PubMed Overview

NLM has been indexing the biomedical literature since 1879, to help provide health professionals access to information necessary for research, health care, and education.

MEDLINE contains journal citations and abstracts for biomedical literature from around the world.

Since 1996, free access to MEDLINE has been available to the public online via PubMed.

PubMed Overview
PubMed is a Web-based retrieval system developed by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine. It is part of NCBI's vast retrieval system, known as Entrez. -database of bibliographic information drawn primarily from the life sciences literature. -contains links to full-text -provides access and links to the integrated molecular biology and chemistry databases maintained by NCBI.
The diagram illustrates the relationships between some of the information resources in Entrez.

What's in PubMed?

Over 20 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. Other records include those in different stages of processing (including records provided directly from the journal publisher) but destined to be MEDLINE citations. A relatively small number of records that are included in PubMed but not selected for MEDLINE

What's in PubMed?
PubMed provides access to MEDLINE, the National Library of Medicine s premier bibliographic database containing citations and author abstracts from approximately 5,400 biomedical journals published in the United States and in other countries. MEDLINE currently contains over 18 million references dating back to 1946. New material is added Tuesday through Saturday. Coverage is worldwide, but most records (about 90%) are from Englishlanguage sources or have English abstracts. Approximately 83% of citations added in the last five years include a published abstract.

MEDLINE Basic Bibliographic Citation

One MEDLINE citation represents one journal article and is composed of fields that provide specific information (Title, Author, Language, etc.) about the journal article. The following information is generally provided: Title of the journal article Names of the Authors Abstract published with the article Controlled Vocabulary search terms (Medical Subject Headings) Journal Source Information First Author Affiliation Language in which the article was published Publication Type (description of the type of article, e.g., Review, Letter, etc.)

Understanding the Vocabulary

MEDLINE uses a controlled vocabulary, meaning that there is a specific set of terms used to describe each article. Familiarity with this vocabulary will make you a better PubMed searcher. The Medical Subject Headings (MeSH) MeSH is the authority list of the vocabulary terms used for subject analysis of biomedical literature at NLM. MeSH vocabulary is used for indexing journal articles for Medline and is also used for cataloging books and audiovisuals. The MeSH controlled vocabulary is a distinctive feature of MEDLINE. It imposes uniformity and consistency to the indexing of biomedical literature. MeSH terms are arranged in a hierarchical categorized manner called MeSH Tree Structures and are updated annually.

The MeSH Tree Structure

MeSH vocabulary is organized by 16 main branches:
A. Anatomy B. Organisms C. Diseases D. Chemical and Drugs E. Analytical, Diagnostic and Therapeutic F. Psychiatry and Psychology G. Biological Sciences H. Natural Sciences I. Anthropology, Education, Sociology J. Technology, Industry, Agriculture K. Humanities L. Information Science M. Named Groups N. Health Care O. Publication Characteristics P. Geographic Locations

Navigating PubMed
PubMed's home page displays: Search features: -a database selection menu, where you can choose between PubMed and other Entrez databases -a search box where you enter your terms -a link to Limits, where you can add criteria to narrow your search -a link to the Advanced Search, where you can construct a tailored search -guided searches and query tools (PubMed Tools) Assistance with PubMed: -a link to PubMed Help -links to specific sections of Help, the FAQ and PubMed Tutorials -Links to related databases (More Resources) -Customization options (My NCBI) -News

Navigating PubMed

Journals Translation Table

Full journal titles MEDLINE title abbreviations International Standard Serial Numbers (ISSN)

If you searched for the journal of cell biology, for example, PubMed would translate this as "J Cell Biol"[Journal] OR "the journal of cell biology"[All Fields].

Full Author Translation Table

Full author names for articles published from 2002 forward, and to journals that publish using the full names of authors. Full author names can be entered in natural or inverted order: Mustafizur Rahman Last Name: Rahman First name initial: M Omit periods after initials, and put all suffixes (e.g., Jr) at the end. However, for some names it is necessary to distinguish which name is the last name Mustafizur R OR Rahman M

Let's see how PubMed searches for the search query rotavirus diarrhea Bangladesh. PubMed will then combine the results (with AND) to produce a single search strategy: Stopwords PubMed also refers to a list of commonly found words that are referred to as "stopwords." Stopwords are words that, if indexed, could potentially return every document in the database if the word was used in a search statement. Consequently, commonly found words are not indexed and PubMed will ignore them. Let s try rotavirus diarrhea in Bangladesh Spell Check Feature Spell check suggests alternative spellings for search terms that include misspellings. Results from a search with the closest common word will display, or an option to link to an alternative spelling to provide users with an easy way to retrieve results for untagged words that are misspelled. Let s try rotavirus diarrhea in Bangladexh

Introduction to Boolean Logic

In the context of database searching, Boolean logic refers to the logical relationships among search terms.

The Boolean operators AND, OR, NOT can be used to combine search terms in PubMed.

Search terms football hockey soccer football OR hockey OR soccer

Results 4819 1058 2517 6090

Introduction to Boolean Logic

NOT: Retrieves a set from which citations to articles containing specified search terms following the NOT operator are eliminated. Example: arthritis NOT letter
Search terms arthritis letter arthritis NOT letter Results 167,933 617,646 159,681

AND Used to retrieve a set in which each citation contains all search terms. Example: salmonella AND hamburger

Search terms salmonella hamburger salmonella AND hamburger

Results 64810 2494 12

Related Citations
The Related Citations link is as straightforward as it sounds. PubMed uses a powerful word-weighted algorithm to compare words from the Title and Abstract of each citation, as well as the MeSH headings assigned. The best matches for each citation are pre-calculated and stored as a set. Note that the first five (most relevant) articles appear to the right of the abstract. If we click on See All, PubMed will display the full list of citations that are related to the original citation. The Related Citations display is in rank order from most to least relevant. The citation you linked from is displayed first. You can refine the Related Citations retrieval set by going to the Advanced Search page History section, then using the search statement number in combination with another concept.

