Medical Subject Headings (MeSH) The NLM Controlled Vocabulary What makes MEDLINE special are the Medical Subject Headings (MeSH) PubMed for Trainers, Fall 2015 U.S. National Library of Medicine (NLM) and NLM Training Center

Objectives By the end of this session, you should be able to: Define MeSH Explain why we use MeSH Explain the hierarchical structure of MeSH Explore MeSH further Here are the objectives for this session Reviewed 2015/10

Medical Subject Headings Defined Represent concepts found in the biomedical literature Like keywords on other systems Used to describe the subject of journal articles for MEDLINE Used for cataloging books and audiovisuals Used by searchers Revised annually Gives uniformity and consistency to the indexing of the biomedical literature MeSH headings represent concepts found in the biomedical literature Similar to keywords on other systems Used for indexing journal articles for MEDLINE and also used for cataloging books, audiovisuals and other library materials Used by searchers Revised annually Gives uniformity and consistency to the indexing of the biomedical literature Reviewed 2015/10

Medical Subject Headings (MeSH® Vocabulary) MeSH Vocabulary Type Examples Headings Body Weight, Kidney, Dental Cavity Preparation, Self Medication, Brain Edema, Oseltamivir Subheadings adverse effects, genetics, contraindications, ultrastructure Publication Types Letter, Review, Practice Guideline, Twin Study Supplementary Concept Records cordycepin, carbon monoxide dehydrogenase, nocturnin We divide the MeSH vocabulary into four types of terms: Headings (topics), subheadings (further describe aspects of the topic), publication types (describe the type of material being indexed), and supplementary concept records We’ve seen examples of the first three. Supplementary Concept Records are topics that are not included as Headings in the vocabulary. The vast majority of these are substances. We’ll return to discuss supplementary concept records in a few minutes. Reviewed 2015/10

MeSH Headings (Examples) Lung Neoplasms Erythrocytes Quality of Life Diabetes Mellitus Ascorbic Acid Birth Order Glycolysis Patient Dropouts NLM’s MEDLINE indexers examine articles and assign the most specific MeSH heading(s) appropriate to describe the main concepts discussed. When there is no single specific MeSH heading for a concept, the indexer will use the closest, more general MeSH heading available. Reviewed 2015/10

MeSH Entry Terms (Example) Lung Neoplasms Tumors or cancer of the LUNG. Entry Terms: Cancer of Lung Cancer of the Lung Lung Cancer Neoplasms, Lung Neoplasms, Pulmonary Pulmonary Cancer Pulmonary Neoplasms One of the features that gives value to MeSH is its use of entry terms. Entry terms are synonymous, or close in scope, to the preferred MeSH Heading. Including the entry terms allows PubMed to account for variations in vocabulary. If a searcher enters lung cancer or pulmonary neoplasms, the correct heading: Lung Neoplasms is brought into the search. This ensures that the relevant indexed citations are retrieved, accounting for variations in vocabulary used by the author of the article and the searcher. Reviewed 2015/10

MeSH Tree Structure Anatomy Organisms Diseases Chemicals and Drugs Analytical, Diagnostic and Therapeutic Techniques and Equipment Psychiatry and Psychology Phenomena and Processes Disciplines and Occupations Anthropology, Education, Sociology and Social Phenomena Technology, Industry, Agriculture Humanities Information Science Named Groups Health Care V. Publication Characteristics Z. Geographicals MeSH headings and Publication Types are arranged in a hierarchical manner called the MeSH Tree Structure The vocabulary is organized into 16 main branches. The most highly used or important branches are probably the first four (anatomy, organisms, diseases and chemicals and drugs). Reviewed 2015/10

MeSH Tree in Use Reviewed 2015/10 Note that melanoma appears in 3 different locations of the tree: Neoplasms, Germ Cell and Embryonal, Neoplasms, Nerve Tissue and Nevi and Melanomas In PubMed, a search of the broader term will automatically include more specific terms. So any narrower terms, in any branch in which they appear, will be included. This is called automatic explosion. In this example, a search of melanoma will include Hutchison’s Melanotic Freckle, Melanoma, Amelanotic and Melanoma, Experimental. Reviewed 2015/10

MeSH Tree in Use Reviewed 2015/10 The context, or branch of the tree, may change what narrower terms appear below it. Here is the example, nose. Nose appears in anatomy as well as sense organs branches. In the anatomy tree, the nose first appears as part of the face. It also appears in that same Anatomy tree, as part of the respiratory system. Under respiratory system, the nose include the nasal bone, cartilages, cavity, mucusa, etc. In the sense organs tree, the nose include the olfactory mucosa and vomeronasal organ; the functional sensory parts of the nose. A search of nose would “explode” to include the specific terms from both face, respiratory system, and sense organs branches. Reviewed 2015/10

