Archive for the ‘PubMed’ Category
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.
English translations of article titles in other languages display in PubMed whenever they are available. In the past, when a translation was not available, the title display in PubMed would read “Not available” or similar wording. PubMed has been updated to display the title in the original language when a translation is not available. Note that this change does not affect PubMed searching. The default title search includes only English titles and title translations. To search titles in the original language, select the “Transliterated Title” field that includes both transliterated and vernacular titles from the Advanced Search page or use the field tag [tt].
PubMed has introduced a new type of link called “Articles Frequently Viewed Together” to assist with locating important articles on a given topic. For some PubMed abstracts, this feature will appear in the “Related Information” section in the right column. Currently, only 1.3 million out of the 24 million records in PubMed have this link. The calculation is based on anonymous click data for the last year, so older articles will be especially underrepresented. To find all articles with these relationships, search PubMed with the query “pubmed_pubmed_alsoviewed[filter]” and add additional terms to narrow the focus to your area of interest.
The NLM exhibit booth at the 2015 Annual Meeting of the Medical Library Association in Austin, TX, featured theater presentations to bring users up-to-date on several NLM products and services. The presentation recordings are captioned and accessible from the NLM Distance Education Program Resources page. The presentations include:
Note: To listen to the voice recordings and view the captions you may need the latest version of Flash® Player (download for free from the Adobe Web site). To maximize the presentation, use the Full Screen button. For more information, go to the NLM Technical Bulletin page.
The PubMed “Related citations” feature will soon be renamed to “Similar articles.” “Similar articles” was chosen because “Related citations” is ambiguous. There are several types of relationships that articles may have. The algorithm to generate the results has not been modified. The link name will be updated on the Summary results. The Abstract display discovery tool title will also be renamed. To see illustrations of the new feature, visit the NLM Technical Bulletin.
The MEDLINE/PubMed Search and Health Literacy Information Resources page and its preformulated Health Literacy Special Query have been updated to keep pace with the growing body of relevant literature. The Health Literacy Special Query now retrieves additional citations to articles about numeracy, comprehension of informed consent, and health insurance comprehension. The dynamic MEDLINE/PubMed health literacy search retrieves more than 8,000 citations to English language journal articles related to Health Literacy. PubMed filters can be used to limit to particular years, research or publication types. To limit citations to a particular subject (such as “decision making”) use the Advanced Search features.
Sometimes called Quantitative Literacy (QL) or Quantitative Reasoning (QR), numeracy involves skills needed to select a health insurance plan, choose treatments, and understand medication instructions. MEDLINE/PubMed may contain citations to articles that discuss numeracy skills of clinicians—physicians, nurses, and other health professionals who must communicate with patients and the public. Informed consent comprehension is of great interest to health literacy advocates and researchers who are concerned with how effectively health care providers communicate disease and treatment risks and benefits to patients. Among the more than 16,000 citations to articles with Informed Consent as a major descriptor, many citations don’t explicitly use the phrase “health literacy,” but are conceptually tied to it.
The selected resources on the right side of the MEDLINE/PubMed Search and Health Literacy Information Resources page includes new links, such as: