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 is sponsoring a free public meeting, SPL/DailyMed Jamboree 2014 Workshop – Practical use of DailyMed and RxNorm Drug Data. Speakers from the Federal government (NLM and IHS), industry (Bayer, Wolters-Kluwer), academia, and non-profit sectors will speak on their experience with Structured Product Label (SPL) drug data as well as RxNorm. The emphasis is on practical and novel ways to use this free data, which is produced cooperatively by NLM and FDA. Topics include SPLs and clinical decision support, extracting indication and drug interaction data from SPLs using natural language processing, e-prescribing experience within the Indian Health Service, Linked Data and SPLs, the use of RxNorm by the United States Pharmacopeia (USP), and more. The proceedings will be webcast and archived.
When: September 18, 9:30 AM to 4:15 PM (ET)
Where: Lister Hill Auditorium, National Library of Medicine, 8600 Rockville Pike, NIH Building 38A, 1st Floor, Bethesda, Maryland 20894
Visit the SPL/DailyMed Jamboree 2014 Workshop webpage to register for the in-person meeting and to view the agenda and speakers. The link to the webcast will be added when available.
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:
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.
Check out the August issue of NIH News in Health, the monthly newsletter bringing you practical health news and tips based on the latest NIH research. In this issue:
- Can You Recognize a Heart Attack or Stroke? What To Do When Every Moment Counts
How would you react to a medical emergency? When it comes to life-threatening conditions like heart attack or stroke, every minute counts. Get to know the signs and symptoms of these health threats. If you think you or someone else might be having a heart attack or stroke, get medical help right away. Acting fast could save your life or someone else’s.
- Surviving Sepsis: Taming a Deadly Immune Response
Many people have never heard of sepsis, or they don’t know what it is. But sepsis is one of the top 10 causes of disease-related death in the United States. The condition can arise suddenly and progress quickly, and it’s often hard to recognize.
- Transplant Reverses Sickle Cell Disease
A specialized bone marrow transplant successfully reversed severe sickle cell disease in adults, in some cases without the need for extensive immune-suppressing drugs. Follow-up testing will be needed to further assess this experimental therapy.
- Mind and Body Therapy for Fibromyalgia
Fibromyalgia is a long-lasting disorder marked by widespread pain, tenderness, fatigue, and other symptoms that can interfere with daily life. An estimated 5 million American adults have the condition. It most often affects women, although men and children also can have the disorder. Unfortunately, despite ongoing research, its causes remain unknown.
- Featured Website: Diabetes Health Sense
About 29 million Americans have diabetes, and many more are at risk because of excess weight, family history, or age. This site offers easy access to resources that can help you eat well, stay active, and meet your health-related goals, whether you have diabetes or are at risk for the condition.
NIH News in Health is available online in both HTML and PDF formats. Print copies are available free of charge for offices, clinics, community centers, and libraries within the U.S. Visit the NIH News in Health Facebook page to suggest topics you’d like to see covered, or share what you find helpful about the newsletter!
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.
ChemIDplus is a dictionary of over 400,000 chemicals (names, synonyms, and structures). It includes links to NLM and other databases and resources, including ones to over 100 federal, state and international agencies. ChemIDplus Lite is designed for simple searching on name or registry number. ChemIDplus Advanced helps users draw their own structures and perform similarity and substructure searches. ChemIDplus records are updated daily. The following new features are now available:
- A new “3D” button on search results pages provides calculated three dimensional structure models for over 300,000 chemicals and 645,000 variations. Users can adjust the rotation speed, the image type (ball and stick, space fill, wireframe), and 3D angle of viewing; dragging the image changes its orientation. Right clicking on the structure box provides other control options such as color, style, measurements, and computation. The open source JSMol program is used for viewing these models. Another feature offers 3D when viewed with Red/Cyan, Red/Green or Red/Blue glasses, allowing for unique visualization of a molecule with depth perception.
- ChemIDplus is now IPhone IOS and Android OS friendly. Buttons collapse to neatly fit the phone screen, and the structures can be displayed.