NCBI Datasets

• NCBI Datasets New Genome AssemblyTriggers when NCBI releases a new genome assembly for a species or wider taxon, with its accession, organism and strain, assembly level, size, submitter and release date

• Get genesLook up one or more genes by NCBI Gene ID and get each one's symbol, full name, organism, chromosome and position on the reference genome, RefSeq summary, synonyms, matching Ensembl, OMIM and UniProt IDs, transcript and protein counts, and Gene Ontology terms.
• Find genes by symbolFind genes by their official symbol, such as BRCA1 or TP53, in one organism, and get the full gene record for each, Gene ID included. Symbols NCBI does not have are listed as not found.
• Find genes by accessionFind the gene behind RefSeq transcript, protein or genomic accessions, such as NM_007294.4 or NP_009225.1, and get its full gene record.
• Search genes in an organismList an organism's genes, optionally only those whose symbol, name, alias or protein name matches some words and only of some kinds, such as protein coding genes or pseudogenes. Returns a page at a time with the total found.
• List gene orthologsList the genes in other species that NCBI groups as orthologs of a gene (the same gene, inherited from a common ancestor), optionally only within a group such as mammals or primates.
• List gene transcripts and proteinsList a gene's RefSeq transcripts and the proteins they encode, the MANE Select transcript first, with lengths, isoforms, matching Ensembl IDs and where each sits on the genome.
• Get gene expression by tissueGet how strongly a gene is expressed in each tissue, in transcripts per million, from the RNA-seq studies NCBI summarises. NCBI holds this for human genes; for others the list is empty.
• Get genome assembliesLook up genome assemblies by accession and get each one's organism, assembly name and level, whether it is the reference genome, release date, submitter, size, GC content, contig and scaffold N50, gene annotation counts and quality scores.
• Search genome assembliesList the genome assemblies of a species or any wider group, newest first, filtered to reference genomes, RefSeq or GenBank, assembly levels, annotated assemblies and a release date range. Returns a page at a time with the total found.
• List genes in a genomeList the genes annotated on a genome assembly, in genome order, optionally only those matching a name, of one kind, or within a region of a chromosome, with each gene's position and the proteins it encodes.
• List genome chromosomesList the chromosomes and other sequences a genome assembly is made of, with their RefSeq, GenBank and UCSC names, lengths and GC content.
• Get genome assembly historyList every version of a genome assembly, newest first, with its name, GenBank and RefSeq accessions and release date.
• Find genome by sequenceFind the genome assembly a chromosome or other sequence accession belongs to, such as NC_000001.11, and get that assembly's record.
• Get a taxonGet a taxon from NCBI Taxonomy by ID or name: its scientific and common names, rank, lineage from domain to species, parent and children, genetic code, and how many genome assemblies and genes NCBI holds for it.
• Search taxa by nameFind taxa whose scientific or common names start with some text, as NCBI's search box suggests them, to get the Taxonomy ID for a species, strain or wider group.
• List taxa within a taxonList the taxa below a taxon, such as the genera of a family or the species of a genus, at every rank or only the ranks chosen.
• Search virus genomesList the genome sequences of a virus, such as SARS-CoV-2 or influenza A, filtered by host, where they were collected, Pango lineage, completeness and release date, with each one's isolate, collection date, length and submitter.
• Get virus genomesLook up virus genome sequences by GenBank or RefSeq accession and get each one's virus, isolate, host, place and date of collection, lineage, length and submitter.
• Get BioSamplesLook up BioSample records by accession and get each sample's organism, owner, dates, BioProjects, where and when it was collected, and every attribute its submitter recorded.
• Search organelle genomesList the mitochondrial, chloroplast and other organelle genomes of a taxon, with their accessions, lengths, shapes and gene counts, optionally only some organelles or a release date range.

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