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MEDLINE®/PubMed® Data Element Descriptions Available

November 04, 2005 [posted]

Detailed descriptions of the major fields in the MEDLINE display format for PubMed MEDLINE records are in a new document entitled MEDLINE® /PubMed® Data Element Descriptions, available at http://www.nlm.nih.gov/bsd/mms/medlineelements.html. This document may be useful to anyone seeking information regarding the data in MEDLINE/PubMed records. The document reflects the 2005 fields, and will be maintained and updated as the data changes. Some of the fields on this list are searchable in PubMed. For searching instructions or more information, see the Search Field Descriptions and Tags section of PubMed Help.

Licensees' Research Use of MEDLINE®/PubMed® Data

November 23, 2005 [posted]

NLM® has created a freely accessible Web site containing summary-level information submitted by NLM's registered licensees about their MEDLINE/PubMed-related research projects. The site includes a brief description and summary of the licensee's research; citations and Web addresses of papers or related sites; and contact information, if permitted. The pages are organized alphabetically by licensees' organization or institution; personal name; country; and by research categories. The site is accessible at: [This link was removed on April 20, 2010, because it is no longer available.].

The overall purpose of the site is to assist in the advancement of science by enabling researchers to 1) be aware of research projects and results from use of NLM's MEDLINE/PubMed data and, 2) contact those who are willing to provide additional information and/or share outcomes of their research.

The Web site is updated at the discretion of NLM based on volume of submissions (licensees are not required to permit their information to be posted on the Web) and feedback.

Information about licensing MEDLINE/PubMed is available.

New Resource: MEDLINE®/PubMed® Baseline Repository (MBR)

November 23, 2005 [posted]

A freely accessible Web site, the MEDLINE/PubMed Baseline Repository (MBR), developed by staff in NLM's Lister Hill Center is now available. The MBR, at http://mbr.nlm.nih.gov/, contains various resources derived from or pertaining to the MEDLINE/PubMed baseline files which are produced after the records have undergone annual maintenance. One MBR resource, the MBR Query Tool, is restricted to use by NLM's registered MEDLINE/PubMed licensees. MEDLINE/PubMed licensees may prefer to search the baseline files via this Web-based Query Tool rather than, or in addition to, locally mounting all the baseline files obtained from NLM's ftp server.


Researchers have expressed interest in having access to MEDLINE citations in the state they were at a given moment in time. The MBR was set up to provide this capability. NLM has stored the end of year baseline MEDLINE/PubMed database for each year maintained with MeSH vocabulary for the upcoming year starting in 2002 along with a selection of the associated MeSH Vocabulary data files. The 2006 baseline files will be available in December 2005.

Resources available via the MBR:

  1. MBR Query Tool Database - Baseline databases 2002 and forward are available for searching by MeSH Headings, Subheadings, MeSH Heading/Subheading combinations, Names of Substances (MeSH Supplementary Concept Records), and PMID. Users can limit or filter by Date Created, Date Completed, Date Last Revised, Publication Year, and Status. Citations retrieved are available in both XML format and PubMed's MEDLINE ASCII display format. The Query Tool is open only to NLM's registered licensees. Access to the Query Tool is controlled by IP address, as is access to the leased MEDLINE/PubMed files from NLM's ftp server.
  2. Frequency counts - Basic frequency counts are sorted into alphabetical and numerical order for MeSH Headings, Subheadings, for MeSH Heading/Subheading combinations, and Names of Substances (MeSH Supplementary Concept Records).
  3. Raw Data Files - Files contain the raw data similar to what was used to create the MBR Query Tool Database for the specific baseline year.
  4. Histogram/Summary Files - Files show the number of MeSH Heading (MH) terms assigned to each of the MeSH Tree top-level and top-level + 1 categories and to each of the UMLS Semantic Type Groupings categories during the latest year to see how assignment of terms might vary from year to year.
  5. Related MeSH Files - Selected MeSH Vocabulary data files and a copy of their associated DTD files for working with the Baseline XML files.
  6. UMLS Semantic Groups File - A coarse-grained set of semantic type groupings designed to reduce the complexity in the UMLS Metathesaurus.

