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Archive for the ‘Data’ Category

NIH Genome Sequencing Program targets the Genomic Bases of common, Rare disease

Wednesday, January 27th, 2016

The National Institutes of Health will fund a set of genome sequencing and analysis centers whose research will focus on understanding the genomic bases of common and rare human diseases. The National Human Genome Research Institute (NHGRI), part of NIH, January 14, 2016 launched the Centers for Common Disease Genomics (CCDG), which will use genome sequencing to explore the genomic contributions to common diseases such as heart disease, diabetes, stroke and autism. NHGRI also announced the next phase of a complementary program, the Centers for Mendelian Genomics (CMG), which will continue investigating the genomic underpinnings of rare, typically inherited diseases, such as cystic fibrosis and muscular dystrophy. “Advances in DNA sequencing are creating tremendous new opportunities for exploring how the genome plays a role in human disease,” said NHGRI Director Eric Green, M.D., Ph.D. “Our continued focus on both rare and common diseases promises to reveal important aspects about the genomic architecture of a wide range of human disorders.”CCDG researchers plan to examine a select group of disorders in order to develop approaches for using genome sequencing to study common disease more broadly. By sequencing an expected 150,000 to 200,000 genomes of individuals with these diseases, the CCDG program aims to improve understanding of how genomic differences among people influence disease risk and to develop models for future studies of common disease.

NHGRI is one of the 27 institutes and centers at the National Institutes of Health. The NHGRI Extramural Research Program supports grants for research and training and career development at sites nationwide. Additional information about NHGRI can be found at

FDA Launches precisionFDA a Cloud-Based, Portal for Scientific Collaboration and Next-Generation Sequencing

Tuesday, December 22nd, 2015

Adapted from: FDA Voice Blog

The U.S. Food and Drug Administration on Tuesday December 15, 2015 has launched the beta version of precisionFDA, its a new collaborative platform designed to foster innovation and to develop the science behind a method of “reading” DNA also known as Next-Generation Sequencing (or NGS).  Next Generation Sequencing allows scientists to compile data on a person’s exact order or sequence of DNA. The precisionFDA includes more than 20 public and private sector participants including National Institutes of Health (NIH), Centers for Disease Control and Prevention, National Institute of Standards and Technology (NIST) and more. Dr. Francis Collins, NIH’s Director stated on that “PrecisionFDA, is a bold and innovative step towards advancing the regulatory science for precision medicine”.

PrecisionFDA allows users to access tools such as “Genome in the Bottle“, a reference sample of DNA for validating genome sequences developed by NIST. These results can be compared with results of previously validated references, and shared with other users, who can track changes and obtain immediate feedback from precisionFDA users. In FDA Voice, Tasha A. Kass-Hout, MD, chief informatics officer at the FDA wrote, “His hope is to grow the community of platform participants and improve the usability of precisionFDA in the coming months and years by placing the code for the precisionFDA portal on the world’s largest open source software repository, GitHub”.


The National Library of Medicine (NLM), Launches Health Literacy Tool Shed Website

Friday, December 18th, 2015
 Adapted from NLM:
The National Library of Medicine, in partnership with Boston University School of Medicine has announced the creation of the Health Literacy Tool Shed. The online database allows users to obtain information of more than 100 health literacy research instruments and compare them to others.
Robert A. Logan Ph.D., senior staff, National Library of Medicine explains, “The new Health Literacy Tool Shed helps users choose the right instrument for their research or practice. It also helps researchers assess core issues, such as the impact of health literacy on health outcomes and health care utilization.”
For more information, please visit the Health Literacy Tool Shed webpage.

NCBI Webinar: “Accessing 1000 Genomes Project Data”

Tuesday, December 8th, 2015

Adapted from the NLM Tech Bull. 2015 Nov-Dec;(407):b9.

To automatically receive the latest news and announcements regarding major changes and updates to NCBI resources and tools please see the subscribe page.

