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_PSYC5131: Meta Analysis: Theory and Practice — Searching PubMed

Library research guide for students in PSYC 5131.

What is PubMed?

PubMed is a free database provided by the US government. It primarily consists of MEDLINE, a database of over 30 million citations from the biomedical literature.

If you've searched MEDLINE on other platforms (like EBSCO or OVID), the difference in content is that PubMed also includes PubMed Central, an archive of full-text journal articles; and the Bookshelf, an archive of books, reports, and other materials. In terms of searching, the technical syntax in PubMed is very different from what you would use in those other platforms, even though the controlled vocabulary is the same.

How Does PubMed Search?

PubMed's default search uses Automatic Term Mapping (ATM) to make an educated guess as to what you're looking for. The most important thing ATM checks for is whether there is a good match for the words or phrases in your search within PubMed's controlled vocabulary (MeSH, or Medical Subject Headings).

ATM is fine, but in a systematic search, you'll want to have more control of what PubMed is doing. That means:

  • Using the Advanced Search page
  • Identifying appropriate controlled vocabulary
  • Constructing your own complex search strings and combining them thoughtfully
  • Using search tags to tell PubMed where to search for terminology

Searching PubMed's Controlled Vocabulary: MeSH

Controlled vocabulary is the specialized language used by a database to describe the citations within it. The controlled vocabulary used in PubMed is called MeSH, or Medical Subject Headings. Below is a video about two ways to locate relevant MeSH headings and use them to further develop your concept table.

Building a Systematic Search in PubMed

This video shows how to build a search strategy in PubMed using keywords and controlled vocabulary, AND and OR, and PubMed's unique search syntax.

For Your Reference: Additional Search Tips for PubMed

PubMed is a database, which means each citation is a record made up of many different fields. Some examples of fields include title, abstract, and MeSH. Search tags allow you to tell PubMed where in the record to search. As you construct your search, you'll usually be looking in a few specific fields:

[mesh]

Searches only the MeSH field.

[mesh:noexp]

Searches only in MeSH, and explicitly excludes the narrower terms underneath your search term in the hierarchy (turns off "exploding").

[tiab]

Searches in title, abstract, and keywords (as well as collection title and other abstract).

[tiab] is the best choice, in most cases, for searching keywords from your concept table. You should also use it to search your MeSH terms as keywords, just in case!

[tw]

This searches in lots of different fields, including title, abstract, MeSH, MeSH subheadings, publication types, substance names, various author name fields, and more.

Because [tw] includes the MeSH field, it has a tendency to duplicate your MeSH search. It may also be too sensitive, returning lots of irrelevant results ("noise"). I recommend using [tiab] instead, in most circumstances. There may be cases in which [tw] is appropriate, but we can work that out together.

In research databases, searching for any ending of a word is called truncation. Frequently you can use * (asterisk) to truncate a word, but the symbol can vary among different databases. In some cases, you can use a wildcard to find alternative spellings that fall inside a word, rather than at the end.

Essential things to know about truncation in PubMed:

  • PubMed does not offer a wildcard symbol to use within a word
  • You can use the asterisk * for truncation at the end of a word: exercis*
  • You can only truncate after 4 or more letters (which means, for example, you can't type run* to find runner or running): xxxx*
  • Truncation disables ATM, which is fine, since you'll generally be avoiding using ATM in your searching
  • You can truncate a phrase, but only the last word in the phrase. To do this:
    • Use a search tag: cardiovascular exercis* [tiab] (this is what I generally recommend)
    • Use double quotes around the phrase: "cardiovascular exercis*"
    • Use a hyphen: cardiovascular-exercis*

Phrase searching works differently in PubMed than in most databases, so see the next tab in this box to learn more about it.

There are three different ways to do phrase searching in PubMed:

Option 1: (this is what I generally recommend)

Use a [search tag]: cardiovascular exercise [tiab]

PubMed first checks to see if the phrase appears in its phrase index. If it does, PubMed executes the search as requested. If it doesn’t, PubMed ignores the search tag and tries to match the words x AND y using ATM.

Option 2

Put "double quotes" around your phrase: "cardiovascular exercise"

PubMed first checks to see if the phrase appears in its phrase index. If it does, PubMed executes the search as requested. If it doesn’t, PubMed tries to match the words x AND y using ATM.

Option 3

Use a hyphen: cardiovascular-exercise

PubMed first checks the phrase index. If it isn't there, PubMed returns no results for your phrase.

Downloading Your PubMed Search History

Most databases allow you to download your search strategy. To do so in PubMed, go to the Advanced Search page and click on the Download option at the top left of the History and Search Details box.

