Writing Tools

Introduction

What is personal citation management software (aka personal bibliographic management software, pbms)? It is software that allows you to organize and retrieve your literature for research, teaching and publications. Possible uses include:

  • Maintain access to reprint collections - both hard copy and virtual file.
  • Compile reading lists for courses.
  • Create bibliographies in a variety of publication styles.
  • Cite sources while you write.
  • Generate list of authors' addresses, email addresses.

EndNote is produced by Thomson ResearchSoft (http://www.endnote.com/), and is one example of personal citation management software. Other examples include:

Should you upgrade to Endnote X1? See EndNote X1 for Windows.

EndNote Library data input and output functions:
EndNote data input and output functions

Build Your Library

Sample EndNote library:

EndNote library display

Journal Term Lists

Before you do anything with your EndNote Library, set up your JOURNAL TERMS LIST. The JOURNAL TERM LIST controls journal title formatting in output styles. EndNote software comes with a number of journal term lists. Use these lists to create your personal JOURNAL TERM LIST.

Other term lists:
Education - locally developed from ISI Journal Citation Report titles by E. Wixson. Right-click and save the file in your EndNote term lists folder (e.g. C:\Program Files\EndNote X1\Term Lists).

NOTE for MAC users: EN9 (MAC) does not recognize imported journal term lists or modifications to the journal term list. There is no patch for this bug, but the problem was corrected with ENX (MAC). As a work-around, open and save your MAC EN9 library on a Windows computer (requires EN9 WIN). If the Journal Term List is empty, import the program's journal term lists following the procedure below. This will convert associated data files. Then reopen your library on a MAC computer. Alternatively, send the .enl file and associated .data folder to Emily to convert for you. I can also send you an empty En9 library populated with chemical and medical journal terms.

  1. Open Endnote library.
  2. Click on TOOLS.
  3. Select OPEN TERMS LIST, then JOURNAL TERMS LIST.
  4. Click on LIST tab in TERMS LIST window.
  5. Highlight JOURNALS.
  6. Click on IMPORT LIST.
  7. Locate the Terms List folder on your hard drive, such as Program Files\EndNote X\Terms Lists, and select appropriate lists to import.

Import journal terms list

Enter Data Manually

To enter a new record,

  1. Choose REFERENCE > NEW.
  2. Choose REFERENCE TYPE.
  3. Enter only raw data. EndNote will format field contents output according to the selected style.
  4. Enter each author's name on a separate line in a consistent way. Enter complete author names to preserve maximum flexibility in formatting future citations and bibliographies.
    Example:
    Casey, Charles P.
    Dzwiniel, Trevor L.
    Kraft, Stefan
    Guzei, Ilia A.

Term Lists are automatically created for authors/editors, journals, and keywords. If you turn on "Suggest terms as you type", EndNote will attempt to complete the term when added.
Suggest terms as you type

EndNote produces a bibliography using font and size of the word processing document. Normally, text is entered using Plain Text font, size and style. If you enter other fonts or styles, those fonts are retained and will appear in your bibliography (e.g. subscripts, Greek letters).

Field-specific Recommendations:

Field Recommendation
Author
  • For maximum flexibility, enter whole names.
  • Enter all authors, one name per line.
  • Preferred format: lastname, firstname, middleinitial
  • Leave blank for anonymous
Journal
  • Import predefined medical and chemistry journal lists.
  • Journal term lists accommodates four variations of a journal name. Typically, column 1 is full name, columns two and three are for standard abbreviations with and without periods. Use column four for special codes. e.g. PNAS
Keyword
  • Separate individual entries with semicolon, backslash, or return
Image
  • (En9) Insert .pdf files into this field.
  • EndNote creates a subdirectory called "images" for all pdfs (plus other images) associated with this library.
  • Display the EndNote record and double-click on the pdf. image to view the pdf.
URL
  • Enter as a recognizable link - e.g. http://…
  • Use "Link To" in record to select file for which file path is inserted when reference is displayed or selected.
  • Use "Open Link" to open the linked file.
PDF (EN X, X1) Drag-and-Drop a PDF file into an EndNote Reference highlighted in the EndNote library display.

Search Databases with EndNote

Use EndNote Connection files to search and retrieve records from remote Z39.50 databases like library catalogs (e.g.MadCat). EndNote searches the available search indexes, not the records. Use this technique for simple searches only. You can also connect to PubMed and Web of Science - this is an easy way to retrieve known citations.

