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Searching PubMed

What is PubMed? PubMed is an interface for searching MEDLINE, the National Library of Medicine’s (NLM) premier bibliographic database.

Getting Started

  1. Go to the Library home page at: http://library.nymc.edu.
  2. Click on the “Login” link and login using your Library barcode and password
  3. Select: "Databases"
  4. Select:"PubMed MEDLINE," from the alphabetical list of databases.
Note: PubMed is made freely available by the NLM, but you must come in via the library web site to take advantage of full-text "LinkOut" to journals.

Searching PubMed - The Basics

To perform a basic search:

  1. Type your keywords into the search box.
  2. Press <ENTER>, or click the GO button to execute your search.
Basic tips:
  • The Boolean operators – AND, OR, NOT -- are useful in structuring your search. PubMed defaults to the AND operator.
  • You can force the database to search for a phrase by putting double quotes around your terms. However, if your search phrase is not on the list of PubMed's indexed phrases, then the quotes are ignored and the phrase is processed using automatic term mapping.
  • After running your search it is useful to click on the DETAILS button to see how PubMed interpreted your search.

Displaying Results
Results will display in the brief Summary Format in reverse chronological order, 20 items per screen.

Printing, Downloading, and Emailing Records
To print, either hit Ctrl-P, click the print icon, or select Print from the File menu on your browser toolbar. All displayed records will print.

To download records to a file, choose File from the drop down box next to the "Send to" button. Then give your file a name with an .html or .fcgi extension.

To email records, choose E-mail from the drop down box next to the "Send to" button. Then fill in the form, specify an email address, and push the "Mail" button.

Searching - Advanced Features

Limits
The Limits feature narrows your search to specified criteria (publication year, publication type, language, age, database subset, etc). To apply a limit, do the following:

  1. After executing a search, click on the word LIMITS under the search box.
  2. Decide and select the limits you wish to apply..
  3. Once all desired limits have been chosen, press <ENTER> or click the GO button to re-execute the search. A checkmark will appear beside the Limits option to remind you that limits are in effect for your search.

See also, Limiting your results to NYMC-owned journals.

Field Searching
The default in PubMed is to search for your term(s) in all fields of a database record -- title, author, abstract, MeSH, etc. This strategy is sometimes called keyword, or free-text searching. It is possible to perform a more specific search in PubMed, by telling the database where to search for term(s) on the record of an article. The database will insert the appropriate field symbol directly into your search for you if you use the Index Feature. Field Abbreviations can also be included in a search by typing them in square brackets [ ] immediately after the term(s) to which they apply as follows:

SELECTED SEARCH FIELDS
Abbreviation:
Searches the:
Explanation/example:
[ti]
Title field warfarin[ti]
[au]
Author field smith ak[au]
[dp]
Date of publication 2003[dp], 1999:2003[dp], 2003/02[dp]
[pt]
Publication Type review[pt], clinical trial[pt]
[la]
Language eng[la]
[ab]
 Abstract diabetes[ab]
[mesh]
 MeSH fluoxetine[mesh]
[majr]
 "Major" MeSH kidney failure[majr]
[jour]
Journal Title (or abbrev) new england journal of medicine[jour], n engl j med[jour]
[ad]
Author affiliation new york medical college[ad]
[sb]
 Subset systematic[sb]

Search Example: ascorbic acid [majr] AND common cold [majr] AND eng [la] AND review [pt]

MeSH Database
The MeSH Database is the thesaurus of subject headings that make up the controlled vocabulary used to index articles in MEDLINE/PubMed. (For more information, see the MeSH tip sheet). To use the MeSH Database:

  1. Select MeSH Database from the blue left-hand side bar.
  2. Type a term into the query box. Select the best heading(s) from the list presented by clicking on the box next to the heading and either:
    1. send to search by clicking on the "Send to" button or
    2. expand a heading by clicking on the heading name and:
      • Click on the box next to the MeSH heading
      • Decide which subheadings, if any, you would like to use and select by clicking on the boxes.
      • Decide whether you would like this MeSH term to be the major focus of your search and if so click to Restrict...
      • Decide whether you would like to also search the more specific terms which come under this term in the MeSH hierarchy. If you would not, click, "Do not explode this term."
  3. Click "Send to" button to send the term to the MeSH Database search box.
  4. Then either repeat the above process to add more MeSH terms or click on "Search PubMed" to execute the search.