Pop Quiz (take a guess) Reviewed 2015/10 POLL: Select all the terms that occur under the broad term Foot in the MeSH tree structure: Ankle Toes Thumb Heel The answer is Ankle, Toes, and Heel Ankle, Toes, and Heel are narrower terms for the term Foot. Thumb is not part of the Foot and therefore not a narrower term. Note there are other narrower terms under Foot. Worth thinking about when you remember that PubMed automatically includes narrower terms when searching broader terms in PubMed. A search for Foot will retrieve citations indexed with the narrower terms Ankle, Toes, and Heel as well as the other terms in this branch of the tree. Reviewed 2015/10

Subheadings (Examples) Lung Neoplasms/diagnosis Erythrocytes/classification Quality of Life/legislation and jurisprudence Diabetes Mellitus/rehabilitation Ascorbic Acid/secretion Birth Order/physiology Glycolysis/genetics Patient Dropouts/psychology Indexers can also assign subheadings to describe the particular aspect of a MeSH concept discussed. Examples of Subheadings are: diagnosis, surgery, metabolism, pathology. They are included with the MeSH heading after a slash. Reviewed 2015/10

In this example we see that the word mortality follows the heading Breast Neoplasms. In other words, the indexer has decided that this article is about mortality from Breast Neoplasms. We also see radiography following Breast Neoplasms. The indexer decided that two aspects of breast cancer are discussed: mortality, and radiography. The MeSH terms that reflect the major points of the article are marked with an asterisk (*) by indexers, as you can see in this example… The main emphases of this article are identified as: mortality from breast neoplasms, radiography of breast neoplasms, adverse effects of mammography, psychology of mammography, and mass screening. In addition to assigning MeSH terms that describe the topic of the article, the indexer provides terms that reflect characteristics of the group being studied (e.g., the age group, human or other animal, male or female) In this example we see adult, female, humans and middle aged. So we know that middle aged women are the subjects of interest. Reviewed 2015/10

Subheading Groupings (Examples) adverse effects poisoning toxicity therapy diet therapy physiology drug therapy genetics nursing growth & development prevention & control immunology radiotherapy metabolism rehabilitation biosynthesis surgery blood transplantation cerebrospinal fluid deficiency enzymology pharmacokinetics urine physiopathology secretion Subheadings have something of a hierarchy of their own. A search of a broader subheading will automatically include the narrower subheadings. In other words, they are exploded. For example, a search of therapy will include diet therapy, drug therapy, radiotherapy, etc. Use the most specific subheading to describe your topic of interest. Where to find? Appendices in PubMed Help Reviewed 2015/10

Publication Types (Examples) Review Editorial Letter Interactive Tutorial Clinical Trial, Phase III Twin Study The indexer also describes the material represented, including the publication format (Editorial, Review) and the characteristics of the research reported by the article (clinical trial, twin study, and ). These terms are listed separately in the record under Publication Types. Reviewed 2015/10

Publication Types in Hierarchy Study Characteristics Clinical Study Clinical Trial Clinical Trial, Phase I Clinical Trial, Phase II Clinical Trial, Phase III Clinical Trial, Phase IV Controlled Clinical Trial Publication Types are part of the MeSH hierarchy. This slide shows an example of the tree structure (in 2016 MeSH). A search of a broader Publication Type will automatically include the narrower Publication Types. In other words, they are exploded. For example, a search for Clinical Trial [pt] will include all the narrower terms shown here. Reviewed 2015/10

We see that this example is a meta-analysis and a review. Reviewed 2015/10

Supplementary Concepts Part of MeSH Database NOT full Headings Used to quickly add vocabulary Substances Protocols Rare Diseases MeSH includes a special subset of terms called Supplementary Concepts. There are currently over 200,000 SCRs. These are primarily substances, but also include some protocols and rare diseases. New substances are identified in the literature regularly by indexers and referred to our staff chemists. These chemists verify that the substance is new to the vocabulary and add them to the database as SCRs. Each substance is mapped to a MeSH Heading. When the supplementary concept is added to a MEDLINE record, the mapped MeSH Heading is added as well. Use the most specific term for searching. Reviewed 2015/10

Here’s an example of a MEDLINE record where plumbagin was applied. Note that the mapped MeSH heading Naphthoquinones is also applied. We’ll talk more about SCRs and how to search with them in the Drug Information presentation in Session 4. Reviewed 2015/10

The MeSH Database Reviewed 2015/10 The MeSH Database, available from any screen in PubMed using the Database Selection menu, provides information about MeSH terms and helps you find appropriate terms for searching. Reviewed 2015/10

The MeSH Database Reviewed 2015/10 A search of the MeSH Database is a search only of the vocabulary: You must search one concept at a time to find relevant terms. Here are the results for a search of falls. We’ll take a look at the term: Accidental Falls. Reviewed 2015/10

Here is the full display format for Accidental Falls in the MeSH Database. Following the term, a definition may be provided. Note that this definition reflects how the term is used for indexing and cataloging. You can use this term to search back to the earliest year displayed. In this case, it is 1987. If you want to search the concept prior to that year, check the Previous Indexing information, below. In this example, you may want to search Accidents for literature between 1966 and 1986. Subheadings specify which aspects of the topic have been applied to MEDLINE records. Note the Entry Terms, below on the screen. These are synonyms that searchers can use for this topic. You may also see a section labeled “See Also” (not on this record) which are terms related to the concept in some way and may be relevant. Reviewed 2015/10

Below that, the MeSH hierarchy surrounding this term is displayed Below that, the MeSH hierarchy surrounding this term is displayed. All branches of the tree where the term appears are listed. Reviewed 2015/10

Here is a MEDLINE record (23663793) Here is a MEDLINE record (23663793). This example shows how the heading Accidental Falls was used with a number of other headings to describe a review article about the prevention of falls. Reviewed 2015/10

Open Quiz (use the MeSH Database) Search for the word Fragaria. 2 polls: What are fragaria better known as? Small pieces of glass Birthmarks Strawberries Disorganized vocalizations   (Answer: Strawberries. Not much discussion on this – an exercise to have them look at the MeSH database record.) Which of the following is NOT a subheading for Fragaria? Adverse effects Blood Genetics Virology (Answer: Blood. This could be treated very simply with the list available in the MeSH Database, but also an opportunity to point out link to MeSH Browser and list of allowable subheadings.) Reviewed 2015/10

Exercises 1. If you search the term Patient Acuity in PubMed, what MeSH terms are also searched? Answer: Severity of Illness Index and Karnofsky Performance Status. This term explodes. Reviewed 2015/10

Exercises 2. How far back can you search PubMed using the MeSH term Hand Disinfection? Answer: 1982. You can search with a term back to the earliest date shown on the MeSH Database record under Year Introduced. If there are multiple dates, that means that something changed about the record, but there is a 1:1 relationship with the old term and the new one. For this example, Hand Disinfection was Handwashing. Because the terms are considered equivalent for MEDLINE purposes, the old term was replaced, so MEDLINE records are searchable back to the earliest use of the previous term. If I wanted to search prior to 1982 what information on this record will help me? Previous Indexing. Reviewed 2015/10

Exercises 3. What ages are included in a search using the MeSH term Adolescent? Answer: 13 to 18. Note the other age groups. Some are “children” of others (e.g., Child, Preschool is under Child). Note also that some terms are newer than others (e.g., Frail Elderly). Be careful when using these for searching. Reviewed 2015/10

Exercises 4. What MeSH term and Subheading combination might find relevant results about the adverse effects of bichloroacetic acid? Answer: Dichloroacetic Acid/adverse effects or Dichloroacetic Acid/ae Bichloroacetic acid is an entry term to dichloroacetic acid. The PubMed syntax is heading forward slash subheading. If you know the two letter abbreviations you can use them in place of the full subheading. Reviewed 2015/10

Exercises 5. What type of MeSH vocabulary is the term CroFab? Answer: CroFab is an entry term to Crotalidae Polyvalent immune Fab. Crotalidae Polyvalent immune Fab is a supplementary concept. Reviewed 2015/10

Exercises 6. What type of MeSH vocabulary is the term Comparative Study? Answer: Comparative Study is a publication type (PT). Specifically, it is under the Study Characteristics branch of Publication Characteristics. Reviewed 2015/10

Exercises: BONUS QUESTION 7. What kind of term is heart attack? Answer: This is kind of a trick question. If you search the MeSH Database, you’ll find that “heart attack” isn’t in MeSH at all. But if you search PubMed, you see that it maps to Myocardial Infarction. This “trickery” (aka: a great feature of PubMed!) is enabled by the use of the Unified Medical Language System (UMLS), which allows PubMed to use terms from a wide range of medical vocabularies to map to MeSH. Reviewed 2015/10

Useful My NCBI features to use when searching with MeSH Click here Reviewed 2015/10

Open Abstract Supplemental Data in My NCBI Reviewed 2015/10

Use of My NCBI /highlighting when searching with MeSH Reviewed 2015/10

Highlighting and open supplemental data Reviewed 2015/10

Summary MeSH is NLM's controlled vocabulary for subject indexing and searching MEDLINE/PubMed There are four types of MeSH: Headings Subheadings Publication Types Supplementary Concept Records MeSH uses synonyms known as Entry terms MeSH is organized in a hierarchy or tree Indexers designate the major points of articles as MeSH Major Topics Use the MeSH Database to find MeSH terms Use My NCBI Site Preferences to customize PubMed displays Reviewed 2015/10

Questions? Reviewed 2015/10