EndNote X7

Class Workbook.

Table of Content EndNote X6

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Getting Started in EndNote

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Creating a New Library

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Understanding the EndNote Interface

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Customizing EndNote’s Look

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Adding References to EndNote

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Method #1: Direct Export from PubMed Method #2: Online Search or Connect Tool Organizing References EndNote Groups:

8  12  14  14 

Creating a New Group

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Adding Citations to a Group

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Using Smart Groups

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Group Icons

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Using References in a Paper

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Insert Selected Citation

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Find Citation(s)

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How to Reformat Your Document

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How to Create a Stand-Alone Bibliography:

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Appendix

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Adding to the Favorites Lists

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Managing Attachments: PDFs & Other Files

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Journal Titles: Abbreviations or Full Names?

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Journal Names Still Not Displaying Correctly?

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NIH – PMCID – NIHMN & EndNote

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Getting Started in EndNote Learn how to create a new library, add a reference, and begin understanding the EndNote interface. EndNote is the most popular bibliographic file management software program being used at UCSD, partly because it is fairly easy to use, and also because it is compatible with MAC computers. In EndNote, your citations are gathered into “libraries.” You can have multiple libraries (as many as needed) with each library having an unlimited number of citations or “records.” We recommend just one library for everything. Organizing citations into “groups” within that library make it manageable.

Creating a New Library After starting EndNote, you may be prompted to open a library or the Sample Library may automatically open. This is a customizable option (see Edit-Preferences on page 4) that gives you control over how EndNote opens. To create a new library Choose File – New to create a new library. Give it a name and decide where you want to save the library. My Documents is a convenient location. You might want to save it to a network or other drive (e.g., dropbox). What is most important is to remember where you put it. FYI: Custom or newly added styles will appear in your My Documents folder. (To open an existing library, click File Open, then Open Library to look for your library. You can also use the quick list that appears under the Open Library option.)

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You have a new, empty, EndNote library. To add a reference by manually entering the information, click on “References” and pick “New Reference.” (Not all options are shown under the References menu bar – just the first few).

Enter the following information:  Sadler, GR.  Health promotion via deaf-friendly ministries.  J Cancer Educ. 2012 Dec, 27(4):606-11 NOTE: When manually entering information, the key is to know the correct order and punctuation. Check the Quick Start Guide for details. A few pointers are:  If you are entering initials instead of full names, be sure to type a period or a space between initials, (for example “Braff, D.L.” or “D L Braff”  Author names can be entered either with the last name followed by a comma and the first name, or the first name followed by the last name. Both are correct  For corporate authors, put a comma after the name to keep it in the correct order. NOTES:

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Understanding the EndNote Interface EndNote is a robust resource and it can take a little while to become comfortable with it. The following highlight some of the key features.

1. Menu bar a. Edit: Output Styles, Import Filters, Connection Styles, Preferences b. References: New & Search References, Show All, Change & Move fields c. Groups: Create, rename, set up a Smart Group, or add references d. Tools: Online Search 2. Output Style – (a.k.a. citation style) choose the one you need (see appendix for customizing the list) 3. Column Headings – click to re-sort the list by that column (e.g., author, title, journal, etc.) 4. Groups – user created & the automatically filled “Smart Groups,” right-click to bring up the group/smart group menu 5. See Reference (& edit, if needed), Preview citation for the selected style (as seen in #2 above), or View (& annotate) attached PDF. 6. EndNote Library Display Modes, a featured EndNote rolled out several years ago that caused many headaches, is now better in version X6. NOTES:

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Customizing EndNote’s Look  Display Fields The Display Fields refer to the columns of information – Title, Author, etc.- and can be re-ordered, taken off the list, or added to – up to 10 column headings. The following are the key ones to know. Under Edit, click on Preferences. 1. Select Display Fields. Rearrange fields as desired using pull down menus. Note: Displaying all authors is an option when selected (see below). For Mac, Preferences in under File instead of Edit.

a. Add fields you would like to be a column and column heading, i.e., Custom 1 field or the Record Number. (Columns 8 or 9 above.) b.

X2 & newer versions will show all authors in the author field. To turn that on, put a check in the box.

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2. Find Full Text – EndNote searches various tools to accomplish this process. Be sure the following are selected: o

Web of Knowledge Full Text Links

o

DOI (Digital Object Identifier)

o

Open URL In the Open URL section, insert the following information: 

o

http://ucelinks.cdlib.org:8888/sfx_local

You do not need to do anything with the Authenticate.

