Genomic research advances our understanding of factors that influence health and disease, and sharing genomic data provides opportunities to accelerate that research through the power of combining large and information-rich datasets. To promote sharing of human and non-human genomic data and to provide appropriate protections for research involving human data, the National Institutes of Health (NIH) issued the Genomic Data Sharing (GDS) Policy on August 27, 2014. The GDS Policy takes effect for grant applications with due dates on or after January 25, 2015, for contracts submitted on or after January 25, 2015, and for intramural research projects generating genomic data on or after January 25, 2015. NIH has also issued a press release regarding the GDS Policy. A publication describing the use and impact of the NIH database for Genotypes and Phenotypes (dbGaP) data under the Policy for Sharing of Data Obtained in NIH Supported or Conducted Genome-Wide Association Studies, from 2007 through 2013, has been published in Nature Genetics.
Archive for the ‘Announcements’ Category
NCBI Discovery Workshops, consisting of four 2.5-hour hands-on training sessions emphasizing NCBI resources such as BLAST and Nucleotide, will be presented by NCBI staff at the University of California, Davis, on September 15-16, and at the University of California, Berkeley, on September 17-18:
- Session 1: Navigating NCBI Molecular Data Through the Integrated Entrez System. 9 am – 11:30 am, 9/15 (UC Davis) & 9/17 (UC Berkeley)
- Session 2: NCBI Genomes, Assemblies and Annotation Products: Microbes to Human. 1 pm – 3:30 pm, 9/15 (UC Davis) & 9/17 (UC Berkeley)
- Session 3: Advanced NCBI BLAST. 9 am – 11:30 am, 9/16 (UC Davis) & 9/18 (UC Berkeley)
- Session 4: Gene Expression Resources at NCBI. 1 pm – 3:30 pm, 9/16 (UC Davis) & 9/18 (UC Berkeley)
For more information or to register:
The National Library of Medicine (NLM) Emergency Access Initiative (EAI) has been activated to support healthcare professionals working on the Ebola public health emergency in West Africa. The EAI is a collaborative partnership between NLM and participating publishers to provide free access to full-text from over 650 biomedical journals and over 4,000 reference books and online databases to healthcare professionals and libraries affected by disasters. It serves as a temporary collection replacement and/or supplement for libraries affected by disasters that need to continue to serve medical staff and affiliated users. It is also intended for medical personnel responding to the specified disaster. EAI is not an open access collection. It is only intended for those affected by the disaster or assisting the affected population. If you know of a library or organization involved in healthcare efforts in response to the Ebola outbreak, please let them know of this service. EAI was activated four times in the past, including following the earthquake and subsequent cholera epidemic in Haiti, flooding in Pakistan and the earthquake and tsunami in Japan.
NLM thanks the numerous participating publishers for their generous support of this initiative: American Academy of Pediatrics, American Association for the Advancement of Science, American Chemical Society, American College of Physicians, American Medical Association, American Society of Health-Systems Pharmacists, ASM Press, B.C. Decker, BMJ, EBSCOHost, Elsevier, FA Davis, Mary Ann Liebert, Massachusetts Medical Society, McGraw-Hill, Merck Publishing, Oxford University Press, People’s Medical Publishing House, Springer, University of Chicago Press, Wiley and Wolters Kluwer.
Resources on Ebola
NLM has several other resources that will be helpful for people working on Ebola:
- Articles in PubMed
- MedlinePlus Ebola Health Topic Page (for the general public)
- International health (for the general public)
HHS agencies, including CDC and ASPR, also provide the latest Ebola information available through social media, including Twitter@phegov, @CDCgov, @CDCEmergency and Facebook Public Health Emergency, CDC, CDC Emergency Preparedness and Response. The CDC also has a comprehensive set of resources on its Ebola Hemorrhagic Fever web page.
PubMed Commons set the stage for commenting on any publication in PubMed, the world’s largest searchable database of biomedical literature. New infrastructure and design enhancements have been implemented to improve the user experience and support the PubMed Commons community, and they are now live on PubMed and PubMed Commons. At center stage is new artwork that has been adopted for the PubMed Commons blog, Twitter account, and homepage, to present a clear, unified identity across platforms. The homepage has also been streamlined to consolidate information about joining and using PubMed Commons in a single page to help users get started. A synopsis of the most recent blog post is now available at the top of the homepage to help users stay up-to-date on PubMed Commons.
For several months, comment rating has given members the chance to weigh in on what comments they find useful. Visitors to PubMed can see these ratings alongside comments. Ratings are a key element in calculating the comment and commenter scores that determine the appearance of comments in the “Selected comments” stream on the homepage. Some new site modifications will highlight contributions to PubMed Commons. On the homepage, “Top comments now” will feature the top three recent comments. On PubMed records, “Selected comments” (from the homepage stream) prompt the appearance of an icon above abstracts, directing readers to comments below. And now the most recent tweet about a PubMed Commons comment appears on the homepage for PubMed searches. Check it out!
The American Library Association has announced the release of Community Conversation Workbook, a resource developed for the ALA’s Libraries Transforming Communities (LTC) initiative, which provides librarians with training and resources to enhance their roles as community leaders and change-agents. The initiative’s goal is to help librarians promote the visibility and value of their libraries within their communities. Public discussions are promoted as key community engagement strategies. The workbook provides invaluable guidance to anyone who wants to conduct discussion groups for community assessment purposes. It provides practical advice on every aspect of convening group discussions, including tips on participant recruitment, a list of discussion questions, facilitator guidelines, note-taking tools, and templates for organizing key findings.
Demonstrating value is currently of considerable interest to many libraries and organizations. Such organizations may be interested in exploring other articles and resources related to the LTC initiative, which are available on the LTC web page. Examples showing how libraries are implementing LTC activities are available from the initiative’s digital portal.
