PubMed

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PubMed
US-NLM-PubMed-Logo.svg
Content
Contact
Research center United States National Library of Medicine (NLM)
Release date January 1996
Access
Website www.ncbi.nlm.nih.gov/pubmed/
Tools
Miscellaneous

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.[1] 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.[2]

Content[edit]

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.[3]
  • PMC citations

Many PubMed records contain links to full text articles, some of which are freely available, often in PubMed Central[4] and local mirrors such as UK PubMed Central.[5]

Information about the journals indexed in PubMed is found in the NLM Catalog.[6]

As of 18 April 2014, 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, 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.[7]

Characteristics[edit]

Standard searches[edit]

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[8] 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.[9]

Comprehensive searches[edit]

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,[10] who are able to select the right type of search and carefully adjust it for recall and precision.[11]

Journal Article Parameters[edit]

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[edit]

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.[12] 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.[13]

Secondary ID[edit]

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).[14]

See also[edit]

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.[15] The 'related articles' function has been judged to be so precise that some researchers suggest it can be used instead of a full search.[16]

Mapping to MeSH headings and subheadings[edit]

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[edit]

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.[17] The "My NCBI" area can be accessed from any computer with web-access. An earlier version of "My NCBI" was called "PubMed Cubby".[18]

LinkOut[edit]

LinkOut, a NLM facility to link (and make available full-text) local journal holdings.[19] 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.[20] 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[edit]

PubMed/MEDLINE can be accessed via handheld devices, using for instance the "PICO" option (for focused clinical questions) created by the NLM.[21] A "PubMed Mobile" option, providing access to a mobile friendly, simplified PubMed version, is also available.[22]

askMEDLINE[edit]

askMEDLINE, a free-text, natural language query tool for MEDLINE/PubMed, developed by the NLM, also suitable for handhelds.[23]

PubMed identifier[edit]

A PMID (PubMed identifier or PubMed unique identifier)[24] is a unique number assigned to each PubMed record. A PMID is not the same as a PMCID which is the identifier for all works published in the free to access PubMed Central.[25]

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[edit]

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.[26] 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[27] of alternative interfaces and 3rd party additions to PubMed, one of a very few large, professionally curated databases which offers this option.

Lu[27] 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;[28] MiSearch;[29]
  • Clustering results by topics, authors, journals etc., for instance: Anne O'Tate;[30] ClusterMed;[31]
  • Enhancing semantics and visualisation, for instance: EBIMed;[32] MedEvi;[33] (Note: CiteXplore was withdrawn from service on 15 February 2013,[34] replaced by Europe PubMed Central.[35])
  • Improved search interface and retrieval experience, for instance: askMEDLINE;[36][37] BabelMeSH;[38] PubCrawler;[39]
  • GoPubMed is a knowledge-based (Gene Ontology and MeSH) search engine for PubMed. GoPubMed is the semantic search engine for the life sciences.
  • Search and ranking of medical and biomedical expertise by specific diagnosis, technique, or other terminology. Results are based on analysis derived from most recent ten years of PubMed data: Expertscape[40]

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.[27]

See also[edit]

References[edit]