  1. Open EndNote Library.
  2. Select TOOLS > ONLINE SEARCH (formerly CONNECT).
  3. Select database.
  4. Perform search. Boolean searches process from top to bottom, so construct your strategy carefully.

Retrieved references appear in a temporary window. You can edit, select, and transfer records to your library from this window.

Results from MadCat search displayed in temporary window

Import References from Online Databases using EndNote Import Filters

Use EndNote import filters to import references downloaded or saved from online databases like SciFinder Scholar, Web of Science, and Medline. Text files may be imported if they conform to a particular format, such as "Tab-delimited" or "Tagged fields". EndNote comes with filters for common databases, but it is important to check the filter to see how it imports record data.

  1. Connect to online database.
  2. Download data in correct format, generally specified as "tagged" format.
    Recommendation: Download ALL fields of each record to preserve EndNote import flexibility. SciFinder Scholar example.
  3. Open EndNote Library
  4. Select FILE > IMPORT.
  5. Click on CHOOSE FILE and select the saved or downloaded records file.
  6. Select IMPORT OPTION and choose the appropriate import filter.
  7. Choose duplicates option, usually "Import All".
  8. Choose text translation option if necessary.
    Import window
  9. Click on IMPORT.

Modify Import Filters

Before importing records, compare the saved or downloaded data file to the EndNote filter to make sure the filter imports fields the way you want.

  1. Open EndNote library.
  2. Select FILE > IMPORT FILTERS > OPEN FILTER MANAGER.
  3. Highlight the filter you want to view.
  4. Click on EDIT.
  5. View individual reference types in TEMPLATES.
  6. Refine filter with Field Editing and Source Parsing.

Field edits in the Beilstein import filter

To import MDL CrossFire Beilstein/Gmelin citations to your Endnote Library, you will need a Beilstein(MDL) filter available from http://library.wisc.edu/endnote/filters-styles.html. Download (to your EndNote\Filters subdirectory) this filter modified by Emily Wixson or develop your own filter.

  1. In MDL CrossFire, search a bibliographic query and display records in the "Citation" context.
  2. Click on EXPORT HITS and select "Procite/Endnote/Reference Manager".
  3. Save as a .txt file.
  4. Follow the procedures above for importing data from online reference databases.

Caution: Citations in Beilstein and Gmelin contain varying amounts of bibliographic information. Newer citation records generally contain more information than older records. Records may not contain starting and ending page numbers. Always compare your EndNote data with the original source.

Manage Your Library

Search Your Library

  1. Open EndNote Library.
  2. Select REFERENCES > SEARCH.
    • Unless "Match Word" or "Use Indexes" is checked, left- and right-truncation are enabled.
    • Boolean operators searches are executed from top to bottom of search window.
    • To search for an empty field, select the desired field, choose "Is" as the comparison operator, and leave search term blank.
    • Use choices in Search Set list to search subsets, combine results, and display certain sets.

Mark a set of references

If your EndNote library includes references on separate but related topics, you might want to "group" or "tag" certain references for those related topics. You can also date or label imported reference sets.

Endnote X1: Create up to 50 custom groups to organize references into subsets.

All versions: View only the targeted reference subset, such as the results of a search or an import. Make sure only the desired references are showing.

  1. Select REFERENCES > CHANGE FIELD .
  2. Specify EndNote field destination, such as Keyword.
  3. Type text.
  4. Select Change option.
  5. Click on CHANGE.

This change adds the character string "*combinatorial" to the keyword field and permits future retrieval of those selected references by that search term.

EndNote also has a "Label" field that can be used for this purpose. The Label field is typically used for in-text citation formats that EndNote cannot create, such as first four letters of an author's name. If this field is not needed for special citation codes, the field may be used for categorizing references or numbering reprints.

Backup EndNote files

Be sure to backup your EndNote Library and any modified styles, filters, and connection files. The library file (filename.enl) is where all of your references are stored. You must also back up the .DATA folder found in the same folder as your library. This folder is considered part of the library and includes images and other files necessary for the library. Modified style, filters, and connection files are saved in the program directory (e.g. C:\Program Files\EndNote X). These should be backed up separately.