NCBI Webinar: “Accessing 1000 Genomes Project Data” on December 17, 2015

December 17, 2015, NCBI staff will demonstrate how to access 1000 Genomes data through SRA, dbVar, SNP and BioProject, as well as through tracks on annotated human sequences in the graphical sequence viewer and Variation Viewer. Attendees will also learn how to display, search, and download individual and genotype level data through the dedicated 1000 Genomes Browser that allows searching by chromosomal position, gene names and other genome markers.

Date and Time: December 17, 2015 11:00a.m. – 12:00p.m. MT; 12:00p.m.-1:00p.m. CST
Registration URL:

After the live presentation, the Webinar will be uploaded to the NCBI YouTube channel. Any related materials will be accessible on the Webinars and Courses page; you can also find information about future Webinars on this page.

Special NHGRI Seminar Series: “A Quarter Century after the Human Genome Project’s Launch: Lessons beyond the Base Pairs”

Tuesday, December 1st, 2015

National Human Genome Research Institute (NHGRI)

The National Human Genome Research Institute (NHGRI) was established originally as the National Center for Human Genome Research in 1989 to lead the International Human Genome Project. NHGRI is part of the National Institutes of Health (NIH), the nation’s medical research agency ( The Human Genome Project, which had as its primary goal the sequencing of the 3 billion DNA letters that make up the human genetic instruction book, was successfully completed in April 2003. Launched in 2012, the NHGRI History of Genomics Program aims to collect and organize historic materials related to the field of genomics and NHGRI as an organization. Efforts include digitization of relevant assets and database development, generation of oral histories chronicling the experiences of genomics leaders and NHGRI staff, production of scholarly work related to major genomics accomplishments, and expansion of the general knowledge about the history of genomics among the scholarly community and the general public. Efforts include digitization of relevant assets and database development, generation of oral histories chronicling the experiences of genomics leaders and NHGRI staff, production of scholarly work related to major genomics accomplishments, and expansion of the general knowledge about the history of genomics among the scholarly community and the general public.


Francis Collins, M.D., Ph.D., Director, National Institutes of Health. Elke Jordan, Ph.D., Former Deputy Director, National Human Genome Research Institute. Mark Guyer, Ph.D., Former Deputy Director, National Human Genome Research Institute. Eric Green, M.D., Ph.D., Director, National Human Genome Research Institute. TITLE:  “A Quarter Century after the Human Genome Project’s Launch:  Lessons Beyond the Base Pairs” DATE:  Thursday, December 3, 2015 TIME:  2:00-3:00 p.m. EST LOCATION:  National Institutes of Health, Bethesda, Maryland, Building 10, Lipsett Amphitheater SPONSOR:  NHGRI History of Genomics Program 

The NHGRI History of Genomics Program: An Archival and Scholarly Initiative

nih genome project

 “Courtesy: National Human Genome Research Institute”

BD2K Updates from NIH and NSF

Tuesday, December 1st, 2015

Big Data to Knowledge (BD2K) updates from NIH and NSF

The National Science Foundation recently posted an article on advances in big data and the management of chronic diseases.

The National Institutes of Health has released new Data Science Funding Opportunities: The new NIH Common Fund program Molecular Transducers of Physical Activity has released funding opportunities including one for a bioinformatics center. Applications are due March 18, 2016.

Article of Interest: How to hijack a Journal.

NIH Open Science Prize for Open Data

Tuesday, November 3rd, 2015

From NIH:

The National Institutes of Health (NIH) Office of the Associate Director for Data Science (ADDS) announces a collaboration with the Wellcome Trust (WT) and the Howard Hughes Medical Institute (HHMI) to launch the “Open Science Prize” (the “Challenge”) to encourage and support the prototyping and development of services, tools and/or platforms that enable open content—including publications, datasets, code and other research outputs—to be discovered, accessed and re-used in ways that will advance research, spark innovation, and generate new societal benefits. The Challenge is necessary to accelerate the field of “open” biomedical research beyond what current funding mechanisms can achieve. For the NIH, this Challenge is being launched under the America COMPETES Reauthorization Act of 2010.

See more at

The Journal of eScience Librarianship

Monday, October 26th, 2015

JESLIB logoThe Journal of eScience Librarianship (JESLIB) is an open access, peer-reviewed journal that advances the theory and practice of librarianship with a special focus on services related to data-driven research in the physical, biological, social, and medical sciences, including public health.

