PubMed

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).

Mapping to MeSH

PubMed automatically links to MeSH terms and subheadings. Examples would be: "bad breath" links to (and includes in the search) "halitosis" and "heart attack" to "myocardial infarction". Where appropriate, these MeSH terms are automatically "expanded", that is, include more specific terms. Terms like "nursing" are automatically linked to "Nursing [MeSH]" or "Nursing [Subheading]". This feature is called Auto Term Mapping and is enacted, by default, in free text searching but not exact phrase searching (i.e. enclosing the search query with double quotes). This feature makes PubMed searches more sensitive and avoids false-negative (missed) hits by compensating for the diversity of medical terminology.

PubMed does not apply automatic mapping of the term in the following circumstances: by writing the quoted phrase (e.g., "kidney allograft"), when truncated on the asterisk (e.g., kidney allograft*), and when looking with field labels (e.g., Cancer [ti]).

My NCBI

The PubMed optional facility "My NCBI" (with free registration) provides tools for

• saving searches
• filtering search results
• setting up automatic updates sent by e-mail
• saving sets of references retrieved as part of a PubMed search
• configuring display formats or highlighting search terms

and a wide range of other options. The "My NCBI" area can be accessed from any computer with web-access. An earlier version of "My NCBI" was called "PubMed Cubby".

LinkOut

LinkOut is an NLM facility to link and make available full-text local journal holdings. Some 3,200 sites (mainly academic institutions) participate in this NLM facility (as of March 2010), from Aalborg University in Denmark to ZymoGenetics in Seattle. Users at these institutions see their institution's logo within the PubMed search result (if the journal is held at that institution) and can access the full-text. Link out is being consolidated with Outside Tool as of the major platform update coming in the Summer of 2019.

PubMed Commons

In 2016, PubMed allows authors of articles to comment on articles indexed by PubMed. This feature was initially tested in a pilot mode (since 2013) and was made permanent in 2016. In February 2018, PubMed Commons was discontinued due to the fact that "usage has remained minimal".

askMEDLINE

askMEDLINE was developed as a free-text language query tool that would allow users to use natural language in their searches. As opposed to using specialized vocabularies that an expert searcher may use, this tool allowed users to conduct an efficient MEDLINE/PubMed search solely with natural language. It was also suitable for handhelds and intended for researchers, clinicians or the general public who may not be familiar with formatting formal queries.

PubMed identifier

A PMID (PubMed identifier or PubMed unique identifier) is a unique integer value, starting at 1, assigned to each PubMed record. A PMID is not the same as a PMCID (PubMed Central identifier) which is the identifier for all works published in the free-to-access PubMed Central.

The assignment of a PMID or PMCID to a publication tells the reader nothing about the type or quality of the content. PMIDs are assigned to letters to the editor, editorial opinions, op-ed columns, and any other piece that the editor chooses to include in the journal, as well as peer-reviewed papers. The existence of the identification number is also not proof that the papers have not been retracted for fraud, incompetence, or misconduct. The announcement about any corrections to original papers may be assigned a PMID.

Each number that is entered in the PubMed search window is treated by default as if it were a PMID. Therefore, any reference in PubMed can be located using the PMID.

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. As of October 2008, 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

Alternative methods to mine the data in PubMed use programming environments such as Matlab, Python or R. In these cases, queries of PubMed are written as lines of code and passed to PubMed and the response is then processed directly in the programming environment. 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.