Cite References and Create Bibliographies

You can create formatted in-text citations and bibliographies from references in your EndNote Library. Depending on the word processor you use, you can use three different approaches:

  1. "Cite While You Write" - MS WORD 97, 2000, XP, 2003, 2007 - or Word 95, Word Perfect 7-10 - EndNote Add-in.
    EndNote X1 is compatible with Word 2007. The EndNote X1 Cite While You Write toolbar should install into the Add ins tab in Word 2007, and the tools should function as designed. If the CWYW tools do not load automatically, click here for instructions on how to install the EndNote toolbar into Word 2007.
  2. Independent bibliographies and other files (e.g. RTF, HTML, Plain Text) - employs copy and paste between document and EndNote Library.
  3. Format Paper (formerly called RTF Document Scan) to cite references and create bibliographies for documents that can be saved as RTF, including WordPerfect

Use "Cite While You Write"

  1. Open EndNote Library(ies).
  2. Start MS WORD and open the paper you want to insert citations.
  3. Place the cursor in the text document where you want to insert the citation.
  4. Go to TOOLS > ENDNOTE.
  5. Choose the appropriate EndNote action.
    Shortcut: Display WORD and EndNote windows side-by-side on your screen. Select references from Endnote and drag them into the WORD document.
EndNote add-in files must be installed in your WORD STARTUP directory. Occasionally these files disappear and EndNote disappears from WORD > TOOLS menu. Occasionally MS WORD "hangs up" with EndNote CWYW. I recommend you disable Instant Formatting.
WORD > Tools > EndNote > Format Bibliography > Instant Formatting

Create Independent Bibliographies

There are several ways to create independent bibliographies or files.

A. Copy formatted references from an EndNote Library and paste them into a word processing document.

  1. Open EndNote Library.
  2. Select desired output style.
  3. Create a subset of records in EndNote with a Custom Group (EN X1) or other means.
  4. Select your references
  5. Select EDIT > COPY FORMATTED.
  6. Paste references into WORD document.

B. Export references from a Library.

  1. In EndNote, select desired output style.
  2. Use FILE > EXPORT to create a file (RFT, text only, HTML).

C. Print references from EndNote.

  1. In EndNote, select desired output style.
  2. Select FILE > PRINT.

Use Format Paper (formerly called RTF Document Scan)

(Refer to your EndNote manual)

Collaborative Writing Projects

Note: These procedures were developed by Jarrod Bogucki in fulfillment of the SLIS Library Instruction Field Placement, Fall 2007. "EndNote" refers to the desktop version of EndNote. Instructions (pdf version) are written for EndNote X and later.

I. When some, but not all, collaborators have EndNote

In EndNote

  1. Create an EndNote library for the manuscript.
  2. Add references cited by collaborators to the EndNote library by entering citation information manually or by searching an online database such as Web of Science from within EndNote. To search Web of Knowledge from within EndNote, your campus must have a subscription to Web of Science AND you must search from a campus IP address.
    • Click on Tools, then Connect, then Web of Science (ISI).
    • Search for keywords in the title.
    • Select correct citation from the results window and transfer to your EndNote library.

In Word

  1. Insert contributed sections into the manuscript.
  2. Insert in-text citations into the manuscript using EndNote.
  3. Format the document and bibliography:
    • Click on Tools, then EndNote, then Format Bibliography.
    • Select desired output style.
    • Save the manuscript. Save a back-up copy of the manuscript.
  4. Remove the EndNote field codes in one copy of the manuscript:
    • Click on Tools, then EndNote, then Remove Field Codes.
    • Save file.
    EndNote Remove Field Codes
  5. Send the version of the manuscript with EndNote field codes removed to collaborators to review.
    Note: The EndNote library does not travel with this version of the manuscript.
  6. Receive revisions from contributors.
  7. Edit the version of the manuscript that contains EndNote field codes.
  8. Repeat steps 3-7 until manuscript is finalized.

II.  When all collaborators have EndNote

Option 1: Multiple EndNote libraries shared among collaborators

  1. Locate the EndNote library file.  NOTE: the file format will vary among EndNote editions.
  2. For EndNote X and later, save the library as a compressed library.
    • In EndNote, click on File, then Send To, then Compressed Library...
    • Save the file as libraryname.enlx.
  3. Transfer the appropriate file or files to the primary author using email, flash drive, or any other means of data storage.
    Note: A paper can be sent either formatted or unformatted.
EndNote Version File(s) Illustration
X and higher compressed file (libraryname.enlx) EndNote compressed file
7, 8, 9 file (libraryname.enl) and associated data folder (libraryname.data) EndNote 7 file and data folder

In EndNote

  1. Open all EndNote libraries associated with the manuscript.

In Word

  1. Edit the compiled manuscript using multiple EndNote libraries.

Option 2: EndNote Traveling Library

Each formatted citation in a Word document is saved with EndNote field codes that embed reference data in the document. The document contains a “Traveling Library” of references cited. To preserve access to the reference data, collaborators must share formatted versions of their manuscripts. Manuscript sections can be combined and reformatted in different output styles, but the combined document cannot be unformatted. Once a manuscript is unformatted, you must have the corresponding EndNote libraries open in order to reformat references.

