Introduction to Hands-on Databases Searches:PubMed & Journal Citation Reports for M1 Students

Presented by Medical Library

Conducted byJonathan Pradubsook with Ong Hong Kiat Medical Resource Librarians

Training Objectives

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• Quality Information Resources• LINC versus Databases eg. PubMed• Journal Citation Reports• PubMed - Learn How to:

• formulate a search strategy• search PubMed effectively• manage search results (citations)• create current awareness profile (optional)• access full-text articles

• Assessment and feedback

Quality Information Resources

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• Resource evaluation criteria• Authority -- author’s credentials, expert?• Accuracy -- valid and reliable• Objectivity and purpose -- any bias?• Review process -- peer-reviewed?• Suitability -- academic/scholarly,

journal – e.g. impact factor• Timeliness -- when information published?

Taken from & accessed 23 Sep 2011: http://libpweb1.nus.edu.sg/lion/s/evaluate.html

• Resources in NUS Libraries have been evaluated by librarianse.g. PubMed and databases & resources listed in Subject Guide (http://libguides.nus.edu.sg/content.php?pid=99257&sid=744804)

Citation for Book

authors

book title

year

publisher

Jonathan Stark. 2010. Building Android apps with HTML, CSS, and JavaScript. Sebastopol, CA : O'Reilly, c2010

place of publicatio

n

Citation for Book Chapter

authors

book chaptertitle

Vladimír Fuka, Josef Brechler & Aleš Jirk. 2010 Modelling of stratified and turbulent flow. In Dragutin T. Mihailovic & Carlo Gualtieri (ed.), Advances in environmental fluid mechanics, 67-86. Singapore: World Scientific.

year

publisher

book title

pages

editors

Citation for Journal Article

author

article title

Qing Li. 2010. Cyberbullying in high schools: A study of students’ behaviors and beliefs about this new phenomenon. Journal of Aggression, Maltreatment & Trauma, 19: 372-392.

year

pages

journal title

volume

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What you CAN

search in LINC

Book Titles:Brown, S. D., & Lent, R. W. (Eds.). (2000). Handbook of counseling psychology. New York: Wiley.

Journal Titles:Asia Pacific Journal of Social Work

What you CAN’T

search in LINC

Journal ArticlesNewspaper Articles

Boey, K. M. (1998). Social network and the subjective well-being of the elderly in Hong Kong. Asia Pacific Journal of Social Work, 8 (2), 5-15.

Examples of Journal titles

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Locating Journal Article If journal title is in abbreviated form, use Advanced Search.

Example: Hum. Pathol. 34(9):950-4

What journals to read?Consideration How to Check

Quality impact journals Impact factor/journal ranking in Journal Citation Reports database

Peer-reviewed journals UlrichsWeb (database), Journal website (editorial process), PubMed (Medline) journals

Reviews (because they often serve as alternatives for earlier literature)

Limit database literature search by document type to review articles

Highly cited papers Citation count ranking in Web of Science, Scopus

Paper authored / recommended by experts in your a field

1. Citation count ranking in Web of Science, Scopus

2. F1000 Medicine Reports

Recommendation from your professors, supervisors10

What is Impact Factor?• Measures how frequently the average article in a journal

has been cited in the past 2 years.• Makes use of citation and article counts from Web of

Science databases.• Journal Citation Reports (JCR) lists impact factors by

alphabetical list or subject categories.• Not be possible to obtain impact factor of a journal not

covered in Web of Science databases. • Youtube video on JCR Impact factor:

http://www.youtube.com/watch?v=IFsHjj7YWwI

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PubMed

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Learn How to:• formulate a search strategy• search PubMed effectively• manage search results (citations)• create current awareness profiles• access full-text articles

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How to Access PubMed

1. Library Portal• http://www.lib.nus.edu.sg• On Campus & Off Campus

Access• Benefit: Directly access to

full-text articles via

electronic journals subscribed by NUS Libraries

2. Google

• Resources are for your research and study• Avoid excessive photocopying or

downloading • Copyright violations may have serious

consequences

COPYRIGHT ACT

photocopying and printing: 10% or 1 chapter of book 1 article in a journal issue

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Navigating Around PubMed

PubMed Layout

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Display Results

• Display Results in Abstract format

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Locate Full-text Articles1. If you accessed PubMed from the Library Portal,

click on publisher icon

2. Use full journal title to check LINC – get full title by mousing over journal abbreviation in PubMed or click on title or use Journals in NCBI Databases

3. Use the proxy bookmarklet http://libguides.nus.edu.sg/content.php?pid=199108&sid=1665215

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Access Full Text

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• Googled leukemia stem cells• Unable to get access to the full text articles?• http://

www.ncbi.nlm.nih.gov/pubmed/15803157• http://dx.doi.org/10.1038/nrc1592

Library Proxy Bookmarklet

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• Google leukemia stem cells• Can you get access to the full text articles?• http://www.ncbi.nlm.nih.gov/pubmed/158031

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Library Proxy Bookmarklet

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Copyright and LicensingTake note of the limitations for copying & downloadingFor personal research or study, can print/download•10% or 1 chapter of book or work

•1 article in a journal issue

No excessive copying or downloading. Penalties imposed for violation.

