BOH 1 Bibliographic Databases

Last update by Mick Draper October 2009

Table of Contents

PubMed

Nutrition Assignment

How to read articles

 

PubMed

PubMed has just changed its format as of yesterday 28th October 2009!

Find citations on the presence of Streptococcus mutans in patients with early childhood caries

This search requires a bit of thought about how to best use language and logic to search PubMed effectively.
I recommend using a logic grid.

There appear to be two concepts S. mutans and early childhood caries.
We can begin our logic grid using these terms.

streptococcus mutans

early childhood caries

The logic grid is used to list all the appropriate terms for each of the concepts we want to search.
List alternative terms and synonyms below each of these concepts to develop columns of terms that can be searched later.

Using PubMed
You can get access to the U of A customized version of PubMed from the Library Home Quick Links.

MeSH Database
PubMed uses subject headings to describe the contents of articles.
These subject headings are added to article citation to make them easier to find.

The great value of subject headings is that no matter what terms are used by authors in their titles and abstracts to describe the contents of their articles, the subject heading are standardised.
If you are able to discover the appropriate subject headings then you should find most of the relevant articles.
You can search for subject headings in the MeSH Database of PubMed.
Click on the link to the MeSH Database under the More Resources heading on the right hand side of the PubMed home.

I find it useful to have separate windows or tabs for the MeSH Database and PubMed.

Type streptococcus mutans into the MeSH search box.

Click on the link to see more details.

To force PubMed to search for this as a subject heading add the field tag [mh] to the term.
For now put this in the logic grid.

streptococcus mutans[mh]

early childhood caries

It's also possible to find citations where this term will appear in the title or abstract of the article.
To make PubMed search in both the title and in the abstract add the term with the field tag [tiab]

streptococcus mutans[mh]	early childhood caries
streptococcus mutans[tiab]

Sometimes authors abbreviate the names of organisms so that Streptococcus mutans can be written as S. mutans.
We should include this term in our search of titles and abstracts too.

streptococcus mutans[mh]	early childhood caries
streptococcus mutans[tiab]
s mutans[tiab]

 

Type early childhood caries into the MeSH search box and click on Go.

Early Childhood Caries is not a MeSH .
When you can't find a MeSH there are a couple of options,
one is to try another similar term in the MeSH database,
another is to search for your term in the PubMed part of the database but restrict your search to the titles of articles.
The idea here is that if a title contains the term then the article is probably about the concept.
Then you can look at the MeSH added to the citations that have the term in the title and see the MeSH used to describe this concept.

This search found 220 citations to articles that have the phrase early childhood caries in the title.
Some of these citations have a note that they are PubMed - in process
This means they don't have MeSH added as yet.

Other citations include the note PubMed - indexed for MEDLINE
These citations have MeSH added.
These MeSH can be viewed by changing the Display Settings to Abstract.
Click on the link or the arrow.

Click in the radio button to the left of Abstract.

Click on Apply.

Then click on MeSH Terms.

 

It looks like there is more than one MeSH used to describe Early Childhood Caries.
One is Dental Caries.
Child, Preschool, or Infant are others.

Just for now, leave the actual phrase early childhood caries out of the logic grid and come back to it later.
Which of the MeSH found above will cover the concept of early childhood?

Are we considering kids between about 8 months and 5 years of age?
If yes, then we have to find which MeSH relating to children are applicable.

Return to the MeSH Database.
Search for infant.

The PubMed definition of Infant tells us that this term probably should be included in our search as many children in this age range will have at least some deciduous teeth.

It's unlikely that the more specific MeSH will be needed in the search but there isn't any need to deliberately exclude these terms.
Add infant to the logic grid as a MeSH.
Also add to the logic grid the terms infant[tiab] and infants[tiab].

streptococcus mutans[mh]	infant[mh]
streptococcus mutans[tiab]	infant[tiab]
s mutans[tiab]	infants[tiab]

Now search in the MeSH database for Child, Preschool.

It looks like Child, Preschool is an appropriate MeSH too.

We can add child, preschool to our logic grid as a MeSH

streptococcus mutans[mh]	infant[mh]
streptococcus mutans[tiab]	infant[tiab]
s mutans[tiab]	infants[tiab]
	child, preschool[mh]

 

Often the Entry Terms can suggest words and phrases authors might use in their titles and abstracts.
Add preschool child*[tiab]

The * here is the truncation symbol in PubMed
It will find any phrase that has preschool as the first word and any second word that begins with the letters c-h-i-l-d.
Truncation is just a convenient short cut.
It's best not to use truncation with MeSH.

streptococcus mutans[mh]	infant[mh]
streptococcus mutans[tiab]	infant[tiab]
s mutans[tiab]	infants[tiab]
	child, preschool[mh]
	preschool child*[tiab]

Return to the MeSH Database and search dental caries.

