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PubMed Central

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985:"The goal of the semantic web is to express real life. Many things in real life, real questions which we will face are not efficiently computable. There are two solutions to this: The classical (pre-web) solution is to constrain the language of expression so that all queries terminate in finite time. The weblike solution is to allow the expression of facts and rules in an overall language which is sufficiently flexible and powerful to express real life. Create subsets fo the web in which specific constraints give you specific computational properties. An anlogy is with the human-information systems which existed before the web. Most forced one to keep ones data in a hierarchy (sometimes of fixed depth or a matrix (often with a specific number of dimensions). This gave consistency properties within the information system. I bet DARPA has many of these systems and still does. They only way they could be integrated was to express them in terms of a much more powerful language - global hypertext. Hypertext did not have any of these reassuring properties. People were frightened about getting lost in it. You could follow links forever. As it turns out, it is true of course that there is a problem that you can follow links forever in the Web. " 316:
National Institutes of Health in the spring of 1999. Varmus envisioned a digital archive of journals, accessible free of charge and with the added value of reference linking. "Our consensus was that publishers should be the ones doing the linking," said Bob Campbell, who chaired the meeting. "Since we were 'higher up the stream,' so to speak, we should be able to link our articles ahead of the NLM as part of the process of producing them. Stefan von Holtzbrinck then set the ball rolling by offering to link Nature publications with anyone else's. We decided to issue an announcement of a broad STM reference linking initiative. It was, of course, a strategic move only, since we had neither plan nor prototype."
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by the physicist Paul Ginsparg and his colleagues at Los Alamos to allow physicists and mathematicians to share their work with one another over the Internet. They were posting "preprints" (articles not yet submitted or accepted for publication) at a publicly accessible website (called LanX or arXiv) for anyone to read and critique. The more I thought about this, the more I was convinced that a radical restructuring of methods for publishing, transmitting, storing, and using biomedical research reports might be possible and beneficial. In a spirit of enthusiasm and political innocence, I wrote a lengthy manifesto, proposing the creation of an NIH-supported online system, called E-biomed.
234:. Earlier data shows that from January 2013 to January 2014 author-initiated deposits exceeded 103,000 papers during a 12-month period. PMC identifies about 4,000 journals which participate in some capacity to deposit their published content into the PMC repository. Some publishers delay the release of their articles on PubMed Central for a set time after publication, referred to as an "embargo period", ranging from a few months to a few years depending on the journal. (Embargoes of six to twelve months are the most common.) PubMed Central is a key example of "systematic external distribution by a third party", which is still prohibited by the contributor agreements of many publishers. 367:(NIH) freely accessible to anyone, and, in addition, many publishers are working cooperatively with the NIH to provide free access to their works. In late 2007, the Consolidated Appropriations Act of 2008 (H.R. 2764) was signed into law and included a provision requiring the NIH to modify its policies and require inclusion into PubMed Central complete electronic copies of their peer-reviewed research and findings from NIH-funded research. These articles are required to be included within 12 months of publication. This is the first time the US government has required an agency to provide 109: 291:, with an external editorial board retaining control over the process of reviewing, curating, and listing papers which would otherwise be freely accessible on the central E-biomed server. Varmus intended to realize the new possibilities presented by communicating scientific results digitally, imagining continuous conversation about published work, versioned documents, and enriched "layered" formats allowing for multiple levels of detail. 496:, the economic consequences of less readership, as well as the effect on maintaining a community of scholars within learned societies. A 2013 analysis found strong evidence that public repositories of published articles were responsible for "drawing significant numbers of readers away from journal websites" and that "the effect of PMC is growing over time". 320:
of the service that would become CrossRef was immediately apparent. Organizations such as AIP and IOP (Institute of Physics) had begun to link to each other's publications, and the impossibility of replicating such one-off arrangements across the industry was obvious. As Tim Ingoldsby later put it, "All those linking agreements were going to kill us."
