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 June 30, 2000 [posted]
 The Transition to New PubMed

T he transition to the new PubMed began in September 1999 when it began running in parallel with the old version. Since our article Highlights of the Beta Version of PubMed was published in the fall of 1999, a few updates are in order. Much of the information provided here may also be found in PubMed's Help and FAQs. This article attempts to bring together information about the most recent changes.


In December 1999, the National Center for Biotechnology Information (NCBI) introduced a new project known as "Books". Books is a collaboration with publishers who provide links to parts of Web versions of reference books. Citations displayed in the Abstract and Citation format may have a Books link that redisplays the same citation but with individual terms linked to a part of a book that discusses the term. You could, therefore, use this feature to obtain information about the term. For example, a student sees the term "nuclear pore complex" in an article abstract, and would like to know more about this concept. The Books feature could be used to see a list of sections from books that address this concept. The listing is in a ranked relevancy order that helps select sections to choose to link. Currently there is only one book in use for this program, but more will be added in the future. For further information please see the article New Books Feature added to New PubMed or NCBI's Overview of Books at NCBI.


As mentioned in the Technical Note New PubMed Limits Added the Limits feature in PubMed was enhanced to allow searchers to limit search retrieval to those citations with abstracts. At the same time three new values were added to the Subset pull-down menu to further limit a search to a predefined set of MEDLINE journals: Abridged Index Medicus (AIM), Dental, and Nursing.

Until recently, the check box next to "Limits" on PubMed's features bar was always present whether or not any Limits had been selected. Now the check box only appears (with a check inside) when Limits have been selected. You can still click on the checkbox, to remove the check, and run a search without Limits.

Text Button

The same Technical Note as above also mentioned the addition of a Text Button on the Search Results page. This button was added in response to some users whose text was running off the right side of pages printed from their browser. The Text Button redisplays the page with just the citation data, not the sidebar, features bar, etc. Printing from this display corrected the problem with truncated text.

All Authors added to Summary Format

Up until early 2000 only the first author was displayed with PubMed's Summary format. In February, all authors were added to the Summary format (to match the Abstract and Citation display formats). [Note: Beginning with publication dates in 2000, NLM has removed the limit on the number of authors that can appear in a citation - see MEDLINE Data Changes Expected].


In March NCBI made changes to the new version of PubMed to give users whose browsers were unable to accept cookies, similar functionality as was available with the old version of PubMed. One of these changes was to the "Select page" function that is used to click to additional pages of search results. This is no longer cookie-dependent. The other change was adding an "Order" button on the search results screen. It is now possible to select items (from the current search) to be ordered through Loansome Doc without first adding the items to the Clipboard. (NLM still encourages users who can, to use the Clipboard to collect items from multiple searches before ordering.)

Some new functions, e.g., History and Clipboard, will continue to require that the user's browser be able to accept cookies.

Clinical Alerts

Also in March PubMed added a link "Clinical Alerts" to the sidebar. This takes you to the page on the NLM site with links to the text of these alerts from NIH institutes.

Ahead of Print Citations

PubMed now accepts citations from publishers for articles that have been published electronically ahead of the printed issue. PubMed displays the rubric "[epub ahead of print]" in the part of the citation where the volume and pagination would ordinarily display.

Example: Proc Natl Acad Sci U S A. 2000 May 2 [epub ahead of print]

When the citation is replaced by one with complete data it can move into the PreMEDLINE processing stage.


In April the Index page was enhanced to include a feature called Preview. Preview shows the number of results of a search before citations are actually displayed. This will appeal to searchers who like to build a search one term at a time to see how each term affects the number of results without waiting for a page full of citations to display. The Preview/Index page displays the last three search statements (which it gets from the History feature).

The Index feature on the same page was also improved. This is the section under "Add Term(s) to Query or View Index:" You can use the pull-down menu to specify a search field for a term you enter. After that, click on a Boolean operator to add the term to your query, or use Preview to just see what the results will be. If you enter a term and Preview it or add it to the query with a Boolean operator, without selecting the term from the Index display, PubMed will utilize its Automatic Term Mapping function. If, however, you use the Index button to find a term in the index, those terms will not be mapped if searched. (The index count reflects the number of records that carry the term, although MeSH terms include the count of the term exploded.)

The other difference you will notice is that when you go to this page the Index is not open. If you enter a term and use the Index button, the Index will then open and display. Also, the bullet, "Multiple terms selected from Index will be ORed; click AND to add to search." appears on the screen only when you use the Index button.

Searches default to new system

Over time more and more users ventured over to the new system. On March 21, 2000, PubMed access went directly to the new version with the old version remaining as a link on the sidebar.

New/Noteworthy Returns

The New/Noteworthy feature in PubMed has returned. Look for this link on the blue sidebar, or try this URL:

New/Noteworthy provides:

  • brief descriptions of the latest PubMed enhancements (with links to Help for more detailed information)
  • announcements of enhancements coming to PubMed in the future

PubMed's URL

When the new version of PubMed becomes the only version the URL will remain the same If you enter the old URL,, it will automatically point to the new URL.

Important Note: Query Links

Many users have created links on other Web sites that search PubMed. They created these links (URLs) using instructions from the old version of PubMed. New PubMed has new instructions for creating query links. These instructions can be found in PubMed's Overview, Creating a Web Link to PubMed.

It is important that all new links be created using the new instructions. Links created using the old instructions will work only for the near future. Please redo these links using the new instructions at your earliest convenience.

Important Note: Bookmarks

In March all "bookmarked" URLs and links created using the old query link technique began pointing to the new version. If you have bookmarks (favorites) created on the old version that you want to keep using, please re-bookmark them in the new version. Even though they may be working now, this is temporary.

What's Next?

Hopefully the next thing we will write about will be the release of PubMed's Cubby. The Cubby will allow PubMed to offer features customized for you. The Cubby will initially provide two features:

  1. Cubby Stored Searches - Store a search on PubMed and update it any time you want.
  2. LinkOut Preferences - Specify which LinkOut providers you want displayed.

Stay tuned for more information about these features.

Why change?

Some users ask us why we change PubMed. NLM's goals have always included improving its products. As technology changes, NLM tries to utilize advancements that help in the retrieval of biomedical information. By and large, however, the changes we make to PubMed are the result of feedback and requests we receive from Pubmed users. Thanks to all of you who have helped make PubMed such a huge success.

By Annette M. Nahin and Margaret McGhee
MEDLARS Management Section

black line separating article from citation information

Nahin AM, McGhee M. The Transition to New PubMed. NLM Tech Bull. 2000 May-Jun;(314):e6.


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Last updated: 12 April 2012