Array ( [0] => {{Short description|Online biomedical database}} [1] => {{cs1 config|name-list-style=vanc|display-authors=6}} [2] => {{Distinguish|PubMed Central}} [3] => {{Use dmy dates|date=September 2020}} [4] => {{infobox biodatabase [5] => |title = PubMed [6] => |logo =[[File:PubMed logo blue.svg|250px]] [7] => |description = [8] => |scope = [9] => |organism = [10] => |center = [[United States National Library of Medicine]] (NLM) [11] => |laboratory = [12] => |pmid = [13] => |released = {{Start date and age|1996|1}} [14] => |standard = [15] => |format = [16] => |url = {{URL|https://pubmed.ncbi.nlm.nih.gov}} [17] => |download = [18] => |webservice = [19] => |sql = [20] => |sparql = [21] => |webapp = [22] => |standalone = [23] => |license = [24] => |versioning = [25] => |frequency = [26] => |curation = [27] => |bookmark = [28] => |version= [29] => }} [30] => [31] => '''PubMed''' is a free [[List of academic databases and search engines|database]] including primarily the [[MEDLINE]] [[bibliographic database|database]] of references and [[Abstract (summary)|abstracts]] on [[life sciences]] and [[Biomedicine|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]].{{Cite web | url=https://www.nlm.nih.gov/bsd/pubmed.html | title=PubMed | access-date=22 February 2019 | archive-date=13 December 2020 | archive-url=https://web.archive.org/web/20201213224006/https://www.nlm.nih.gov/bsd/pubmed.html | url-status=live }} [32] => [33] => From 1971 to 1997, online access to the MEDLINE database had been primarily through institutional facilities, such as [[academic library|university libraries]].{{cite journal | vauthors = Lindberg DA | title = Internet access to the National Library of Medicine | journal = Effective Clinical Practice | volume = 3 | issue = 5 | pages = 256–60 | date = 2000 | pmid = 11185333 | url = http://www.acponline.org/clinical_information/journals_publications/ecp/sepoct00/nlm.pdf | archive-url = https://web.archive.org/web/20131102194044/http://www.acponline.org/clinical_information/journals_publications/ecp/sepoct00/nlm.pdf| url-status = dead | archive-date = 2 November 2013 }} PubMed, first released in January 1996, ushered in the era of private, free, home- and office-based MEDLINE searching.{{cite web |title=PubMed Celebrates its 10th Anniversary |website=Technical Bulletin |publisher=[[United States National Library of Medicine]] |date=2006-10-05 |url=https://www.nlm.nih.gov/pubs/techbull/so06/so06_pm_10.html |access-date=2011-03-22 |archive-date=23 April 2018 |archive-url=https://web.archive.org/web/20180423152104/https://www.nlm.nih.gov/pubs/techbull/so06/so06_pm_10.html |url-status=live }} The PubMed system was offered free to the public starting in June 1997. [34] => {{TOC limit|3}} [35] => [36] => ==Content== [37] => In addition to MEDLINE, PubMed provides access to: [38] => * older references from the print version of ''[[Index Medicus]]'', back to 1951 and earlier [39] => * references to some journals before they were indexed in Index Medicus and MEDLINE, for instance [[Science (journal)|''Science'']], ''[[BMJ]]'', and ''[[Annals of Surgery]]'' [40] => * very recent entries to records for an article before it is indexed with [[Medical Subject Headings]] (MeSH) and added to MEDLINE [41] => * a collection of books available full-text and other subsets of NLM records{{cite web |title=PubMed: MEDLINE Retrieval on the World Wide Web |website=Fact Sheet |publisher=United States National Library of Medicine |date=2002-06-07 |access-date=2011-03-22 |url=https://www.nlm.nih.gov/pubs/factsheets/pubmed.html |archive-date=1 September 2018 |archive-url=https://web.archive.org/web/20180901170358/https://www.nlm.nih.gov/pubs/factsheets/pubmed.html |url-status=live }} [42] => * [[PubMed Central|PMC]] citations [43] => * [[National Center for Biotechnology Information#NCBI Bookshelf|NCBI Bookshelf]] [44] => [45] => Many PubMed records contain links to full text articles, some of which are freely available, often in [[PubMed Central]]{{cite journal | vauthors = Roberts RJ | title = PubMed Central: The GenBank of the published literature | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 98 | issue = 2 | pages = 381–2 | date = January 2001 | pmid = 11209037 | pmc = 33354 | doi = 10.1073/pnas.98.2.381 | bibcode = 2001PNAS...98..381R | doi-access = free }} and local mirrors, such as [[Europe PubMed Central]].