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Archive for the ‘PubMed’ Category

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.

Sara Tybaert Appointed as New Head of NLM’s MEDLARS Management Section!

Sara Tybaert begins her new position as Head of MEDLARS Management Section (MMS) in NLM’s Bibliographic Services Division (BSD) on October 6, 2013. Sara has been with MMS since 1990, filling many roles. Since 2011, Sara has been the Head of the Bibliographic Data Management Unit within MMS. In this position she has overseen the daily MEDLINE data verification process for the nightly exports of MEDLINE data to PubMed and to MEDLINE licensees. Her work includes oversight of the various systems used in the data quality control work performed within MMS. She also supports the ongoing development and testing of data input and maintenance systems for MEDLINE. And perhaps most importantly, Sara has been the project manager for the annual Year End Processing (YEP) efforts within BSD.

Sara has provided support and oversight for several key projects within MMS during her tenure at NLM. She serves as the MMS representative to the Shared Serials Group. Sara also currently serves as the MMS representative to the NLM COGNOS Team Leads group, and participates on the MEDLINE Processing Working Group and NLM DTD Group. She has participated on the MMS PubMed team with NCBI, including system testing and support for MEDLINE/PubMed customer service. In addition, she has often represented NLM at the NLM Exhibit Booth at the MLA annual meeting. Over the years, one of Sara’s greatest accomplishments was serving as the COR/COTR for the NLM Bioethics Contract with the Kennedy Institute of Ethics. Under her guidance, NLM was eventually able to reduce and eventually discontinue this contract, providing significant savings to NLM and Library Operations.

2014 Medical Subject Headings (MeSH) Now Available

What do air travel, dandruff, patient harm, and social determinants of health have in common? They are all new 2014 MeSH descriptors!

The Introduction to MeSH 2014 is now available, including information on its use and structure, as well as recent updates and availability of data. MeSH vocabulary changes for 2014 lists include:

Additionally, the entire MeSH vocabulary is available to download in XML and ASCII format.

My NCBI Curriculum Vitae Web Application: SciENcv

SciENcv is a new feature in My NCBI that helps users create an online professional profile that can be made public to share with others. In SciENcv users can document their education, employment, research activities, publications, honors, research grants, and other professional contributions. In addition, the SciENcv profile may include an ORCID iD, when registered with ORCID. eRA Commons account holders who have linked their eRA account to My NCBI will find their SciENcv profile automatically populated with the information stored in their eRA Commons profile. The information transferred from eRA Commons to SciENcv profiles can be changed, hidden, augmented, or deleted.

The SciENcv Web application is the end product of a request made by the Federal Demonstration Partnership (FDP) to reduce the administrative burden associated with federal grant submissions. It is being developed under the aegis of an interagency workgroup composed of members from the Department of Defense, the Department of Energy, the Environmental Protection Agency, the National Institutes of Health, the National Science Foundation, The Smithsonian, and the United States Department of Agriculture.

For additional information, please visit the My NCBI Help: SciENcv webpage or the NLM Technical Bulletin.

NTC Classes: PubMed for Trainers, TOXNET, and PubMed Update

On December 12, 2013, staff from the National Library of Medicine Training Center (NTC) and NLM will present NLM Express: A PubMed® Update for PSR Network members and others who register. Learn about recently added PubMed features and interface changes from the last six months, and bring your PubMed questions to this online webinar!

PubMed® for Trainers is coming to our region (San Francisco) in February, 2014. The hybrid sessions run from Thursday, February 6, 2014 – February 26, 2014. Three of the session are online, with the final one conducted in-person at the UCSF Library and Center for Knowledge Management. Class participants are eligible for 15 MLA CE credits. The class is an in-depth look at PubMed and a chance to share training ideas with your fellow participants! This hands-on course consists of lectures, individual exercises, group work, and discussions, with approximately 2-3 hours of independent work to be done outside of class time. All sessions must be attended to receive credit. The in-person Session Four is in San Francisco on February 26, 2014, 9 am – 4:30 pm PT. Registration is now available!

TOXNET® and Beyond is designed to convey the basics of searching the NLM’s TOXNET®, a Web-based system of databases in the areas of toxicology, environmental health, and related fields. TOXNET® is a free class, offering 6.0 MLA continuing education credits. This daylong in-person course will be held Thursday, February 27, 2014, beginning at 9:00 AM PT in San Francisco at UCSF. Registration is now available!

For questions about the Pacific Southwest Region training program, please contact Kay Deeney, Educational Services Coordinator.