1. David Abdy Academic Liaison Librarian
Searching with PubMed
David Abdy Academic Liaison Librarian

2. What’s in PubMed?
More than 27 million records representing articles in the biomedical literature and a small selection of items from the NCBI Books database.
Most PubMed records are Medline citations.
Records in different stages of processing that are destined to become Medline citations.
A small number of records are included in PubMed but not selected for Medline.

3. Understanding the vocabulary
PubMed uses a controlled vocabulary, meaning there is a specific set of terms used to describe each article in the database.
MeSH – Medical Subject Headings.
MeSH terms are arranged in a hierarchical categorised system called MeSH Tree Structures.

4. Understanding the vocabulary
This example displays part of the hierarchy that includes the term Face. Narrower terms are indented under the broader terms.
When PubMed searches a MeSH term, it will automatically include narrower terms in the search, if applicable. This is also called "automatic explosion."

5. Understanding the vocabulary
Articles have as many MeSH headings as appropriate to cover the topics of the article (generally between 5 and 15).
When there is no exact heading available, the closest general heading will be used.
Headings may also cover the group being studied (age group, gender, etc.) and the publication type (review, clinical trial, editorial, etc.)
Major subjects are marked with an asterisk.

6. Automatic Term Mapping
PubMed uses an Automatic Term Mapping feature to search for:
Subjects (using MeSH)
Journals
Authors
in that order.
As soon as PubMed finds a match, the mapping stops. That is, if a term matches a subject, PubMed does not continue to look for that term as a journal.
If no match is found, PubMed breaks apart the phrase and repeats the process until a match is found.
The phrases and individual terms are also searched in all fields (title, abstract, corporate author, etc.)

7. Automatic Term Mapping
Your Search details, accessible from the results screen, shows you how PubMed translated your search.
Click See more to view the details in a larger screen.

8. Automatic Term Mapping
When PubMed finds a match in the MeSH vocabulary, it automatically searches the more specific terms underneath that heading (if there are any) in the MeSH hierarchy. This is referred to as exploding the term. This is important to know because the Explosion is NOT shown in the Search details. For example, in this search, PubMed found a match for Glaucoma. If we look in the MeSH Database, we see that Glaucoma has several more specific terms underneath it in the MeSH hierarchy. These terms are automatically included in the PubMed search.

9. Automatic Term Mapping: Journals
If PubMed fails to find a match for a term as a subject, the Automatic Term Mapping process then searches for journals using the Journals Translation table.
The Journals Translation Table contains:
Full journal titles
MEDLINE title abbreviations
International Standard Serial Numbers (ISSN)
If you searched for the journal, Cancer Research, for example, PubMed would translate
this as "Cancer Res"[Journal] and also search the terms in [All Fields].
When searching by journal title (rather than by title abbreviation or ISSN), you must use the FULL journal title (the journal of cell biology).
What if a journal name also maps to a MeSH heading -- cell, for example? PubMed will first check in the MeSH Translation Table, find all matches (in this case, the terms cells) and stop the mapping process. The search will also include [All Fields], therefore it will find the journal name, but the results will include many more citations than from the journal, Cell.

10. Automatic Term Mapping: Authors
If PubMed fails to find a term as a subject or a journal, the term is then searched as an author or investigator. Author and investigator names exist in the format lastname initials in all PubMed records, therefore you should use this format for searching. Consider using the Advanced Search or Single Citation Matcher to find author names.

11. Automatic Term Mapping
Because of the power of Automatic Term Mapping, you can enter combinations of terms, including subjects, journals and author names, and PubMed will find matches for you. In this example, graham c maps to an author name, nutr rev maps to a journal, and obesity maps to the MeSH term, Obesity.

12. Automatic Term Mapping: No Match
There are times when PubMed is unable to match a search term with the subject, journal or author indexes. PubMed will then search the individual words in All Fields. These will then be combined. For example, pressure point is not found in any of the PubMed indexes as a phrase. Therefore, the two words are searched separately. Pressure is mapped to MeSH, but point does not match anywhere, so is just searched in All Fields. When a medical term does not map to MeSH, try to find another term to describe your topic.

13. Similar Articles
The Similar Articles link is as straightforward as it sounds. PubMed uses an algorithm to compare words from the Title and Abstract of each citation, as well as MeSH headings. The best matches for each citation are pre-calculated and stored as a set. You may see a few citations without the Similar Articles link, which simply means that these citations have not yet gone through the algorithm. This process may take several days.

