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Search Clinic: Chemicals and Drugs in PubMed®
Questions and Answers

The following questions were posed to the trainers during or immediately after the August 23, 2007 Search Clinic: Chemicals and Drugs in PubMed. Answers are provided by NLM staff. Please note that changes are made to PubMed regularly. See the NLM Technical Bulletin for news and announcements about changes to MEDLINE/PubMed data and PubMed functions and features.

Note: Questions numbered 10 through 14 were added and notations to questions 3 and 6 were made on September 27, 2007. Question 15 was added November 5, 2007.

1. What is a “preferred” MeSH® heading?
A “preferred” MeSH heading is the form that you see in the MH data element in a MEDLINE citation. MeSH Headings, which can be found in the MeSH Database, also have entry terms or synonyms that may be used to search the concept; those entry terms map to the preferred form of the concept for searching. The preferred MeSH heading may change over time. NLM maintains all older citations to have the current preferred form of the heading.

For example, in 2007 MeSH:
MeSH Heading – Matrix Metalloproteinase 1
Year introduced: 2007(2000)
Entry Terms:
Metalloproteinase 1, Matrix
Interstitial Collagenase
Matrix Metalloproteinase-1
MMP-1 Metalloproteinase
[plus more Entry Terms exist]

The preferred MH, effective in 2007, is Matrix Metalloproteinase 1. You may search that term or any of its entry terms and get the same retrieval back through the 2000 indexing year. The term that displays in PubMed on the citations is the preferred term.

This concept was introduced to MeSH for the first time as a descriptor in 2000 when the preferred term was Interstitial Collagenase. Effective for 2007 MeSH, the preferred term was changed to Matrix Metalloproteinase 1 and NLM maintained all the citations to have this new, preferred term for display.

This particular concept existed first in MeSH as a Supplementary Concept Record (SCR) as of 1991. For 2000 MeSH, it was elevated to MeSH Descriptor status. All of the citations indexed with SCR from 1991 – 1999 also have the current preferred form of the MH so that searches actually retrieve citations back through 1991.

2. How are items added to the Pharmacologic Action list?
Pharmacological Action terms are added to new or existing substances if the following three criteria are met:

  • There are more than 20 citations in PubMed discussing the Pharmacological Action being exhibited by that drug;
  • There is substantial evidence that the Pharmacological Action is in effect in humans (i.e., the drug is used clinically); and
  • A reasonable proportion of the literature (greater than or equal to 10%) on that drug accounts for those effects.

3. Do all substance records include a registry number (RN)?
No. In 1996-1997, the National Library of Medicine ceased adding registry numbers (RNs) to substance records that appear in the MeSH database.
[Note added 9/27/07: If an existing substance record has an RN, that RN will continue to be applied to new citations indexed with that substance.]

4. In the aspirin example you used Pharmacological action with an [mh] tag but there are [pa] tags. How do you know which tag to use?
Use the pharmacological action with an [mh] tag if you are interested in a specific action of a particular substance (e.g., folate AND antioxidants [mh]). Search the pharmacological action with a [pa] tag if you want to search all substances identified as having that action (e.g., bladder cancer AND antioxidants [pa]).

5. How would I search for the use of beta blockers in patients with MI (myocardial infarction)? Do I use Pharmacological action or MeSH?
Beta-blockers are described in MeSH with the term Adrenergic beta-Antagonists. To search for all substances identified as adrenergic beta-antagonists, search the term as a pharmacologic action [pa]. To search for adrenergic beta-antagonists as a subject, search the term as a MeSH heading [mh].

In this particular example where there is a large body of literature, take advantage of the fact that an indexer describing an article about using beta-blockers to treat patients with myocardial infarction would use the MeSH heading Adrenergic beta-Antagonists with the subheading therapeutic use as a major topic, and the heading Myocardial Infarction with the subheading drug therapy as a major topic. We recommend the targeted search:

adrenergic beta-antagonists/therapeutic use[majr] AND myocardial infarction/drug therapy[majr]

For a more comprehensive, broader search that would also include all of the substances identified as adrenergic beta-antagonists, use:

adrenergic beta-antagonists AND myocardial infarction/drug therapy [majr]
(see PubMed Details tab to see how PubMed translates the unqualified phrase)

6. Does anti-infective agents [pa] get every article about any of the substances that can be used as an antibiotic OR does it get only those articles in which the anti-infective agent aspects/use of those substances are being discussed?
Anti-infective agents [pa] will retrieve any article indexed with any of the substances identified as an anti-infective, regardless of the slant of the article. To retrieve articles indexed since 1996 discussing the anti-infective aspects of a substance, use anti-infective agents [mh]. [Note added 9/27/07: To retrieve articles discussing the antibiotic aspects of a substance, use anti-bacterial agents[mh].] For more information see NahinAM. Pharmacologic Action Headings: PubMed®. NLM Tech Bull. 2003 Jul-Aug;(333):e6.