{{cite journal | vauthors = McEntyre JR, Ananiadou S, Andrews S, Black WJ, Boulderstone R, Buttery P, Chaplin D, Chevuru S, Cobley N, Coleman LA, Davey P, Gupta B, Haji-Gholam L, Hawkins C, Horne A, Hubbard SJ, Kim JH, 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, Rupp CJ, Stoehr P, Vaughan P | title = UKPMC: a full text article resource for the life sciences | journal = Nucleic Acids Research | volume = 39 | issue = Database issue | pages = D58-65 | date = January 2011 | pmid = 21062818 | pmc = 3013671 | doi = 10.1093/nar/gkq1063 }} [46] => [47] => Information about the journals indexed in MEDLINE, and available through PubMed, is found in the NLM Catalog.{{cite web |title=NLM Catalogue: Journals referenced in the NCBI Databases |url=https://www.ncbi.nlm.nih.gov/nlmcatalog/journals |publisher=NCBI |date=2011 |access-date=8 September 2017 |archive-date=13 October 2023 |archive-url=https://web.archive.org/web/20231013093717/https://www.ncbi.nlm.nih.gov/nlmcatalog/journals |url-status=live }} [48] => [49] => {{As of|2023|05|23}}, PubMed has more than 35 million citations and abstracts dating back to 1966, selectively to the year 1865, and very selectively to 1809. {{As of|2023|05|23|alt=As of the same date}}, 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).{{Cite web|title=PubMed|url=https://pubmed.ncbi.nlm.nih.gov/|access-date=2023-01-05|website=PubMed|language=en|archive-date=6 January 2022|archive-url=https://web.archive.org/web/20220106115855/https://pubmed.ncbi.nlm.nih.gov/|url-status=live}} The search query "1800:2100[dp]" retrieves all results whose date of publication is between 1800 and 2100 inclusive. Over the last 10 years (ending 31 December 2019), an average of nearly one million new records were added each year. [50] => [51] => In 2016, NLM changed the indexing system so that publishers are able to directly correct typos and errors in PubMed indexed articles.{{cite journal | journal = NLM Technical Bulletin | date = July–August 2016 | issue = 411 | page = e1 | url = https://www.nlm.nih.gov/pubs/techbull/ja16/ja16_medline_pm_production.html | title = MEDLINE/PubMed Production Improvements Underway | access-date = 29 July 2016 | archive-date = 29 March 2023 | archive-url = https://web.archive.org/web/20230329194413/https://www.nlm.nih.gov/pubs/techbull/ja16/ja16_medline_pm_production.html | url-status = live }} [52] => [53] => 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.{{cite journal | vauthors = Manca A, Moher D, Cugusi L, Dvir Z, Deriu F | title = How predatory journals leak into PubMed | journal = CMAJ | volume = 190 | issue = 35 | pages = E1042–E1045 | date = September 2018 | pmid = 30181150 | pmc = 6148641 | doi = 10.1503/cmaj.180154 }} The National Library of Medicine had respond that individual journal articles can be included in PMC to support the public access policies of research funders and that rigorous policies about journals and publishers ensure integrity of NLM literature databases.{{Cite journal |last1=Topper |first1=Lauren |last2=Marill |first2=Jennifer |last3=Kelly |first3=Christopher |last4=Funk |first4=Kathryn |date=2019-03-11 |title=Rigorous policies ensure integrity of NLM literature databases |journal=CMAJ |volume=191 |issue=10 |pages=E289 |doi=10.1503/cmaj.71602 |issn=1488-2329 |pmc=6411471 |pmid=30858186}} [54] => [55] => ==Characteristics== [56] => [57] => ===Website design=== [58] => 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.{{cite journal | vauthors = Clarke J, Wentz R | title = Pragmatic approach is effective in evidence based health care | journal = BMJ | volume = 321 | issue = 7260 | pages = 566–7 | date = September 2000 | pmid = 10968827 | pmc = 1118450 | doi = 10.1136/bmj.321.7260.566/a }} 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.{{cite journal | vauthors = Fatehi F, Gray LC, Wootton R | title = How to improve your PubMed/MEDLINE searches: 2. display settings, complex search queries and topic searching | journal = Journal of Telemedicine and Telecare | volume = 20 | issue = 1 | pages = 44–55 | date = January 2014 | pmid = 24352897 | doi = 10.1177/1357633X13517067 | s2cid = 43725062 }} [59] => [60] => The PubMed website design and domain was updated in January 2020 and became default on 15 May 2020, with the updated and new features.{{cite web|url=https://nlmdirector.nlm.nih.gov/2020/01/21/a-new-and-improved-pubmed/|title=A New and Improved PubMed®|work=NLM Musings From the Mezzanine|last=Trawick|first=Bart|date=21 January 2020|access-date=23 May 2020|archive-date=7 October 2023|archive-url=https://web.archive.org/web/20231007120743/https://nlmdirector.nlm.nih.gov/2020/01/21/a-new-and-improved-pubmed/|url-status=live}} There was a critical reaction from many researchers who frequently use the site.{{cite news|url=https://www.science.org/content/article/they-redesigned-pubmed-beloved-website-it-hasn-t-gone-over-well|title=They redesigned PubMed, a beloved website. It hasn't gone over well|first=Michael|last=Price|date=22 May 2020|work=Science|access-date=30 June 2022|archive-date=21 May 2022|archive-url=https://web.archive.org/web/20220521200855/https://www.science.org/content/article/they-redesigned-pubmed-beloved-website-it-hasn-t-gone-over-well|url-status=live}} [61] => [62] => ====PubMed for handhelds/mobiles==== [63] => PubMed/MEDLINE can be accessed via handheld devices, using for instance the [[PICO process|"PICO"]] option (for focused clinical questions) created by the NLM.{{cite web |title=PubMed via handhelds (PICO) |url=https://www.nlm.nih.gov/pubs/techbull/mj04/mj04_pico.html |publisher=United States National Library of Medicine |website=Technical Bulletin |date=2004 |access-date=7 April 2016 |archive-date=30 May 2023 |archive-url=https://web.archive.org/web/20230530094234/https://www.nlm.nih.gov/pubs/techbull/mj04/mj04_pico.html |url-status=live }} A "PubMed Mobile" option, providing access to a mobile friendly, simplified PubMed version, is also available.{{cite web |title=PubMed Mobile Beta |url=https://www.nlm.nih.gov/pubs/techbull/ma11/ma11_pm_mobile_beta.html |publisher=United States National Library of Medicine |website=Technical Bulletin |date=2011 |access-date=7 April 2016 |archive-date=11 April 2023 |archive-url=https://web.archive.org/web/20230411072800/https://www.nlm.nih.gov/pubs/techbull/ma11/ma11_pm_mobile_beta.html |url-status=live }} [64] => [65] => ===Search=== [66] => ====Standard search==== [67] => Simple searches on PubMed can be carried out by entering key aspects of a subject into PubMed's search window. [68] => [69] => 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.{{Citation needed|date=August 2022}} [70] => [71] => The examples given in a PubMed tutorial{{cite web|title=Simple Subject Search with Quiz|url=https://www.nlm.nih.gov/bsd/viewlet/search/subject/subject.html|publisher=NCBI|date=2010|access-date=7 April 2016|archive-date=11 May 2020|archive-url=https://web.archive.org/web/20200511005916/https://www.nlm.nih.gov/bsd/viewlet/search/subject/subject.html|url-status=live}} demonstrate how this automatic process works: [72] => [73] => {{quote|'''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])}} [74] => [75] => Likewise, [76] => {{quote|'''soft [77] => 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])}} [78] => [79] => ====Comprehensive search==== [80] => 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.{{cite journal | vauthors = Jadad AR, McQuay HJ | title = Searching the literature. Be systematic in your searching | journal = BMJ | volume = 307 | issue = 6895 | pages = 66 | date = July 1993 | pmid = 8343701 | pmc = 1678459 | doi = 10.1136/bmj.307.6895.66-a }}{{cite journal | vauthors = Allison JJ, Kiefe CI, Weissman NW, Carter J, Centor RM | title = The art and science of searching MEDLINE to answer clinical questions. Finding the right number of articles | journal = International Journal of Technology Assessment in Health Care | volume = 15 | issue = 2 | pages = 281–96 | date = Spring 1999 | pmid = 10507188 | doi = 10.1017/S0266462399015214 | s2cid = 11023273 | url = https://escholarship.umassmed.edu/qhs_pp/130 | access-date = 13 December 2019 | archive-date = 19 February 2022 | archive-url = https://web.archive.org/web/20220219071643/https://escholarship.umassmed.edu/qhs_pp/130/ | url-status = live }} [81] => [82] => 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.{{cite journal | vauthors = Campos-Asensio C |date=2018|title=Cómo elaborar una estrategia de búsqueda bibliográfica|journal=Enfermería Intensiva|language=es|volume=29|issue=4|pages=182–186|doi=10.1016/j.enfi.2018.09.001|pmid=30291015|s2cid=188132546 }} [83] => [84] => ===Journal article parameters=== [85] => 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). [86] => [87] => ====Publication Type: Clinical queries/systematic reviews==== [88] => Publication type parameter allows searching by the [[Scientific journal#Types of articles|type of publication]], including reports of various kinds of clinical research.