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[交流] 【分享】利用endnote实现文献管理【已搜索无重复】

Using EndNote for Manuscript Management (version 6)
Robin R. Sewell, DVM, MLS
979-845-7499
rsewell@medlib.tamu.edu
The purpose of this lecture is to address the most important features available in EndNote.  It is by no means an exhaustive coverage of the software.  The best way to use the lecture is to install EndNote and follow along opening and closing the menus, and creating and modifying references.  I have found that playing with software is one of the best ways to learn how to use it.  This will be directed play.  If you have any questions, please feel free to contact me.

What is bibliographic software?

Bibliographic software is designed to make an author’s life easier.  Basic, bare bones bibliographic software packages provide database storage of manually created citations and format the bibliography when a document is complete.  More sophisticated bibliographic programs allow importation of existing citations from text files or files created by other bibliographic programs, allow citations to be directly imported from an online journal or database, and format the document and bibliography according to a given style based on standards such as those set by the American Psychological Association Manual or by professional journals.  Programs may also have utilities that allow direct Internet connection from the program to online indexes, such as PubMed, allowing the database to be searched directly from the bibliographic software.

Why EndNote?

In the beginning there were three main bibliographic software options, EndNote, Procite and Reference Manager.  Then ISI Research Soft, creator of Reference Manager, gobbled up EndNote and Procite and created a mini-monopoly.  There are other bibliographic software programs out there, but none are as well recognized at Reference Manger, EndNote and Procite.  Below is a table from ISI comparing the functionality between the products.

So why are we using EndNote and not one of the other ISI products?  In my experience, Reference Manager is more difficult to learn.  Unless you need unlimited database size, or the ability to search across multiple citation databases, EndNote is a better option.  I have used Procite in the past and have had problems with its ability to import citations.  What took me two days of tinkering with the most recent Procite version at the time, version 4, I was able to do with EndNote in 2 minutes.  The latest release, EndNote 6, has added features allowing management of tables and figures within a document and stores the tables and figures at the end of the document in the manner preferred by most journals requiring electronic submission.  Reference Manager and Procite are available on a 30 day free trial basis from the ISI Research Soft website if anyone wants to comparison shop.  While the details may be different, the overlying concepts I am presenting will apply to all three software applications.

Feature comparison between EndNote, Procite, and Reference Manager

http://thomsonisiresearchsoft.com/compare/

Getting EndNote

Download the evaluation copy of EndNote 6 and follow the steps for installation.  The trial version is the same as the full version, but access to the program is limited to 30 days.  If you wish to purchase a copy at a later date, any files created with the trial version will work with the registered installation, just be sure to save copies of your work at a location other than the EndNote directory.  You will find the trial version download at:
http://www.endnote.com/

Setting EndNote Preferences

Start EndNote and create a new library.

The EndNote library is where your citations will be stored.  EndNote cannot search for citations across different libraries, so it is best to store all the citations you will need for a particular project or subject in one library.  The maximum number of references EndNote will store is 32,000.  This is should be more than enough space for anyone.

The EndNote library display can be customized to need your needs.  Go to

Edit->Preferences.

Most of these settings are self-explanatory.  The ones I would like you to look at are Libraries, Reference Types, Display Fields, and Duplicates.  I will not talk about Temporary Citations.

Libraries – allows you to enter the path to one or more libraries that you would like to have open and ready to go when EndNote is started.  Clicking Add Open Libraries will add all the libraries that are currently open to the list.  Libraries may be added and removed at any time.

Select Reference Types – sets the default reference type.  Because most citations in scholarly articles are from journal articles, leave the default set at Journal Article.  If you are adding a citation from a book or thesis, be sure to change the type when creating your citation.  As you can see when you click on the drop down menu, there are a lot of options.  ProCite offers 50+ types while EndNote only has 28.  The 28 that EndNote offers should be more than sufficient.  Reference types may be modified, changing the information that is captured and stored.  It is best to leave these setting alone until you have more experience with EndNote.  Changing them could alter the way the bibliography is formatted.

Display Fields - determine how the library will look and allow the references to be sorted based on the fields displayed.  The default is Author, Year and Title.  You can change the order of display or include and exclude other fields.  I add Journal/Second Title to my display.