7. In searching PubMed for chemical names, you said to not use parentheses... [but to instead] use a hyphen... Did you also say it was okay to do a space instead?
Substitute a space for parentheses or brackets, unless there is already a hyphen. If there is an adjacent hyphen, simply delete the parenthesis or bracket. For example, edit
1-[(3,5-dichloro)-2,6-dihydroxy-4-methoxyphenyl]-1-hexanone to:

8. What exactly is the [mhda] tag? How is it used?
The date entered in the MHDA field is initially the date the record entered the database (matching the EDAT). Then, when a record is indexed with MeSH terms, the MHDA field is updated. In other words, for MEDLINE records, the MHDA reflects the date of indexing. Search tags are described in PubMed Help.

9. Is it preferable to search for chemical entities under RN (registry number) in PubChem?
Not all PubChem Substance records include registry numbers; therefore we would hesitate to suggest this as a preferred search method. It is one of several search options.

10. Why is RN not being added [to MeSH records]? Where did the RNs come from?
RNs were supplied by the Chemical Abstracts Service (CAS®). About a decade ago, NLM ceased adding RNs to MeSH records because we were unable to negotiate a satisfactory contract with CAS. Note that RNs that were already included in MeSH continue to be added to MEDLINE citations and can be used to search MEDLINE records in PubMed.

11. Are there any problems with the consistency with which indexers enter pharmacological actions in records?
The pharmacological action heading applied with a specific substance may vary from article to article, depending on the subject matter of the article in hand. For example, some articles about methotrexate require that the pharmacological action Antimetabolites, Antineoplastic be applied, while other articles would require that Antirheumatic Agents be applied. Some articles might require application of a pharmacological action heading that is not one of those listed in the MeSH record for Methotrexate. Sometimes no pharmacological action heading is applied because the article is only about the isolation or purification of a substance, and does not substantively discuss any pharmacological properties of the substance. Finally, remember that the policy to coordinate with the pharmacological action heading was not instituted until 1996; citations prior to that date are not routinely indexed with a pharmacological action.

12. How would I search for the side effects of celebrex, and contraindications between celebrex and aspirin?
For side effects of celebrex, try:

celebrex AND sulfonamides/ae[mh:noexp]
celebrex AND ae[sh] AND sulfonamides/ae[mh:noexp]

For contraindications between celebrex and aspirin try:

aspirin/ct AND celebrex AND sulfonamides/ct[mh:noexp]

Please note that search celebrex AND sulfonamides/ct[mh:noexp] currently retrieves 10 citations.

13. How do you search for melamine poisoning?
Melamine is a substance name with a mapped MeSH heading of Triazines. To search for a substance using a concept represented by a subheading in MeSH, you would generally apply the subheading to the mapped MeSH heading, such as:

melamine AND triazines/po

However, this example has no results. Because there are few articles related to this subject, a better search might currently be the broader:

melamine AND triazines/ae
melamine food contamination

if that is appropriate.

14. When or why does a substance name change to a MeSH term?
A Substance Name (or Supplementary Concept Record) may be upgraded to a preferred MeSH Heading based on various criteria, including importance to clinical care and research and the frequency of occurrence in the journal literature. According to MeSH Section staff, NLM rarely promotes individual chemicals that are Supplementary Concepts to Descriptors "until the analogs and derivatives become a major issue."

15. How best to search for adverse effects of any antibiotic ... anti-infective agents/ae? But individual antibiotics are not in the MeSH trees any longer. So, this will not get ampicillin/ae. So I'm left with anti-infective agents (so that will map to antibiotics and also to the pa AND ae which isn't great because it's floating).

To find articles about the adverse effects of any antibiotic where the article was indexed since the beginning of the 1996 indexing year, use anti-bacterial agents/ae. This heading is applied in addition to the specific substance concept when relevant.

Try this:

(anti-bacterial agents/ae AND 1995/10/20:2007 [dcom]) OR (anti-bacterial agents [pa] AND ae [sh:noexp] NOT anti-bacterial agents/ae AND 1800:1995/10/19 [dcom])

Note:  The date completed value [dcom] of 1995/10/20 is the first date of the 1996 indexing year.