Biomedical Engineering and Design
The Welch Medical Library has a YouTube Channel.
- how to use the Welch library website
- tutorials about how to search PubMed
- how to use other tools such as EndNote
- recordings from their classes
The User Guide is under the SEARCH button on the home page:
To see the icons for links to the full text: always use https://databases.library.jhu.edu/databases/proxy/JHU07224
To find that PubMed address:
- MSEL home page: Databases --> PubMed (New Interface)
- Welch library page: on the left, under "Literature Databases"
- 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
"Best Match" is 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
(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):
Here is the complete list of field tags (as of July 2022), such as [au] for author.
Use the FILTERS on the left of your results list, including
- 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 only MeSH terms will give you *fewer* results than using only text words -- this is because MEDLINE items have MeSH indexing, but they only make up about 85% of PubMed. If you use text words, you'll find *all* articles with those words in the text.
- Field Tags - The list of abbreviations for finding words in the TITLE of the article, or to search by "first author" [1AU], "pharmacological action" [PA], "place of publication" [PL], and more
- Major Topics - "Asterisks on MeSH headings and subheadings (e.g., Wound Healing/radiation effects*) means that that is a major topic of the article. Non-major (non-asterisked) headings/subheadings are usually additional topics substantively discussed within the article, terms added to qualify a major topic, or check tags. Check tags are never major topics."
- Near other words ("proximity searching") - Searches for words that are near each other, in any order, in the [Title] or [Title/Abstract] fields.
Use this format: "search terms"[field:~N]-- Search terms = Two or more words enclosed in double quotes (e.g., "chicken pox")
-- Field = The search field tag for the Title or Title/Abstract fields (i.e., [ti] or [tiab])
-- N = The maximum number of words that may appear between your search terms. For example, to search PubMed for citations where the terms "hip" and "pain" appear with no more than 2 words between them in the Title/Abstract search field: "hip pain"[Title/Abstract:~2]
-- Search results may include hip pain, hip-related pain, hip joint pain, hip/groin pain, hip biomechanics and pain, pain after total hip arthroplasty, pain in right hip, and more
- ---See the PubMed User Guide and view the proximity searching tutorial for more examples and information about proximity searching in PubMed.
- Publication Types - On the left is "article types," such as "clinical trial, Phase IV"
- Textbooks - Online, searchable biomedical textbooks
Here are two ways to export citations from PubMed to RefWorks:
1. Export many documents
2. Export one document
Exporting many documents from PubMed to RefWorks
- Search PubMed
- Check the boxes next to the citations you want to export to RefWorks
- Click "Send To" and then "Citation Manager"
4. It will show you how many citations you have selected.
Choose "Create file."
- Save the file to your computer. (The file name will have a word in it to help you identify it, but remember where you put it.)
- Now open RefWorks
- Click the "+" sign on the top left, to ADD citations
- "Import references"
- You want to Import from a file --> "select a file from your computer"
- Wait! You always want "NLM PubMed." So always click in the box to see options, and choose box for "NLM PubMed."
- Now you can either (a) click IMPORT to send your file your computer into RefWorks, OR (b) if you have more than one RefWorks folder, you can choose which folder to send them to
From PubMed to Google Scholar to RefWorks (which is how to export one citation at a time to RefWorks)
- Find an article in PubMed
- Copy its title
- Paste the title into Google Scholar, and find the correct citation
- 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.
Basically, you go to PubMed (make sure you're using the correct address) and click "Sign in to My NCBI," on the top right
- Do a search
- 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)
- 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 vs MEDLINE
What are the differences in coverage between Embase and PubMed?
(as of May 2022)
- Embase indexes more than 8,100 journals, and 2,900 are not indexed by PubMed.
- Embase is produced in Europe and has more European journal coverage than PubMed.
- "MeSH" (Medical Subject Headings) is PubMed's thesaurus, and "Emtree" is Embase's thesaurus.
MeSH has about 30,000 subject headings but Emtree has about 60,000.
- Those extra Emtree terms are mainly for drugs and medical devices; therefore Embase is much better if you are searching for a drug name, drug class, or type of medical device.
- Embase indexes routes of drug administration and medical device trade names and manufacturers, while PubMed does not.
(Thanks to library at University of Bath)
Refine your search -- Choose words to put in the article TITLE, or searching by AUTHOR, or other specific choices.
- Here is the list of all Embase field codes
Focus your search -- Use "Add field" and/or "Limit to:
Focus your search -- Use the headings given*: