PubMed Central

PubMed Central

Encyclopedia

Tutorials

Encyclopedia

Dictionary

Directory

Email this to a friend PubMed_Central

PubMed Central

PubMed Central is a free digital database of full-text scientific literature in biomedical and life sciences.

It grew from the online Entrez PubMed biomedical literature search system. PubMed Central was developed by the U.S. National Library of Medicine as an online archive of biomedical journal articles. The full text of all PubMed Central articles is available free. Some participating journals, however, delay release of their articles for a set time after paper publication (often 6 months).

As of June 2007, the archive contains approximately 1,000,000 items, including articles, editorials, letters, and so on. It appears to be growing by at least 7% per year.

The minutes of the NIH Board of Regents at http://www.nlm.nih.gov/od/bor/bor904.pdf#search=%22%20terabytes%20%22per%20day%22%22 indicate that as of September, 2004, PubMedCentral, PubMed, and related NLM service were handling approximately 1300 hits per second, and supplying 1.3 Terabytes of data per day; no doubt the numbers are much higher today (hit rates would likely rise faster than archive size).

Adoption
PubMed Central Technology
References
See also
External links

Adoption

This repository has grown rapidly, as the U.S. NIH's "Policy on Enhancing Public Access to Archived Publications Resulting from NIH-Funded Research" ^[1] is designed to make all research funded by NIH freely accessible to anyone, and, in addition, many publishers are working cooperatively with the NIH to provide free access to their works.

Some publishers may be reluctant to make works freely available online in any form, including archives such as PubMed Central, fearing that it will reduce traffic to their journals, and ultimately harm sales. There may be a positive impact on citations, as some studies have found open access papers to be more highly cited^[2]. However, the first randomised trial of open access found that there was no citation advantage for open access papers^[3], and that the perceived benefit was likely due to other factors.

Scientific Societies have also expressed reservations about the implementation of the policy, particularly as many rely on the income from journals to survive^[4]. See also Open Access for more information on this debate.

In late 2007, the Consolidated Appropriations Act of 2007 (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 the their research to PubMed Central. ^[5]

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.

The National Library of Medicine "NLM Journal Publishing DTD" http://dtd.nlm.nih.gov/publishing/ is freely available, and appears to be the most widely used journal article markup language. The Association of Learned and Professional Society Publishers http://www.alpsp.org has held seminars titled A Standard XML Document Format: The case for the adoption of NLM DTD? http://www.alpsp.org/events/2006/DTD/default.htm, commenting that "it is likely to become the standard for preparing scholarly content for both books and journals." A related DTD is available for books http://dtd.nlm.nih.gov/book/.

The Library of Congress and the British Library have announced support for the NLM DTD http://www.loc.gov/today/pr/2006/06-097.html. It has also been popular with journal service providers http://www.inera.com/nlmresources.shtml.

PubMed Central Technology

(not all information in this section has been verified)

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 http://dtd.nlm.nih.gov/. 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.

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; alternate names for organisms, diseases, anatomical parts; and so on.

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 PMC using the NIH Manuscript Submission (NIHMS). Articles thus submitted typically go through XML markup in order to be converted to NLM DTD.