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Archive for the ‘PubMed’ Category

New 2016 MeSH Headings: Zika Virus Infection and Zika Virus

On January 27, 2016, two new MeSH headings were added to the 2016 MeSH Browser in response to increased reports in the literature about the Zika virus outbreak and its tentative association with microcephaly in newborns as well as possible paralysis and Guillain-Barre Syndrome in adults:

The terms also appeared in the MeSH export file available to licensees on January 27, 2016. Indexing for the new headings began January 28, 2016. In addition, NLM Indexing staff will review citations previously indexed on this topic to determine if the new headings should be applied to the citations. Here is a suggested interim PubMed search strategy to retrieve citations on Zika until the review of previously indexed citations is completed:

Zika [tiab]

Using the [tiab] search tag finds citations that have already been indexed with MeSH or are still in process. The tag restricts retrieval to the article title, abstract, or author keyword fields and prevents false drops from other fields such as author name.

A Zika Virus Health Information Resources page, from the Disaster Information Management Research Center at NLM, gathers resources on the emerging health issues arising from the Zika Virus. For additional information see the article, NLM Disaster Information Management Research Center Resource List Updates.

NIH Author Manuscripts Available for Text Mining

NIH-supported scientists have made over 300,000 author manuscripts available in PMC. Now NIH is making these papers accessible to the public in a format that will allow robust text analyses.

You can download the PMC collection of NIH-supported author manuscripts as a package in either XML or plain-text format. The collection encompasses all NIH manuscripts posted to PMC that were published in July 2008 or later. While the public can access the manuscripts’ full text and accompanying figures, tables, and multimedia via the PMC website, the newly available XML and plain-text files include full text only. In addition to text mining, the files may be used consistent with the principles of fair use under copyright law. Please note that these author manuscript files are not part of the PMC Open Access Subset.

The NIH Office of Extramural Research developed this resource to increase the impact of NIH funding. Through this collection, scientists will be able to analyze these manuscripts, further apply NIH research findings, and generate new discoveries. For more information, please visit the PMC author manuscript collection webpage.

MeSH Webinar: “2016 MeSH Highlights” on January 20

On January 20, join NLM staff for a highlights tour of the 2016 Medical Subject Headings (MeSH). A 30-minute presentation will feature a MeSH tree clean-up project; a new Clinical Study publication type; changes to the trees for diet, food and nutrition; restructuring in pharmacology and toxicology; and new terms in psychology and health care. Following the presentation, Indexing and MeSH experts will be available to answer your questions.

Webinar: 2016 MeSH Highlights
Date and time: Wednesday, January 20, 2016, at 9:00 am PST
View a recording of the presentation.

For more information about 2016 MeSH, see What’s New for 2016 MeSH and the Introduction to MeSH – 2016.

Search PubMed with 2016 MeSH!

As of December 15, PubMed/MEDLINE citations (including the backlog of citations indexed since November 18 with 2016 MeSH), the MeSH database, and the NLM Catalog were updated to reflect 2016 MeSH. The MeSH translation tables were also updated on December 15. Now that end-of-year activities are complete, MEDLINE/PubMed may be searched using 2016 MeSH vocabulary. See MEDLINE Data Changes — 2016 for details on the data changes. On December 16, NLM resumed daily MEDLINE updates to PubMed.

PubMed for Nurses: New Tutorial Available

The PubMed for Nurses Tutorial is available now from the PubMed Online Training page on the NLM Web site. This tutorial was created specifically to help nurses efficiently find literature using PubMed. Its concise, targeted content consists of five videos with exercises to test your knowledge. The tutorial was designed to be completed in less than 30 minutes.

The PubMed for Nurses Tutorial was researched, designed and developed by Megan Kellner from Maryland’s iSchool, the College of Information Studies at the University of Maryland, in consultation with nurses and librarians who serve nurses around the United States.

Updated PMC Journal Review Process and Minimum Requirements

The PMC Overview and FAQ have been updated to provide more information on the Scientific Quality Review Process for journals that apply to participate in PMC. In 2014, PMC implemented a scientific and editorial quality review procedure whereby expert consultants from outside the National Library of Medicine (NLM) conduct an independent review of journals seeking to participate in PMC. This was in response to a significant increase in new publishers and journals applying to participate in PMC, many of which are unknown to NLM in terms of quality and publishing practices. The independent review, which was approved by the PMC National Advisory Committee (see minutes from June 10, 2014), follows an assessment by NLM that the journal meets NLM’s criteria for its collection, as outlined in the Collection Development Manual.

PMC also recently updated the minimum requirement on the number of substantive, peer-reviewed articles needed before a journal can apply to PMC. The new 25-article minimum ensures that the reviewers have a sufficient amount of content on which to base their recommendation for inclusion in PMC. The new minimum article requirement takes effect on January 1, 2016. Publishers are encouraged to use the 25-article minimum as a guideline in the interim when submitting applications.

