Handout

Introduction to MEDLINE/PubMed

CDENT 5141: Dental InformaticsSpring 2009

John Siegel, MLS, Reference LibrarianLiaison to the School of Dental Medicine

Game On!“The Price is Right”

Two contestants….if I call your raffle ticket number, come on down!

“Name That Price” Guess the correct price and win a prize! Each contestant will have the opportunity to

take away up to two incorrect prices by answering two questions correctly.

“Name That Price!”

According to Jay Friedman (2007), what is the average fee for 1 upper and 1 lower wisdom tooth extraction charged by a general dentist?

1. $250

2. $300

3. $400

4. $500

“Name That Price!”Elimination Question #1

What is a citation?

a. Information required to identify a particular

library, such as a university or public

b. Information required to identify a particular

resource, such as a book or journal

c. Good question!

d. None of the above.


What information is included in a citation for

a journal article?

a. Authors

b. Title of Article

c. Title of Journal

d. All of the above


According to Jay Friedman (2007), what is the average fee for 1 upper and 1 lower wisdom tooth extraction charged by a general dentist?

Correct Answer: $300


According to Jay Friedman (2007), what is the average fee for 1 upper and 1 lower wisdom tooth extraction charged by an oral and maxillofacial surgeon (not including x-rays or anesthesia)?

1. $4002. $4503. $5004. $600


In addition to or besides the title, how can you distinguish a scholarly journal from a magazine?

a. A scholarly journal does not include articles on current topics.

b. A scholarly journal generally has a panel of subject experts review the articles.

c. A scholarly journal has more interesting articles than a magazine.

d. None of the above.


Which of the following is true about a

journal article abstract?

a. It includes a reference list for the reader.

b. It is usually several pages long.

c. It summarizes the article for the reader.

d. None of the above


According to Jay Friedman (2007), what is the average fee for 1 upper and 1 lower wisdom tooth extraction charged by an oral and maxillofacial surgeon (not including x-rays or anesthesia)?

Correct Answer: $500

Friedman Article Citation

Friedman, J. W. (2007). The prophylactic extraction of third molars: A public health hazard. American Journal of Public Health, 97(9), 1554-1559.

“Bonus Question”

You are performing a routine examination on one of patients, who is 17 years old. You determine from x-rays that his wisdom teeth are impacted.

You ask the patient if he is having any symptoms, such as pain, and he says no.

“Bonus Question”

Knowing that it is a commonly accepted and performed procedure, yet given possible complications (i.e. pain, time missed from work/school) and cost, would you recommend extraction of this patient’s wisdom teeth?

Why or why not?

How would you decide?

Common “Ways of Knowing”

Ask a colleague Legacy – always done it this way Internet resources Textbooks, other books Professional meeting papers/presentations Journal literature – scientific studies

Evidence-Based Dentistry

“An approach to oral health care that requires the judicious integration of systematic assessments of clinically relevant scientific evidence, relating to the patient's oral and medical condition and history, with the dentist's clinical expertise and the patient's treatment needs and preferences.”

Source: American Dental Association. (2008). Evidence Based Dentistry: Glossary of Terms. Retrieved February 27, 2008, from http://www.ada.org/prof/resources/ebd/glossary.asp.

Evidence-Based Dentistry

Clinician’s Clinical

Expertise

Patient’s Needs and Preferences

Assessment of Scientific Literature

Database

Organized Searchable Contains information about

something specific (individual iTune songs, pictures of Chicago, etc.)

It doesn’t have to be, but often electronic

Bibliographic Databases at the Library

Information about Joseph (Joe)

Schmoe’s accepted journal article

Information about Junior’s accepted

journal article

Information about other journal articles,

and sometimes magazines, newspapers

Bibliographic Database

Bibliographic Databases:What information are we talking here?

Author Date article was published Title of article Title of journal, magazine,

or newspaper that article appeared in

Volume, Issue Page numbers

ARTICLE

CITATION

In addition to article citations, bibliographic databases generally also contain the following useful pieces of information:

Abstract = Brief synopsis of article

Think of as “Coming Attraction”

Subject headings = Standardized vocabulary

“You say tomato, I say to-ma-to”

Bibliographic Databases:What information are we talking here?

MEDLINE

Electronic bibliographic database maintained by the National Library of Medicine

Contains citations (not-full text) to biomedical literature (including dentistry)

Citations date back to 1950s Most newer citations include

abstracts All citations include subject

headings: Medical Subject Headings (MeSH)

Subject Headings:You Say Tomato, I Say To-ma-to

Article A

Title:

Wisdom tooth extraction.

Article B

Title:

Third molar extraction.

Medical Subject Heading (MeSH) for both titles:

Molar, Third

PubMed: MEDLINE and More

National Library of Medicine’s interface to access MEDLINE

PubMed also allows you to search citations that have not been assigned controlled vocabulary (MeSH) – Generally newest citations

Accessing PubMed

Two ways to access PubMed Freely: www.pubmed.gov Through your university health sciences library

It is recommended that you access PubMed through your university health sciences library to take advantage of full-text links

Searching PubMed

Notice “Search Box” (similar to Google) Best not to overload search box: Use a few

selective keywords

Formulating Your Search:Building Block Approach

Refer to your research question

For example, let’s refer back to your patient with the asymptomatic, impacted wisdom teeth:

In the case of asymptomatic, impacted wisdom teeth, is extraction a viable treatment?


Pull out the major concepts (either single words or phrases) that will serve as keywords

Use the BOOLEAN operator “AND” (must be capitalized) to combine concepts



What keywords would you use? Keyword #1: ____________________ Keyword #2: ____________________ Keyword #3: ____________________ Keyword #4: ____________________



What keywords would you use? Keyword #1: wisdom teeth Keyword #2: asymptomatic Keyword #3: impacted Keyword #4: extraction


Search strategy for the previous question, with BOOLEAN operator “AND” inserted between keywords:

wisdom teeth AND asymptomatic AND impacted AND extraction

We’re using the BOOLEAN operator “AND” because we want citations to articles that contain all of these concepts

Formulating Your Search:Building Block Approach/Nesting

You may want to consider adding synonyms for one or more concepts.

If you add synonyms, you must incorporate a search technique known as nesting, which uses parentheses (as shown below)

In addition to nesting, you must include the BOOLEAN operator “OR” (capitalized) between synonyms

Formulating Your Search:Building Block Approach/Nesting

Example:Concept #1: wisdom teethConcept #2: (asymptomatic OR prophylactic)Concept #3: impactedConcept #4: extraction

Search strategy, with nesting and BOOLEAN operator “OR” inserted between synonyms:

wisdom teeth AND (asymptomatic OR prophylactic) AND impacted AND extraction

Some Tips…

Avoid quotation marks around phrases, as this turns off one part of PubMed’s search function – stay tuned!

Wildcard/truncation search – i.e. dental cleaning* to retrieve dental cleaning, dental cleanings – also turns off one part of PubMed’s search function – continue to stay tuned!

Search Statement Recap

wisdom teeth AND asymptomatic AND impacted AND extraction

Running Your Search in PubMed

Must say “PubMed”

Enter your search statement, making sure that BOOLEAN operators (AND, OR, NOT) are CAPITALIZED, then hit “Go”

Examining PubMed Results

To view the abstract for a particular article, click on the authors link

Change the Show feature from “20” to “50” by using the small down arrow to the right.

Limits in PubMed

Limits are an excellent way to target your citation retrieval

Example of limits you might use: Language: Since MEDLINE/PubMed contains

citations for articles beyond English journals (global coverage), limit your search to English

Age Type of article: Includes limits for evidence-based

dentistry (i.e. meta-analysis, practice guidelines, clinical trials, randomized control trials)

Applying Limits to PubMed Searches

Click once on the “Limits” tab


To apply the “English” Language limit, click once in the small box to the left of “English”


Be sure to click once on the “Go” button at the bottom of the screen after you have selected your limits


If limits are applied successfully, you should see the above

The PubMed Record:A Closer Look

To find similar articles, click on the “See all Related Articles”

NOTE: DO NOT USE FOR WRITTEN ASSIGNMENT!

To obtain the full title of a journal, scroll over the journal abbreviation.

To find similar citations (for other research and review articles) – DO NOT USE THESE LINKS FOR YOUR ASSIGNMENT!

Link to full-text

“Displays” in PubMed

PubMed has a variety of “Display” options, which affect how citations and other information appear

Common “Displays”: Summary – default view; shows citation, Abstract –Citation and abstract, link to full-text at

HSLS AbstractPlus – same as Abstract + related links Citation – Citation, abstract, and subject headings MEDLINE – Use to import citations into citation

management software (i.e. EndNote, RefWorks)

Citation Output Options

You have a variety of options for working with your citations away from PubMed:

Text – Allows you to copy and paste citations into another document

File – Allows you to save citations to a text file Printer – Allows you to print citations E-mail - Send selected citations Collections – Set up a free MyNCBI account to

save citations online for future reference

PubMed History: Record of Searches

Exploring Medical Subject Headings (MeSH)

Approximately 25,000 terms Human indexers assign these terms to

citations, based on reading the abstract or complete article

Provides a controlled means of searching – a concept may be referred to in several different ways, allows standardization

Compare to keywords – not standardized PubMed’s default is to combine keyword and

MeSH searching

Exploring Medical Subject Headings (MeSH)

Title #1: Title #2:

Review of the current Clinical challenges

status and challenges for and the relevance

dental posterior restorative of materials testing

composites: Clinical, for posterior

chemistry, and physical composite

behavior considerations restorations

MeSH headings for both titles:

Composite Resins

Dental Restoration, Permanent

Exploring MeSH:The MeSH Database

To access MeSH database

Important Things to Know About the MeSH Database

You aren’t searching PubMed when you search the MeSH database

The MeSH database contains records about the MeSH terms

These records include the following fields: MeSH term Scope note (definition) – though a scope note

may not always be present Entry terms

Exploring MeSH:The MeSH Database

Enter each keyword individually in the search box, then hit “Go” button

The MeSH Database:MeSH Records – Things to Know

ENTRY TERMS ARE NOT THE SAME AS MESH TERMS!

“Entry terms” are keywords/text words, which are not standardized. If you search the MeSH database for one of these “entry terms” OR your PubMed search statement includes one of these “entry terms,” PubMed automatically searches the MeSH heading. In this case, we searched for “wisdom teeth,” which PubMed “translated” and then searched as MeSH term, “Molar, Third.”

Scope note: Definition of MeSH term – May not always be present

MeSH term – answer(s) for question #4

The MeSH Database:List of Possible MeSH terms

Generally you will not see a MeSH record “pop-up” when you enter a term, as in the previous slide.

You are more likely to get a list of MeSH terms and you will have to pick the term that fits your concept.

Again, remember that in the MeSH database, you’re only searching MeSH terms. PubMed isn’t actually doing a search.

The MeSH Database:List of Possible MeSH terms

MeSH term

Scope note

If you don’t find a MeSH term that matches in your list, try clicking on one of the MeSH terms that appears as a

“Suggestion”

MeSH Database Exercise

Using the MeSH database, identify MeSH terms for the remainder of the keywords in the wisdom teeth example. [HINT: There may not be a MeSH term for one keyword]

Tooth Extractions ____________________ Dental cleaning _______________________ Sleep _______________________________ Asymptomatic

________________________

MeSH Database Exercise

Using the MeSH database, identify MeSH terms for the remainder of the keywords in the wisdom teeth example. [HINT: There may not be a MeSH term for one keyword]

Tooth extractionsTooth extraction Dental cleaning Dental prophylaxis Sleep Sleep Asymptomatic No MeSH match

MeSH Database:Final Reminders

Remember, when you search the MeSH database you’re not searching PubMed

You generally will get a list of possible MeSH terms – you will need to pick-out the MeSH term that best fits your concept

An entry term is NOT the same as the MeSH term

Sometimes the keyword you type in may be the same as the MeSH term (i.e. keyword sleep = MeSH term Sleep

PubMed Behind the Scenes

Two components of PubMed search:

When you do a search in PubMed, PubMed will search for the terms you enter [keyword/text word searching]

AND PubMed will attempt to “translate” the terms you

enter into Medical Subject Headings (MeSH), then it will search any “translated”/”mapped” MeSH terms [subject searching via PubMed’s automatic term mapping feature]

Understanding How PubMed Processed Your Search

Click once on the “Details” tab

Understanding How PubMed Processed Your Search

Wherever you see the phrase “MeSH Terms” in brackets, PubMed automatically searched these MeSH terms.

In this case, by “wisdom teeth” PubMed thought we were referring to the MeSH term “molar, third.” PubMed searched the MeSH term “molar, third.” Note that PubMed did not map to any other MeSH terms in this example (see “Translations” section below).

Be sure to look for the “MeSH Terms” in brackets throughout the translation section. Any words in quotes in front of the “MeSH Terms” in brackets is a MeSH term that PubMed searched.

Single Citation Matcher: When You Have an Incomplete Citation…

Single Citation Matcher: When You Have an Incomplete Citation…

Will allow you to “plug in” the information you have to find the citation

Type author’s names (if applicable) as Last Name<space>First Initial

For date, you can type a month and year or just a year – enter as YYYY/MM OR YYYY

Process of trial and error – If there is no citation “match,” try revising the information you typed (i.e. just enter the Author’s last name, without first initial; just enter the year, without the month)

Identifying Citation Information

To obtain the full title of a journal, scroll over the journal abbreviation

In this example: 204 is volume; 4 is issue (in parentheses); E7 is page number

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