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Archive for the ‘Search Tools’ Category

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 resource for Alaska Natives and American Indians: NativeOneStop.gov

The White House, in collaboration with the Department of the Interior and the Bureau of Indian Affairs, has announced a new resource for American Indians and Alaska Natives. NativeOneStop.gov was launched in an effort to provide American Indians and Alaska Natives with easy, online access to Federal resources and programs. It is a partnership of many Federal agencies and organizations with a shared vision – to provide improved, personalized access to Federal resources and programs for American Indians and Alaska Natives. NativeOneStop.gov will make it easier for tribes, Alaska Natives, and American Indians to find services, receive consistent information, and streamline outreach and services by Federal agencies.

Upcoming NCBI Webinars: Advanced Search in dbGaP and 1000 Genomes Project Data

Join NCBI staff for the upcoming webinars on dbGaP and the 1000 Genomes Project Data.

NCBI Minute: New Advanced Search in dbGaP Provides Easy Access to Relevant Data
Wednesday, December 16, 2015, 9:00-9:15 am PST
The new advanced search interface to dbGaP makes finding relevant data much easier. In this webinar you will learn how to access the new faceted search and to quickly find human subject data by study, variables, datasets, documents, and genotypes.

Accessing the 1000 Genomes Project Data at the NCBI
Thursday, December 17, 2015, 10:00-11:00 am PST
The 1000 Genomes Project data now include small-scale and structural variant calls from 2,504 individuals representing 26 human populations. In this webinar you will see how to access 1000 Genomes data through the SRA, dbVar, SNP and BioProject resources, as well as through tracks on annotated human sequences in the Graphical sequence viewer and the Variation Viewer. Most important you will learn how to display, search, and download individual and genotype level data through the dedicated 1000 Genomes Browser that allows searching by chromosomal position, gene names and other genome markers.

Visit the NCBI Webinars and Courses webpage to view archived webinars and materials, and to learn about future webinars. Archived webinars can also be accessed on the NCBI YouTube channel.

NLM Releases New Health Literacy Tool Shed Website

Health Literacy Tool Shed HomepageThe U.S. National Library of Medicine (NLM), in collaboration with Boston University School of Medicine is pleased to announce the launch of the Health Literacy Tool Shed. The Health Literacy Tool Shed is a free, user-friendly, unique, curated online database of more than 100 empirically validated health literacy instruments. The Tool Shed serves as an interactive, one-stop shop where researchers use provided filters to select a health literacy research instrument. The website was developed following user-centered design methods to ensure the site’s relevance and ease of use.

The Health Literacy Tool Shed provides background information about each instrument and enables users to compare them. Each instrument within the Health Literacy Tool Shed is peer reviewed by health literacy research experts including: Michael Paasche-Orlow, M.D., M.P.H., Boston University School of Medicine; and Lauren McCormack, Ph.D., M.S.P.H., RTI International. The selected instruments vary in terms of user accessibility and cost, as mandated by the original investigator.

NIH Manuscript Collection Optimized for Text-Mining and More

NIH-supported scientists have made over 300,000 author manuscripts available on PubMedCentral (PMC) since 2008. Now, NIH is making these papers accessible to the public in a format that will allow robust text analyses. You can download the entire PMC collection of NIH-supported author manuscripts as a package in either XML or plain text formats. The collection will encompass all NIH manuscripts posted to PMC since July 2008. While the public can access the articles’ full text and accompanying figures, tables, and multimedia on the PMC website, the newly available article packages include full-text only, in a form that facilitates text-mining. This resource was developed to increase the impact of NIH funding. Through this collection, scientists will be able to analyze these manuscripts, further apply the findings of NIH research, and generate new discoveries. For more information visit the PMC author manuscript collection web site.

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

NLM Cataloging News for 2016

The National Library of Medicine (NLM) adopted the 2016 MeSH vocabulary for cataloging on November 23, 2015. Accordingly, MeSH subject headings in LocatorPlus were changed to reflect the 2016 MeSH vocabulary and appear in that form as of November 23, 2015. When year-end processing (YEP) activities are completed in mid-December, the NLM Catalog, MeSH database, and translation tables will be updated to reflect 2016 MeSH. Until then, there will be a hiatus in the addition of new and edited bibliographic records to the NLM Catalog. The Index to the NLM Classification will not reflect 2016 MeSH changes until Spring 2016. In general, the Cataloging Section implemented the vocabulary changes in NLM bibliographic records for books, serials, and other materials, as they were applied for citations in MEDLINE. Highlights of the changes are available in the NLM Technical Bulletin.

Subject Changes in NLM Distributed Records

The National Library of Medicine (NLM) reminds libraries that beginning with the December 2015 distribution of new records in CATFILE and SERFILE, NLM subject terms (MeSH) will be distributed with topical subjects recorded in 650 $a or 650 $a $x; geographic subjects recorded in 651 $a or 651 $a $x; and publication type/genre terms record in 655 $a. In January 2016, the entire CATFILE and SERFILE databases will be released with these updates made to all the records. NLM recommends that libraries that want their data to be consistent with the NLM files download the full update.

Catalogers in other libraries that use MeSH are encouraged to follow NLM practice in assigning their subjects. Under no circumstances should a library edit a record in OCLC to re-create a string and remove the 651 and 655 fields. Any desired editing should be done only in your local catalog. After January 2016, libraries will be required to establish medical subjects in a deconstructed format in OCLC. OCLC will be updating all records with 650 fields with a second indicator of 2 to follow the new NLM practice in January. NLM is working with authority vendors to provide guidance on how local catalogs can be updated. The Program for Cooperative Cataloging will soon be issuing guidelines for BIBCO and CONSER libraries that use MeSH. The new guidelines will take effect January 1, 2016.

Structured Abstracts in MEDLINE: Newly Identified and Mapped Labels Available

The National Library of Medicine (NLM) has updated its list of structured abstract labels. This updated list, along with the NLM-assigned broader category mappings, can be downloaded for free from the Structured Abstracts resource page which also provides NLM guidelines and other background information to assist licensees or researchers. A grand total of 4,702 citations (whether in process, MEDLINE, or PubMed-not-MEDLINE status) were revised so that the new labels include the NLM Category mapping in the XML data, effective on or about October 26, 2015. Of interest, the new label ‘TWEETABLE ABSTRACT’ (mapped to the NLM Category ‘CONCLUSIONS’) illustrates the impact of social media. Read more about Structured Abstracts in MEDLINE/PubMed.