PubMed Central
Encyclopedia
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 (NLM) as an online archive of biomedical journal articles.
The full text of all PubMed Central articles is available free. Some participating publishers, however, delay release of their articles for a set time after paper publication (often six months).
, the archive contains approximately 2.2 million items, including articles, editorials and letters. It appears to be growing by at least 7% per year. , PubMed Central, PubMed, and related NLM services were handling approximately 1,300 hits per second, and supplying 1.3 terabytes of data per day.
's "Policy on Enhancing Public Access to Archived Publications Resulting from NIH-Funded Research" 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 the their research to PubMed Central.
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 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. 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." A related DTD
is available for books. The Library of Congress
and the British Library have announced support for the NLM DTD. It has also been popular with journal service providers.
or SGML, using a variety of article DTD
s. 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.
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.
The change in procedure has received criticism. The American Physiological Society has expressed reservations about the implementation of the policy.
Bibliographic database
A bibliographic database is a database of bibliographic records, an organized digital collection of references to published literature, including journal and newspaper articles, conference proceedings, reports, government and legal publications, patents, books, etc...
of full-text scientific literature
Scientific literature
Scientific literature comprises scientific publications that report original empirical and theoretical work in the natural and social sciences, and within a scientific field is often abbreviated as the literature. Academic publishing is the process of placing the results of one's research into the...
in biomedical and life sciences. It grew from the online Entrez
Entrez
The Entrez Global Query Cross-Database Search System is a powerful federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information website...
PubMed
PubMed
PubMed is a free database accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez information retrieval system...
biomedical literature search system. PubMed Central was developed by the U.S. National Library of Medicine (NLM) as an online archive of biomedical journal articles.
The full text of all PubMed Central articles is available free. Some participating publishers, however, delay release of their articles for a set time after paper publication (often six months).
, the archive contains approximately 2.2 million items, including articles, editorials and letters. It appears to be growing by at least 7% per year. , PubMed Central, PubMed, and related NLM services were handling approximately 1,300 hits per second, and supplying 1.3 terabytes of data per day.
Adoption
The repository has grown rapidly, as the U.S. National Institutes of HealthNational Institutes of Health
The National Institutes of Health are an agency of the United States Department of Health and Human Services and are the primary agency of the United States government responsible for biomedical and health-related research. Its science and engineering counterpart is the National Science Foundation...
's "Policy on Enhancing Public Access to Archived Publications Resulting from NIH-Funded Research" 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 the their research to PubMed Central.
A UK version of the PubMed Central system, UK PubMed Central (UKPMC), has been developed by the Wellcome Trust
Wellcome Trust
The Wellcome Trust was established in 1936 as an independent charity funding research to improve human and animal health. With an endowment of around £13.9 billion, it is the United Kingdom's largest non-governmental source of funds for biomedical research...
and the British Library
British Library
The British Library is the national library of the United Kingdom, and is the world's largest library in terms of total number of items. The library is a major research library, holding over 150 million items from every country in the world, in virtually all known languages and in many formats,...
as part of a nine-strong group of UK research funders. This system went live in January 2007. The Canadian member of the PubMed Central International network, PubMed Central Canada
PubMed Central Canada
PubMed Central Canada is a Canadian national digital repository of peer-reviewed health and life sciences literature. It joins UK PubMed Central as a member of the PubMed Central International network...
, was launched in October 2009.
The National Library of Medicine "NLM Journal Publishing Tag Set" journal article markup language
Markup language
A markup language is a modern system for annotating a text in a way that is syntactically distinguishable from that text. The idea and terminology evolved from the "marking up" of manuscripts, i.e. the revision instructions by editors, traditionally written with a blue pencil on authors' manuscripts...
is freely available. 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." A related DTD
Document Type Definition
Document Type Definition is a set of markup declarations that define a document type for SGML-family markup languages...
is available for books. The Library of Congress
Library of Congress
The Library of Congress is the research library of the United States Congress, de facto national library of the United States, and the oldest federal cultural institution in the United States. Located in three buildings in Washington, D.C., it is the largest library in the world by shelf space and...
and the British Library have announced support for the NLM DTD. It has also been popular with journal service providers.
Technology
Articles are sent to PubMed Central by publishers in XMLXML
Extensible Markup Language is a set of rules for encoding documents in machine-readable form. It is defined in the XML 1.0 Specification produced by the W3C, and several other related specifications, all gratis open standards....
or SGML, using a variety of article DTD
Document Type Definition
Document Type Definition is a set of markup declarations that define a document type for SGML-family markup languages...
s. 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
XSLT
XSLT is a declarative, XML-based language used for the transformation of XML documents. The original document is not changed; rather, a new document is created based on the content of an existing one. The new document may be serialized by the processor in standard XML syntax or in another format,...
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.
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
Medical terminology
Medical terminology is a vocabulary for accurately describing the human body and associated components, conditions, processes and process in a science-based manner. Some examples are: R.I.C.E., trapezius, and latissimus dorsi. It is to be used in the medical and nursing fields...
, 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
HTML
HyperText Markup Language is the predominant markup language for web pages. HTML elements are the basic building-blocks of webpages....
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
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. A randomised trial found that an increase in content downloads of open access papers, with no citation advantage over subscription access one year after publication.The change in procedure has received criticism. The American Physiological Society has expressed reservations about the implementation of the policy.
See also
- MEDLINEMEDLINEMEDLINE is a bibliographic database of life sciences and biomedical information. It includes bibliographic information for articles from academic journals covering medicine, nursing, pharmacy, dentistry, veterinary medicine, and health care...
, an international literature database of life sciences and biomedical information - PMID (PubMed Identifier)