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Tools for your Biological Sciences Research (Life Sciences Year II Students). Kenneth Lim slblekk@nus.edu.sg 30 & 31 Jul 2013 With acknowledgements to NUS Libraries EndNote Team. Outline. Using the Library Overview of Search Strategies Information Sources & Evaluation

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tools for your biological sciences research life sciences year ii students

Tools for your Biological Sciences Research (Life Sciences Year II Students)

Kenneth Lim

slblekk@nus.edu.sg

30 & 31 Jul 2013

With acknowledgements to

NUS Libraries EndNote Team

outline
Outline
  • Using the Library
  • Overview of Search Strategies
  • Information Sources & Evaluation
  • Citations & Plagiarism
  • Bibliographic Software & Introduction to EndNote
  • Guides, Tools and Tips
loan entitlement for undergraduates
Loan Entitlement for Undergraduates
  • 20 items 14 days 3 renewals

How do I Borrow a Book?

FAQ: http://libfaq.nus.edu.sg/a.php?qid=79581

http://www.battenkillbooks.com/wp-content/uploads/2011/10/stack_of_books21.jpg

literature search cycle
Literature Search Cycle

http://libguides.nus.edu.sg/content.php?pid=165681&sid=1733290

types of database searches
Types of Database Searches
  • Keyword / Phrase Searche.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 aMeSH (Medical Subject Headings) term in PubMed
boolean connectors
Boolean Connectors
  • OR- eitherof the terms may be present. Used for broadening a searche.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 worde.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)
exact vs wildcard search
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 characterse.g. behavio$r , colo$r , vapo$r (useful for finding both British & American spellings)
production of limulus amebocyte lysate lal
Production of Limulus Amebocyte Lysate (LAL)

Source: http://www.wired.com/magazine/2011/06/st_processcrab/?pid=5836&viewall=true

alternative recombinant factor c r fc
Alternative: recombinant Factor-C (r-FC)

http://media.drugdevcompare.com/m/7/Product/57499-1-400x300.jpg

http://media.drugdevcompare.com/m/7/Product/57499-2-400x300.jpg

research topics
Research Topics

Topic 1:

Population studies of Asian Horseshoe Crabs

Topic 2:

Limulus Amebocyte Lysate (LAL) and Recombinant Factor C (rFC) as tests for airborne endotoxins

Image Source: http://animals.m-y-d-s.com/aquatic/horseshoe_crab/

construction of search statement
Construction of Search Statement
  • Step 1: Identify concepts/keywords
  • Limulus Amebocyte Lysate (LAL) and Recombinant Factor C (rFC)as tests for airborne endotoxins
  • Step 2: Generate synonyms, alternate terms, abbreviations
  • airborne: air, aerial, dust, aerosol endotoxin: pyrogen, lippopolysaccharide, LPS
  • Step 3: Construct search statement (initial search)
  • (endotoxin*AND(air* OR dust*))AND("limulus amebocyte lysate"OR"recombinant factor c")
slide17

“Good artists copy, great artists steal”

- Steve Jobs (1994)

“…competitors should create their own original technology, not steal ours.”

- Steve Jobs (2010)

http://www.apple.com/pr/library/2010/03/02Apple-Sues-HTC-for-Patent-Infringement.html

plagiarism
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/
    • Proper citation of information sources
    • turnitin software
citations bibliography
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)
why cite
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
endnote online guide
EndNote Online Guide

http://libguides.nus.edu.sg/endnote

http://libguides.nus.edu.sg/endnote

introduction to endnote
Introduction to 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
installing endnote for pc
Installing EndNote for PC

http://libguides.nus.edu.sg/endnote

For installation issues, contact NUS IT Care

Tel: 6516-2080, Email: itcare@nus.edu.sg

installing endnote for mac
Installing EndNote for Mac

Email software administrator for instructions

the endnote library
The EndNote Library
  • Contains all your references. No limit to number of references, but <100,000 is recommended
step 1 create an endnote library

Hands-on

Step 1: Create an EndNote Library
  • All programs > EndNote > EndNote Program
  • File > New
  • Filename: Test (*.enl)
  • Save
step 2 add references to the library
Step 2: Add References to the Library

Import PDF

Direct

Export

Import Text File

Online Search

Manual Inputting

EndNote Library

Cite While You Write

MS Word

method 1 direct export
Method 1: Direct Export
  • Export references directly from database
  • At the database, select the records you want
  • Save, output, export or send to EndNote (Look for “RIS format”)
  • Click Open to transfer records to your EndNote library
method 1 direct export wos
Method 1: Direct Export (WOS)