The MBR resources may be of particular interest to researchers. Please explore the resources including documentation available from the main MBR site at http://mbr.nlm.nih.gov/. Only NLM's registered MEDLINE/PubMed licensees may use the Query Tool which is available from a link on the main page. Comments about use of the MBR site are welcome and may be directed to NLMdatadistrib@nlm.nih.gov.

AHRQ Evidence Reports Added to NCBI Bookshelf

November 25, 2005 [posted]
December 08, 2005 [editor's note added]

The National Center for Biotechnology Information (NCBI) has recently added two new AHRQ (Agency for Healthcare Research and Quality) Evidence Reports to the HSTAT collection on the Bookshelf. HSTAT, Health Services/ Technology Assessment Text, is a free, Web-based resource of full-text documents that provide health information and support health care decision making.

75. Effect of the Supplemental Use of Antioxidants Vitamin C, Vitamin E, and Coenzyme Q10 for the Prevention and Treatment of Cancer

116. Effects of Omega-3 Fatty Acids on Mental Health

[Editor's Note: Two additional AHRQ (Agency for Healthcare Research and Quality) Evidence Reports were added to the HSTAT collection on the Bookshelf.]

117. Effects of Omega-3 Fatty Acids on Eye Health

118. Effects of Omega-3 Fatty Acids on Child and Maternal Health

The books in Bookshelf may be searched directly from the Bookshelf site, via links from the Links pull-down menu from relevant PubMed® citations, or through the Entrez cross-database search page.

New Book Added to NCBI Bookshelf

November 25, 2005 [posted]
December 20, 2005 [editor's note added]

The National Center for Biotechnology Information (NCBI) has recently added a new book to the Bookshelf:

Blood Groups and Red Cell Antigens [Internet].
Dean, Laura
Bethesda (MD): National Library of Medicine (US), NCBI; 2005.

[Editor's Note: Two additional books were added to the Bookshelf.]

Collective Expert Evaluation Reports.
INSERM Collective Expertise Centre
Paris: Institut National de la Sante et de la Recherche Medicale (INSERM); c2000-2004.
Available from: http://www.ncbi.nlm.nih.gov/books/bv.fcgi? call=bv.View..ShowTOC&rid=inserm2.TOC&depth=2

Ecology, Epidemiology, and Evolution of Parasitism in Daphnia [Internet].
Ebert, Dieter
Bethesda (MD): National Library of Medicine (US), NCBI; 2005.
Available from: http://www.ncbi.nlm.nih.gov/books/bv.fcgi? call=bv.View..ShowTOC&rid=daph.TOC&depth=2

The books in Bookshelf may be searched directly from the Bookshelf site, via links from the Links pull-down menu from relevant PubMed® citations, or through the Entrez Global query feature.

NLM Resource Update: TOXNET

December 08, 2005 [posted]

[Editor's Note: This Technical Note is a reprint of an announcement published on NLM-Tox-Enviro-Health-L, an e-mail announcement list available from the NLM Division of Specialized Information Services. To subscribe to this list, please see http://sis.nlm.nih.gov/enviro/envirolistserv.html.]

TOXNET now can dynamically generate specific "multi-database" searches via simple Web links. Information about creating these links can be found in the TOXNET FAQ "How do I create a link to the results when I search all the databases in TOXNET?"

Specific "chemical links" to records in a TOXNET database can also be created. For details, see the TOXNET FAQ "How do I create a link to a record in a TOXNET database?"

TOXNET now can be accessed from a Web browser on a PDA device with a network connection.

TOXNET (TOXicology Data NETwork) is a collection of databases from the National Library of Medicine (NLM) covering toxicology, hazardous chemicals, environmental health and related areas.

NLM® Announces a New Version of the PubMed® Tutorial

December 08, 2005 [posted]

The National Library of Medicine is pleased to release a new version of the PubMed Tutorial. As always, the tutorial is available from the PubMed sidebar.

This new version incorporates changes to PubMed through October 2005 including full author searching, first author searching, and updated links to PubMed Help on the Bookshelf. Please see PubMed's New/Noteworthy to view a list of recent PubMed changes.

