Change to PubMed’s Automatic Term Mapping (Janice Contini, UCLA; PubMed Resource Liaison)

March 27, 2003 Author: CDLCategories:

Change to PubMed’s Automatic Term Mapping will affect phrase searching. NLM plans to improve the ability of PubMed to find appropriate Medical Subject Headings (MeSH terms) by removing the phrase list table from the Automatic Term Mapping.

What is MeSH and why does this matter?
Indexers use the MeSH terms to describe the subject content of articles as they are added to MEDLINE in PubMed. We can then retrieve citations relevant to our topic no matter what terminology the author used to describe the subject. So, usually when PubMed interprets our query into MeSH, our results are more complete.

How will removing the phrase list help?
Currently PubMed searches the words input against a MeSH translation table, then against the journals translation table, then against the phrase list table, and finally against the author index. If the complete phrase as entered in the query is not found in the MeSH table, but is found in the phrase list, the system stops the Automatic Term Mapping process. An example of a search query that currently retrieves a phrase but not a MeSH is chronic urinary tract infections. Currently the query retrieves 141 citations covering all years (1965 to present) containing the exact phrase. When the Automatic Term Mapping no longer includes the phrase list, the query will retrieve 2475 citations covering all years containing the word chronic, the MeSH urinary tract infections, and the phrase urinary tract infections.

What are the adverse effects of this change?
You may find that PubMed interprets terms in your query inappropriately to MeSH. For example, if you are interested in mongolian spots, currently PubMed interprets your query as a phrase and retrieves 44 citations covering all years. When the Automatic Term Mapping no longer includes the phrase list, the query will retrieve 92 citations covering all years containing the MeSH down syndrome or the word mongolian as well as the MeSH exanthema or the word spots. To retrieve ONLY the concept mongolian spots (the 44 citations containing that exact phrase,) you will need to use quotation marks: “mongolian spots”.

What action should you take?
If you use either the PubMed Cubby or BioMail to regularly update your results on a topic, you may wish to check your strategies now and once again following the change to Automatic Term Mapping.

For the PubMed Cubby, to find out if your stored strategies include phrases or terms that will be affected by this change,
1. Log into the Cubby
2. On the list of your stored searches, click on the name of a search. This takes you to the Stored Search Information screen for that search.
3. Click on the Search button to retrieve citations for that query (without updating it)
4. On the screen with the search results, click on Details; look for multi-word terms in the PubMed Query box that are tagged with [All Fields].

After the change is implemented, you should check again to make sure that terms have not retrieved inappropriate MeSH for your topic.

For BioMail,
1. Log into BioMail
2. Highlight your strategy and copy it
3. Go to PubMed and paste it into the search box
4. Click on Go; follow the instructions above for checking Details

We recommend checking to see how PubMed interpreted your query by clicking Details anytime you are searching PubMed.

Updated URL 2011 http://www.cdlib.org/services/info_services/instruct/index.html#p