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Pubmed Particulars

The MeSH Database

The newest Entrez Database is the MeSH Database. It has a new look, some new functionality, and has sparked some questions and confusion. Personally, I think it is a huge improvement over the old PubMed MeSH Browser, so this column will address some of the questions that have come up about the MeSH Database.

Since it is an Entrez database, it has some familiar features: Limits, Preview/Index, History, Clipboard, and Details. It also has Send to, Display, and Show options similar to those in PubMed (another Entrez database).

As always, the MeSH Database is designed to point users to MeSH terms including Headings, Subheadings, and Publication Types.

Users type a word or words into the search box and either click on Go or hit Enter on their keyboard. Here's where things start getting a bit confused. For example, if we look for a MeSH term for "heart attack", the results page looks like this:

The first thing many notice is the list of Suggestions that appear under the search box toward the top of the page. What the heck are these? This part of the MeSH Database has prompted more questions than any other feature to date, so here are some explanations. The Suggestions are MeSH terms or Entry terms that have been generated by an algorithm. For our purposes, it is helpful to understand that part of the algorithm involves looking for similar 3-letter groups. (For a detailed description of the algorithm, please see http://www.ncbi.nlm.nih.gov/entrez/query/static/trigram_explanation.html.) This explains why, for example, "Bird" is one of the Suggestions for "Birth Control." Doesn't seem particularly related to the idea being searched, but has been generated by the algorithm.

The Suggestions can be particularly helpful if the user has misspelled a word. They can also be helpful simply as suggestions - perhaps you didn't know that there were also these other terms available in the MeSH vocabulary. So, they have their uses.

Some of these suggested terms are Entry terms. What, exactly, does that mean? In any controlled vocabulary, a single term is designated as the preferred term for a certain concept. In PubMed, certain other (non-preferred, if you will) terms will map directly to the one preferred term. The terms that map to the preferred term are the Entry terms. Entry terms are synonyms, or near synonyms, abbreviations, alternate spellings, and other alternate forms of the MeSH term (the preferred term).

Accessing the Full Record for "Myocardial Infarction" in the MeSH Database will give you a list of the Entry terms for this MeSH Heading. They are:

If any of the Entry terms listed above are used in the MeSH Database or in the PubMed search box, they will automatically map to the appropriate MeSH term (Myocardial Infarction).

The astute among you will notice that "heart attack" is NOT an Entry Term for Myocardial Infarction. So, how did the MeSH Database know how to map this correctly? That has to do with something called UMLS: the Unified Medical Language System. But, that's another subject altogether. Suffice it to say for now that UMLS is working behind the scenes to help make the Entrez Databases as good as they are.

So, the suggestions are MeSH terms or Entry terms. Clicking on any of these hyperlinked terms will bring up the appropriate records.

And this is where additional confusion seems to be generated. For example, if "dog" is typed into the search box in the MeSH Database, one of the suggested terms is "Dogbane." Click on "Dogbane," the following screen appears:

In the search box, it says "Dogbane[MeSH]" and yet the MeSH term given is "Apocynum." What's going on here?

Entry terms. Dogbane is an Entry term. In fact, it is the only Entry term for the MeSH Heading Apocynum.

The information in the search box seems to give the impression that Dogbane is a MeSH term. I'm not sure why the designers of this database decided to have the [MeSH] designation appear in the search box when a suggested term is clicked, but they did. Don't let it throw you.

What's most important here? While the suggestions have been causing some confusion, they can be helpful at times. For the most part, however, what we are really interested in are the search results, not the suggestions.

Results in the MeSH Database are returned in relevance-ranked order. If the search term(s) exactly match a MeSH term, that MeSH term will be the first result.

Results are displayed in summary format. Clicking on any hyperlinked result will display the full record for the chosen term. The full record includes subheadings, entry terms, the MeSH tree structure, the option to restrict the search to Major Topic heading only, and the do not explode option.

The Links menu in the MeSH Database offers additional functionality. Two options are presented:

Selecting the PubMed option from the Links list will automatically do a PubMed search for that term.

Selecting the NLM MeSH Browser option will pull up the term's record from the MeSH section's browser located at http://www.nlm.nih.gov/mesh/MBrowser.html. While the two records (the MeSH Database and the NLM MeSH section's browser) contain much of the same information, the MeSH section's browser contains a bit more information and may be useful.

Using the Send to option allows users to build a PubMed search in the MeSH Database. Select a term and click on Send to: Search Box with AND. A box will appear showing the search term chosen. Additional terms may be added. Here, one search term has been chosen (hypertension) and appears in the query box while another has been searched in the MeSH Database (fish oils). The fish oils term may be added to the hypertension search by selecting it and then clicking on Send to: Search Box with AND.

While the language in the Send to option may seem a bit clumsy, it is basically allowing users to build a search using AND, OR, or NOT as the combining terms.

Send to also includes some familiar options: text, file, Clipboard. These are similar to the PubMed options.

Clipboard and History function the same way they do in PubMed. Please note, however, that the MeSH Database has its own Clipboard and History. They function the same way but they are separate. In other words, when you search MeSH terms in the MeSH Database, those terms will not show up in PubMed's History. They will show up in the MeSH Database's History.

This has been an overview of the new MeSH Database. Use it. Explore it. It's an incredibly powerful tool for PubMed searchers.

And, if you're in the mood for even more information about the MeSH Database, please see the NLM Technical Journal article: http://www.nlm.nih.gov/pubs/techbull/ma03/ma03_mesh.html

Donna Berryman, Outreach Coordinator