PubMed® Online Training Page Now Available

December 08, 2005 [posted]

Access to the growing body of online instructional resources for PubMed, including the PubMed Tutorial and Quick Tours, is now available at http://www.nlm.nih.gov/bsd/disted/pubmed.html. This page is now available directly from the Tutorials link on the PubMed sidebar.

Comments, suggestions and questions regarding the PubMed Tutorial and Quick Tours are always welcome and may be sent to custserv@nlm.nih.gov.

NLM's® Household Products Database and HazMap® Updated

December 08, 2005 [posted]

[Editor's Note: This Technical Note is a reprint of an announcement published on NLM-Tox-Enviro-Health-L, an e-mail announcement list available from the NLM Division of Specialized Information Services. To subscribe to this list, please see http://sis.nlm.nih.gov/enviro/envirolistserv.html.]

The National Library of Medicine's (NLM) Household Products Database has been updated and now includes 6000 brand name products.

The Household Products Database is a consumer guide that provides information on the potential health effects of chemicals contained in more than 6,000 common household products used inside and around the home. This resource helps scientists and consumers learn about ingredients in brand-name products.

NLM's HazMap has been updated with two new features:

  1. A new disease category "Infection, Travel" has been added. It includes:
    African Trypanosomiasis
    American Trypanosomiasis
    Cyclospora cayetanensis infection
    Dengue fever
    Entamoeba histolytica infection
    Enterotoxigenic Escherichia coli infection
    Hepatitis E
    Schistosomiasis, hepatic and intestinal
    Schistosomiasis, urinary
    Severe acute respiratory syndrome

  2. Images of skin lesions and X-rays have been added for some diseases:

    HazMap Skin Lesion Images:
    Candida paronychia
    Atypical mycobacterium skin infections
    Herpetic whitlow
    Orf (Contagious ecthyma)
    Acquired immunodeficiency syndrome
    Lyme disease
    Cutaneous larva migrans
    Dengue fever
    American Trypanosomiasis
    Boutonneuse fever

    HazMap X-ray Images:
    Lung cancer
    Mesothelioma, pleural
    Asthma, occupational
    Severe acute respiratory syndrome
    Dengue fever

Haz-Map is an occupational health database designed for health and safety professionals and for consumers seeking information about the health effects of exposure to chemicals and biologicals at work. Haz-Map links jobs and hazardous tasks with occupational diseases and their symptoms.

Newly Maintained MEDLINE® Now Available in PubMed®

December 13, 2005 [posted]

As of December 12, PubMed's MEDLINE citations, translation tables, and the MeSH® database have been updated to reflect 2006 MeSH. Now that end-of-year activities are complete, MEDLINE via PubMed may be searched using 2006 MeSH vocabulary. See MEDLINE® Data Changes - 2006. NLM Tech Bull. 2005 Nov-Dec;(347):e7. and PubMed® Notes for 2006. NLM Tech Bull. 2005 Nov-Dec;(347):e11. for details on data changes. These articles include links to other relevant MEDLINE and MeSH-related articles. On December 13, NLM resumed the daily (Tuesday-Saturday) MEDLINE updates to PubMed (including the backlog of citations indexed since November 17 with 2006 MeSH but not yet added to PubMed).

Systematic Reviews Subset Strategy Revised for 2006

December 13, 2005 [posted]

The strategy used to create PubMed®'s systematic reviews subset was revised to address changes to MeSH® vocabulary for 2006. Other subject subset strategies will likely be revised in the coming weeks, notice of which will be published here.

Updated NLM Gateway and ClinicalTrials.gov Training Manual Available

December 14, 2005 [posted]

The recently updated edition of the NLM Gateway and ClinicalTrials.gov training workbook is now available for downloading from the NLM Web site. This edition reflects changes since July 2005.

The November 2005 manual is available for downloading in Portable Document Format (PDF) and Microsoft® (MS) Word formats. It is broken down into sections so you can choose the areas of interest to you. The material corresponds to the NLM's National Training Center and Clearinghouse training courses described at: http://nnlm.gov/mar/online/description.html.

Feel free to use any part of the workbook - you may customize parts for training programs, demonstrations, or workshops you conduct. These workbooks are not copyrighted.

