PubMed

Content

In addition to MEDLINE, PubMed provides access to:

• older references from the print version of Index Medicus, back to 1951 and earlier
• references to some journals before they were indexed in Index Medicus and MEDLINE, for instance Science, BMJ, and Annals of Surgery
• very recent entries to records for an article before it is indexed with Medical Subject Headings (MeSH) and added to MEDLINE
• a collection of books available full-text and other subsets of NLM records
• PMC citations
• NCBI Bookshelf

Many PubMed records contain links to full text articles, some of which are freely available, often in PubMed Central and local mirrors, such as Europe PubMed Central.

Information about the journals indexed in MEDLINE, and available through PubMed, is found in the NLM Catalog.

, PubMed has more than 35 million citations and abstracts dating back to 1966, selectively to the year 1865, and very selectively to 1809. , 24.6 million of PubMed's records are listed with their abstracts, and 26.8 million records have links to full-text versions (of which 10.9 million articles are available, full-text for free). Over the last 10 years (ending 31 December 2019), an average of nearly one million new records were added each year.

In 2016, NLM changed the indexing system so that publishers are able to directly correct typos and errors in PubMed indexed articles.

PubMed has been reported to include some articles published in predatory journals. MEDLINE and PubMed policies for the selection of journals for database inclusion are slightly different. Weaknesses in the criteria and procedures for indexing journals in PubMed Central may allow publications from predatory journals to leak into PubMed.

On March 4, 2025, there was a temporary global outage of the PubMed database. The outage lasted about a day and ‘stoked fears about the database’s future’ because researchers worldwide depend on PubMed to access peer-reviewed scientific literature. The disruption was apparently not deliberate, and services were restored, but the event highlighted concerns about the reliability and contingency planning for essential research infrastructure

Characteristics

Website design

A new PubMed interface was launched in October 2009 and encouraged the use of such quick, Google-like search formulations; they have also been described as 'telegram' searches. By default the results are sorted by Most Recent, but this can be changed to Best Match, Publication Date, First Author, Last Author, Journal, or Title.

The PubMed website design and domain was updated in January 2020 and became default on 15 May 2020, with the updated and new features. There was a critical reaction from many researchers who frequently use the site.

PubMed for handhelds/mobiles

PubMed/MEDLINE can be accessed via handheld devices, using for instance the "PICO" option (for focused clinical questions) created by the NLM. A "PubMed Mobile" option, providing access to a mobile friendly, simplified PubMed version, is also available.

Search

Standard search

Simple searches on PubMed can be carried out by entering key aspects of a subject into PubMed's search window.

PubMed translates this initial search formulation and automatically adds field names, relevant MeSH (Medical Subject Headings) terms, synonyms, Boolean operators, and 'nests' the resulting terms appropriately, enhancing the search formulation significantly, in particular by routinely combining (using the OR operator) textwords and MeSH terms.

Comprehensive search

For optimal searches in PubMed, it is necessary to understand its core component, MEDLINE, and especially of the MeSH (Medical Subject Headings) controlled vocabulary used to index MEDLINE articles. They may also require complex search strategies, use of field names (tags), proper use of limits and other features; reference librarians and search specialists offer search services.

The search into PubMed's search window is only recommended for the search of unequivocal topics or new interventions that do not yet have a MeSH heading created, as well as for the search for commercial brands of medicines and proper nouns. It is also useful when there is no suitable heading or the descriptor represents a partial aspect. The search using the thesaurus MeSH is more accurate and will give fewer irrelevant results. In addition, it saves the disadvantage of the free text search in which the spelling, singular/plural or abbreviated differences have to be taken into consideration. On the other side, articles more recently incorporated into the database to which descriptors have not yet been assigned will not be found. Therefore, to guarantee an exhaustive search, a combination of controlled language headings and free text terms must be used.

Journal article parameters

When a journal article is indexed, numerous article parameters are extracted and stored as structured information. Such parameters are: Article Type (MeSH terms, e.g., "Clinical Trial"), Secondary identifiers, (MeSH terms), Language, Country of the Journal or publication history (e-publication date, print journal publication date).

Publication Type: Clinical queries/systematic reviews

Publication type parameter allows searching by the type of publication, including reports of various kinds of clinical research.

Secondary ID

Since July 2005, the MEDLINE article indexing process extracts identifiers from the article abstract and puts those in a field called Secondary Identifier (SI). The secondary identifier field is to store accession numbers to various databases of molecular sequence data, gene expression or chemical compounds and clinical trial IDs. For clinical trials, PubMed extracts trial IDs for the two largest trial registries: ClinicalTrials.gov (NCT identifier) and the International Standard Randomized Controlled Trial Number Register (IRCTN identifier).

Alternative interfaces

The National Library of Medicine leases the MEDLINE information to a number of private vendors such as Embase, Ovid, Dialog, EBSCO, Knowledge Finder and many other commercial, non-commercial, and academic providers. , more than 500 licenses had been issued, more than 200 of them to providers outside the United States. As licenses to use MEDLINE data are available for free, the NLM in effect provides a free testing ground for a wide range of alternative interfaces and 3rd party additions to PubMed, one of a very few large, professionally curated databases which offers this option.

Lu identifies a sample of 28 current and free Web-based PubMed versions, requiring no installation or registration, which are grouped into four categories:

1. Ranking search results, for instance: eTBLAST; MedlineRanker; MiSearch;
2. Clustering results by topics, authors, journals etc., for instance: Anne O'Tate; ClusterMed;
3. Enhancing semantics and visualization, for instance: EBIMed; MedEvi.
4. Improved search interface and retrieval experience, for instance, askMEDLINE BabelMeSH; and PubCrawler.

As most of these and other alternatives rely essentially on PubMed/MEDLINE data leased under license from the NLM/PubMed, the term "PubMed derivatives" has been suggested. Without the need to store about 90 GB of original PubMed Datasets, anybody can write PubMed applications using the eutils-application program interface as described in "The E-utilities In-Depth: Parameters, Syntax and More", by Eric Sayers, PhD. Various citation format generators, taking PMID numbers as input, are examples of web applications making use of the eutils-application program interface. Sample web pages include Citation Generator – Mick Schroeder, Pubmed Citation Generator – Ultrasound of the Week, and Cite this for me.

In 2025, the ZBMed, the German National Library of Medicine, announced plans to develop an internationally supported open source version of PubMed.

Data mining of PubMed

Code can be automated to systematically query with different keywords such as disease, year, organs, etc.

For bulk processing, the full PubMed database is available as XML which can be downloaded from an FTP server. The annual baseline is released in December, followed by daily update files.

In addition to its traditional role as a biomedical database, PubMed has become common resource for training biomedical language models.

The data accessible by PubMed can be mirrored locally using an unofficial tool such as MEDOC.

Millions of PubMed records augment various open data datasets about open access, like Unpaywall. Data analysis tools like Unpaywall Journals are used by libraries to assist with big deal cancellations: libraries can avoid subscriptions for materials already served by instant open access via open archives like PubMed Central.

References

References

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