WM ZAHIRUDDIN WAN MOHAMMAD

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1 Intensive Course for MMed/Msc/PhD USM December 2014 Referencing with Assoc. Prof. Dr WM ZAHIRUDDIN WAN MOHAMMAD M.D, M.Comm. Med. (Epid. & Biostats) USM 1

2 Referencing in scientific writing Time consuming Writing proposal and publishing research require gathering references and creating properly formatted bibliographic citations. Keeping track of your bibliography as your research into a subject becomes deeper, and the literature base expands to thousands of articles. Standard formatting almost every journal requires a different format for citations (numbered or alphabetized) and you can find yourself reformatting (and retyping) your citations time and time again. 2

3 Using bibliography softwares Reference list or bibliography must: be in alphabetical order by author s surname (Harvard system) or by ordered numbers (Vancouver) have all elements of the reference in the correct order with consistent syntax and punctuations throughout Consistency is the rule in any system of referencing....it S BEST TO USE A BIBLIOGRAPHIC SOFTWARE! There are many software's that can be used for writing manuscripts and research papers. Endnote is one of the most popular software among students and researchers. 3

4 In today s session Part 1 - how to create an Endnote library, enter new references, download references from online databases and sort your library. Part 2 - how to create bibliographies and to insert citations into your thesis/documents using different referencing styles by Endnote. 4

5 Part I Introduction, creating and managing Endnote 5

6 Introduction to Endnote Endnote is a software developed by ISI Research Soft. ( Endnote is not a freeware, need to purchase. Current version (licensed) is EndNote X7. If your institution subscribes it, get the CDROM This software is useful for Creating and managing your own personal bibliography Managing pdf files Online search tool for articles (import or export files) Bibliography maker (> 4,000 journal templates formats) Cite while you write (CWYW) Writing manuscript /thesis/research papers formatting citations and manuscript template 6

7 Words compatibility and Tutorials EndNote s Cite While You Write (CWYW) is compatible with following word processing and text formats: Microsoft Word OpenOffice.org Writer 3 (EndNote only) WordPerfect/word processors with Rich Text Format (RTF). Macintosh: compatible with Microsoft Word X, 2004, Go to Endnote s FAQ website to learn more. One of the best Endnote X7 website tutorial/handout: 7

8 Checking your installation: If EndNote & MS Word are properly installed, both will be accessible via the menu toolbars Accessing Endnote X7 through menu toolbar in MS Word Accessing MS Word through Tools from Endnote X7 program 8

9 Opening an existing Endnote library An Endnote library has two files: *.Data (folder-like file) *.enl (endnote database) 9

10 How to view a sample Endnote library Go to C: drive and click Open. Select Program Files; looks for EndNote X7 folder, then click the Example s shortcut 10

11 Viewing an Endnote library EndNote X7 Windows icon toolbar Groups pane lists various groups of references for easy retrieval. Reference List pane displays a multi-column list of references. This window displays a Preview tab to view formatted references (Abstracts or Output styles), manage PDF file and insert attachments 11

12 How to view an abstract Highlight selected reference to view the abstract (use Annotated view & click Preview) 12

13 How to view the Output styles Highlight selected reference and click the output styles (e.g APA 6 th format) 13

14 General steps in using Endnote Getting References (eg. PubMed, online databases, manually) Import / Export Microsoft Word Cite while you write Selected citation styles formatting Other citation styles

15 Creating an Endnote library 1. Open Endnote program 2. Create a new Endnote library (..name and save it!) 3. Getting references into your EndNote library: Search from Pubmed website and import it Export references from subscribed online databases (e.g Ovid, ProQuest, Science Direct etc) Export from Google Scholar Direct pdf files import or download Online retrieval through EndNote Manual entry of references 15

16 i. Search and import from PubMed First, search your references (using keywords, Boolean methods or your search strategy) from PubMed website. E.g Search AIDS Malaysia Knowledge as keywords Search for references in pubmed 16

17 Use Citation manager to send selected (ticked boxes) Pubmed file(s) to your Endote library Note: the selected files will be created automatically to your open Endnote program 17

18 Importing to Endnote Note: You may be asked to Save file as citations.nbib in a folder, then import into an open Endnote thru PubMed(NLM) option. 18

19 ii. Getting references from USM-subscribed Online Databases (use Ez-proxy if off-campus login) Examples: Proquest, Ovid, Science Direct, ISI Web of Knowledge etc 19

20 From PROQUEST, tick/select the retrieved references, then click Export/Save to Endnote (follow the instructions) 20

21 Proquest database: Export and save the file in your Endnote Scroll down, then click Continue. Save the file (or open through RIS files), and it will automatically be imported to an active Endnote library 21

22 Exporting and saving from Ovid database Click Export after selecting the references Choose Endnote. Citation + Abstract. Export citation(s) Then save the file (ovidweb.cgi), then double click it to import it to your active Endnote library 22

