EndNote X6 Basics Guide (Mac) - Scripps Research · EndNote X6 Basics (Mac) - 2 - A. Getting Started 1. EndNote Web • The first time you open EndNote X6, you will see an EndNote

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TSRI, 400-S [email protected]

858-784-8705

EndNote X6 Basics Guide (Mac) Contact Angela Murrell Outreach and Instruction Librarian Kresge Library [email protected] 858-784-8705 Download 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...........................................................................................................2 1. EndNote Web ...................................................................................2 2. New Library .....................................................................................2 3. Import Journal Term Lists ...............................................................3 4. Set display fields ..............................................................................4 5. Duplicate record handling ................................................................5 6. Setting Default Libraries ..................................................................5 7. Output Styles ....................................................................................6 8. Import Filters ...................................................................................6

B. Importing records ........................................................................................... 1. Web of Science ...............................................................................7 2. PubMed (Manual Importing) ...........................................................8 3. SciFinder Scholar ...........................................................................10

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

1. Setting PDF preferences ................................................................12 2. Finding Full Text ...........................................................................13

E. Exporting References .................................................................................14 F. Sharing Libraries ........................................................................................15 G. Global Changes ..........................................................................................16 H. Using Groups .............................................................................................17 I. CWYW ......................................................................................................18 J. Format paper (for non-Word, non-Papers) ................................................19

EndNote X6 Basics (Mac)

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A. Getting Started 1. EndNote Web

• The first time you open EndNote X6, you will see an EndNote Web option box. • EndNote Web is a web based version of EndNote that you can access from any Internet

computer. EndNote Web is now fully synced with the desktop 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.

• Click Cancel.

2. Create a new Library

• Open EndNote • Select Create a new EndNote library in the window that opens (or choose New… from

the File menu) • Click OK. • In the next window, enter a name in Save As:. • Select location (use desktop for this training) in Where:.

• You can select Save as Package to combine the .enl and .DATA folder. However, this is

not recommended if you will be sharing this with Windows users. • Click Save.


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3. Import Journal Term Lists (required step, best before entering citations, do for each library)

Adding these will allow standard journal titles and abbreviations to link together. • Go to Tools > Open term Lists > Journal Term List • Click on the Lists tab.

• Be sure Journals is highlighted, then click Import List… • The lists should be found in Applications\EndNote X6\Terms • Select one. (medical.txt for biologists, chemical.txt for chemists) • Click Choose. • Repeat the process for the other list(s) you wish to add. • Click Close when done.

• 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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4. Set Display Fields • Go to the EndNote X6 menu and select Preferences • 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 can remove the “Read/unread” fields and rating fields here.

• You may also change the heading name for the column. The default is the Generic name

for the field selected. • Click Save.


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5. Duplicate record handling • Go to the EndNote X6 menu and select Preferences • 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. • Decide if EndNote should Automatically discard duplicates when searching online. • This does not apply when searching outside of EndNote.

6. Setting Default Libraries

• Go to the EndNote X6 menu and select Preferences • 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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7. Output Styles Output styles are used to create bibliographies or format Word documents. Currently there are over 5000 Output styles available. Only 400+ Styles are downloaded with EndNote.

• You can browse the downloaded Styles: • Go to Edit > Output Styles > Open Style Manager… • In the window that opens, mark the box next to any styles you might use.

• Close the window after you have selected your styles. Do not click Edit. • These will appear now in the Edit > Output Styles drop down list. • If you would like to download additional Styles, go to

http://endnote.com/downloads/styles • New Styles will open in EndNote. • Go to File > Save As > remove the word “copy” and the space after the file name • Files are saved to an EndNote folder created in your Documents folder

8. Select Import Filters (optional step, convenience for later) Import filters convert citations from databases and .txt files into EndNote records.

• Go to Edit > Import Filters > Open Filter Manager… • In the window that opens, mark the box next to filters you might use often.

• Close the window after you have selected your filters.


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B. Importing records into EndNote Recommended: Use Firefox or Netscape.

1. Web of Science

2. Mark records from your search 3. Select “EndNote” from the “Send To:” option menu. 4. In the pop up, choose “Full Record” 5. Click Send 6. Click Cancel when complete

For Firefox: select Open with: and choose the EndNote program at Applications > EndNote

X6 > EndNote X6

If the file does not automatically import, or for Internet Explorer or Safari: • A .ciw file will be saved. • Locate the file. (Location set in Preferences of Safari) • Or select “Show in Finder from Downloads window

• Drag the file to the EndNote icon in the Dock, OR • Right click (or hold the ctrl button and click) on the file. • Select Open with then select Other… • Then select “EndNote X6” (located in Applications > EndNote X6 > EndNote X6)


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7. 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)

o If you choose “File” instead, you have to choose Format as “Medline” • Click Create File.

For Firefox users:

• Select the “Open with” option and click on Choose… • Locate the EndNote program (Applications > EndNote X6 > EndNote X6 ) • Click Open. Then click Ok.


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• Select “PubMed (NLM)” from the list in the Choose an Import Filter window.

• Click Choose.

For IE or Safari users:

• A nbib file will be saved to your computer. • Go to EndNote:

o Select File >Import. o In the Import box that opens, select the file (usually called “citations.nbib”). o Use the pull down list next to Import Options. o Select Other filters… o Then select “Pubmed (NLM)”.

o Click Import.


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8. SciFinder Web

• Search SciFinder as usual. • Once you have marked the citations you wish to import. • Click on Export on the menu bar of the result set. • Name the file. • Under For: select “Citation export format (*.ris)”.

• Click Export. • Depending on the browser you are using, a popup window may appear.

• For FireFox: Mark “Open with” and

click Choose • Select the EndNote Program • Click OK.

• For Safari: click SAVE. • Go to EndNote, File>Import • Select the file. • Choose “Reference Manager (RIS)” as

the Import Option • Click Import


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C. Search databases from within EndNote If you are on the TSRI Network, you can connect through EndNote to our databases

that have connection files. Be sure you use the database name and the provider from the list below: Medline (OVID) Web of Science (ISI) PubMed (NLM)-free

• First the library should open in “My Library” mode. If not you can go there by

clicking on the house icon. If you close the library in “My Library” mode, the library will open in “My Library” mode the next time you open it.

• Then select the Online Search Mode (Globe) then click on the database:

PubMed(NLM)

• If the database you want is not listed under “Online Search” click “more…” • Or use Tools> Online Search… > New Search to begin an online search.

o Highlight the database and click CHOOSE o No password is required, so click OK and the database should open.

• Perform the search • Results are imported into a temporary window

• Select the desired reference(s) • Go to References > Copy references to… then select the library Hint: To save time, use the combined mode when you know only 1 record will be found, i.e., you have the PMID. But be careful, ALL results go directly into the Library.


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D. Finding Full text

1. Set PDF Preferences a. PDF attachments: • Go to the EndNote X6 menu and select 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

a. Using the Find Full Text… feature • This feature does not work on all references, but is an aid to getting the PDFs that are free

or that Kresge Library subscribes to. • Highlight one or more references. • Go to References > Find Full Text > 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 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. • Go to the EndNote X6 menu and select Preferences … • Select Find Full Text from the left menu

• Check the box next to Enable OpenURL. • Delete current text in OpenURL Path: box. • Type in: http://sfxhosted.exlibrisgroup.com/scripps/ • Click Apply.

c. Using the OpenURL Link resolver (SFX@TSRI)

• Highlight a reference, • Then go to References > 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 ILLiad to order articles we do not own. (See a librarian for

more information.)


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E. Exporting references 1. Export references

• Selected references can be exported directly from EndNote into an RTF. • If any references are highlighted only those will export. • To print all be sure all references are showing (References > Show all

References) • Or search for certain references using a keyword, author, keyword, etc. • Or use the COMMAND or 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. • Name the file. • Save file as type: “Rich Text Format” to have a word processing ready formatted list. • Select Output Style. • Click Save.

• Now go to Edit > Output Styles and select the style, it should now be in the drop

down list. • Finally, go to File > Print…

F. 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” (will open Entourage) • 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 Web 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. • HOWEVER, the group you share will not sync to the other users desktop version. It will

sync on your desktop, but it will only be available to them online. They can add the records to their library, but this could change the record number.

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 EndNote X6 menu >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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G. 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 > Change text

• 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 and Move 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 between entries. • 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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H. Using Groups EndNote X6 allows you to group references within a library.

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 lerner, r • Click on the Search tab at the bottom of the library window. • Set up a search (e.g., author Contains learner, r), click Search • Click on the gear button next to the Search button.

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

3. Using Group Sets

For an extra level of organization, EndNote X6 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.


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I. CWYW - Cite While You Write Cite While You Write (CWYW) is a feature in EndNote that allows you to insert

citations into a paper and format the MS Word, or Apple Pages ’09 document to the journal publication style requirements of hundreds of journals and publishers.

Please refer to the additional handout for your word processor. All the functionality is the same, but some of the tools names and how you access them may have changed from older versions of EndNote.

NOTE: If you use any other word processing program use the “Format Paper” tool to

format an .rtf document. J. Format Paper (for use with unsupported word processed documents)

• When using another word processing software, insert references into the paper in the following format:

{author last name, year #reference number} Example: {Agah, 2005 #105} • The reference number is found in the header of the record in the EndNote library.

• This number can also be displayed in the Display Fields showing at the top of the library. • To do this, go to EndNote > Preferences and choose Display Fields. • Select Reference Number from near the top of the pull down menu list.

• When the paper is finished, save it as an rtf (rich text format) file.


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• Close the paper. • Open the EndNote library the references from the paper come from. • Go to Tools > Format Paper> Format Paper. • Select the rtf file you just saved. • Select the Output Style.

• Click Format. • The default name will be the paper name with the output style name tacked on (for

example: mypaper-ACS). This is recommended. (To format in a different style you will need to have the original unformatted file.)

• Choose Where to save the file and click Save. • To save in another Output Style format, repeat these steps with the original, unformatted

rtf file.