Archive for the ‘PubMed’ Category
The PMC Overview and FAQ have been updated to provide more information on the Scientific Quality Review Process for journals that apply to participate in PMC. In 2014, PMC implemented a scientific and editorial quality review procedure whereby expert consultants from outside the National Library of Medicine (NLM) conduct an independent review of journals seeking to participate in PMC. This was in response to a significant increase in new publishers and journals applying to participate in PMC, many of which are unknown to NLM in terms of quality and publishing practices. The independent review, which was approved by the PMC National Advisory Committee (see minutes from June 10, 2014), follows an assessment by NLM that the journal meets NLM’s criteria for its collection, as outlined in the Collection Development Manual.
PMC also recently updated the minimum requirement on the number of substantive, peer-reviewed articles needed before a journal can apply to PMC. The new 25-article minimum ensures that the reviewers have a sufficient amount of content on which to base their recommendation for inclusion in PMC. The new minimum article requirement takes effect on January 1, 2016. Publishers are encouraged to use the 25-article minimum as a guideline in the interim when submitting applications.
Earlier this year PubMed Health was expanded with research on research methods. These are studies and guidance for doing systematic reviews and helping them make an impact. A new resource takes this process a step further; the PubMed Systematic Review Methods Filter, as well as a new section at PubMed Health “For Researchers.” Also available are new glossary pages especially for research methods for anyone who wants to understand more about the mechanics of health research. The glossary will grow to cover the most common research terms used in PubMed Health.
Whenever you search in PubMed Health, you also get results from PubMed using the new filter. They will appear to the right of the main search results, in a box called “Systematic Review Methods in PubMed.” It’s below a box called “Systematic Reviews in PubMed,” which is a search for systematic reviews themselves. The filter searches through a subset of PubMed records that are either research or guidance on systematic review methods. The publications could relate to the development or evaluation of any step in doing or using systematic reviews. To use the filter in PubMed, enter sysrev_methods [sb] in the search box. You can use it like any search term, for example, sysrev_methods [sb] AND “network meta-analysis.”
The methods filter is a result of collaboration between the PubMed Health team and the Scientific Resource Center (SRC) for the U.S. Agency for Healthcare Research and Quality (AHRQ). The SRC team selects the publications, after scanning widely every day looking for new candidates. When you see a systematic review at PubMed Health, there will often be a methods box to the right. That links to the relevant methods guide from the organization behind the review. Six groups so far have started contributing their methods guidance and research to PubMed Health. You can see the list on the new “For Researchers” page.
Navigation isn’t the only part of PubMed Health with a new look. The homepage also has a new design. For further details, visit the PubMed Health Blog.
MeSH, the National Library of Medicine’s controlled vocabulary thesaurus, is updated annually. It is used to index articles from thousands of biomedical journals for the MEDLINE/PubMed database and for the cataloging of books, documents, and audiovisuals acquired by NLM. Changes for 2016 MeSH include: 438 new Descriptors, 17 Descriptor terms replaced with more up-to-date terminology, 9 deleted Descriptors, and deletion of the Subheading “diagnostic use.” Content of MeSH now includes 27,883 Descriptors; 87,028 Descriptor entry terms; 82 Qualifiers (Subheadings); and 230,872 Supplementary Concept Records. Three new Publication Types were added for catalogers; Blogs, Graphic Novels, and Public Service Announcements. The Publication Type Clinical Study was added mainly for use by indexers. Additional changes involve the MeSH Trees and Scope Notes. For a complete list of changes, visit the NLM Technical Bulletin.
Creative Commons (CC) licenses are types of copyright licenses that allow free distribution of a work. PubMed Central (PMC), the NLM archive of full text journal articles, includes articles that have a Creative Commons license or are in the public domain. The latter covers those articles authored by staff of U.S. government agencies. NLM now offers a filter for both PubMed Central and PubMed to find articles with unrestricted Creative Commons or public domain (CC0) licenses:
These filters are based on license information that is provided to PubMed Central by publishers. There are many more articles cited in PubMed but not deposited in PMC that have CC0 licenses, but that information is not part of PubMed. You can view the detailed copyright information for an article in PubMed Central by clicking on Copyright and License Information at the top:
For more information, see the PubMed Central Open Access Subset page. You may use and reproduce these articles without special permission. It is requested that you properly cite and acknowledge the source. Please bear in mind that these articles, although made available under a CC0 license, may still contain photographs or illustrations copyrighted by other commercial organizations or individuals that may not be used without obtaining prior approval from the holder of the copyright.
The NN/LM Middle Atlantic Region has announced two webinar opportunities that are open to anyone wishing to attend:
Tuesday, December 8: Hospital Libraries: Challenges and Opportunities – This session will include discussion of the current state of hospital libraries and consider their future in light of the Affordable Care Act, Meaningful Use, and budget cuts. It will also consider the role the librarian plays and their effect on these changes, as well as ways the library’s resources (including the librarian) can help offset the expenses hospitals are facing. Speaker: Heather N. Holmes, MLIS, AHIP, Clinical Informationist, Summa Health System, Akron, OH.
