PubMed Central

PubMed Central (PMC) is a free digital repository that archives publicly accessible full-text scholarly articles that have been published within the biomedical and life sciences journal literature. As one of the major research databases within the suite of resources that have been developed by the National Center for Biotechnology Information (NCBI), PubMed Central is much more than just a document repository. Submissions into PMC undergo an indexing and formatting procedure which results in enhanced metadata, medical ontology, and unique identifiers which all enrich the XML structured data for each article on deposit.[1] Content within PMC can easily be interlinked to many other NCBI databases and accessed via Entrez search and retrieval systems, further enhancing the public's ability to freely discover, read and build upon this portfolio of biomedical knowledge.[2]

PubMed Central is very distinct from PubMed.[3] 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 physically resides elsewhere (in print or online, free or behind a subscriber paywall).

As of December 2018, the PMC archive contained over 5.2 million articles,[4] with contributions coming directly from publishers or authors depositing their own manuscripts into the repository per the NIH Public Access Policy. Older data shows that from Jan 2013 to Jan 2014 author-initiated deposits exceeded 103,000 papers during this 12-month period.[5] PMC also identifies about 4,000 journals which now participate in some capacity to automatically deposit their published content into the PMC repository.[6] Some participating publishers will delay the release of their articles on PubMed Central for a set time after publication, this is often referred to as an "embargo period", and can range from a few months to a few years depending on the journal. (Embargoes of six to twelve months are the most common.) However, PubMed Central is a key example of "systematic external distribution by a third party"[7] which is still prohibited by the contributor agreements of many publishers.

PubMed Central
ProducerUnited States National Library of Medicine (United States)
History2000 to present
Access
CostFree
Coverage
DisciplinesMedicine
Record depthIndex, abstract & full-text
Format coverageJournal articles
Links

Adoption

Launched in February 2000, the repository has grown rapidly as the NIH Public Access Policy is designed to make all research funded by the National Institutes of Health (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 open access to research and is an evolution from the 2005 policy, in which the NIH asked researchers to voluntarily add their research to PubMed Central.[8]

A UK version of the PubMed Central system, UK PubMed Central (UKPMC), has been developed by the Wellcome Trust and the British Library as part of a nine-strong group of UK research funders. This system went live in January 2007. On 1 November 2012, it became Europe PubMed Central. The Canadian member of the PubMed Central International network, PubMed Central Canada, was launched in October 2009.

The National Library of Medicine "NLM Journal Publishing Tag Set" journal article markup language is freely available.[9] The Association of Learned and Professional Society Publishers comments that "it is likely to become the standard for preparing scholarly content for both books and journals".[10] A related DTD is available for books.[11] The Library of Congress and the British Library have announced support for the NLM DTD.[12] It has also been popular with journal service providers.[13]

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.[14] This includes NASA content, with the interface branded as "PubSpace".[15][16]

Technology

Articles are sent to PubMed Central by publishers in XML or SGML, using a variety of article DTDs. Older and larger publishers may have their own established in-house DTDs, but many publishers use the NLM Journal Publishing DTD (see above).

Received articles are converted via XSLT 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 database, along with associated files for graphics, multimedia, or other associated data. Many publishers also provide PDF of their articles, and these are made available without change.[17]

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 of these sources, are tracked in the database and automatically come "live" when the resources become available.

An in-house indexing system provides search capability, and is aware of biological and medical terminology, such as generic vs. proprietary drug names, and alternate names for organisms, diseases and anatomical parts.

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 HTML 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.

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.

Reception

Reactions to PubMed Central among the scholarly publishing community range between a genuine enthusiasm by some,[18] to cautious concern by others.[19] 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 version-of-record, the economic consequences of less readership, as well as the effect on maintaining a community of scholars within learned societies.[20] 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 result of taxpayer support.[21]

The Antelman study of open access publishing found that in philosophy, political science, electrical and electronic engineering and mathematics, open access papers had a greater research impact.[22] A randomised trial found an increase in content downloads of open access papers, with no citation advantage over subscription access one year after publication.[23]

The change in procedure has received criticism.[24] The American Physiological Society has expressed reservations about the implementation of the policy.[25]

PMCID

The PMCID (PubMed Central identifier), also known as the PMC reference number, is a bibliographic identifier for the PubMed Central database, much like the PMID is the bibliographic identifier for the PubMed database. The two identifiers are distinct however. It consists of "PMC" followed by a string of seven numbers. The format is:[26]

  • PMCID: PMC1852221

Authors applying for NIH awards must include the PMCID in their application.