223:. PubMed Central is a free digital archive of full articles, accessible to anyone from anywhere via a web browser (with varying provisions for reuse). Conversely, although PubMed is a searchable database of biomedical citations and abstracts, the full-text article resides elsewhere (in print or online, free or behind a subscriber 277:
But my views broadened abruptly one morning in December of 1998 when I met Pat Brown for coffee, at the café that was formerly the famed Tassajara Bakery, on the corner of Cole and Parnassus, during a visit to San Francisco. A few weeks before our coffee, Pat had learned about the methods being used
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Libraries, universities, open access supporters, consumer health advocacy groups, and patient rights organizations have applauded PubMed Central, and hope to see similar public access repositories developed by other federal funding agencies so to freely share any research publications that were the
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Bibliographic citations are parsed and automatically linked to the relevant abstracts in PubMed, articles in PubMed Central, and resources on publishers' Web sites. PubMed links also lead to PubMed Central. Unresolvable references, such as to journals or particular articles not yet available at one
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A small group led by Arnoud de Kemp of Springer-Verlag met in an adjacent room immediately following the Board meeting to draft the announcement, which was distributed to all attendees of the STM annual meeting the following day and published in an STM membership publication. The potential benefit
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Under pressure from vigorous lobbying from commercial publishers and scientific societies who feared for lost profits, NIH officials announced a revised PubMed Central proposal in August 1999. PMC would receive submissions from publishers, rather than from authors as in E-biomed. Publications were
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At the Board meeting of the STM association, held the afternoon of Monday, October 11, before the fair's Wednesday opening, discussion focused on an emerging U.S. National Library of Medicine (NLM) initiative called E-Biomed (later PubMed Central) that had been proposed by Harold Varmus of the
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to the very similar NLM Archiving and Interchange DTD. This process may reveal errors that are reported back to the publisher for correction. Graphics are also converted to standard formats and sizes. The original and converted forms are archived. The converted form is moved into a relational
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and create their own indexing system was a wholly new idea. Major commercial publishers had begun experimenting with an indexing system for scientific papers shared across publishers as early as 1993, and were spurred to action following the E-biomed proposal. At the October 1999
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When a user accesses a journal issue, a table of contents is automatically generated by retrieving all articles, letters, editorials, etc. for that issue. When an actual item such as an article is reached, PubMed Central converts the NLM markup to
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In a separate submission stream, NIH-funded authors may deposit articles into PubMed Central using the NIH Manuscript Submission (NIHMS). Articles thus submitted typically go through XML markup in order to be converted to NLM DTD.
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While PMC is a welcome partner to open access publishers in its ability to augment the discovery and dissemination of biomedical knowledge, that same truth causes others to worry about traffic being diverted from the published
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With the release of public access plans for many agencies beyond NIH, PMC is in the process of becoming the repository for a wider variety of articles. This includes NASA content, with the interface branded as "PubSpace".
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The goal of E-biomed was to provide free access to all biomedical research. Papers submitted to E-biomed could take one of two routes: either immediately published as a preprint, or through a traditional
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papers had a greater research impact. A randomised trial found an increase in content downloads of open access papers, with no citation advantage over subscription access one year after publication.
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To support this initiative, NLM is adapting its standard procedures for depositing articles into PMC to provide greater flexibility that will ensure coronavirus research is readily available.
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As of December 2018, the PMC archive contained over 5.2 million articles, with contributions coming from publishers or authors depositing their manuscripts into the repository per the
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The proposal to create a central index of biomedical research was a radical departure from prevailing publishing norms. Prior to the internet, publication indexes operated largely like
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for delivery, and provides links to related data objects. This is feasible because the variety of incoming data has first been converted to standard DTDs and graphic formats.
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Ashburner, Michael; Brown, Patrick O.; Eisen, Michael; Kirschner, Marc; Khosla, Chaitan; Nusse, Roel; Roberts, Richard J.; Scott, Matthew; Varmus, Harold; Wold, Barbara.
