EndNote Reference Manager and Literature Searching

MODULE LABORATORY EndNote Reference Manager and Literature Searching Name of Course/ Module Course Code Semester and Year offered Credit Value : CRP V : C10A.117 : 5 and 3 rd year : 1 SCU Learning Objective : At the end of learning process in CRP V, the students will have the competence to apply basic clinical epidemiology and evidence-based medicine. Specific Learning Objective : 1. Explain how EndNote can help search online bibliographic databases and retrieve the references. (C2) 2. Apply how to get started with the software of EndNote, Setting EndNote Preferences, Entering References, Searching Remote Databases,Importing References,Searching EndNote Libraries and Printing References, Using EndNote While Writing a Paper (C2, P2) Faculty : Lulu Eva Rakhmilla, dr., M.KM Lola Ilona FAH, dr., Mkes Kurnia Wahyudi, dr. Introduction EndNote is an online search tool, it provides a simple way to search online bibliographic databases and retrieve the references directly into EndNote. EndNote is a reference and image database, it specializes in storing, managing, and searching for bibliographic references in your private reference library. You can organize images, including charts, tables, figures, equations, and assign each image its own caption and keywords. EndNote is a bibliography and manuscript maker, it formats citations, figures, and tables in Microsoft Word with the Cite While You Write feature. Watch the reference, figure, and table lists grow as you insert citations in your manuscript. Microsoft Word templates guide you through the exacting manuscript requirements of publishers. This softwares are very helpful for medical practitioners, it s simple way to search online bibliographic databases and retrieve the references directly into EndNote Methods : Computer Exercise LER 2012 Page 1

EndNote Reference Manager Every scientist has to cope with the problem of managing references (or citations, or notes, or literature, or whatever you call it.) When writing his second paper he discovers that he has to type a number of references that he already typed in when preparing his first paper. This repetitive action calls for a repository of references. In an ideal world many group members submit their references to this repository and after some time a very efficient storage medium has been EndNote is a reference database, it specialises in storing, managing, and searching for bibliographic references in your private reference library. A critical part of the research process is keeping track of where you found a particular idea, picture, fact, or quote so you can properly cite it in your work according to an accepted style. Reference management software programs are tools to help you do this easily and efficiently. EndNote is a bibliography maker, it builds lists of cited works automatically. Use EndNote to insert citations into word processing documents to compile a bibliography in any format that you need. EndNote is an online search import tool, it provides a simple way to capture references from online bibliographic databases, library catalogues etc and import them directly into EndNote. 1. Opening EndNote and Creating a Library 1.1 Start EndNote and Create a Library Note: In EndNote databases of references are called libraries. Click on the Start button, then click on All programs, followed by EndNote and then EndNote Program.The first time you open Endnote, you will be asked for 3 choices Tip: Setting a default library You can choose whether you wish EndNote to open with a specific library or to allow you to choose a library by setting a default. If you don t want to work with EndnoteWeb, simply cancel and click on File and New. Save the file at your PC, and than continue to explore Endnote. From the Edit menu, click on LER 2012 Preferences and choose Page your 2 favoured option beside When EndNote starts.

Double-click the icon to create a new library. You will be asked to save the library to a suitable location, for example to your Z drive or to a memory stick. The next time you open Endnote, the library that you have created will automatically open. Tip: Creating one Endnote library It is recommended that you only create one library in Endnote. You can use groups to organise references together (see the last point) 1.2 Understanding the toolbars 2. Adding References Start adding references to your new library. There are two ways of adding references: Typing in references manually Importing references automatically from an online database 2.1 Create a New Reference Manually Open a library and choose New Reference from the References menu or click on the symbol. An empty Reference window opens with the words "New Reference" displayed at the top. New references always appear as journal articles but can be changed to any other type of reference using the Reference Type drop down menu at the top of the New Reference window. LER 2012 Page 3

