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.
A new PubMed search option “hasdatabanklist” has been created to retrieve citations that carry a value in the Secondary Source ID [SI] field regardless of what the specific value(s) may be. Typically, the SI field contains information about where additional data related to an article are deposited. Please see MEDLINE Databank Sources to view the list of repository values.
To limit a search to citations that may have deposited data in a repository and acknowledged that deposit in the full text of the article, search using AND hasdatabanklist; for example: randomized controlled trial [pt] AND hasdatabanklist.
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.
According to recent studies, and despite new private insurance coverage over the past year, many people do not understand the very terms and concepts necessary to make informed choices. A new Alliance for Health Reform Toolkit, Health Literacy and Health Insurance Literacy: Do Consumers Know What they are Buying? addresses the extent and significance of both health literacy and health insurance literacy for Americans buying and using health insurance.
A few highlights from the Toolkit:
- Nearly nine out of ten adults have difficulty using health information to make informed decisions about their health.
- Half of Americans don’t understand such basic health insurance terms as premium, deductible and copay.
- Thirty-seven percent of marketplace enrollees did not know their deductible, and 47% of those receiving subsidies did not know the amount of federal assistance they were getting.
- The cost of low health literacy in the United States currently represents between 7% and 17% of all personal health care expenditures.
Contents of the Toolkit include:
- An overview of problems associated with health literacy as well as studies analyzing their impact.
- Links to reports and news articles explaining and analyzing the issue.
- Contact information for leading experts on the issue.
The publisher of science magazines Nature and Scientific American is merging with private equity-owned peer Springer Science+Business Media, creating a group with 1.5 billion euros ($1.75 billion) in annual sales and 13,000 employees. Germany’s Holtzbrinck, which owns Nature publisher Macmillan Science and Education, will combine the majority of its activities with BC Partners’ Springer unit, which publishes scientific, technical, and medical books and journals. Springer Science Chief Executive Derk Haank will head the new merged company, which will have an enterprise value of more than 5 billion euros. Macmillan Science and Education Chief Executive Annette Thomas will serve as Chief Scientific Officer. The deal is expected to close in the first half of 2015.
Macmillan’s English language school books and social sciences publisher Palgrave Macmillan will be part of the merged entity, as will Springer’s publications and data for professionals. Holtzbrinck’s investments in IT and software businesses, its consumer books unit Macmillan Publishers, and its U.S. higher education business will not be part of the transaction. Springer Science is a separate company from German publisher Axel Springer owning leading tabloid Bild, while Holtzbrinck Publishing is a different company than Dieter von Holtzbrinck Medien, which publishes German business daily Handelsblatt.
The National Library of Medicine’s (NLM) Alternatives to Animal Testing (ALTBIB) portal provides access to PubMed/MEDLINE citations relevant to alternatives to the use of live vertebrates in biomedical research and testing. The ALTBIB topics and subtopics are aligned with current U.S. and international approaches. For example, information is provided on in silico, in vitro, and refined or improved animal testing methods. Strategies that incorporate validated methods and other approaches are also covered. In addition to the topic areas for PubMed searches, the ALTBIB portal includes a searchable bibliographic collection of alternatives to animal testing, including citations from published articles, books, book chapters, and technical reports published from 1980 to 2000.
The Hazardous Substances Data Bank (HSDB), part of NLM’s Toxicology Data Network (TOXNET), now includes subheadings (“/alternative/ and /in vitro tests/”) in the Human and Non-Human Toxicity Excerpts fields. These subheadings allow users to locate data from in vitro and other alternative methods. For example, users can search “ALTERNATIVE IN VITRO TESTS” to locate records with this data. Coverage includes results from methods validated by the Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM) and the European Union Reference Laboratory for Alternatives to Animal Testing (EURL-ECVAM).
The University of Arizona (UA) libraries developed an open-source tool called Guide on the Side for creating interactive tutorials. The left frame of the screen contains instructions and can also have quizzes or links to other information, and the larger, right side has the live website to interact with, without losing your place in the tutorial. A four-minute introductory video about the software is available for viewing on the NLM National Training Center (NTC) web site.
Guide on the Side is an open source PHP and MySQL program and needs to be installed on a server. The program requires a handful of common PHP packages enabled. Once installed, it is very easy for someone without programming experience to create interactive tutorials, which can be easily updated if the interface of the database or other web resource changes. Several examples of Guide on the Side tutorials for TOXNET resources are available on the NTC web site. The UA Libraries have developed more than 25 tutorials using the tool, which have received nearly 73,000 uses in one year. Other libraries have installed the software, begun creating tutorials, and joined a discussion group to continue improving the software.
The National Agricultural Library (NAL) has unveiled PubAg, a user-friendly search engine that provides public enhanced access to research published by the U.S. Department of Agriculture (USDA) scientists. NAL is part of USDA’s Agricultural Research Service (ARS), and has one of the world’s largest and most comprehensive compilations of agricultural information available.
PubAg is a new portal for literature searches and full-text access of more than 40,000 scientific journal articles by USDA researchers, mostly from 1997 to 2014. New articles by USDA researchers will be added almost daily, and older articles may be added if possible. There is no access fee, and no requirement for a username, password or any other form of registration to use PubAg. Phase I of PubAg provides access for searches of 340,000 peer-reviewed agriculturally related scientific literature, mostly from 2002 to 2012, each entry offering a citation, abstract and a link to the article if available from the publisher. This initial group of highly relevant, high-quality literature was taken from the 4 million bibliographic citations in NAL’s database. Phase II of PubAg, planned for later in 2015, will include the remainder of NAL’s significant bibliographic records. PubAg has been specifically designed to be easy to use and to serve a number of diverse users including the public, farmers, scientists, academicians and students.
SciENcv enhancements will include the new NIH biographical sketch format as a choice for creating SciENcv profiles. SciENcv will continue to support the current NIH biographical sketch format; however, NIH encourages researchers to use the new format with their grant submissions. Researchers will be required to employ the new NIH biographical sketch starting May 25, 2015. Users will be able to utilize their existing Science Experts Network Curriculum Vitae (SciENcv) profiles to create profiles in the new NIH biographical sketch format, as well as be able to select the new NIH biographical sketch format when creating profiles manually or through a data feed from an external source. The Personal Statement section of the NIH biographical sketch has been updated to include an option to list up to four peer-reviewed citations. A new section, Contribution to Science, replaces the former section Selected Peer-Reviewed Publications, and it aims to give researchers a place where they can describe five of their most significant contributions to science.
SciENcv users will also soon be able to create profiles in the National Science Foundation (NSF) biographical sketch format. This newly added format will be available to download in PDF, MS Word or XML, and users will be able to share their SciENcv NSF profiles through a public URL. In addition, by linking your NSF account to an NCBI account, you will be able to populate SciENcv profiles with information stored in your NSF account. The NSF biographical sketch is the official format used for grant submissions to the NSF and consists of five sections: Professional Preparation, Appointments, Products, Synergistic Activities, and Collaborators & Other Affiliations.
For more information visit the NLM Technical Bulletin articles: My NCBI – New NIH Biographical Sketch Available in SciENcv and My NCBI – National Science Foundation Biographical Sketch and Data Integration with SciENcv.
The Public Access Compliance Monitor (PACM or “compliance monitor”) is a service from the National Library of Medicine that helps users at NIH-funded institutions locate and track the compliance of funded papers with the NIH Public Access Policy at an institutional level. Whether you are looking for a quick snapshot of your institution’s compliance rate or want to take an active role in helping your investigators comply with the policy, PACM can help you get the information you need.
To gain access to the compliance monitor, users must first be assigned a compliance reports role (“PACR”) role by an administrator at their institution who is authorized to assign roles in the NIH eRA Commons grants administration system. Users with a PACR role will then have access to the compliance reports for their institution.
PACM provides users with a list of all PubMed citations associated with an institution’s NIH funding and classifies the articles according to compliance status (i.e., Compliant, Non-Compliant, In Process). The compliance monitor also provides detailed information about each article including:
- a full citation including the PMID (PubMed ID) and link to the PubMed record
- associated grants and principal investigators
- NIHMSID (NIH Manuscript Submission Reference Number), where available
- PMCID (PubMed Central ID), where available
- key names and dates in the NIHMS, where available
- article compliance status
- method A status
- journal publisher
Compliance reports can be downloaded from these lists and the data filtered based on an institution’s needs.
For more information on the PACR role, the compliance monitor, and the available reports, see the User Guide. Additonally, an overview video of PACM from The NIH Public Access Policy for Librarians Webinar and a four-minute Look at the NIH Public Access Policy Compliance Monitor are available.