Duplicates – settings allow you to select the parameters that are used to determine if an article is a duplicate.  Remember that this is based on how the information is presented in the source database.  The same citation from two different databases may not match exactly.  For example if one database uses “last name” “first initial” and the other uses “last name” “first and middle initial,” EndNote will not see them as a match and you may still have duplicates.  It is always a good idea to sort your references by last name and check for duplicates that way.  Because I have found articles by the same author with very similar titles published in different journals, I include Journal/Second Title in the display field.  You may also come across papers from Conference Proceedings that are later included as a full journal article and have the same authors, title and year.  Saving duplicates can have advantages.  Some databases have more information in the citations, such as the month of the publication, which may be required by some journals.  Saving duplicates allows you to select the citation with the most detail.

A Quick Word About Vendors

Some people get confused by all the different names they see for databases, such as OVID, OCLC, Ebsco, Medline, Biosis, and CAB Abstracts.  OVID, OCLC, and Ebsco are vendors.  Vendors buy the rights to various databases, such as Medline, Biosis, and CAB, and then repackage them with their own interface.  When you search Medline provided by the vendor OVID, it is the same Medline provided by OCLC.  They look different because of the proprietary interface of the vendor, and may perform differently because of features the vendor has incorporated as search options, such as combining searches, setting limits and using Boolean AND, OR, or NOT.  Libraries buy subscriptions to the databases from the different vendors based on price, functionality, and the number and type of databases included in the package.  For example, MSL gets Medline, CAB Abstracts, and Biosis from OVID.

Importing References

We will not be covering the connect function that allows you to automatically connect to certain databases.  This feature requires that you use the EndNote search interface, which is not as efficient as doing a direct search.  If anyone in interested in finding out how to do this, please feel free to contact me.

When you are not working at your own computer with EndNote installed, you may have to save citations to a disk or email them to yourself.  To use them in EndNote, they will have to be imported.  EndNote provides several filters based on the way different database vendors format information.  These filters look for tags to identify pertinent information such as author, title, and publisher.  Go to

EndNote -> Edit -> Import Filters -> Open Filter Manager

You will see a long list of available filters based on database type followed by the provider name in parentheses.  Scroll down to Medline(OVID).  Highlight it and click Edit.  This is the information that allows you to import a file into EndNote and have it make sense to the program.  Select Templates.  This is the most important feature of the Filter Manager.  Due to our limited time, we will not talk about the other options. The current Reference Type should be Journal Article.  On the right hand side are columns for tags and fields.  Tags identify the information that follows so the system knows that anything after AU is an author in the Medline(OVID) format.  If you compare the tags for Medline(OVID) to the output of the Medline(OVID) search below you will see that there are differences.

UI  - 12228823
MI  - 22215553
AU  - Crump JA
AU  - Griffin PM
AU  - Angulo FJ
IN  - Foodborne and Diarrheal Diseases Branch, Division of Bacterial and Mycotic Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA. jcrump@cdc.gov
TI  - Bacterial contamination of animal feed and its relationship to human foodborne illness.
SO  - Clinical Infectious Diseases. 2002 Oct 1;35(7):859-65
AB  - Animal feed is at the beginning of the food safety chain in the "farm-to-fork"……..

These differences do not effect EndNote ability to import the information.  Extra tags in the citation or tags in the filter template that are missing from the citation will not effect importation.  In this example, the Medline(OVID) filter template does not have a UI tag, but the record does.  When the citation is imported into EndNote, UI and the information after it on the same line is ignored.  More than one AU tag is present in the citation telling EndNote that all of these are authors.  The field associated with the SO, source, tag contains a large amount of information.  This particular citation would match the first SO in the filter template.  More than one SO is contained in the template to accommodate changes in the Medline citation style over the years and differences in the amount of information available for a type of publication.  These differences can be subtle, but are important.  SO contains the journal title, volume, number, pages, and date.  To be correctly identified, the SO field of the citation must exactly match one of the SO fields in the template.  The only available options for the Medline(OVID) filter are:

Tag Medline(OVID) Template Medline Citations

SO- Journal Year;Volume(Issue)

ages JAMA. 2001 Dec 5;286(21):2655-6
SO- Journal Year;Volume Issue

ages No example of this style could be found
SO- Journal Year;Volume

ages Annual Review of Public Health. 1980;1:121-36

The periods at the end of the source title are retained.  They will be removed automatically if it is required by the selected style format.

If you have trouble importing a file the first thing you need to check is the filter template and compare its tags to the tags on your citation.  A discrepancy in the tags is the primary source of import failure.  If the file is imported, but the year doesn’t show up or there is too much information on the source line, it is probably due to an error in the source field of the filter template.

Exercise - Importing a Citation

For this exercise we will use Medline(OVID) accessed through the MSL homepage (msl.tamu.edu).
In the Information Resources block select the OVID Medline link.  A menu for all the OVID databases will be displayed.  Select one of the Medline databases.  It doesn’t matter which one.

Since you will have to do a presentation incorporating references at the end of this class, it would be a good idea to start with a search for information relating to your topic.  Find at least six articles, even if you have to check the boxes randomly.  This will give you more citations to work with as we go over EndNote features.  If you have more than one page of citations in Medline, be sure to use the interface “Next Citations” and “Previous Citation” buttons to move back and forth, not the browser back button, or you will loose some of your selections.  When you are finished, scroll down to the bottom of the page.  Under “Fields” select “Citation + Abstract + Subject Headings.” Select “Citation Format” OVID.  At this point the file may be saved to disk or sent to an email address.  Ignore the Direct Export for now.  Save the file as ovid.cgi by clicking “Save” under Actions and following the instructions.  Once the file has been saved, go back one page using the browsers back button or by clicking the Titles button at the top of the page.  You are going to repeat this process for Citation Formats BRS/Tagged and Reprint/Medlars saving the files with appropriate names.

CGI files are text files.  They can be saved with the cgi extension, or you can save it as a text file by changing the file type to All Files and entering the .txt extension on the name line, FileName.txt.

Import the files into your library (don’t use the automatic export feature).  Don’t worry about duplicates.  What happened?  If there was a problem, what caused it?

If you open the files you saved in a word processing program you can see that the saved OVID format is not represented in the Medline(OVID) filter template.  This means that any files saved in this format will not import into EndNote.  Further more, it is impossible to create a template to cover this formatting style because there are no tags.  Tags must be on the same line as the beginning line of the field they represent.  The OVID format inserts a carriage return after the tag.

Now look at the BRS/Tagged citation file.  The tags are different.  The BRS/Tagged format lacks a hyphen after the letters designating the tag.  BRS/Tagged format SO JAMA. does not match the Medline(OVID) format SO - JAMA.  Look at some of the different Medline filters available in the Style Manager.  Is there another Medline filter that you could use?  You may run into this problem if some one gives you a file of citations, but you don’t know which output format was used or which database vendor it is from.

Evidently there was not good communication between EndNote and OVID.  OVID does provide the direct export feature that bypasses the problem, but it does require EndNote to be installed on the machine you are using.  Try to do a direct export to see how it works.  Select the Direct Export button and click save.  I have not found any problems with the other database providers.

When you import references the library display shows only the references that were just imported.  This allows you to review the references and make any changes before you include them in the library.  Citations may be deleted by selecting the citation and clicking on

References->Delete References

If you wish to see all of the references and incorporate the new imports into the library, go to

References->Show All References
Or
Ctrl-H

Term Lists

Term lists accommodate the different bibliographic citation styles required by journals.  The most important term list is the Journal List.

