In this part of the training the use of keywords (MeSH terms) in PubMed will be explained.
This information is useful once you start collecting references on your own topic.
Read the text in the text box 'MeSH terms' at the right hand side of this screen.
Go back to the results of your search from assignment 2 (use the 'Back' function of your browser).
Select a few references and have a look at the MeSH terms assigned to these articles.
Read the text in the text box : 'MeSH database' at the right hand side of the screen.
Return to the homepage of PubMed by clicking on at the top left.
Open the 'MeSH database' (under More resources at the right) and enter the search term: AIDS. Select the first option by clicking on the keyword underlined in blue. Have a look at the result.
Please note: Now you are NOT searching the articles database, but the keywords database!
Search in PubMed for the MeSH term AIDS in the MeSH Database as is explained in the text box 'MeSH Database'.
How many hits do you get? Compare this to the earlier search for AIDS you performed in Assignment 1.
How do you explain the difference?
(click on the question to view the answer)
Read the text in the text box 'Automatic Term Mapping'.
In PubMed return to the homepage via the back button of your browser. Enter the term Alzheimer in the search box and click on Search. Now have a look at 'Search details' to find out how PubMed "translates" the search. As you can see the corresponding MeSH term is automatically included in your search.
Now do the same for the search term Besnier-Boeck (Besnier-Boeck Disease is synonymous with sarcoidosis). How do you expect PubMed to "translate" this search term? And does it? (Check 'Search details' again to find out).
Now enter Besnier-Boeck Disease instead of Besnier-Boeck and again check 'Search details'. What is the difference?
Recently the National Library of Medicine launched a new tool: MeSH on Demand.
Based on pieces of text (for example, a protocol, or a summary of a key article), it generates MeSH terms.
See: MeSH on Demand
To each reference in PubMed keywords are assigned. This is called 'indexing'. The keywords in PubMed are known as 'MeSH terms' (MeSH = Medical Subject Headings).
At each reference in the list of results and below the abstract, you can see if the article has been indexed yet or in other words, has been given keywords. In that case it says: [PubMed - indexed for MEDLINE]:
Recent references have not been given keywords yet, at these articles you will find: [PubMed – as supplied by publisher] or [PubMed - in process].
If you click on the title of a reference in the list of results you will see a pull-out menu ‘Publication Types, MeSH Terms, Substances…’below the abstract. If you pull out this menu, you will see which keywords have been given to this reference.
There is a separate database of MeSH terms: the MeSH Database. In this database you will find all MeSH terms which may be used as keywords in PubMed. The MeSH Database can be found on the right at the bottom of the PubMed-homepage, under the heading: ‘More Resources’
In the MeSH Database you will find the exact definition for each keyword, refinements ('Subheadings'), search terms that are automatically translated into these MeSH term ('Entry Terms'), sometimes also 'Previous Indexing' (when another keyword was used in the past) and 'See Also' (references to other MeSH terms). Finally you will find an overview of the relations between the index terms. MeSH terms are organised in a tree structure, and as you can see: a MeSH term can occur in several 'trees'.
You can use the information in the MeSH Database to adjust your search: sometimes you will find synonyms, or ideas to refine or extend your search.
From the MeSH Database you can search directly in PubMed: at the top of the right column you will find the 'PubMed Search Builder'. Via the button ‘Add to Search Builder’ the selected MeSH term appears in this search box. Clicking on the button ‘Search PubMed‘ starts a search for the MeSH term in PubMed. If you want to search with the MeSH term in combination with certain 'Subheadings', you must first tick the 'Subheading(s)' in question
Please note: there are several disadvantages to the exclusive search on MeSH terms:
1. The MeSH database is updated each year. MeSH terms are added and removed. However, to already indexed articles, new MeSH terms will not be added automatically. So these articles won't be found when you are searching on new MeSH terms.
2. To the most recent articles no index terms have been assigned yet. So you will also miss out on these articles when you are searching on MeSH terms.
Where possible, PubMed turns entered search terms into MeSH keywords. This is called Automatic Term Mapping. Moreover PubMed also searches the exact search terms in the tag 'All Fields'. Please note that you do not always have to agree with this 'translation' by PubMed.
To check how PubMed interpretes the search terms entered by you, always have a look at the ‘Search details' (at the right hand column of the screen).
The translation of search tems by PubMed is not always carried out logically and consistently. So do not forget to check under ‘Search details’ how PubMed treats the search terms entered by you! You can adjust the search you carried out in the 'Search details' screen.