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Archive for the ‘PubMed’ Category

NLM to Update MEDLINE/PubMed Daily!

Beginning June 2, 2014, the National Library of Medicine will add new and updated citations to PubMed seven days a week. Daily updating is a welcome enhancement to PubMed. Prior to this change, NLM updated PubMed five times a week on Tuesday through Saturday.

Likewise, new MEDLINE/PubMed update files for NLM data licensees will appear on the ftp server daily by noon ET. More than one update file may become available on the same day. The update files are available all hours seven days per week throughout the year.

For more information, visit the NLM Technical Bulletin.

MLA Theater Presentations Available!

The NLM theater presentation recordings are available from the NLM Web site and have been announced in the NLM Technical Bulletin. The Technical Bulletin article lists the topics. Besides the usual PubMed Update, there are The ACA, Hospital Community Benefit and Needs Assessment: NLM Resources and NLM Resources Used in Disasters. The recordings are also available from the NLM Distance Education Resources page.

Lori Tagawa and Kay Deeney were available for the Using the ClinicalTrials.gov Results Database presentation because the speaker hadn’t been able to attend MLA. We answered questions from the audience!

MeSH on Demand Tool: An Easy Way to Identify Relevant MeSH Terms

The National Library of Medicine is pleased to announce the launch of MeSH on Demand, a new feature that uses the NLM Medical Text Indexer (MTI) to find MeSH terms.

Currently, the MeSH Browser allows for searches of MeSH terms, text-word searches of the Annotation and Scope Note, and searches of various fields for chemicals. These searches assume that users are familiar with MeSH terms and using the MeSH Browser. Wouldn’t it be great if you could find MeSH terms directly from your text such as an abstract or grant summary? MeSH on Demand has been developed in close collaboration among MeSH Section, NLM Index Section, and the Lister Hill National Center for Biomedical Communications to address this need.

Use MeSH on Demand to find MeSH terms relevant to your text up to 10,000 characters. One of the strengths of MeSH on Demand is its ease of use without any prior knowledge of the MeSH vocabulary and without any downloads. From the MeSH on Demand homepage, add your text, such as an abstract, into the box labeled “Text to be Processed.” Then, click the “Find MeSH Terms” button. Please read the Helpful Hints section of the homepage to improve your results.

For example, the abstract below contains the phrase “treatment-resistant depression.” The relevant MeSH Heading found for that concept is Depressive Disorder, Treatment-Resistant. MeSH on Demand finds MeSH Headings, Publication Types, and Supplementary Concepts, but not Qualifiers (Subheadings). Select the green question mark button next to the MeSH term or the MeSH term itself to open a new window with the MeSH Browser for that MeSH term.

The MeSH on Demand results page

Please note the Disclaimer that these MeSH terms are machine generated by MTI and do not reflect any human review. While the results will be different from human-generated indexing, MeSH on Demand does find relevant MeSH terms that can help jump-start finding MeSH terms in your search area. NLM welcomes your feedback on MeSH on Demand and MTI. Please send comments and questions to NLM Customer Service with “MeSH on Demand” in the subject box. NLM also looks forward to seeing your ideas for other helpful tools to utilize the MeSH vocabulary and NLM resources more easily. Please contact NLM at meshsugg@nlm.nih.gov.

NLM and Wellcome Library Establish Agreement to Make 150 Years of Biomedical Journals Freely Available Online!

Representatives of the US National Library of Medicine (NLM) and the Wellcome Trust recently signed a memorandum of understanding to work together to make thousands of complete back issues of historically-significant biomedical journals freely available online. The terms of the MOU include a donation of £750,000 ($1.2 million) to the NLM that will support coordination of the three-year project to scan original materials from NLM’s collection at the article level, and Wellcome’s work to secure copyright clearances and permissions for electronic deposit from publishers. NLM will undertake conservation of the original material to ensure its preservation for future generations. Key journals charting the development of modern medicine over the last 150 years will be digitized in their entirety and made available on the National Institutes of Health life sciences repository PubMed Central (PMC) and its European counterpart, Europe PMC. The project builds on the Medical Journal Backfiles Digitization Project (2004-2010) and will contribute substantially to the current PMC archive of over 3 million articles from medical journals.

Part of the project will concentrate on mental health journals, supporting a major archive digitization program also being undertaken by the Wellcome Trust. Journals to be digitized include Mental Health, Mental Hygiene, and the Journal of Psychological Medicine and Mental Pathology. Other journals have been selected for their general relevance, such as the Indian Medical Gazette, the British and Foreign Medico-Chirurgical Review and the Transactions of the Epidemiology Society of London. In addition to images and searchable text, NLM will also create article-level citations for PubMed. Digitization is expected to start in late 2014 and to be completed by 2017. Material will be added to PMC and Europe PMC as it is digitized.

