Archive for the ‘Search Tools’ Category
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.
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.
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 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.
NLM’s HIV/AIDS Portal now offers the ability to search for multilingual content. The new Multilingual Search interface searches specifically for HIV/AIDS related topics from the multilingual and multicultural content of HealthReach (formerly RHIN). HealthReach offers easy access to quality health information to individuals for whom English is not the primary language. It is also an important resource for health professionals as well as public health administrators. Users can search by subject/topic, language, and format. The default for the search is always HIV/AIDS so there is no need for these terms to be included in the search. There is also an Advanced Search capability to further refine retrieval. The content is available in audio and video formats as well as text. For text documents there is a feature that allows viewing the document in a split screen with one side being English and the other being the language requested in the search.
As part of the omnibus budget measure signed by President Obama in December 2014, Congress changed the name of NCCAM to the National Center for Complementary and Integrative Health, or NCCIH. The change was made to more accurately reflect the Center’s research commitment to studying promising health approaches that are already in use by the American public. Since the Center’s inception, complementary approaches have grown in use to the point that Americans no longer consider them an alternative to medical care. The name change is in keeping with the Center’s existing Congressional mandate and is aligned with the strategic plan currently guiding the Center’s research priorities and public education activities. The mission of the organization will remain unchanged.
Large population-based surveys have found that the use of “alternative medicine,” unproven practices used in place of conventional medicine, is actually rare. By contrast, integrative health care, which can be defined as combining complementary approaches into conventional treatment plans, has grown within care settings across the nation, including hospitals, hospices, and military health facilities. The goal of an integrative approach is to enhance overall health, prevent disease, and to alleviate debilitating symptoms such as pain and stress and anxiety management that often affects patients coping with complex and chronic disease.
The Office of Alternative Medicine (OAM) was established in 1992 within the Office of the Director, NIH, to facilitate the study and evaluation of complementary and alternative medical practices and to disseminate the resulting information to the public. In 1998, NCCAM was established by Congress, elevating OAM to the status of an NIH center. In February 2011, NCCAM released Exploring the Science of Complementary and Alternative Medicine: Third Strategic Plan 2011–2015, which continues to guide NCCIH’s work.
As of December 15, PubMed/MEDLINE citations (including the backlog of citations indexed since November 19 with 2015 MeSH), the MeSH database, and the NLM Catalog were updated to reflect 2015 MeSH. The MeSH translation tables were also updated on December 15. Now that end-of-year activities are complete, MEDLINE/PubMed may be searched using 2015 MeSH vocabulary. Highlights of MEDLINE Data Changes for 2015 were previously published in the NN/LM PSR Latitudes blog. On December 16, NLM resumed daily MEDLINE updates to PubMed.
The National Library of Medicine (NLM) TOXMAP’s new Flash-based beta now includes 2013 coal emissions data published by the US EPA’s Clean Air Markets program. Data was obtained from the Air Markets Program Data (AMPD) tool, a publicly-available data system for searching and downloading data collected as part of EPA’s emissions trading programs. In 2013, about 2.1 billion metric tons of carbon dioxide emissions were attributable to electricity generated from coal.
TOXMAP is a Geographic Information System (GIS) from the National Library of Medicine (NLM) that uses maps of the United States to help users visually explore data from the EPA’s Toxics Release Inventory (TRI) and Superfund Programs.
The National Library of Medicine (NLM) adopted the 2015 MeSH vocabulary for cataloging on November 24, 2014. Accordingly, MeSH subject headings in LocatorPlus were changed to reflect the 2015 MeSH vocabulary and appear in that form as of November 24. When year-end processing (YEP) activities are completed in mid-December, the NLM Catalog, MeSH database, and translation tables will be updated to reflect 2015 MeSH. Until then, there will be a hiatus in the addition of new and edited bibliographic records to the NLM Catalog. The Index to the NLM Classification will not reflect 2015 MeSH changes until Spring 2015. In general, the Cataloging Section implemented the vocabulary changes in NLM bibliographic records for books, serials, and other materials, as they were applied for citations in MEDLINE. Following are a few highlights:
Death vs. Mortality
New terms were created: Infant Death and Perinatal Death. These terms complement the existing MeSH terms Infant Mortality and Perinatal Mortality. Death terms are used for biological, physiological, or psychological concepts while mortality terms are used for statistical concepts. There is some overlap with the perinatal terms. Catalogers should follow the annotations carefully.
The new term Sociological Factors, formerly an entry term (ET) to the specialty term Sociology, now serves as an overall heading for specific sociological characteristics and phenomena. Other new “social” terms include Social Theory, Social Capital, Social Norms, and Social Skills.
Missions Terms and Religious Personnel
The 2014 MeSH Missions and Missionaries was deleted. For 2015 MeSH, the concept of missions was separated from the persons involved in missionary work. Two new terms were created: Religious Missions and Missionaries. The automated MeSH changes that took place November 22-23 replaced the term Missions and Missionaries with Religious Missions. Cataloging staff will conduct additional manual processing in December to add Missionaries to the set of records that also have PT Biography, Autobiography, or Personal Narratives. Note that the existing term Medical Missions, Official is still available. Religious Personnel was created as an overall term under which Clergy and the new terms Monks and Nuns are treed. Several entry terms were created for the existing term, Clergy: Chaplains, Clerics, Deacons, Imams, Ministers, Pastors, Priests, and Rabbis.
The new term Manufacturing Industry, formerly an entry term to Industry, now serves as an overall heading for specific manufacturing industries.
Publication Types (PTs) and Related Terms
No new Publication Types were created for 2015.
Rural and medically underserved areas often have challenges including both increased health disparities and population health issues combined with limited resources and healthcare providers to help meet these challenges. The use of appropriate program evaluation measures can help to assess what actually works for rural health settings since many evidence-based strategies are based on urban and non-rural populations.
The Rural Assistance Center has recently issued a freely available online guide, which is intended to help an organization:
- Identify the similarities and differences among rural health research, assessment, and evaluation
- Discuss common methods, such as surveys and focus groups
- Provide contacts within the field of rural health research
- Address the importance of community-based participatory research to rural communities
- Look at the community health needs assessment (CHNA) requirements for non-profit hospitals and public health
- Examine the importance of building the evidence-base so interventions conducted in rural areas have the maximum possible impact