Enter the information in the relevant fields: author, title date etc. Move between fields by pressing Tab. Except for authors which are entered Surname, initials (e.g., Smith, J. E.) no extra punctuation is entered into the reference; EndNote adds the necessary punctuation and text style changes to the references when it creates a bibliography. Tip: Entering author names Write Author names in the order of Last, First Middle e.g. Jacobson, Carol May or First Middle Last e.g. Carol May Jacobson. Whichever you choose, be consistent! List multiple authors, one underneath the other by pressing the Return key between typing each name in the Author field. Use capital letters where necessary e.g. author s names. EndNote does not correct capitalisation for you. For references with a corporate author rather than a named individual put a full stop and a comma after the organisation s name to make sure it appears correctly in the resulting reference, like this: Department of Health, You do not need to fill in every field - just those important details you will require for your bibliography or for your own notes. When you close the reference window, you will be prompted to save the information and the reference is then automatically saved as a new reference in your library. LER Tip 2012 : Knowing when a reference was added Page 4 To see when a reference was added or updated, open the reference and see the footer

2.2 Other rules and exceptions Author Multiple last names: Van Tets, Gerald Frederick Titles such as Jr: Smith, Alfred, Jr Enter all authors when there are several. Enter et al., (note the comma) only as a last resort if you don't know the names of later authors. Leave the author field blank for anonymous works (but use Anonymous if "Anonymous" is printed on the title page) Institutions as authors - University of Adelaide, (i.e. add a comma) Institutions with a division - University of Adelaide,, School of Chemistry and Physics (i.e. add a double comma) If possible, enter full author names rather than initials. Year If appropriate, enter in press or in preparation or similar. Title and Journal details Use plain text without using italics or bold formatting or capitals, except when you know capitals or italics appear regardless of the citation style. Examples of such exceptions: Capitalise proper names like Australia. Capitalise the first letter of each key word in a journal title (Australian Journal of Botany) because most styles do. Use italics for a species name - Drosophila melanogaster. Use superscripts or subscripts if necessary - H 2 O - by selecting the text and choosing EDIT > STYLE > SUBSCRIPT. If possible, enter full journal titles. Abbreviated journal titles are better entered in the Alternate journal field. See Unit 4.4 for more on the handling of abbreviations through the Journals term list. Enter volume and issue numbers without v., vol., :, ( ) and so on City and Publisher, Pages and Edition Do not add punctuation such as a full stop at the end of city or publisher. Otherwise enter publisher data as you want to see it in your bibliography. Capitalize publisher or place names. For pages enter 1098 not 1,098. For edition do not add ed. enter 2nd, not 2nd ed. Page ranges can be full 1442-1449 or abbreviated 1442-9. Keywords, Abstract, Notes, Label Data can be entered here much as you like, since they do not appear in your bibliography. LER 2012 Page 5

By default use semi-colon(;), backslash (\), or ENTER as the delimiter that separates individual keywords. [The default can be changed using the Define Term Lists command in the TOOLS menu.] The Abstract and Notes fields can hold up to 16 pages of text. If your work covers more than one topic, consider adding a topic category to the Label field so that you can search for a subset of that topic's references if you need to. URL Enter a URL for a web document you will want to link to later. To link to a document on your own computer. Exercise 1 (Adding references manually) 1. Reference Type: Journal Article Authors: Peter McGill Daniel McDougall Year: 2001 Title: How to cite Journal: Journal of Academic Studies Volume: 16 Issue: 3 Pages: 34-52 Keywords: Research; Citation; Bibliography 2. Reference Type: Book Author: Zina O Leary Year: 2004 Title: Essential guide to doing research City: London Publisher: Sage Keywords: EndNote; Bibliography; Research Abstract: The authors demonstrate the correct methods of citation for publishing in academic journals in the United Kingdom. 3. Reference Type: Book Author: Department for Transport Year: 1992 Title: Increasing bus use for journeys to school: a guide to best practice within existing legislation City: London Publisher: Department for Transport 4. Reference Type: Book Section Author: Richard Harrington LER 2012 Page 6

