Archive for the ‘E-Science’ Category
The NIH Big Data to Knowledge (BD2K) program and the NIH Library are pleased to join the Johns Hopkins (JHU) Bloomberg School of Public Health Department of Biostatistics in announcing the first JHU DaSH, Data Science Hackathon, on September 21-23, 2015, in Baltimore.
The event organizers, Drs. Brian Caffo, Leah Jager, Jeff Leek and Roger Peng, include JHU professors who teach the popular Coursera Data Science Specialization. This Data Science Hackathon will provide an opportunity for hands-on training that reinforces and builds on data management and analysis skills, and provides a local opportunity for NIH scientists and trainees to participate in a data science Hackathon. For questions about the Hackathon, contact Lisa Federer at the NIH Library.
A new Big Data to Knowledge (BD2K) funding opportunity (FOA) is available, Development of Software Tools and Methods for Biomedical Big Data in Targeted Areas of High Need, with an October 6 application due date. This FOA solicits development of innovative analytical methods and software tools with the objective of addressing critical current and emerging needs of the biomedical research community for using, managing, and analyzing the larger and more complex data sets inherent to biomedical big data, focusing on the three topic areas of Data Privacy, Data Repurposing, and Applying Metadata, all as part of the overall BD2K initiative. This FOA aims to support the development of innovative tools and approaches to tough problems, as opposed to having fully fledged software tools developed for less-daunting problems. It is not expected that software and methods developed under this FOA will be fully hardened, but rather that investigators show a novel approach to a difficult problem and show some proof-of-concept for this new approach using relevant biomedical big data. While this FOA is intended to foster new development, submissions consisting of significant adaptations of existing methods and software are also invited.
It is anticipated that a single application will have a primary focus on one of the three topic areas. Applicants can submit multiple independent applications, each addressing a separate topic area. The award mechanism will be a Cooperative Agreement, used used when there will be substantial Federal scientific or programmatic involvement. Substantial involvement means that, after the award, NIH scientific or program staff will assist, guide, coordinate, or participate in project activities. NIH intends to fund 8-12 awards in fiscal year 2016, corresponding to a total of $5 million. The maximum project period is three years, and direct costs are limited to a maximum of $300,000 in each year. Scientific Merit Reviews of applications are expected in February 2016, and the earliest award start date is expected in July, 2016.
NLM is announcing on behalf of the IHTSDO (International Health Terminology Standards Development Organization) the formation of seven new IHTSDO Advisory Groups (AGs). The AGs are the successors of the IHTSDO Standing Committees, which will allow for a more agile and flexible structure. The AGs will conduct specific activities that will contribute to the fulfillment of the IHTSDO Management Team’s responsibilities or the organization’s mandate.
The IHTSDO is seeking volunteers to serve on the following AGs:
- Content Managers Advisory Group
- E-Learning Advisory Group
- Modeling Advisory Group
- SNOMED CT Editorial Advisory Group
- Software Developers Advisory Group
- Terminology Release Advisory Group
- Tooling User Advisory Group
For additional information on the different Advisory Groups as well as the nomination and application process, please see the IHTSDO news note, Join an Advisory Group. The nomination period is open until August 14, 2015.
The National Library of Medicine’s ChemIDplus Lite and ChemIDplus Advanced interfaces have been enhanced with the following features:
- Valid chemical names and CAS RN completions are displayed as the user types in the search box. If no data are found, suggestions are provided.
- The ChemIDplus Registry Number field now includes the FDA UNII code.
- The InChIKey is now directly searchable. It can be used for the interchange of structural data and as input for search engines such as Google.
- The ChemIDplus Formula field now accepts molecular formulas with spaces between elements and their counts and without the hyphens previously required.
Examples of these new features may be viewed at the ChemIDplus Help pages. ChemIDplus is a free, web search system that provides access to the structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases, including the TOXNET® system. ChemIDplus also has structure searching and direct links to resources at NLM, federal agencies, U.S states, and scientific sites. The database contains more than 400,000 chemical records, of which over 300,000 include chemical structures.
Have you ever wanted to be able to use mapping for your outreach needs, but thought that making maps would be too expensive, time-consuming, or just too difficult? The main goal of the National Library of Medicine’s Community Health Maps: Information on Low Cost Mapping Tools for Community-based Organizations blog is facilitating the use of geographic information system (GIS) mapping by providing information about low cost mapping tools, software reviews, best practices, and the experiences of those who have successfully implemented a mapping workflow as part of their work. The blog is moderated by Kurt Menke, a certified GIS professional.
Here are some examples of the kinds of things you can find on the Community Health Maps blog:
- A short guide for using iForm for field data collection. iForm is an app that can be used on iPads, iPhones and Android devices, and has a free version. Using this app, you can go to different locations, gather data (for example, demographic information about attendance at your program), and view it in tabular or map format.
- A description of a project using youth in the Philippines to collect data on the needs of their communities. Technology + Youth = Change showed how a dozen donated phones helped 30 young adults survey and map information on access to water, electricity, jobs, and more.
