EndNote X7 Basics Guide (Win) - Scripps ResearchEndNote X7 Basics (Win) - 3 - 3. Import Journal Term Lists - Required step, best before entering citations, for each library. Adding

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EndNote X7 Basics Guide (Win) Contact Kresge Library 858-784-8705 EndNote Technical Support 1-800-336-4474 (press 4, then 1) TSRI Download/Support site http://library.scripps.edu/endnote Must be TSRI faculty, postdoc, student, or staff Use your TSRI email account (without the @scripps.edu part) to sign in EndNote Training Guide Page

A. Set up ............................................................................................................. 1. EndNote Web ...................................................................................2 2. New Library .....................................................................................2 3. Import Journal Term Lists ...............................................................3

B. Preferences ..................................................................................................... 1. Find Full Text set up ........................................................................4 2. PDF Handling ..................................................................................4 3. Set Display Fields ............................................................................5 4. Read/Unread Settings .......................................................................5 5. Duplicate record handling ................................................................6 6. Setting default Libraries ...................................................................6

C. Importing records ........................................................................................... 1. Web of Science ................................................................................7 2. PubMed ............................................................................................8 3. SciFinder Web ..............................................................................10

D. Search databases from with EndNote ........................................................11 E. Find Full Text ...............................................................................................

1. Set PDF Preferences ......................................................................12 2. Finding Full Text ..........................................................................12

F. Exporting References .................................................................................14 G. Sharing EndNote Libraries ........................................................................14 H. Global Changes ..........................................................................................16 I. Using Groups .............................................................................................17

EndNote X7 Basics (Win)

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A. Set Up

1. EndNote Web • The first time you open EndNote X7, you will see an EndNote information box. • EndNote has a web-based version of EndNote that you can access from any Internet

computer. EndNote is now fully synced with a web, iPad and desktop version of EndNote. If you already have a personal account in Web of Science, this is also your EndNote Web login. You can also create or connect your EndNote Web account to the desktop in the future. You do not need to set up an account at this time.

• You can sign up now or later. • To register later, go to Edit> Preferences>Sync • Click Enable Sync • Use your Web of Science personal account from TSRI if you have one.

• If you are creating a new account, you will be asked for some information. • Then click OK.

2. Create a new Library:

• Go to File > New. • In the next window, enter a File name:. • Select location (use desktop for this training) in the Save in: box at the top. • Click Save.


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3. Import Journal Term Lists - Required step, best before entering citations, for each library. Adding these will allow standard journal titles and abbreviations to link together.

• Go to Tools > Open Term Lists > Journals Term List.

• Click on the Lists tab. • Be sure Journals is highlighted, and then click Import List…

• The lists will be found at Local Disc C:\\Program Files\Endnote X7\Terms Lists\

(use the pull down for look in:) • Select one (medical.txt is the best list for journals from PubMed). • Click Open. • To edit Journal terms, click on the Terms tab.

• Highlight a journal name and click Edit term. • You can add or edit abbreviations • Close the Term List window when done.


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B. Preferences 1. Find Full Text - Important – turn this off when beginning or importing large numbers of

citations. While this feature seems helpful, it will look to publishers like we are violating our agreements and doing systematic downloads of their content.

• Select Find Full Text. • Uncheck the box next to “Automatically invoke Find Full Text on newly-imported

references”

2. PDF Handling • Select PDF Handling from the left menu • Here you can select how to name the PDFs added to EndNote • Use Custom to select up to 3 fields to create the PDF name • Tip - don’t make the PDF name too long (i.e., don’t use the article title)


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3. Set Display Fields • Select Display Fields from the left menu. • Choose the field displayed from the pull down list for up to 8 columns displayed. You

may also select [Do not display] to exclude a column.

• You may also change the heading name for the column. The default is the Generic name for the field selected. You can type in a heading for a field to be displayed in the main EndNote library display.

• Fields can be removed by selecting another Field to display in the columns. 4. Read/Unread settings

• Select Read/Unread • To remove the bold from all references, uncheck the box next to “Show unread

references in bold text.”


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5. Duplicate record handling • Select Duplicates from the left menu • Mark the fields to be compared when EndNote looks for Duplicates

• The fields must match exactly; abbreviations do NOT match full journal names for duplicate purposes.

• Decide if EndNote should automatically discard duplicates when searching online from inside of EndNote (see page 10). This does not apply when searching outside of EndNote.

6. Setting Default Libraries • Select Libraries from the left menu • Next to the text “When EndNote starts:” the pull down gives several options

• Set how you want EndNote to handle opening libraries. Note: Be careful when using

“Open the most recently used library” if you tend to pass a library back and forth on email, you may not be editing the copy of the library you think you are!!