Limits
Limits allow you to set commonly used parameters for your query, which may result in more relevant retrieval. Click Limits above the search box on any PubMed screen to bring up the Limits feature.

Multiple selections are allowed. Note that active Limits appear above your search results. To return to the Limits page to change your selections, click Change. To clear your Limits selections, click Remove.

Dates
Limit your search to articles Published in the Last pre-set date range, OR Specify a date range using yyyy/mm/dd format. Month and days are optional.

Note that PubMed will search both electronic and print publication dates when range searching. If using a single date, PubMed will search only the earliest publication date.

PubMed displays search results in descending date of entry order, i.e., last in, first out.

History
Your PubMed Search History is available on the Advanced Search page. The History section displays the search, the time of the search, the number of citations in your search results, and a search statement numbers menu for combining searches. History can hold a maximum of 100 search statements. Once that number is reached, PubMed will remove the oldest search to add the most current. Search History is automatically lost after 8 hours of inactivity. Use the Clear History button to remove all searches from the History. Use the Delete option from the search statement number menu to delete an individual search from History.

Review - Search Tools

Exercise 1
Use the MeSH Database to build a strategy that will find citations to references discussing the economics of community-acquired pneumonia.

Exercise 2
Use the NLM Catalog Journal search page to see if PubMed includes the journal, Molecular Microbiology. If so, retrieve all PubMed citations from this journal.

Exercise 3
Use the Clinical Queries to find systematic reviews for accidents caused by sleep deprivation.

Display Settings
To view the full display of a record in PubMed, click on the title link. Use the Display Settings menu to change the display format, the number of citations per page and the sort order of your results. To view selected citations: Click on the box found to the left of each item number of interest. Select your display settings. Title of the article: Note: Foreign language titles are translated into English and placed within brackets. Author name(s): All authors from the MEDLINE record are displayed. Corporate Author: Identifies the corporate authorship of an article. Corporate names display exactly as they appear in the journal. Note: Citations indexed pre-2000 and some citations indexed in 2000-2001 retain corporate authors at the end of the title field.

Source: Provides the journal title abbreviations, date of publication, volume, issue, and page numbers of the article. A mouseover of the journal title abbreviation displays the full journal title. Additional notations: Original language (if other than English); Publication Type (if the article is a review or retracted publication); and the notation "No abstract available . Tags: [PubMed - as supplied by publisher], [PubMed - in process], [PubMed - indexed for MEDLINE], or [PubMed] tags. Identification number: A PubMed Unique Identifier (PMID) is included on each record. Related Citations: Free full text: The availability of free full text is indicated.

Saving Articles
Send to:
- can be used to send or copy PubMed records to a file, to the Clipboard, to Collections, to E-Mail, to order, or to My Bibliography.

Collections
Use My NCBI Collections to save PubMed citations for future use in PubMed. Create a Collection Step 1: Select the search result items you wish to save. This can be done from a results screen or from the Clipboard. Note: If no items are checked, all (up to 5000*) 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: Choose to create a new collection. Rename your collection. Click Save.

My Bibliography
My Bibliography is a special kind of collection designed to make it easier for authors to search and collect citations for their publications. To create your bibliography: 1. Go to the My Saved Data section of My NCBI and click on the link to My Bibliography. 2. On the My Bibliography page, select the article (s) to create or add items to a bibliography. You can choose to add journal article citations from citations in PubMed or manually, and add other citations manually. For this example, we will choose to add citations from PubMed. Click Continue. 3. Create a search for your citations. Hit the Enter key on your keyboard to run the search. 4. Select your citations using the Add buttons to the left. 5. When finished selecting your citations from all pages of results, Click Done at the bottom of the page. You can add items to the bibliography by selecting My Bibliography from the Send to... menu or returning to Saved Data > My Bibliography

Exercise 1 -- Basic
Find citations to articles about the ethics of liver transplantation. Check Details to see how the terms are mapped. Filter to review articles. Select a few items and add them to the Clipboard. Go to the Clipboard and view the selected items in Abstract format to see the assigned MeSH terms.

Exercise 2 Advanced
Part A In one search, find references about the relationships between circadian rhythms and either cortisol or melatonin in humans.

Part B Find references about heart surgery. Notice how the term is mapped using the Search Details box on your results screen. Using History on the Advanced Search screen, combine this search with the previous search to find references about heart surgery, circadian rhythms and cortisol or melatonin in humans.

Exercise 3 - MeSH Database

Use the MeSH Database to build a strategy that will find citations to articles about schizophrenia resulting from prenatal exposure to influenza. Schizophrenia and influenza should be the major topics of the articles.

Exercise 4 -- Finding Specific Citations

This exercise is in three parts. Use the search box, the Single Citation Matcher or Advanced Search and the information below to find the citations. Part A: I think the article was published in 2000 in the New England Journal of Medicine. It is about using a hip protector to prevent hip fractures. Part B: Find citations to references where A. M. Adelman is the first author. Part C: I want to see all of the citations from Volume 5, issue 4 of PLoS Pathogens.

END OF PUBMED