Tools->Open Term Lists->Journals Term List

The Journals List is generated each time you import citations.  If you scroll to the right you will see that there is a column for Full Journal and three columns for abbreviations of the journal title.  When you import a journal from Medline(OVID) it will have the full title in the citation and this will be inserted into your Journal List for this particular library.  If the citation is imported from PubMed, which uses abbreviations, the abbreviated title will be imported and will be placed in the Full Journal title slot.  EndNote has no way of knowing which titles are abbreviations unless you tell it.  When you format a bibliography that requires a full journal title, the citation from PubMed will only have the abbreviation.  Conversely, if the format requires an abbreviation, the Medline(OVID) citation will only have full title, while PubMed will have the correct title display.  Fortunately EndNote has a list of journal titles and abbreviation for several subjects including medicine.  The medicine list has over 8,000 titles.  To import the EndNote medicine list, click the List tab and click the Import List in the lower right part of the box.  If you have followed the standard program installation, the file is located at

C:\Program Files\EndNote\Term Lists

Click open and the list will import.  It is a large file and takes about a minute to install.  You will see that the file has the complete journal name as well as two abbreviations, one with periods and one without.  This covers all of the style requirements of the different journals.  It must be imported or copied into each library you wish to use it in.

Automatic Export

Automatic export is another reason for selecting EndNote.  The OVID automatic export feature will open EndNote and ask you which library you would like to store the references in.  It does not require you to mess with filters or worry about the reference type.  Many of the electronic journals have a feature that allows you to export the citation directly to EndNote.  Go to the following URL

http://msl.tamu.edu/Redirects2/p70.htm

This is the electronic journal “Public Health Reports.”  If you are off campus you will be prompted for a username and password.  Select an issue.  Check several of the boxes to the left of the article titles and click on “Get All Checked Abstracts.”  One the right hand side of the new display is a link

Download ALL Selected Citations to Citation Manager

When you click the link, you will see that there are several download option, one of which is EndNote.  Click on EndNote.  Select a library and click Open.

Searching Your References

Endnote allows you to search your references to locate citations by various fields.  Go to

References->Search References

The search box allows you to select the field or fields to search.  Changing the default Contains to Is will find an exact match.  Contains allows you to find an author if you only know part of the name, or a title containing a keyword.

When I asked you to save the Medline(OVID) searches, I instructed you to select Citation + Abstract + Subject Headings.  The reason for saving the abstract is obvious.  The abstract can be an important reference for you later on.  Saving the subject headings in a Medline search can also be beneficial.  If you save the subject headings for the citation, you can do a subject search of your citations using the subject headings and gather a subset of your citation library based on subject.  Subject searching has benefits not found in keyword searching.  Keyword searching will only look for the keyword entered.  It is up to the searcher to think of all the possible synonyms and spelling variations.  Subject searching relies on subject headings.  Subject Headings are applied to citations based on an indexer’s interpretation of what the article is about.  This allows articles to be retrieved even if they do not have a keyword in the title or abstract.  Subject searching also prevents retrieval of a large number of citations that mentioned a keyword in passing, but are not about that subject.  For example doing a keyword search of your library to find articles about Salmonella, and getting a citation back that says, “Salmonella was ruled out….” in the abstract.

Book Citations, Figures and Charts

Unless you can find a citation to a book in a database, such as CAB Abstracts, it will need to be created manually.  Figures and Charts will also need to be added to the EndNote library manually.  Go to

References->New References

Be sure to select the correct reference type.  The reference type will effect how the bibliography is formatted.  Some publications use different formatting styles for the various reference types such as books, journals and electronic references.

Create a chart in Excel using existing or fictitious data and save the chart as a separate worksheet.  To make the information available through reference manager, you need to create

References->New References

Change the reference type to chart.  Fill in the information for Author etc.  When you get to image go to

References->Insert Object
Or
Click the right mouse button and select Insert Object from the menu

Use the Choose File button to locate and select the Excel file containing your chart. Click okay.  An Excel icon will be placed in the image box.  This icon will refer to your chart.  If you double click the icon it will open the image/object it refers to.  You can use the same process to include pictures, figures, tables, and equations, just be sure to change to reference type.  EndNote can import the following files types as objects:

Excel Chart
Excel Worksheet
MS Visio Drawing
MS Power Point Slide or Presentation

Charts and equations can be created in MS Word by selecting

Insert -> Object -> New Object ->

But, keep in mind that only the files types listed above will work with EndNote Objects.

