|Research center||United States National Library of Medicine (NLM)|
|Release date||January 1996|
PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine (NLM) at the National Institutes of Health maintains the database as part of the Entrez system of information retrieval.
From 1971 to 1997, MEDLINE online access to the MEDLARS computerized database had been primarily through institutional facilities like medical libraries. PubMed, first released in January 1996, ushered in the era of private, free, and home-computerized MEDLINE searching. The PubMed system was offered free to the public in June, 1997, when MEDLINE searches via the web were demonstrated, in a ceremony, by Vice President Al Gore.
- 1 Content
- 2 Characteristics
- 2.1 Standard searches
- 2.2 Comprehensive searches
- 2.3 Journal Article Parameters
- 2.4 See also
- 2.5 Mapping to MeSH headings and subheadings
- 2.6 My NCBI
- 2.7 LinkOut
- 2.8 PubMed for handhelds/mobiles
- 2.9 askMEDLINE
- 2.10 PubMed identifier
- 3 Alternative interfaces
- 4 See also
- 5 References
- 6 External links
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; and
- a collection of books available full-text and other subsets of NLM records.
- PMC citations
Information about the journals indexed in PubMed is found in the NLM Catalog.
As of 3 October 2013[update], PubMed has over 23 million records going back to 1966, selectively to the year 1865, and very selectively to 1809; about 500,000 new records are added each year. As of the same date[update], 13.1 million of PubMed's records are listed with their abstracts, and 14.2 million articles have links to full-text (of which 3.8 million articles are available full-text for free for any user). To see the current size of the database type "1800:2100[dp]" or "all[sb]" into the PubMed search window.
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.
The examples given in a PubMed tutorial demonstrate how this automatic process works:
- Causes Sleep Walking is translated as ("etiology"[Subheading] OR "etiology"[All Fields] OR "causes"[All Fields] OR "causality"[MeSH Terms] OR "causality"[All Fields]) AND ("somnambulism"[MeSH Terms] OR "somnambulism"[All Fields] OR ("sleep"[All Fields] AND "walking"[All Fields]) OR "sleep walking"[All Fields])
- Heart Attack Aspirin Prevention is translated as ("myocardial infarction"[MeSH Terms] OR ("myocardial"[All Fields] AND "infarction"[All Fields]) OR "myocardial infarction"[All Fields] OR ("heart"[All Fields] AND "attack"[All Fields]) OR "heart attack"[All Fields]) AND ("aspirin"[MeSH Terms] OR "aspirin"[All Fields]) AND ("prevention and control"[Subheading] OR ("prevention"[All Fields] AND "control"[All Fields]) OR "prevention and control"[All Fields] OR "prevention"[All Fields])
The new PubMed interface, launched in October 2009, encourages the use of such quick, Google-like search formulations; they have also been described as 'telegram' searches.
For comprehensive, optimal searches in PubMed, it is necessary to have a thorough understanding of 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, and are best carried out by PubMed search specialists or librarians, who are able to select the right type of search and carefully adjust it for recall and precision.
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, Keywords (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 enables many special features. A special feature of PubMed is its "Clinical Queries" section, where "Clinical Categories", "Systematic Reviews", and "Medical Genetics" subjects can be searched, with study-type 'filters' automatically applied to identify substantial, robust studies. As these 'clinical queries' can generate small sets of robust studies with considerable precision, it has been suggested that this PubMed section can be used as a 'point-of-care' resource.
Since July 2005, the MEDLINE article indexing process extracts important 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).
A reference which is judged particularly relevant can be marked and "related articles" can be identified. If relevant, several studies can be selected and related articles to all of them can be generated (on PubMed or any of the other NCBI Entrez databases) using the 'Find related data' option. The related articles are then listed in order of "relatedness". To create these lists of related articles, PubMed compares words from the title and abstract of each citation, as well as the MeSH headings assigned, using a powerful word-weighted algorithm. The 'related articles' function has been judged to be so precise that some researchers suggest it can be used instead of a full search.
