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 March 06, 2003 [posted]
  September 11, 2003 [updated]
  Change to PubMed's® Automatic Term Mapping Affects Phrase Searching

drop cap letter for p ubMed optimizes searches using a process known as Automatic Term Mapping (ATM). ATM compares terms from the search query with lists of terms: MeSH (including UMLS mappings), journal titles, author names, and phrases. The list of phrases includes many with embedded MeSH terms, e.g., acute otitis media. If a searcher's query includes a phrase found on the phrase list, it halts further comparisons with other lists and searches the complete phrase "acute otitis media" rather than mapping to:

acute[All Fields] AND ("otitis media"[MeSH Terms] OR otitis media[Text Word])

To resolve this problem and improve searching, the phrase list will be removed from Automatic Term Mapping. At that time ATM will work with:

  1. The MeSH Translation Table
  2. The Journals Translation Table
  3. The Author Index

[Editor's Note: This change to Automatic Term Mapping was implemented on April 10, 2003.]

Phrase Searching
PubMed will continue to search for phrases under these conditions:

  • The phrase is entered with a search tag:
           kidney allograft [tw]
  • The phrase is enclosed in double quotes. (The absence of a search tag indicates the search should be conducted in All Fields.):
           "kidney allograft"
  • The term is hyphenated:
  • The term is truncated:
           kidney allograft*

These formats for phrase searching instruct PubMed to bypass ATM and look for the phrase in PubMed's Index of searchable terms. If the phrase is in the Index, PubMed will retrieve citations that contain the phrase.

The Index, which includes phrases from the former ATM phrase list, can be browsed on PubMed's Preview/Index screen. For more information about Phrase searching on PubMed, please see Help. (If you are unable to search a phrase in PubMed, please write to and let us know.)

Check Searches
If you have Cubby stored searches, you may want to see if they include terms that will be affected by this change. To do this, log into the Cubby. 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. Click on the Search button to run your search (without updating it). 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] (see Figure 1). Phrases with embedded MeSH terms are probably best left alone as these will translate in accordance with ATM (see Figure 2).

  Translation of chronic urinary tract infections with current version of Automatic Term Mapping (ATM)

  New version of ATM will recognize MeSH

If, after this change is implemented, you find that terms have mapped in an undesirable way (see Figure 3), you may want to consider re-storing your search with the phrase in quotes (see Figure 4) to ensure a phrase search in All Fields.

  Translation of mongolian spots with new version of ATM

  Search term with quotes to ensure phrase search

After you have re-stored a search, use the Delete Selected Searches option in the Cubby to remove the old strategy. For more information about using the Cubby, see PubMed's Help and also our article, Revising PubMed® Cubby Stored Searches.

This change is expected to go into effect in early April. Watch PubMed's Home Page for an announcement or check New/Noteworthy.

To quote or not to quote? It is important that searches be entered initially without quotes around terms to benefit from Automatic Term Mapping. Use the Details feature to see how the terms were mapped. If the mapping is not appropriate, or the retrieval was not as specific as desired, quoting terms can then be considered.

By Annette M. Nahin
MEDLARS Management Section

black line separting article from citation

Nahin AM. Change to PubMed's Automatic Term Mapping Affects Phrase Searching. NLM Tech Bull. 2003 Mar-Apr;(331):e3.


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Last updated: 11 April 2012