  1. ^ "PubMed Celebrates its 10th Anniversary". Technical Bulletin. United States National Library of Medicine. 2006-10-05. Retrieved 2011-03-22. 
  2. ^ Hisory of PubMed and MEDLINE
  3. ^ "PubMed: MEDLINE Retrieval on the World Wide Web". Fact Sheet. United States National Library of Medicine. 2002-06-07. Retrieved 2011-03-22. 
  4. ^ Roberts, R. J. (2001). "PubMed Central: The GenBank of the published literature". Proceedings of the National Academy of Sciences 98 (2): 381–382. Bibcode:2001PNAS...98..381R. doi:10.1073/pnas.98.2.381. PMC 33354. PMID 11209037.  edit
  5. ^ McEntyre, J. R.; Ananiadou, S.; Andrews, S.; Black, W. J.; Boulderstone, R.; Buttery, P.; Chaplin, D.; Chevuru, S.; Cobley, N.; Coleman, L. -A.; Davey, P.; Gupta, B.; Haji-Gholam, L.; Hawkins, C.; Horne, A.; Hubbard, S. J.; Kim, J. -H.; Lewin, I.; Lyte, V.; MacIntyre, R.; Mansoor, S.; Mason, L.; McNaught, J.; Newbold, E.; Nobata, C.; Ong, E.; Pillai, S.; Rebholz-Schuhmann, D.; Rosie, H.; Rowbotham, R. (2010). "UKPMC: A full text article resource for the life sciences". Nucleic Acids Research 39 (Database issue): D58–D65. doi:10.1093/nar/gkq1063. PMC 3013671. PMID 21062818.  edit
  6. ^ "NLM Catalogue: Journals referenced in the NCBI Databases". NCBI. 2011. 
  7. ^ "PubMed Help. NCBI Help Manual". NCBI. 2005. 
  8. ^ "Simple Subject Search with Quiz". NCBI. 2010. 
  9. ^ Clarke J, Wentz R (September 2000). "Pragmatic approach is effective in evidence based health care". BMJ 321 (7260): 566–567. doi:10.1136/bmj.321.7260.566/a. PMC 1118450. PMID 10968827. 
  10. ^ Jadad AR, McQuay HJ (July 1993). "Searching the literature. Be systematic in your searching". BMJ 307 (6895): 66. PMC 1678459. PMID 8343701. 
  11. ^ Allison JJ, Kiefe CI, Carter J, Centor RM (Spring 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. 
  12. ^ "Clinical Queries Filter Terms explained". NCBI. 2010. 
  13. ^ Glasziou, P. (2007). "Do all fractures need full immobilisation?". BMJ 335 (7620): 612–613. doi:10.1136/bmj.39272.565810.80. PMC 1988981. PMID 17884906.  edit
  14. ^ Huser, V.; Cimino, J. J. (2013). "Evaluating adherence to the International Committee of Medical Journal Editors' policy of mandatory, timely clinical trial registration". Journal of the American Medical Informatics Association. doi:10.1136/amiajnl-2012-001501.  edit
  15. ^ "Computation of Related Articles explained". NCBI. 
  16. ^ Chang AA, Heskett KM, Davidson TM (February 2006). "Searching the literature using medical subject headings versus text word with PubMed". Laryngoscope 116 (2): 366–340. doi:10.1097/01.mlg.0000195371.72887.a2. PMID 16467730. 
  17. ^ "My NCBI explained". NCBI. 13 December 2010. 
  18. ^ "PubMed Cubby". Technical Bulletin. United States National Library of Medicine. 2000. 
  19. ^ "LinkOut Overview". NCBI. 2010. 
  20. ^ "LinkOut Participants 2011". NCBI. 2011. 
  21. ^ "PubMed via handhelds (PICO)". Technical Bulletin. United States National Library of Medicine. 2004. 
  22. ^ "PubMed Mobile Beta". Technical Bulletin. United States National Library of Medicine. 2011. 
  23. ^ "askMedline". NCBI. 2005. 
  24. ^ "Search Field Descriptions and Tags". National Center for Biotechnology Information. Retrieved 15 July 2013. 
  25. ^ Keener, Molly (19 May 2008). "PMID vs. PMCID: What's the difference?". University of Chicago. Retrieved 19 January 2014. 
  26. ^ "Leasing journal citations from PubMed/Medline". NLM. 2011. 
  27. ^ a b c 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.  edit
  28. ^ 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.  edit
  29. ^ 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.  edit
  30. ^ Smalheiser, N. R.; Zhou, W.; Torvik, V. I. (2008). "Anne O'Tate: A tool to support user-driven summarization, drill-down and browsing of PubMed search results". Journal of Biomedical Discovery and Collaboration 3: 2. doi:10.1186/1747-5333-3-2. PMC 2276193. PMID 18279519.  edit
  31. ^ "ClusterMed". Vivisimo Clustering Engine. 2011. 
  32. ^ 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.  edit
  33. ^ 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.  edit
  34. ^ CiteXplore
  35. ^ Europe PubMed Central
  36. ^ Fontelo, P.; Liu, F.; Ackerman, M.; Schardt, C. M.; Keitz, S. A. (2006). "AskMEDLINE: A report on a year-long experience". AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium 2006: 923. PMC 1839379. PMID 17238542.  edit
  37. ^ Fontelo, P.; Liu, F.; Ackerman, M. (2005). "MeSH Speller + askMEDLINE: Auto-completes MeSH terms then searches MEDLINE/PubMed via free-text, natural language queries". AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium 2005: 957. PMC 1513542. PMID 16779244.  edit
  38. ^ 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.  edit
  39. ^ Hokamp, K.; Wolfe, K. H. (2004). "PubCrawler: Keeping up comfortably with PubMed and GenBank". Nucleic Acids Research 32 (Web Server issue): W16–W19. doi:10.1093/nar/gkh453. PMC 441591. PMID 15215341.  edit
  40. ^ "Expertscape". Expertscape. 

External links[edit]