JESLIB explores the many roles of librarians in supporting eScience and welcomes articles by contributors from all areas of the globe related to education, outreach, collaborations, policy, tools, and best practices. The journal includes peer-reviewed articles discussing topics such as research data management, librarians embedded on research teams, data services, data curation, and data sharing and re-use. Submissions covering both theoretical and practical applications are welcomed.

JESLIB does not charge subscription, submission, or author fees and authors retain ownership of the copyright for their content.

Edited by Elaine Martin, Director of the NN/LM New England Region, JESLIB is a product of the eScholarship@UMMS digital repository and supports the National Institute of Health’s big data missions, including the BD2K (Big Data to Knowledge) initiative.

NIH Data Science Webinar Presentation: Data-level Metrics

Monday, October 26th, 2015

LECTURE TITLE: Data-Level Metrics
DATE: Wednesday, October 28, 2015, 8:00-10:00am Mountain, 9:00-11:00am Central
SPEAKER: Martin Fenner

Martin Fenner has been the DataCite Technical Director since August 2015. From 2012 to 2015 he was the technical lead for the PLOS Article-Level Metrics project. Dr. Fenner has a medical degree from the Free University of Berlin and is a Board-certified medical oncologist.


The Office of the Associate Director for Data Science (ADDS) is launching a new “Frontiers in Science” webinar series.  NCI Center for Biomedical Informatics and Information Technology (CBIIT) is pleased to co-host one of the first sessions as part of our bi-weekly Speaker Series.

The DataONE repository network, California Digital Library, and Public Library of Science (PLOS) from October 2014 – October 2015, worked on an NSF-funded project to explore metrics – including citations, downloads and social media –  for about 150,000 datasets. This presentation will summarize the major hurdles to complete this work, the most important findings, and some ideas for moving forward, including implementation as a production service.

Individuals with disabilities who need Sign Language Interpreters and/or reasonable accommodation to participate in this event should contact Sonynka Ngosso, at 301-402-9816. Requests should be made at least 5 business days in advance of the event.

Please join us for this exciting talk!

Webinar Details:

Online link:
Password: $Peakerseries15

Dial-In for Audio Only: 1-855-244-8681
Event number: 733 789 875

On-site:  Shady Grove, room 2W910 – 912

NLM Informatics Lecture Series: Use of Clinical Big Data to Inform Precision Medicine

Thursday, October 22nd, 2015

Shared from NIH:

The next session of the National Library of Medicine Informatics Lecture Series will be held on November 4, 12:00-1:00pm Mountain, 1:00-2:00pm Central.  This talk will be broadcast live and archived at The feature presentation is Use of Clinical Big Data to Inform Precision Medicine with speaker Joshua Denny, MD, Associate Professor in the Departments of Biomedical Informatics and Medicine at Vanderbilt University Medical Center.

For more details and to add the event to your calendar, visit

Abstract: Precision medicine offers the promise of improved diagnosis and more effective, patient-specific therapies. Typically, clinical research studies have been pursued by enrolling a cohort of willing participants in a town or region, and obtaining information and tissue samples from them. At Vanderbilt, Dr. Denny and his team have linked phenotypic information from de-identified electronic health records (EHRs) to a DNA repository of nearly 200,000 samples, creating a ‘virtual’ cohort. This approach allows study of genomic basis of disease and drug response using real-world clinical data. Finding the right information in the EHR can be challenging, but the combination of billing data, laboratory data, medication exposures, and natural language processing has enabled efficient study of genomic and pharmacogenomic phenotypes. The Vanderbilt research team has put many of these discovered pharmacogenomic characteristics into practice through clinical decision support. The EHR also enables the inverse experiment – starting with a genotype and discovering all the phenotypes with which it is associated – a phenome-wide association study (PheWAS). PheWAS requires a densely-phenotyped population such as found in the EHR. Dr. Denny’s research team has used PheWAS to replicate more than 300 genotype-phenotype associations, characterize pleiotropy, and discover new associations. They have also used PheWAS to identify characteristics within disease subtypes.

This event will be broadcast at when the event is live.