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Template:Infobox biodatabase PubMed is a free database 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 information retrieval system. PubMed was first released in January 1996.[1]

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; and
  • a collection of books available full-text and other subsets of NLM records.[2]

Many PubMed records contain links to full text articles, some of which are freely available, often in PubMed Central[3] and local mirrors such as UK PubMed Central.[4]

Information about the journals indexed in PubMed is found in the NLM Catalog.[5]

As of 13 May 2012 (2012 -05-13), PubMed has over 21.78 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; 12.38 million of these articles are listed with their abstracts, and 12.81 articles have links to full-text (of which 3.54 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.[6]

Characteristics

Standard searches

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 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[7] 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])

Likewise,

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.[8]

Comprehensive 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,[9] who are able to select the right type of search and carefully adjust it for recall and precision.[10]

Clinical queries/systematic reviews

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.[11] 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.[12]

Related articles

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.[13] The 'related articles' function has been judged to be so precise that some researchers suggest it can be used instead of a full search.[14]

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.

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.[15] The "My NCBI" area can be accessed from any computer with web-access. An earlier version of "My NCBI" was called "PubMed Cubby".[16]

LinkOut

LinkOut, a NLM facility to link (and make available full-text) local journal holdings.[17] 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.[18] 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.[19] A 'PubMed Mobile' option, providing access to a mobile friendly, simplified PubMed version, is also available.[20]

askMEDLINE

askMEDLINE, a free-text, natural language query tool for MEDLINE/PubMed, developed by the NLM, also suitable for handhelds.[21]

PubMed identifier

A PMID (PubMed identifier or PubMed unique identifier)[22] is a unique number assigned to each PubMed record.

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.

Alternative interfaces

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.[23] As of October 2008, 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[24] of alternative interfaces and 3rd party additions to PubMed, one of a very few large, professionally curated databases which offers this option.

Lu [24] 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;[25] MiSearch;[26]
  • Clustering results by topics, authors, journals etc., for instance: Anne O'Tate;[27] ClusterMed;[28]
  • Enhancing semantics and visualisation, for instance: CiteXplore; EBIMed;[29] MedEvi;[30]
  • Improved search interface and retrieval experience, for instance: askMEDLINE;[31][32] BabelMeSH;[33]PubCrawler;[34]

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.[24]

See also

References

  1. ^ "PubMed Celebrates its 10th Anniversary". Technical Bulletin. United States National Library of Medicine. 2006-10-05. Retrieved 2011-03-22. 
  2. ^ "PubMed: MEDLINE Retrieval on the World Wide Web". Fact Sheet. United States National Library of Medicine. 2002-06-07. Retrieved 2011-03-22. 
  3. ^ PubMed
  4. ^ PubMed
  5. ^ "NLM Catalogue: Journals referenced in the NCBI Databases". NCBI. 2011. 
  6. ^ "PubMed Help. NCBI Help Manual". NCBI. 2005. 
  7. ^ "Simple Subject Search with Quiz". NCBI. 2010. 
  8. ^ Clarke J, Wentz R (2000). "Pragmatic approach is effective in evidence based health care". BMJ. 321 (7260): 566–567. PMC 1118450Freely accessible. PMID 10968827. doi:10.1136/bmj.321.7260.566/a.  Unknown parameter |month= ignored (help)
  9. ^ Jadad AR, McQuay HJ (1993). "Searching the literature. Be systematic in your searching". BMJ. 307 (6895): 66. PMC 1678459Freely accessible. PMID 8343701.  Unknown parameter |month= ignored (help)
  10. ^ Allison JJ, Kiefe CI, Carter J, Centor RM (1999). "The art and science of searching MEDLINE to answer clinical questions. Finding the right number of articles.". Int J Technol Assess Health Care. 15 (2): 281–296. PMID 10507188.  Unknown parameter |month= ignored (help)
  11. ^ "Clinical Queries Filter Terms explained". NCBI. 2010. 
  12. ^ PubMed
  13. ^ "Computation of Related Articles explained". NCBI. 
  14. ^ Chang AA, Heskett KM, Davidson TM (2006). "Searching the literature using medical subject headings versus text word with PubMed". Laryngoscope. 116 (2): 366–340. PMID 16467730. doi:10.1097/01.mlg.0000195371.72887.a2.  Unknown parameter |month= ignored (help)
  15. ^ "My NCBI explained". NCBI. 13 December 2010. 
  16. ^ "PubMed Cubby". Technical Bulletin. United States National Library of Medicine. 2000. 
  17. ^ "LinkOut Overview". NCBI. 2010. 
  18. ^ "LinkOut Participants 2011". NCBI. 2011. 
  19. ^ "PubMed via handhelds (PICO)". Technical Bulletin. United States National Library of Medicine. 2004. 
  20. ^ "PubMed Mobile Beta". Technical Bulletin. United States National Library of Medicine. 2011. 
  21. ^ "askMedline". NCBI. 2005. 
  22. ^ "Search Field Descriptions and Tags". National Center for Biotechnology Information. Retrieved 27 November 2008. 
  23. ^ "Leasing journal citations from PubMed / Medline". NLM. 2011. 
  24. ^ a b c PubMed
  25. ^ PubMed
  26. ^ PubMed
  27. ^ PubMed
  28. ^ "ClusterMed". Vivisimo Clustering Engine. 2011. 
  29. ^ PubMed
  30. ^ PubMed
  31. ^ PubMed
  32. ^ PubMed
  33. ^ PubMed
  34. ^ PubMed

External links



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