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Archive for the ‘Search Tools’ Category

Connecting to NLM’s Hazardous Substances Data Bank Using PubMed and LinkOut

The National Library of Medicine’s LinkOut filters feature provides PubMed users with connections to web-accessible resources, including full-text articles, consumer health information, and supplementary data related to a PubMed citation. PubMed users can access information for over 5,700 Hazardous Substances Data Bank (HSDB) chemical substances via LinkOut. HSDB focuses on the toxicology of potentially hazardous chemicals.

To set up LinkOut to retrieve HSDB information:

  • If you don’t already have a free MyNCBI account, create one;
  • In the Filters box on your MyNCBI account page, click the “Manage filters” link;
  • Click on LinkOut from the “Select Category” option;
  • Click on the + next to the Chemical Information option;
  • Then click on the + next to the Toxicology option;
  • Check the two boxes next to HSDB–this saves these options.

Then run a search:

  • Log into your MyNCBI account and go to PubMed;
  • Run your search;
  • On the upper right side of the results page find “Filter your results;”
  • Click on the HSDB link;
  • Then click on a result;
  • Click on the HSDB icon. The link takes you to the HSDB record for chemical(s) mentioned in the article.

Please note that LinkOut is not available for citations marked as “In process.”

Redesigned FTP Site for MeSH Downloads

The Medical Subject Headings (MeSH) FTP download site has been updated to include separate directories for each release year of MeSH. The FTP directories include:

  • A single directory for earlier files from 1999-2010.
  • The yearly release directories from 2011 to the latest full release which occurs in November of the preceding year.
  • The directory “MESH_FILES” with the latest release files that are updated every morning Monday – Friday.
  • File names ending with .nt and .ttl extensions that are for the MeSH RDF format.

Hopefully making these archive copies more readily available to the public will be useful for anyone interested in studying the history of MeSH terminology as it has progressed over the years. Distributed MeSH files are freely available to the public with agreement to NLM’s Memorandum of Understanding. For further information and illustrations, refer to the NLM Technical Bulletin.

Images from NLM’s History of Medicine Now Available in NLM Digital Collections

Beginning today, Images from the History Medicine (IHM), the National Library of Medicine’s History of Medicine Division’s (HMD) online database of historical images, will be decommissioned from its current Luna Imaging platform, and formally launched in its new home in NLM’s Digital Collections, the Library’s free online resource of over 16,000 biomedical books and moving images. IHM is a collection of historical portraits, photographs, fine prints, caricatures, posters, and other graphic art that illustrates the social and historical aspects of medicine from the Middle Ages to the present. The collection covers subjects ranging from medieval medical practice to 19th century slum conditions to World War I hospitals to the international fight against drug abuse and AIDS. Now this entire image collection is more easily searchable, alongside digitized books and videos, and images can be downloaded more seamlessly. For more details, visit NLM’s Circulating Now blog.

My NCBI Has New Features for My Bibliography and Other Citations

NCBI has enhanced My Bibliography and Other Citations to include the following two improvements: a search and select tool to add citations from PubMed and an option to add citations in bulk using files that have citations in the MEDLINE or RIS (Research Information Systems) format. These features were developed to help manage My Bibliography and Other Citations collections allowing you to add PubMed citations directly in My Bibliography and Other Citations collections, and to upload citations in bulk using a file, which is especially useful for publications that are not present in PubMed. For further details, visit this NLM Technical Bulletin article.

Newly Redesigned UMLS Homepage

The Unified Medical Language System (UMLS) has a new homepage that features an updated design for a better user experience. It highlights the license sign-up link and content downloads as well as the browser and API, organizes training and documentation material, and provides links to related terminology resources at NLM. Additionally, the page features a new “Local Installation” menu. The new design is responsive to varying screen sizes.

NCBI Minute Webinar on May 4: Linking PubMed and ClinicalTrials.gov

Registration is available for the next NCBI Minute webinar on Wednesday, May 4, at 9:00 AM PDT. The presentation will include a short tutorial that will teach two ways to filter PubMed searches for publications linked to clinical trials in clinicaltrials.gov; you’ll also learn how to use the ClinicalTrials database to get more information on trials of interest.

After registering, you will receive a confirmation email with information about attending the webinar. After the live presentation, the webinar will be uploaded to the NCBI YouTube channel. Any related materials will be accessible on the Webinars and Courses page; future webinars are also listed on this page.

Images from the NLM History of Medicine Division Now Available in Open-i Search Engine

On March 22 the NLM History of Medicine Division’s image database, Images from the History of Medicine (IHM), launched in Open-iSM, the National Library of Medicine’s open access biomedical image search engine from the Lister Hill National Center for Biomedical Communications (LHNCBC). Open-iSM enables search and retrieval of abstracts and images (including charts, graphs, clinical images, etc.) from open source literature and biomedical image collections. IHM’s nearly 70,000 images now join over 1.6 million images already available through Open-iSM from sources including the open access subset of PMC, a free full-text archive of biomedical and life sciences journal literature at the National Library of Medicine, the Indiana University hospital network, and the Orthopaedic Surgical Anatomy Teaching Collection at the University of Southern California (USC) Digital Library. For additional details, visit NLM’s Circulating Now blog posting.

NLM VSAC Publishes Updated Electronic Clinical Quality Measure Value Sets for 2017 Reporting

On April 6 the National Library of Medicine (NLM) Value Set Authority Center (VSAC), in collaboration with the Office of the National Coordinator for Health Information Technology (ONC) and Centers for Medicare & Medicaid Services (CMS), published the 2016 annual update for the electronic clinical quality measure (eCQM) value sets for eligible hospitals and eligible professionals. Providers will use these updated eCQM value sets to electronically report 2017 quality data for CMS quality reporting programs. CMS updates these electronic reporting specifications annually to improve alignment with current clinical guidelines and code systems so that they remain relevant and actionable within the clinical care setting. CMS has re-specified all of the updated measures using Quality Data Model (QDM) 4.2 based-HQMF version R 2.1.

Access to the VSAC suite of tools requires a free Unified Medical Language System® Metathesaurus License.

  • Application Programming Interface (API): Programmatically retrieve value sets. Find VSAC API documentation in the VSAC Support Center.
  • VSAC Web Page: Browse and download specific eCQM value sets. Filter by specific CMS eMeasure ID, QDM Category, or Meaningful Use Measure type (EH or EP). Accessible from the Search Value Sets tab on the VSAC Web page.
  • Data Element Catalog: Data element names (value set names) required for capture in electronic health record (EHR) technology certified under the 2014 Edition of the ONC Standards and Certification Criteria.
  • VSAC Collaboration Tool: Interactive and centralized collaboration among VSAC authors and collaborators. Find VSAC Collaboration documentation in the VSAC Support Center.

The updated eCQM measure specifications are available in the CMS eCQM Library and the Electronic Clinical Quality Improvement (eCQI) Resource Center.

PubMed Subject Filter Strategies Updated for 2016

PubMed subject filter strategies are reviewed each year to determine if modifications are necessary. Modifications may include revisions due to changes in Medical Subject Heading (MeSH) vocabulary or MEDLINE journals, adding or deleting terms, and changing parts of a strategy to optimize retrieval. The following subset strategies were recently revised:

  • AIDS
  • Bioethics
  • Cancer
  • Complementary Medicine
  • Dietary Supplements
  • Space Life Sciences
  • Systematic Reviews
  • Toxicology

NLM Announces Pill Image Recognition Challenge

The National Library of Medicine (NLM) announced its Pill Image Recognition Challenge January 19, 2016 in the Federal Register. The Pill Image Recognition Challenge will also be posted on Challenge.gov. The submission period for the Challenge is April 4, 2016 to May 31, 2016, with winners announced August 1, 2016.

The Pill Image Recognition Challenge is a National Institutes of Health (NIH) Challenge under the America COMPETES (Creating Opportunities to Meaningfully Promote Excellence in Technology, Education, and Science) Reauthorization Act of 2010 (Public Law 111-358). Through this Challenge the National Library of Medicine (NLM) seeks algorithms and software to match images of prescription oral solid-dose pharmaceutical medications (pills, including capsules and tablets). The objective of the Challenge is the development and discovery of high-quality algorithms and software that rank how well consumer images of prescription pills match reference images of pills in the authoritative NLM RxIMAGE database. NLM will use the Challenge entries (i.e., algorithm and software) to create a future API (Application Programming Interface) and a future software system for pill image recognition; the API will be freely accessible and the system will be freely usable.

For further details, visit the NLM News & Events page.