Module 4: how to Use pubMed




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  1. HINARI Access to Research in Health Programme

MODULE 4.4: HOW to UsE PubMed

-- MeSH: THE MEDICAL SUBJECT HEADINGS



Table of Contents – Module 4.4:

    • Using MeSH in PubMed

    • The MeSH database

      • Major Topic Headings and Explode

      • Using MeSH terms

      • Geographic regions

This module continues the mastering of the skills necessary to utilize the PubMed database as means to identify e-journals within HINARI. It will emphasize the use of the MeSH controlled vocabulary as a tool to retrieve information from PubMed.


You must login to HINARI and then go to search for articles through PubMed (Medline) or you will not have access to the full-text articles (see section 1. Connecting to PubMed)
Note: Remember that you must keep your sign on to HINARI open; do note close this tab on the bottom of your Internet browser’s screen.


  1. Connecting To PubMed

HINARI users can search and access full-text articles directly from the PubMed database. You will need to have your HINARI log in details to do this.


  • First go to the HINARI website found at www.who.int/hinari where you can select the LOGIN hyperlink which will take you to the HINARI login page.

  • When the login page opens, enter your institutional HINARI User Name and Password into the login boxes and then select the “Loginbutton to access the HINARI site.

  • If you do not register in HINARI using your institution’s User Name and Password, you will not have access to the HINARI publishers’ full-text articles at the completion of your PubMed search.

  • From the HINARI Contents page, select the hyperlink Search inside HINARI full-text using PubMed.

The home page for PubMed displays giving you access to PubMed databases.





  1. MeSH Or Medical Subject Headings and Using MeSH In PubMed

MeSH is the controlled vocabulary used to index articles for Medline. The MeSH vocabulary provides a consistent way to retrieve information that may use different terminology to describe the same concept. It is important to realize that if an article is indexed for MEDLINE the MeSH terms will be assigned as keywords to each of the indexed articles.
If you search for articles using MeSH headings alone, you only will find those articles that have been indexed for MeSH terms. You will miss those articles that are PubMed, but not indexed for MEDLINE, as they will not have MeSH terms assigned to their records.
This module will guide you through using the MeSH or Medical Subject Headings. There are exercises incorporated within the module to illustrate the use of MeSH in the search process.


  1. The MeSH Database

To access the MeSH Database from the initial PubMed page, click on the MeSH Database link in the More Resources listing that is in the bottom right column of the initial PubMed search page. You can also open the MeSH Database by selecting it from the databases ‘dropdown’ menu to the left of the PubMed “Search” box.
To search the MeSH database you need to ensure that the box adjacent to Search displays MeSH and that you enter your search terms in the longer search box.

To search for the MeSH term that applies to your topic enter your search statement in the search box click on Go to run your search. The database will then display the results that match your term.



Exercise 1

  • Select and open the MeSH Database.

  • In this exercise we will look for a MeSH term for Cancer

  • In the empty MeSH Search query box, type in the following statement: Cancer. Then click on the adjacent Search button.

  • From the results found you can see that the MeSH term for cancer is Neoplasms.

  • To display the full definition, check the Neoplasms box. Open the Display Setting drop down menu, click on Full format and Apply.

  • What is the definition supplied for the term Neoplasms?

The record for a MeSH term contains a definition of the term, associated subheadings, a list of entry terms and the tree view of MeSH. You will see the description and the subheadings which are associated with the term.




    1. Major Topic Headings and Explode

Below the subheadings are two check boxes. One refers to Major Topic Headings only and the other to instruct PubMed not to Explode a term. Under this section there are entry terms with see also references. Each record also has a tree view of MeSH displaying the term and its position in the MeSH tree structure.

Exercise 2

  • Select and open the MeSH Database.

  • In this exercise, we will look for a MeSH term for Dengue

  • In the empty MeSH Search query box, type in Dengue and click on Search. From the results found, you can see that there are multiple MeSH terms for Dengue.

  • Check the initial Dengue box, open the Display Setting drop down menu and click on Full format and Apply.

  • Look at the definition and the subheadings.

  • Click on Add to search builder, after "Dengue"[Mesh] is displayed in the PubMed search builder box, click on Search PubMed.

  • List three Entry Terms for Dengue.