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The Antelman study of open access publishing found that in philosophy, political science, electrical and electronic engineering and mathematics,
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Reactions to PubMed Central among the scholarly publishing community range between a genuine enthusiasm by some, to cautious concern by others.
441:. Older and larger publishers may have their own established in-house DTDs, but many publishers use the NLM Journal Publishing DTD (see above). 329:
up to one year. PMC would only allow peer-reviewed work — no preprints. The then-unnamed publisher-led linking system shortly thereafter became
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to research and is an evolution from the 2005 policy, in which the NIH asked researchers to voluntarily add their research to PubMed Central.
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search and retrieval systems, further enhancing the public's ability to discover, read and build upon its biomedical knowledge.
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as part of a nine-strong group of UK research funders. This system went live in January 2007. On 1 November 2012, it became
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comments that "it is likely to become the standard for preparing scholarly content for both books and journals". A related
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and the British Library have announced support for the NLM DTD. It has also been popular with journal service providers.
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database, along with associated files for graphics, multimedia, or other associated data. Many publishers also provide
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of these sources, are tracked in the database and automatically come "live" when the resources become available.
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Proceedings of the International Symposium on XML for the Long Haul: Issues in the Long-term Preservation of XML
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Beck J (2010). "Report from the Field: PubMed Central, an XML-based Archive of Life Sciences Journal Articles".
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structured data for each article. Content within PMC can be linked to other NCBI databases and accessed via
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In March 2020, PubMed Central accelerated its deposit procedures for the full text of publications on
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Saunders, Jonny (September 1, 2022). "Decentralized Infrastructure for (Neuro)science". p. 26.
2188: 2146: 511: 461: 414: 108: 1708:"The National Library of Medicine expands access to coronavirus literature through PubMed Central" 844:"E-Biomed: A Proposal for Electronic Publications in the Biomedical Sciences (Draft and Addendum)" 2557: 2193: 2165: 2073: 1827: 966: 181: 1346: 1204:"ALPSP Technology Update: A Standard XML Document Format: The case for the adoption of NLM DTD" 2613: 2501: 2468: 2289: 2210: 2048: 2023: 1868: 1840: 1689: 1551: 1497: 1488:
Davis PM (October 2012). "The effect of public deposit of scientific articles on readership".
933: 650: 493: 1154: 2602: 2516: 2238: 2160: 1921: 1679: 1671: 1638: 1612: 1541: 1531: 896: 884: 642: 465: 1740: 1086:"The Scholars Rebellion Against Scholarly Publishing Practices: Varmus, Vitek, and Venting" 885:"The real stakes of virtual publishing: The transformation of E-Biomed into PubMed central" 2577: 2374: 2364: 2311: 2294: 2220: 2104: 2033: 402: 383: 308: 288: 1117:"Letter from the Public Library of Science [to signers of the PLoS open letter]" 2526: 2496: 2432: 2399: 2369: 2318: 2205: 2200: 2063: 2018: 2008: 2003: 1858: 1850: 1684: 1660:"Open access publishing, article downloads, and citations: randomised controlled trial" 1659: 1546: 1519: 557:
database. The two identifiers are distinct however. It consists of "PMC" followed by a
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An in-house indexing system provides search capability, and is aware of biological and
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and international scientists to improve access for scientists, healthcare providers,
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reached a hurried conference room consensus to launch their competitor prototype:
253:. The idea came to him "abruptly" in December 1998, inspired by the early use of 2562: 2420: 2379: 2233: 2043: 1863: 1259: 671: 646: 518: 368: 299: 284: 185: 17: 927: 2442: 2344: 1916: 1813: 1782: 988: 699: 542: 189: 150: 2463: 2306: 1911: 1643: 1626: 843: 1693: 1555: 1501: 1293: 2536: 2531: 2458: 2248: 1617: 1600: 1536: 468:
names, and alternate names for organisms, diseases and anatomical parts.
