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NCBI INSIGHTS

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NOW AVAILABLE: REFSEQ RELEASE 223

Check out RefSeq release 223, now available online and from the FTP site. You
can access RefSeq data through NCBI Datasets.

WHAT’S INCLUDED IN THIS RELEASE?

As of March 4, 2024, this full release incorporates genomic, transcript, and
protein data containing:

 * 425,594,654 records
 * 316,329,937 proteins
 * 60,886,133 RNAs
 * sequences from 147,591 organisms 

Continue reading “Now Available: RefSeq Release 223” →

 * NCBI Staff
 * March 11, 2024March 11, 2024

 * Comparative Genomics Resource (CGR)
 * Eukaryote Genome Annotation Pipeline (EGAP)
 * Eukaryotic genome annotation
 * RefSeq


FOREIGN CONTAMINATION SCREEN TOOL: NOW AVAILABLE IN GALAXY!


CHECK OUT OUR LATEST ENHANCEMENTS 

Do you submit genome assembly data to GenBank? If so, try out NCBI’s Foreign
Contamination Screen (FCS) tool, a quality assurance process that you can run
yourself. We will screen all prokaryotic and eukaryotic genome submissions to
GenBank with this tool, but we encourage you to screen your data before
submitting to save time. FCS offers sensitive contaminant detection to increase
the quality of your genome submissions to GenBank. As part of our ongoing effort
to improve your experience, we recently made several enhancements.  Continue
reading “Foreign Contamination Screen Tool: Now Available in Galaxy!” →

 * NCBI Staff
 * March 7, 2024March 7, 2024

 * Comparative Genomics Resource (CGR)
 * Foreign Contamination Screen (FCS) Tool
 * GenBank


CELEBRATING THE BUILDING TRANSPARENT ML/AI SOLUTIONS FOR BIOLOGICAL RESEARCH
CODEATHON

Machine Learning and Artificial Intelligence (ML/AI) are reshaping data science
and scientific discovery. Recognizing the important role of collaboration and
knowledge sharing in this space, NCBI hosted the “Building transparent ML/AI
solutions to advance biological research codeathon” from February 26 to March 1,
2024. This virtual event brought together biologists, developers, and data
scientists passionate about using responsible AI in biological research. 
Continue reading “Celebrating the Building Transparent ML/AI Solutions for
Biological Research Codeathon” →

 * NCBI Staff
 * March 5, 2024March 5, 2024

 * Codeathon


SUBMIT YOUR SOMATIC VARIATION DATA TO CLINVAR

NCBI’s ClinVar is now accepting submissions for somatic variants classified for
cancer. As recently announced, we updated the ClinVar website as part of our
effort to better support the display of submitted somatic variation data.  

Access to somatic variation data is essential for understanding tumor biology
and will help researchers advance cancer treatment. It also helps clinical
cancer testing laboratories provide better patient reports. Make ClinVar as
useful for somatic variants as it is for germline by contributing your data! To
submit your data, use our new somatic spreadsheet template
(SubmissionTemplateSomatic.xlsx) and follow these step-by-step instructions.
Once your submission is prepared, you can go to the ClinVar Submission Portal to
upload and send your file. See an example below.   Continue reading “Submit Your
Somatic Variation Data to ClinVar” →

 * NCBI Staff
 * February 29, 2024

 * ClinVar


JOIN NCBI AT TAGC 2024


MARCH 6-10 IN WASHINGTON, D.C. 

We look forward to seeing you in person at The Allied Genetics Conference
(TAGC), March 6-10, 2024, in the Washington D.C. metro area. NCBI staff will
participate in a variety of activities and events, including hosting a hands-on
workshop: Exploring and downloading NCBI data with NCBI Datasets. We’re also
excited to share our recent efforts on the NIH Comparative Genomics Resource
(CGR) in a talk during Sunday’s Technology, Tools, and Resources session. 

