Archive for the ‘Search Tools’ Category
PubMed users can now see the icon that links to the full text deposited at an institutional repository (IR) using LinkOut. The LinkOut service provides links to full text, library holdings, and other relevant external resources from PubMed and other NCBI databases. Until this year, there were three quick ways to access full text articles from PubMed:
- the publisher icon links to the journal web site (may require a subscription to the journal)
- the PMC icon links to free full text in PubMed Central (PMC)
- the DOI (Digital Object Identifier) links to the article on the journal web site (may require a subscription to the journal)
The new institutional repository icons will link to free full text of the article at an institutional repository that it is not freely available from the journal or PMC. When an IR is participating in this new LinkOut feature, the linking icon will display in the “Full text links” section next to the abstract in PubMed for any publication with a direct link to a full text that does not have another free full text link. The “LinkOut – more resources” section expands to show the same direct links to full text as the icons. All links to participating IRs will appear whether or not there is a free full text icon displayed in the “Full text links” section. There are only a few IRs participating in the free full text LinkOut at this time but these few already expand access to about 25,000 publications. Some academic and research institutions encourage or require authors to submit their publications in the IR, making them publicly accessible within the terms of publication at a journal. This is often called “green open access.” There might be an embargo period or delay after publication, as there can be with NIH-authored manuscripts in PMC. However, free full texts can be available as soon as an article is published.
LinkOut resources come from organizations that have applied to join LinkOut, providing information or data that are relevant to that specific publication. LinkOut participants include libraries, biological data repositories, and repositories like Dryad and Figshare. If you know of an IR that has publicly available free full texts beyond those available in PMC, please let them know about this service. A list of participating institutional repositories is available from the LinkOut Web site. Instructions for institutional repositories to join LinkOut are also available. For questions about participating in LinkOut, contact NLM. Additional details and sample screen displays are available in the NLM Technical Bulletin.
The NLM Catalog left sidebar facets have been updated to improve users’ ability to combine filters when searching. For example, “Journals referenced in the NCBI DBs” (databases) now appears as its own category so that it can be combined easily with any other filter. Users are also able to customize the sidebar to display additional facets, including “PubMed/PMC journals” and “All MEDLINE journals.” For further details, visit the NLM Technical Bulletin.
Health professionals often need to locate health statistics and data and to visualize that data in chart, graph, or map format. The following resources related to health data, statistics, and data visualization tools may be useful:
- NLM’s MedlinePlus: The Health Statistics page provides a summary of health statistics and links to a wide variety of reliable health statistics resources.
- 2010 Census Data: The most detailed information available from the 2010 Census about a community’s entire population, including cross-tabulations of age, sex, households, families, relationship to householder, housing units, detailed race and Hispanic or Latino origin groups, and group quarters.
- Healthdata.gov: Comprehensive catalog of health-related data sets relevant to all aspects of health, for a broad array of users, supplied by a wide range of federal agencies, and available for free.
- CDC Data Resources: Reference list of nationally funded data systems with a relationship to environmental public health; highlights the major data systems with a national scope where public health and environmental data can be directly downloaded.
- Visualize Toxic Chemical Data: Use NLM’s TOXMAP to visualize locations of US EPA Toxics Release Inventory facilities, US Superfund sites, Environment Canada’s National Pollutant Release Inventory sites, US nuclear plants, and EPA coal plants. Additional layers of US census and health data can be added to the map.
- Learn How to Create Maps with Low/No Cost Tools: Use NLM’s Community Health Maps to learn about free and low cost methods for collecting field data, combining field data with other organizational data, and visualizing the data through online mapping tools.
AIDSource is a portal to HIV/AIDS-related resources, reviewed and selected by expert information specialists from the National Library of Medicine. Users can easily locate HIV/AIDS resources for special populations under the Specific Populations section of AIDSource, including:
Users can also choose the “Select Audience” menu on AIDSource to view lists of HIV/AIDS resources for specific audiences, such as the general public, health professionals, multilingual speakers, researchers/scientists, Spanish speakers, or students/educators.
On March 8 NLM implemented four new enhancements to PubMed:
- Conflict of Interest Statements (COIS): PubMed includes conflict of interest statements below the abstract when these statements are supplied by the publisher.
- Editorial Expressions of Concern: NLM has added editorial expressions of concern as a new pair of linking elements in the Comments/Corrections suite in PubMed. Expressions of concern, previously handled as comments, are labeled explicitly in the abstract display.
