contents€¦ · endnote permits the importing of properly formatted files or even folders of files...

EndNote X7 WINDOWS / May 2015 Peter Shipman [email protected]

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EndNote X7 Technical Support http://endnote.com//support/contact-support

Training Videos http://endnote.com/training#video

Download Output Styles http://endnote.com/downloads/styles

Contents

Create an EndNote Library

Edit Preferences

Standardize Journal title names in every Library

To freeze updating of future journal name changes in the Journal Terms List

EndNote Library Modes to work inside or outside the Library

Exporting (i.e. Direct Export) from database to Library

Browser and/or computer settings to enhance success of direct export

Traveling Library Export from Word document to Library

Export PubMed records to Library

Importing to Library: from PDF from PubMed from Ovid MEDLINE from EndNote Library

Adding references manually to Library

Editing EndNote references (repairing improper data or adding data to a Library reference)

Attaching Full Text PDFs to an EndNote reference manually

Find Full Text – attaching links or PDF to EndNote reference using Greenblatt Library link resolver

Organize References into Groups to quickly locate a tagged subset of records in a Library

Output Styles – format citations in a Word document to a specified style

Cite While You Write – inserting citations in a Word document

Edit and Manage References in the Word document to change formatting

EndNote Manuscript Templates to quickly setup Word in a specific Output Style

PDF Handling – setup Preferences to hold PDFs in a specific folder

Back Up Libraries

EndNote Online - server-based EndNote from Web of Science

Miscellaneous facts about Libraries

Sharing an EndNote Library through EndNote Online

mailto:[email protected]

http://endnote.com/support/contact-support

http://endnote.com/training#video

http://endnote.com/downloads/styles


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Groups – tag references

for retrieval by groups

Search – to search for

references in a Library

Reference List –

customize display

Tabs – edit references,

view formatted

references, view PDFs,

and attach PDFs

Create an EndNote X7 Library Open the EndNote program.

In EndNote: File > New

When New Reference Library Window opens, create an EndNote Library at File Name.

Name the EndNote Library, select the Save In location, click Save.

The file type is EndNote Library (*.enl).

What is the EndNote Library?

An EndNote Library is a file with the extension ENL with a corresponding DATA folder created automatically with

the ENL file. The ENL file and the DATA folder may be stored like any other file, including copying a backup. The

DATA file hold PDF, sound files, and video files attached to references in the Library. The Library collects and holds

references transferred online from files or databases, or created manually.

EndNote Library panels The EndNote Library window contains four panels that can be configured using the Layout link in the lower right-

hand corner of the window (Groups “Left” / Reference Panel “Right” is displayed below). Choosing Layout of

Reference Panel Right – Split or Reference Panel Bottom - Split will display the PDF tab in a separate panel.

Edit > Preferences to customize EndNote “Display Fields” and “Display

Fonts” – other features may also be configured.

The Search Panel link in the upper right-hand corner can be toggled to either Show

or Hide that specific panel as needed; toggling to Hide the rarely-used Search Panel

is a good way to manage screen space.



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Standardize journal title names in every Library

An EndNote Output Style refers to how a reference is formatted in a References section of a journal

article or a bibliography. There are hundreds of Output Styles – examples are “APA 6th,” “New England

Journal of Medicine,” “JAMA,” “Stroke,” etc.)

APA 6th

van Werkhoven, J. M., Schuijf, J. D., Gaemperli, O., Jukema, J. W., Boersma, E., Wijns, W., . . . Bax, J. J. (2009). Prognostic value of multislice computed tomography and gated single-photon emission computed tomography in patients with suspected coronary artery disease. Journal of the American College of Cardiology, 53(7), 623-632. doi: 10.1016/j.jacc.2008.10.043

Stroke

1. van Werkhoven JM, Schuijf JD, Gaemperli O, Jukema JW, Boersma E, Wijns W, et al. Prognostic value of multislice computed tomography and gated single-photon emission computed tomography in patients with suspected coronary artery disease. J. Am. Coll. Cardiol. 2009;53:623-632

Journal names in some Output Styles may be full (APA 6th):

Journal of the American College of Cardiology

Journal names in some Output Styles may be abbreviated (Stroke): J. Am. Coll. Cardiol.