Index Feature
The Index allows you to view a list of terms within a search field, select a term(s) to add to your search directly from the list, and provides you with information about the number of records in which your term(s) occurs. This tool is not an online thesaurus. You should use the MeSH Database to determine an appropriate subject heading for use in your search.

To browse an index:

  1. Click on "Preview/Index" from the menu bar under the search box.
  2. Select the search field you wish to browse by using the pull-down menu.
  3. Key your search term into the query box, click on the INDEX button. A box will appear listing the term you entered (if found), and the number of articles in which the term appears.
  4. Select your term by clicking on it. You can select multiple terms by holding down the <CTRL> key on your keyboard and then clicking on each term you wish to include.
  5. Click on the appropriate Boolean operator -- AND, OR, or NOT -- to add the term(s) to your search.
  6. Click on GO next to the search box at the top of the screen to execute the search.

Single Citation Matcher
When you know some combination of specific information about what you are looking for, e.g. you know the author and the journal name, or the journal and the first page of the article, or some article title words and the year, etc.

  1. Select Single Citation Matcher on the blue left hand bar under PubMed Services.
  2. Enter the values you know into the correct fields.
  3. Click on Search.

Journals Database
This is useful when you need to know if a particular journal is indexed in PubMed, to find out its ISSN number or title abbreviation, and to execute a search on that title in PubMed.

  1. Click on Journals Database on the blue left hand side bar.
  2. Type in the title of the journal (or part of the title) and click "Go". You will be presented with a list of journals with their ISSNs, Index Medicus abbreviations, and NLM IDs.
  3. If you wish to execute a PubMed search a particular title, you need to use the "Links" link to the far right of that title -- from the dropdown menu, click on PubMed.
  4. Clicking on the journal title will give more information.
  5. Clicking on the NLM ID will search for that title in the NLM's Locator catalog.

History
Each time you perform a search, the database stores it as part of your search history. The history feature allows to review searches previously executed, and to combine them to perform new searches. Your search history will be lost after eight hours of inactivity on the database.

  1. To review your search history, click on "History" in the list of options under the search box at the top of the page.
  2. To combine previously executed searches, either:
    • Combine them in the search box using the appropriate Boolean operators. You must use the # before each search set number. Example. #2 AND (#3 OR #4) or
    • Click on the search number, indicate the Boolean operator you would like to use to combine the search sets, and click on the next search number, etc.

Clipboard
As you review the results of your search it is possible to put aside citations for future review, printing, or downloading. Selected items will be stored on your "Clipboard". A maximum of 500 records can be stored on the clipboard, for up to eight hours of inactivity.

Limiting your results to NYMC-owned journals using My NCBI

Note: The link from the Databases page currently uses shared My NCBI settings, so individuals should not have to do this individually, unless you wish to also set up alerts and other personalized settings via My NCBI.

To limit your search results to NYMC-owned journals, simply click on the "nymclib" tab at the top of your results.

If you set up a personalized “My NCBI” service you will need to set up the filter for the "nymclib" tab yourself:

1) Go into PubMed
2) In the upper right corner of the screen, either log in using your old cubby password or register and log in to cubby
3) On the blue sidebar, click on “My NCBI”
4) Then on the blue left sidebar, click on “Filters”
5) Choose PubMed as the database you wish to configure by clicking on it from the list
6) Click on the resulting “Browse” tab
7) Click on “Libraries” under LinkOut
8) Scroll down to “New York Medical College Library” and click on it
9) Check “Add a result tab for all items that match this filter ”

Now when you are in “My NCBI”, am “nymclib” tab will appear which will limit results to NYMC holdings. NOTE: after logging in you will need to click on “My NCBI” on the left sidebar to see this tab.

See also the following tipsheets:
PubMed LinkOut for information on accessing full-text journal articles via PubMed
Medical Subject Headings (MeSH)

The Reference and Information Services department offers classes (register online) and one-on-one consultations on searching PubMed and using the other resources of the Health Sciences Library. To schedule one-on-one consultations, please call 914-594-4210.

Updated M.Ascher 10/10/07

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