3. Libraries provides a box where you can specify the library or libraries to open. 4. Read/Unread, if you like this feature, you have options for customizing when something is counted as read. 5. Sync is where your EndNote Web details can be entered and sync enabled – only available starting with EndNote X6. Earlier versions have a manual update feature. 6. URLs & Links – you might find an updated “Open URL Argument will increase your Find Full Text success. Copy the link from our webpage: http://bit.ly/enopenurl. 7. Choose another preference or click OK if finished.

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Adding References to EndNote There are 4 ways to get references into EndNote: 1. Direct export is available from some database providers, including PubMed (NEW!), ISI (Web of Science, BIOSIS) and many others. This enables the saving of records directly into EndNote rather than having to save to a file on the desktop and then importing. It saves a few clicks. Note: This option is the preferred method when subject searching – it gives a more powerful, accurate database search, such as using PubMed, BIOSIS, etc. then it is easy to Import or Directly Export the references from your searches into EndNote in a few simple steps. Option 3 may be needed if direct export is not available. 2. Online Search can search databases from inside EndNote. (Formerly called Connect.) Note: Option #2 works well when you are going after “known item” references that you expect will be in that database and you have specific details to use. 3. Search for your desired references in an article database. Download references to your computer and Import them into EndNote. 4. Type references in using the New Reference template. Note: Option #4 is needed only when you cannot find articles or books in a database (i.e., PubMed) or a library catalog (i.e., Roger) – for details on entry, see page 2.

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Method #1: Direct Export from PubMed  PubMed Example 1. Go to PubMed Database (Link available under “Library Quicklinks” at http://biomed.ucsd.edu) and search for articles on your topic or use the example topic – Jurassic park).

2. When your results are displayed, select those that you would like to save in EndNote.

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3. Use the options under the Send to: to send the selected results to Citation manager. Then click the button – Create File.

 The first time, you will need

to select Open with – Other… and point it to EndNote. Any other time, it will automatically be selected.

NOTE: Chrome & Safari automatically save it as a file that needs to be opened. Firefox & IE will let you specify that EndNote should open it. 4. The articles should now be in your library.  If it asks you to select a filter, you have an older version of EndNote (or an unpatched X6). Simply point to PubMed and the articles will appear.  The records will import, and at first, you will see only these new references. (Remember, you can use the Show All command in the References menu to show the entire library.) 5. If you are using groups to organize your library, now would be a good time to organize them where you want them. NOTES:

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 Web of Science Example 1. Go to Web of Science (Link available from the Quick Links list at http://biomed.ucsd.edu)  Perform a search or use the Cited Reference example search below. 2. A cited reference search starts with a known article and asks to find any articles that have used it in their references.  Find articles by JBC Jackson, published in Science in 2001 & the starting page is 2401.

 At the intermediary page – look for the article that starts on page 2401, click to select it and click on the “Finish” button to bring up the results.

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3. Mark some of your result. Under Output Records - select Authors plus abstract, then click the Save to EndNote, RefMan ... button.

 If a series of citations are needed, they can be specified in the Output Records option.  Results can also be sent to the Marked List so you can select more than just the citations on the first page. The direct export process must then be started from the Marked List page. 4. The export process should begin automatically once the button is clicked.  If prompted to save or open the file, select Open with ... It might be EndNote or ResearchSoft – either is fine.  EndNote will open, and select the library you want the records to go in to.  The records will import, and at first you will see only these new references. (Remember, you can use the Show All command in the References menu to show the entire library.)

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Method #2: Online Search or Connect Tool  Connect through EndNote to PubMed 1. Click on the “globe” (top left corner) to bring up the online search options. 2. Click on PubMed a. If what you want is not showing, click more and find what you need. Note: Not all items in the list are accessible – just those to which UCSD subscribes or are freely available (e.g.,BIOSIS, CINAHL, or PubMed).

3. Start the search – a new box appears above the citations. Fill in the form as seen or change the first field to “All Fields” and enter all your search terms in one box – see example below.

Note: In X2 – X5, using the Online Search Mode, the search box will appear below where the citations usually appear.

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4. The Confirm Remote Search dialog box will appear to inform you of how many references were found. Click on OK to retrieve all of the found references (or if a large number, adjust the numbers to retrieve fewer references).

5. A list of possible matches will appear. Select the one(s) you want using either the Ctrl key or the Shift key and then clicking on the ones you want.

Right click to make the little menu appear with the option to “Copy References To” the library of your choice or use Add to sent them to a custom group. The command can also be found under References on the menu bar.