A collaborative project between the National Library of Medicine’s National Center for Biotechnology Information (NCBI) and several other federal and state partners, to reduce the time and improve the accuracy of detecting foodborne pathogens by using whole genome sequencing (WGS) techniques, received the HHSinnovates award on July 21, 2014. The HHSinnovates program was initiated in 2010 to recognize new ideas and solutions developed by HHS employees and their collaborators. Six finalist teams were recognized at the awards ceremony. The WGS Food Safety Project, which also involved the Centers for Disease Control and Prevention (CDC), the Food and Drug Administration (FDA), the US Department of Agriculture (USDA), and state public health laboratories, was one of three projects to be honored as “Secretary’s Picks” by HHS Secretary Sylvia Mathews Burwell. The award went to the specific individuals leading the project in the various agencies; in the case of NCBI, Senior Scientist William Klimke, PhD, was honored for his work in heading NCBI’s part of the project.
WGS provides greater specificity than other techniques, such as the commonly used pulsed-field gel electrophoresis (PFGE), in identifying the DNA fingerprint of bacteria. It also can more rapidly determine whether isolates are related to a foodborne disease outbreak. The demonstration project involves real-time sequencing of Listeria monocytogenes isolates from human DNA as well as the food supply chain. In the project, the whole genomes of isolates are sequenced and the sequencing data are sent to NCBI, which performs assembly, annotation and analysis, and then sends results back to CDC, FDA, USDA and the labs. Collaborative projects using WGS for other pathogens related to food safety are also underway.
The National Center for Advancing Translational Sciences (NCATS) has announced the Toxicology in the 21st Century (Tox21) Data Challenge 2014 competition.
The goal of the challenge is to crowdsource data analysis by independent researchers in order to develop computational models that can better predict chemical toxicity. It is designed to improve current toxicity assessment methods, which are often slow and costly. The model submission deadline is November 14, 2014. NCATS will showcase the winning models in January 2015. Registration for the challenge and more information is available on the web site.
Tox21 scientists are currently testing a library of more than 10,000 chemical compounds in NCATS’s high-throughput robotic screening system. To date, the team has produced nearly 50 million data points from screening the chemical library against cell-based assays. Data generated from twelve of these assays form the basis of the 2014 challenge. For more information on the Tox21 Modeling Challenge and Tox21 Program, contact Anna Rossoshek.
Shaping Outcomes: Making a Difference in Libraries and Museums is available as a free online course that learners can start anytime and work on at their own self-navigated pace. While there are library and museum-specific examples provided in the course, the concepts of learning more about target audience needs, how to clarify desired results, developing logic models, and evaluating outcomes are applicable for most any organization’s outreach projects. Modules of the class are broken into five sections; Overview, Plan, Build, Evaluate, and Report, with a helpful Glossary to learn outcomes-based planning and evaluation (OBPE) terminology, and a Logic Model template. Shaping Outcomes was developed by the Institute of Museum and Library Services (IMLS) and Indiana University/Purdue University Indianapolis (IUPUI) and previously was available as an instructor-led class.
More information specific to developing logic models in health information outreach programs is available from NN/LM Outreach Evaluation Resource Center (OERC) Booklet Two: Planning Outcomes-Based Outreach Projects. Additional information is available on the OERC Evaluation Guides page.
The National Library of Medicine Training Center (NTC) is offering an online, asynchronous Moodle class called Discovering TOXNET from October 20 – November 14, 2014. Register now to discover TOXNET and other NLM environmental health databases through videos, guided tutorials, and discovery exercises! The class is taught online in thirteen independent modules. Participants work on their own time over a period of four weeks to complete the modules of interest. There is one required module; the remaining are optional. This class is offered for variable MLA Continuing Education credit. Each module will be offered for 0.5 to 2.0 credit hours, for a total of up to 12 hours. Credit will not be awarded for partial completion of a module. Total credit awarded will be based on completed modules with a minimum of 1.0 credit hours.
TOXNET is a web-based system of databases covering hazardous chemicals, environmental health, toxic releases, chemical nomenclature, poisoning, risk assessment and regulations, and occupational safety and health. The independent modules cover TOXLINE, ChemIDplus, TRI, TOXMAP, Hazardous Substances Data Bank (HSDB), IRIS, Haz-Map, LactMed, WISER, CHEMM, REMM, LiverTox, and more.
The modules are:
- Introduction to TOXNET: 0.5 hour (Required)
- TOXLINE: 1.0 hour
- ChemIDplus: 2.0 hours
- Integrated Risk Information System & Risk Assessment: 1.0 hour
- Hazardous Substances Databank: 1.5 hours
- Toxic Release Inventory: 1.0 hour
- TOXMAP: 1.5 hours
- Household Products Database: 0.5 hour
- LactMed: 0.5 hour
- Haz-Map: 0.5 hour
- WISER & CHEMM: 1.0 hour
- REMM: 0.5 hour
- LiverTox: 0.5 hour
Space in the class is limited, so don’t delay registering! For questions, contact the NTC.
Community Health Maps Blog is an initiative designed to share information about free and low cost and easy-to-use applications of Geographic Information Systems (GIS) mapping tools. The goal is to help community-based and other types of small organizations collect and visualize information about their communities with an eye towards using these techniques to support planning and decision-making about community health. The tools discussed on the Community Health Maps Blog can support the collection and visualization of health statistics, demographic information, community resources, and events, thereby facilitating a better understanding of community conditions.
The interactive nature of blogging helps Community Health Maps share information about hardware platforms and software applications available to communities as they consider how, or if, they might use GIS. NLM encourages the submission of blog postings by those who use such resources to carry out projects within their communities, as well as those who have identified additional applications that may be of interest for this purpose.