Search Strategy• Define/Given search topic• Identify relevant database (s)

–e.g. PubMed• Construct search statement• Run search• Refine search if necessary

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PubMed Search

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MeSH (Medical Subject Heading)

Keyword

Refine a search

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Keyword versus MeSH SearchKeyword MeSH

Broader, less precise Specific - Restrict Search to Medical Subject Heading [MeSH]Even more specific – Restrict to major medical subject headings (major topic heading) [majr]

Retrieves all kinds of records, including the latest (as supplied by publisher) = PubMed

Retrieves citations indexed with MeSH terms (time lag, older) = Medline

Useful there is no MeSH term available to represent the concept

Consistent way to retrieve information that may use different terminology for the same concept

Comparing Keyword, MeSH and Major MeSH Searches

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keyword

Major MeSH

MeSHbroadest, least precise, current

narrowest, most precise, slightly dated

Using Advanced Search for Specific Field Searching

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• Choose the field you want to search and add your search term to the search box

• Do this for each individual search term

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AND is used to indicate that both terms must be presente.g. A AND Barticles containing both A and B

OR is used to indicate that either terms maybe presente.g. A OR B articles containing either A or B

Boolean Operators

A B

A B

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Fast Food and the Risk of Heart Disease

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1. Find just this article

2. Find related articles

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Concept A AND Concept B AND Concept C

(A1 OR A2 OR A3) AND (B1 OR B2) AND (C1 OR C2 OR C3)

Concept A

Concept B

Concept C

Term ‘A1’ OR Term ‘A2’ OR Term ‘A3’

Term ‘C1’ OR Term ‘C2’ OR Term ‘C3’

Term ‘B1’ OR Term ‘B2’

“Block Building”

AND

AND

AND

AND

Question: Is A related to B and C?

(vaccination) AND (autism)

(vaccination OR immunization OR vaccines) AND (autism OR autistic OR kanner’s syndrome)

vaccination

autism

vaccination OR immunization OR vaccines

autism OR autistic OR kanner’s sydrome

“Block Building”

ANDAND

Is vaccination related to autism?

Search Statement

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Topic

(vaccination OR immunization OR vaccines) AND (autism OR autistic OR Kanner’s syndrome)

Search Statement

Concepts

Keywords

Is vaccination related to autism?

vaccination autism

vaccine autistic

vaccines Kanner’s syndrome

Search Statement

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Topic

(vaccination OR vaccine OR vaccines OR vaccin*) AND (autism OR autistic OR kanner’s syndrome OR autis* )

Search Statement

Concepts

Keywords

Is vaccination related to autism?

vaccination autism

vaccine autistic

vaccines Kanner’s syndrome

vaccin* autism*

Truncation

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Vaccine* - vaccine, vaccines…

Vaccin* - vaccination,vaccinations, vaccinator, vaccinating…

Vac* - vacation, vaccine… vacuum, vacuole…

Take Note: PubMed only searches the first 600 variations

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Hands-on – PubMed Keyword Search1. Type vaccination .

Click Go. Note results. Click Details. Note ATM. Click Clear.

2. Type vaccination OR vaccine OR vaccines OR vaccine* .

Click Go. Note results. Click Clear.

3. Type autism OR autistic OR kanner’s syndrome .

Click Go. Note results. Note wildcard search message. Click Details. Note ATM. Click Clear.

PubMed Keyword Search• Search vaccination

• Search results – broad, not precise, current

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Keyword Search – Search History• Click Advanced Search to display Search History

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Keyword Search – Combining Search Sets• Combine sets numbers (prefixed #) with boolean operator

AND in upper case.

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(A1 OR A2 OR A3 OR A4) AND (B1 OR B2 OR B3)

MeSH Search – MeSH Database

• Clear previous search

• Select MeSH from databases drop-down menu

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click MeSH

MeSH Search – Finding Valid MeSH

• Search for valid MeSH for concept 1

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Valid MeSH terms with definitions

Searching Major MeSH Term

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Tick checkbox

Entry Terms in MeSH Database

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If you need to expand your search, consider these synonyms in keyword search

• Entry terms are non MeSH terms – not authorised vocabulary

Searching Major MeSH in PubMed• Send selected MeSH Term to PubMed Search Box

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Comparing Keyword, MeSH and Major MeSH Searches

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keyword

Major MeSH

MeSHbroadest, least precise, current

narrowest, most precise, slightly dated

Refine a Search using Filters

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• Located at the left side of the search results

• Choose suitable filters depending on what you are looking for

• Select additional filters if necessary

• Most commonly used: Article Types, Language

• Review search history and pick best search for alerts to new results

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Create Search Alerts

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Search Alerts

• Save your search

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Search Alerts - settings

• Set your settings for your search alert

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Search Alerts - settings

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Search Alerts - settings• Manage your saved searches by clicking on “My NCBI” to access

the NCBI dashboard

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Avoid Plagiarism – Cite Properly

• Avoid Plagiarism : NUS Honour Code• Acknowledge intellectual debt• Lend support to arguments by referring to

authoritative sources • Help readers verify your claims• Show research done• “Makes you look good on paper”

A software that:• stores & organizes citations found from

many sources• inserts these citations into a Word

document• automatically formats your references

according to a predefined citation style• http://libguides.nus.edu.sg/endnote

Summary

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• Quality Information Resource• LINC versus Databases eg. PubMed• Journal Citation Reports• PubMed - Learn How to:

• formulate a search strategy• search PubMed effectively• manage search results (citations)• create current awareness profile (optional)• access full-text articles

• Assessment and feedback

57

We are always here for you!

Medical / Science Library Information Desk: 6516 2046Email : mdlib@nus.edu.sg or Website: www.lib.nus.edu.sg