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Line 1: {{Short description\|Online biomedical database}} {{cs1 config\|name-list-style=vanc\|display-authors=6}} {{Distinguish\|PubMed Central}} {{Use dmy dates\|date=September 2020}} Line 29 ⟶ 30: }} '''PubMed''' is a free [[List of academic databases and search engines\|~~search engine~~database]] ~~accessing~~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]] ~~maintain~~maintains the database as part of the [[Entrez]] system of [[information retrieval]].<ref>{{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 }}</ref> From 1971 to 1997, online access to the MEDLINE database had been primarily through institutional facilities, such as [[academic library\|university libraries]].<ref name="pmid11185333">{{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 }}</ref> PubMed, first released in January 1996, ushered in the era of private, free, home- and office-based MEDLINE searching.<ref>{{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 }}</ref> The PubMed system was offered free to the public starting in June 1997.<ref name="pmid11185333"/> Line 43 ⟶ 44: * [[National Center for Biotechnology Information#NCBI Bookshelf\|NCBI Bookshelf]] Many PubMed records contain links to full text articles, some of which are freely available, often in [[PubMed Central]]<ref>{{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 }}</ref> and local mirrors, such as [[Europe PubMed Central]].<ref>{{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 ~~\| display-authors = 6~~ \| 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 }}</ref> Information about the journals indexed in MEDLINE, and available through PubMed, is found in the NLM Catalog.<ref>{{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 }}</ref> Line 51 ⟶ 52: In 2016, NLM changed the indexing system so that publishers are able to directly correct typos and errors in PubMed indexed articles.<ref>{{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 }}</ref> 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.<ref>{{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 }}</ref> 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.<ref>{{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}}</ref> ==Characteristics== Line 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}} The examples given in a PubMed tutorial<ref>{{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}}</ref> demonstrate how this automatic process works: {{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])}} ~~Likewise,~~ ~~{{quote\|'''soft~~ 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])}} ====Comprehensive search==== Line 92 ⟶ 85: === See also === 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.<ref>{{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 }}</ref> 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.<ref name="pmid16467730">{{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 = ~~http~~https://~~www.~~escholarship.org/uccontent/~~item~~qt8cn089mk/~~8cn089mk~~qt8cn089mk.pdf?t=nxc986 \| access-date = 11 September 2018 \| archive-date = ~~2 April 2023~~ \| archive-url = ~~https://web.archive.org/web/20230402175315/https://escholarship.org/uc/item/8cn089mk~~ \| url-status = ~~live~~ \| doi-access = free }}</ref> ===Mapping to MeSH=== Line 120 ⟶ 113: === PubMed identifier ===<!-- PMID redirects here --> {{For\|help using PubMed identifiers within Wikipedia\|Wikipedia:PMID}} A '''PMID''' (PubMed identifier or PubMed unique identifier)<ref>{{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 }}</ref> is a [[unique identifier\|unique integer value]], starting at <code>1</code>, 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]].<ref name="PMCID">{{cite web \|last=Keener \|first=Molly ~~\| name-list-style = vanc~~ \|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 }}</ref> 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. Line 142 ⟶ 135: 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. <!-- Citation and link to examples needed! --> Code can be automated to systematically query with different keywords such as disease, year, organs, etc. In addition to its traditional role as a biomedical database, PubMed has become common resource for training biomedical [[Language_model\|language models]].<ref>{{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 }}</ref> 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. The data accessible by PubMed can be mirrored locally using an unofficial tool such as MEDOC.<ref name="MEDOC">{{GitHub \|MrMimic/MEDOC}}</ref> Line 167 ⟶ 160: {{DEFAULTSORT:Pubmed}} [[Category:Internet properties established in 1996]] [[Category:1996 establishments in the United States]] [[Category:American medical websites]] [[Category:Bibliographic databases and indexes]] Line 172 ⟶ 167: [[Category:Databases in the United States]] [[Category:Medical search engines]] [[Category:National Institutes of Health\|PubMed]] [[Category:Online databases]] [[Category:United States National Library of Medicine]\|PubMed]