23 Other subscribed databases You may retrieve references from many other subscribed databases, and look for Export to Endnote menu ISI Web of Knowledge Scopus Science Direct Specific journal database 23

24 From ISI Web of Science 24

25 iii. Exporting from Google Scholar directly (customize the setting preferences for EndNote) Set the Scholar Preferences. Select Show links to import citations into, select EndNote from the drop-down. Click Save Preferences. 25

26 Exporting from Google Scholar directly via Import into EndNote Use Open to import the selected references into the Endnote (for IE and Firefox). For Google chrome, save as scholar.enw files then click it to import. Note: - Can only import one citation at a time into EndNote. - Imported references may not follow proper bibliographic formatting! 26

27 iv. Importing PDF articles You can import publisher-created PDFs into EndNote and, in many cases, EndNote will create a reference in your EndNote library at the same time. EndNote can extract the reference information using its Digital Object Identifier (DOI). If the DOI is not present the PDF will be imported, but you will need to do extensive editing in required fields of the reference. 27

28 Importing and attached a pdf file (or folder) to selected reference Choose to import the selected file using Import Option PDF, then click Import 28

29 Importing PDF file with DOI Using Import procedure in EndNote, it can extract the reference information using its Digital Object Identifier (DOI). 29

30 Need to edit information in selected fields of the imported pdf file without DOI Need to edit in reference preview 30

31 Finding full-text pdf articles EndNote X7 can automatically locate and download full text files by accessing several sources. But with conditions. 1. If the articles are FREELY AVAILABLE online, they will most likely be found and attached. 2. You are connected to your library website s subscribed databases The retrieved the full text file is saved as pdf files in the library s DATA folder and linked as attachment. 31

32 How to find the full text article (pdf) of selected reference from internet 32

33 v. Online search directly from EndNote (make sure online for remote searching) Type the appropriate key words based on your search strategy (e.g Bolean seacrh techniques) in Any Field. 33

34 Choose the online database (preferably PubMed NLM) Valid only for selected databases This method is good for known citations Choose connection file: Connect to PubMed (NLM), public access version of MEDLINE. 34

35 vi. Manual entry of references Some references are not available through online or databases e.g unpublished thesis, proceedings, books, annual reports etc. Need to add the references manually into existing Endnote library. Click on the New Reference button or on the toolbar. 35

36 Choose type of reference, then fill in required fields Fill in the required information based on the reference types Select the type of reference you want to create, e.g Journal (as default), proceedings, books, reports etc. 36

37 Manual entry: Write only relevant information in the fields Individual author name must be entered one per line (3 ways to do it). Last, First Middle First Middle Last Last, (abbr) Middle.Last. As you type, Endnote will suggest names similar name as entering. If the name appears in RED, it indicates a new name for authors in your library. For institution or corporate authors, you may write the name followed by a coma e.g Universiti Sains Malaysia,, World Health Organization, 37

38 Manual entry: Closing and saving Save it from the File menu or Closing the Reference window by clicking the close button (smaller x). All information is automatically saved into your active library when you close a window. 38

39 Important points to remember when entering data manually! The output styles can only format data correctly if the data is entered correctly. Just add the basic data, in the default EndNote font. The output style will change this to bold or italics and add extra text such as "vol." or "Ed." (if required by the style) Fields such as Abstract, Notes, Research Notes are for your use Use the URL field to link to an electronic version of the document Use the File Attachments field to add a PDF version of the document to your library If you use abbreviated journal titles in your publications, you can set up a Journal Term list to store the abbreviations 39

40 Managing Endnote (demonstration) Copy output styles into the Endnote folder Remove reference duplicates Sort ascending, descending Copy paste references between libraries Compress a Library and to colleague Attach files (pdf, word, jpeg etc) Organize references into Groups (or folders) 40

41 Create a compressed library to Compressed the Endnote Library ( *.enl and *.Data files together) as *.enlx. Save or send compressed files to it (with/without attachments) 41

42 Attach files (pdf, Word or jpeg) Store PDF and other files with your EndNote library: In Endnote X7, there is unlimited size for external files attachments per reference. You may copy-paste or Drag and drop files in "File Attachment" field onto a reference for auto-linking and storage. 42

43 Find duplicates It is important to try to avoid duplicates of references in your EndNote Library. To check, go to References and select Find Duplicates. You may sort references by title to ensure no duplicate records have been missed. To delete duplicate records, select duplicate records, right click, then select Move References to Trash. In addition, when importing in PDF files EndNote gives you the option to Import into Duplicates Library 43

44 Organize references into Groups Adding a Group to your Group Set You can create several groups under a group set. Adding References to a group Drag and drop the references to a group. Smart Groups When new references are added to the library, they are searched by each of the smart groups. If the references fit the search criteria they are automatically added to that group. 44

45 Let s take a break! 45

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