Biomedical Engineering and Design

Information specific to BME and BME/CBID design teams.

PUBMED

For links to the full text:  Always use  https://databases.library.jhu.edu/databases/database/JHU07224
 
To find that PubMed address:
  • MSEL home page:  Articles and Databases --> DATABASES --> PubMed (New Interface)
  • Welch library page: on the left, under "Key Resources," go to "Literature Databases"

New PubMed is now the default. (More information here.)

Searching  

  • To search, you can use the single box on the main page, or the Advanced search screen
  • You can go back and forth between those pages, because each of your searches is being saved on the Advanced screen

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BE AWARE:

"Best Match" is now the default -- it will give you ONLY a few highly relevant articles.
("'Best Match' is not designed for comprehensive or systematic searches.")

  • If you want to see a broader range of articles about a topic, change the sort to something else (as shown below)

Filters -- Your filters may still be ON from the last time you used PubMed, so make sure to check every time

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The "User Guide" is under the SEARCH button on the home page:

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(NOTE: TOXNET was retired in November 2019. Here is the list of databases where that content can now be found.)

You've gotten too many results -- how do you narrow your search?

Put some of your search words or phrases into the TITLE of the article, by adding   [ti]   after the word or phrase (or by choosing TITLE on the advanced search screen):

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Here is the complete list of "field" abbreviations, such as [ab] for abstract.
Here is the HELP page for NEW PubMed.

ALSO:  Use the FILTERS on the left of your results list, including

  • date
  • associated data
  • article types [such as "clinical trial" and "review"]
  • all of the others, such as "species" and "language" -- click "Additional filters

 

You only got a few results -- how do you broaden your search to get more?

Brainstorm similar words for one concept, and put them in parentheses connected by OR:

You can also remove some of the words from your search, or remove them from the TITLE to being just anywhere, or removing some of your filters.

Here are some very useful pages for HELP and other things:

  • Latest treatments for a disease or disorder -- This 2-minute interactive video shows how to use Clinical Queries. (When the talking stops, click the arrow to go to the next slide.)
     
  • Use the Thesaurus (called MeSH, for Medical Subject Headings) -- This will give you specific terms for your topic, so you may find some articles that you might have missed otherwise; e.g., Developing Countries, Neglected Diseases, Cost of Illness
    -- You can also use MeSH to add subheadings, such as "instrumentation," "mortality," "prevention and control," and "therapy"
    -- NOTE: Using MeSH terms will give you *fewer* results than using just text words -- this is because MEDLINE items have MeSH indexing, but they only make up about 85% of PubMed, but if you use text words, you'll find *all* articles with those text words.
    Using subheadings will narrow your search even further, even though they can be helpful.
     
  • Field Tags - How to put your search words in the TITLE of the article, or to search by "first author" [1AU], "pharmacological action" [PA}, "place of publication" [PL], and more
     
  • Publication Types - On the left is "article types," such as "clinical trial, Phase IV." Here are the definitions.
     
  • Textbooks - Online, searchable biomedical textbooks

Here are two ways to export citations from PubMed to RefWorks.

From PubMed to RefWorks (which allows you to export many documents at once)
  1. Search PubMed
  2. Check the boxes next to the citations you want to export to RefWorks


     
  3. It will show how many citations you have selected.
    Choose "Create file."


     
  4. Then save the file to your computer. (The file name will have a word in it to help you identify it.)


     
  5. Now open RefWorks
  6. Click the "+" sign on the top left, to ADD citations


     
  7. "Import references"


     
  8. You want to "select a file from your computer"


     
  9. Wait! No, you do not want the format shown below ("RefWorks Tagged Format").
    You want "NLM PubMed." So choose "search for the format."


     
  10. Click in the box to see the available formats, choose "NLM PubMed," then "Import"


     
  11. Now you can either
    (a) click IMPORT to send your citations from your computer into RefWorks, OR,
    (b) if you have more than one RefWorks folder, you can choose which folder to send them to

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From PubMed to Google Scholar to RefWorks (which is how to export one citation at a time to RefWorks)
  1. Find an article in PubMed
  2. Copy its title
  3. Paste the title into Google Scholar, and find the correct citation
  4. Under the article, click the quotation marks

5. Click "RefWorks" (which is at the bottom)

OR, just configure Scholar so that it ALWAYS sends your citations to RefWorks:  go to the menu (the 3 lines) at the top left of Scholar, choose Settings, scroll down to this, and choose RefWorks

Once you build a search that you like, you can save it and run it again whenever you wish.

Here are the steps for how to do that.