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Davis PM, Lewenstein BV, Simon DH, Booth JG, Connolly MJ (July 2008).
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Journal of the American Society for Information Science and Technology
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identifier for the PubMed Central open access database, much like the
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Maloney C, Sequeira E, Kelly C, Orris R, Beck J (December 5, 2013).
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Launched in February 2000, the repository has grown rapidly as the
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journals. As one of the major research databases developed by the
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of their articles, and these are made available without change.
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The NIH policy and open access repository work has inspired a
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process. The peer review process was to resemble contemporary
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which has sparked action in other federal agencies as well.
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Repository of freely accessible biomedical journal articles
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Association of Learned and Professional Society Publishers
1601:"Do Open-Access Articles Have a Greater Research Impact?" 932:. New york: W.W. Norton & Company. pp. 255–256. 188:
full-text scholarly articles that have been published in
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Annual Frankfurt Conference, several publishers led by
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Kling, Rob; Spector, Lisa B.; Fortuna, Joanna (2004).
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Articles are sent to PubMed Central by publishers in
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awards must include the PMCID in their application.
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Health Insurance Portability and Accountability Act
1849: 1820: 1741:"Include PMCID in Citations | publicaccess.nih.gov" 521:. The NLM did so upon request from the White House 145: 121: 116: 98: 90: 82: 74: 69: 61: 56: 48: 37: 1421:"PLOS Applauds Congress for Action on Open Access" 1339:"Public Access to Results of NASA-Funded Research" 1179:. National Center for Biotechnology Information. 401:"NLM Journal Publishing Tag Set" journal article 545:), also known as the PMC reference number, is a 341:went on to found the Public Library of Science ( 363:is designed to make all research funded by the 275: 1937:Participative decision-making in organizations 1308:"Public Access Plans of U.S. Federal Agencies" 2131: 1798: 1391:"Journal Archiving and Interchange Tag Suite" 198:National Center for Biotechnology Information 8: 337:system. Varmus, Brown, and others including 32: 374:A UK version of the PubMed Central system, 2727:United States National Library of Medicine 2138: 2124: 2116: 1805: 1791: 1783: 1021:The Formation of CrossRef: A Short History 837: 835: 613:(similar project focused on Latin America) 208:, and unique identifiers which enrich the 107: 42:United States National Library of Medicine 1683: 1642: 1616: 1545: 1535: 970: 246:, initially proposed in May 1999 by then- 1147:"Public access to NIH research made law" 553:is the bibliographic identifier for the 1513: 1511: 1455:Office of Science and Technology Policy 629: 523:Office of Science and Technology Policy 261:after a presentation from Pat Brown of 1751:from the original on December 29, 2020 1718:from the original on December 21, 2020 1465:from the original on February 13, 2017 31: 2646:Academic databases and search engines 1965:Health information on Knowledge (XXG) 1631:College & Research Libraries News 1240:from the original on October 16, 2020 1210:from the original on October 26, 2020 1183:from the original on October 16, 2020 1127:from the original on October 30, 2023 1123:. 