Tools for your Biological Sciences Research

(Life Sciences Year II Students) Kenneth Lim [email protected]

29, 30 & 31 Jul 2014

• • • • • •

Outline

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

NUS Libraries Portal

( http://www.lib.nus.edu.sg

)

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Loan Entitlement for Undergraduates

20 14 3

items days 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

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Literature Search Cycle

Breakdown the Research topic into concepts Manage Citations Identify key Information Sources Locate Additional Information Sources Develop a Search Strategy http://libguides.nus.edu.sg/content.php?pid=165681&sid=1733290

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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 ( Me dical S ubject H eadings) term in PubMed 6

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

A

OR

B

) AND (

B

AND

C C

)

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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 biol ogy , biol ogical , biol ogist , biol ogists

?

- represent any single character (useful for singular/plural forms) e.g. cat

?

- for cat, cat s

$

- 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

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Types of Information Sources

Information Sources Primary Sources

Presents the original research information and empirical data.

Current Secondary Sources

Review or restate information in Primary Sources or other Secondary Sources.

Examples

• Experimental results • Theses & Dissertations • Conference Proceedings • Journal articles • Review articles • Bibliographies • Databases

Tertiary Sources

Provides overviews of topics by synthesizing information gathered from other sources.

• Dictionaries • Encyclopedias • Textbooks

Dated

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Recommended Online Resources

Type of Information

Multi-disciplinary Bibliographic Databases Biomedical & Life Sciences Animal Biology & Taxonomic Reference Medicine, Dentistry, Pharmacy, Healthcare & Life Sciences Experimental Protocols and Demonstration Videos Chemical Substance Structure / Properties & Reaction Searching Newspaper Articles / Local Content

Recommended E-Resource

Web of Science / Scopus BIOSIS Previews Zoological Record PubMed (MEDLINE) Springer Protocols Wiley Current Protocols JoVE (Journal of Visualized Experiments) Reaxys / SciFinder (registration) Factiva / Lexis-Nexis / NewspaperSG 10 10

Guidelines for Evaluation of Resources Criteria Authority Questions

Author’s Credentials, Subject Expert?

Accuracy Objectivity & Purpose Review process

Information is Valid and Reliable Any Bias?

Publication Peer-Reviewed?

Suitability

Academic /Scholarly Journal (Journal Impact Factor, Immediacy Index)

Timeliness

When was the Information published?

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Production of Limulus Amebocyte Lysate (LAL)

Source: http://www.wired.com/magazine/2011/06/st_processcrab/?pid=5836&viewall=true 12

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

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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

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

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

* )) ( "

limulus amebocyte lysate

" OR " AND

recombinant factor c

" )

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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

turn it in

software Plagiarism Spectrum http://turnitin.com/assets/en_us/media/plagiarism_spectrum.php

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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

) 17

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 18

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

Comparison of Reference Management Software

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EndNote Online Guide

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

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

EndNote Workflow

1. Create an EndNote Library 2. Add references to the EndNote Library 3. Manage references: using groups & finding duplicates 4. Insert references in MS Word (Cite While You Write) 5. Change citation style and edit preferences

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Step 1: Create an EndNote Library

a. All programs > EndNote > EndNote Program b.

File > New c. Filename: Test d.

Save (*.enl)

Hands-on

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Step 2: Add References to the Library

Direct Export Import Text File Online Search Import PDF Manual Inputting EndNote Library

MS Word

Cite While You Write 23

Method 1: Direct Export

Export references directly from database a. At the database, select the records you want b.

Save, output, export or (Look for “RIS format”) send to EndNote c. Click Open library to transfer records to your EndNote 24

Method 2: Import .txt File

Used when references cannot be exported to EndNote.

Very few databases e.g. Factiva a. At the database, select the records you want b. Export text (.txt) file and save on desktop c. In EndNote, go to File > Import d. Browse and select the .txt file e. Select Import option > Other filters

Which filter to use?

http://libguides.nus.edu.sg/content.php?pid=96551&sid=3508846 25

NATL

Method 3: Online Search

Search free databases (e.g. PubMed) and library catalogues (e.g. LINC, Library of Congress) a. Go to Online Search Mode > More b. Select a free database or catalogue, e.g. NATL U of

Singapore

c. In the online search pane, search by exact title of book or conference proceeding d. Copy the reference to Local Library Mode 26

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)

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Method 5: Manual Inputting

Video: http://youtu.be/30u5_b9d5D4

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Step 3: Duplicate References

• To set criteria: Edit > Preferences > Duplicates • To find duplicates: References > Find Duplicates 29

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 30

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 31

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.

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Inserting Citations

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) 33

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 34

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 35

Backing Up Library (1)

Method 1: Save a Copy

• Creates an exact copy of the library  and xxx Copy.enl

xxx Copy.Data File > Save a Copy… 36

Online Database Guides & Resources

• Biological & Life Sciences Subject Guide http://libguides.nus.edu.sg/biology • PubMed Resources http://www.nlm.nih.gov/bsd/disted/pubmedtutorial/ • Web of Science (includes BIOSIS Previews & Zoological Record) http://wokinfo.com/training_support/training/ • Scopus Resources http://help.scopus.com/Content/h_tutorials.htm

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Library Proxy Stem/Bookmarklet

NUS Libraries Proxy Stem

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 38

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 39

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 40

Thank You!



Please fill in the feedback form at: http://bit.ly/bsf31Jul14 Contact me at: Kenneth Lim [email protected]

Science Library [email protected]

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NUS Libraries Games & Lucky Draws

28 Aug 2014 10am - 5pm

Book Sale

Proceeds go to NUS Annual Giving Bursary 28 - 29 Aug 2014 http://j.mp/erdd2014 Knowledge Without Boundaries!