Edit menu + point at Output Styles + Open Style Manager and then find the citation style that you are using. Select the style and click the Edit button. In the Style Editing window click Journal Names toward the top of the left column. At the right it shows what of the 3 abbreviations is being used. (It is necessary that all the abbreviations for all of the journals being cited have the abbreviation in that abbreviation field in the Journals term list--meaning that all the required abbreviations be all in field 1 or all in field 2 or all in field 3, all in the same column.) To find the correct abbreviation, you may be able to do a Google search for the journal title (in double quotes) and the word abbreviation. (Different disciplines use different abbreviation guidelines, so the abbreviation from one discipline might not be what is needed for your field of study.)
  • the journal title as it is listed in your EndNote reference has to be exactly the same as in the Journals term list. If the reference has an ampersand (&) it won't match the word "and" in the term list. If there is a period in the title, it won't match a term without a period. The same with spacing or punctuation differences. One option to resolve this is you could edit the journal name in the reference to match the journal listing in the term list.
  • some databases, in particular PubMed, seem to send the journal abbreviation to EndNote as the journal name. This can cause problems with not matching the journal names in the term list and also in cases where one needs the journal name in the citation and not the abbreviation. You could edit the references in EndNote and put the full journal name in the journal name field. There is also an Alternate Journal field in EndNote Journal Article references and you could copy the abbreviation to that field (to keep track of the abbreviation).

Backing up EndNote Libraries and Word Documents

EndNote strongly recommends backing up EndNote Libraries and papers. (This is recommended in EndNote desktop's online help under "Backing Up Your EndNote Files".) One way to backup the EndNote library is to create a compressed library. To do that from EndNote desktop, click the File menu + Compressed Library. The compressed library window should open and you can decide to include all references, references in a group or group set, or references that are selected and also whether to include file attachments.

There are different strategies for how often a library should be backed up. You could backup by time period or after significant work that you would not want to lose. If saving file space is important, it is probably safe to include the file attachments less often and usually just back up the references without file attachments. You could use part of the date of the backup in the compressed library name to distinguish the file names, for example, 063017EndNoteLibrary.enlx or a counting number EndNoteLibrary1.enlx.

Backing up the Word documents is also important. It is possible for errors to be introduced in a Word document that can make it difficult to continue using that copy.

Unformatted Citations

There are some cases when you may want to unformat your citations in Word. Some cases include:

  • when combining files with citations (for example, chapters of a document) when it is desired that the bibliography appear at the last of the combined file
  • when adding formatted citations is taking too much computer time (this is more likely when there are numerous citations in a document, perhaps over 30, because EndNote is scanning the entire document and reformatting all of the citations when you add one formatted citation). In some cases, people have found it to be unworkable because of the delay. Working in unformatted mode may resolve that. (And one does not typically see the bibliography being updated while editing in the document, anyway, because the bibliography is usually not in the same screen view as the content being edited.)

When working in Word you can choose to unformat your citations or to work in Unformatted Citations mode where citations are not formatted (and items are not added to the bibliography in the document) until you later Format Citations. Unformatted citations by default appear as {Jones, 1970 #435}. If the EndNote record doesn't have an author or year, that data will not appear in the unformatted citation. The number is the record number in EndNote which can be seen in the EndNote library if you double-click a reference. The record number appears at the top of the window.

In a Word document with formatted citations, to unformat the citations in Word go to the EndNote ribbon and click Convert Citations and Bibliography and then click Convert to Unformatted Citations. Another function that is related is the setting for Instant Formatting. If you unformat citations, Instant Formatting may automatically be turned off so that new citations will be added as unformatted citations. When the citations are unformatted the bibliography is not displayed (it is not created) though it will be created when the citations are formatted..

At any time you can format the citations and that will also display the bibliography. To format the citations, one option is to click Update Citations and Bibliography in the EndNote ribbon. This may also turn Instant Formatting on, so that additional citations will be added as formatted.

Convert to Plain Text

Sometimes you may need to submit a version of a document without any EndNote fields in the document. When EndNote adds citations to a document, the data for the citations is included within the document in Word fields that are not visible in the usual document view. Another instance when you might want to convert the document is if there are certain references that cannot be correctly formatted by EndNote. In both of these cases you might want to Convert the document to plain text. To do this, in Word from the EndNote ribbon, click Convert Citations and Bibliography and then Click Convert to Plain Text. EndNote X8 displays a window saying that it "will create a new copy of your Word document and remove all special EndNote markers from it. The new document will appear in a new unsaved document window. The original file will remain opened and untouched."

The new document without EndNote codes keeps most of the text formatting but not the EndNote codes. The resulting document is editable. (One change I noticed was that the original document had clickable blue URLs and the text document did not treat the URLs as links.)

One problem with Converting to Plain Text in order to allow making some editing changes to references is that if you later want to add more references from EndNote, EndNote will not recognize the earlier citations in the text version of the document and cannot revise or use them. If you use EndNote to add new references, it will treat the existing bibliography as part of the text of the document and will add the new references after it. You might have to return to the most recent EndNote version of the document, add the new references, convert to plain text and make all the editing changes again.

Annotated Review Style

The Annotated Review Style is based on EndNote's Annotated Style and can be used to read the Research Notes and Abstracts for your references. Unlike how most styles are used for citing references the Annotated Review style is intended for reading. When you add the Annotated Review Style to EndNote's styles and select it in EndNote, the reference preview shows a basic citation for the selected reference and your Research Notes (if any) for that reference and the Abstract (if any). All references have a Research Notes field that is reserved for your use. EndNote does not transfer data into that field when automatically creating new references. The Research Notes field can contain up to 64,000 characters (about 16 pages of text). You could--as examples--put your thoughts about the significance of a reference, the main themes, (possibly) listing other related sources, methodologies used, how the reference relates to your project, how you intend to use the source, and so on. When the Annotated Review style is selected and you are viewing the Preview of a reference, you can use the up and down arrow keys to move from reference to reference, so it allows easy browsing through references.

