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Archive for 2014

PubMed Commons Update

@PubMedCommonsPubMed 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!

ALA Publishes Guide for Conducting Community Conversations

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.

NLM’s National Center for Biotechnology Information Receives HHSinnovates Award!

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.

NCATS Announces the Toxicology in the 21st Century (Tox21) Data Challenge 2014 Competition

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.

Free Online Course–Shaping Outcomes: Making a Difference in Libraries and Museums

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.

Exciting New Features Added to ChemIDplus!

3D model of DigoxinChemIDplus 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.
  • The ChemIDplus structure box now uses quick-loading Marvin for JavaScript (free; requires IE9 or above). The Marvin Applet version is also available in a pull-down for legacy browsers.
  • ChemIDplus is now IPhone IOS and Android OS friendly. Buttons collapse to neatly fit the phone screen, and the structures can be displayed.

National Library of Medicine Training Center (NTC) Offers Free Online TOXNET Class This Fall!

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:

  1. Introduction to TOXNET: 0.5 hour (Required)
  2. TOXLINE: 1.0 hour
  3. ChemIDplus: 2.0 hours
  4. Integrated Risk Information System & Risk Assessment: 1.0 hour
  5. Hazardous Substances Databank: 1.5 hours
  6. Toxic Release Inventory: 1.0 hour
  7. TOXMAP: 1.5 hours
  8. Household Products Database: 0.5 hour
  9. LactMed: 0.5 hour
  10. Haz-Map: 0.5 hour
  11. WISER & CHEMM: 1.0 hour
  12. REMM: 0.5 hour
  13. LiverTox: 0.5 hour

Space in the class is limited, so don’t delay registering! For questions, contact the NTC.

NIH MedlinePlus the Magazine Summer 2014 Issue Available Online!

Cover of Summer 2014 issue of NIH MedlinePlus the MagazineThe Summer 2014 issue of NIH MedlinePlus the Magazine features information on treating cataracts, understanding rheumatoid arthritis (RA), screening for breast cancer, and The Children’s Inn at NIH turning 25. The cover features Amy Robach, who was diagnosed as the one of 1-in-8 women in America who will be affected by breast cancer in their lifetimes. After receiving the first-ever mammogram on live television, she received a surprising breast cancer diagnosis. She now speaks out in support of others facing the disease. The magazine goes into further detail about breast cancer, looking at detection, diagnosis, screening, staging, and treatment, as well as some relevant National Cancer Institute research.

The magazine also highlights The Children’s Inn at NIH. The Children’s Inn enhances opportunities for groundbreaking medical discoveries by providing a free “place like home” that reduces the burdens of illness through a supportive environment, including therapeutic, educational, and recreational programming. President George H. W. Bush and his wife, Barbara, are serving as honorary chairpersons for the year of celebrations for The Children’s Inn’s 25th Anniversary, which kicked off on June 21, 2014, and will continue throughout the anniversary year of 2015. The Bushes presided over the ribbon cutting ceremony when The Inn became a reality in June 1990.

NIH MedlinePlus the Magazine is the free, trusted consumer guide to the vast array of authoritative online health and medical information at MedlinePlus. Published four times a year, the magazine showcases the National Institutes of Health’s (NIH) latest medical research and healthcare information. NIH MedlinePlus the Magazine is freely available as a print subscription, e-mail alerts, and online.

Visualization Literacy

With an increase of technology tools available for data reporting and visualization sometimes it’s challenging to know how to best use them to clearly communicate the intended meaning of the data. The concept of visualization literacy and a broader theme of visual literacy are often not included as part of the instructions guiding people in the steps to create their own visualization design. A recent entry by Andrew Kirk on the blog of Seeing Data, a research project in the United Kingdom studying how people understand big data visualizations shown in the media, offers a great review of 8 Articles Discussing Visual and Visualization Literacy that are freely available and well worth a read to better understand both visual and visualization literacy. Their featured articles include resources ranging from the importance of Visual Literacy in an Age of Data to How to Be an Educated Consumer of Infographics, and Seeing Data has asked that you share additional ones with them via blog comments or their Twitter social media account @SeeingData.

Low Cost Mapping Tools for Community-Based Organizations!

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.