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New PDA Version of Genes and Disease Added to NCBI Bookshelf

Technical Notes

New PDA Version of Genes and Disease Added to NCBI Bookshelf

Systematic Evidence Reviews Added to NCBI Bookshelf

My NCBI Quick Tours Available

Resolving Page Expired Error Message in PubMed®

Updated Training Manuals Available

New NLM Mobile Link in PubMed®

PubMed® Help Now Available Only on the Bookshelf

PubMed® Citation Status Tag

New Version of TOXMAP Available

TOXNET® TRI 2003 Released

Healthy People 2010 Added to PubMed® Special Queries

Addition of Spell Checking Feature to the NLM Catalog®

NLM® Adopts 2005 Amendments to Anglo-American Cataloguing Rules®

"What you see is not what you get! DNA barcoding is helping scientists unveil nature's most hidden diversity" Added to Coffee Break

New Book Added to NCBI Bookshelf

Online Mendelian Inheritance in Animals (OMIA) Added to Entrez Databases

Funding Support Web Page Revised

July 8, 2005 [posted]

A PDA version has been added to the NCBI Bookshelf for Genes and Disease. On the Table of Contents page (or any page of the book) at the end of regular text, you'll see:

"Download this book for your handheld computer (requires the MobiPocket Reader)." Available from: http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=gnd.TOC.

For more information on PDA versions available on the NCBI Bookshelf and how to install MobiPocket Reader, see: http://www.ncbi.nlm.nih.gov/entrez/query/
Books.live/Help/mobile.html
.

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.

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Systematic Evidence Reviews Added to NCBI Bookshelf

July 8, 2005 [posted]

The National Center for Biotechnology Information (NCBI) has recently added six Systematic Evidence Reviews, from the Guide to Clinical Preventive Services, 3rd ed., 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.

The six new reviews are:

10. [This link was removed because it is no longer valid] Postmenopausal Hormone Replacement Therapy and Cardiovascular Disease

12. [This link was removed because it is no longer valid] Hormone Replacement Therapy and Osteoporosis

17. [This link was removed because it is no longer valid] Screening for Postmenopausal Osteoporosis

21. [This link was removed because it is no longer valid] Screening and Interventions for Overweight and Obesity in Adults

23. [This link was removed because it is no longer valid] Screening for Thyroid Disease

32. [This link was removed because it is no longer valid] Screening for Suicide Risk: Systematic Evidence Review for the U.S. Preventive Services Task Force

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.

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My NCBI Quick Tours Available

July 8, 2005 [posted]

NLM announces three new animated tutorials, now called "quick tours," on My NCBI with PubMed®. The quick tours are brief, narrated demonstrations in Flash format, on the following topics:

  • Getting Started with My NCBI: How to register, sign in and out, change your password, and what to do if you've forgotten your password.
  • Saving Searches: How to save a PubMed search to run later or to have results sent to your e-mail account.
  • Filters: How to create filters to group your search results.

In addition, the Searching PubMed for an Author quick tour has been updated to include information on searching by full author name.

The My NCBI Quick Tours are available from the My NCBI sidebar. All PubMed Quick Tours are available at: http://www.nlm.nih.gov/bsd/dist_edu.html. They require the Macromedia Flash Player and were created using Qarbon's ViewletBuilder.

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Resolving Page Expired Error Message in PubMed®

July 22, 2005 [posted]

NCBI is using HTTP1.1 compression/content encoding with Entrez databases (e.g., PubMed). Data compression allows data to be sent faster - a big help for users who have slower connections.

Most recent versions of popular browsers are by default enabled to use HTTP1.1. If, however, users see the message, "Warning: Page has Expired," after using the back button in their browser, they should enable HTTP1.1 compression in their browser. The steps to enable HTTP1.1 compression in Microsoft® Internet Explorer (MSIE) are:

  1. From the Tools menu, select Internet Options.
  2. Click the Advanced Tab.
  3. Scroll down to HTTP1.1 settings.
  4. Check the following checkboxes: Use HTTP1.1 and Use HTTP1.1 via proxy connections.
  5. Click OK.
  6. Close MSIE and re-open it.

If, after enabling HTTP1.1 compression (be sure to close and re-launch the browser), users still see the "Warning: Page has Expired" message, it is possible that another application is responsible. For example, we have determined that, even with HTTP1.1 compression enabled, Symantec's firewall program, Norton Internet Security can cause the browser to display the error message if the firewall is configured to monitor HTTP connections, which is the default configuration.

If, in the case of a firewall program, users wish to disable HTTP monitoring, they should fully understand the consequences of doing so. We suggest users either consult the product documentation or contact the vendor.

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Updated Training Manuals Available

July 22, 2005 [posted]

Recently updated editions of the PubMed®, NLM Gateway, and ClinicalTrials.gov training workbooks are now available for downloading from the NLM Web site. The current edition of the PubMed workbook reflects changes since March 2005. The Gateway workbook has been completely updated for instruction on the newly designed Gateway interface.

The manuals are available for downloading in Portable Document Format (PDF) and Microsoft® (MS) Word formats. They are broken down into sections so you can choose the areas of interest to you. These materials correspond 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 workbooks - you may customize parts for training programs, demonstrations, or workshops you conduct. These workbooks are not copyrighted.

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

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New NLM Mobile Link in PubMed®

August 1, 2005 [posted]

A new link, NLM Mobile, will be added to PubMed's blue side bar. Like the Text Version link that takes you to a page providing specialized PubMed searches for text browsers, the NLM Mobile link provides access to a directory of PubMed tools that are appropriate for mobile devices. These include Palm Powered and Pocket PC handheld computers as well as newer smartphones and Blackberry devices.

The directory links to:

  • PubMed for Handhelds Web site, which is designed for the small screen and Web browser of any mobile device.
  • PubMed on Tap software, an application that works on Palm Powered and Pocket PC handheld computers. It allows user-customized searching.
  • Wireless System for Emergency Responders (WISER), software for Palm Powered or Pocket PC devices to assist first responders in hazardous material incidents.
  • NCBI Bookshelf, with downloadable versions of books from the NCBI Bookshelf for any mobile device.
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PubMed® Help Now Available Only on the Bookshelf

August 3, 2005 [posted]

The PubMed Help is now available only on the NCBI Bookshelf. The former PubMed Help document has been retired. Links created to the former Help will automatically go to the Bookshelf Help.

For further information on PubMed Help on the Bookshelf see: PubMed® Help Added to NCBI Bookshelf. NLM Tech Bull. 2005 May-Jun;(344):e16.

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PubMed® Citation Status Tag

August 9, 2005 [posted]

All citations in PubMed with the status tag [PubMed] have had the bibliographic data (e.g.: authors, article title, source information, abstract) reviewed for accuracy. The coverage of this status tag has now been expanded. It includes:

  • A citation for an article in a journal from which NLM regularly indexes articles, but this article is on a topic considered outside the scope of MEDLINE®

    Example in Summary format:

    Monnin E, Indermuhle A, Dallenbach A, Fluckiger J, Stauffer B, Stocker TF, Raynaud D, Barnola JM.
    Atmospheric CO2 concentrations over the last glacial termination.
    Science. 2001 Jan 5;291(5501):112-4.
    PMID: 11141559 [PubMed]


  • A citation for an article from issues of journals published prior to their selection for MEDLINE indexing and submitted to NLM since late 2003

    Example in Summary format:

    Kajita J, Fuse E, Kuwabara T, Kobayashi H.
    The contribution of cytochrome P450 to the metabolism of tegafur in human liver.
    Drug Metab Pharmacokinet. 2003;18;(5):303-9.
    PMID: 15618749 [PubMed]


  • A citation for an article in a journal that is not indexed for MEDLINE. These are typically citations to articles from journals that deposit their full text articles in PubMed Central®, but have not yet been recommended for indexing in MEDLINE

    Example in Summary format:

    Lauffart B, Vaughan MM, Eddy R, Chervinsky D, DiCioccio RA, Black JD, Still IH.
    Aberrations of TACC1 and TACC3 are associated with ovarian cancer.
    BMC Womens Health. 2005 May 26;5(1):8.
    PMID: 15918899 [PubMed]

The third category above is the newest addition to the [PubMed] tag, beginning in late June 2005 for prospective citations.

To search for citations with the [PubMed] citation status tag use:

pubmednotmedline [sb]
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New Version of TOXMAP Available

August 15, 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 version of TOXMAP was released July 25, 2005.

TOXMAP 2.4 contains the following new features:

TOXMAP is an interactive web site from the National Library of Medicine that shows the amount and location of reported toxic chemicals released into the environment on maps of the United States. TOXMAP allows users to visually explore information about releases of toxic chemicals by industrial facilities around the United States as reported annually to the Environmental Protection Agency (EPA). It also integrates the map display with access to relevant bibliographic references and other data on these chemicals, providing a map-based portal to these resources.

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TOXNET® TRI 2003 Released

August 15, 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 2003 Toxics Release Inventory (TRI) was released on TOXNET® on June 13, 2005. The new release (1987-2003) contains 1,461,916 records.

The EPA's TRI provides information on the releases of over 600 specific chemicals into the environment as reported annually by industrial facilities around the United States.

NLM's TOXNET® is a group of databases on hazardous chemicals, environmental health, and toxic releases.

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Healthy People 2010 Added to PubMed® Special Queries

August 18, 2005 [posted]

A link to the search interface providing searches for published literature related to the Healthy People 2010 focus areas of the HP2010 Information Access Project was added to the Special Queries resource page available from PubMed's blue sidebar.

The National Library of Medicine® and the Public Health Foundation staff have worked together to develop pre-formulated search strategies for selected Healthy People 2010 focus areas. The purpose of these searches is to make information and evidence-based strategies related to the Healthy People 2010 objectives easier to find. Select a focus area and see a list of specialized searches for the objectives. The "PubMed search" icons on the focus area page search PubMed.

Healthy People 2010 is a set of health objectives for the Nation to achieve over the first decade of the new century. It can be used by many different people, States, communities, professional organizations, and others to help them develop programs to improve health.

For more information on the Special Queries Resource in PubMed see Technical Notes. NLM Tech Bull. 2005 Mar-Apr;(343):e1.

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Addition of Spell Checking Feature to the NLM Catalog®

August 18, 2005 [posted]

On August 4, 2005, a new spell checking feature was implemented in the NLM Catalog. This feature, similar to one implemented in PubMed® in February 2005, provides suggested alternative spellings for NLM Catalog search terms that include possible English misspellings. Terms entered with a search tag (e.g., [mh]; [majr]; [tw]) do not generate alternative spellings.

The initial NLM Catalog retrieval display now includes results from a search along with an option to link to the alternative English spelling, providing users with an easy way to retrieve results for untagged words that are misspelled.

For a complete description of the spell checking feature, see New PubMed® Spell Checking Feature. NLM Tech Bull. 2004 Nov-Dec;(341):e12.

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NLM® Adopts 2005 Amendments to Anglo-American Cataloguing Rules®

August 18, 2005 [posted]

The NLM Cataloging Section implemented the 2005 amendments to the Anglo-American Cataloguing Rules, 2nd edition, 2002 revision, on August 1, 2005, in tandem with the Library of Congress. Most changes, this year, consist of clarifications to and amplifications of existing rules and appendices. For a complete description of the changes see http://www.loc.gov/catdir/cpso/2005upd.html.

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"What you see is not what you get! DNA barcoding is helping scientists unveil nature's most hidden diversity" Added to Coffee Break

August 26, 2005 [posted]

NCBI's Coffee Break is a collection of short stories and interactive tutorials about recent biomedical discoveries. These snapshots of science are short enough to be enjoyed over a cup of coffee but also give a detailed report on a molecular topic.

The latest Coffee Break, "What you see is not what you get! DNA barcoding is helping scientists unveil nature's most hidden diversity," describes DNA barcoding and how it is expected to precisely identify every species on our planet in the next 20 years. To see a complete list of all available Coffee Break reports click on the contents link.

You can read more about Coffee Break in the NLM Technical Bulletin article, Dean L. Take a Coffee Break. NLM Tech Bull. 2003 Nov-Dec;(335):e5.

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New Books Added to NCBI Bookshelf

August 26, 2005 [posted]

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

Alternative Medicine and Rehabilitation: A Guide for Practitioners.
Wainapel, Stanley F.; Fast, Avital, editors
New York: Demos Medical Publishing; c2003
Available from: http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=altrehab.TOC&depth=2

Parkinson's Disease: Diagnosis and Clinical Management.
Factor, Stewart A.; Weiner, William J., editors
New York: Demos Medical Publishing; c2002
Available from: http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=parkinsons.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.

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Online Mendelian Inheritance in Animals (OMIA) Added to Entrez Databases

August 26, 2005 [posted]

In August 2005, NCBI debuted an Entrez version of the Online Mendelian Inheritance in Animals (OMIA) database. OMIA contains information and references for genes, inherited disorders, and traits in animal species and is authored by Frank Nicholas at the University of Sydney, Australia. The Entrez version of OMIA has been enhanced with links to other NCBI databases including OMIM, Entrez Gene, Protein, Taxonomy, UniSTS, HomoloGene, UniGene, PubMed, and soon to PhenoDB. Novel features of the Entrez version of OMIA include links to the Mammalian Phenotype Ontology and the computation of many additional links to Entrez Gene via linked OMIM records and HomoloGene clusters.

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Funding Support Web Page Revised

August 26, 2005 [posted]

The National Library of Medicine® has updated its electronic resource that explains the various research funding support tags that are searchable in PubMed®. See New Research Support MeSH® Headings Introduced mid-Year to 2005 MeSH®. NLM Tech Bull. 2005 May-Jun;(344):e12. for additional details.

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