How to search PubMed for citations that are assigned MeSH supplemental concept records in MEDLINE?
dhimmel opened this issue · 2 comments
Based on the MEDLINE online training docs, it sounds like MEDLINE assigns MeSH supplemental concept records (SCRs) to citations:
1-benzylpiperazine is a supplementary chemical concept. It is mapped to the MeSH descriptor PIPERAZINES. That means that the article indexed with 1-benzylpiperazine will appear in PubMed under both 1-benzylpiperazine and PIPERAZINES. The indexer needs ONLY to index the SCR; the Heading Mapped to is added automatically.
The indexing of SCR terms is identical to the indexing of MeSH descriptors. In the IMS Browser, they appear in the scroll-down list alphabetically along with MeSH descriptors. The indexer can search the MeSH browser for complex SCR terms in the same manner as for complex MeSH terms. The Pharmacological Action of the SCR term must be added, if appropriate.
The MeSH browser for 1-benzylpiperazine shows a frequency of 57, leading me to believe it is actually assigned as a topic in MEDLINE.
But searching pubmed for "1-benzylpiperazine" [MeSH Terms:noexp] returns zero results and the message:
Your search was processed without automatic term mapping because it retrieved zero results.
So is there a way to search PubMed for MeSH SCRs?
Sent a question to the NCBI helpdesk (case number is CAS-706823-M2K8C1):
Greetings, I have a PubMed / MEDLINE / MeSH question.
I would like to search PubMed for articles that are assigned as having the topic "1-benzylpiperazine" in MEDLINE. "1-benzylpiperazine" is a MeSH supplementary concept record with ID C006737.
However, searching pubmed for
"1-benzylpiperazine" [MeSH Terms:noexp]returns zero results. I am guessing the search is failing because 1-benzylpiperazine is an SCR rather than a Descriptor.But it appears MEDLINE is actually indexing at the level or SCR. So is there a way to search PubMed for articles based on a MeSH SCR?
My end goal is to get the list of pubmed IDs that have a MeSH SCR as a MEDLINE. I can use the API and or download datasets if needed.
Ryan Cohen, Customer Service Librarian for NLM, provided the following response:
You may search for 1-benzylpiperazine as a SCR by tagging the phrase, i.e.,
"1-benzylpiperazine" [Supplementary Concept]
Please see the User Guide for Search Field descriptions and tags
Additionally, you may enter the phrase in PubMed and it will automatically map to the SCR.
Please see the User Guide for automatic term mapping
Search Details (including individual term translations) are available on the Advanced Search page under "History". Click the chevron icon " > " next to a query in History to expand the Search Details.
For more information about Search Details, please see the PubMed User Guide
Supplementary Records, also called Supplementary Chemical Records (SCRs), are used to index chemicals, drugs, and other concepts such as rare diseases for MEDLINE and are searchable by Substance Name [NM] in PubMed. Unlike Descriptors, SCRs are not organized in a tree hierarchy. Instead each SCR is linked to one or more Descriptors by the Heading Mapped To (HM) field in the SCR. They also include a Indexing Information (II) field field that is used to refer to other descriptors that are from related topics. SCRs are created daily and distributed nightly Monday-Thursday. There are currently over 230,000 SCR records with over 505,000 SCR terms. Like all MeSH records, SCRs are searchable in the MeSH Browser. Four classes of SCRs exist.
Secondly, an article may refer to the use of a drug or chemical that is an occasional or novel use. That would suggest use of a pharmacological action but not treatment as a MeSH heading.
Only those drugs or chemical regularly recognized in standard reference sources or very high and regular use are assigned a MeSH heading.
See also: