1. Kenneth Lim Kenneth.lim@nus.edu.sg 29 & 30 Jul 2015 Tools for your Biological Sciences Research (Life Sciences Year II Students)

2. Outline Using the Library Overview of Search Strategies Information Sources & Evaluation Citations & Plagiarism Bibliographic Software & Introduction to EndNote Guides, Tools and Tips 2

3. NUS Libraries Portal (http://www.lib.nus.edu.sg)http://www.lib.nus.edu.sg 3

4. FindMore@NUSL & LINC 4 What is the difference between FindMore & LINC? http://libfaq.nus.edu.sg/faq/71517http://libfaq.nus.edu.sg/faq/71517

5. Outline Using the Library Overview of Search Strategies Information Sources & Evaluation Citations & Plagiarism Bibliographic Software & Introduction to EndNote Guides, Tools and Tips 5

6. Literature Search Cycle 6 Breakdown the Research topic into concepts Identify key Information Sources Develop a Search Strategy Locate Additional Information Sources Manage Citations

7. Types of Database Searches Keyword / Phrase Search e.g. Using “horseshoe crab” in Web of Science /Google Field Search e.g. Using Raffles Bulletin of Zoology in the Publication Name field in Zoological Record Subject Heading / Thesaurus Search e.g. Using neoplasms (instead of cancer) as a MeSH (Medical Subject Headings) term in PubMed 7

8. Boolean Connectors OR - either of the terms may be present. Used for broadening a search e.g. roundworms OR nematodes AND - both terms must be present. Used for narrowing a search. e.g. parasites AND intestine NOT - eliminate an unwanted concept or word e.g. parasites NOT flatworms ( ) – grouping words or phrases and specifying the order in which Boolean operations occur when multiple operations are present e.g. (A OR B) AND C A OR (B AND C) 8

9. Exact vs. Wildcard Search “ ’’- searches the exact phrase enclosed within the quotes e.g. “avian influenza” * - represent any group of characters or no characters (useful for representing various forms of a term) e.g. biol* - for biology, biological, biologist, biologists ? - represent any single character (useful for singular/plural forms) e.g. cat? - for cat, cats $ - represent one character or no characters e.g. behavio$r, colo$r, vapo$r (useful for finding both British & American spellings) Note: Wildcards and usage are dependent on the database 9

10. Sample Quiz Q. What did you drink for breakfast today? a.Coffee b.Tea c.Milo d.I haven’t had breakfast  Click this link to answer (http://bit.ly/ls2q0)http://bit.ly/ls2q0 10

11. Quiz on Search Strategies Q1. To broaden our search results we may make use of all of the following: Synonyms of keywords Truncation “*” and Wildcard Symbols “?” Boolean operator “AND” Is this statement (a) True or (b) False? Click this link to answer (http://bit.ly/ls2q1)http://bit.ly/ls2q1 11

12. Outline Using the Library Overview of Search Strategies Information Sources & Evaluation Citations & Plagiarism Bibliographic Software & Introduction to EndNote Guides, Tools and Tips 12

13. Types of Information Sources Information SourcesExamples Primary Sources Presents the original research information and empirical data. Experimental results Theses & Dissertations Conference Proceedings Journal articles Secondary Sources Review or restate information in Primary Sources or other Secondary Sources. Review articles Bibliographies Databases Tertiary Sources Provides overviews of topics by synthesizing information gathered from other sources. Dictionaries Encyclopedias Textbooks 13 Current Dated

14. Recommended Online Resources 14 Type of InformationRecommended E-Resource Multi-disciplinary Bibliographic Databases Web of Science Web of Science / ScopusScopus Biomedical & Life Sciences BIOSIS Previews Animal Biology & Taxonomic Reference Zoological Record Medicine, Dentistry, Pharmacy, Healthcare & Life Sciences PubMed (MEDLINE) Embase Experimental Protocols and Demonstration Videos Springer Protocols Wiley Current Protocols JoVE JoVE (Journal of Visualized Experiments) Chemical Substance Structure / Properties & Reaction Searching Reaxys Reaxys / SciFinder (registration)SciFinder (registration) Newspaper Articles / Local Content FactivaFactiva / Lexis-Nexis / NewspaperSGLexis-NexisNewspaperSG 14

