How many hamsters does it take? Under the hood at PMC

2017 ◽  
Author(s):  
Jeffrey D. Beck
Keyword(s):  
Full Text ◽  
Life Sciences ◽  
National Library ◽  
Pubmed Central ◽  
Journal Literature ◽  
True Story ◽  
The U.S

PubMed Central (PMC) is a free full-text XML-based archive of biomedical and life sciences journal literature at the U.S. National Library of Medicine. Publishers submit XML, images, and supplemental files for their articles, the text converts to a common JATS XML, and they load to the database cleanly. The power of XML compels it! But that is not the whole story (or even a true story). Policies, miscommunications, and technical misunderstandings conspire against our Utopian XML workflow. We will share the details of how we get 30,000 new articles into the archive each month.

scholarly journals Attempts to modernize XML conversion at PubMed Central

2021 ◽  
Author(s):  
Martin Latterner ◽  
Dax Bamberger ◽  
Kelly Peters ◽  
Jeffrey D. Beck
Keyword(s):  
Full Text ◽  
Life Sciences ◽  
National Library ◽  
Pubmed Central ◽  
Journal Literature ◽  
Conversion Operation ◽  
The U.S

PubMed Central® (PMC) is a free full-text archive of biomedical and life sciences journal literature at the U.S. National Institutes of Health's National Library of Medicine. PMC receives about 70,000 XML articles every month and uses XSLT to convert them into its preferred format. In 2021, PMC started to explore options to modernize its extensive conversion codebase leveraging XSLT 3.0. This paper describes XML conversion and its challenges at PMC. It then outlines the first approach that PMC is evaluating: breaking a single conversion operation into multiple, dynamic transformations using fn:transform, one of the powerful new tools available with XSLT 3.0.

Report from the Field: PubMed Central, an XML-based Archive of Life Sciences Journal Articles

2010 ◽  
Author(s):  
Jeff Beck
Keyword(s):  
Full Text ◽  
Life Sciences ◽  
Evaluation Process ◽  
Public Access ◽  
Data Evaluation ◽  
Journal Articles ◽  
Pubmed Central ◽  
Journal Literature ◽  
The U.S

PubMed Central (PMC) is an XML-based archive of life sciences journal literature at the U.S. National Institutes of Heath that allows public access to full-text journal articles. The archive was created in 2000 and has grown steadily to over 2 million records. The project has been successful in part because of the strict XML control and the flexibility that PMC givesre its submitters. This paper gives an overview of the PMC data evaluation process; the XML processing model; the PMC philosophy toward XML use, including use of the NLM DTD, XML Taggging Style, usability or reusablilty of the XML, public XML tools, and our people; and some challenges we continue to face maintaining the archive.

scholarly journals Better Normal, A Silver Lining in 2020: JAFES is Accepted for Indexing in PubMed Central

2020 ◽  
Vol 35 (2) ◽  
pp. 151-152
Author(s):  
Elizabeth Paz-Pacheco ◽  
Keyword(s):  
Open Access ◽  
Full Text ◽  
Citation Index ◽  
Life Sciences ◽  
Journal Articles ◽  
National Library ◽  
Pubmed Central ◽  
The Us ◽  
Print Journal ◽  
Silver Lining

Amid the uncertainties and challenges brought on by the COVID-19 pandemic, we celebrate another major milestone in the continuing journey of the JAFES. We formally announce here our acceptance to PubMed Central after being included in Scopus and Clarivate Analytics Emerging Sources Citation Index in the last 2 years. Launched in 2000, PubMed Central is a free archive of full-text biomedical and life sciences journal articles, serving as a digital counterpart to the print journal collection of the US National Library of Medicine. As a participating journal, JAFES shall be depositing full text articles starting from 2017 and these shall be available 100% open access and searchable also in MedLine.

scholarly journals UK PubMed Central: Interview with Phil Vaughan

2009 ◽  
Author(s):  
Martin Fenner
Keyword(s):  
Life Sciences ◽  
National Institutes Of Health ◽  
Digital Archive ◽  
Journal Articles ◽  
Pubmed Central ◽  
The U.S

PubMed Central was launched in February 2000 by the U.S. National Institutes of Health (NIH) as a free digital archive of journal articles. Just as PubMed, PubMed Central covers research in the life sciences, but not other areas of research, e.g. ...