History and Search Details box, with an arrow pointing to the Download link.

This downloads your search history as a csv file. Because Excel has a character limit for each cell, you may need to open your csv file in a text editor like Notepad to see the full text of all your search strings.

Downloading your searches allows you to easily see and document how you searched as well as to re-execute searches by copying and pasting search strings.

Using Search Hedges in PubMed

Search hedges are designed to narrow your results based on specific criteria, such as publication type. This video demonstrates how to use a search hedge, specifically the CADTH hedge which limits to systematic reviews and other evidence syntheses. You can find the full hedge to copy and paste into your PubMed search in the next box on this page.

Don't forget to acknowledge and cite any hedges you use in your searches!

Common Search Hedges & How to Find Others

Below is the CADTH search hedge to limit to systematic reviews and other evidence syntheses in PubMed. To use this, as with most search hedges, follow these steps:

  1. Do a search for the full text of the hedge in the PubMed Advanced Search query box.
  2. Use AND to combine the results of the search hedge with the search or searches that reflect the concepts in your research question.

You can copy and paste the text below to execute the first step above.

"systematic"[filter] OR "meta-analysis"[pt] OR "meta-analysis as topic"[mh] OR meta analy*[tw] OR metanaly*[tw] OR metaanaly*[tw] OR met analy*[tw] OR integrative research[tiab]  OR integrative review*[tiab] OR integrative overview*[tiab] OR research integration*[tiab] OR research overview*[tiab] OR collaborative review*[tiab] OR collaborative overview*[tiab] OR "systematic review"[pt] OR "systematic reviews as topic"[mh] OR systematic review*[tiab] OR technology assessment*[tiab] OR technology overview*[tiab] OR technology appraisal*[tiab] OR "Technology Assessment, Biomedical"[mh] OR HTA[tiab] OR HTAs[tiab] OR comparative efficacy[tiab] OR comparative effectiveness[tiab] OR outcomes research[tiab] OR indirect comparison*[tiab] OR Bayesian comparison[tiab] OR ((indirect treatment[tiab] OR mixed-treatment[tiab]) AND comparison*[tiab]) OR Embase*[tiab] OR Cinahl*[tiab] OR systematic overview*[tiab] OR methodological overview*[tiab]  OR methodologic overview*[tiab]  OR methodological review*[tiab]  OR methodologic review*[tiab] OR quantitative review*[tiab] OR  quantitative overview*[tiab] OR quantitative synthes*[tiab] OR pooled analy*[tiab] OR Cochrane[tiab] OR Medline[tiab] OR Pubmed[tiab] OR Medlars[tiab] OR handsearch*[tiab] OR hand search*[tiab] OR meta-regression*[tiab] OR metaregression*[tiab] OR data synthes*[tiab] OR data extraction[tiab] OR data abstraction*[tiab] OR mantel haenszel[tiab] OR peto[tiab] OR der-simonian[tiab] OR dersimonian[tiab] OR fixed effect*[tiab] OR multiple treatment comparison[tiab] OR mixed treatment meta-analys*[tiab] OR umbrella review*[tiab] OR ((multiple paramet*[tiab]) AND (evidence synthesis[tiab]))  OR ((multi-paramet*[tiab]) AND (evidence synthesis[tiab])) OR ((multiparameter*[tiab]) AND (evidence synthesis[tiab])) OR "Cochrane Database Syst Rev"[Journal] OR "health technology assessment winchester, england"[Journal] OR  "Evid Rep Technol Assess (Full Rep)"[Journal] OR "Evid Rep Technol Assess (Summ)"[Journal] OR "Int J Technol Assess Health Care"[Journal] OR "GMS Health Technol Assess"[Journal] OR "Health Technol Assess (Rockv)"[Journal] OR "Health Technol Assess Rep"[Journal]

Sometimes you'll notice you're getting a lot of results on animal research that are making it hard to find the relevant human research studies. Because humans are technically animals, asking PubMed to limit to human research is harder than you might expect. 

This hedge is designed to identify research on humans.

To use this hedge:

  1. Start with a set of results that represents your full search strategy, in which you've used AND to combine all your main concepts. In the image below, that results set is represented by #1.
  2. In the PubMed Advanced Search query box, combine that search set with the full text of the search hedge below. Because this hedge uses NOT, you won't need to put AND between your search and the hedge.

Full text of the hedge to use in your search:

NOT ("animals"[MeSH Terms] NOT "humans"[MeSH Terms])

PubMed query showing how to combine your search with the human research hedge

In future searches, you may need additional search hedges. This is my most-used source of hedges, although it's certainly not the only place to find them.