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Archived from 1270:from the original on April 17, 2016 1260:"News from the Library of Congress" 1121:Harold Varmus - Profiles in Science 2416:Academic journal publishing reform 1957:Health information on the Internet 1580:from the original on June 12, 2018 1371:from the original on July 27, 2020 1096:from the original on July 30, 2020 680:from the original on July 28, 2020 25: 842:Varmus, Harold (April 19, 1999). 1605:College & Research Libraries 1290:"Inera Inc. - NLM DTD Resources" 1055:"Public Library of Science post" 747:NIH Manuscript Submission System 394:, was launched in October 2009. 219:PubMed Central is distinct from 2090:Open-source healthcare software 929:The Art and Politics of Science 86:Index, abstract & full-text 1625:Stemper J, Williams K (2006). 99: 1: 2707:National Institutes of Health 2676:Category:Scientific documents 437:, using a variety of article 365:National Institutes of Health 2671:Category:Academic publishing 1177:"Journal Publishing Tag Set" 500:result of taxpayer support. 413:is available for books. The 399:National Library of Medicine 378:, has been developed by the 1907:Doctor–patient relationship 1814:Telemedicine and telehealth 1202:French D (August 4, 2006). 1053:Public Library of Science. 647:10.4242/BalisageVol6.Beck01 561:of numbers. The format is: 512:2013 presidential directive 2743: 2489:Indexes and search engines 1942:Patient Activation Measure 1599:Antelman, Kristin (2004). 541:The PMCID (PubMed Central 533:, and the general public. 352: 2014:Remote patient monitoring 531:AI healthcare researchers 405:is freely available. The 376:UK PubMed Central (UKPMC) 1970:Online patient education 1874:Electronic health record 1365:preview.ncbi.nlm.nih.gov 1337:Kovo Y (July 22, 2016). 1059:The Harold Varmus Papers 361:NIH Public Access Policy 355:NIH Public Access Policy 242:PubMed Central began as 232:NIH Public Access Policy 2666:Style/formatting guides 2568:Scholarly communication 2268:Other publication types 1644:10.5860/crln.67.11.7720 1027:. CrossRef. p. 8. 926:Varmus, Harold (2009). 728:"Openness by Default", 325:allowed time-embargoed 2608:Least publishable unit 2280:Collection of articles 2095:Patient opinion leader 1947:Shared decision-making 1884:Personal health record 1518:Davis PM (July 2013). 1153:. 2007. Archived from 527:data mining innovators 464:, such as generic vs. 322: 280: 2598:Electronic publishing 2573:Scientific literature 2350:Article-level metrics 1927:Knowledge translation 1894:Patient participation 1296:on February 19, 2013. 854:(99). 101584926X356. 706:. September 9, 2019. 606:PubMed Central Canada 583:Europe PubMed Central 569:Authors applying for 392:PubMed Central Canada 388:Europe PubMed Central 313: 2712:Open-access archives 2697:Biological databases 2641:Open-access journals 2588:Open scientific data 2395:SCImago Journal Rank 2355:Author-level metrics 2340:Acknowledgment index 2100:Research participant 1745:publicaccess.nih.gov 1618:10.5860/crl.65.5.372 1574:www.autismspeaks.org 1537:10.1096/fj.13-229922 753:on February 10, 2014 2636:Scientific journals 2147:Academic publishing 1821:Background concepts 1349:on August 19, 2016. 1318:on October 18, 2020 1264:Library of Congress 1230:"NCBI Book Tag Set" 602:(PubMed Identifier) 462:medical terminology 415:Library of Congress 34: 2656:Copyright policies 2651:University presses 2558:Scientific writing 2426:Citation advantage 2333:Impact and ranking 2166:Scientific journal 2074:Telerehabilitation 1828:Health informatics 1714:. March 25, 2020. 