Mapping to MeSH headings and subheadings
A strong feature of PubMed is its ability to automatically link to MeSH terms and subheadings. Examples would be: "bad breath" links to (and includes in the search) "halitosis", "heart attack" to "myocardial infarction", "breast cancer" to "breast neoplasms". 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 important feature makes PubMed searches automatically more sensitive and avoids false-negative (missed) hits by compensating for the diversity of medical terminology.
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
LinkOut, a 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[update]), from Aalborg University in Denmark to ZymoGenetics in Seattle. Users at these institutions see their institutions logo within the PubMed search result (if the journal is held at that institution) and can access the full-text.
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.
askMEDLINE, a free-text, natural language query tool for MEDLINE/PubMed, developed by the NLM, also suitable for handhelds.
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.
The National Library of Medicine leases the MEDLINE information to a number of private vendors such as Ovid, Dialog, EBSCO, Knowledge Finder and many other commercial, non-commercial, and academic providers. As of October 2008[update], more than 500 licences had been issued, more than 200 of them to non-US providers. As licences 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:
- Ranking search results, for instance: eTBLAST; Hakia; MedlineRanker; MiSearch;
- Clustering results by topics, authors, journals etc., for instance: Anne O'Tate; ClusterMed;
- Enhancing semantics and visualisation, for instance: EBIMed; MedEvi; (Note: CiteXplore was withdrawn from service on 15 February 2013, replaced by Europe PubMed Central.)
- Improved search interface and retrieval experience, for instance: askMEDLINE; BabelMeSH; PubCrawler;
- GoPubMed is a knowledge-based (Gene Ontology and MeSH) search engine for PubMed. GoPubMed is the semantic search engine for the life sciences.
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.
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- Hisory of PubMed and MEDLINE
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- "askMedline". NCBI. 2005.
- "Search Field Descriptions and Tags". National Center for Biotechnology Information. Retrieved 15 July 2013.
- "Leasing journal citations from PubMed/Medline". NLM. 2011.
- Lu, Z. (2011). "PubMed and beyond: A survey of web tools for searching biomedical literature". Database 2011: baq036–baq036. doi:10.1093/database/baq036. PMC 3025693. PMID 21245076.
- Fontaine, J. -F.; Barbosa-Silva, A.; Schaefer, M.; Huska, M. R.; Muro, E. M.; Andrade-Navarro, M. A. (2009). "MedlineRanker: Flexible ranking of biomedical literature". Nucleic Acids Research 37 (Web Server issue): W141–W146. doi:10.1093/nar/gkp353. PMC 2703945. PMID 19429696.
- States, D. J.; Ade, A. S.; Wright, Z. C.; Bookvich, A. V.; Athey, B. D. (2009). "MiSearch adaptive pubMed search tool". Bioinformatics 25 (7): 974–976. doi:10.1093/bioinformatics/btn033. PMC 2660869. PMID 18326507.
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- "ClusterMed". Vivisimo Clustering Engine. 2011.
- Rebholz-Schuhmann, D.; Kirsch, H.; Arregui, M.; Gaudan, S.; Riethoven, M.; Stoehr, P. (2007). "EBIMed--text crunching to gather facts for proteins from Medline". Bioinformatics 23 (2): e237–e244. doi:10.1093/bioinformatics/btl302. PMID 17237098.
- Kim, J. -J.; Pezik, P.; Rebholz-Schuhmann, D. (2008). "MedEvi: Retrieving textual evidence of relations between biomedical concepts from Medline". Bioinformatics 24 (11): 1410–1412. doi:10.1093/bioinformatics/btn117. PMC 2387223. PMID 18400773.
- Europe PubMed Central
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- Fontelo, P.; Liu, F.; Leon, S.; Anne, A.; Ackerman, M. (2007). "PICO Linguist and BabelMeSH: Development and partial evaluation of evidence-based multilanguage search tools for MEDLINE/PubMed". Studies in health technology and informatics 129 (Pt 1): 817–821. PMID 17911830.
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