See also

References

  1. ^ Beck, Jeff. "Report from the Field: PubMed Central, an XML-based Archive of Life Sciences Journal Articles". Proceedings of the International Symposium on XML for the Long Haul: Issues in the Long-term Preservation of XML. doi:10.4242/BalisageVol6.Beck01.
  2. ^ Maloney, Chris; Sequeira, Ed; Kelly, Christopher; Orris, Rebecca; Beck, Jeffrey (5 December 2013). "PubMed Central". National Center for Biotechnology Information (US).
  3. ^ "MEDLINE, PubMed, and PMC (PubMed Central): How are they different?". www.nlm.nih.gov.
  4. ^ "Openness by Default", Inside Higher Ed, 16 January 2017.
  5. ^ "NIHMS Statistics". nihms.nih.gov.
  6. ^ "Home - PMC - NCBI". www.ncbi.nlm.nih.gov.
  7. ^ Ouerfelli, Noureddine. "Author rights: what's it all about" (PDF).
  8. ^ "Public access to NIH research made law". Science Codex. 2007. Archived from the original on 4 March 2016. Retrieved 6 November 2013.
  9. ^ "Journal Publishing Tag Set". National Center for Biotechnology Information. Retrieved 6 November 2013.
  10. ^ French, Diane (4 August 2006). "ALPSP Technology Update: A Standard XML Document Format: The case for the adoption of NLM DTD". ALPSP. Retrieved 6 November 2013.
  11. ^ "NCBI Book Tag Set". dtd.nlm.nih.gov.
  12. ^ "News from the Library of Congress". Library of Congress. 19 April 2006. Retrieved 6 November 2013.
  13. ^ "Inera Inc. - NLM DTD Resources". archive.org. 19 February 2013.
  14. ^ "Public Access Plans of U.S. Federal Agencies". cendi.gov.
  15. ^ Kovo, Yael (22 July 2016). "Public Access to Results of NASA-Funded Research". nasa.gov.
  16. ^ "NASA in PMC". preview.ncbi.nlm.nih.gov.
  17. ^ NLM Journal Archiving and Interchange Tag Suite, National Center for Biotechnical Information, National Library of Medicine
  18. ^ PLOS Applauds Congress for Action on Open Access
  19. ^ "ACS Submission to the Office of Science and Technology Policy Request for Information on Public Access to Peer-Reviewed Scholarly Publications Resulting from Federally Funded Research" (PDF). whitehouse.gov. Archived from the original (PDF) on 2012-07-11. Retrieved 2014-02-07.
  20. ^ Davis PM. The effect of public deposit of scientific articles on readership. Physiologist. 2012 Oct;55(5):161, 163-5
  21. ^ "Autism Speaks Announces New Policy to Give Families Easy, Free Access to Key Research Findings - Press Release - Autism Speaks". www.autismspeaks.org. 25 July 2012.
  22. ^ Kristin Antelman (September 2004). "Do Open-Access Articles Have a Greater Research Impact?". College & Research Libraries 65(5). pp. 372–382. and summarized by C&RL News
  23. ^ Davis, Philip M.; Lewenstein, Bruce V.; Simon, Daniel H.; Booth, James G.; Connolly, Mathew J. L. (31 July 2008). "Open access publishing, article downloads, and citations: randomised controlled trial". BMJ. 337: a568. doi:10.1136/bmj.a568. PMID 18669565.
  24. ^ C&RL News: Scholarly Communication in Flux: Entrenchment and Opportunity Kate Thomes, Science & Technology Libraries 22, no. 3/4 (220): 104 "Many faculty see the current system of scholarly communication as an effective, known, and reliable system that is not broken and therefore does not need to be fixed".
  25. ^ The American Physiological Society "Although the American Physiological Society (APS) supports the principle of public access, the NIH approach is a mallet rather than a scalpel. It is likely to harm publishers, which will in turn harm the dissemination of science through the literature".
  26. ^ "Include PMCID in Citations | publicaccess.nih.gov". publicaccess.nih.gov. Retrieved 2017-07-01.

