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.
Archive for the ‘Search Tools’ Category
As part of its ongoing work to develop an infrastructure and tools for identifying prescription pills, the National Library of Medicine has announced a new Request for Information (RFI). This is NOT a solicitation for proposals, proposal abstracts, or quotations. The purpose of this RFI is to obtain knowledge and information for project planning purposes. The government will not award a contract on the basis of this notice, or otherwise pay for information solicited by it. Proprietary information should be clearly marked. The requested information is for planning and market research purposes only and will not be publicly released. This Request for Information (RFI) is a pilot for a forthcoming Pill Image Recognition Challenge for visually identifying pills. The Challenge has as its main objective the development and discovery of high-quality software that matches images of unknown prescription pills to images in the RxIMAGE database. The pilot will help ensure that the Challenge is successful.
The National Library of Medicine (NLM) Computational Photography Project for Pill Identification (C3PI) is developing infrastructure and tools for identifying prescription pills. The infrastructure includes NLM’s RxIMAGE database of freely available, high quality prescription pill images and associated pill data. One tool is the freely accessible RxIMAGE API (Application Programming Interface) for text-based search and retrieval of images and data from the RxIMAGE database.
NLM now seeks to expand the toolset to include smart phone apps to visually search for and retrieve pill images and data. A person will photograph an unknown prescription pill, possibly under poor lighting conditions, from an angle, or at low resolution. The app will return one or more RxIMAGE images and data that are most likely to match the photographed pill. Respondents to the RFI are asked to submit executable software that matches consumer images – photos of pills taken by cell phone digital cameras – with reference images obtained from images in the RxIMAGE database.
The start date for accepting responses to this RFI is April 6, 2015. The end date for accepting responses to this RFI is May 15, 2015. For full information about the RFI, visit the NLM News & Events and NLM Pill Image Recognition Pilot (PIR Pilot) websites.
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:
- The Culture Framework for Health: An integrative approach for research and program design and evaluation (OBSSR, NIH, 2015, PDF version)
- Measuring Health Insurance Literacy: A Call to Action. A Report from the Health Insurance Literacy Expert Roundtable of Consumers Union (2012, PDF version)
- ACOG Health Literacy Committee Opinion Number 585 (February 2014)
- Always Use Teach-back! training toolkit (IHS Center for Clinical Transformation, Health Literacy Iowa and Des Moines)
- 2015 Health Literacy Annual Research Conference (updated page for the HARC VII Conference)
The CDC just released the updated Community Health Status Indicators (CHSI), an interactive online tool that provides public health profiles for all 3,143 counties in the United States. Each profile includes key indicators of health outcomes, which describes the population health status of a county and factors that have the potential to influence health outcomes, such as health care access and quality, health behaviors, social factors, and the physical environment. First issued in 2000, CHSI 2015 represents the collaboration of public health partners in the public, non-profit and research communities. The re-designed online application includes updated peer county groups, health status indicators, a summary comparison page, and U.S. Census tract data and indicators for sub-populations (age groups, sex, and race/ethnicity) to identify potential health disparities. In this new version of CHSI, all indicators are benchmarked against those of peer counties, groups of counties that are similar to each other based on 19 variables, the median of all U.S. counties, and Healthy People 2020 targets. CHSI 2015 is designed to complement other available sources of community health indicators including the Robert Wood Johnson Foundation’s County Health Rankings and Roadmaps. Organizations conducting community health assessments can use CHSI data to:
- Assess community health status and identify disparities;
- Promote a shared understanding of the wide range of factors that can influence health; and
- Mobilize multi-sector partnerships to work together to improve population health.
To promote awareness of the new tool, the CDC and the National Library of Medicine are co-hosting two sessions of a one-hour briefing that will provide an overview of the new features and redesign of CHSI. Registration is available for either March 24, 12-1:00 PM PDT, or March 26, 8-9:00 AM PDT. Once your registration request is approved, you will receive instructions for joining the meeting.
The NCBI homepage has six new buttons on it: Submit, Download, Learn, Develop, Analyze, and Research. Each of these leads to an action page devoted to a particular set of services. These action pages allow easy access to the pages and resources you need to complete tasks. For instance, you can: Find information about the Entrez API; Find an upcoming NCBI webinar, Find an NCBI tool that designs PCR primers, and much more! On the new action pages, you’ll also see six categories in the header: Literature, Health, Genomes, Genes, Proteins, and Chemicals. These category pages highlight useful databases, tools and resources for each of the topics all in one place.
Also included is a blue Feedback button on the left side of the Download, Learn, Develop, and Analyze pages so that you can send comments to NCBI. More information about the new homepage will be released on NCBI News and to the blog, NCBI Insights.
Do you know any stories about people using NLM resources to find out something interesting, forge a new path, or improve their lives in a unique or dramatic way? Or, more simply, have you ever found just the right information at just the right time, for yourself or for a patron? For this year’s theater presentations at the Medical Library Association annual meeting in Austin, TX, NLM staff members who develop the resources are interested in teaming with the librarians who use them. They are interested in stories (great and small) about any NLM resource, but especially:
- Health Services Research Resources on Comparative Effectiveness, Patient Centered Outcomes, Health Technology Assessment
- DIMRC and other disaster resources
- BIBFRAME and Linked Data
- History of Medicine social media (e.g., Circulating Now)
- PubMed Central
- PubMed Health
Anyone interested in sharing their story should contact Kate Majewski at NLM.
The List of Serials Indexed for Online Users (LSIOU), 2015 edition, is now available in XML format. The 2015 edition contains 14,856 serial titles, including titles currently indexed for MEDLINE as well as titles indexed over time which have ceased or changed titles. The titles are listed alphabetically by the journal title abbreviation. Tailored lists of indexed journals may be generated from the NLM Catalog. While the XML version of the LSIOU is a snapshot in time, the results of a search in the NLM Catalog will provide a “real time” list for the LSIOU.
For a “real time” list for the LSIOU, enter reportedmedline in the search box and click “Search.” For a list of only the currently indexed MEDLINE journals, enter currentlyindexed in the search box and click “Search.” Display and sort formats are selected from the results page; click on the Display Settings pull-down menu to choose a display format (for example, the Journal display) and an appropriate sort (for example, Title or Title Abbreviation). To save the entire list as one document, click on the “Send to” pull-down menu, with “File” as the destination, choose a format and sort order, and then click “Create File.” Click “Save” in the File Download pop-up box. Provide your directory location and desired file name.
Additional information about journals indexed for MEDLINE can be found via the links from the MEDLINE/PubMed Resources web page. This page includes Journals Recently Accepted by NLM for Inclusion in MEDLINE, a list of titles selected by the Literature Selection Technical Review Committee (LSTRC) that meets three times per year in February, June, and October. Results from those meetings appear online about six weeks after each meeting, both on the web page and in the NLM Catalog. For additional details about searching the NLM Catalog, visit NLM Catalog Quick Tours and Searching for Journals in the NLM Catalog.
The National Library of Medicine (NLM) has issued a call for participation in a Pill Image Recognition (PIR) Request for Information (RFI). Unidentified and misidentified prescription pills present challenges for individuals and professionals. Unidentified pills can be found by family members, health professionals, educators, and law enforcement. The nine out of 10 US citizens over age 65 who take more than one prescription pill can be prone to misidentifying those pills.
This PIR RFI is a pilot for a forthcoming PIR Challenge whose goal is to develop smart phone apps that individuals can use to take pictures of prescription pills and then search for and retrieve pill images and associated data of likely matches in an NLM database. NLM anticipates that respondents will include professionals and students, individually or in teams, in computer vision and computer graphics working on content-based image retrieval. Instructions for responding to the RFI are available on the PIR website.
The deadline for submissions to this RFI is Monday, April 27, 2015.
The 22nd annual edition of the Nucleic Acids Research Database Issue features nine free full-text papers from NCBI staff that present recent updates to the databases, including GenBank, Gene, and RefSeq. These papers describe the state of NCBI databases as well as future plans to improve their use, from new reference resources created to improve the usability of viral sequence data to in-house curation efforts in the Conserved Domain Database, and much more. The articles are all available from PubMed.
- “Database Resources of the National Center for Biotechnology Information” by NCBI Resource Coordinators. (PMID: 25398906)
- “GenBank” by Dennis A. Benson et al. (PMID: 25414350)
- “Gene: a gene-centered information resource at NCBI” by Garth R. Brown et al. (PMID: 25355515)
- “CDD: NCBI’s conserved domain database” by Aron Marchler-Bauer et al. (PMID: 25414356)
- “Expanded microbial genome coverage and improved protein family annotation in the COG database” by Michael Y. Galperin, Kira S. Makarova, Yuri I. Wolf and Eugene V. Koonin. (PMID: 25428365)
- “HIV-1, human interaction database: current status and new features” by Danso Ako-Adjei et al. (PMID: 25378338)
- “NCBI Viral Genomes Resource” by J. Rodney Brister, Danso Ako-Adjei, Yiming Bao and Olga Blinkova. (PMID: 25428358)
- “Update on RefSeq microbial genomes resources” by Tatiana Tatusova et al. (PMID: 25510495)
- “Type material in the NCBI Taxonomy Database” by Scott Federhen. (PMID: 25398905)
The National Library of Medicine (NLM) LiverTox resource is a free website providing up-to-date, comprehensive and unbiased information about drug-induced liver injury caused by prescription and nonprescription drugs, herbals, and dietary supplements. LiverTox represents a collaborative effort by medical and scientific specialists to provide a central repository of clinical information in support of clinical and basic research on the prevention and control of drug-induced liver injury. The site also provides guidance to clinicians and healthcare providers on the diagnosis and management of this important cause of liver disease. LiverTox contains approximately 850 drug and herbal records. It is a joint effort of the Liver Disease Research Branch of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) and the Division of Specialized Information Services (SIS) of NLM.
Look for these LiverTox updates in the coming months:
- Addition of about 100 new records.
- New histopathologic imaging (microscopic structure of diseased tissue) from the National Cancer Institute (NCI) included in drug records.
- Section providing public access to reference cases, initially populated with clinical cases from the Drug-Induced Liver Injury Network, a consortium of eight academic medical centers throughout the United States. This repository will allow for statistical analyses of trends in drug-induced liver disease, as well as better characterization of clinical patterns of injury.