Skip all navigation and go to page content
NN/LM Home About PSR | Contact PSR | Feedback |Site Map | Help | Bookmark and Share

Archive for the ‘PubMed’ Category

Nucleic Acids Research Database 2015 Issue Features NCBI Databases

The 22nd annual edition of the Nucleic Acids Research Database Issue features nine free full-text papers from NCBI staff that present recent updates to the databases, including GenBank, Gene, and RefSeq. These papers describe the state of NCBI databases as well as future plans to improve their use, from new reference resources created to improve the usability of viral sequence data to in-house curation efforts in the Conserved Domain Database, and much more. The articles are all available from PubMed.

New Secondary Source ID (Databank) Search Value

A new PubMed search option “hasdatabanklist” has been created to retrieve citations that carry a value in the Secondary Source ID [SI] field regardless of what the specific value(s) may be. Typically, the SI field contains information about where additional data related to an article are deposited. Please see MEDLINE Databank Sources to view the list of repository values.

To limit a search to citations that may have deposited data in a repository and acknowledged that deposit in the full text of the article, search using AND hasdatabanklist; for example: randomized controlled trial [pt] AND hasdatabanklist.

Public Access Compliance Monitor

The Public Access Compliance Monitor (PACM or “compliance monitor”) is a service from the National Library of Medicine that helps users at NIH-funded institutions locate and track the compliance of funded papers with the NIH Public Access Policy at an institutional level. Whether you are looking for a quick snapshot of your institution’s compliance rate or want to take an active role in helping your investigators comply with the policy, PACM can help you get the information you need.

To gain access to the compliance monitor, users must first be assigned a compliance reports role (“PACR”) role by an administrator at their institution who is authorized to assign roles in the NIH eRA Commons grants administration system. Users with a PACR role will then have access to the compliance reports for their institution.

PACM provides users with a list of all PubMed citations associated with an institution’s NIH funding and classifies the articles according to compliance status (i.e., Compliant, Non-Compliant, In Process). The compliance monitor also provides detailed information about each article including:

  • a full citation including the PMID (PubMed ID) and link to the PubMed record
  • associated grants and principal investigators
  • NIHMSID (NIH Manuscript Submission Reference Number), where available
  • PMCID (PubMed Central ID), where available
  • key names and dates in the NIHMS, where available
  • article compliance status
  • method A status
  • journal publisher

Compliance reports can be downloaded from these lists and the data filtered based on an institution’s needs.

For more information on the PACR role, the compliance monitor, and the available reports, see the User Guide. Additonally, an overview video of PACM from The NIH Public Access Policy for Librarians Webinar and a four-minute Look at the NIH Public Access Policy Compliance Monitor are available.

2015 MeSH Now Available in PubMed!

As of December 15, PubMed/MEDLINE citations (including the backlog of citations indexed since November 19 with 2015 MeSH), the MeSH database, and the NLM Catalog were updated to reflect 2015 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 2015 MeSH vocabulary. Highlights of MEDLINE Data Changes for 2015 were previously published in the NN/LM PSR Latitudes blog. On December 16, NLM resumed daily MEDLINE updates to PubMed.

Thai Clinical Trials Registry Added to the MEDLINE Databank Sources

NLM will be including the databank name for the Thai Clinical Trials Registry (TCTR) starting with citations to articles published in 2014. TCTR is a World Health Organization (WHO) primary clinical trial registry. The MEDLINE Databank Sources webpage has been updated to include this new listing.

Other clinical trial databank sources that appear in the Secondary Source ID [SI] element in the PubMed MEDLINE display include:

  • ClinicalTrials.gov Database (NIH/NLM)
  • Australian New Zealand Clinical Trials Registry
  • Chinese Clinical Trials Registry
  • Clinical Research Information Service, Republic of Korea
  • Clinical Trials Registry – India
  • German Clinical Trials Register
  • EU Clinical Trials Register
  • Iranian Registry of Clinical Trials
  • International Standard Randomized Controlled Trial Number (ISRCTN.org) Register
  • Japan Primary Registries Network
  • The Netherlands National Trial Register
  • Pan African Clinical Trial Register
  • Brazilian Clinical Trials Registry
  • Cuban Public Registry of Clinical Trials
  • Sri Lanka Clinical Trials Registry

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.