New PubMed Health Resources!

Earlier this year PubMed Health was expanded with research on research methods. These are studies and guidance for doing systematic reviews and helping them make an impact. A new resource takes this process a step further; the PubMed Systematic Review Methods Filter, as well as a new section at PubMed Health “For Researchers.” Also available are new glossary pages especially for research methods for anyone who wants to understand more about the mechanics of health research. The glossary will grow to cover the most common research terms used in PubMed Health.

Whenever you search in PubMed Health, you also get results from PubMed using the new filter. They will appear to the right of the main search results, in a box called “Systematic Review Methods in PubMed.” It’s below a box called “Systematic Reviews in PubMed,” which is a search for systematic reviews themselves. The filter searches through a subset of PubMed records that are either research or guidance on systematic review methods. The publications could relate to the development or evaluation of any step in doing or using systematic reviews. To use the filter in PubMed, enter sysrev_methods [sb] in the search box. You can use it like any search term, for example, sysrev_methods [sb] AND “network meta-analysis.”

The methods filter is a result of collaboration between the PubMed Health team and the Scientific Resource Center (SRC) for the U.S. Agency for Healthcare Research and Quality (AHRQ). The SRC team selects the publications, after scanning widely every day looking for new candidates. When you see a systematic review at PubMed Health, there will often be a methods box to the right. That links to the relevant methods guide from the organization behind the review. Six groups so far have started contributing their methods guidance and research to PubMed Health. You can see the list on the new “For Researchers” page.

Navigation isn’t the only part of PubMed Health with a new look. The homepage also has a new design. For further details, visit the PubMed Health Blog.

Check Out What’s New for 2016 MeSH!

MeSH, the National Library of Medicine’s controlled vocabulary thesaurus, is updated annually. It is used to index articles from thousands of biomedical journals for the MEDLINE/PubMed database and for the cataloging of books, documents, and audiovisuals acquired by NLM. Changes for 2016 MeSH include: 438 new Descriptors, 17 Descriptor terms replaced with more up-to-date terminology, 9 deleted Descriptors, and deletion of the Subheading “diagnostic use.” Content of MeSH now includes 27,883 Descriptors; 87,028 Descriptor entry terms; 82 Qualifiers (Subheadings); and 230,872 Supplementary Concept Records. Three new Publication Types were added for catalogers; Blogs, Graphic Novels, and Public Service Announcements. The Publication Type Clinical Study was added mainly for use by indexers. Additional changes involve the MeSH Trees and Scope Notes. For a complete list of changes, visit the NLM Technical Bulletin.

New PubMed and PMC Filters for Creative Commons Articles

Creative Commons (CC) licenses are types of copyright licenses that allow free distribution of a work. PubMed Central (PMC), the NLM archive of full text journal articles, includes articles that have a Creative Commons license or are in the public domain. The latter covers those articles authored by staff of U.S. government agencies. NLM now offers a filter for both PubMed Central and PubMed to find articles with unrestricted Creative Commons or public domain (CC0) licenses:

These filters are based on license information that is provided to PubMed Central by publishers. There are many more articles cited in PubMed but not deposited in PMC that have CC0 licenses, but that information is not part of PubMed. You can view the detailed copyright information for an article in PubMed Central by clicking on Copyright and License Information at the top:

Copyright information for an article in PubMed Central.

For more information, see the PubMed Central Open Access Subset page. You may use and reproduce these articles without special permission. It is requested that you properly cite and acknowledge the source. Please bear in mind that these articles, although made available under a CC0 license, may still contain photographs or illustrations copyrighted by other commercial organizations or individuals that may not be used without obtaining prior approval from the holder of the copyright.

December Webinar Opportunities Hosted by NN/LM Middle Atlantic Region

The NN/LM Middle Atlantic Region has announced two webinar opportunities that are open to anyone wishing to attend:

Tuesday, December 8: Hospital Libraries: Challenges and Opportunities – This session will include discussion of the current state of hospital libraries and consider their future in light of the Affordable Care Act, Meaningful Use, and budget cuts. It will also consider the role the librarian plays and their effect on these changes, as well as ways the library’s resources (including the librarian) can help offset the expenses hospitals are facing. Speaker: Heather N. Holmes, MLIS, AHIP, Clinical Informationist, Summa Health System, Akron, OH.
When: December 8, 2015, 9:00-10:00am PST
Where: https://webmeeting.nih.gov/boost2/
No Registration Required
Eligible for 1 MLA CEU

Thursday, December 17: Saving time with PubMed Subject-specific Queries – Want to boost your PubMed prowess? Looking for preformulated searches on drugs, health information technology, public health and other topics? Spend an hour with NN/LM MAR Outreach Coordinator, Kate Flewelling, to save hours on your searches!
When: December 17, 2015, 9:00-10:00am PST
Where: https://webmeeting.nih.gov/nlmfocus/
No Registration Required
Eligible for 1 MLA CE