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C. Importing records into EndNote

1. Web of Science

• Mark records from your search • Select “Save to EndNote desktop” • In the pop up, choose “Full Record” • Click Send

For IE users:

• Endnote X7 will import the record(s) into the open library. Note: if you see a yellow bar, click it and choose “Download file”. You may need to click “Send” again.

• The new records are added to the “All references” group, but are displayed in the Imported References group until you perform another import.

• To view all records in the library select the All References group.

For Firefox users: • Firefox will display a prompt, select “open with: ResearchSoft Direct Export helper”. • Click OK

• If EndNote does not open click “send” on the Web of Science screen. • Otherwise click “Close” in the Web of Science page once the import is complete.


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2. PubMed

• First open the EndNote library. • Go to PubMed and perform your search. • Next, Mark the citation(s) you wish to save to EndNote. • Click on the arrow next to the Send to: link. • Select “Citation Manager” (note: limited to 200 records at a time) • Click Create File.

IE 8+ users:

For Firefox users:

• Click Open. • The browser may prompt you to approve the

use of a program (the EndNote.exe file). • Click Allow. Note: This only works in Windows 7, or if IE recognizes the file type nbib. Otherwise use the IE 7 procedure above. You can set the file type in the browser settings.


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• From the “Open With” pull down menu choose Other…(or it may say Browse) • Select the EndNoteX7 program from the list. (DO NOT select the library.) • Click OK.

For both Firefox and IE 8: • The first time, EndNote may open and the Choose an Import Filter window will appear. • Select “PubMed (NLM)” from the list. • Click Choose. • Records are imported into the library that is open.

For IE 7 users:

• A File Download window appears

• Click Save. • Select a location (recommend the desktop). • In the File name box type the name of the file (or use the default “citation.nbib”). • Click Save. • You can set your browser to always open these files with EndNote, or you can use the

manual import below

• In EndNote:

• An EndNote window with just the imported records should appear. • To view all records in the library select References >Show All References (or use

CTRL-M).

o Select File >Import>File… o In the Import box that opens, click Choose

file… to search for the file. o Select file in the box that opens and click

Open. o Next select the “PubMed (NLM)” filter from

the pull down list of Import Option. Choose to delete duplicate records from Duplicates pull down list.

o Click Import.


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3. SciFinder Web Step 1:

• Search SciFinder as usual. • Once you have marked the citations you wish to import. • Click on Export.

• Name the file. • Under For: select “Citation export format (*.ris)”. • Click on Export. • Depending on the browser you are using, a popup window may appear.

Firefox IE 8+

• Choose “Open with” and select “ResearchSoft Direct Export Helper (default)”. • Click OK. • Or simply choose Open. (for IE 8 and Windows 7) • Since the file is .ris, EndNote knows what Import Filter to use and will not ask you. • The records will be imported into the open library. • Or you can save the .ris file and then use the Manual Import step (above), selecting the

“RIS” filter instead of the “PubMed” filter. (IE 7 and Windows Xp, Vista)


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D. Search databases from within EndNote

If you are on the TSRI Network, you can connect through EndNote to our databases that have connection files: Medline (OVID), Web of Science (ISI). Or you can search PubMed (NLM) from any computer, as it is freely available on the Internet.

• The library should be in “Local Library Mode” - the books icon.

• Then select the “Online Search Mode” – the globe icon in the library menu.

• Or go to Tools > Online Search, highlight the database and click Choose. • The search box is in the bottom of the temporary library window. • Select the records, and right click or go to References. • Select Copy References To and choose the library (must be open to be listed) or

select “Choose Library” to select a library that is not open.

• To return to your library, click the “Local Library Mode”. • When you leave the “Online” mode, you may be prompted to discard the results from the

online search.


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E. Finding Full Text

1. Set PDF preferences a. PDF attachment preferences: • Go to Edit > Preferences … • Select URL & Links from the left menu. • This box is checked by default, which will create copies of PDFs and store them in the

library.

• If you uncheck this box, adding a PDF file will only create a link to its current location

on your computer. (Does not apply to PDFs found with “Find Full Text” feature.)

2. Finding Full text NOTE: This feature is set to automatically run in the latest update to EndNote X7. This could be an issue with computing times and license restrictions!! Go to Edit >Preferences > Find Full Text and uncheck the box to automatically enable this feature.

a. Using the Find Full Text… feature • Highlight one or more references. • Go to References > Find Full Text…

• The search will run in the background. • In some cases a URL will be added to the URL field instead of a PDF.


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b. Set SFX as the OpenURL tool: You can set up for EndNote to use the Kresge Library’s OpenURL tool, SFX, if the built in “Find Full Text” feature does not find anything. This will not only help you find more PDFs but also facilitate ordering via ILLiad, Kresge Library’s interlibrary loan service. • Select Find Full Text from the left menu. • Check the box next to OpenURL.