The Updated Label List and NLM Category Mappings file contains 2,799 labels: 2,454 labels (from the 2013 Label List) and 345 new labels. Each label has a map to one of five corresponding broader NLM Categories (i.e., BACKGROUND, OBJECTIVE, METHODS, RESULTS, or CONCLUSIONS) and an indication of whether the label is classed as an “Ending Label” concept. The 345 new label entries have a timestamp of “|20141113”. This file does not contain labels that map to UNASSIGNED as an NLM Category (see explanation). A grand total of 4,514 citations in PubMed (whether in process, MEDLINE, or PubMed-not-MEDLINE status) were revised to reflect the new labels effective on or about November 13, 2014.

Read more about Structured Abstracts in MEDLINE/PubMed.

PMC Citation Exporter Feature Now Available!

PMC (PubMed Central) is happy to announce the addition of a citation exporter feature. This feature makes it easy to retrieve either styled citations that you can copy/paste into your manuscripts, or to download them into a format compatible with your bibliographic reference manager software.

When viewing a search results page, each result summary will now include a “Citation” link. When, clicked, this will open a pop-up window that you can use to easily copy/paste citations formatted in one of three popular styles: AMA (American Medical Association), MLA (Modern Library Association, or APA (American Psychological Association). In addition, the box has links at the bottom that can be used to download the citation information in one of three machine-readable formats, which most bibliographic reference management software can import. The same citation box can also be invoked from an individual article, either in classic view (with the “Citation” link among the list of formats) or the PubReader view, by clicking on the citation information just below the article title in the banner.

Citation Exporter Feature screenshot

These human-readable styled citations, and machine-readable formats, will be available through a public API. Further details will be provided in another announcement, on the pmc-utils-announce mailing list. Please subscribe to that list if you are interested in updates.

MeSH Browser Now Updated More Frequently

Beginning on September 4, 2014, the MeSH Browser is being updated each business day. The MeSH XML and ASCII format files for Supplementary Concept Records (SCRs) will be available on this same Monday through Friday schedule starting the week of September 15, 2014. Prior to this change, the MeSH Browser and MeSH XML and ASCII files for SCRs were updated and made available once per week.

This new update schedule releases new and edited SCRs, mostly for chemicals and drugs, in a more timely way for use by both indexers and searchers. Descriptors and qualifiers are changed only on an annual basis.

2015 Medical Subject Headings (MeSH) Now Available!

MeSH Vocabulary Changes for 2015 is now available! Lists of new descriptors, changed descriptors, deleted descriptors, and new descriptors by tree subcategory are available on the NLM website. For more information about MeSH use and structure, as well as recent updates and availability of data, visit the updated Introduction to MeSH – 2015 webpage.

Note: The default year in the MeSH Browser remains 2014 MeSH for now, but the alternate link provides access to 2015 MeSH. The MeSH Section will continue to provide access via the MeSH Browser for two years of the vocabulary; the current year and an alternate year. Sometime in November or December, the default year will change to 2015 MeSH and the alternate link will provide access to the 2014 MeSH.

Population Health Added to Special Queries

The NLM PubMed Special Queries page includes a link to a new MEDLINE/PubMed Population Health search. A definition for population health is “the health outcomes of a group of individuals, including the distribution of such outcomes within the group. The field of population health includes health outcomes, patterns of health determinants, and policies and interventions that link these to differences between groups of people.” 1

The Population Health Special Query is a PubMed search of relevant MeSH headings and text words combined strategically to retrieve PubMed citations. MeSH headings were selected with the assistance of members of the Institute of Medicine Board on Population Health and Public Health.

1 Kindig D, Stoddart G. What is population health? Am J Public Health. 2003 Mar;93(3):380-3. PubMed PMID: 12604476.