- A review of a pilot project done by the Seattle Indian Health Board’s Urban Indian Health Institute on noise pollution and health in the urban environment.
On May 1, 2015, The National Library of Medicine (NLM) Value Set Authority Center (VSAC), in collaboration with the Office of the National Coordinator for Health Information Technology (ONC) and Centers for Medicare & Medicaid Services (CMS), published the annual update for the 2014 electronic clinical quality measures (eCQMs) value sets for eligible hospitals and eligible professionals. Providers will use these updated eCQM value sets to electronically report 2016 quality data for CMS quality reporting programs, including the Physician Quality Reporting System (PQRS), Inpatient Quality Reporting Program (IQR), and the EHR Incentive Programs. CMS updates these electronic reporting specifications annually to improve alignment with current clinical guidelines and terminologies and to remain relevant and actionable within the clinical care setting.
The VSAC offers a Downloadable Resource Table, accessible from the Download tab on the VSAC Web page, that provides prepackaged downloads for the most recently updated and released eCQM value sets, as well as for previously released versions. Access to the VSAC requires a free Unified Medical Language System® Metathesaurus License. NLM also provides the Data Element Catalog that identifies data element names (value set names) required for capture in electronic health record (EHR) technology certified under the 2014 Edition of the ONC Standards and Certification Criteria.
The NLM update of the VSAC eCQM value sets coincides with the CMS posting of the annual update for the 2014 eCQMs for eligible hospitals and eligible professionals, available in the CMS eCQM Library. CMS has re-specified all of the 2015 updated measures using Quality Data Model (QDM) 4.1.2 based-HQMF version R 2.1. 2014 Clinical Quality Measure Resources.
The following resources are available to help health care providers and vendors navigate the 2014 eCQMs.
The FDA, in partnership with the National Library of Medicine, has announced that data submitted to FDA’s Global Unique Device Identification Database (GUDID) is now publicly available through a website called AccessGUDID. By using AccessGUDID, anyone can search or download information that device labelers have submitted to the GUDID about their medical devices. Because the UDI system is being phased in over the next several years, labelers are currently submitting data on only the highest risk medical devices, a small subset of marketed devices. But as the system is implemented according to the UDI compliance timeline, the records of all medical devices required to have a UDI will be included.
With the launch of this beta version of AccessGUDID, everyone is encouraged—health care systems, clinicians, patients, researchers, industry and others—to explore its contents, assess its functionality and provide feedback. This feedback will shape future enhancements, including advanced search and web services. To submit feedback, use the Contact Us link at the bottom of the AccessGUDID landing page or the FDA UDI Help Desk.
The National Library of Medicine needs your help reaching out to current and potential users of low-cost and easy-to-use online mapping tools (GIS). The Community Health Maps (CHM) project identifies and promotes tools that seek to meet the mapping needs of communities and community organizations such as clinics, schools, libraries, health departments, faith-based and community-based groups. These tools can be used to collect and visualize health statistics and local resources, to compare data across locations, and to explore trends. In order to improve CHM and better tailor it for the specific requirements of users, please share this GIS user needs survey!
Both versions of TOXMAP, classic and beta, now include the Toxics Release Inventory (TRI) 2013 National Analysis data, as well as recent cancer and disease mortality data from NCI SEER. This is the first version of the TOXMAP beta with health data, whereas mortality data in TOXMAP classic has been updated. To view national county-level cancer and disease mortality data from 2007-2011 in TOXMAP beta, bring up the US Census & Health Data window and navigate to the Mortality tab. Two sub-tabs list cancer and disease mortality layers that can be overlaid on the map (one at a time).
TOXMAP maps the TRI chemicals reported to the EPA, as required by the Emergency Planning and Community Right to Know Act (EPCRA). A complete list of TRI chemicals required to be reported to the EPA can be found on the Toxics Release Inventory (TRI) Program website.
Fifty years ago, Marshall W. Nirenberg, PhD, deciphered the genetic code. It led to a Nobel Prize—the first for a scientist at the National Institutes of Health. Dr. Nirenberg’s family recently donated his Nobel Prize medal to the National Library of Medicine to be added to the papers and other items that chronicle his contributions to science. NLM’s History of Medicine Division hosted the first of three events at NIH that will celebrate the legacy of Marshall Nirenberg, who died in 2010, and the fiftieth anniversary of his deciphering of the genetic code. Subsequent events will be announced by the NIH Office of Intramural Research.
A Tribute to Marshall Nirenberg was filled with personal stories from his wife; from a scientist in his lab; and from a historian who helped develop NLM’s Nirenberg collection. The event, held March 17, was recorded and can be viewed on demand. One of the most significant pieces in the Nirenberg collection is the chart that is the first summary of the genetic code. Dated January 18, 1965, when more than half of the code had been deciphered, the document, with curatorial notes provided by Serlin, was recently added to NLM’s Turning the Pages project, which is available online and as an iPad app. Dr. Nirenberg won the Nobel Prize for Physiology or Medicine in 1968. He shared the award with Har Gobind Khorana of the University of Wisconsin and Robert W. Holley of the Salk Institute.