• Delete current text in OpenURL Path: box. • Type in: http://sfxhosted.exlibrisgroup.com/scripps/ • Click Apply.

c. To find full text using the OpenURL Link resolver (SFX): • Highlight only one reference and right-click or go to References menu • Select URL > OpenURL Link.

• A window will open with the SFX services. • If electronic access is available, it will be the first link. • Otherwise, use the link to the Library catalog to search for print, or the link to ILLiad to

order articles we do not own. • See a librarian for more information.

Select “OpenURL Link”, NOT “Open URL”

Uncheck to turn off automatic Find Full Text

http://sfxhosted.exlibrisgroup.com/scripps/


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F. Exporting references to Word

1. Exporting references to use in Word (biosketch, stand alone reference list)

• Selected references can be exported from EndNote in a Word format. • Select the references you want to print:

• To print all references click on the All References group. • Or click on a Group to export that group. • Or search for certain references using a keyword, author, keyword. • Or use the CTRL key to highlight more than one reference. Then References >

Show Selected References. • Go to File > Export…

Be sure to note the location the file is saved. Default is where ever the EndNote program is saved.

• Name the file. • Select Output Style. • Save as type: “Rich Text Format (*.rtf)” to have a word processing ready formatted

list. • Click Save.

G. Sharing EndNote Libraries EndNote is designed as a single-user software, however, there may be times when you wish

to share your library, for example with an admin who will add records to your library. 1. Compressed Library

• With the library open, go to File>Compressed Library (.enlx)

• You have the option to “Create” or “Create & Email” (works if you use Outlook) and the option to include attachments (be mindful of copyright!)

• Then choose which references: “All references in the Library”, or you may send only a Group, or some selected references. (Sending references this way maintains the Record Number, which is essential when working with Word documents.)

• Click Next • Choose where to save the compressed library.


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2. EndNote Online /Basic

EndNote now comes with a free 2 year access to EndNote online, an online version of EndNote that you can sync with your desktop library (only one library can be synced) but you can share groups with collaborators. • This is great for keeping your library up to date on several computers. • You can assign read and read/write access to your groups so collaborators can add or

remove references from your shared group. • You can use Cite-While-You-Write directly from the Online version and you and your

collaborators can cite from the shared group online. • Syncing is improving, so test before using. • Required to sync to iPad version (can buy in the Apple store, not part of our license).

To set up your EndNote Web account:

• Open the library you want to sync with the web version. • If you already have a Web of Science alert account, that is also your EndNote Web

login. • To sign up for an EndNote Web account, go to Tools > Sync • Click the Sign up button and follow the instructions to register for an account. • This information should be populated in the Sync menu. • Go to Edit > Preferences • Select Sync • Click Enable Sync

• Enter your email and password you used to create the EndNote Online account. • Select your sync preferences.

3. Another option is to put the library on a shared drive.

• Only one user will be able to open EndNote at a time, and all users must have permissions to read and write to it (see IT for more information about permissions).


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H. Global Changes There are times when it would be useful to make a change to a set of references in a library,

or even to all references in a library. Here are a few examples. CAUTION: There is no “Undo” feature for these global changes. Be sure to read all windows before clicking OK. 1. Edit > Find and Replace

• This will change the text (like a find/replace) in “any field” or in a selected field. Great

for misspellings or adapting subject terms 2. Tools > Change/Move/Copy Fields…

• Used for adding the same term(s) to multiple records at once, or moving the contents of a field to another in multiple records.

• Be sure to select the field, e.g., “Keywords”

o Keywords is a special field that gets indexed (like “Author” and “Journal”) so you want to be sure new terms are on a separate line, or separated by a semicolon ;

• Use the “Insert Special” drop down menu to put a Carriage Return to create a separate line.

• Click OK • Read the pop-up window to be sure it is only editing the records you are showing

• Click OK


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I. Using Groups

1. Custom Groups • Highlight the references (hold the ctrl key while marking several references). • Go to Groups > Add References to…

• Choose a Group listed or select Create Custom Group. • Type in a name (for new group).

2. Using Smart Groups

You can also set up smart groups that will automatically update with new records you import when the search criteria match. E.g., author is bloss • Set up a search (e.g., author Contains bloss). • Click on Options.

• Select Convert to Smart Group. • Type in a name for the Smart Group.

3. Using Group Sets

For an extra level of organization, EndNote X7 allows you to create Group Sets, which are simply folders for placing multiple Groups and/or Smart Groups together.

• Go to Groups > Create Group Set. • Type in a name for the new Group Set. • Drag Groups and Smart Groups to the Group Set.

Documents

EndNote X7 Basics Guide (Win) - Scripps ResearchEndNote X7 Basics (Win) - 3 - 3. Import Journal Term Lists - Required step, best before entering citations, for each library. Adding