1266:. April 19, 2006. 987:Berners-Lee, Tim. 743:"NIHMS Statistics" 732:, 16 January 2017. 182:digital repository 2717:Medical databases 2684: 2683: 2661:Preprint policies 2631:Academic journals 2614:Publish or perish 2469:Version of record 2409:Reform and access 2211:Literature review 2113: 2112: 2049:Teleophthalmology 2039:Telemental health 2024:Tele-epidemiology 1869:De-identification 1841:Telecommunication 1576:. July 25, 2012. 1496:(5): 161, 163–5. 1475:National Archives 1018:CrossRef (2009). 993:Web design issues 939:978-0-393-06128-4 901:10.1002/asi.10352 656:978-1-935958-02-4 619:(similar service) 565:PMCID: PMC1852221 494:version of record 171: 170: 16:(Redirected from 2734: 2603:Ingelfinger rule 2517:Semantic Scholar 2239:Technical report 2161:Academic journal 2140: 2133: 2126: 2117: 1922:Health education 1807: 1800: 1793: 1784: 1779: 1778: 1776:Official website 1761: 1760: 1758: 1756: 1737: 1731: 1730: 1725: 1723: 1704: 1698: 1697: 1687: 1676:10.1136/bmj.a568 1655: 1649: 1648: 1646: 1623:, summarized by 1622: 1620: 1596: 1590: 1589: 1587: 1585: 1566: 1560: 1559: 1549: 1539: 1515: 1506: 1505: 1490:The Physiologist 1485: 1479: 1478: 1472: 1470: 1464: 1451: 1443: 1437: 1436: 1434: 1432: 1423:. Archived from 1417: 1411: 1410: 1408: 1406: 1387: 1381: 1380: 1378: 1376: 1357: 1351: 1350: 1345:. Archived from 1334: 1328: 1327: 1325: 1323: 1314:. 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Archived from 739: 733: 730:Inside Higher Ed 726: 720: 719: 717: 715: 696: 690: 689: 687: 685: 667: 661: 660: 634: 466:proprietary drug 289:overlay journals 167: 164: 162: 160: 158: 156: 154: 152: 141: 138: 136: 134: 132: 130: 128: 112: 111: 101: 94:Journal articles 35: 21: 18:PMC (identifier) 2742: 2741: 2737: 2736: 2735: 2733: 2732: 2731: 2687: 2686: 2685: 2680: 2619: 2578:Learned society 2541: 2483: 2447: 2404: 2375:Journal ranking 2365:Citation impact 2328: 2263: 2221:Grey literature 2215: 2177: 2149: 2144: 2114: 2109: 2105:Virtual patient 2078: 2034:Teledermatology 1984: 1951: 1888: 1845: 1816: 1811: 1774: 1773: 1770: 1765: 1764: 1754: 1752: 1739: 1738: 1734: 1721: 1719: 1706: 1705: 1701: 1657: 1656: 1652: 1637:(11): 692–696. 1624: 1598: 1597: 1593: 1583: 1581: 1568: 1567: 1563: 1517: 1516: 1509: 1487: 1486: 1482: 1468: 1466: 1462: 1449: 1445: 1444: 1440: 1430: 1428: 1419: 1418: 1414: 1404: 1402: 1395:dtd.nlm.nih.gov 1389: 1388: 1384: 1374: 1372: 1359: 1358: 1354: 1336: 1335: 1331: 1321: 1319: 1306: 1305: 1301: 1288: 1287: 1283: 1273: 1271: 1258: 1257: 1253: 1243: 1241: 1234:dtd.nlm.nih.gov 1228: 1227: 1223: 1213: 1211: 1201: 1200: 1196: 1186: 1184: 1175: 1174: 1170: 1160: 1158: 1145: 1144: 1140: 1130: 1128: 1114: 1113: 1109: 1099: 1097: 1083: 1082: 1078: 1068: 1066: 1052: 1051: 1047: 1037: 1035: 1031: 1024: 1017: 1016: 1012: 1002: 1000: 986: 984: 980: 964: 963: 959: 949: 947: 940: 925: 924: 920: 910: 908: 882: 881: 874: 864: 862: 858: 841: 840: 833: 823: 821: 817: 806: 801: 800: 796: 786: 784: 771: 770: 766: 756: 754: 741: 740: 736: 727: 723: 713: 711: 704:www.nlm.nih.gov 698: 697: 693: 683: 681: 669: 668: 664: 657: 641:. 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Index

PMC (identifier)
United States National Library of Medicine
Edit this on Wikidata
www.ncbi.nlm.nih.gov/pmc/
www.ncbi.nlm.nih.gov/pmc/journals/
digital repository
open access
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life sciences
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XML
Entrez
PubMed
paywall
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E-biomed
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Harold Varmus
arXiv
preprints
Stanford
David Lipman
NCBI
peer review
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ISBNs
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STM

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