Search, Download, and Visualize Human RNA-Seq Gene Expression Data in NCBI’s Gene Expression Omnibus (GEO)

Are you interested in accessing consistently computed gene expression count matrices across thousands of experimental studies for half a million samples? Now you can! We are pleased to announce the availability of gene expression count matrices generated from all the human RNA-seq studies in GEO.

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You can find studies with RNA-seq counts by searching GEO Datasets with “rnaseq counts”[Filter]. Continue reading “Search, Download, and Visualize Human RNA-Seq Gene Expression Data in NCBI’s Gene Expression Omnibus (GEO)” →

Putting Content into Context: Clarifying PubMed Central’s Role as an Archive

The role of a library in a digital world continues to evolve and expand. NLM’s PubMed Central (PMC) has a large and diverse user base that includes students and the public, as well as researchers, clinicians, and librarians. We recognize that these different audiences have varying levels of familiarity with PMC as an archive of literature published by other organizations, as well as with NLM, the National Institutes of Health (NIH), and the scholarly publishing process. That’s why we recently updated how we describe, display, and share articles in PMC to provide our users with more context and help them more accurately cite the correct source of an article made available in PMC.

Here are the updates made to PMC:

Continue reading “Putting Content into Context: Clarifying PubMed Central’s Role as an Archive” →

New annotations in RefSeq!

In February and March, the NCBI Eukaryotic Genome Annotation Pipeline released forty-two new annotations in RefSeq for the organisms listed below. Additionally, interim builds for over sixty species were run during that time period to fix some issues with gene symbol assignment.

Agelaius phoeniceus (red-winged blackbird)
Anastrepha ludens (Mexican fruit fly)
Anopheles marshallii (mosquito)
Anopheles nili (mosquito)
Anoplopoma fimbria (sablefish)
Artibeus jamaicensis (Jamaican fruit-eating bat)
Bombina bombina (fire-bellied toad) Continue reading “New annotations in RefSeq!” →

ClinicalTrials.gov Modernization Public Meeting

Join us virtually on April 25 at 12:30 p.m.

Want to learn more about the upcoming changes to the ClinicalTrials.gov website and the new Protocol Registration and Results System (PRS)? We’re hosting a virtual public meeting on Tuesday, April 25 from 12:30 p.m. to 3 p.m. ET to provide a detailed look at the current beta sites and share our overall progress on modernization.

Register Now

This meeting is part of an effort by the National Library of Medicine (NLM) to keep stakeholders and the public informed about the ClinicalTrials.gov modernization, which seeks to deliver an improved user experience on an updated platform that will accommodate growth and enhance efficiency. During the meeting, you will have the opportunity to hear from and interact with modernization team members and other stakeholders. Please register using the link above.

Meeting Agenda

ClinicalTrials.gov modernization team members and members of the NLM Board of Regents Public Service Working Group on ClinicalTrials.gov Modernization will engage with attendees in relation to the following:

How We Got Here: A Summary of Our User-Centered Process for the Design and Development of the ClinicalTrials.gov Website
Get to Know ClinicalTrials.gov Beta and PRS Beta
Breakout Rooms for ClinicalTrials.gov Beta and PRS Beta (attendees may join one)

Who Should Attend

The meeting is open to the public. We particularly aim to reach study sponsors and investigators who submit clinical trial information using the PRS. In addition, we hope to reach ClinicalTrials.gov public website users, including patients, families, health care providers, academics, industry representatives, members of nonprofit and advocacy organizations, staff of government agencies, and data researchers.

The meeting will be recorded, and the recording and presentation slides will be available on the ClinicalTrials.gov Modernization webpage after the meeting.

Stay Up to Date 

Celebrating 10 Years of ClinVar: Why it is More Important Than Ever!

Identifying genetic variants and their impact on health is key to tailoring patient care. However, most variants are rare! As such, it is imperative for health care professionals to compare findings from multiple labs, examine evidence, and read related publications to provide accurate interpretations of genetic testing results as well as to develop treatment plans for their patients. ClinVar, a free and publicly available database, was established 10 years ago with this fundamental need in mind.

10 years of ClinVar

The field of variant discovery and classification for diseases has increased rapidly in the last decade! Continue reading “Celebrating 10 Years of ClinVar: Why it is More Important Than Ever!” →

dbSNP Enhances Scalability, Data Diversity, and Accessibility

As part of the Human Genome Project, NCBI, part of the National Library of Medicine, and the National Human Genome Research Institute (NHGRI) established the Single Nucleotide Polymorphism database (dbSNP) in 1998. Over the last 25 years, dbSNP has evolved into a reliable central public repository for genetic variation data. dbSNP is a community-accepted reference data set for genetic research, analysis pipelines, and for both open-source and commercial tools. It is also an essential part of genetic research and discovery. For example, dbSNP data are used in nearly all human genetic variation research workflows and it serves as the foundation for commercially available ancestry testing products.

Current dbSNP statistics include:

3,800 submitters from all over the world
3.3 billion submitted SNP records
1.1 billion Reference SNP records
1.0 billion Reference SNP records with population frequency
dbSNP accessions are cited in over 65K publications

Continue reading “dbSNP Enhances Scalability, Data Diversity, and Accessibility” →

NCBI Virus Extends Dashboard Visualizations to all Virus Sequences!

Do you want to be able to quickly filter your virus search results based on important attributes? Good news, now you can! We are pleased to announce the extension of Dashboard Visualizations for any virus in the NCBI Virus collection (Figure 1). Dashboard Visualizations allow data to be quickly visualized in a graphical presentation based on a few highly sought-after attributes to prefilter your dataset.

What are Dashboard Visualizations?

Dashboard Visualizations allow you to filter your search by geographic location, collection time, and release time. Each feature on the Dashboard is interactive, so when a filter is applied, it limits the data shown in the other features. When using these filters, the top summary section updates to provide you a snapshot of the number of records in NCBI RefSeq, Nucleotide, and Protein that fit the combined conditions of your search in the NCBI Virus database. Continue reading “NCBI Virus Extends Dashboard Visualizations to all Virus Sequences!” →

New Improvements! Try out our Foreign Contamination Screen (FCS) Tool

Want to submit high-quality data quickly and easily to GenBank? Check out our Foreign Contamination Screen (FCS) tool, a quality assurance process that you can run yourself. FCS offers enhanced contaminant detection sensitivity to improve your genome assemblies and facilitate high-quality data submissions to GenBank. We recently made several improvements to make the tool even easier to use!

What’s New?

Now quicker and easier to run!
Decontaminate your genome with just one extra step.
- Save the removed sequences in a separate file, if desired.
More accurate!
Find more contaminants with improved coverage of prokaryotes, protists, and more.
Screen your genome on the cloud in minutes.

Continue reading “New Improvements! Try out our Foreign Contamination Screen (FCS) Tool” →

NCBI’s Genome Decoration Page (GDP) to Retire in September 2023

As of September 2023, NCBI’s Genome Decoration Page (GDP) will no longer be available. Due to low usage of GDP, we are focusing our development efforts on our more popular resources and tools.

If you are using GDP to view your data mapped to genomes, we encourage you to check out our Genome Data Viewer (GDV) if you haven’t already. You can upload your data for display in GDV and export PDF or SVG images of your view.

Stay up to date 

Follow us on Twitter @NCBI and join our mailing list to keep up to date with our visualization tools and other NCBI news.  

Questions?

Feel free to contact our help desk at [email protected] if you have any questions or concerns.

New Way to View and Download Related Genes

Effective June 2023, the HomoloGene records will redirect to the Datasets Gene Table

Do you use HomoloGene to view and download data? You can now access updated homology data from NCBI Datasets through the Datasets Gene Table with connections to NCBI Orthologs. Go directly from a HomoloGene record to the Datasets Gene Table that will give you access to up-to-date sequence data and metadata. NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.

The Datasets Gene Table provides connections to the NCBI Ortholog interface (Figure 1) that provides the following data:

Orthology data based on an updated algorithm that identifies orthologs spanning > 500 vertebrate species
Similar gene data based on protein architectures that spans all eukaryotes

Continue reading “New Way to View and Download Related Genes” →