Legacy pages will be redirected effective July 2023
In July 2023, NCBI’s Assembly and Genome record pages will be redirected to new Datasets pages as part of our ongoing effort to modernize and improve your user experience. NCBI Datasets is a new resource that makes it easier to find and download genome data.
We will update the following pages:
- The NCBI Assembly pages will be redirected to the new Datasets Genome pages that describe assembled genomes and provide links to related NCBI tools such as Genome Data Viewer and BLAST.
- The NCBI Genome pages will be redirected to the Datasets Taxonomy pages that provide a taxonomy-focused portal to genes, genomes and additional NCBI resources.
- During this transition, you will have the option to return to the legacy Genome and Assembly pages.
These updates are part of our larger NIH Comparative Genomics Research (CGR) project mission to facilitate reliable comparative genomics analyses for all eukaryotic organisms in collaboration with the genomics community. For an example of the new NCBI Datasets updates in action, feel free to browse the Genome and Taxonomy pages for Ursus arctos (brown bear) data.
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We are very excited about these enhancements and welcome your feedback as we continue to improve and transition to our new pages! Feel free to email us with questions or feedback. For more information, check out our help documentation.
Hello,
In what ways will the Genome and Taxonomy database APIs change with this update? I am working on a tool that uses the Rentrez package, and I am not able to find a changelog for this.
Thanks
Thanks for asking. These changes will not affect the Genome and Taxonomy database APIs.
Will this affect the eutils and/or edirect utilities when I download an assembly, e.g.,
`esearch -db assembly -query “$assembly_acc NOT refseq[filter]” | elink -target nuccore -name assembly_nuccore_insdc | efetch -format fasta`
Thank you for the question. The EDirect/E-Utilities access to the assembly, genomes, and taxonomy databases will be unaffected by this change for the foreseeable future.
Where can exact values for assembly statistics be found in the new page design?
Thanks for the question. The genome page linked in the blog has an option to download the assembly data report with the statistics. We’re working on a way for you to view the exact values on the web page. If you have additional questions, please contact our Help Desk at info@ncbi.nlm.nih.gov.
Would it be possible to include a link to the FTP directory of all associated files for an assembly on the new genome page? I find these very useful and always have to click back to the legacy page to access.
Thanks for the suggestion. Actually the link to the FTP site is present on the new pages. It’s under the Actions menu. Click the three dots. See for example https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001405.40/
Thank you for the information!
Would it also be possible to make available under the Actions menu on the genome page by taxon? For example here
https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=9606
Thank you for suggestion. We will pass it along to the product team!
Previously, I could download protein annotation (protein table) in the strain for each strain as an excel file, but is it now impossible?
Hello, Thanks for your question. Please contact our help desk so we can assist you: info@ncbi.nlm.nih.gov
Hello,
How can we easily recognize those datasets with both assembly and annotation deposited in NCBI? Traditionally, annotation is referred as “genome” in NCBI…now, it appears to be more confusing to identify them…
Cheers
maxmaronna
Hello! Thank you for your question. Please contact our help desk so we can assist you: info@ncbi.nlm.nih.gov