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<H1>[Utilities-announce] NCBI Datasets command-line and API</H1>
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<B>utilities-announce at ncbi.nlm.nih.gov</B>
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<A HREF="mailto:utilities-announce%40ncbi.nlm.nih.gov?Subject=Re%3A%20%5BUtilities-announce%5D%20NCBI%20Datasets%20command-line%20and%20API&In-Reply-To=%3Cmailman.5110.1606246118.4761.utilities-announce%40ncbi.nlm.nih.gov%3E"
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TITLE="[Utilities-announce] NCBI Datasets command-line and API">utilities-announce at ncbi.nlm.nih.gov
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<I>Tue Nov 24 14:28:20 EST 2020</I>
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<PRE>NCBI announces improved programmatic access to gene, genome, and virus datasets with an updated command-line tool and RESTful API.
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Command-line tool: <A HREF="https://www.ncbi.nlm.nih.gov/datasets/docs/command-line-access/">https://www.ncbi.nlm.nih.gov/datasets/docs/command-line-access/</A>
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Get started with datasets - ncbi.nlm.nih.gov<<A HREF="https://www.ncbi.nlm.nih.gov/datasets/docs/command-line-access/">https://www.ncbi.nlm.nih.gov/datasets/docs/command-line-access/</A>>
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The NCBI Datasets project has developed a command-line tool, datasets, that is used to query and download biological sequence data across all domains of life from NCBI databases. datasets is currently in alpha and will be updated frequently to add new features, fix bugs, and enhance usability ...
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www.ncbi.nlm.nih.gov
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RESTful API: <A HREF="https://api.ncbi.nlm.nih.gov/datasets/v1alpha/">https://api.ncbi.nlm.nih.gov/datasets/v1alpha/</A>
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You can find genomic data by entering an assembly accession, NCBI Taxonomy ID, or taxonomic name (scientific or common) for any tax rank (for example, 'apes' or 'Lactobacillus’). You can then customize the download to include sequence, metadata, and annotations in various formats including GFF, GBFF, and (coming soon) GTF. For large download requests we provide options for a 'dehydrated' dataset that can be 'hydrated' when you need the data.
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You can find gene data by entering a RefSeq accession, gene ID, or gene symbol plus a taxonomic identifier (for example ‘mouse’ or the NCBI Taxonomy ID ‘10090’) and get gene, transcript, and protein sequences along with detailed metadata.
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We also provide programmatic access to SARS-CoV-2 datasets that include genomic sequence, protein sequence, annotations, and metadata.
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The Datasets command-line tool and API are still in alpha, and we're updating them often to add new functionality, fix bugs, and make other small changes to enhance usability. Please try them out and let us know what you think!
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Please contact <A HREF="http://www.ncbi.nlm.nih.gov/mailman/listinfo/utilities-announce">info at ncbi.nlm.nih.gov</A> with questions or feedback.
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