PubMed Central

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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 ontologies, 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 should not be confused with PubMed. These are two very different services at their core.[3] While PubMed is a searchable database of biomedical citations and abstracts, the full-text article referenced in the PubMed record will physically reside elsewhere. (Sometimes in print, sometimes online, sometimes free, sometimes behind a toll-wall accessible only to paying subscribers). PubMed Central is a free digital archive of articles, accessible to anyone from anywhere via a basic web browser. The full text of all PubMed Central articles is free to read, with varying provisions for reuse.

As of February 2014, the PMC archive contained over 2.9 million articles, with contributions coming directly from publishers or authors depositing their own manuscripts into the repository per the NIH Public Access Policy. Recent data shows that in the past year (Jan 2013 – Jan 2014) author initiated deposits exceeded 103,000 papers during just this 12 month period.[4] PMC also identifies about 4,000 journals which now participate in some capacity to automatically deposit their published content into the PMC repository.[5] 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).

Adoption[edit]

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.[6]

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.[7] 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".[8] A related DTD is available for books.[9] The Library of Congress and the British Library have announced support for the NLM DTD.[10] It has also been popular with journal service providers.[11]

Technology[edit]

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.[12]

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[edit]

Reactions to PubMed Central among the scholarly publishing community range between a genuine enthusiasm by some,[13] to cautious concern by others.[14] 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.[15] 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.[16]

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.[17] A randomised trial found an increase in content downloads of open access papers, with no citation advantage over subscription access one year after publication.[18]

The change in procedure has received criticism.[19] The American Physiological Society has expressed reservations about the implementation of the policy.[20]

See also[edit]

  • JATS (technology)
  • MEDLINE, an international literature database of life sciences and biomedical information
  • PMID (PubMed Identifier)
  • SciELO (similar service)

Notes[edit]

  1. ^ Beck, Jeff. Report from the Field: PubMed Central, an XML-based Archive of Life Sciences Journal Articles.
  2. ^ NCBI Handbook: PubMed Central. Chris Maloney, Ed Sequeira, Christopher Kelly, Rebecca Orris, and Jeffrey Beck Dec 2013
  3. ^ MEDLINE, PubMed, and PMC (PubMed Central): How are they different?
  4. ^ NIH Manuscript Submission Statistics
  5. ^ PubMedCentral
  6. ^ "Public access to NIH research made law". Science Codex. 2007. Retrieved 6 November 2013. 
  7. ^ "Journal Publishing Tag Set". National Center for Biotechnology Information. Retrieved 6 November 2013. 
  8. ^ 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. 
  9. ^ NLM-NCBI Book Tag Set
  10. ^ "News from the Library of Congress". Library of Congress. 19 April 2006. Retrieved 6 November 2013. 
  11. ^ Inera NLM DTD Resources
  12. ^ NLM Journal Archiving and Interchange Tag Suite, National Center for Biotechnical Information, National Library of Medicine
  13. ^ PLOS Applauds Congress for Action on Open Access
  14. ^ 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
  15. ^ Davis PM. The effect of public deposit of scientific articles on readership. Physiologist. 2012 Oct;55(5):161, 163-5
  16. ^ Autism Speaks Announces New Policy to Give Families Easy, Free Access to Key Research Findings
  17. ^ 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
  18. ^ Open access publishing, article downloads, and citations: randomised controlled trial
  19. ^ 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".
  20. ^ 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".

External links[edit]