{{cite book|url=https://www.ncbi.nlm.nih.gov/entrez/query/static/clinicaltable.html|title=Clinical Queries Filter Terms explained|publisher=NCBI|date=2010|access-date=8 September 2017|archive-date=29 November 2022|archive-url=https://web.archive.org/web/20221129143847/https://www.ncbi.nlm.nih.gov/entrez/query/static/clinicaltable.html|url-status=live}} [89] => [90] => ====Secondary ID==== [91] => 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).{{cite journal | vauthors = Huser V, Cimino JJ | title = Evaluating adherence to the International Committee of Medical Journal Editors' policy of mandatory, timely clinical trial registration | journal = Journal of the American Medical Informatics Association | volume = 20 | issue = e1 | pages = e169-74 | date = June 2013 | pmid = 23396544 | pmc = 3715364 | doi = 10.1136/amiajnl-2012-001501 }} [92] => [93] => === See also === [94] => 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.{{cite web |url=https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.section.pubmedhelp.Appendices#pubmedhelp.Computation_of_Relat |title=Computation of Related Articles explained |publisher=NCBI |access-date=8 September 2017 |archive-date=18 December 2008 |archive-url=https://web.archive.org/web/20081218184920/http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.section.pubmedhelp.Appendices#pubmedhelp.Computation_of_Relat |url-status=live }} The 'related articles' function has been judged to be so precise that the authors of a paper suggested it can be used instead of a full search.{{cite journal | vauthors = Chang AA, Heskett KM, Davidson TM | title = Searching the literature using medical subject headings versus text word with PubMed | journal = The Laryngoscope | volume = 116 | issue = 2 | pages = 336–40 | date = February 2006 | pmid = 16467730 | doi = 10.1097/01.mlg.0000195371.72887.a2 | s2cid = 42510351 | url = https://escholarship.org/content/qt8cn089mk/qt8cn089mk.pdf?t=nxc986 | access-date = 11 September 2018 | archive-date = | archive-url = | url-status = | doi-access = free }} [95] => [96] => ===Mapping to MeSH=== [97] => PubMed automatically links 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 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).{{cite journal | vauthors = Fatehi F, Gray LC, Wootton R | title = How to improve your PubMed/MEDLINE searches: 3. advanced searching, MeSH and My NCBI | journal = Journal of Telemedicine and Telecare | volume = 20 | issue = 2 | pages = 102–12 | date = March 2014 | pmid = 24614997 | doi = 10.1177/1357633X13519036 | s2cid = 9948223 }} This feature makes PubMed searches more sensitive and avoids false-negative (missed) hits by compensating for the diversity of medical terminology. [98] => [99] => 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]). [100] => [101] => ===My NCBI=== [102] => The PubMed optional facility "My NCBI" (with free registration) provides tools for [103] => * saving searches [104] => * filtering search results [105] => * setting up automatic updates sent by e-mail [106] => * saving sets of references retrieved as part of a PubMed search [107] => * configuring display formats or highlighting search terms [108] => and a wide range of other options.{{cite book |title=My NCBI explained |chapter=My NCBI Help |url=https://www.ncbi.nlm.nih.gov/books/NBK3842/ |publisher=NCBI |date=13 December 2010 |access-date=8 September 2017 |archive-date=26 July 2023 |archive-url=https://web.archive.org/web/20230726213825/https://www.ncbi.nlm.nih.gov/books/NBK3842/ |url-status=live }} The "My NCBI" area can be accessed from any computer with web-access. [109] => An earlier version of "My NCBI" was called "PubMed Cubby".{{cite web |title=PubMed Cubby |url=https://www.nlm.nih.gov/pubs/techbull/so00/so00_hands_on_register.html |publisher=United States National Library of Medicine |website=Technical Bulletin |date=2000 |access-date=7 April 2016 |archive-date=20 February 2023 |archive-url=https://web.archive.org/web/20230220053836/https://www.nlm.nih.gov/pubs/techbull/so00/so00_hands_on_register.html |url-status=live }} [110] => [111] => ===LinkOut=== [112] => LinkOut is an NLM facility to link and make available full-text local journal holdings.{{cite web| title=LinkOut Overview| url=https://www.ncbi.nlm.nih.gov/projects/linkout/| publisher=NCBI| date=2010| access-date=8 September 2017| archive-date=10 September 2023| archive-url=https://web.archive.org/web/20230910152532/https://www.ncbi.nlm.nih.gov/projects/linkout/| url-status=live}} Some 3,200 sites (mainly academic institutions) participate in this NLM facility ({{As of|2010|03|lc=on}}), from [[Aalborg University]] in Denmark to [[ZymoGenetics]] in Seattle.{{cite web|title=LinkOut Participants 2011|url=https://www.ncbi.nlm.nih.gov/projects/linkout/journals/htmllists.cgi?type_id=6|publisher=NCBI|date=2011|access-date=8 September 2017|archive-date=14 October 2017|archive-url=https://web.archive.org/web/20171014080855/https://www.ncbi.nlm.nih.gov/projects/linkout/journals/htmllists.cgi?type_id=6|url-status=live}} 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.{{Cite web | url=https://www.nlm.nih.gov/pubs/techbull/ma19/ma19_pubmed_update.html | title=An Updated PubMed is on its Way | access-date=1 April 2019 | archive-date=16 May 2023 | archive-url=https://web.archive.org/web/20230516020452/https://www.nlm.nih.gov/pubs/techbull/ma19/ma19_pubmed_update.html | url-status=live }} [113] => [114] => ===PubMed Commons=== [115] => 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.{{cite web|url=https://pubmedcommonsblog.ncbi.nlm.nih.gov/2015/12/17/commenting-on-pubmed-a-successful-pilot/|title=Commenting on PubMed: A Successful Pilot|author=PubMed Commons Team|date=17 December 2015|access-date=29 July 2016|archive-date=25 October 2017|archive-url=https://web.archive.org/web/20171025190236/https://pubmedcommonsblog.ncbi.nlm.nih.gov/2015/12/17/commenting-on-pubmed-a-successful-pilot/|url-status=dead}} In February 2018, PubMed Commons was discontinued due to the fact that "usage has remained minimal".{{Cite news|url=https://ncbiinsights.ncbi.nlm.nih.gov/2018/02/01/pubmed-commons-to-be-discontinued/|title=PubMed Commons to be Discontinued|date=2018-02-01|work=NCBI Insights|access-date=2018-02-02|language=en-US|archive-date=28 August 2023|archive-url=https://web.archive.org/web/20230828064342/https://ncbiinsights.ncbi.nlm.nih.gov/2018/02/01/pubmed-commons-to-be-discontinued/|url-status=live}}{{Cite web|url=http://retractionwatch.com/2018/02/02/pubmed-shuts-comments-feature-pubmed-commons/|title=PubMed shuts down its comments feature, PubMed Commons|date=2018-02-02|website=Retraction Watch|access-date=2018-02-02|archive-date=28 June 2022|archive-url=https://web.archive.org/web/20220628195915/https://retractionwatch.com/2018/02/02/pubmed-shuts-comments-feature-pubmed-commons/|url-status=live}} [116] => [117] => ===askMEDLINE=== [118] => askMEDLINE, a free-text, natural language query tool for MEDLINE/PubMed, developed by the NLM, also suitable for handhelds.{{cite web|title=askMedline|url=http://askmedline.nlm.nih.gov/ask/ask.php|publisher=NCBI|date=2005|access-date=3 April 2011|archive-date=17 July 2013|archive-url=https://web.archive.org/web/20130717121944/http://askmedline.nlm.nih.gov/ask/ask.php|url-status=live}} [119] => [120] => === PubMed identifier === [121] => {{For|help using PubMed identifiers within Wikipedia|Wikipedia:PMID}} [122] => A '''PMID''' (PubMed identifier or PubMed unique identifier){{Cite web |url=https://www.ncbi.nlm.nih.gov/books/NBK3827/#pubmedhelp.Search_Field_Descrip |title=Search Field Descriptions and Tags |access-date=15 July 2013 |publisher=National Center for Biotechnology Information |archive-date=11 July 2013 |archive-url=https://web.archive.org/web/20130711005252/http://www.ncbi.nlm.nih.gov/books/NBK3827/#pubmedhelp.Search_Field_Descrip |url-status=live }} is a [[unique identifier|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]].{{cite web |last=Keener |first=Molly |title=PMID vs. PMCID: What's the difference?|url=http://chess.uchicago.edu/docs/PMCIDinPubMed.pdf | archive-url = https://web.archive.org/web/20140706060933/http://chess.uchicago.edu/docs/PMCIDinPubMed.pdf | archive-date = 6 July 2014 | url-status = dead |publisher=University of Chicago |access-date=19 January 2014 }} [123] => [124] => 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 [[Letter to the editor|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 [[Retractions in academic publishing|retracted]] for fraud, incompetence, or misconduct. The announcement about any [[correction (newspaper)|corrections]] to original papers may be assigned a PMID. [125] => [126] => 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. [127] => [128] => ==Alternative interfaces== [129] => [[File:MEDLINE via PubMed.png|thumb|upright=1.4|MEDLINE is one of the databases which are accessible via PubMed. Several companies provide access to MEDLINE through their platforms.]] [130] => The National Library of Medicine leases the MEDLINE information to a number of private vendors such as [[Embase]], [[Ovid Technologies|Ovid]], [[Dialog (online database)|Dialog]], [[EBSCO Publishing|EBSCO]], [[Knowledge Finder]] and many other commercial, non-commercial, and academic providers.{{cite web |title=Leasing journal citations from PubMed/Medline |url=https://www.nlm.nih.gov/databases/journal.html |publisher=NLM |date=2011 |access-date=7 April 2016 |archive-date=9 July 2023 |archive-url=https://web.archive.org/web/20230709080814/https://www.nlm.nih.gov/databases/journal.html |url-status=live }} {{As of|2008|10}}, 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{{cite journal | vauthors = Lu Z | title = PubMed and beyond: a survey of web tools for searching biomedical literature | journal = Database | volume = 2011 | pages = baq036 | date = 2011 | pmid = 21245076 | pmc = 3025693 | doi = 10.1093/database/baq036 }} of alternative interfaces and 3rd party additions to PubMed, one of a very few large, professionally curated databases which offers this option. [131] => [132] => Lu identifies a sample of 28 current and free Web-based PubMed versions, requiring no installation or registration, which are grouped into four categories: [133] => # Ranking search results, for instance: [[eTBLAST]]; MedlineRanker;{{cite journal | vauthors = Fontaine JF, Barbosa-Silva A, Schaefer M, Huska MR, Muro EM, Andrade-Navarro MA | title = MedlineRanker: flexible ranking of biomedical literature | journal = Nucleic Acids Research | volume = 37 | issue = Web Server issue | pages = W141-6 | date = July 2009 | pmid = 19429696 | pmc = 2703945 | doi = 10.1093/nar/gkp353 }} MiSearch;{{cite journal | vauthors = States DJ, Ade AS, Wright ZC, Bookvich AV, Athey BD | title = MiSearch adaptive pubMed search tool | journal = Bioinformatics | volume = 25 | issue = 7 | pages = 974–6 | date = April 2009 | pmid = 18326507 | pmc = 2660869 | doi = 10.1093/bioinformatics/btn033 }} [134] => # Clustering results by topics, authors, journals etc., for instance: [[Anne O'Tate]];{{cite journal | vauthors = Smalheiser NR, Zhou W, Torvik VI | title = Anne O'Tate: A tool to support user-driven summarization, drill-down and browsing of PubMed search results | journal = Journal of Biomedical Discovery and Collaboration | volume = 3 | pages = 2 | date = February 2008 | pmid = 18279519 | pmc = 2276193 | doi = 10.1186/1747-5333-3-2 | doi-access = free }} ClusterMed;{{cite web |title=ClusterMed |url=http://demos.vivisimo.com/clustermed |publisher=Vivisimo Clustering Engine |date=2011 |access-date=3 July 2011 |archive-url=https://web.archive.org/web/20110811122944/http://demos.vivisimo.com/clustermed |archive-date=11 August 2011 |url-status=dead }} [135] => # Enhancing semantics and visualization, for instance: EBIMed;{{cite journal | vauthors = Rebholz-Schuhmann D, Kirsch H, Arregui M, Gaudan S, Riethoven M, Stoehr P | title = EBIMed--text crunching to gather facts for proteins from Medline | journal = Bioinformatics | volume = 23 | issue = 2 | pages = e237-44 | date = January 2007 | pmid = 17237098 | doi = 10.1093/bioinformatics/btl302 | doi-access = free }} MedEvi.{{cite journal | vauthors = Kim JJ, Pezik P, Rebholz-Schuhmann D | title = MedEvi: retrieving textual evidence of relations between biomedical concepts from Medline | journal = Bioinformatics | volume = 24 | issue = 11 | pages = 1410–2 | date = June 2008 | pmid = 18400773 | pmc = 2387223 | doi = 10.1093/bioinformatics/btn117 }} [136] => # Improved search interface and retrieval experience, for instance, askMEDLINE{{cite journal | vauthors = Fontelo P, Liu F, Ackerman M, Schardt CM, Keitz SA | title = askMEDLINE: a report on a year-long experience | journal = AMIA ... Annual Symposium Proceedings. AMIA Symposium | volume = 2006 | pages = 923 | date = 2006 | pmid = 17238542 | pmc = 1839379 }}{{cite journal | vauthors = Fontelo P, Liu F, Ackerman M | title = MeSH Speller + askMEDLINE: auto-completes MeSH terms then searches MEDLINE/PubMed via free-text, natural language queries | journal = AMIA ... Annual Symposium Proceedings. AMIA Symposium | volume = 2005 | pages = 957 | date = 2005 | pmid = 16779244 | pmc = 1513542 }} BabelMeSH;{{cite journal | vauthors = Fontelo P, Liu F, Leon S, Anne A, Ackerman M | title = PICO Linguist and BabelMeSH: development and partial evaluation of evidence-based multilanguage search tools for MEDLINE/PubMed | journal = Studies in Health Technology and Informatics | volume = 129 | issue = Pt 1 | pages = 817–21 | date = 2007 | pmid = 17911830 | url = http://booksonline.iospress.nl/Extern/EnterMedLine.aspx?ISSN=0926-9630&Volume=129&SPage=817 | access-date = 31 May 2014 | archive-date = 18 October 2023 | archive-url = https://web.archive.org/web/20231018105123/https://ebooks.iospress.nl/publication/11089 | url-status = live }} and PubCrawler.{{cite journal | vauthors = Hokamp K, Wolfe KH | title = PubCrawler: keeping up comfortably with PubMed and GenBank | journal = Nucleic Acids Research | volume = 32 | issue = Web Server issue | pages = W16-9 | date = July 2004 | pmid = 15215341 | pmc = 441591 | doi = 10.1093/nar/gkh453 | author-link2 = Kenneth H. Wolfe }} [137] => [138] => 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.{{Cite book | author=Eric Sayers, PhD | title=The E-utilities In-Depth: Parameters, Syntax and More | url=https://www.ncbi.nlm.nih.gov/books/NBK25499/ | publisher=NCBI | date=24 October 2018 | access-date=8 September 2017 | archive-date=23 June 2023 | archive-url=https://web.archive.org/web/20230623132148/https://www.ncbi.nlm.nih.gov/books/NBK25499/ | url-status=live }} 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 [https://mickschroeder.com/citation/ Citation Generator – Mick Schroeder], [https://www.ultrasoundoftheweek.com/citation/ Pubmed Citation Generator – Ultrasound of the Week], [https://www.pmid2cite.com/ PMID2cite], and [http://www.citethisforme.com/citation-generator/ama Cite this for me]. [139] => [140] => ==Data mining of PubMed== [141] => [142] => Alternative methods to mine the data in PubMed use programming environments such as [[Matlab]], [[Python (programming language)|Python]] or [[R (programming language)|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. [143] => [144] => In addition to its traditional role as a biomedical database, PubMed has become common resource for training biomedical [[Language_model|language models]].{{cite journal |last1=Singhal |first1=Karan |last2=Azizi |first2=Shekoofeh |last3=Tu |first3=Tao |last4=Mahdavi |first4=S. Sara |last5=Wei |first5=Jason |last6=Chung |first6=Hyung Won |last7=Scales |first7=Nathan |last8=Tanwani |first8=Ajay |last9=Cole-Lewis |first9=Heather |last10=Pfohl |first10=Stephen |last11=Payne |first11=Perry |last12=Seneviratne |first12=Martin |last13=Gamble |first13=Paul |last14=Kelly |first14=Chris |last15=Babiker |first15=Abubakr |last16=Schärli |first16=Nathanael |last17=Chowdhery |first17=Aakanksha |last18=Mansfield |first18=Philip |last19=Demner-Fushman |first19=Dina |last20=Agüera y Arcas |first20=Blaise |last21=Webster |first21=Dale |last22=Corrado |first22=Greg S. |last23=Matias |first23=Yossi |last24=Chou |first24=Katherine |last25=Gottweis |first25=Juraj |last26=Tomasev |first26=Nenad |last27=Liu |first27=Yun |last28=Rajkomar |first28=Alvin |last29=Barral |first29=Joelle |last30=Semturs |first30=Christopher |last31=Karthikesalingam |first31=Alan |last32=Natarajan |first32=Vivek |title=Large language models encode clinical knowledge |journal=Nature |date=3 August 2023 |volume=620 |issue=7972 |pages=172–180 |doi=10.1038/s41586-023-06291-2|pmid=37438534 |pmc=10396962 |arxiv=2212.13138 |bibcode=2023Natur.620..172S }} Recent advancements in this field include the development of models like PubMedGPT, a 2.7B parameter model trained on PubMed data by Stanford CRFM, and Microsoft's BiomedCLIP-PubMedBERT, which utilizes figure-caption pairs from PubMed Central for [[vision-language processing]]. These models demonstrate the significant potential of PubMed data in enhancing the capabilities of AI in medical research and healthcare applications. Such advancements underline the growing intersection between large-scale data mining and AI development in the biomedical field. [145] => [146] => The data accessible by PubMed can be mirrored locally using an unofficial tool such as MEDOC.{{GitHub |MrMimic/MEDOC}} [147] => [148] => 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 (subscription model)|big deal]] cancellations: libraries can avoid subscriptions for materials already served by instant [[open access]] via [[open archive]]s like PubMed Central.