When: December 8, 2015, 9:00-10:00am PST
No Registration Required
Eligible for 1 MLA CEU
Thursday, December 17: Saving time with PubMed Subject-specific Queries – Want to boost your PubMed prowess? Looking for preformulated searches on drugs, health information technology, public health and other topics? Spend an hour with NN/LM MAR Outreach Coordinator, Kate Flewelling, to save hours on your searches!
When: December 17, 2015, 9:00-10:00am PST
No Registration Required
Eligible for 1 MLA CE
Join NCBI staff for the upcoming webinars on PubMed and ClinVar:
PubMed for Scientists
Thu, Nov 12, 2015 9:30 AM – 10:30 AM PST
Search the biomedical literature more efficiently with PubMed. In this Webinar designed for scientists you will learn to search by author; explore a subject; use filters to narrow your search; find the full text article; and set up an e-mail alert for new research on your topic. Bring your questions about searching PubMed.
NCBI Minute: The New ClinVar Submission Wizard
Wed, Nov 18, 2015 9:00 AM – 9:30 AM PST
ClinVar is the NCBI archive of submitted interpretations of variants relative to diseases and other phenotypes. Submission to ClinVar has been through the Variation Submission Portal, which is useful for groups who frequently submit large number of variants but may not be convenient for infrequent submitters of small numbers of variants. This webinar will introduce and demonstrate the new ClinVar Submission Wizard, a guided interface for direct data entry, targeted to research laboratories that infrequently want to submit a small number of records. The Submission Wizard is designed to support all types of submissions to ClinVar, including structural variants, pharmacogenomics variants, somatic variants, as well as interpretations based on functional rather than clinical significance.
NCBI Minute: Finding Genes in PubMed
Wed, Dec 2, 2015 9:00 AM – 9:15 AM PST
Learn to quickly find literature about a gene of interest using PubMed. Take advantage of the links between gene data and literature, and leverage the vocabulary used to describe gene information in PubMed to build a better search.
Visit the NCBI Webinars and Courses webpage to view archived webinars and materials, and to learn about future webinars. Archived webinars can also be accessed on the NCBI YouTube channel.
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. A grand total of 4,702 citations (whether in process, MEDLINE, or PubMed-not-MEDLINE status) were revised so that the new labels include the NLM Category mapping in the XML data, effective on or about October 26, 2015. Of interest, the new label ‘TWEETABLE ABSTRACT’ (mapped to the NLM Category ‘CONCLUSIONS’) illustrates the impact of social media. Read more about Structured Abstracts in MEDLINE/PubMed.
On October 7, 2015, the “Write to the PubMed Help Desk” customer service form was revised. The new form includes prompts to provide necessary request information. This information will enable NLM to address customer needs more efficiently. For example, the “What are you writing about?” line has a drop down list of options for a user to select. One choice is “Misspelling or error in PubMed.” If this option is selected, the form prompts the user for the PMID of the citation. The form will display citation information for the user to confirm, and then require the “Current text in PubMed” and the “Correct text.” The selected topic, along with the PMID information when provided, automates the routing of the question for appropriate review and action at NLM. There are also information buttons that link to explanations of related NLM policies.
The National Center on Health Services Research and Health Care Technology (NICHSR) of the National Library of Medicine (NLM) has released a new health services research resource on domestic violence, to complement the new NLM exhibition, Confronting Violence, Improving Women’s Lives. The new resource can be found on the Web portal, Health Services Research Information Central (HSR Info Central). It is intended to support health services researchers, policymakers, administrators, and practitioners involved in detection, prevention and treatment services for this underserved and often unnoticed community. The scope of this “topic page” includes Intimate Partner Violence, Reproductive and Sexual Coercion, Child Abuse and Maltreatment, and Elder Abuse.
The Domestic Violence topic page assists researchers, both novice and advanced, by providing detailed search queries for key NLM databases: PubMed, PubMed Health, HSRProj (Health Services Research Projects in Progress), and HSRR (Health Services and Sciences Research Resources). These searches will enable users to readily discover relevant published medical literature, clinical effectiveness research, ongoing HSR projects, and related datasets, instruments and other tools. In addition, the resource identifies important guidelines, assessment instruments and measures, and includes a structured query for the Agency for Healthcare Research and Quality’s National Guidelines Clearinghouse.
The National Library of Medicine (NLM) is currently involved in MEDLINE year-end processing (YEP) activities. These include changing the Medical Subject Headings (MeSH) main headings and subheadings as well as Supplementary Concept Records that standardize names and associated numbers for chemicals, protocols, and diseases that are not main headings. The MeSH edits include maintaining existing MEDLINE citations to conform with the 2016 version of MeSH, and other global changes.
- November 18, 2015: NLM expects to temporarily suspend the addition of fully-indexed MEDLINE citations to PubMed. NLM will continue to add Publisher-supplied and in process citations.
- Mid-December 2015: PubMed MEDLINE citations, translation tables, and the MeSH database will have been updated to reflect 2016 MeSH.
For details about the impact on searching from November 19 to mid-December, see: Annual MEDLINE/PubMed Year-End Processing (YEP): Impact on Searching During Fall 2015. For background information on the general kinds of changes made annually, see: Annual MEDLINE/PubMed Year-End Processing (YEP): Background Information.