15. Guidelines for Evaluation of Resources CriteriaQuestions Authority Author’s Credentials, Subject Expert? Accuracy Information is Valid and Reliable Objectivity & Purpose Any Bias? Review process Publication Peer-Reviewed? Suitability Academic /Scholarly Journal (Journal Impact Factor, Immediacy Index) Timeliness When was the Information published? 15 NLB S.U.R.E Campaign

16. Production of Limulus Amebocyte Lysate (LAL) 16 Source: http://www.wired.com/magazine/2011/06/st_processcrab/?pid=5836&viewall=true

17. Alternative: recombinant Factor-C (r-FC) 17 http://media.drugdevcompare.com/m/7/Product/57499-1-400x300.jpg http://media.drugdevcompare.com/m/7/Product/57499-2-400x300.jpg

18. Research Topics 18 Topic 1: Conservation of Horseshoe crabs in Malaysia and Singapore Topic 2: Application of Limulus Amoebocyte Lysate assay for detection of bacterial endotoxins Image Source: http://animals.m-y-d-s.com/aquatic/horseshoe_crab /

19. BIOSIS Previews Demo Topic: Conservation of Horseshoe crabs in Malaysia and Singapore 19

20. Construction of Search Statement Step 1: Identify concepts/keywords Application of Limulus Amoebocyte Lysate assay for detection of bacterial endotoxins Step 2: Generate synonyms, alternate terms, abbreviations limulus amebocyte lysate: LAL endotoxin: pyrogen, lippopolysaccharide, LPS Step 3: Construct search statement (initial search) ("limulus amoebocyte lysate" OR LAL) AND (endotoxin OR (lipopolysaccharide OR LPS)) 20

21. Quiz on Search Statements Q2. Which of the following search statements would be the best one for searching articles on bird flu? a.(“bird flu”) b.(bird AND flu) c.(bird OR avian) AND (flu OR influenza) Click this link to answer (http://bit.ly/ls2qn2)http://bit.ly/ls2qn2 21

22. Web of Science Demo Topic: Application of Limulus Amoebocyte Lysate assay for detection of bacterial endotoxins 22 ("limulus amoebocyte lysate" OR LAL) AND (endotoxin OR (lipopolysaccharide OR LPS))

23. Outline Using the Library Overview of Search Strategies Information Sources & Evaluation Citations & Plagiarism Bibliographic Software & Introduction to EndNote Guides, Tools and Tips 23

24. Plagiarism What is Plagiarism? A piece of writing that has been copied from someone else and presented as being your own work. The American Heritage Dictionary of the English Language (4th Ed.) The act of taking someone’s words or ideas as if they were your own. Avoiding Plagiarism CIT Preventing Plagiarism site http://www.cit.nus.edu.sg/plagiarism-prevention/ http://www.cit.nus.edu.sg/plagiarism-prevention/ Proper citation of information sources turnitin software Plagiarism Spectrum http://turnitin.com/assets/en_us/media/plagiarism_spectrum.php http://turnitin.com/assets/en_us/media/plagiarism_spectrum.php 24

25. Citations & Bibliography Two places to cite the references you have used: within a sentence (in-text citation) at the end of the document (bibliography/references) 25 Bibliography/Reference 4. Ding JL, Navas III MA, Ho B. Molecular cloning and sequence analysis of factor C cDNA from the Singapore horseshoe crab, Carcinoscorpius rotundicauda. Mol Mar Biol Biotechnol 1995; 4: 90 Bibliography/Reference 4. Ding JL, Navas III MA, Ho B. Molecular cloning and sequence analysis of factor C cDNA from the Singapore horseshoe crab, Carcinoscorpius rotundicauda. Mol Mar Biol Biotechnol 1995; 4: 90 In-text Citation …Mangrove horseshoe crab ( Cacinoscorpius rotundicauda ) was recently developed (4) In-text Citation …Mangrove horseshoe crab ( Cacinoscorpius rotundicauda ) was recently developed (4)

26. Quiz on Citations Q3. The following Bibliographic Reference is an example of a: a.Journal article citation b.Book citation c.Book Chapter citation Click this link to answer (http://bit.ly/ls2qsn3)http://bit.ly/ls2qsn3 26

27. Why cite? To acknowledge the contributor(s) of ideas used in writings To lend support to arguments by referring to authoritative sources To help readers verify your claims To show research done 27

28. Outline Using the Library Overview of Search Strategies Information Sources & Evaluation Citations & Plagiarism Bibliographic Software & Introduction to EndNote Guides, Tools and Tips 28

29. Introduction to Bibliographic Software & EndNote A software that: stores and organises references from many sources inserts these references into a Word document, and automatically formats your references according to a predefined citation style 29 Comparison of Reference Management Software

30. EndNote Online Guide http://libguides.nus.edu.sg/endnote

31. EndNote Workflow 31 1. Create an EndNote Library2. Add references to the EndNote Library3. Manage references: using groups & finding duplicates4. Insert references in MS Word (Cite While You Write)5. Change citation style and edit preferences

32. Step 1: Create an EndNote Library a.All programs > EndNote > EndNote Program b.File > New c.Filename: Test (*.enl) d.Save 32 Hands-on

33. Step 2: Add References to the Library 33 Direct Export Direct Export Import Text File Manual Inputting EndNote Library Cite While You Write MS Word Import PDF Online Search

34. Method 1: Direct Export Export references directly from database a.At the database, select the records you want b.Save, output, export or send to EndNote (Look for “RIS format”) c.Click Open to transfer records to your EndNote library 34

35. Method 4: Import PDF Files Extracts references from PDF files PDF must contain a Digital Object Identifer (DOI) and is not a scanned document. a.In EndNote, go to File > Import b.Choose either file or folder, and change Import Option > PDF Note: If the author, title, journal, etc, fields are not auto-populated, the PDF could be of the wrong format or have an incorrect DOI New in X7 - PDF auto-import folder Whats new in EndNote X7 (Video) Whats new in EndNote X7 (Video) 35

36. Step 3: Duplicate References To set criteria: Edit > Preferences > Duplicates To find duplicates: References > Find Duplicates 36

37. Managing References: Custom vs. Smart Groups Custom Groups Create folders to group (categorise) references Smart Groups Automatically group references based on your search criteria, e.g.: author/year/title contains/is/word begins with… Note: Any references added to EndNote will be automatically filed in the group, with immediate effect 37

38. Outline NUS Libraries and Services for Graduate Students Overview of online databases for Life Sciences Plagiarism, Citations and Publishing Introduction to bibliographic software & EndNote Adding references to your library Managing references: Groups & Duplicates Cite While You Write Backing up Guides and Tips 38

39. Step 4: Cite While You Write (CWYW) 39 Use MS Word to insert citations into your paper Create a paper with properly formatted references, bibliography, figures & tables Tip: Do NOT edit the citations and bibliographies in Word. Edit the reference in the EndNote Library only Tip: To locate citation and bibliography fields, change the MS Word’s Field Shading option

40. EndNote Tab & Field Shading If EndNote is properly installed, you will see the EndNote tab in Word After you add references, Field shading shows up as text highlighted in grey. 40