External links

Entrez

The Entrez (pronounced ɒnˈtreɪ) Global Query Cross-Database Search System is a federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website. The NCBI is a part of the National Library of Medicine (NLM), which is itself a department of the National Institutes of Health (NIH), which in turn is a part of the United States Department of Health and Human Services. The name "Entrez" (a greeting meaning "Come in!" in French) was chosen to reflect the spirit of welcoming the public to search the content available from the NLM.

Entrez Global Query is an integrated search and retrieval system that provides access to all databases simultaneously with a single query string and user interface. Entrez can efficiently retrieve related sequences, structures, and references. The Entrez system can provide views of gene and protein sequences and chromosome maps. Some textbooks are also available online through the Entrez system.

Europe PubMed Central

Europe PubMed Central (Europe PMC) is an on-line database that offers free access to a large and growing collection of biomedical research literature. It was known as UK PubMed Central until 1 November 2012. The Europe PMC project was originally launched in 2007 as the first 'mirror' site to PMC, which aims to provide international preservation of the open and free-access biomedical and life sciences literature. It forms part of a network of PMC International (PMCI) repositories that includes PubMed Central Canada. Europe PMC is not an exact "mirror" of the PMC database but has developed some different features. On February 15, 2013, CiteXplore was subsumed under Europe PubMed Central.The resource is managed and developed by the European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), on behalf of an alliance of 27 biomedical and life sciences research funders, led by the Wellcome Trust. The Europe PMC funders group requires that articles describing the results of biomedical and life sciences research they have supported be made freely available in Europe PMC within 6 months of publication to maximise the impact of the work that they fund.

International Journal of Medical Sciences

The International Journal of Medical Sciences is a peer-reviewed open access medical journal published by Ivyspring International Publisher covering research in basic medical sciences. Articles include original research papers, reviews, and short research communications. Full text of published articles is archived in PubMed Central. The current editor-in-chief is Dennis D. Taub (National Institute on Aging).

Journal of Bacteriology

The Journal of Bacteriology is a peer-reviewed medical journal established in 1916. It is published by the American Society for Microbiology (ASM) and the editor in chief is Thomas J. Silhavy. The journal is delayed open access, content is available free at the journal's website and at PubMed Central after a six-month embargo. The journal is also hybrid open access allowing authors to pay $3,000 ($2,000 for ASM members) for their articles to be available free immediately.

NIH Public Access Policy

The NIH Public Access Policy is an open access mandate, drafted in 2004 and mandated in 2008, requiring that research papers describing research funded by the National Institutes of Health must be available to the public free through PubMed Central within 12 months of publication. PubMed Central is the self-archiving repository in which authors or their publishers deposit their publications. Copyright is retained by the usual holders, but authors may submit papers with one of the Creative Commons licenses.

PubMed

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 Online computerized database primarily had been through institutional facilities, such as university libraries. PubMed, first released in January 1996, ushered in the era of private, free, home- and office-based MEDLINE searching. The PubMed system was offered free to the public starting in June 1997.

PubMed Central Canada

PubMed Central Canada (PMC Canada) was a Canadian national digital repository of peer-reviewed health and life sciences literature, taken offline in February 2018. It joined Europe PubMed Central (formerly UK PubMed Central) as a member of the PubMed Central International network. PMC Canada was a partnership between the Canadian Institutes of Health Research (CIHR), the Canada Institute for Scientific and Technical Information (NRC-CISTI, the Canadian National Science Library), and the United States National Library of Medicine (NLM).PMC Canada included an interface in both English and French, to support the use of Canada's two official languages. PubMed Central Canada provided free access to content, and was one of the locations where CIHR researchers could deposit their peer-reviewed research articles, in order to meet with the open-access requirements of the CIHR Policy on Access to Research Outputs.

Schadenfreude

Schadenfreude (; German: [ˈʃaːdn̩ˌfʁɔʏ̯də] (listen); lit. 'harm-joy') is the experience of pleasure, joy, or self-satisfaction that comes from learning of or witnessing the troubles, failures, or humiliation of another. It is one of four related emotions or concepts.

Schadenfreude is a complex emotion, where rather than feeling sympathy towards someone's misfortune, schadenfreude evokes joyful feelings that take pleasure from watching someone fail. This emotion is displayed more in children than adults, however adults also experience schadenfreude, they are just better at concealing their expressions.

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