Barr Smith Library
Obstetrics & Gynaecology EndNote Training
Compiled by Mick Draper
Latest update July 2009
Table of Contents
This training site mostly follows the Library EndNote Tutorial
Importing Citations from PubMed Into EndNote
First run your PubMed search. If you'd like extra help with how to search PubMed, there are a couple of tutorials you can view.
BSL Basic PubMed Tutorial Covers searching using MeSH, MeSH and title and abstract terms, limits and displaying results
BSL Advanced PubMed Tutorial Includes more details on searching and saving
Official PubMed Tutorial A very detailed tutorial From the US National Library of Medicine
Or you can ask Mick Draper for help.
If you're not sure what to search today I've used
ovarian failure, premature/prevention and control[majr]
You could search on an author.
Remember most searches by author will be in the form last name space first initial[au]
Selecting PubMed Citations to Import
Select the citations you want by clicking in the boxes to the left of the titles.
If you don't click in any of the boxes all of the citations are selected!
PubMed doesn't have direct export.
You'll have to save your citations in the MEDLINE format as a text file then import them into the EndNote program.
Change the Display format to MEDLINE
Click anywhere in the Display box
The menu will display.
Click once on MEDLINE.
The selected citations will appear in MEDLINE style.
Click on the Send to box.
Click on File.
Click on OK in the Dialogue box to save the results.
You might have to fight with Vista to be able to download the citations.
Rename the file of PubMed citations to something like delete, or rubbish, or throwout etc but retain the .txt file extension.
Save the file in gntrain on the Desktop today.
Open EndNote from the start button.
Open a new EndNote library.
It's safer to put new citations into a new temporary library rather than into an existing EndNote library.
After checking that the citations are not corrupted you can copy and save them to your permanent library.
Today you can save this on Gntrain on the Desktop.
Call it something like deleteme, or junk etc
Now we'll attempt to import the PubMed citations into this new library.
In your EndNote Library click on File (top left of the the screen)
Click on Import.
Check to see that the PubMed filter is showing as the Import Option.
If not then click in the Import Option box and see if the PubMed (NLM) filter is listed.
If it is, click on it.
If not, click on Other Filters and scroll through to find the PubMed filter.
Now click on the EndNote Choose File button.
Can you remember where you put your PubMed results, and what you called the file?
Find the file.
Double click on the file.
Your citations should flow into your EndNote library.
It's probably a good idea to save the actual PubMed search terms you use (though not in today's session)
Use MyNCBI for this.
There's a tutorial on how to save searches and set up alerts on the PubMed Saving Searches tutorial
Making copies of EndNote Libraries
When you have your own library, you should make copies.
Copies should be backed up on a server, on a usb, at home, etc
To do this
Click on File.
Click on Save a Copy ...
Don't actually do this now.
Make sure all your copies aren't on one machine or in one place.
You'll have to remember to keep all your copies up to date by deleting older copies or changing their names as you change your main EndNote library.
Setting Library Preferences
There are several preferences you can set to make your library suit your needs.
Click on Edit.
Click on Preferences.
The figure below shows the Preferences available.
Libraries
You can set up EndNote to open your library every time you open the EndNote program.
If you want to do this click on Add Open Libraries.
Display Fonts
You can change the font of the citations in your library.
Display Fields can be important.
Most EndNote users like to have (Figures, File Attachments,) Record Numbers, Authors, Years, & Titles displaying in order in their Libraries.
You can adjust the order using Display Fields in the Preferences.
Click on the pull down menu for the Column you want to change.
Click on the field to display in the column.
When finished with changing preferences click on the Apply button, then on the OK button.
Note that you can view and revert to the EndNote defaults.
Sorting citations in a library
You can sort the order of citations in any library by clicking on a column heading.
To sort citations by record number simply click on that heading within the library.
The citations will now be listed in Record Number order
[EndNote assigns the record numbers as new records are imported or created in your EndNote library]
Clicking the same column heading again will reverse the order.
To change the default sort settings [Author, Year, Record Number] click on References.
Click on Sort References...
You can choose which elements of the citations are used to sort and the order A to Z, or Z to A etc.
Viewing individual citations
Click once on an individual citation within your EndNote library to view it in the style that will display in your bibliography
Changing the Output Style
Click Edit>Output Styles>Open Style Manager
Click on a style.