The Wellcome Library is one of the world’s leading libraries of medical history, housing 2.5 million items of extraordinary range and diversity, and a growing collection of contemporary biomedical information resources relating to consumer health, popular science, biomedical ethics and the public understanding of science. The Wellcome Library is part of the Wellcome Trust, a global charitable foundation dedicated to achieving extraordinary improvements in human and animal health. It supports the brightest minds in biomedical research and the medical humanities. The Trust’s breadth of support includes public engagement, education and the application of research to improve health. It is independent of both political and commercial interests.

New NCBI Bookshelf Item: The Art and Politics of Science, a Memoir

Dr. Harold Varmus’ memoir, The Art and Politics of Science, chronicles his path from a graduate student in English literature at Harvard to co-recipient of the Nobel Prize for cellular origin of retroviral oncogenes, to director of the National Institutes of Health, to President and CEO of Memorial Sloan-Kettering Cancer Center. The memoir is now freely available on the NCBI Bookshelf:

The Art and Politics of Science, by Dr. Harold Varmus. There are sections on PubMed: Virtues and Limitations and journal publishing from Chapter 15, Science Publishing and Science Libraries in the Internet Age.

Three Million Articles are Now in PMC!

PMC logoAs of February 21, 2014, PMC (formerly known as PubMed Central) became home to three million articles! PMC is a free archive of biomedical and life sciences journal literature at the U.S. National Institutes of Health’s National Library of Medicine. The content has been provided in part by 1,445 full participation journals, 277 NIH Portfolio journals, and 2,477 selective deposit journals. PMC hit the one million milestone in 2007, and the two million milestone in 2010. Congratulations PMC!

Trials in PubMed Linking to Systematic Reviews

PubMed Health’s curated collection of systematic reviews now has an important new role: enabling PubMed users to go straight from a clinical trial to systematic reviews that have considered it. Visitors to records of many thousands of trials will now see a new section to the right, called a portlet. It will show links to systematic reviews in PubMed that have cited that trial. This new portlet does not replace “Related citations in PubMed”: that will follow as usual. All of PubMed Health’s 31,100 systematic reviews since 2003 are not yet included. If there is no portlet showing, it does not mean for certain that there is no systematic review that includes the trial. There are enough reviews included, though, that this portlet should become a familiar sight when using PubMed. For additional information, visit the latest issue of the NLM Technical Bulletin.

What’s New for 2014 MeSH

Three hundred four (304) new MeSH Headings were added in 2014. Forty-eight (48) MeSH Headings were either changed or deleted and replaced with more up-to-date terminology. Three new publication types have been introduced for 2014 MeSH:

  • Dataset: This publication type is defined as “An organized collection of values stored permanently in a formalized manner suitable for communication, interpretation, or processing.” This publication type will not be used in combination with any other publication type as it is not to be used for journal articles that contain or produce datasets as part of the publication (including Supplemental Materials). Rather, it will be used on citations to items that are stand-alone descriptions of the metadata of a particular dataset.
  • Observational Study: The scope note defines this publication type as “A clinical study in which participants may receive diagnostic, therapeutic, or other types of interventions, but the investigator does not assign participants to specific interventions (as in an interventional study).” This publication type should not be confused with the MeSH Heading “Observation” which is used for a scientific method. There is a related new MeSH Heading “Observational Studies as Topic,” which is used for general design, methodology, economies, etc. of observational studies.
  • Pragmatic Clinical Trial: This publication type refers to “Randomized clinical trials that compare interventions in clinical settings and which look at a range of effectiveness outcomes and impacts.” There is a related new MeSH Heading, “Pragmatic Clinical Trial as Topic,” which is used for general design, methodology, economics, etc. of pragmatic clinical trials.

Additional details are available by consulting the 2014 online Introduction to MeSH and the NLM Technical Bulletin.

PubMed Relevance Sort

PubMed now includes a new relevance sort option! The “Relevance” sort option is available from the “Display Settings” menu under the “Sort by” selections. The relevance sort order for search results is based on an algorithm that analyzes each PubMed citation that includes the search terms. For each search query, “weight” is calculated for citations depending on how many search terms are found and in which fields they are found. In addition, recently-published articles are given a somewhat higher weight for sorting.

Easy access to the relevance sort will also initially be provided under a “New feature” discovery tool:

PubMed Summary results with

Users may either choose “Relevance” from the “Display Settings Sort by” menu or click the “Sort by Relevance” link in the New Feature discovery tool. For additional information, please visit the NLM Technical Bulletin.

PubMed Commons: A New Forum for Scientific Discourse

PubMed Commons HomepageNCBI has released PubMed Commons, currently in pilot phase, which is a system that enables researchers to share their opinions about scientific publications. Researchers can comment on any publication indexed by PubMed, and read the comments of others. PubMed Commons is a forum for open and constructive criticism and discussion of scientific issues. It will thrive with high quality interchange from the scientific community. PubMed Commons is currently in a closed pilot testing phase, which means that only invited participants can add and view comments in PubMed.

For the current pilot testing phase there is a limited facility for joining that may work for you. Several organizations have provided lists of approved author e-mail addresses. If you are included on the list, you can request an invitation to join. Additional options for joining will be provided in future releases.

For additional information, visit the NCBI Insights blog.