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Organizing References Starting with EndNote X3, the “Groups” or “My Groups” features were added to help keep your citations organized for the different projects you work on, or grouped by the different people you support. “Groups” lets you easily get to a select list of citations.

EndNote Groups: 

The permanent Groups that you will see under “My Library” are: All References, Unfiled, and Trash. You can’t remove or rename these groups.



The temporary Groups hold references until you move them to another Group, or end the session, are: Copied References, Imported References, Search Results, and Find Full Text.



Unfiled Groups are created by the system when you sync with your EndNote Web account and bring in a group of references that does not fit into your existing EndNote Groups. These groups that were imported from EndNote Web, should be moved to your Groups section.

My Groups, Custom & Smart Group Sets: 

Older versions of EndNote (X3-X5) had limits of 300 to 500 groups, with EndNote X6 you can have up to 5,000 groups per library.



Each Group can be its own group (



A reference can be in more than one Group.



Deleting a record from a Group will remove it from the Group but keep it in All References.



Deleting a record from All References will completely remove it, including from any Groups, and will move it to the Trash section. References in Trash cannot be searched or cited, but can be retrieved, moved back, and will not be deleted until you Empty Trash by right clicking on Trash, or selecting “Empty Trash”, from the References menu.

) or contain a combination of Custom Groups and Smart Groups (

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Creating a New Group Groups can be created ahead of time or they can be created as soon as you have references that need a new group. To create a new, empty Group: 1. Click Groups from the Menu Bar, & Create New Group, or simply right click in the My Groups pane to create it. 2. In the box that appears, name your group. 3. You can create a Group, a Smart group (based on a search strategy) or even group your Groups.

Adding Citations to a Group You may already have a library that needs organizing into groups or you may want to start out organized by making sure to put new citations into groups. Either method is very simple. 1. Adding citations already in your library if you have a group already:  Highlight the citations you want and drag them to the Group. 2. Adding citations already in your library and you need to create a group:  Highlight the citations you want and right click them.

 Select Add References To and choose Create New Group & name the group.

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Using Smart Groups Use Smart Groups to organize your existing library and automatically add any new citations that match your search criteria. Under Groups, click Create Smart Group. In the Smart Group search box, give your group a name, add your search terms, and choose where EndNote is to search – including the attached PDF. Click the Create button.

This Smart Group will save the term “cancer” as a search of any field including attached PDFs. All existing references will be searched AND new references added to EndNote will automatically be scanned for possible addition to this group. In addition, any time an existing record is edited to add the term “cancer” to keywords, notes, or any field, this changed record will now appear in this Smart Group.

Group Icons EndNote has a couple of visual reminders about the type of groups you create, because unlike the following example, the name you give it will not tell you what it is.

 Combination Groups: a group of groups, has the overlapping circles. (ANDs & ORs matter here.)

 A regular group has the folder icon  Smart groups have the lightbulb-magnifying glass search icon.

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Using References in a Paper Now that you have all these references in EndNote, you can use them in papers you are writing or to create a stand-alone bibliography. Inserting citations into a paper can be accomplished in two different ways and creating a stand-alone bibliography requires just a couple of clicks. In Microsoft Word, you may need to use the EndNote toolbar or the EndNote ribbon, depending upon which version of MS Word you have.

Insert Selected Citation 1. Make sure you have the correct reference highlighted in EndNote. (Always the first step). 2. Place your cursor at the point in the document where you would like the reference to appear. 3. Click Insert Citation - right over the text not the top icon (this is a 2-part button) - & choose Insert Selected Citation.

Your citation should automatically format and a reference list automatically start at the end of the document. NOTES:

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Find Citation(s) You may also search for a specific reference in EndNote from within Word, and then insert the reference into your document. The search term can be an author’s name, any title word, or word in the abstract or notes field. 1. Place your cursor at the point in the document where you would like the reference to appear. 2. Click on

to Find Citations in your EndNote library (e.g., West).

For Word 2003, the button is just the magnifying glass. 3. Highlight the citation or citations you want to add (use the shift or ctrl key while clicking) and click the Insert button. Author-date style of writing my need the options in the drop-down list.

How to Reformat Your Document As you enter references into a Word document, your bibliography is automatically formatted. You may format (or reformat) your bibliography according to any output style. 1. Adjust citation Style in ribbon and click Update Citations & Bibliography. If the one you want is not on the list, click on the arrow of the box showing the current style, then choose “Select Another Style” to bring up the full list.