CHECK OUT NCBI’S SCHEDULE OF ACTIVITIES AND EVENTS:

Continue reading “Join NCBI at TAGC 2024” →

 * NCBI Staff
 * February 22, 2024

 * Comparative Genomics Resource (CGR)
 * Gene Expression Omnibus (GEO)
 * NCBI Datasets
 * RefSeq


SIGNIFICANT UPDATES COMING TO THE NCBI DATASETS APIS AND COMMAND-LINE TOOLS

As part of our ongoing effort to enhance your experience, we are updating the
NCBI Datasets application programming interfaces (APIs). Beginning in June 2024,
the v2alpha APIs will be promoted to the stable v2 version. At this time, the v1
API, the command-line interface (CLI) version 13 and older versions, and the
Python library v1 will be deprecated and thus no longer supported for bug fixes
or updates. Effective December 31, 2024, these will no longer be available for
use. 

Our updated APIs and CLI tools include new features and functionality based on
your feedback. We’re committed to making this transition as smooth as possible
and encourage you to review our FAQs for more details. If you use NCBI Datasets
web pages and command-line tools v14+, no action is required.   Continue reading
“Significant Updates Coming to the NCBI Datasets APIs and Command-Line Tools” →

 * NCBI Staff
 * February 20, 2024February 20, 2024

 * API
 * NCBI Datasets


NCBI CELEBRATES INTERNATIONAL LOVE DATA WEEK


PROVIDING FREE AND OPEN ACCESS TO SCIENTIFIC LITERATURE AND DATA 

Do you love biological data? Join NCBI in celebrating International Love Data
Week, February 12-16, 2024! Love Data Week is an international celebration of
data, which takes place every year during the week of Valentine’s Day. This
year’s theme is “My Kind of Data,” focusing on data equity and inclusion,
disciplinary communities, and creating a kinder world through data. 

NCBI is one of the largest sources of free and open biological data on the web
with over 300 TB retrieved every day. There’s something for everyone to love! 
Continue reading “NCBI Celebrates International Love Data Week” →

 * NCBI Staff
 * February 12, 2024February 13, 2024

 * Biomedical data
 * data


NEW REFSEQ ANNOTATIONS NOW AVAILABLE!

During October to January, the NCBI Eukaryotic Genome Annotation
Pipeline released seventy new annotations in RefSeq!

NEW ANNOTATIONS

 * Alnus glutinosa (eudicot)
 * Amyelois transitella (moth)
 * Anolis sagrei ordinatus (Brown anole)
 * Apis cerana (Asiatic honeybee)
 * Balaenoptera ricei (Rice’s whale)
 * Bombus pascuorum (bee)
 * Bos javanicus (banteng)
 * Bos taurus (cattle) 

Continue reading “New RefSeq Annotations Now Available!” →

 * NCBI Staff
 * February 7, 2024

 * Comparative Genomics Resource (CGR)
 * Eukaryote Genome Annotation Pipeline (EGAP)
 * Genome Data Viewer (GDV)
 * NCBI Datasets
 * RefSeq


ENHANCEMENTS TO CLINVAR WEBSITE NOW LIVE

Important Note: Support for both the old XML formats has been extended through
the end of June 2024.

As previously announced, we updated the ClinVar website as part of our effort to
better support the display of submitted somatic variation data. 

WHAT CHANGED? 

Continue reading “Enhancements to ClinVar Website Now Live” →

 * NCBI Staff
 * January 31, 2024February 20, 2024

 * ClinVar


HOMOLOGENE NOW REDIRECTS TO NCBI DATASETS GENE


A NEW WAY TO VIEW AND DOWNLOAD RELATED GENES 

As previously announced, HomoloGene now automatically redirects to the NCBI
Datasets Gene page giving you easy access to up-to-date sequence and homology
data. The NCBI Datasets Gene Table provides a link to NCBI Orthologs with
expanded gene and protein information and links to tools. NCBI Orthologs
includes more genes and sequences for a growing range of taxa. See an example
below. Legacy HomoloGene data remains available on the FTP site. Continue
reading “HomoloGene Now Redirects to NCBI Datasets Gene” →

 * NCBI Staff
 * January 30, 2024

 * Comparative Genomics Resource (CGR)
 * Gene
 * Homologs
 * NCBI Datasets


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