The Traveling Library can be used to share references. References can be exported from a document into an existing or new EndNote Library.

  1. Send formatted manuscript to collaborator.

In Word

  1. Open the manuscript in Word and run the 'Export Traveling Library' command.
    • Click on Tools, then EndNote, then Export Traveling Library.
    • Choose to add citations to an existing EndNote library or to create a new EndNote library.
Exported references are renumbered and do not retain their original reference numbers. These numbers will not match the temporary citation numbers in the manuscript.

The default temporary citation format is:
{Author, Year #Record Number}

Beginning with EndNote X1, "#Record Number" can be replaced with "Pages".
Endnote X1 temporary citation
If all collaborators have EndNote X1, and they agree to use {Author, Year Pages}, the Traveling Library feature can be used to create a project library whose references will match the temporary citation numbers in the manuscript.

Option 3: EndNote Web (https://www.myendnoteweb.com)

For scholarly research and writing, EndNote Web is intended to complement desktop EndNote. It is useful for storing references for eventual download to desktop EndNote as well as storing references from ISI Web of Knowledge searches. EndNote Web folders can be shared with collaborators, but collaborators cannot edit records in a shared folder. All collaborators must have login information to be able to fully edit references. Given limitations of the current version, we do not recommend EndNote Web for professional collaborative writing.

EndNote Web

  • Web-based (http://www.myendnoteweb.com/)
  • Requires registration.  If you have already registered with Web of Knowledge for search alerts or table of contents alerts, you can use the same username and password for EndNote Web.
  • Collect, group, and manage up to 10,000 citations
  • Share groups of reference online with colleagues or group project members (from the Organize tab).
  • Transfer records directly between your desktop EndNote X and higher and your EndNote Web account for access when you are away from your office. Transfers are initiated through EndNote. Refer to the EndNote documentation for detailed instructions.
  • Compatible with MS WORD (requires free Cite While You Write plug-in)
  • 1,300+ output styles
  • Compare EndNote - EndNote Web features

To import a file:

  1. From the Collect tab, click the Import link.
  2. For the File field, click the Browse button to find and select the file containing reference data.
  3. For the Filter field, select the import filter that matches the reference data format.
    See Import Filter Favorites to customize this list.
  4. Click on Import.

To create, manage, or share a group of references:

  1. Click the Organize tab to display the Manage My Groups page.
  2. Select appropriate action.

Glossary

Cite While You Write - add-in that integrates an EndNote submenu of commands into the Tools menu of MS Word.. Provides quick and easy insertions and formatting of citations and bibliographies.

Connection File (also Connect File) - EndNote files used to connect and search online databases while in EndNote.

Delimiters - punctuation that separates one term or field from another.

Field - a section of a record, such as author, title, or publication year. Fields may have multiple entries. Each Endnote record can have a maximum of 38 fields. Each field is limited to 32,000 characters.

Filter - instructs EndNote how to interpret and import data into corresponding EndNote fields. Can be modified and can create new filters.

Information Provider - service that provides access to online databases (e.g. ISI).

Library - your EndNote database of references.

  • No limit to number of libraries. EndNote recommends one library per user rather than one library for each topic.
  • (EndNote X1) There is no limit to the number of references you can create in an EndNote library. It is recommended that the number not exceed 100,000 to maintain efficient performance managing the database.
  • (EndNote X1) A reference may have up to a total of 52 fields per reference, including the reference type name.
  • (EndNote X1) Can generate a bibliography from more than one library at a time.
  • (EndNote X1) You can attach one graphic or file attachment to the Figure field of a record.

Reference Type - type of information source, such as journal article, patent, book, manuscript, web page.

Style - a file used by EndNote to format references for publication, such as Science, ACS, etc.

Template - used by styles and filters to control how EndNote outputs or imports bibliographic information. Each reference type has its own template.

Traveling Library - When using "Cite While You Write", each formatted citation is saved in your Word document as a "traveling library".