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Use of MeSH in Online Retrieval

The MeSH vocabulary is designed for use by NLM for indexing and searching of the MEDLINE database of journal citations and other data. This enables retrieval systems, such as NLM's PubMed, to provide subject searching of the data. The following includes features of MeSH used for searching. See also Use of MeSH in Indexing.

1. Combining specific MeSH Descriptors in searching for complex subjects

Often a particular subject of a journal article is represented by multiple MeSH Descriptors or Qualifiers. For example, the subject of jejunal enteritis is expressed by the use of the Descriptors Jejunum and Enteritis, so in PubMed a searcher would combine these Descriptors in a query. Similarly Qualifiers can be used in conjunction with appropriate Descriptors. For example, a deficiency of monoamine oxidase is retrieved by the Descriptor Monoamine Oxidase combined with the Qualifier /deficiency. Information about combining a particular MeSH Descriptor is sometimes stored in the Annotation field, which may be viewed in the MeSH Browser.

Not all complex subjects require a combination of terms. When a particular complex subject occurs frequently in the indexed literature, a single Descriptor may be created. For example, to search the subject of arm injuries, instead of combining the Descriptor Arm with the Qualifier/injuries, the single Descriptor Arm Injuries is used.

2. Inclusive retrieval and MeSH Tree Structures

When using a MeSH Descriptor to search, PubMed automatically searches on narrower Descriptors indented under it in the MeSH Tree Structures. Thus, for example, searching Pneumoconiosis retrieves not only articles indexed with that Descriptor but also citations indexed to each of the specific pneumoconioses under it in the Tree Structures:

         Caplan's Syndrome

(The Tree Structure for a given Descriptor is automatically displayed in the MeSH Browser.) This type of search is sometimes called "exploding" the Descriptor. If a PubMed searcher wants to search only the broader subject - without the indented subjects, the search is qualified with the tag "[mh:noexp]".

3. Finding the desired MeSH indexing concept by iterative searching of citations

If the searcher has no idea what MeSH term or terms have been used in indexing relevant literature, a useful strategy is to begin with a text word search. Having found a few good citations, then the searcher may look at the MeSH terms used in indexing and identify those that will retrieve further relevant citations. One of the greatest advantages of an online system is the opportunity it affords one to perform a heuristic iterative search in this manner. This is particularly helpful for the occasional searcher or when searching in areas of very rapid change where MeSH may be less developed or indexing less consistent. For example, if a user is interested in "scalp diseases" - a term not in MeSH, they could search this term in PubMed (title and/or abstract). Then seeing citations that looked particularly relevant, the user could look at the citation record (MEDLINE format), and find the MH term Scalp Dermatoses. This term would then be the basis of a new search.

4. Using the MeSH Browser to find an appropriate MeSH search term

If a searcher is not familiar with the MeSH vocabulary the MeSH Browser provides an excellent means for searching MeSH to find an appropriate Descriptor.

4.1 Text word searching of MeSH terms and notes

For example, if you are interested in "SARS" [Severe Acute Respiratory Syndrome], a search of the MeSH Browser will retrieve all MeSH terms containing the text word "sars", including synonyms and other entry terms. In this example, the user will easily see SARS Virus on the list, which will have additional information. Searching MeSH Scope Notes (definitions) can also be helpful, particularly if the text word is not common. Using the "SARS" example, if a user checks the radio button "Search as text words in Annotation & Scope Note."

screen shot of MeSH Browser

4.2 Navigating the MeSH Tree Structures

The MeSH Tree Structures are a hierarchical display so that broader and narrower Descriptors are displayed. For example,

    Neoplasms [C04]>
      Neoplasms by Site [C04.588]
      Abdominal Neoplasms [C04.588.033] +
      Anal Gland Neoplasms [C04.588.083]
      Bone Neoplasms [C04.588.149] +
      Breast Neoplasms [C04.588.180]
            Breast Neoplasms, Male [C04.588.180.260]
            Carcinoma, Ductal, Breast [C04.588.180.390]
            Phyllodes Tumor [C04.588.180.762]
      Digestive System Neoplasms [C04.588.274] +

A user might begin the search with Breast Neoplasms but realize after viewing the hierarchy that they really wanted the more specific Descriptor Breast Neoplasms, Male.