{{cite web|access-date=2020-04-18|title=SUNY Negotiates New, Modified Agreement with Elsevier – Libraries News Center University at Buffalo Libraries|url=https://library.buffalo.edu/news/2020/04/07/suny-negotiates-new-modified-agreement-with-elsevier/|website=library.buffalo.edu|author=Denise Wolfe|publisher=[[University at Buffalo]]|date=2020-04-07|archive-date=6 December 2020|archive-url=https://web.archive.org/web/20201206111125/https://library.buffalo.edu/news/2020/04/07/suny-negotiates-new-modified-agreement-with-elsevier/|url-status=live}} [149] => [150] => == See also == [151] => * [[Europe PubMed Central]] [152] => * [[JournalReview.org]] [153] => * [[List of academic databases and search engines]] [154] => * [[PubMed Central]] [155] => * [[PubMed Central Canada]] [156] => [157] => == References == [158] => {{Reflist}} [159] => [160] => == External links == [161] => {{Wikidata property |1=P698}} [162] => * {{Official|https://pubmed.ncbi.nlm.nih.gov/}} [163] => * [https://www.ncbi.nlm.nih.gov/books/NBK3827/table/pubmedhelp.Tn/ PubMed search tags & field qualifiers] [164] => [165] => {{Telemedicine navbox}} [166] => {{Academic publishing}} [167] => [168] => {{DEFAULTSORT:Pubmed}} [169] => [[Category:American medical websites]] [170] => [[Category:Bibliographic databases and indexes]] [171] => [[Category:Biological databases]] [172] => [[Category:Databases in the United States]] [173] => [[Category:Medical search engines]] [174] => [[Category:National Institutes of Health]] [175] => [[Category:Online databases]] [176] => [[Category:United States National Library of Medicine]] [] => )
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PubMed

PubMed is a free search engine for accessing a vast collection of biomedical literature, including scientific journals, clinical research papers, and articles on health-related subjects. Developed and maintained by the National Center for Biotechnology Information (NCBI), it is widely used by healthcare professionals, researchers, and students to access credible and up-to-date information in the field of medicine and life sciences.

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Developed and maintained by the National Center for Biotechnology Information (NCBI), it is widely used by healthcare professionals, researchers, and students to access credible and up-to-date information in the field of medicine and life sciences. PubMed provides access to over 32 million citations from the fields of biomedicine, nursing, pharmacology, dentistry, veterinary medicine, and more. It covers topics ranging from fundamental basic science to clinical trials and systematic reviews. The database includes articles published in various languages from multiple countries around the world. Users can search PubMed using keywords, author names, specific journals, or MeSH (Medical Subject Headings) terms, which help categorize articles based on their subjects. The search results typically display the title, authors, abstract, and citation details of each article, allowing users to assess its relevance and quality before accessing the full text. PubMed Central (PMC), a related database, is a digital repository that houses full-text articles from PubMed, with an emphasis on open access publications. As of 2021, PMC contains over 6. 7 million full-text articles. Users can directly access the full-text articles when available or link to the respective journal's website for access. PubMed provides various additional features, such as filters for narrowing search results, citation tools for creating bibliographies, and options for saving searches. Its user-friendly interface and powerful search capabilities make it an invaluable resource in the medical and scientific community, enabling researchers to stay updated with the latest literature, discover relevant articles for their research, and facilitate evidence-based practice. Overall, PubMed is a prominent platform for accessing biomedical literature, offering a comprehensive and reliable database of articles in the field of medicine and life sciences. Its free and easily accessible nature has made it an indispensable tool for individuals involved in healthcare, scientific research, and academia.

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Biomedicine

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MEDLINE

MEDLINE (Medical Literature Analysis and Retrieval System Online, or MEDLARS Online) is a bibliographic database of life sciences and biomedical information.

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