14. Filters
Filters add search terms to narrow your results. Filter options appear to the left of your results. Click on a filter to apply it to your search. Active filters appear above your search results. Filters "stick" and are applied to future searches until you turn them off. Only the most popular filters display by default. Click Show additional filters to view more options. Selecting multiple filters from one category will add the filters with "OR," expanding your results. Only filters which are valid for your search results will appear. For example, if no Clinical Trials are in your results, the filter for Clinical Trials will not appear.

15. Boolean Operators
You may use the Boolean operators AND, OR and NOT in PubMed. Boolean operators must be entered in UPPERCASE. AND is the default operator used in PubMed. AND will automatically be added between your search terms in PubMed. PubMed processes Boolean connectors left-to-right. You can change the order of processing by nesting an individual concept in parentheses. The terms inside the parentheses will be processed as a unit and then incorporated into the overall strategy.

16. Search History
Your PubMed Search History is available on the Advanced Search page. This page shows your search strategies and number of items found for each search. The search statement numbers can be combined with each other or with new search terms using Boolean logic (e.g., #1 AND #2).

17. Phrase Searching and Truncation
PubMed automatically searches for phrases during Automatic Term Mapping.
Finding all terms that begin with a given string of text, is generally not a recommended search technique for PubMed.
When you are having trouble finding good MeSH vocabulary for a concept, forcing a phrase search to identify records containing a phrase, and then exploring how they are indexed can be a useful search technique. But...
Truncation bypasses Automatic Term Mapping and automatic explosion. Also, in such a large database, variations of a text string can become overwhelming and unmanageable. Especially when multiple terms are truncated, PubMed may even time out and fail in an attempt to run the search.
Do NOT use quotes (“…”) until you first try your search without them.

18. Managing Your Results
The Send to: menu can be used to send or copy PubMed records to the following locations: File: Use to save citations as a file on your computer. You can send individual, selected, or all citations to a file in any of the PubMed formats such as Abstract, Summary or MEDLINE formats. Collections: Use Collections to build collections of records, to save indefinitely. Order: Use to order a copy of the article. Citation Manager: Use to export your search results to a citation management program such as EndNote, RefWorks or Mendeley. The export will be in MEDLINE (tagged) format. Clipboard: Use the Clipboard to store records for today – to do something with before you sign out or close PubMed. Use to send results to an address. My Bibliography: Use My Bibliography if you are an NIH-funded researcher and are responsible for public access reporting. Or, use if you’d like to have a separate place to build a bibliography that contains citations from outside of PubMed.

19. Collections
Use My NCBI Collections to save PubMed citations for future use in PubMed. To save items in a Collection, you have two options: Send to Collections Step 1: From your Summary display of results, use the checkboxes to select the search result items you wish to save. If no items are checked, all (up to 1000*) items are included. Step 2: Click Send to and select Collections. Click Add to Collections. If you are not already signed into My NCBI, you will be prompted to do so. Step 3: Either choose to create a new collection or append to an existing one. Click Save.

20. Collections
Use My NCBI Collections to save PubMed citations for future use in PubMed.
To save items in a Collection, you have two options:
Select Favorite from the Abstract Display
Step 1: While viewing an abstract in PubMed, click Favorite in the right column. A collection called "Favorites" is displayed at the top. If you are signed in to My NCBI, all of your collections are listed.
Step 2: Choose the collection to which you want to add items. The star next to the collection name will turn blue when the item is added.
To remove this item from the collection, click on the collection name a second time. The star will revert to clear.

21. Saving the Search Using My NCBI First run your search in PubMed.
From the Results screen, click on the Create alert link below the search box. You will be taken to a Saved Search screen where you can select your options. (If you are not already signed into My NCBI, you will be prompted to do so.
Select how often you want updates, the format of the and the records, and the number of items you would like included in the message. The will include a link that takes you to the total update results in PubMed. alerts can be turned off if required.
Once you have made all your selections, click Save. This search will now be included on your list of Saved Searches in My NCBI.

22. Saving the Search Send to RSS
The RSS (Really Simple Syndication) function in PubMed allows you to generate an RSS feed of a PubMed search to display new results, with links back to the citations in PubMed.
To create an RSS feed and enter it into a feed reader:
Run your search.
Click Create RSS, below the search box.
Select the number of items to be sent daily to the feed reader, and rename the feed, if desired.
Click Create RSS.
Drag and drop the XML icon onto the feed reader interface. OR
Click on the orange XML icon, and copy the URL in the address box of the resulting browser window. Follow the instructions of your feed reader software .
Note that your RSS feed will only display new items. Also, if your results exceed the maximum number of items you selected, the feed will only display a link back to your results in PubMed.