2021 MeSH Highlights
Every year, updates are made to MeSH, the NLM controlled vocabulary thesaurus used for indexing articles for PubMed. This annual webinar aims to introduce those changes and provide examples of how the changes may affect you as a PubMed searcher. For more information about MeSH, see the MeSH homepage.
A: Any publications indexed with COVID-related SCRs will now be retrievable with the new MeSH heading. However, we recommend leaving off the [MeSH] tag (search simply COVID-19) to map most comprehensively and retrieve both indexed and non-indexed records.
Q: Is LitCovid still getting updated?
A: Yes, LitCovid is active, tracking scientific literature about the 2019 novel Coronavirus. Consider also using the PubMed Clinical Queries filter for COVID-19 articles, where you can select categories of literature to search (e.g., Treatment, Mechanism, Transmission, Diagnosis, etc.).
Q: When do you create a Supplementary Concept Record (SCR)? Can you talk more about the reason/function of SCRs? I've never quite understood this part of MeSH.
A: The Medical Subject Headings and trees are only updated once per year. Supplementary Concept Records (SCRs), on the other hand, are added on a weekly basis. This allows us to add new terms throughout the year for describing the literature. This has been particularly useful for describing new drugs and chemicals, and this past year, for adding COVID-related terms. Note that every SCR is also mapped to a preferred MeSH term which is also added automatically to the MEDLINE record. This means that the literature will also be described and retrievable with MeSH preferred terms, with the SCRs often adding important specificity.
Q: When is it better to use a MESH term vs. just typing in a term?
A: Limiting your searches to MeSH provides precision that “keyword” searching cannot. MeSH searches allow you to search the set of indexed records with some assurance that the results are really about the topic you are searching, limiting the “false hits.” This is particularly true if you apply the Major Topic [majr] designation. However, because not all PubMed records are indexed, you are also eliminating some potentially relevant records, particularly the most recently added records, if you search only with MeSH.
Expert searchers who intend to search PubMed as comprehensively as possible will use iterative approaches, using untagged searching to explore terminology in their search details and results and investigating the Best Matches; then often tagging their searches with MeSH to retrieve indexed records; and searching the non-indexed records by adding NOT medline[sb] to keyword searches.
Q: Do you recommend using the MeSH database search over MeSH Browser? What’s the difference?
A: The MeSH Database is built so that you can craft PubMed searches from the Database, so it’s the best choice for PubMed searching. If you’re looking for more in-depth (e.g., historical) information about a particular term or its relationship to other MeSH terms, that’s when you’ll want to consult the MeSH Browser.
Q: Is it possible to prevent a term from exploding?
A: You can use the [mh:noexp] tag to search a broad term without including the narrower term automatically. Please use this with caution. Indexers use the most specific term available and you often risk eliminating relevant results with this method. Please refer to our How PubMed Works series of classes.
Q: When would searchers use a taxonomy ID search vs PubMed search?
A: Searching taxonomy IDs (txid) within the NCBI Taxonomy Browser may be more useful for researchers seeking data from across NLM’s various sequence databases. Although you can find datasets attached to PubMed articles, PubMed focuses on literature.
Q: Is there a resource that links MH tree ids to their unique id other than the individual term pages? For instance, I want to be able to have a list of all unique ids under Diseases (C).
Try using the MeSH RDF SPARQL endpoint at https://id.nlm.nih.gov/mesh/sparql. A web browser interface is available https://id.nlm.nih.gov/mesh/query. Documentation is available at https://hhs.github.io/meshrdf/sparql-and-uri-requests.
Q: Why the inconsistency in Negative-*Sense* vs Positive-*Strand* RNA Viruses? Is the use of -sense vs -strand not synonymous?
Sense and strand are synonyms in our usage. Thank you for your suggestion. We will change these records to make them consistent.
Q: Why aren't specific types of pets (dogs, cats, etc.) narrower terms under the Pets MeSH term? This requires us to search those pets ORed together (Dogs[MH] OR Cats[MH] ... OR Pets[mh].
Articles about a specific species of pets (e.g. “pet dogs” or “pet cats”) are indexed with both the “Pets” heading AND the specific species heading (e.g. “Dogs” or “Cats”). Therefore, while “Dogs” and “Cats” are not considered narrower terms of “Pets,” your search for “Pets” should retrieve the relevant articles.
Q: Do human indexers index all the Medline entries, or is any indexing automated?¬ How extensive is automated indexing (% of journals/content)? Is there a list of journals being indexed this way available?
We use a combination of automated and semi-automated methods to index articles for MEDLINE. You can read about the MEDLINE Indexing Initiative and find the current list of journals for which we use automated indexing methods on the NLM Indexing Initiative web site.
Q: How are publication types indexed? Often authors are not so clear when mentioning their study design.
A: Since 1991, Publication Types (PTs) have been assigned by NLM indexers to describe the form of presentation of materials that are indexed. Some PTs reflect the format and editorial practices of the individual journal; others reflect the indexer's analytical judgment. Items indexed prior to 1991 have had a limited number of PTs added by machine rather than by re-indexing. Publishers are also permitted to include publication types in their submissions to PubMed. This publisher-supplied data is checked during the Indexing process.
For more information about indexing publication types, please see the MEDLINE Indexing Online Training Course section on Category V.
Questions & Answers
Q: Will the new Covid-19 MeSH term capture results from 2020 or just going forward from 2021? When searching with "COVID-19"[MeSH] , do I also find publications about Covid-19 from Nov 2019?A: Any publications indexed with COVID-related SCRs will now be retrievable with the new MeSH heading. However, we recommend leaving off the [MeSH] tag (search simply COVID-19) to map most comprehensively and retrieve both indexed and non-indexed records.
Q: Is LitCovid still getting updated?
A: Yes, LitCovid is active, tracking scientific literature about the 2019 novel Coronavirus. Consider also using the PubMed Clinical Queries filter for COVID-19 articles, where you can select categories of literature to search (e.g., Treatment, Mechanism, Transmission, Diagnosis, etc.).
Q: When do you create a Supplementary Concept Record (SCR)? Can you talk more about the reason/function of SCRs? I've never quite understood this part of MeSH.
A: The Medical Subject Headings and trees are only updated once per year. Supplementary Concept Records (SCRs), on the other hand, are added on a weekly basis. This allows us to add new terms throughout the year for describing the literature. This has been particularly useful for describing new drugs and chemicals, and this past year, for adding COVID-related terms. Note that every SCR is also mapped to a preferred MeSH term which is also added automatically to the MEDLINE record. This means that the literature will also be described and retrievable with MeSH preferred terms, with the SCRs often adding important specificity.
Q: When is it better to use a MESH term vs. just typing in a term?
A: Limiting your searches to MeSH provides precision that “keyword” searching cannot. MeSH searches allow you to search the set of indexed records with some assurance that the results are really about the topic you are searching, limiting the “false hits.” This is particularly true if you apply the Major Topic [majr] designation. However, because not all PubMed records are indexed, you are also eliminating some potentially relevant records, particularly the most recently added records, if you search only with MeSH.
Expert searchers who intend to search PubMed as comprehensively as possible will use iterative approaches, using untagged searching to explore terminology in their search details and results and investigating the Best Matches; then often tagging their searches with MeSH to retrieve indexed records; and searching the non-indexed records by adding NOT medline[sb] to keyword searches.
Q: Do you recommend using the MeSH database search over MeSH Browser? What’s the difference?
A: The MeSH Database is built so that you can craft PubMed searches from the Database, so it’s the best choice for PubMed searching. If you’re looking for more in-depth (e.g., historical) information about a particular term or its relationship to other MeSH terms, that’s when you’ll want to consult the MeSH Browser.
Q: Is it possible to prevent a term from exploding?
A: You can use the [mh:noexp] tag to search a broad term without including the narrower term automatically. Please use this with caution. Indexers use the most specific term available and you often risk eliminating relevant results with this method. Please refer to our How PubMed Works series of classes.
Q: When would searchers use a taxonomy ID search vs PubMed search?
A: Searching taxonomy IDs (txid) within the NCBI Taxonomy Browser may be more useful for researchers seeking data from across NLM’s various sequence databases. Although you can find datasets attached to PubMed articles, PubMed focuses on literature.
Q: Is there a resource that links MH tree ids to their unique id other than the individual term pages? For instance, I want to be able to have a list of all unique ids under Diseases (C).
Try using the MeSH RDF SPARQL endpoint at https://id.nlm.nih.gov/mesh/sparql. A web browser interface is available https://id.nlm.nih.gov/mesh/query. Documentation is available at https://hhs.github.io/meshrdf/sparql-and-uri-requests.
Q: Why the inconsistency in Negative-*Sense* vs Positive-*Strand* RNA Viruses? Is the use of -sense vs -strand not synonymous?
Sense and strand are synonyms in our usage. Thank you for your suggestion. We will change these records to make them consistent.
Q: Why aren't specific types of pets (dogs, cats, etc.) narrower terms under the Pets MeSH term? This requires us to search those pets ORed together (Dogs[MH] OR Cats[MH] ... OR Pets[mh].
Articles about a specific species of pets (e.g. “pet dogs” or “pet cats”) are indexed with both the “Pets” heading AND the specific species heading (e.g. “Dogs” or “Cats”). Therefore, while “Dogs” and “Cats” are not considered narrower terms of “Pets,” your search for “Pets” should retrieve the relevant articles.
Q: Do human indexers index all the Medline entries, or is any indexing automated?¬ How extensive is automated indexing (% of journals/content)? Is there a list of journals being indexed this way available?
We use a combination of automated and semi-automated methods to index articles for MEDLINE. You can read about the MEDLINE Indexing Initiative and find the current list of journals for which we use automated indexing methods on the NLM Indexing Initiative web site.
Q: How are publication types indexed? Often authors are not so clear when mentioning their study design.
A: Since 1991, Publication Types (PTs) have been assigned by NLM indexers to describe the form of presentation of materials that are indexed. Some PTs reflect the format and editorial practices of the individual journal; others reflect the indexer's analytical judgment. Items indexed prior to 1991 have had a limited number of PTs added by machine rather than by re-indexing. Publishers are also permitted to include publication types in their submissions to PubMed. This publisher-supplied data is checked during the Indexing process.
For more information about indexing publication types, please see the MEDLINE Indexing Online Training Course section on Category V.
Useful Links:
- PubMed Online Training
- Learn about MeSH
- MeSH Database
- Tybaert S. MEDLINE Data Changes – 2021. NLM Tech Bull. 2020 Nov-Dec;(437):e3a.
- COVID-19 and SARS-CoV-2 MeSH Terms—2021. NLM Tech Bull. 2020 Nov-Dec;(437):e3b.
- New 2021 MeSH Headings
- NCBI Taxonomy database
- Cho, D. NCBI Taxonomy Identifiers Added to MeSH. NLM Tech Bull. 2020 Nov-Dec;(437):e2.
Last Reviewed: February 17, 2021