EndNote X5 Basics Guide (Win)

TSRI, 400-S [email protected] 858-784-8705

EndNote X5 Basics Guide (Win) 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 ............................................................................................................. 1. EndNote Web ...................................................................................2 2. New Library .....................................................................................2 3. Import Journal Term Lists ...............................................................3 4. Set Display Fields ............................................................................4 5. Duplicate record handling ................................................................4 6. Output Styles....................................................................................5 7. Import Filters ...................................................................................5 B. Importing records ........................................................................................... 1. Web of Science ................................................................................6 2. PubMed ............................................................................................7 3. SciFinder Web ................................................................................9 C. Search databases from with EndNote ........................................................10 D. Find Full Text ............................................................................................... 1. Set PDF Preferences ......................................................................11 2. Finding Full Text ..........................................................................12 E. Exporting References .................................................................................13 F. Sharing EndNote Libraries ........................................................................14 G. Global Changes ..........................................................................................15 H. Using Groups .............................................................................................16 I. CWYW (see additional handout) ...............................................................17 J. Format paper (for non-Word documents) ..................................................17

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EndNote X5 Basics (Win)

A. Set Up 1. EndNote Web • The first time you open EndNote X5, 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. Right now it is not fully synced with the desktop EndNote. You can set up an EndNote Web account from within Web of Science. You can create or connect your EndNote Web account to the desktop in the future.

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Simply click Finish.

2. Create a new Library: • Go to File> New.

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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.

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

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The lists will be found at Local Disc C:\\Program Files\Endnote X5\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.

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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 Edit 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.

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You may also change the heading name for the column. The default is the Generic name for the field selected. Click Apply. Click OK.

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

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The fields must match: exactly abbreviations do NOT match full journal names. 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. -4-


6. 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.

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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.

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7. Import Filters 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.

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Close the window, do NOT click Edit. -5-


B. Importing records into EndNote 1. Web of Science • Mark records from your search • Scroll to the bottom (or click “more options” at the top.) • Step 1: select which records to export: e.g., “Selected Records on page” • Step 2: select what details to export: “Authors, Title, Source” or “Full Record” o Note: selecting “plus Cited References” imports the citations for the reference list into the NOTES field, it does not import each cited reference into it’s own record. • Step 3: click the EndNote button.

For IE users: • Endnote X5 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 “export” again.

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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: Web Export helper”. • Click OK

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If EndNote does not open click “Export” on the Web of Science screen. Otherwise click “Back to Results” 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.

For IE 7 users: • A File Download window appears

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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.

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In EndNote:

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. • 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). IE 8 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. • •

For Firefox users:

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From the “Open With” pull down menu choose Other…(or it may say Browse) Select the EndNoteX5 program from the list. (DO NOT select the library.) Click OK.

For both Firefox and IE 8: • EndNote will 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. -8-


3. SciFinder Web Step 1: • Search SciFinder as usual. • Once you have marked the citations you wish to import. • Click on Export.

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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

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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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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: Medline (OVID), Web of Science (ISI). Or you can search PubMed (NLM) from any computer, as it is freely available on the Internet. •

First set the library to “Local Library” mode by clicking on the books icon. If you close the library in “Local Library” mode, choosing Tools>Online Search will automatically open the Online mode with the temporary library.

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Then select the Online Search Mode icon in the library menu.

NOTE: In EndNote X5 (and X2 – X4), if you do not select the “Online” mode, all results from the search will be automatically imported into the open library. • 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.

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To return to your library, click the “Integrated” mode or “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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D. Finding Full Text EndNote can now assist you with locating and downloading the full text PDF or URL link for articles in your library. There are a few settings associated with PDF downloading and viewing. 1. Set PDF preferences a. PDF attachment preferences: • Go to Edit > Preferences … • Select URL & Links from the left menu. • The Box is checked for Copy new PDF files to the default file attachment folder and create a relative link.

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PDFs are saved in the File Attachment field, simply drag and drop the PDF into the field. Any PDFs found automatically via the “Find Full Text” feature (see below) will be copied to the Data folder by default.

b. New PDF preview X5 has a quick view that allows you to view and edit attached PDFs. • Select PDF on the left. • The default setting is to have the PDF preview on (option is checked). • To remove the PDF quick view panel, uncheck the box.

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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. • You can use this feature before using the URL > OpenURL Link tool. • Highlight one or more references. • Go to References > Find Full Text…

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

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.

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

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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.

Select “OpenURL Link”, NOT “Open URL”

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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.

E. 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 other field

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search, using References > Search References or click . • 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.

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F. Sharing EndNote Libraries EndNote is designed as single-user software; however, it allows multiple authors to insert their own references from different libraries. EndNote will look for duplicates and merge these within the Word document. There is no need to share the actual library, or to create a new library for each paper you write. 1. Compressed Library However, there may be times when you wish to share your library, for example with an admin who will add records to your library. To do so you will want to create a “Compressed Library (.enlx)” and sent that. NOTE: A word of caution, as with Word or Excel files, once you send an EndNote library to someone, any changes they make on their copy are not reflected in the copy you have on your computer. If you both make changes independently, the changes you made will be lost when the library is passed back to you and you open it. To create the compressed library: • With the library open, go to File>Compressed Library (.enlx)

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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. The default library name is the original library name, but uses the extension “.enlx” For example, “Murrell.enl” becomes “Murrell.enlx” To open from the compressed library, simply double click the .enlx file from the folder you wish the library to be stored in. It will automatically expand and create the .enl and .Data folders using the name of the .enlx. For example: double clicking “Murrell.enlx” in My Documents folder would create both the “Murrell.enl” and “Murrell.Data” in My Documents REPLACING the existing “Murrell.enl” and Murrell.Data” files if they are stored in the same folder (My Documents in this example).

2. 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). - 14 -


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

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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.

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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

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Click OK

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H. Using Groups EndNote X4 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…

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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 on Options.

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

3. Using Group Sets For an extra level of organization, EndNote X4 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. - 16 -


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 OpenOffice.org Writer 3) document to the journal publication style requirements of hundreds of journals and publishers. Word 2003/2007: See the handouts provided. Word 2010: see online tutorial OpenOffice.org Writer 3: The functionality is the same, but some of the tools names and how you access them have changed. Toolbar and menu in OpenOffice.org Writer 3:

NOTE: CWYW does not work with WordPerfect. If you use WordPerfect you must 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 (WordPerfect, etc.) insert references into the paper in the following format: {author last name, year #reference number} Example: {Agah, 2005 #105}

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The reference number is found in the header of the record in the EndNote library.

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

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

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Click Format. The default name will be the paper name with the output style name tacked on (for example: cwyw-Nature.rtf). This is recommended. (To format in a different style you will need to have the original unformatted file.)

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Choose the location (default is where the original file is saved) and click Save. To save in another Output Style format, repeat these steps with the original, unformatted rtf file.

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