Problem: databases send full and abbreviated journal names inconsistently to the EndNote record,

creating an unstable Journal Term List for the EndNote Library. This means abbreviated journal names

appear in the Full Journal column of the Journal Term List, and full journal names appear incorrectly in

the Abbreviated Journal column of the Journal Term List. The formatting of full and abbreviated journal

names in Word documents are inconsistent when the source of the journal names are databases.

Solution: override the database-provided journal names by importing the Medical Journal Terms List

into the EndNote Library, and then freezing the updating of the Journal Term List for the EndNote

Library. It is a best practice to import the Medical Journal Terms List into the empty EndNote Library

before populating the library with references.

Importing the Medical Journal Terms List into an EndNote Library will provide the proper journal

names to over 13K journal titles;

the Medical List is based on the National Library of Medicine’s official names and abbreviations

of journals.

To view an EndNote Library’s Journal Terms List Tools > Term Lists > Journal Terms List

Each EndNote Library has its own Journal Terms List

If an EndNote Library contains references and the Medical Journal Terms List has not been imported into

the EndNote Library, delete the Library’s existing Journal Terms List: Tools > Open Term Lists > Journals Term List

Select all titles, click Delete Term; close List.

When creating NEW Libraries or when a Library has an empty Journals Term List, import the Medical

Journals Term List:



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Tools > Define Term Lists highlight Journals and click Import List

C:\ProgramFiles\EndNoteX7\TermLists highlight Medical.txt and click Open.

Click OK; click Close in the Term Lists window.

To FREEZE updating of future journal name changes in the Journal Terms List for the EndNote Library: Edit > Preferences > Term Lists

uncheck “Update lists when importing or pasting references”

uncheck “Update lists during data entry”

Click OK

EndNote Library Modes to work inside or outside the Library

Three icons designating a specific mode appear in the upper left-hand corner of

EndNote:

Book icon – Local Library Mode - preferred default – depress icon to engage

Globe icon – Online Search Mode (Temporary Library) – use sparingly

Globe + Books icon – Integrated Library and Online Search Mode - avoid

Why Local Library Mode is preferred: EndNote encourages Online Search Mode to transfer database

records to an EndNote Library, essentially searching the database from the Search Panel in EndNote.

Searching from the Search Panel is discouraged because it only works with free databases (i.e. PubMed).

Other useful Greenblatt Library databases are subscription-based and the Online Search Mode and the

Intregrated Library and Online Search Mode do not work. Solution: do all searching of databases outside

of the EndNote program.

Exporting (i.e. Direct Export) from database to Library

Exporting is the preferred choice to transfer records from a database to an EndNote Library. While

exporting records is normally a reliable method that is fairly easy to do, some users may not be able to

export records in all instances because of operating systems, choice of browser, personal computer

settings, or database limitations.

Open an EndNote Library to receive the records. Search the database and mark records to be

transferred to the EndNote Library. Follow the steps to export the record to EndNote.

Commonly used biomedical databases that Export records to EndNote

PubMed: Send To > Choose Destination: Citation manager, click Create File

CINAHL Plus: Open Folder View > Direct Export in RIS Format

Ovid MEDLINE: Export link > Export to EndNote > Complete Reference > click Export Citations

Web of Science: send references to the Marked List > Step 2. Output Records (also select Abstract

content), Step 3. Send to EndNote desktop

SciFinder: Click “Export” at top menu bar. In Export window, move radio buttons as needed,

Export: Selected; For: Citation Manager – Citation export format (*.ris); click Export button.



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Export (the transfer of records from a database to the EndNote Library) is successful when marked

records are spontaneously added and displayed in the Reference List panel of the EndNote Library.

Browser and/or computer settings to enhance success of direct export

Associate a file type (NBIB formatted file [PubMed], OVID Direct, RIS) to open (export) database records

with a specific program (ResearchSoft Direct Export Helper OR EndNote X7)

Firefox browser: Tools > Options. At Options, go to Applications. At Applications, choose

ResearchSoft Direct Export Helper or EndNote X7 to open NBIB formatted file (PubMed) or OVID

Direct.

WINDOWS 7

Start > Control Panel > Default Programs

Click Associate a file type or protocol with a program

Select .nbib

Use recommended ResearchSoft Direct Export Helper

Note: in the example below all are directed to open the output files from those databases with

the ResearchSoft Direct Export Helper. EndNote X7 can also be used to open these types of files.

