EndNote X4 Basics Guide (Win) - Scripps Research …scripps.edu 858-784-8705. EndNote X4 Basics Guide (Win) Contact . Angela Murrell . Outreach and Instruction Librarian . Kresge Library

endnotex4trainguidepc Created by amurrell

TSRI, 400-S [email protected]

858-784-8705

EndNote X4 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 ...........................................................................................................2 1. New Library .....................................................................................2 2. Import Journal Term Lists ...............................................................2 3. Set Preferences .................................................................................3 4. Output Styles ....................................................................................4 5. Import Filters ...................................................................................4

B. Importing records .........................................................................................5 1. Web of Science ................................................................................5 2. PubMed ............................................................................................6 3. SciFinder Web ................................................................................8

C. Search databases from with EndNote ..........................................................9 D. Find Full Text ...........................................................................................10 E. Exporting References .................................................................................12 F. Sharing EndNote Libraries ........................................................................13 G. Global Changes ..........................................................................................14 H. Using Groups .............................................................................................15 I. CWYW (see additional handout) ...............................................................16 J. Format paper (for non-Word documents) ..................................................16

Questions Please feel free to ask questions throughout the workshop. If you have questions that occur to you after the workshop, or that you wish to discuss individually, please feel free to contact me at any time.

mailto:[email protected]

http://www.scripps.edu/library/Endnote.html

EndNote X4 Basics (Win)

A. Set Up

1. Create a new Library: • Go to File> New. • Click OK. • 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.

2. 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, then click Import List…

• The lists will be found at Local Disc C:\\Program Files\Endnote X4\Terms Lists\ (use

the pull down for look in:). • Select one (medical.txt is the best list for journals from PubMed). • Click Open. • Repeat the process for the other list(s) you wish to add. • 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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3. Set Preferences

a. Set EndNote default Library to open when EndNote starts: • Go to Edit > Preferences… • Select Libraries from the left menu. • Next to “When EndNote starts:” choose an option:

1. Open the most recently used library 2. Open the specified library 3. Prompt to select a library 4. Do nothing

b. Rearranging the columns in the library window view: • 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.

• Click Apply. • Click OK.

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4. Select Output Styles (optional step, convenience for later) Output styles are used to create bibliographies or format Word documents.

• 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.

5. 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.

• You can always select a filter when you use it. • Close the window after you have selected your filters (do NOT click Edit).

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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.) • Select “Selected Records on page” in the Output Records Step 1. • Select “Full Record”

o Note: selected “plus Cited References” imports the citations for the records into the NOTES field of the marked record, it does not import each cited reference into it’s own record.

• Click “Export to EndNote, RefMan or other reference software”

For IE users: • Endnote X4 will import the record(s) into the open library. • 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

• 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 “File”. • Then select “MEDLINE” for Format. • Select the sort order. • Click Create File.

For IE 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 “pubmed_result.txt”). • 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 filter from the pull down list of Import Option. If the filter has

not already been used it will not show in the list. Select Other filters… to search for the appropriate filter (list of filters for TSRI databases given below).

o 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). For Firefox users:

• From the “Open With” pull down menu choose Other… • Locate the EndNoteX4 program (or navigate to C:/Program Files/EndNote

X4/EndNote.exe ) DO NOT select the library. • Click OK. • The Choose An Import Filter window will open. • Select “PubMed (NLM)” from the list. • Click Choose. • Records are imported into the library that is open.

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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. • 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.

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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.

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

NOTE: In EndNote X4 (and X2 or X3), 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.

• 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 1. Set PDF 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.

• PDFs are saved in the File Attachment field, simply drag and drop the PDF into the field.

2. 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…

• 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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Sometimes EndNote cannot locate a PDF. There could be a problem with the journal’s website that does not allow EndNote to go directly to the PDF, or it may be that the publisher requires a subscription, and the TSRI Library does not purchase that journal subscription. For records where no PDF is found, you can use an alternative method: the OpenURL Linker. 3. Set SFX as the OpenURL tool:

• 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.

4. 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”

• 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.

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E. Exporting references

1. Printing references • Selected references can be printed directly from EndNote. • 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

search, using References > Search References or click . • Or use the CTRL key to highlight more than one reference. Then References >

Show Selected References. • Next select the Output Style to print the references. Go to Edit > Output Styles.

• The style checked is the current style. Select the style you want to use. • If you do not see the style you want to use in the list, select Open Style

Manager… at the top of the list. • Scroll through and put a check in the box next to the style you want. • Close the window (DO NOT click Edit). • Now go to Edit > Output Styles and select the style, it should now be in the drop

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

2. Export References to Word: • Select references as above. • 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.

3. Export references to Import into another EndNote library: • Select references and show references as above. • Go to File > Export… • Name the file. • Save as type: “Text file (*.txt)” • Select Output Style as “EndNote Export”. • Click Save. • To Import the file, open the destination EndNote library. • Select File> Import. • Select “EndNote Import” as the Import Option.

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F. Sharing EndNote Libraries EndNote is designed as a 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)

• 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).

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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 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…

• 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.

• 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.

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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 OpenOffice.org Writer 3) document to the journal publication style requirements of hundreds of journals and publishers.

Word 2003/2007: See the handouts provided. 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 may wish to try Reference Manager software, or 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}

• 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 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.

• 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.)

• 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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