Health Sciences Research Skills

Proximity Searching

You cannot perform proximity searching within PubMed. However, you can in Embase - another reason to search multiple databases. Proximity searching is searching for keywords within X number of words from each other.

In Embase,

NEAR/n requests terms that are within 'n' words of each other in either direction.

NEXT/n requests terms that are within 'n' words of each other in the order specified.

For example: (chemotherapy) NEAR/2 (related OR associated) NEXT/2 (diarrh*)

Truncation & Wildcards

In basic search design we discussed using truncation at the end of a word to find variations. In Embase you can use truncation (also refererred to as "wildcards") to find alternative spellings within words. You can also use them while phrase searching in Embase - something you cannot do in PubMed.

This can be extremely helpful when searching for words that have slight spelling variations between countries or pharmaceutical names.

For one or more letters use *

For a single letter use ?

Example:

"heart attack*" finds heart attack, heart attacks

sul*r finds sulfur and sulphur

f*cal finds fecal and faecal

sulf?nyl finds 'sulfonyl' and 'sulfinyl'

PubMed: Medical Subject Headings

In PubMed each article is manually labeled with a set of subject headings that describe the "aboutness" of the article. If you use a Medical Subject Heading (MeSH) for each concept of your search and each MeSH is assigned to a given article that article should be extremely relevant to your topic. MeSH help narrow and define your searching further.

Sometimes subject headings and keywords are the same, but often they aren't. The MeSH heading in MEDLINE for support groups is Self-Help Groups. Using only the keyword "support groups" will leave out some articles tagged with the subject heading, but using only the subject heading will leave out some articles that use the keyword. For a comprehensive search, always use both subject headings and keywords.

From the University of Toronto Gerstein Health Information Centre

Embase: Emtree Subject Headings

Like PubMed, Embase has its own subject headings called Emtree. These are similar to MeSH and are applied manually and are used for the same purpose.

To combine field codes use a comma ,

To search the title and abstract use :ti,ab

Every database uses unique field syntax to tell the search algorithm WHERE to search in an article's record. These can be powerful, when used correctly, and help narrow and make your search more precise. They often include a container element like square brackets or colons and abbreviations.

PubMed

PubMed puts search field tags in square brackets [  ].

The major syntax we learned above was for Medical Subject headings, [MeSH]. Here are a few more:

[Majr] - use this if you want your MeSH subject heading to be the major focus of the article. Either click the check box in the MeSH term record that says "restrict to major topic" or replace the [Mesh] with [Majr] at the end of your subject heading.

[tiab] - put this after a key term, either singular or a phrase in quotations, to only search for it in the title and abstract fields. This prevents PubMed from "automatic term mapping" which can artificially broaden your results and introduce irrelevant results.

Embase

Embase has similar syntax to PubMed. Instead of square brackets it uses a colon or / and an abbreviation.

Some commonly used field codes are:

 mj for major term    /mj

ab to search only in the abstract     :ab

ti to search only in the title field     :ti

Subheadings are a useful but often misused component to advanced searching in PubMed.

When you choose a MeSH term there is an option to select a subheading to go along with it. This further narrows the potential results because the results will only include that specific subset of articles.

For example, if your research questions was about (strictly) the surgical treatment or outcomes for heart attacks you would search for:

"Myocardial Infarction/surgery"[Mesh]

The word after the / is the subheading. A list of all the potential subheadings can be found below but will not be available for all MeSH because of indexing choices.

Instead of using the limits in PubMed to select only humans instead you will want to add in a "hedge" or search string. If you select the "humans" filter this will remove studies that include humans AND animals. These could still be relevant to your topic.

Use this instead: NOT (("Animals"[Mesh] NOT ("Animals"[Mesh] AND "Humans"[Mesh]))

The hedge/filter for humans in PubMed comes from the Cochrane Handbook for Systematic Reviews of Interventions http://www.cochrane-handbook.org/ Chapter 2, section 6.4.11 in Box 6.4.a.

In Embase use this: NOT ((exp animal/ or nonhuman/) NOT exp human/)

If you find an article that is exactly what you are looking for and you want to find more like it one way to do this is to use citation chaining. This is an additional way to augment searching databases and ensure higher recall of relevant research.

Backward citation chaining: look at the article's bibliography and see what they cited, odds are many are quite relevant to the topic you are researching too.

Forward citation chaining: sometimes called 'snowballing', you can use search engines to find who cited the article you like. This is a great way to find new research including conference proceedings and reports your search may have missed.

There are two main products out there that do this, Web of Science and GoogleScholar. In Web of Science type in the articles title to the search box, making sure that "all databases" is selected, and the click the "cited by" link to the right of the title on the results page.

In GoogleScholar type in the title of the article and click the "cited by" link underneath the title.

Both of these sites will generate a list of results of articles that have cited your chosen article and which, in theory, should be highly relevant to the topic you are currently searching.