Year: 1992 Title: Regional policy Editors: Simon Bulmer Stephen George Andrew Scott Book title: The United Kingdom and EC membership evaluated City: London Publisher: Pinter Pages: 57-64 5. Reference Type: Newspaper Article Reporter: Phil Baty Year: 2005 Title: Data row sparks research debate Newspaper: The Times Higher Education Supplement Volume: 1719 Issue date: 25 November 2005 Pages: 1 6. Reference Type: Edited Book Editors: David Murphy, Robb Walker, Graham Webb Year: 2001 Title: Online learning and teaching with technology City: London Publisher: Kogan Page 7. Reference Type: Web page Authors: Sarah Currier, Sharron Brown, F Cuna Ekmekioglu Year: 2001 Title: INSPIRAL: Investigating portals for information resources and learning (Final report.) Publisher: University of Strathclyde City: Glasgow Access Year: 2007 Access Date: 3 December URL: http://inspiral.cdlr.strath.ac.uk/documents/documents.html 3. Importing references from databases (direct) You can use Endnote to save references from bibliographic databases or from library catalogues by importing them electronically into your EndNote library. There are two methods, as explained below, a direct import facility is LER 2012 Page 7

available for some databases but other require you to save a file of references which are then imported using an appropriate filter. For references to be imported with any of the EndNote filters, the data must be consistently "tagged," with each tag starting on a new line, and the file saved as a text file, as in these examples importing citations into your EndNote library and finding full text PubMed. Exercise 2 (Adding references directly, topic: Prevention of Obesity) 1. Follow all the step correctly at Google Scholar Go to Google Scholar - http://scholar.google.com Click on Scholar Preferences In the Library Links box, type university of california berkeley Click on Find Library. Click in the box next to University of California Berkeley - UC-eLinks Scroll down to Bibliography Manager, select Show links to import citations into and choose EndNote in the drop down box. Click on the Save Preferences button. Type obesity prevention workplace into the search box and click Search. Choose a citation and import it into EndNote by clicking on Import into EndNote. Choose about 3 or so more and import them into EndNote. Include some non-article citations. Select your library to save the citations into. You may need to select Open With EndNote.exe to download citations into your EndNote library from Firefox. Check the citations as they import to make sure they import correctly. Edit as necessary since not all information is imported into EndNote. 2. Please perform importing references from Google Books! 4. Importing references from databases (non-direct) You can use a reference manager to organize your references by research project. No longer will you have to look through scraps of paper or email messages for that reference you need. Your references will be in your own searchable database. You can import references from online databases, library catalogs, and journal indexes. You can also include references from full-text sources like JSTOR and from Web sites. These programs make it much easier to keep track of and use your references, and it eliminates the need to type the references into your research paper. The programs will automatically format LER 2012 Page 8

your references in any style you choose, such as MLA, APA or the style of a particular journal. Examples of uses: Collect and organize references from many different resources into your own personal, searchable database Create formatted bibliographies and reading lists Develop lists of cited papers as footnotes or as endnotes at the conclusion of scholarly papers Exercise 3 (Adding references non-directly, topic: Prevention of Obesity) Follow all the step correctly: Open up the web browser and go to the PubMed for UCB: http://uclibs.org/pid/17708 Type "chronic disease prevention" AND nutrition into the search box and click Go. Choose some citations (about 5 or so) by clicking in the box to the left of the citation number. Use the drop-down menu to the right of the Display button to choose MEDLINE. Use the Send to menu to send the results to File. Save and name the file. Keep the file suffix.txt. Save to your desktop. Go back to EndNote. Make sure your library is open. Choose Import from the File menu. Next to Import Data File: click on the Choose File button to choose the text file you have just saved to the desktop. Select the file and click OK. Click on the down arrow to choose PubMed (NLM) as the Import Option. If it is not listed, choose Other Filters... and choose the PubMed (NLM) filter. Leave the Duplicates options as Import All. Ignore the Text Translation box. Click the Import button. 5. Search for a Set of References Choose Search Library from the Tools menu to open up a search box in the bottom pane. Type in a search word in the first search item and select the field in which you wish to search. To use automatic word stemming use the option Word begins with from the drop down menu under Contains. To find references from e.g. 2001 or later, type in the date in the search window, choose Year from the drop down field list in the second search item. LER 2012 Page 9