Training materials used in training on PubMed®, Toxicology and Environmental Health Web Resources, the Unified Medical Language System® (UMLS® ), and Molecular Biology Information Resources are also available from this Web site.

NLM® WebWISER Makes WISER Available on the Internet

December 19, 2005 [posted]

[Editor's Note: This Technical Note is a reprint of an announcement published on NLM-Tox-Enviro-Health-L, an e-mail announcement list available from the NLM Division of Specialized Information Services. To subscribe to this list, please see http://sis.nlm.nih.gov/enviro/envirolistserv.html.]

WISER is an application designed to assist first responders in hazardous material incidents. It provides a wide range of information on hazardous substances, including chemical identification support, physical characteristics, human health data, and containment and suppression information.

WebWISER provides the WISER functionality via the Internet, without downloading of software or data to the desktop. It has a consistent look and feel of the WISER for Windows desktops/laptops and PDAs. WebWISER supports Web browsers for both PCs and PDAs, including BlackBerry®.

For free downloads of WISER for PDAs and Window PC platforms, a tutorial, and links to other useful information for emergency responders, go to the general WISER Web site.

NLM® Adds Herbal and Dietary Supplement Information to MedlinePlus®

December 19, 2005 [posted]

On December 13, NLM released another enhancement to its Web-based consumer health resource, MedlinePlus. In addition to information on thousands of prescription and over-the-counter medicines, MedlinePlus now includes over 100 herbal and dietary supplement monographs in English and Spanish from Natural Standard. Natural Standard is an evidence-based, peer-reviewed collection of information on alternative treatments. Each monograph includes a table of uses of the supplement based on scientific evidence. The herbal or supplement receives a grade ranging from A (strong scientific evidence for this use) to F (strong scientific evidence against this use) for diseases or conditions it treats. In addition, each monograph provides information on dosing, safety, interactions, and selected references. Many monographs also contain illustrations.

You can find Natural Standard monographs by choosing Drugs & Supplements from the MedlinePlus homepage. Search results for Natural Standard pages have the label (supplement) following the name of the monograph.

Journals Database Link Modified

December 20, 2005 [posted]

The Journals database currently includes a link on the Summary and Full display from the NLM ID to the NLM LocatorPlus Details display. This link will be changed to go to the NLM Catalog Expanded display. Users may go directly to the LocatorPlus Holdings information from the NLM Catalog by clicking the NLM ID link, by selecting NLM LocatorPlus under the Links menu, or by clicking the NLM Holdings in LocatorPlus button on the Expanded display.

OLDMEDLINE MeSH® Mapping Project

December 20, 2005 [posted]

As explained in New Feature for OLDMEDLINE. NLM Tech Bull. 2005 Sep-Oct;(346):e1, NLM® began an OLDMEDLINE Other Term-to-MeSH mapping project. OLDMEDLINE Other Terms are the original subject headings assigned to the citations when they appeared in the print indexes. This project maps those terms to current MeSH vocabulary and will be maintained each year during year end processing. NLM estimates that approximately 92% of the OLDMEDLINE citations now have at least one MeSH term (86% of the Other Terms are mapped). All current MeSH headings added to these records have been added as major MeSH headings. Additional work on this project will continue. See the OLDMEDLINE description for more information about the MeSH Mapping Project and about searching OLDMEDLINE citations using MeSH.

New Enviro-Health Links Resources on Lead

December 27, 2005 [posted]

[Editor's Note: This Technical Note is a reprint of an announcement published on NLM-Tox-Enviro-Health-L, an e-mail announcement list available from the NLM Division of Specialized Information Services. To subscribe to this list, please see http://sis.nlm.nih.gov/enviro/envirolistserv.html.]

A new Web page that addresses the relationship between lead and human health has been added to the National Library of Medicine's® (NLM) Enviro-Health Links. This page provides links to selected Web sites on exposure, treatment, and prevention of lead poisoning.

Lead is a naturally-occurring element that can be harmful to humans when ingested or inhaled. Lead poisoning can cause a number of adverse human health effects, but is particularly detrimental to the neurological development of children. People can be exposed to lead through the air, as well as through accidentally or intentionally eating soil or paint chips, and food or water contaminated with lead.

NLM also offers other Enviro-Health Links on topics such as:

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