Tag: Open data

Introducing SARS-CoV-2 Variants Overview, NLM’s latest tool in the fight against COVID-19

The National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM) has released a new resource, called the SARS-CoV-2 Variants Overview, that aggregates data related to SARS-CoV-2 variants from sequences available in NCBI’s GenBank and Sequence Read Archive (SRA) databases.

SARS-CoV-2 Variants Overview, a freely available online dashboard, was developed with guidance from the TRACE Working Group as part of NLM’s participation in the National Institutes of Health (NIH) Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV) initiative, a public-private partnership for a coordinated research strategy to support and speed up the development of COVID-19 treatments and vaccines.

One impetus for development of the dashboard is that unassembled SRA data cannot be processed through Pango tools, and many SARS-CoV-2 samples are only represented in SRA. The Pango nomenclature is being used by researchers and public health agencies worldwide to track the transmission and spread of SARS-CoV-2, including variants of concern. Thus, we developed a uniform approach to making variant calls from SRA records and assigning Pangolin lineages on the basis of these results. This means that submission groups do not have to go through the effort of creating assemblies. Continue reading “Introducing SARS-CoV-2 Variants Overview, NLM’s latest tool in the fight against COVID-19 “ →

NCBI’s Open Data – A Source of Experimental Data for Important Discoveries

On a typical day, researchers download about 30 terabytes of data from NCBI in an effort to make discoveries. NCBI began providing online access to data in the early 1990s, starting with the GenBank database of DNA sequences. Over the years we’ve greatly expanded the types and quantity of data available. You can now find on our site descriptions and data from experimental studies such as next-generation sequencing projects, bioactivity assays for small molecules, microarray datasets and genome-wide association studies.

The White House recently recognized these efforts by awarding NCBI Director David J. Lipman with the “Open Science” Champion of Change Award [1]. The scientific community has recognized the benefits of open data. Access to this information serves as a source of both original and supplemental data for exploration and validation [2-4], which improves the power of experimental data [5] while increasing the speed and decreasing the cost of discovery [6].

In this post, we summarize three recent cases where researchers used data from an NCBI resource/database to make significant discoveries.

Continue reading “NCBI’s Open Data – A Source of Experimental Data for Important Discoveries” →