.ciw (Web of Science)

.nbib (PubMed)

.ovd (OVID Direct)

.ris (RIS Formatted File) are

Traveling Library export from Word document to Library

When EndNote references are inserted into Word documents, such a Word document is embedded with

the core EndNote reference information and Word document is termed as containing and EndNote

Traveling Library. When this Word document is shared with research colleagues also using similar

versions of EndNote, the embedded EndNote records (the Traveling Library) in the Word document can

be exported to a colleague’s EndNote Library.



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Open the Word document.

In the Word ribbon on top of the document, click the EndNote X7 tab.

At the pull-down menu at Export to EndNote, select Export Traveling Library.

When the Export Traveling Library window opens, use the

pull-down menu or Browse options to locate the EndNote

Library to receive the references. Click OK.

Export PubMed records to Library 1. Open the EndNote Library to receive PubMed

records.

2. Open PubMed from the Greenblatt Library home

page.

3. Search PubMed. At search results pages, check the

records to be exported from PubMed to the

Library (see image at right).

4. At top of search result page, click Send to pull-

down menu. Select Citation manager, and click

Create File.

5. Records should transfer and display in the open EndNote Library. Each browser may handle the export in

a different manner.


http://www.gru.edu/library/greenblatt/

http://www.gru.edu/library/greenblatt/


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Importing to Library

EndNote permits the importing of properly formatted files or even folders of files into a Library.

Import from PDF

In some instances, EndNote can scrape information from a PDF - creating an EndNote reference and

attaching the PDF to the EndNote reference (storing the PDF in the Library’s DATA folder). Some of

references imported this way are equivalent to information from a database record, and some of the

information is much less than the database record. Sometimes no information can be scraped from the

PDF into an EndNote reference, often from books or white papers, and should be entered into EndNote

manually.

The process for PDF import:

Open an EndNote Library File > Import > File

OR File > Import > Folder (of PDFs)

At Import File window:

Import File: (Choose PDF)

Import Option: PDF

Click Import.

When to Import from database

When Export does not transfer database records directly to an EndNote Library, or when not at a

workstation with the EndNote program, save database search results in a properly formatted file and

Import the records into an EndNote Library.



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Import process

Search the database.

Save the records in a formatted file.

Import the file to an open EndNote Library: File > Import

In the Import File window, at Import File field click Choose to locate the saved file.

At Import Option, choose the database or format that matches to the saved file best.

If also asked to select an Import Filter to open the saved file, choose the name of the database

and name of the vendor providing the database [ex: Cochrane Library, MEDLINE (OvidSP),

WorldCat (OCLC)]

Click Import.

OR, more quickly, right-click on formatted file and left-click Open with the EndNote program to import.

Import from PubMed

Mark records from search results.

At the Display Settings pull-down window,

change Format from Summary to

MEDLINE; click Apply.

Use browser’s Save As command to:

Name the file

Select File Type as Text File or Plain

Text.

Remember the saved location of the file.

Open the EndNote Library.

Begin the Import Process (File > Import), locate the

saved file and place it in Import File field.

At Import Option, choose PubMed (NLM).

If PubMed (NLM) is not visible as an option, click Other

Filters link to select PubMed (NLM).

Click Import.



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Import from Ovid MEDLINE

Mark records from search results.

Click Export link at Results page.

Export To Reprint/Medlars

Select Fields to Display Complete Reference

Click Export Citation(s).

Plain text file (“Medlars”) is created in default download folder.

OR, more quickly, go to the default download folder:

Right click on Medlars > Open With > (left click) EndNote X7

Import from an EndNote Library

Import an EndNote Library from a research colleague.

Open an EndNote Library to receive the colleague’s EndNote

Library.

File > Import

Import File field: Choose the EndNote Library (.enl) file to be received.

Import Filter field: select EndNote Library

Click Import

Adding references manually to Library

Some records or sources for a document are not present in a database and EndNote references have to

be created manually:

Open the EndNote Library.

References > New Reference

At the New Reference window, select a Reference Type from the pull-down menu (Journal

Article is the default); other common Reference Types are web page and edited book.

Enter information into the fields of the record.

Each author gets a separate line; place a comma after any group author.

Close the New Reference window to save the record to the Library.