Click on the Style Info/Preview button to view examples of citations in the new style.
Note that these citations are from a list of examples in the EndNote program.
The style info box will usually have a link to the advice to authors for the journal, or give you some details of the advice.
Click on the Style Info/Preview button again to return to this.
Opening citations (for editing)
Open an individual citation by double clicking on it in your EndNote Library.
When you import from a database you should check each citation you are going to include in your bibliography.
Scroll down the fields of the citation you've opened checking that all is well.
Check that the spelling of authors' names includes appropriate diacritics etc.
Continue scrolling
until you get to Keywords.
If the citation you imported from PubMed has MeSH they will appear here.
You can delete any keywords you don't want, but more importantly add your own.
Close the citation when you are finished editing.
You can edit lists of terms such as Keywords more quickly by clicking on Tools>Open Term Lists>Keyword Term Lists (or Authors, or Journal Titles)
Here you can delete any terms that aren't relevant for your searches, and add new terms that you'll want to include in some citations.
Finding citations (references) within EndNote
You can search any field of the citations in your library.
Click References>Search References.
Type in what you're looking for, e.g. fertility
Specify the citation field(s) to search, e.g. keywords (or title, or journal title etc).
Click on Search.
Adding Citations (by hand)
Click on References.
Click on New Reference.
Follow the instructions in the Library EndNote tutorial 2.2
To open the EndNote tutorial in a new window right click on the link above.
Click on Open in new window.
Linking pdfs
You can link a citation to a pdf stored anywhere on your computer.
In gntrain there's a pdf called lourenco.
Normally this would be the pdf of the article
I'll link the pdf to the EndNote citation of the article you can link it to any citation if you're not searching on Ovarian Failure, Premature
First I find the citation using Search References.
Click once (or twice) on the citation to select it.
Click on References>File Attachments>Attach File
If you select the alternative Convert to relative links the pdf will be able to be transferred with the EndNote Library to another computer.
Inserting Figures in EndNote
You can attach a figure to an EndNote citation and add it later to a word document
Open the citation in EndNote (double click) that is to receive the figure stored on your computer
Click References>Figure>Attach Figure
The figure should now be added to the Library.
You can add a caption.
To inset a figure in EndNote into Word
Find out which citation has the figure.
In Word click on EndNote
Click on the downward arrow in Insert Citation (top left)>Find Figure
Search for the figure using some aspect of the record.
Adding citations from another database
Now we'll open a temporary library and import more citations, this time from Scopus.
Right click here to open Scopus in a new window
I'll be searching "premature ovarian failure" as keywords
AND
prevention or control as keywords
Copy the Scopus citations in the temporary Library by using Edit>Select All then,
Edit>Copy
Switch to the permanent library and use Edit>Paste
to add these citations.
To remove duplicate citations, click References>Find Duplicates>Delete duplicates
Notice that the more recent citations (larger record numbers) are the ones deleted.
If the new duplicate citations have something you want to keep such as better keywords, an abstract, etc cut and paste these to the older citation before deleting the newer citation.
Once the new citations are added to the permanent library, delete them from the temporary library.
Connection Files
Now use the temporary library to connect to the Library Catalogue and find a book in the Library Catalogue
The abnormal menstrual cycle / edited by Margaret Rees, Sally Hope and Veronica Ravnikar.
In EndNote click on Tools>Online Searches>New Search>U Adelaide
Click on the Choose button.
Search for the book (by title, or some other field)
Click on OK.
Close the Search dialogue box.
Click on the book record.
Click on Copy Selected to
Click on your temporary library
Check that the citation is OK.
Copy to your permanent library and delete from the temporary library.
Using a connection file to search PubMed is not recommended unless you know which specific citations you are after.
Editing an Output Style
In the EndNote program
Click on the Edit drop down menu
Point at Output Styles
Click on Open Style Manager
Scroll to find the style you want to customise e.g. Vancouver
Double click on the style.
The Citations section (see the left panel) refers to the in text part of the citations. In this style it's a number.
Click on Templates under Citations.
If you want to change this to no brackets and superscript first delete the brackets from (Bibliography Number).
Highlight the text Bibliography Number
Click on A1 (superscript) in the tool bar.
