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Archive for the ‘PubMed’ Category

The National Library of Medicine Wants Your Stories!

Do you know any stories about people using NLM resources to find out something interesting, forge a new path, or improve their lives in a unique or dramatic way? Or, more simply, have you ever found just the right information at just the right time, for yourself or for a patron? For this year’s theater presentations at the Medical Library Association annual meeting in Austin, TX, NLM staff members who develop the resources are interested in teaming with the librarians who use them. They are interested in stories (great and small) about any NLM resource, but especially:

  • HSRProj
  • Health Services Research Resources on Comparative Effectiveness, Patient Centered Outcomes, Health Technology Assessment
  • DIMRC and other disaster resources
  • BIBFRAME and Linked Data
  • History of Medicine social media (e.g., Circulating Now)
  • MedlinePlus
  • PubMed Central
  • PubMed
  • PubMed Health

Anyone interested in sharing their story should contact Kate Majewski at NLM.

PubMed Subject Filter Strategies Updated for 2015

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:

List of Serials Indexed for Online Users, 2015 Edition, Now Available in XML

The List of Serials Indexed for Online Users (LSIOU), 2015 edition, is now available in XML format. The 2015 edition contains 14,856 serial titles, including titles currently indexed for MEDLINE as well as titles indexed over time which have ceased or changed titles. The titles are listed alphabetically by the journal title abbreviation. Tailored lists of indexed journals may be generated from the NLM Catalog. While the XML version of the LSIOU is a snapshot in time, the results of a search in the NLM Catalog will provide a “real time” list for the LSIOU.

For a “real time” list for the LSIOU, enter reportedmedline in the search box and click “Search.” For a list of only the currently indexed MEDLINE journals, enter currentlyindexed in the search box and click “Search.” Display and sort formats are selected from the results page; click on the Display Settings pull-down menu to choose a display format (for example, the Journal display) and an appropriate sort (for example, Title or Title Abbreviation). To save the entire list as one document, click on the “Send to” pull-down menu, with “File” as the destination, choose a format and sort order, and then click “Create File.” Click “Save” in the File Download pop-up box. Provide your directory location and desired file name.

Additional information about journals indexed for MEDLINE can be found via the links from the MEDLINE/PubMed Resources web page. This page includes Journals Recently Accepted by NLM for Inclusion in MEDLINE, a list of titles selected by the Literature Selection Technical Review Committee (LSTRC) that meets three times per year in February, June, and October. Results from those meetings appear online about six weeks after each meeting, both on the web page and in the NLM Catalog. For additional details about searching the NLM Catalog, visit NLM Catalog Quick Tours and Searching for Journals in the NLM Catalog.

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:

  • 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 ( 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.