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Cognitive Science 1: Searching PubMed

Accessing PubMed

URL of this guide: guides.lib.berkeley.edu/pubmed.

Use this UC Berkeley PubMed URL (not "pubmed.gov"); this link will appear on all Library web pages and it facilitates access to online articles from licensed/subscribed journals via UC-eLinks  UC-eLinks icon or Get it at UC Get it at UC icon

This PubMed exercise set (docx) will help get you started using PubMed's search features, including filters, field tags, MeSH, and more.

The PubMed FAQ and User Guide is your best bet for up-to-date PubMed help.

  PubMed home page image

Search Tips

Looking for a known article?
In the Search box, simply type the article title, or a combination of article title words with author and/or journal name words, and click Search. PubMed's citation sensor will automatically analyze your query for citation information to return the correct citation. More information in the PubMed User Guide.

Subject Searching:
For most literature reviews, it may be best to search narrowly: think of your topic in specific concepts: Who is your population? Are you looking at a specific outcome or intervention? Are you interested in a specific geography? Do you only want studies that used a particular method? Build your search using the concepts that describe what you want, then broaden or narrow the search as needed. Consult our Searching the Public Health Literature More Effectively Guide for more literature searching tips.

Search specific fields (author name or affiliation, word in title and/or abstract, journal name, etc.):
Two methods: Field Tags or Advanced Search

Field tags exist for every field in a PubMed record. For example, type cell[ta] to search for articles in the journal Cell. Affiliation (tag is [ad]) can include any field in an author's address. Type cell[ta] AND (berkeley[ad] OR 94720[ad]) to find articles in Cell by Berkeley authors. A complete list of field tags (there are several dozen) is in the PubMed User Guide.

Click Advanced under the search box to be taken to PubMed's Advanced Search page where you can use a drop-down menu to specify fields to be searched. Click Add to add the term to the search box. You may then use the drop-down menu to add another field to be searched; click AND (or change to OR or NOT), to add it to the Query box:

More information in the PubMed User Guide

Search History

Click Advanced (under the Search box) and scroll down to see your search history.
Click > in the Details column to see how PubMed translated your query. Click the number in the Results column to go back to the search results for that search. You can build new searches or revise past searches here; details in the PubMed User Guide. It is highly recommended that you download your search history by clicking the Download button. This will help you keep track of what and when you searched; this is especially important when doing a systematic review.

Exporting Citation to Reference Management Software

EndNote:
Open your EndNote library. Select the PubMed citations to export by clicking in the checkbox to the left of each. Click Send to (just under the search box) and choose Citation manager, then click Create file. The first time you do this, make sure EndNote or Research Soft Direct Export is selected as the Open with program; navigate to the EndNote program on your computer if necessary. Click OK.

RefWorks:
Note: Currently, RefWorks Save to RefWorks bookmarklet does not work with the New PubMed.
In PubMed, select the citations to export by clicking in the checkbox to the left of each. Click Save, and make sure Selection (number) is what you see on that drop-down menu. Choose PubMed in the Format menu, and then Create file. Save the file to somewhere you will remember. In RefWorks, select Add > Import references. Select a file from your computer or drag and drop it onto the import page, then click Import. You can select which folder to import into.

Zotero:
Note: Currently the Zotero Connector does not always work with the New PubMed.
In PubMed, select the citations to export by clicking in the checkbox to the left of each. Click Save, and make sure Selection (number) is what you see on that drop-down menu. Choose PubMed in the Format menu, and then Create file. Save the file to somewhere you will remember. In Zotero, click File > Import... > A File, and navigate to the file you saved. Select it and click Open.

Mendeley:
In PubMed, select the citations to export by clicking in the checkbox to the left of each. Click Save, and make sure Selection (number) is what you see on that drop-down menu. Choose PubMed in the Format menu, and then Create file. Save the file to somewhere you will remember. In Mendeley, select the folder you want to import into, and click Add Files. Select the search results file.

Others:
Most citation managers will let you import a text file in RIS format. In the New PubMed, the PubMed format is comparable to RIS format. Save citations in PubMed format, then import into your citation manager.

More information in the PubMed User Guide.

Using Search Filters

After running a search, use the filters on the left side to limit your search results. Click Additional filters to add filtering options such as article type, language and age groups. Note that selected filters will "stick" for future searches until you de-select them. More information is in the PubMed User Guide.

Important note: Using filters will have the effect of limiting your search results to include only citations with MeSH terms applied; see below on what will be excluded by limiting your search to only include citations with MeSH terms.

Using MeSH (Medical Subject Headings)

Why MeSH?
Using Medical Subject Headings, or MeSH, may help you retrieve more relevant search results. MeSH are the subject terms applied to nearly all PubMed citations. However, it is important to remember that some PubMed citations - including the very newest citations - do not have MeSH terms applied to them, and therefore will not appear in a search that exclusively uses MeSH terms.

Three ways to search using MeSH:

  • Use the MeSH terms from a known, relevant article: Search for a known article, click to open the full record, then scroll down to see the MeSH terms applied to that article. Clicking on a MeSH term will allow you to either search PubMed using only that term, or add that term to the search box; you can then add additional terms and execute your search.
  • Use the MeSH Database to find terms, then build a search using those terms: Step-by step instructions may be found in the PubMed User Guide.
  • Use Advanced Search to search using known MeSH terms: If you know the MeSH terms you want for your search, click Advanced under the Search box, then use the drop-down menu in Advanced Search. Instructions in the PubMed User Guide.

To see suggested MeSH terms based on a block of submitted text (ie, an abstract or article, etc.), use the MeSH on Demand tool. MeSH on Demand also lists similar PubMed articles relevant to your submitted text, thus MeSH on Demand can help you find articles similar to a known, relevant article.

MeSH Subheadings (or "Qualifiers") help focus your search results more precisely.
In the MeSH Database, select desired subheadings, then click Add to search builder, then click Search PubMed:

Help & Tutorials

The PubMed User Guide is updated frequently. It includes FAQs on most common search issues, as well as search tips and more. Examples:

PubMed's Online Training website includes numerous tutorials, guides, and handouts.

Alternative PubMed Search Interfaces

The Medline subset of PubMed, which consists of articles assigned MeSH terms, and comprises the overwhelming majority of PubMed citations, is available for searching in both Ovid Medline and in Embase.

PubMed PubReMiner lets you enter a search, and the results will list terms in a frequency order: you will see lists of MeSH terms, title words, abstract words, authors, journals, etc., in the frequency order each of these appears in your search result. This can help you come up with additional terms to include in your search, as well as top publishing authors and journals on your topic.

Use PubMed by Year to see a graph the number and rate per 100,000 citations of your search terms, and to compare to the frequency of various terms over time. PubMed by Year searches from the oldest citations in PubMed (1781) to the current year.  Data downloadable to csv or svg.

My NCBI: Customizing PubMed & More

My NCBI allows you to save searches and citations, customize PubMed, and more.
Click Log in (top right); you will be presented with several options; unless you already use an eRA or NIH logon, we strongly suggest you select more login options, then start typing berkeley and choose UC Berkeley. You can then log in using CalNet. Once logged in, click your user name (top right) then select Dashboard (My NCBI). Here will be your:

  • Saved Searches (which you can have re-run as an "alert" on a schedule);
  • Collections (citations you have saved, which you can share if desired);
  • Custom filters you have created;

and more. Detailed instructions may be found in My NCBI Help. If you already are a NCBI user, please note: Important Changes to NCBI Accounts Coming in 2021.