Then change Contains to is greater than or equal to from the drop down comparison list in the Search window. Search terms can be linked with AND and OR. The search below is for references containing the word extinction published since 1990: Extra lines to combine more than three searches can be added by using the + button. You can also choose to search by added to library or last updated and enter a date. To return to the preview view, click on the preview tab in the bottom pane. To carry out a quick search, use the quick search box at the top of the page and type in your search term. Exercise 4 There are two ways of importing from PubMed, importing references directly and nondirectly. Make some appropiate steps, how you generate this problems. Use topics based on this problems belows: A 28 years old Canadian tourist, male, is evaluated for a prolonged fever and cough following a three-week visit to his grandparents in Kenya. Four years before, he got pulmonary tuberculosis but the treatment does not continued (only in 3 weeks). A Mantoux (5 tuberculin units) test produces 22 mm of induration at 72 h. A chest x-ray is reported probably normal, the radiologist notes only poor inspiration. Three sputum smear were obtained, as an outpatient, on successive mornings. All were smear negative. In Kenya Hospital have new procedure for clinical diagnosis tuberculose, which is microscopic-observation drug-susceptibility (MODS). But this patient not sure about this test because he doesn t have enough money. What the best decision for this patient? Which one have better performance between MODS test and standard test? LER 2012 Page 10

a. Searching this article from Endnote, import references directly and nondirectly! b. Write the title of journal and the authors, and then put into your Endnote Library! c. Please answer the patients problems! Exercise 5 a. With the same clinical scenario how many journal in NEJM (New England Journal of Medicine) was appropiate to answer the Canadian tourist problems? b. Write the title of journal and the authors, and then put into your Endnote Library! 6. Managing references There are a couple of ways of editing multiple references in EndNote, for example to insert the name of the database where you found them (in previous step). You can also edit references which have already been added to your library. 6.1 Displaying references You can create a new reference by typing or copying and pasting text directly into an EndNote record. You must follow certain entry rules. This tip sheet will help you learn how to do customize the display font, customize the displayed fields within your library, sort your library display. Open a new reference window By default, EndNote displays first a column to indicate whether an Image file is attached to each reference, then a column to indicate whether a PDF files is attached to each reference, then the first author, year, title, journal title, reference type and URL for each reference. However, you can customize your Library Display to include any of the EndNote fields, in any order, with a maximum of five displayed columns. For the purposes of this example, assume you want to customize the display to include reference types instead of URLs. This will help you distinguish journal articles from books, conference proceedings from theses, etc When you open a Library you see the Library window listing all of the references that the library contains: LER 2012 Page 11

For each reference, the Library window displays the first author's last name, the year, and as much of the title as will fit in the window. (The default display can be altered in the Display Fields menu under Edit Preferences and Display Fields). If you highlight a particular reference more detail is shown in the lower half of the window in the chosen style. You can browse through your reference library by using the scroll bar, the scroll arrows, or the Page Down, Page Up, Home, End, and Arrow keys. 6.2 Editing a Reference To work with specific references you must first select them in the Library window by double clicking on a selected reference in the list. Chose one of the references you have retrieved from a database. The Reference window opens to display all of the information associated with the reference. This is where you enter or edit information for a reference. The citation information displayed at the top of the Reference window (e.g. Argus, 1991 #11) is used by EndNote to match citations in a paper to references in a library. LER 2012 Page 12

To view the rest of the reference, use the mouse to scroll down through the Reference window. Note that you can hide empty fields with the button at the top right of the window. EndNote will prompt you to save any changes made to a reference when the Reference window is closed. Basic editing Endnote manager are sorting references and changing display fields, creating a custom groups, make linking files. (Exercises 6 8). The Sort References command is used to sort the references in the library window. By default, the library window is sorted alphabetically by first author. You can sort by displayed fields by clicking on the column headings. To sort references by other fields: Choose Sort Library from the Tools menu. Use the drop-down menus to choose the field(s) to be used for sorting. Click on the button to the right of the field to specify ascending or descending order. Click on OK. In order to print the references with their abstracts, you first select references by highlighting them with the mouse, using the Ctrl key to highlight several. Then select a reference style e.g. Author-Date or Numbered from the drop-down Style list at the top of the screen. Note that a sample of the reference style is shown in the lower display window. Choose Print from the File menu. A standard print dialog will appear. Click OK to begin printing. Groups can be created to collect together references on a particular topic. Click on the groups option on the menu bar and select create group. Enter a name for your group. You can then simply drag and drop references from your main library into any of your groups. The references will show in your group, but also remain in the main library. Smart groups allow you to set up a search strategy and any references that match that search strategy will automatically be moved to the relevant smart group. To set up a smart group, go to Groups and Create smart group and enter your search strategy, or use the Search function to enter your search LER 2012 Page 13