Editing EndNote references (repairing improper data or adding data to a Library reference)

Because data elements are not always uniform in databases, or as database records are modified over

time such as those in PubMed that undergo processing and final indexing, EndNote references should

be inspected for quality so the reference inserted into a Word document is formatted properly by

EndNote. Below is a group author with a comma that needs moving:

Plain Text

options



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Other parts of EndNote references that often require editing:

- Title in Headline Format should be edited to sentence format

- Author names should follow Last, First format

- DOI information should only contain the number

- Author names with suffixes require a second comma

Attaching PDFs to an EndNote reference

PDFs can be inserted into the File Attachments field of an EndNote reference manually or by applying

the Find Full Text feature in EndNote.

File Attachments enhancement EndNote documentation indicates up to forty-five (45) files may be attached to a single EndNote reference. Sound files and video files may also be added to the File Attachment field.

Manual method: Cut/Paste or Drag/Drop the PDF into the File Attachments field of the EndNote

reference.

Find Full Text: set-up Preferences to use the Library’s link resolver to attach PDFs to the EndNote

reference.

NOT ALL PUBLISHERS ALLOW ENDNOTE TO MINE PDF FULL-TEXT DOCUMENTS; NOT ALL LIBRARY- OWNED FULL-

TEXT CONTENT CAN BE LOCATED USING THE “FIND FULL TEXT” METHOD IN ENDNOTE.

Edit > Preferences > Find Full Text

Insert the Open URL Path http://sfx.galib.uga.edu/sfx_med1 At the “Authenticate with” field, insert the URL http://ezproxy.gru.edu/login?url= Click Apply. Click OK.


http://sfx.galib.uga.edu/sfx_med1

http://ezproxy.gru.edu/login?url


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Find Full Text

EndNote has a Find Full Text feature that attempts to mine the Greenblatt Library eJournal collection, to

attach the matching full-text document to the EndNote reference.

Highlight the references in the Reference List panel; CTRL + A.

At the Tool Bar, click Find Full Text icon (GLOBE + RED ARROW + DOCUMENT icon)

If appropriate, logon to Off-Campus Access to Greenblatt Library.



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Monitor process of full-text mining at the Groups Panel (Paper Clip icon in Library panel

indicates a found PDF)

Organize References into Groups to quickly locate a tagged subset of records in a Library

Tag References by Groups to quickly locate relevant References without using the Search Panel. In the

image above, under My Groups, three Custom Groups were created: Diet-LowCarb, Diet-Medit, and

Exercise with the corresponding number of records appearing in each group in parentheses. Smart

Groups can be created to tag new References based on specific criteria; Combination Groups can

combine existing Custom or Smart Groups with Boolean operators (AND, OR).

Custom Group

[right-click] My Group > Create Group, name group

Highlight references in Reference Panel, drag/drop OR right-click to Add to [group name]

Smart Group

[right-click] My Group > Create Smart Group

Complete search statement, click Create



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Combination Group

[right-click] My Group > Create From Groups

Complete Create From Groups search box to combine existing My Groups.

Output Styles – format citations in a Word document to a specified style

EndNote contains hundreds of output styles to take the data from an EndNote reference and insert that

data in a Word document in the specified style: examples would be JAMA, New England Journal of

Medicine, APA 6th, Vancouver, etc. Create a custom menu of desired Output Styles in EndNote; EndNote

loads several default styles. To select or deselect an Output Style from the menu in EndNote:

Edit > Output Styles > Open Style Manager

Check or un-check Output Styles [image at left] to appear in EndNote menu bar [image at right].

Cite While You Write – inserting citations in a Word document

Installing EndNote X7 enables EndNote’s Cite While You Write in Microsoft Word (2007, 2010, 2013); an

EndNote X7 tab appears in the MS Word ribbon. Cite While You Write inserts and embeds the EndNote

reference in the Word document and outputs the reference in the Output Style selected.



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Edit and Manage References in the Word document to change formatting

Because EndNote X7 embeds coded information into a Word document, do not attempt to use the

keyboard to overwrite or delete embedded content. In Word, at the EndNote X7 tab, always use Edit &

Manage Citation(s) to modify or remove references inserted in the document.

The Edit & Manage Citations window permits:

the removal of the reference from the document;

when multiple references share the same insertion point, allow a reordering of the references

when the Output Style allows;

editing the display of in-text elements at the insertion point, such as year of publication or

author name(s), when the Output Style allows.

The Edit & Manage Citations windows has two panes: the upper panel removes or reorders References,

the lower panel modifies the in-text appearance of References.



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Click the Edit and Manage Citation(s) link in Word’s EndNote X7 tab ribbon to open the edit window:

The lower pane pull-down menu allows the exclusion of elements of the in-text citation such as author

or year:



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EndNote Manuscript Templates to quickly setup Word in a specific Output Style

To save time in the formatting of the Word document, EndNote contains several Word Manuscript

Templates. The Templates are found at the Tools menu and at the EndNote Support web site. When

opening the templates, enable the set-up wizard to add title, author, etc. information easily. For

example, a formatted APA 6th Word template with author, title, running head, headings, etc. can be set

up in less than ten minutes.

PDF Handling – setup Preferences to hold PDFs in a specific folder

In EndNote Preferences, (Edit > Preferences > PDF Handling) a specific folder can be

designated to hold new PDF’s. When new PDF’s are added to the designated folder, an open EndNote

Library can have references imported automatically from information scraped from the new PDF’s; the

PDF’s could then be attached to the corresponding EndNote reference by cut/paste or drag/drop.

The Search Panel can not only search any part of the EndNote reference, but it can search any text in a

PDF File Attached to the EndNote Reference.

When the PDF tab in the Tabs Panel for a reference is selected, a toolbar in the Tabs Panel allows the

saving, printing, and emailing of the PDF, as well as a highlighting tool and a sticky note tool to annotate

the PDF document. A search box is also present to search the PDF toolbar.

Back Up Libraries

keep several copies of critical EndNote Libraries and Word documents

do not actively use or store an EndNote library in a cloud environment or in a distant server to

avoid corruption of the Library; an active working EndNote program should only be accessed

from a computer’s hard drive. (EndNote documentation is contradictory on this point.)

back up EndNote Libraries to an external hard drive or thumb drive.



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File > Save A Copy to create a backup of the ENL and DATA files

To send a library as an email attachment File > Compressed Library > Create will

compress the ENL and DATA files to single file, in an ENLX format:

o keep ENLX file size down by not including File Attachments when compressing (4GB

limit)

o those receiving ENLX click to open the Library into the ENL and DATA portions

EndNote Online - server-based EndNote from Web of Science

EndNote X7 is workstation-based; for a more portable server-based version of EndNote, go to Web of

Science and download EndNote [Online]. At the Web of Science database, click EndNote and register

with gru.edu email address. It provides an option for saving Web of Science content into EndNote

Online.

Miscellaneous facts about Libraries

There is no limit to the size of a Library; there are limits to the size of a Library that needs to be

compressed to attach to an email or store.

Each Reference in a Library is unique to that Library and is numbered sequentially as they are

brought into a Library.

Libraries can be moved, but always move the ENL file and corresponding DATA folder together.

Libraries can be renamed, but remember to rename the DATA folder as well.

Libraries can be deleted, but remember to delete both the ENL file and the DATA folder.

Only one person can work in a Library at a time.

More than one Library can be open at the same time.

Libraries can be imported (as described earlier in this document), but copy/paste and drag/drop

work well.

MS PowerPoint contains an EndNote X7 tab that allows the insertion of the reference onto a

PPT slide.

See Edit > Preferences > Folder Locations to view the location of (Output) Styles,

Filters, and Connection Files. As some of these files are updated, go to the EndNote Support site

to download the updated file and replace the outdated file in the appropriate folder.

In the References Tab, click on column headers to toggle the sorting of references. For example,

clicking on Author column will toggle A-Z or Z-A by first author’s last name; clicking on Title will

toggle the alphabetical order of the title information.

References > Find Duplicates to locate potentially duplicate records in an EndNote

Library; however, deleting any EndNote references used previously in Word documents will

break the link between the Library and that reference in the document.



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Sharing an EndNote Library through EndNote Online

With version X7.2, a user may share direct access to their EndNote library with up to fourteen other

EndNote X7.2 users, regardless of operating system (Windows or Mac).

All users must have EndNote X7.2 and all users must have EndNote Online accounts.

Library owner invites others by email to access the Library

View video at http://www.youtube.com/watch?v=ZJ1DpcEeTLw

Access can be revoked at any time by Library owner


http://www.youtube.com/watch?v=ZJ1DpcEeTLw

contents€¦ · endnote permits the importing of properly formatted files or even folders of files...

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