2.

Click OK once new style is selected. Your citations should automatically update. If not, click on “Update Citations & Bibliography.”

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How to Create a Stand-Alone Bibliography: In some cases you need to create a bibliography in the absence of an accompanying manuscript (e.g. your annotated bibliography, or a publications list for your resume). In other words, you need references but no in-text citations. 1. In EndNote, choose the citation style you want. 2. Select the references you want to use. You can select all, view the ones in one of your groups, or use the Shift or Ctrl key to select multiple references. 3. Use the Copy Formatted command from the Edit menu.

4. In Word, paste the references into the document.

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Appendix The following are additional topics with step-by-step instructions that may be covered during the EndNote session or may be included because they address some of the frequently asked questions about using EndNote.

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Adding to the Favorites Lists  Database Import Filters (Very helpful if you use more than one database). 1. In EndNote, under Edit click on Import Filters. 2. Select Open Filter Manger. 3. Put a check in the boxes of the filters you would like to add your favorites list as seen below. 4. Simply close the box (use the X) after selecting – there is no OK button

5. The selected filters should now appear in your favorites list. You will see the list when you use the File – Import option and click on pull-down menu for the Import Option.

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 Output Styles (For use in EndNote or from the Word Tools menu). 1. In EndNote, under Edit, click on Output Styles. 2. Select Open Style Manager. 3. Put a check in the boxes of the output (or citation) styles you would like to add your favorites list as seen below. 4. Simply close this box after selecting – there is no OK button.

5. The selected styles should now appear in your output favorites lists. In EndNote

In Word

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Managing Attachments: PDFs & Other Files You can link a file on your computer (or network drive),— such as a graphic, a word processing document, a spreadsheet, or a PDF file—to an EndNote reference. You can also attach the PDF or other file so that it goes along with the traveling library. Starting with X5 you can also add comments to PDFs. Attach a File 1. Select a reference – highlight it by clicking on it or open it. 2. From the References menu, choose File Attachments > Attach File.

3. In the dialog box, select a file to link to the selected reference and click open. 4. Note the check box along the bottom titled, "Copy this file to the default file attachment folder and create a relative link."  Leave it selected to copy the original file and place the copy in the EndNote folder and the EndNote Traveling library.  Uncheck it to always pull it from its original location, not from EndNote space.

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Import PDFs to EndNote & EndNote Creates a Record You can point EndNote to a specific file or a folder of PDFs that are not yet part of your EndNote library. Then EndNote will create a record for each PDF and use a process like Find Full Text to search the Internet to create the details of that record.

1. From the File menu select Import. 2. Then select File if you want to import a single PDF, or select Folder to import a folder containing your PDFs. 3. Click on Choose to find the File or Folder to import. 4. Select PDF as the Import Option, and then click the Import button.

Note: EndNote can import PDF files containing a DOI (Digital Object Identifier) in the metadata, or the first 2 pages of the PDF. It uses the free databases PubMed or CrossRef to look up the reference using the DOI, imports the bibliographic information, and then attaches the PDF to that record. Your PDF must have a DOI, and EndNote must have access to the Internet, for this process to be successful.

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Journal Titles: Abbreviations or Full Names? Always be sure to check the instruction to author’s for details on a journal’s preferred citation style. For those times when the style requires a full journal names in the bibliography, you may need to do a little work to make sure EndNote has that information. Depending upon the database you used, EndNote may not have that in the record – it may only have a journal abbreviation or vice versa. Use EndNote’s pre-filled Term Lists to add that information to your library. (If you are starting with an empty library, you can skip steps one & two). 1. From Tools, click on Open Term Lists – choose Journals Term Lists. 2. You will see a list of the journals used in your library in the box that opens. Select the first one and then scroll down to the last and hold Shift before clicking. This will select all in the list and then click Delete Term. 3. Click on the tab Lists and make sure Journals is highlighted. 4. Click on Import List button and select the list you want. a. You will need to navigate to where the Terms Lists folder lives to find the files. Usually, it will be in C:\Program Files\EndNote X3. b. If you want to import more than one list, after picking the first one, simply go back and select as many as you think you need. 5. Click close and now all citations should be able to use either full text or the abbreviation

Journal Names Still Not Displaying Correctly? Sometimes, the Terms List will need to be manually edited and this is easily done by Opening Term Lists. Select the one you want and click Edit Term. 1. Add abbreviation. 2. Revise an abbreviation. 3. Use New Term button to add a journal not already on the list.

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