41. Inserting Citations 41 Method 1: Find Citation a.EndNote X7 tab: Insert citation > Find Citation b.Search for a word in any field (e.g. title, author) c.Select the references that you want to insert into your paper Method 2: Insert Selected Citation(s) a.In EndNote library, select a citation b.Go to Word and place cursor at insertion point c.Click on Insert Citation > Insert Selected Citation(s)

42. Editing Citations & References Edit & Manage Citation(s) E.g. add page numbers, exclude author, exclude year Edit Library Reference(s) Place cursor in the citation, click on Edit library references and make the necessary changes. Next, click on Update citations and bibliography 42

43. Step 5: Change Style & Create a Bib Section To change the citation style EndNote X7 tab: Click on Style > Select Another Style… To create bibliography section* a.Bottom right corner of Bibliography group > Layout > Bibliography title b.Type References (or Bibliography) *The bibliography section appears only when you insert a citation *New in X7 - Create sections within Bibliography 43

44. Backing Up Library Save a Copy Creates an exact copy of the library  xxx Copy.Data and xxx Copy.enl File > Save a Copy… 44

45. Outline Using the Library Overview of Search Strategies Information Sources & Evaluation Citations & Plagiarism Bibliographic Software & Introduction to EndNote Guides, Tools and Tips 45

46. Online Database Guides & Resources Biological & Life Sciences Subject Guide http://libguides.nus.edu.sg/biology http://libguides.nus.edu.sg/biology PubMed Resources http://www.nlm.nih.gov/bsd/disted/pubmedtutorial/ http://www.nlm.nih.gov/bsd/disted/pubmedtutorial/ Embase Getting Started http://help.elsevier.com/app/answers/list/p/9754/c/9540,9541 http://help.elsevier.com/app/answers/list/p/9754/c/9540,9541 Web of Science (includes BIOSIS Previews & Zoological Record) http://wokinfo.com/training_support/training/http://wokinfo.com/training_support/training/ Scopus Resources http://help.scopus.com/Content/h_tutorials.htm http://help.scopus.com/Content/h_tutorials.htm 46

47. Library Proxy Stem/Bookmarklet NUS Libraries Proxy Stem http://libproxy1.nus.edu.sg/login?url= http://libproxy1.nus.edu.sg/login?url e.g. Prefix a URL with the NUS Libraries Proxy Stem http://www.springerlink.com/content/e440n0431724460v/ http://libproxy1.nus.edu.sg/login?url=http://www.springerlink.c om/content/e440n0431724460v/ Installing the NUS Libraries Proxy Bookmarklet: FAQ: http://libguides.nus.edu.sg/content.php?pid=199108&sid=1665223 FAQ: http://libguides.nus.edu.sg/content.php?pid=199108&sid=1665223 47

48. Accessing Full-Text via Google Scholar Setting up NUS Libraries access in Google Scholar : FAQ: http://libfaq.nus.edu.sg/a.php?qid=260648 FAQ: http://libfaq.nus.edu.sg/a.php?qid=260648 Alternate direct link: http://scholar.google.com/schhp?hl=en&inst=13660462560571941651 http://scholar.google.com/schhp?hl=en&inst=13660462560571941651 48

49. Accessing Full-Text via PubMed Setting up NUS Libraries access in PubMed: FAQ: http://libfaq.nus.edu.sg/a.php?qid=260692#.US2nFFeQg8k Direct link: http://libproxy1.nus.edu.sg/login?url=http://www.ncbi.nlm.nih.gov/pubmed? myncbishare=nuslib&holding=isgnuslib_fft http://libproxy1.nus.edu.sg/login?url=http://www.ncbi.nlm.nih.gov/pubmed? myncbishare=nuslib&holding=isgnuslib_fft 49

50. Thank You! Please fill in the feedback form at: http://bit.ly/bsf30Jul15 Contact me at: Kenneth Lim kenneth.lim@nus.edu.sgkenneth.lim@nus.edu.sg Science Library sclib@nus.edu.sgsclib@nus.edu.sg 50