4.3 Pharmacological Action

A user interested in a particular drug may also be interested in the pharmacological activity of the drug. For example, a searcher interested in aspirin, might be interested in the common pharmacological actions of the drug as noted in the MeSH Browser:

MeSH Heading Aspirin
Tree Number D02.455.426.559.389.657.410.595.176
Pharm. Action Anti-Inflammatory Agents, Non-Steroidal
Pharm. Action Antipyretics
Pharm. Action Cyclooxygenase Inhibitors
Pharm. Action Fibrinolytic Agents
Pharm. Action Platelet Aggregation Inhibitors
Unique ID D001241

5. Entry Terms

Entry terms, sometimes called "See cross-references" in printed listings, are synonyms, alternate forms, and other closely related terms in a given MeSH record that are generally used interchangeably with the preferred Descriptor term* for the purposes of indexing and retrieval. This greatly increases the access points to the citations since a searcher may not know the exact preferred term for a MeSH Descriptor and there are frequently terms which mean the same thing when the article is indexed. For example, the entry terms Lung Cancer and Pulmonary Cancer are entry terms to the Descriptor Lung Neoplasms. When an entry term is used, the computer automatically substitutes the MeSH descriptor to which the entry term refers. See also Entry Vocabulary.

* The preferred term is one of possibly several equivalent terms in a MeSH Descriptor record. See Concept Structure in XML MeSH. The MeSH preferred term is tagged as [MeSH Term] in a PubMed query.

6. Using MeSH in Searching PubMed - the [mh] and other MeSH record tags

A searcher may constrain a query in the PubMed query box by using specific tags, such as [mh] and [pa]. (See PubMed Search Field Descriptions and Tags.) Both the [mh] and [pa] are used in searching for MeSH Descriptors. Searching is also enhanced by the MeSH Translation tables.

6.1 Terms in the MeSH Records

A principal method of searching PubMed is by using the terms in MeSH records. To ensure a search by a MeSH term the query uses the [mh] tag, for example:

   Asthma [mh]

This query retrieves every citation indexed with this Descriptor. It also retrieves citations indexed to Descriptors which are narrower in the MeSH Tree Structures, in this case:

         Asthma, Exercise-Induced   
         Status Asthmaticus

If a PubMed searcher wants to search only the broader subject - without the indented subjects, the search uses the tag "[mh:noexp]".

Entry terms may be used interchangeably with the preferred term in the record. For example

   Bronchial Asthma [mh]

As an entry term to Asthma, this term is equivalent to Asthma for purposes of indexing and searching in PubMed.

MeSH Qualifiers and Supplementary Concept Records (SCRs) may also be used in PubMed. A query using an SCR would be:

   Agent Orange [nm]

Notice that a distinct tag is used for SCRs. Inclusive searching ("exploding") is not available for SCRs since these records are not part of the MeSH Tree Structures.

An example of a MeSH Qualifier search would be:

   adverse effects [sh]

However, Qualifiers in MEDLINE are always used in conjunction with a Descriptor record, so a more likely search would be like:

   Adverse effects [sh] AND Anticoagulants [mh]

Note that PubMed has a "Details" feature which displays the query in the format actually used by PubMed. For example the entry term search:

   Bronchial Asthma [mh]


   "asthma" [MeSH Terms]

Note the mapping to the MeSH preferred term as well as the different tag.

For more on the three main types of records see MeSH Record Types.

6.2 The MeSH Translation Table

Additional retrieval capabilities in PubMed are provided by an internal table which includes terms not available in the MeSH database itself.

"PubMed's logic for parsing unqualified terms entered in the query box involves automatic translation tables, one of which incorporates not only MeSH but also enhancements from the Unified Medical Language System (UMLS®). . . . NLM has made UMLS mapping available through the PubMed query box with no additional steps or clicks needed by the user. For example, a user's search for "heart attack" maps as: "myocardial infarction" [MeSH Terms] OR heart attack [Text Word]." (Lou Knecht and Stuart J. Nelson. J Med Libr Assoc. 2002 October; 90(4): 475. Mapping in PubMed.