The only other thing to change with a numbered style is the Numbering.
If you include the tick in Use number ranges for consecutive citations, then citation numbers in the text for citations 1, 2, 3, 5, 10 will appear as 1-3, 5, 10 in a formatted bibliography.
Note this citation order isn't the same as the record number of references in an EndNote Library.
The unformatted document
The formatted document
Bibliography Section
Templates
You can change the order of the elements of the citation, delete elements you don't want, and insert extra elements
In the graphic above Year and Date are alternatives in the Journal Article reference type.
Non-Breaking Space
Notice in the journal article template that both Year and Date are included as fields. If the Year field is missing from a citation the content of the Date field will be used in the bibliography. The diamond shaped special character links these two fields. EndNote calls this a non-breaking space and allows alternative field contents in a citation to fill a field in the bibliography.
To add a nonbreaking space between two linked fields:
Insert the cursor where you want the character
Click on the Insert Field button
Click on Link Adjacent Text
Alternatively keyboard Ctrl+Alt+Space
Vertical Bar
The vertical bar seen in the templates tells EndNote to separate the following punctuation from the preceding field.
In the Journal Article template above the first full stop is linked to the Author, the second to the Title.
The full stop after the Volume is not linked to it because of the vertical bar.
The full stop will appear after the Volume, only if there is data in the Issue field.
The space after issue will appear if there is data in the Year field.
Carats and Graves
Carats can be used to allow singular and plural bibliography text options for particular fields.
In the template for a book citation (with an author but not an editor) there is a place for an author, a title and an edition statement. Then follows an area for a Series Editor or Series Editors. If there is a single name in the Series Editor field then the word editor will appear after the name in the bibliography. If there is more than one name in the Series Editor field then the word editors will appear after after the names. The carat ^ allows you to enter both variations and have the correct word appear in the bibliography. If there is no data in the Series Editor Field then neither word will appear.
The graves around each of these words `editor`^`editors` tell EndNote that these are words to be added to the bibliography text and are not field names. EndNote would treat both of these words as the field name for Editor if they didn't have the graves.
More detailed information on editing output styles is available in the EndNote Manual.
Click on the computer Start icon.
Start typing EndNote in the Start Search box.
EndNote program options will appear.
Click on EndNote Manual.
The manual has a pretty good index.
Cite While You Write Preferences
In Word click on Preferences in the EndNote area.
I recommend that you delete all the ticks except for Return to document after inserting citations.
Cite While You Write
In Word
begin writing a document, or find the document called My Article in gntrain on the Desktop and open that.
When you need to add a reference click on the EndNote tab in Word.
Click on Go to EndNote.
Scroll or Search to find the citation(s) you want to add.
Click once on the citation.
If you want multiple citations you can hold down the Ctrl key while you click.
Click on Tools.
Point at Cite While You Write.
Click on Insert Selected Citation(s).
The citations are added to your article.
They appear with the author, date, and record number enclosed in curly brackets.
This isn't the final format for the citations, but it makes it easier for you to identify citations and edit them if necessary.
This is what's called an 'unformatted' document. You can edit this including editing the citations.
Continue writing and adding citations remembering to save the article regularly in several locations.
When you have finished your article do all the editing and update all your copies of this unformatted document.
Formatting a bibliography
Method 1
Click on Go to EndNote.
Click on Tools.
Point at Cite While You Write.
Click on Format Bibliography.
The style of the bibliography will be in the style you selected earlier.
If you want this style then click on OK.
To change the style click on the Browse button and scroll to find your style.
Click on the name of the style.
Click on OK.
Click on OK on the Format Bibliography dialogue box.
Your formatted document with bibliography will appear.
Method 2
Make sure your selected output style is showing in the Style box.
If it isn't click on the drop down menu to find the style.
If you still can't find your style of choice, click on Select Another Style.
This will take you to the area shown in the graphic above
Click on the style you want and then on OK.
Click on Update Citations and Bibliography.
This produces your formatted document that includes a bibliography.
Sharing formatted documents
Convert to Plain Text to send to a publisher.
First make copies of the formatted document (you don't have to do this in today's session)
In Word, click on Convert Citations and Bibliography
Click on Convert to Plain Text.
Keep practicing, and contact me if you have any problems.