Note: When your term is entered in the search box you can add further keywords or MeSH terms to the search. If you wish to search using subheadings select the appropriate subheading by checking the selection box next to it.



Exercise 3




  • Select and open the MeSH Database.

  • Return to the Dengue MeSH results page. (If necessary, enter Dengue in the MeSH search box and click on Search.. Check the initial Dengue box, open the Display Setting drop down menu and click on Full format and Apply.)

  • Look at the the subheadings, check the ones for prevention and control and transmission,

  • Click on Add to search builder, after "Dengue/prevention and control"[Mesh] or “Dengue/transmission”[Mesh] are displayed in the PubMed search builder box, click on Search PubMed.

  • In the completed PubMed search, what is the result (# of citations) from this search?

  • Is this the same, somewhat smaller or significantly smaller that the # of citations for the original Dengue search?

  • After the PubMed results are shown, open the Display Settings drop down menu. In the display format column, click on Abstract and apply.

  • The new display format will appear. At the bottom of any abstract, click on MeSH Terms.

  • Once displayed, look at the MeSH terms on the records. You will notice the occurrence of your terms in the MeSH list.

  • What is the result (# of citations) from this search?


3.2 Restricting to Major Topic Headings Only


Restricting a search to the Major Topic Headings means that the items found will be primarily about that Major Term and will not be those that relate to the subject in secondary terms or just mention it in passing. For example if we restrict Dengue to a Major Topic Heading we will be finding articles whose primary subject matter is about dengue.
Exercise 4


  • Return to the Dengue MeSH results page. (If necessary, enter Dengue in the MeSH search box and click on Search.. Check the initial Dengue box, open the Display Setting drop down menu and click on Full format and Apply.)Then click on the adjacent Go button.

  • For the same (initial) Dengue search, check the box for Restrict Search to Major Topic Headings Only. Then click on Add to search builder and Search PubMed.

  • What is the result (# of citations) from this search?

  • Is this the same, somewhat smaller or significantly smaller that the # of citations for the second search you completed - “Dengue/prevention and control” or “Dengue/transmission”? Why do you think you obtained this answer?


Identifying Major MeSH terms in retrieved records

In the citation format, Major MeSH terms are identified with an asterisk next to them e.g. Dengue.



3.3 Using MeSH terms

If you look at your search history you can compare the difference in numbers of the records found searching as a keyword, MeSH term and Major MeSH term. The MeSH term describes the content of an article using consistent terminology and is valuable for finding relevant items with some degree of specificity. Restricting a search to Major MeSH Terms can improve the specificity of a search although you may miss some items where your topic is not the main focus of the article.


3.4 Geographical regions

There are also MeSH terms assigned to geographical regions and countries.


Exercise 5


  • Select and open the MeSH Database.

  • In the empty MeSH Search query box, type in Asia and click on Search. From the results found, you can see that there are multiple MeSH terms for Asia.

  • Check the initial Asia box, open the Display Setting drop down menu and click on Full format and Apply.

  • Look at various sub-geographic locations listed.

  • Click on Vietnam or a country of interest to you. Note the Entry Terms.

  • Click on Add to search builder. After "Vietnam"[Mesh] is displayed in the PubMed search builder box, click on Search PubMed.

  • In the completed PubMed search, what is the result (# of citations) from this search?



Exercise 6 (A summary)


  • Select and open the MeSH Database.

  • In the empty MeSH Search query box, type in Developing Countries and click on Search. From the results found, you can see that there are multiple Entry Terms for Developing Countries.

  • Click on Add to search builder, after "Developing Countries"[Mesh] is displayed in the PubMed search builder box, click on Search PubMed.

  • In the completed PubMed search what is the result (# of citations) from this search?

  • From the PubMed search results page, click on Advanced (below the Search box).

  • In the Advanced Search Builder Page, locate the History option (at the bottom of the page).

  • Locate the # for the “Developing Countries”[Mesh] search and click on Add. Locate the # for the “Dengue”[Mesh] search and click on ADD.

  • Note how the #s are displayed in the Builder fields as Recent Query and connected by the AND operator. Click on Search.

  • What is the result (# of citations) from this search?


Assignment

You now have completed module 4.4 and finished six exercises. You have learned what MeSH terms are and how they can be applied to retrieve information in PubMed.


Updated 2012 11



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