Assuming we are happy to get citations to articles on dental fissures or root caries, then we can add a new column to the logic grid that begins with dental caries[mh].
Using some of the Entry Terms and other terms we can complete the grid

streptococcus mutans[mh]	infant[mh]	dental caries[mh]
streptococcus mutans[tiab]	infant[tiab]	caries[tiab]
s mutans[tiab]	infants[tiab]	dental decay[tiab]
	child, preschool[mh]	tooth decay[tiab]
	preschool child*[tiab]

Now (with the exception of the phrase early childhood caries) the language of the search is done.
Next apply the LOGIC RULES.

Terms in the same column are joined using OR logic.
Terms in the same column are enclosed in round brackets.
Terms from different columns are joined by AND logic.

This will organise the search logic to

(streptococcus mutans[mh] OR streptococcus mutans[tiab] OR s mutans[tiab]) AND (infant[mh] OR infant[tiab] OR infants[tiab] OR child, preschool[mh] OR preschool child*[tiab]) AND (dental caries[mh] OR caries[tiab] OR dental decay[tiab] OR tooth decay[tiab])

Now we come to the slightly tricky bit of adding early childhood caries[tiab] to this search.
It's tricky because this phrase covers two columns of our logic grid.

Use brackets to add the phrase so that it's is ORed to the terms from the second and third column, while ANDed to the terms in the first column.

(streptococcus mutans[mh] OR streptococcus mutans[tiab] OR s mutans[tiab]) AND ((infant[mh] OR infant[tiab] OR infants[tiab] OR child, preschool[mh] OR preschool child*[tiab]) AND (dental caries[mh] OR caries[tiab] OR dental decay[tiab] OR tooth decay[tiab]) OR early childhood caries[tiab])

Now you can enter this search strategy into the PubMed database to find citations.

You might like to compare this with the naive search

early childhood caries AND streptococcus mutans

 

Nutrition Assignment

The Nutrition assignment asks you to consider particular groups in Australia and some aspect of their biology.
Before beginning a database search you might like to look at

Australian Bureau of Statistics web site to search for
National Nutrition Survey: Nutrient Intakes and Physical Measurements, Australia, 1995 
Click on Downloads to view the tables
Find the section on Region of Birth.

You might also find it useful to look at nutrition tables and food composition tables held in the Library.
You can search the catalogue for these subject headings.

There are also plenty of these tables on the internet.
NUTTAB 2006 Australian Food Composition Tables

Or search for a particular food in these tables

 

Example Question
What are the significant aspects of nutrition in Australian youths with eating disorders.

nutrition

youth

eating disorders

For this assignment there is an emphasis on the Australian population.
There is a group of databases that might be especially useful.
There are several Informit databases that cover health and wellbeing.
I've grouped these together and you can find them by clicking on the Databases tab on the Library Home.

Click on Dentistry.

Scroll down and click on Informit Health Databases

Remember that it can be useful to use the MeSH database to search for terms that describe these concepts, even if you use other databases for searching.

nutriti	youth*	"eating disorder"
diet	adolescen*	"eating disorders"
diets	teen*	anorexi*
vitamin*		bulimi*
mineral*		coprophagi*
food*		pica

Are there other terms you could add to any of these columns?
What about adding eat* to the first column, and "young adults" to the second?

Notice that in these Informit databases that phrases are enclosed in straight double quotes "eating disorder" (not curly double quotes “eating disorder”)

Enter terms from each column of the logic grid into a separate search query box.
No need for brackets.

Click on the Add more terms link to enter the final column search terms

 

You can also elect to search in the full text of articles, you can change the date range.
Click on the Search button.

All the databases are searched and duplicates aren't removed, so the same citations can turn up more than once.
You may care to link directly to pdfs from the database.
If you can't see a link to full text on the screen click on the Check fulltext options button.

You can search for the same topic in PubMed using a PubMed field tags.
You may want to include an extra column in your logic grid to search for australia[mh] OR australia*[tiab], or if you are having trouble finding citations you could leave this out.

Migrant Groups Search
You can use the same databases to do your migrant group searches. One thing that might be useful to remember is that most countries don't have homogeneous populations. Before searching in the Informit databases it might be useful to do a Google or other search engine search to find the different groups that might be represented in the migrant populations.

Here's an example of how you might search for populations in Laos.

How to read a paper (pdf 17kB)
A short document on the basics of critically reading a journal article by Mick Draper

Trisha Greenhalgh's series of articles called How to read a paper.
Barr Smith Library has the 3 editions of Greenhalgh's book How to read a paper: the basics of evidence-based medicine.
The third edition is in the Main Collection of the Library at 616 G813h.3

Sources for Finding Journal Articles
Barr Smith Library databases for finding journal articles in the health sciences

Journal Title Abbreviations

PubMed Tutorials

Full Text Journals

Uni of Adelaide Library Full Text Dentistry Journals
Access outside The Barr Smith Library for Uni of Adelaide Community only