1. Mark the records

2. Click on EndNote

method 1 direct export pubmed
Method 1: Direct Export (PubMed)

1. Mark the records

2. Send to>Choose Destination>Citation Manager

method 2 import txt file
Method 2: Import .txt File
  • Used when references cannot be exported to EndNote.
  • Very few databases e.g. Factiva
  • At the database, select the records you want
  • Export text (.txt) file and save on desktop
  • In EndNote, go to File > Import
  • Browse and select the .txt file
  • Select Import option > Other filters

Which filter to use?

http://libguides.nus.edu.sg/content.php?pid=96551&sid=3508846

method 3 online search

NATL

Method 3: Online Search
  • Search free databases (e.g. PubMed) and library catalogues (e.g. LINC, Library of Congress)
  • Go to Online Search Mode > More
  • Select a free database or catalogue, e.g. NATL U of Singapore
  • In the online search pane, search by exact title of book or conference proceeding
  • Copy the reference to Local Library Mode
method 3 online search1
Method 3: Online Search

Search by the exact title

2. Select more

1. Click on Online Search Mode (Temporary Library)

method 4 import pdf files
Method 4: Import PDF Files
  • Extracts references from PDF files
  • PDF must contain a Digital Object Identifer (DOI) and is not a scanned document.
  • Steps:
  • In EndNote, go to File > Import
  • 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
method 5 manual inputting
Method 5: Manual Inputting

Link to the video: http://youtu.be/30u5_b9d5D4

step 3 duplicate references
Step 3: Duplicate References
  • To set criteria:
  • Edit > Preferences > Duplicates
  • To find duplicates:
  • References > Find Duplicates
managing references custom groups
Managing References: Custom Groups
  • Create folders to group (categorise) references

Go back to All References.

Select references and drag into custom group. Alternatively, right click on the references > Add References To > My Groups

managing references smart groups
Managing 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

1

2

44

attaching files to references
Attaching Files to References
  • To set criteria:
  • References > File Attachment > Attach Files
step 4 cite while you write cwyw
Step 4: Cite While You Write (CWYW)
  • 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
inserting citations
Inserting Citations

Method 1: Find Citation

a. EndNote X6 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)

In EndNote library, select a citation

Go to Word and place cursor at insertion point

Click on Insert Citation > Insert Selected Citation(s)

editing citations references
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
change style create a bib section
Change Style & Create a Bib Section
  • To change the citation style
  • EndNote X6 tab:
  • Click on Style > Select Another Style…
  • To create bibliography section*
  • Bottom right corner of Bibliography group > Layout > Bibliography title
  • Type References (or Bibliography)
  • *The bibliography section appears only when you insert a citation
backing up library 1
Backing Up Library (1)
  • Method 1: Save a Copy
  • Creates an exact copy of the library  xxx Copy.Data and xxx Copy.enl
  • File > Save a Copy…
backing up library 2
Backing Up Library (2)
  • Method 2: Compress Library
  • Saves the .enl file and .Data folder into one compressed file
  • File > Compressed Library (.enlx)
  • To restore: File > Open > Open Library…
more information on endnote
More Information on EndNote
  • EndNote LibGuide
  • EndNote X6 User’s Guide
  • Endnote Training YouTube Channel
  • EndNote Updates
  • Output Styles
  • Connection Files
  • Microsoft Word Templates
  • Frequently Asked Questions
  • Contact NUS Libraries’ EndNote team: askalib@nus.edu.sg
online database guides resources
Online Database Guides & Resources
  • Biological & Life Sciences Subject Guidehttp://libguides.nus.edu.sg/biology
  • PubMed Resourceshttp://www.nlm.nih.gov/bsd/disted/pubmedtutorial/
  • Web of Science / BIOSIS Resourceshttp://science.thomsonreuters.com/training/wos/http://science.thomsonreuters.com/training/biosis/
  • Scopus Resourceshttp://help.scopus.com/Content/h_tutorials.htm
library proxy stem bookmarklet
Library Proxy Stem/Bookmarklet
  • NUS Libraries Proxy Stemhttp://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.com/content/e440n0431724460v/
  • Installing the NUS Libraries Proxy Bookmarklet:FAQ:http://libguides.nus.edu.sg/content.php?pid=199108&sid=1665223
accessing full text via google scholar
Accessing Full-Text via Google Scholar
  • Setting up NUS Libraries access in Google Scholar : FAQ: http://libfaq.nus.edu.sg/a.php?qid=260648
  • Alternate direct link:http://scholar.google.com/schhp?hl=en&inst=13660462560571941651
accessing full text via pubmed
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