NCBI Datasets, the new set of services for downloading genome assembly and annotation data (previous Datasets posts), has redesigned and reorganized web pages to make it easier to find and access the services and documentation you need. NCBI Datasets has a fresh new homepage (Figure 1) highlighting the types of data available through our tools. Available … Continue reading New NCBI Datasets home and documentation pages provide easier access
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You can now retrieve genome data using the NCBI Datasets command-line tool and API by simply providing a BioProject accession. You can go directly from a BioProject accession to genome data even when the BioProject accession is the parent of multiple BioProjects (Figure 1). Figure 1. Command-lines using BioProject accessions with the datasets command-line tool and sample metadata. Top … Continue reading Retrieve genome data by BioProject using the Datasets command-line tool
Do you need to download a lot of genomic data? Maybe you need all primate reference genomes or maybe you need just a few really big genomes? Prior to the advent of NCBI Datasets, downloading such a large amount of data could be a frustrating and time consuming experience involving failed downloads and writing custom scripts. NCBI Datasets … Continue reading Easily download large amounts of genomic data with NCBI Datasets
You can now get gene ortholog data using the NCBI Datasets command-line tool using a gene ID, gene symbol, or RefSeq nucleotide or protein accession. Data are available for vertebrates and insects. The vertebrate orthologs includes a specialized set for fish. (See our recent post for more information on the orthologs for fish and insects.) You … Continue reading The Datasets command-line tool now provides ortholog data
In March, we announced NCBI Datasets, a new resource that lets you easily retrieve and download data from across NCBI databases. Did you know you can now fetch NCBI Gene data programmatically using the NCBI Datasets API or command-line tool? Quickly retrieve both metadata and gene sequence data for multiple Gene records including transcripts and proteins … Continue reading Programmatic access to Gene data using Datasets command-line and API
NCBI introduces Datasets, a new resource that lets you easily gather data from across NCBI databases. Our first release allows you to find and download genomic sequence and annotation data for all eukaryotic organisms through our user-friendly web interface. Our web interface also provides an interactive taxonomy tree that lets you browse for your favorite organism. We … Continue reading Announcing NCBI Datasets – try it out!
While searching for SARS-CoV-2 sequences, have you longed for a COVID-focused SRA dataset? Great news — now there is one! We are happy to announce the addition of COVID-focused datasets (including source and normalized SRA file formats) to the AWS Public Dataset Program. These data can now be explored at the Registry of Open Data … Continue reading NIH’s COVID-focused Sequence Read Archive (SRA) datasets are now open access on AWS!
NCBI Datasets now offers Gene tables: customizable tables of the genes you specify, with key gene information, and the ability to easily download a dataset of genomic, transcript and protein sequences. Drag and drop a list of Gene IDs or gene symbols, and the data table shows your genes with up to 15 columns of metadata, … Continue reading NCBI Datasets now provides downloads of gene data for more than 30 thousand organisms
Are you interested in mining literature about COVID-19 and the novel SARS-Cov-2 virus? You may want to check out the COVID-19 Open Research Dataset (CORD-19). CORD-19 is a collection of more than 13,000 full text articles that focus on COVID-19 and coronaviruses and that were assembled from PMC, the WHO, bioRxiv, and medRxiv. To produce … Continue reading CORD-19: A New Machine Readable COVID-19 Literature Dataset
It’s time we do another roundup of what’s been happening on YouTube! First up, the NCBI YouTube channel has merged with the NLM YouTube channel. You’ll now be able to find diverse content all on one channel, from tips on using resources to fascinating moments in the history of medicine and more!