Equations require the MS Equation Editor.  It is not automatically installed as part of MS Office.  To install it select

Start -> Settings -> Control Panel -> Add/Remove Programs -> Microsoft Office

You will need your MS Office CD.  The Equation Editor is listed under Office Tools.  To use an equation it must be copied and pasted into MS Paint.  The Paint document can be saved as an image file and the image file can be imported and inserted into the EndNote reference by selecting Insert Picture instead of Insert Object.  The view of the image in the EndNote reference may look blurry, but it will look like the original image when it is inserted.

Another option is to scan the equations, figures, tables, and charts and save the image files.  The image files can be stored in an EndNote reference as described above.

Exporting References

Exporting references can be a handy way of taking them with you to the library as a paper copy, on a diskette, or on your PDA.  In electronic format, the references can also be easily shared.

To export references to your PDA you will need to install the output style to the PocketCites(EN4) output style located in the same WebCT folder as this lecture.  Save the file to your hard disk at the following location

C:\Program Files\EndNote\Styles\PocketCites(EN4)

To export your library to PDA go to

Edit -> Output Styles -> Open Style Manager

Select PocketCites(EN4).  It will save the library as a text file.

To export only a portion of the library, select the references for export and go to

References -> Show Selected References

This opens up a new window containing the selected references.  As long as this is the active (selected) window, when you follow the export procedures, only these references will be exported.  This same selection feature can also be used to Edit, Delete References, or Search References.  It cannot be used to Link Out.

The Linking Feature

The linking feature in EndNote allows you to connect the reference to a web page through a URL or to a source document.  For example you can connect a citation to an article saved as a PDF file or a URL.

To link a reference, select a reference in your EndNote library.  Only one reference can be selected at a time.  Go to

References->Link To
Select a file and Open

The information for the file location is inserted into the URL field.  To open the linked file go to

References->Open Link

The file and associated program will be opened.  It is important to remember that the link is not dynamic.  If you move the location of the file, the link will be broken.

To create a link to a web page, the URL can be pasted directly into the URL field.

Using Word – Inserting Citations

When you install EndNote toolbar is open and ready to use in Word.  The EndNote tool bar in Word has an icon that allows you to go directly to EndNote as part of the “Cite as You Write” feature.  If EndNote is not open it will open the program for you.  There is also an icon to go back to Word from EndNote.  It has a blue W over a yellow triangle located on the left side of the bottom EndNote tool bar.

Open Word and create a test document to practice inserting references.  Place the cursor where you would like to insert a reference.  Select the EndNote icon to go to your EndNote library.  Highlight the citation or citations you wish to include.  (Holding down the control key while you select citations allows you to select more than one.)  Use the Word icon to return to Word.  Select the icon for inserting citations, fourth from the left on the EndNote tool bar in Word.  The citation will be inserted and formatted according to a default format.  Don’t worry; this format can be changed easily.

Now go back to EndNote and select a figure or chart to insert.  Return to Word and use the Insert Figure icon, fourth from the right.  The caption you selected and the image will be placed at the end of the document, but the reference mark for the figure will be at the point of insertion.

An optional method of inserting citations and figures is to select the corresponding insert buttons from the EndNote tool bar in EndNote after you highlight your selections.  The citation or figure will be inserted and you will be sent back to Word to continue writing.

Using Word – Formatting the Style

The style manager resides in EndNote.  Go to

Edit -> Output Styles -> Open Style Manager

Select the check box of the styles that you want quick access to.  These styles will appear in the drop down menu making formatting quicker.

In Word, select the icon for formatting the bibliography, the third icon from the left.  Click on the With Output Style drop down menu. Notice that the styles you selected in EndNote appear in this menu.  You can also access the Style Manager directly from this menu.  Select one of the styles and click OK.  Your Word document will be formatted according to that style.

When submitting a manuscript, always compare the formatted manuscript with the journal requirement.  Journal requirement may change and the current version of EndNote may not reflect those changes.

Task
Find and evaluate another piece of bibliographic software.  Based on your experience with EndNote, what are your recommendations?  Some points to address are:

What are the features?
Are there any obvious bugs?
What is the price and is academic pricing available?

Submit a short summary of your findings.  Short is less than a page.

http://library.tamu.edu/vgn/portal/tamulib/content/renderer/0,2174,1724_2334600,00.html

[ Last edited by ratio on 2008-11-28 at 21:46 ]

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