Editorial

2003 ◽  
Vol 9 (2) ◽  
pp. 95-95
Author(s):  
Charles E. Lyman
Keyword(s):  
Impact Factor ◽  
Scientific Information ◽  
Life Sciences ◽  
Editorial Board Member ◽  
Initial Letter ◽  
Strong Impact ◽  
National Library ◽  
The Past ◽  
Number Of Citations

Microscopy and Microanalysis has made significant strides forward over the past year, and I would like to comment on two of these. First, the Institute for Scientific Information (ISI) ranked this journal third among the nine microscopy journals it indexes. The ranking was in terms of ISI's Impact Factor, which tracks the number of citations to papers published in the journal. A strong Impact Factor indicates that information in the journal is of interest to other workers in the field. Second, the National Library of Medicine (NLM) has selected Microscopy and Microanalysis to be indexed in MEDLINE (PubMed), beginning with the first issue of 2003. As any biologist will tell you, this listing is essential for the electronic visibility of papers in the fast-moving world of life sciences research. I thank Editorial Board member Dave Piston for his efforts in writing the initial letter of application to the NLM.

scholarly journals Database citation in supplementary data linked to Europe PubMed Central full text biomedical articles

2015 ◽  
Vol 6 (1) ◽  
pp. 1 ◽  
Author(s):  
Şenay Kafkas ◽  
Jee-Hyub Kim ◽  
Xingjun Pi ◽  
Johanna R McEntyre
Keyword(s):  
Full Text ◽  
Supplementary Data ◽  
Pubmed Central

scholarly journals Ebola Outbreak Response: The Role of Information Resources and the National Library of Medicine

2014 ◽  
Vol 9 (1) ◽  
pp. 82-85 ◽  
Author(s):  
Cynthia B. Love ◽  
Stacey J. Arnesen ◽  
Steven J. Phillips
Keyword(s):  
Social Media ◽  
Information Resources ◽  
Free Access ◽  
Outbreak Response ◽  
National Library ◽  
Online Data ◽  
Journal Literature ◽  
The Us ◽  
Variation Database ◽  
Disaster Event

AbstractThe US National Library of Medicine (NLM) offers Internet-based, no-cost resources useful for responding to the 2014 West Africa Ebola outbreak. Resources for health professionals, planners, responders, and researchers include PubMed, Disaster Lit, the Web page “Ebola Outbreak 2014: Information Resources,” and the Virus Variation database of sequences for Ebolavirus. In cooperation with participating publishers, NLM offers free access to full-text articles from over 650 biomedical journals and 4000 online reference books through the Emergency Access Initiative. At the start of a prolonged disaster event or disease outbreak, the documents and information of most immediate use may not be in the peer-reviewed biomedical journal literature. To maintain current awareness may require using any of the following: news outlets; social media; preliminary online data, maps, and situation reports; and documents published by nongovernmental organizations, international associations, and government agencies. Similar to the pattern of interest shown in the news and social media, use of NLM Ebola-related resources is also increasing since the start of the outbreak was first reported in March 2014 (Disaster Med Public Health Preparedness. 2014;0:1-4)

Knowledge for Medicine and Health Care

2005 ◽  
Vol 44 (04) ◽  
pp. 596-600
Author(s):  
Jan H. van Bemmel
Keyword(s):  
Health Care ◽  
American Medical ◽  
Medical Informatics ◽  
Health Sciences ◽  
International Medical ◽  
Honorary Doctorate ◽  
National Library ◽  
American Medical Informatics Association ◽  
The University ◽  
The U.S

SummaryDr. Donald A. B. Lindberg, Director of the U.S. National Library of Medicine, received an honorary doctorate from UMIT, the University for Health Sciences, Medical Informatics and Technology in Innsbruck, Tyrol. The celebration took place on September 28, 2004 at an academic event during a conference of the Austrian, German, and Swiss Societies of Medical Informatics, GMDS2004. Dr. Lindberg has been a pioneer in the field of computers in health care from the early 1960s onwards. In 1984 he became the Director of the National Library of Medicine in Bethesda, the world’s largest fully computerized biomedical library. Dr. Lind-berg has been involved in the early activities of the International Medical Informatics Association (IMIA), among others being the chair of the Organizing Committee for MEDINFO 86 in Washington D.C. He was elected the first president of the American Medical Informatics Association (AMIA), and served as an editor of Methods of Information in Medicine.

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