strategy and then click on the options button and select Convert to Smart Group. To edit the search terms for the smart group, right-click on the group name in the groups panel and select Edit group. Note that smart groups are a temporary location for references. There is no facility to manually move references from all references or from a custom group into a smart group. It is advisable to move references from a smart group into a custom group if you wish to be able to manually move references as well as dynamically populate the group. A smart group can have the same name as a custom group. Exercise 6 (Sorting References and Changing Display Fields) 1. Sorting your references by author (alphabetical order) and put reference type on display fields! Click on All References from the Groups window to see your entire library Click on the field names at the top of the columns (Author, Title ) to change the sort order. To change the display fields: Under the Edit menu, choose Preferences. Click on Display Fields. Using the drop-down menu, change the Field in Column 1 to Reference Type You can change the Heading text to display what text you would like. Click on OK. You should now see the new display field. Exercise 7 (Creating Group) 2. Make 2 group of references, Tuberculosis and Obesity. Under the Groups menu, select Create Group. Name the group and press Enter. Click on the All References group. Click on a reference you would like to add to the group. Holding the mouse button down, drag the reference to your new group. Click on your group name in the Groups column to see the references you have in your group To remove a reference from a group, click on the reference and then hit the Delete key or under the Reference menu select Remove References from Group. 3. Make a smart group only for Diagnosis Test for Tuberculosis! LER 2012 Page 14

Exercise 8 (Linking Files) 4. Make linking files by word document Open up Word and create a new document. Type "My test document" into it. Save the document to your desktop. Call the document anything you wish. Go to your EndNote Library. Click on a reference. Under the References menu, select File Attachments Attach File Use the dialog box to locate and select the file you just created. To create a file link, uncheck the box next to: Copy this file to the default file attachment folder and create a relative link. If you do NOT uncheck this box the file will be added to your EndNote library. Click Open. Double click on the reference you added the file to. Scroll down to the File Attachment field and you should see an icon. When you mouse over the icon, you should see the file pathname to that document appear. To open the linked document, double click on it. Close the reference window. 5. Make linking files by pdf. File formatted 6.3 Linking to the Full-text Endnote provides several ways of linking to the full-text of an article. In remote database, EndNotes enables you to connect, search, retrieve, and save references from other databases (remote) to add to your library. Try to finding full text for your references. Exercise 9 Searching from Endnote based on this problems: An 18-month-old girl entered your practice having recently been adopted from Mainland China. An initial Mantoux test produces 18 mm of induration. She had Bacille Calmette-Guerin at birth, and the mother believes this is the likely cause of her positive test. She is hepatitis B surface antigen negative. Should she have treatment for latent TB infection? 1. Put the appropiate keyword when you searching (Serching in Pubmed) Select all the references by holding the Shift key down and clicking on the first then last reference. Under References menu, select Find Full Text. Click on Continue. In the Groups window, you now see Full Text (#). Full text was found for the highlighted references. LER 2012 Page 15

How many full text references do you have? Click on All References from the Groups window to see your entire library. 2. With the same procedure how many full text references do you have, if you find in Medline (Ovid) and Oxford U (Library Catalog). Each reference type (journal article, book, etc) has a template with its own set of fields (author, title, publisher etc). Click the Reference Type drop box to choose the reference type you need. Use Book for books written by one or more authors. Use Edited Book for books edited by one or more editors. Use Book Section for parts of edited or non-edited books - for example a chapter or an article in published conference proceedings. Use Journal article for electronic or print journal articles. Use Conference Proceedings for a whole conference proceedings not a single conference article. Use Electronic Source for a Web page that isn't a book of journal article. Use Personal Communication for all correspondence including email. Exercise 10 Put 10 references (books) to your Endnote Library manually, based on assignment from web CRP in previous day. Use appropiate reference type! Goodluck and practice by yourself... LER 2012 Page 16