- Results Display: The “Per page” menu, which allows users to customize the number of items that appear on the results screen, appears at the top of the results list.
- Status Tag: The status tag [PubMed – indexed for MEDLINE] has been replaced with the tag [Indexed for MEDLINE]. The Abstract display in PubMed includes a status tag only if the citation is indexed for MEDLINE. Additional status tags still appear in the MEDLINE and XML displays. The citation status search strategies continue to function as they always have.
For additional details and illustrations of these updates, visit the NLM Technical Bulletin.
Join the one-hour NN/LM Webinar, What’s New in Post-Publication Activities in PubMed, on March 15, 1:00-2:00 PM PDT. Hilda Bastian from the National Center for Biotechnology Information (NCBI) will present a discussion of the changing visibility and accessibility of post-publication activity in PubMed. The webinar is part of the PNR Rendezvous monthly webinar series from the NN/LM Pacific Northwest Region.
The National Library of Medicine has announced the addition of CVX (Vaccines Administered) as a new data source to RxNorm. The addition of CVX data to RxNorm helps facilitate the electronic exchange of vaccine information in electronic health records. CVX includes both active and inactive vaccines available in the United States. CVX codes for inactive vaccines allow electronic transmission of historical immunization records. CVX is maintained and developed by the Centers for Disease Control and Prevention (CDC), National Center of Immunization and Respiratory Diseases (NCIRD).
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:
- Complementary Medicine
- Dietary Supplements
- Systematic Reviews
A prototype online platform that uses real-time visualization and viral genome data to track the spread of global pathogens such as Zika and Ebola is the grand prize winner of the Open Science Prize. The international team competition is an initiative of the National Institutes of Health, in collaboration with the Wellcome Trust and the Howard Hughes Medical Institute (HHMI). The winning team, Real-time Evolutionary Tracking for Pathogen Surveillance and Epidemiological Investigation, created its nextstrain.org prototype to pool data from researchers across the globe, perform rapid phylogenetic analysis, and post the results on the platform’s website. The winning team will receive $230,000 to fully develop their prototype with NIH awarding $115,000 to the U.S. members of the winning team, and the Wellcome Trust and HHMI also contributing $115,000.
The Open Science Prize is a global competition designed to foster innovative solutions in public health and biomedicine using open digital content. The prize, which was launched in October 2015, aims to forge new international collaborations that bring together open science innovators to develop services and tools of benefit to the global research community. All six finalist teams were considered exemplary by the funders and are to be commended for their tenacity in developing creative approaches to applying publicly-accessible data to solve complex biomedical and public health challenges. The topics spanned the breadth of biomedical and public challenges, ranging from understanding the genetic basis of rare diseases, mapping the human brain, and enhancing the sharing of clinical trial information. As evidenced from the six Open Science Prize finalists, public health and biomedical solutions are enriched when data are combined from geographically diverse sources. Further details are available in the NIH Press Release.
Health outreach professionals often need to locate health statistics and data, to learn what kinds of health issues affect specific populations. The data may need to be visualized in chart, graph, or map format, to include in reports for policy makers and for the general public. Where can you find the raw data related to public health, and what tools are available to visualize the data? Following are a few resources related to health data, statistics, and data visualization that may be useful:
- Learn about Health Statistics on MedlinePlus: Your first stop can be the Health Statistics page on MedlinePlus, where you can read a quick summary about health statistics and access links to a wide variety of reliable health statistics resources.
- Find Public Datasets Related to Health Disparities: The Office of Minority Health (OMH) at the U.S. Department of Health and Human Services (HHS) recently announced the release of the National Partnership for Action (NPA) Compendium of Publicly Available Datasets and Other Data-Related Resources, a free resource that compiles descriptions of and links to 132 public datasets and resources that include information about health conditions and other factors that impact the health of minority populations.
- Visualize Toxic Chemical Health Data on TOXMAP: The TOXMAP tool can be used to visualize locations of Toxic Release Inventory facilities, Superfund sites, Environment Canada’s National Pollutant Release Inventory data, location of nuclear plants, and location of EPA coal plants, with additional layers of US census and health data added to the map to illustrate environmental health disparities in specific locations.
- Learn How to Create Community Health Maps: Use the Community Health Mapping Lab Exercises to learn free and low cost methods for collecting field data, combining field data with other organizational data, and visualizing the data through online mapping tools.