LM is modifying the way PubMed searches for Pharmacologic Action MeSH headings. We are also introducing a new search tag, [PA], to search for substances known to have a particular pharmacologic action. These changes are expected to be completed later this summer. [Editor's Note: These changes were completed on September 22, 2003.]
While many substances are known to have multiple pharmacological actions (PA), much of the published research looks at one action of a drug. Effective with the 1996 MeSH Vocabulary year, NLM's indexing policy was changed to require that articles about the action of a drug or chemical be indexed with the respective drug/substance MeSH heading and the MeSH heading for the pharmacologic action(s) being studied.
An article about the ability of aspirin to prevent platelets clumping together would be indexed with:
MH - Aspirin
MH - Platelet Aggregation Inhibitors
(Subheadings omitted for brevity.)
An article about the anti-inflammatory effect of aspirin would be indexed with:
MH - Anti-Inflammatory Agents, Non-Steroidal
MH - Aspirin
At the same time the Pharmacologic Action (PA) indexing policy was implemented, NLM changed the MeSH Tree Structure so that the specific drugs/chemicals were no longer treed under a function (pharmacologic action) heading. This means that in MeSH there is no branch containing all drugs with a particular effect (e.g., all the antioxidants). (For historical background, albeit from the ELHILL perspective, please see, Willis J, et al. New MeSH and Indexing Policy Change for 1996 MeSH Chemical and Pharmacologic Action Headings and Trees. NLM Tech Bull. 1995 Sep-Oct;(286):9-16.
The PA/PX System
To allow searchers to continue to easily search for citations to articles indexed with any drug/substance term for a particular pharmacologic action, the Pharmacologic Action/Pre-Explosion (PA/PX) system was developed and later incorporated by PubMed. The Pre-Explosion worked by ORing the "action" term (e.g., Antioxidants), with all the drugs/substances terms with that action as noted in MeSH. Up until April 2003, PubMed's MeSH Browser displayed the associated drug/substance terms under the respective action term in the hierarchical display - even though these indentions did not exist in the MeSH tree structure.
This arrangement (merging the PA/PX list of terms with the MeSH tree) is not optimal for searching. You cannot, for example, retrieve a particular drug only with a particular action (e.g., aspirin [mh] AND platelet aggregation inhibitors [mh]) because the action term would invoke the Pre-Explosion, which retrieves the drug (see previous paragraph). This results in ANDing the drug term with a list that contains the drug -- so you end up with all the citations for the drug - not limited to those with the action term. (See "Search with [MH]" below for solution.) Another problem is that the PA lists do not include Supplementary Concept Records (SCRs).
Changes to PubMed
Display of MeSH Hierarchy
When the PubMed MeSH Database replaced the Browser (see Canese K. New Entrez Database: MeSH. NLM Tech Bull. 2003 Mar-Apr;(331):e13.) the display of the hierarchy for PA terms was changed. It includes only those indentions for PA terms found in the actual MeSH tree structure, not (as before) terms that had the effect, but were not true indentions. In this way, the hierarchy shown by the PubMed MeSH Database, matches that shown by the NLM MeSH Browser.
Search with [PA]
A new search tag, [PA], and an associated index for Pharmacologic Action terms has been created (see this index on the Preview/Index screen). Use of a term with the [PA] tag, (e.g., plasminogen activators [pa]) instructs PubMed to OR together terms from a list. Each list is made up of a PA term and the drug/substance terms known to have that effect. This includes both MeSH headings and terms for Supplementary Concept Records. Any MeSH terms on the lists are searched with the no explode specification, [mh:noexp], so as not to include any possible indentions of the term that might not share the pharmacologic action. Use this search method when you want to include retrieval for all MeSH terms with a particular action.
Example: neoplasms [mh] AND antioxidants [pa]
Pharmacologic Action Lists
To see what substances are included in a PA list, use the NLM MeSH Browser. Enter the "action" term in the query box, check the Pharmacological Action (PA) box, and click on Find Exact Term. (See Figures 1 and 2.)
For information about how PAs are assigned to SCRs, see "Pharmacological Action (PA) for Supplementary Concept Records" in the article, Rosov J. MEDLINE® Data Changes - 2003. NLM Tech Bull. 2002 Nov-Dec;(329):e4.
The following lists are also available in XML format:
- Pharmacologic Actions of a given substance
- Substances with a given Pharmacologic Action
Search with [MH]
Terms tagged with [MH] will retrieve the term and true indentions (PubMed automatically explodes MeSH headings). For example, a search for food additives [mh] will retrieve citations with the MeSH heading, Food Additives or any of its indented terms in the MeSH hierarchy (Fat Substitutes, Food Coloring Agents, and Food Preservatives).
Because the retrieval for the [mh] tag will no longer additionally retrieve terms from the old PA/PX system, you can now successfully retrieve citations about a drug or substance with a specific action back through 1996.
edetic acid [mh] AND food additives [mh]
(See Recommendations for pre-1996 retrieval.)
Search with No Tag
If you enter a MeSH Heading (or Entry Term) that happens to be a Pharmacologic Action Term and do not use a search tag, PubMed will search the term as [MH], [PA], and [TW].
For example, if you enter food additives, PubMed will translate this to:
food additives [mh] OR food additives [pa] OR food additives [tw]
- Searchers who use drug, substance, or pharmacologic action terms in searches are advised to review strategies (e.g., Cubby stored searches) to see if revisions are necessary based on these changes.
- Check the Details screen after running searches to see how PubMed translated your query.
- Prior to the 1996 MeSH year, NLM treed specific drugs/substances under the pharmacologic action MeSH heading. Indexing policy stipulates that indexers assign the most specific heading; a broader heading is typically not added. Therefore, citations to articles about pharmacologic actions indexed before 1996 usually carry only the specific drug/substance heading and not the pharmacologic action heading. If you need comprehensive searches to include citations for articles indexed before 1996, do a search for the substance ANDed with the PA term as well as a search for the substance alone, i.e., do not combine with PA term. The following example strategy is suggested for doing comprehensive searching:
- aspirin [mh] AND platelet aggregation inhibitors [mh]
- aspirin [mh] NOT platelet aggregation inhibitors [mh] NOT 1996:current year [dp]
- Combine #2 with subject search terms for the action concept, or manually check items to find those about the drug/substance with this desired action. Add these items to results of #1 to obtain comprehensive results.
[Editor's note: please see Nahin AM. Pharmacological Action Terms Identified in MeSH Database. NLM Tech Bull. 2003 Nov-Dec;(335):e7. for updated information on Pharmacological Action headings.]
By Annette M. Nahin
MEDLARS Management Section
Nahin AM. Pharmacologic Action Headings: PubMed®. NLM Tech Bull. 2003 Jul-Aug;(333):e6.