To add the Annotated Review Style to your installation of EndNote, click the link below the following graphic for the Annotated Review Style and download the file. Then on your computer browse to the downloaded file and open the file with EndNote. EndNote will display the file in its Style Editing window. Then click EndNote's File menu + Save as. If you have not yet added the Annotated Review Style, you can delete the word "Copy" from the style name. Once you have save the file within EndNote, you can select the style and view references in the Preview panel. (You have to write the Research Notes for them to appear in the preview.)

The change made to EndNote's Annotated style can be seen (and reused to base the style on a citation style beside the Annotated style) in the Style Editing window. With Annotated Review selected as the style in EndNote, click the Edit menu + point at Output Styles and then click Edit "Annotated Review". In the Bibliography section at the left, click Layout. Some of the data in the Layout field includes (in the lower "End each reference with") section: two line returns, a tab, the bold text for Research Notes (you can quote a field name with single back quotes), the diamond-shaped (four dots) connector "Link Adjacent Text" (which I copied from another template under Bibliography since it does not appear when editing the Layout section with the Insert Field button at the top right of the lower section). If you click on Templates under the Bibliography section, the "Link Adjacent Text" connector is likely used in most or all of the Reference Type templates.

Screen copy of EndNote desktop showing the citation preview when using the Annotated Review style. This shows one's own  Research Notes and the Abstact.

Using EndNote with LaTex and BibTex

I do not have direct experience with using LaTeX or related tools, so I researched this subject when asked about it. I later in communication with students asking about EndNote and LaTeX wrote some notes piecing together a workflow that might work, that seemed to address certain issues in the process (going from EndNote to LaTeX). I don't know what faults there may be in any of this information. The first section is from an email a student sent me after I had sent him some information letting me know what he had found. If you discover additional information, I'd like to know!

http://libguides.mit.edu/content.php?pid=234127&sid=1937425

EndNote is not designed to be used with Latex at all. So, the only way to use them together is to export EndNote libraries to BibTeX. BibTeX can then be embedded in the the LaTeX document. 

The problem is EndNote doesn't insert citations in the correct format to work directly with BibTeX. So, there is a program called JabRef (free open source software). This program is like EndNote but for LaTeX and LyX. 

After you export the EndNote library, you open it with JabRef. Then from the tools menu, you select (clean entries) and then select (auto-generate BibTeX entries). This commands fixes all errors with the export process. Some of the entries will not be fixed yet. In this case, you need to manually import them from another source, for example, Google Scholar.

Using LaTeX natively is a difficult process. So, most LaTeX users use a front end processor such as LyX. 

In LyX, you can select insert/list or TOC/BibTeX bibliography. 

After that you are done! You can insert the citations in your LyX document using the insert citation button!

Reference managing software is always necessary to manage your references when writing a big project. I used endnote because I used to give my adviser copies of my papers in Microsoft Word. Endnote is not preferred if you work with LaTeX. 

I had to use both since I give my adviser the paper in Word so that he could edit and comment on it. But when I submit it to journal it has to be formatted in a certain way and required LaTeX or LyX to get the job done.

I already had my database of references in Endnote so I needed a translator from Endnote to JabRef. 

Other software performs the same task as EndNote. Programs differ in capabilities. The choice of reference managing program will be dictated by the needs of the researcher. EndNote offers excellent support for Microsoft Word but no support whatsoever for LaTeX. On the other hand, JabRef offer the same capabilities as Endnote but almost no support for Microsoft Word. In Word you hit the insert citation button in the Endnote ribbon and you are done. In LyX it is the same, you hit insert citation and you are done. There is no integration between Endnote and LyX.

And so now I will continue after quoting what the student told me above and also include my original notes to the student and other comments.

I've talked with EndNote and RefWorks support and they said that it made sense to use a reference manager even if citations could not be automatically sent from the reference manager to a LaTeX document. I think the general process might be to gather references in EndNote, then export them to BibTex and use BibTex with Latex to add the citations.

I’m going to describe a process that may help. Whether my description is helpful and more efficient probably depends on there being enough records (references) in the EndNote library. (What I meant was that if there are only a few records, then it might be easier to do the work a different way. This method might only be efficient if there are a high enough number of references. Again, though, I do not know what the work will involve to be able to recommend any particular process.) If you have over 200 records, maybe this is still a good bit of work.

Refering to MIT’s information about using the Label field--the label field is one of the data fields for each record in EndNote. You can double-click a record in Endnote and if you scroll through the fields you should see the label field. It does not tend to be automatically used, so there should not tend to already be data in that field. It looks like unique data needs to be in the label field to identify the record.

One method for getting unique data in the label field is to copy the unique EndNote record number into the label field. You can see the record number if you double-click a record in the EndNote library and view the window with all the fields. At the top of that window there should be a number sign and the record number, for example, #624. Record numbers are automatically assigned as references are added to a library. If the reference is deleted, the number is not reused. So, if one put the record number in the label field, that would be one way to have a unique number in the label field. (Of course, it may be just as well to simply put a counting number in the label field.)

To automatically transfer the record number to the label field you can use the command Change/Move/Copy Fields. (EndNote Tools menu + Change/Move/Copy Fields + Move/Copy Fields tab + select Copy Field + select the “From” field to be “Record Number” + select the “To” field to be “Label”).

I do not know whether this is all set up to easily cite in BibTex. It just seems like it meets a requirement that a quick review of the MIT guide suggested.