Basically, you go to PubMed (make sure you're using the correct address) and click "Sign in to My NCBI," on the top right

  1. Do a search
  2. Click on "Create Alert" (on top, underneath the search box), and fill in your preferences (this is where you can schedule automatic searches and ask for notifications of the results)
  3. You can "manage" your saved searches with the link on the bottom right

MeSH (Medical Subject Headings) is PubMed's excellent thesaurus. (Here is a fact sheet.)

 

MeSH headings will:
  • list all of the articles about a topic, even when your search words are not used in the title or abstract (including alternate spellings such as "paediatric" and "orthopaedic")
     
  • list all of the subcategories of your concept so that you can focus your search, such as those for "cardiovascular" (e.g., Cardiovascular System; Cardiovascular Infections; Cardiovascular Surgical Procedures; Models, Cardiovascular)
     
  • catch all of the articles whose concepts have synonyms (e.g., if you put in "undernutrition," you will still get the right MeSH heading, which is "malnutrition")
     
  • tell you what kind of entity your concept is -- scroll to the bottom to see the "tree" structure that shows you the concepts that are both broader and narrower than yours

MeSH gives definitions, which you should cite if you use them.

This APA page provides the following example for citing a word from a dictionary, which is close enough to use for citing MeSH:

  • "Heuristic. (n.d.). In Merriam-Webster’s online dictionary (11th ed.). Retrieved from http://www.m-w.com/dictionary/heuristic"

Following this example, a citation to a MeSH term would look like this:

  • Prosthesis and Implants. (n.d.) In MeSH (Medical Subject Headings; National Center for Biotechnology Information). Retrieved from https://www.ncbi.nlm.nih.gov/mesh/68019736

EMBASE

EMBASE is the world's other great database for biomedical topics. It includes articles, conference papers, and post-market surveillance reports, among other things.
  • It has greater coverage in some areas than PubMed, especially in the areas of pharmacology and toxicology
  • It has some specialized search features for medical devices, including "manufacturers," "comparisons," "economics,"

EMBASE also has content that PubMed does not have, so always search *both* databases.

Saving Searches -- To save your searches, you must register for a free username and password.

  • During the registration process, you will be asked to enter an "institutional key," which is Johns Hopkins University
In BASIC search, focus your search results by putting words in the TITLE, by adding a colon and "ti" :


Using ADVANCED SEARCH will be a big help for focusing your search.
  • Click on "Search" on the right above the blue line at the top of the page, and pull down "Advanced Search":

Now you can do a comprehensive search with the limits that you want:

  • date -- the years during which articles were published
  • sources -- either EMBASE or MEDLINE (the *published* articles from PubMed, not those in press)
  • fields -- author, title, etc.; e.g., for articles with your search words in the article *Title*, add  :ti  to your search
  • quick limits -- limits such as "humans," "only in English" and a few others
  • EBM -- "evidence-based medicine"; choose "Cochrane review," "systematic review," "controlled clinical trial," "randomized trial," and/or "meta-analysis"
  • pub types -- for example, review articles, editorials, and a few more choices
  • languages -- choose from among lots of languages
  • gender -- male, female, or articles about both men and women
  • age -- choose from among given age ranges
  • animal -- "animal cell," "animal experiment," "animal model," and/or "animal tissue"

Your searches can also use:

  • AND -- Every article must include *all* search words (e.g., dog AND cat)
  • OR -- Articles must include at least one of the search words (dog OR cat OR bird). The articles do not need to have all of these words in them. 
  • NOT -- You do not want articles with that search word(s) in it (e.g., dog NOT cat)
  • NEAR/n – The words must be within some number of words of another word (e.g., e: symptom NEAR/5 headache gets articles with the word "symptom" within 1, 2, 3, or 4 words near "headache," no matter which comes first)
  • NEXT/n – Same thing as above, except the order *does* matter (e.g., symptom NEXT/5 headache will get articles with the word "symptom" *before* the word "headache," with 1, 2, 3, or 4 words between them)

There are two ways to focus on finding device information:

  1. Do an advanced search and then use the left column to choose *Device,* and narrow it down from there
    -- OR --
  2. Start with a "Device" search:

Device Fields includes

  • device manufacturers
  • device trade names

Device Subheadings includes

  • adverse device effect
  • device comparison
  • device economics
  • clinical trial

 

There are two ways to focus on finding drug information:

  1. SEARCH (word in the middle of the top of the page) --> Choose Advanced (word under the second blue line at the top of the page), then use the left column to choose *Drugs,* and narrow it down from there
  2. SEARCH --> Drug (word under second blue line at the top of the page)

Drug Fields includes

  • drug manufacturers
  • drug trade names

Drug Subheadings has 17 choices, including

  • adverse drug effect
  • drug analysis
  • drug dose
  • pharmacokinetics

Routes has many choices, including

  • buccal
  • inhalational
  • intramuscular
  • intravenous
  • intraspinal
  • oral
  • sublingual