Thus the query term "heart attack" functions in PubMed like a MeSH entry term though the term itself is not part of the MeSH thesaurus. The search "heart attack [mh]" produces the query:

  "myocardial infarction" [MeSH Terms]

Another situation addressed by the Translation Table is when a term may have multiple meanings. For example:

"The MeSH term, Cold is the concept of 'an absence of warmth or heat or a temperature notably below an accustomed norm.' However, the word 'cold' is used by many people to mean the 'common cold'.

The MeSH thesaurus does not allow identical terms having the same meaning so the Translation Table maps the query for "cold" to Descriptor Cold [temperature], the Descriptor Common Cold, and the Descriptor Chronic Obstructive Lung Disease. The PubMed query is:

   "pulmonary disease, chronic obstructive"[MeSH Terms] OR
   "common cold"                           [MeSH Terms] OR
   "cold"                                  [MeSH Terms]

6.3 Search by PubMed [pa] tag (Pharmacological Action)

Some MeSH Descriptors refer to the Pharmacological Action of a given drug or substance. For example, an article about the anti-inflammatory effect of ibuprofen would be indexed with Ibuprofen and Anti-Inflammatory Agents, Non-Steroidal. Like other MeSH Descriptors, these are searchable in PubMed by the search field tag [mh]. However, a search is also available using the search tag [pa] which consists in citations indexed to MeSH Descriptor substances having that pharmacological action in the MeSH Pharmacological Action (PA) field. For example, the following PubMed search:

   Anti-Inflammatory Agents, Non-Steroidal [pa]

retrieves not only citations retrieved by the [mh]-tagged search but also retrieves citations like the following:

   PMID- 16818845
   MH  - Ibuprofen/*administration & dosage/adverse effects

This is because the Descriptor Ibuprofen has Anti-Inflammatory Agents, Non-Steroidal in the MeSH PA field:

Example from the MeSH Browser:

MeSH Heading Ibuprofen
Tree Number D02.241.223.701.430
Scope Note A nonsteroidal anti-inflammatory agent with
analgesic properties used in the therapy of
rheumatism and arthritis.
Pharm. Action Analgesics, Non-Narcotic
Pharm. Action Anti-Inflammatory Agents, Non-Steroidal
Pharm. Action Cyclooxygenase Inhibitors
Unique ID D007052

PAs are added to the record when the MeSH Section determines that the specific chemical is known to have these pharmacological effects.

Note that while a [pa] query and [mh] query may overlap, they are not the same queries and must be specifically combined (OR-ed) if both are desired.

The MeSH PA data used by PubMed are available as separate XML files. See under Files Available to Download. Note PA XML documentation. For historical background to the [pa] tag, see Pharmacologic Action Headings: PubMed®. NLM Technical Bulletin. July - August, 2003.

6.4 MeSH Treetops - "category" key word

The highest level of the MeSH Tree Structures consists of 16 broad categories, such as "Anatomy". (See the MeSH Browser, "Navigate from tree top".) These terms are not part of MeSH data as maintained and distributed, however, they can be used to search PubMed by use of the search word "category". For example, the search "anatomy category [mh]" will retrieve all citations indexed to any MeSH Descriptor in any of the A category. See Searching MeSH® Treetops. NLM Technical Bulletin. March - April, 2005.

7. PubMed searching without tags

As likely as not a PubMed searcher will not use tags in a search but will just enter the plain term. In this situation PubMed applies a number of rules to expand the search behind the scenes. NLM refers to the application of these as "Automatic Term Mapping. " For these rules see the following:

PubMed's® Automatic Term Mapping Enhanced. NLM Technical Bulletin, November-December, 2004.

How PubMed works: automatic term mapping.

PubMed's® Enhanced Translation for Entry Terms Expands to Substance Names. NLM Technical Bulletin, March-April, 2005.