Author: NCBI Staff

NCBI dbVar releases updated human reference structural variation (SV) data files and tutorials

NCBI dbVar releases updated human reference structural variation (SV) data files and tutorials

Would you like to compare and analyze your data with known structural variants (SV) in NCBI’s database of genomic structural variation (dbVar)? Now there are easy-to-use files containing non-redundant (NR) deletions, duplications, and insertions aggregated from across studies in dbVar.  The files are available for human assembly versions GRCh37 and GRCh38.   Descriptions of the NR data are available on GitHub.

The NR files are available for FTP download in BED, BEDPE, and custom tab-separated formats, designed to be compatible with many popular tools and browsers. To help users get started, we have developed tutorials for UCSC Genomic Browser, Galaxy web-based analysis platform, NCBI Sequence Viewer, and command-line BEDtools.

An upcoming release will include annotations including genes, regulatory regions, and more. Have a favorite annotation you’d like to see? Send us your suggestions by contacting dbVar directly or open a GitHub issue. We also welcome comments and other improvement suggestions.

Discover GTR at AMP 2018 (Nov 1-3)

Discover GTR at AMP 2018 (Nov 1-3)

Starting this Thursday, November 1st, NCBI staff from projects like ClinVar, GTR, MedGen, Medical Genetics Summaries and OSIRIS will be ready to hear your feedback at the Association for Molecular Pathology (AMP) 2018 Annual Meeting & Expo in San Antonio, Texas. Come to booth #1810 and tell us how to make our resources better for you or ask questions about how to participate and use these resources!

Staff will also present on their current work at AMP 2018. We will present our analyses of current GTR tests and discuss how GTR data aims to reflect the current genetic testing landscape.

Below is a sneak peek on two different presentations to learn about “The NIH Genetic Testing Registry (GTR): Test Methodologies as a Sensor of the Precision Medicine Environment”:

  • Poster TT046 – Friday, November 2 from 2:30 – 3:30 PM
  • Technical Topics Platform Presentation – Saturday, November 3 from 7:45 – 8:00 AM

Continue reading “Discover GTR at AMP 2018 (Nov 1-3)” →

Improved search for eukaryotic and viral proteins and gene names

NCBI previously announced improved search functionality to provide users with better results for common language queries. We have expanded this search capability beyond queries for species-qualified gene symbols (e.g. human GhrI) to support species-qualified protein names (e.g. human obestatin) and gene names (e.g. human ghrelin and obestatin prepropeptide) in eukaryotes and viruses. Whether you are searching for a gene, transcript, or protein, our updated featured results panel displays the relevant information. The results panel for the selected gene includes quick links to many resources including transcripts, protein products, and publications.
Search results for peptide hormone 'rat obestatin' in NCBI's All Databases search page
Figure 1. Search results for peptide hormone ‘rat obestatin’ in NCBI’s All Databases search page
Try these example queries to see the improved search results.
Join NCBI at ASHG 2018, October 16-20

Join NCBI at ASHG 2018, October 16-20

Putting your schedule together for ASHG? Don’t forget to look at all of NCBI’s activities, which include 1 GRC Workshop, 1 Booth (#315), 2 Co-Labs, and 10 Poster presentations. We created a handy schedule below, with links to posts where we’ve highlighted events.

Booth #315, Exhibit Hall:

  • Wednesday, October 17, 10:00 AM – 4:30 PM
  • Thursday, October 18, 10:00 AM – 4:30 PM
  • Friday, October 19, 10:00 AM – 4:30 PM

Visit us at the booth to provide feedback, have questions answered or just to chat!

Continue reading “Join NCBI at ASHG 2018, October 16-20” →

Try out a new version of My Bibliography in NCBI Labs

My Bibliography is a component of My NCBI and allows you to create an online collection of your published work. You can import citations directly from PubMed or add them manually. For accounts linked to eRA Commons, you can associate citations with awards and manage compliance with the NIH Public Access Policy.

Are you a My Bibliography user?

We are working on a new My Bibliography and want your feedback! The new trial version of My Bibliography is an NCBI Labs experiment. It incorporates many improved features over the existing My Bibliography, including a color-coded view of compliance status, filtering by compliance status, and functionality on your phone.

mybib on labs

Anything you try or change in the NCBI Labs My Bibliography site will not affect content in your existing My Bibliography account, so feel free to experiment.

After trying the new My Bibliography, please let us know what you think.

Matched Annotation by NCBI and EMBL-EBI (MANE): a new joint venture to define a set of representative transcripts for human protein-coding genes

The RefSeq project at the NCBI and the Ensembl/GENCODE project at EMBL-EBI have provided independent high-quality human reference gene datasets to biologists since the sequencing of the human genome.

Now we’re joining together on an exciting new project we’re calling Matched Annotation from the NCBI and EMBL-EBI or MANE, to provide a matched set of well-supported transcripts for human protein-coding genes and define one representative transcript for each gene. Both RefSeq and Ensembl will continue to provide a rich set of alternate transcripts per gene.

Continue reading “Matched Annotation by NCBI and EMBL-EBI (MANE): a new joint venture to define a set of representative transcripts for human protein-coding genes” →

See improvements in NCBI’s genome visualization and analysis tools at ASHG

GDV_homepage

In 2016, NCBI introduced the Genome Data Viewer (GDV). This past May, the GDV replaced the aging Map Viewer. Over the past year, NCBI has kept you updated about GDV through announcements, webinars, and blogs. Now you can gather information and get an overview of all the changes to GDV in person at ASHG!

Check out Poster 1670F “What’s new with NCBI tools for genome visualization and analysis.” on Friday, Oct. 19 from 3 PM to 4 PM
(Exhibit Hall, Ground Level)

Continue reading “See improvements in NCBI’s genome visualization and analysis tools at ASHG” →

NCBI at ASHG 2018: Data and Clinical CoLabs introduce interactive graphical displays and medical genetics resources

As you know, NCBI will be attending American Society of Human Genetics (ASHG) 2018 in San Diego.

This year, we have two CoLabs – interactive sessions where you can learn about freely available NCBI tools and resources. Read on below for a description of each CoLab and join us at ASHG in two weeks!

Continue reading “NCBI at ASHG 2018: Data and Clinical CoLabs introduce interactive graphical displays and medical genetics resources” →

Abstract display option added for PubMed Labs search results

Thank you for your feedback! The community response to our launch of PubMed Labs has been outstanding. We are continuing to test new features at PubMed Labs, like the addition of a new view for search results.

In response to your input, we’ve added “Abstract” to the Display Options of your PubMed Labs search results.

view pubmed labs search results by abstract
Figure 1. PubMed Labs search. Click the ‘gear’ icon at the top of your results page and click “Abstract” to see the new view.

Be sure to let us know how this and other new features in PubMed Labs work for you.

Please note that PubMed Labs includes only a limited set of features, and not the full set of PubMed tools. The absence of a PubMed tool in PubMed Labs does not mean it is planned for elimination.