Get gene metadata

Gene metadata is available through the easy-to-use website and command-line tool (CLI). For an overview of what metadata is available, see the report schemas for the gene primary and gene product reports.

Using NCBI gene IDs

Retrieve gene metadata by providing one or more gene IDs (space delimited). If using the --inputfile option instead, each gene ID should be on a separate line.

datasets summary gene gene-id 1 2 3 9 10 11 12 13 14 15 16

Using gene symbols

Run the following command to retrieve gene metadadata by gene symbols.

datasets summary gene symbol ACRV1 A2M --taxon human

Using RefSeq transcript or protein accessions

Retrieve gene metadata by RefSeq nucleotide or protein accession.

datasets summary gene accession NM_020107.5 NP_001334352.2

Using species name

Retrieve gene metadata by species name or Taxonomy ID. Run the following command to get gene metadata for all human genes.

datasets summary gene taxon human

Retrieve the gene product report

The gene product report contains information about record identifiers, genomic locations, transcripts, and products.

datasets summary gene symbol ACRV1 --report product

Create a tsv output of gene metadata using dataformat

datasets summary gene symbol ACRV1 A2M --as-json-lines | dataformat tsv gene --fields symbol,gene-id,synonyms

Output:

Symbol  NCBI GeneID     Synonyms
A2M     2               A2MD,CPAMD5,FWP007,S863-7
A2M     2               A2MD,CPAMD5,FWP007,S863-7
ACRV1   56              SP-10,SPACA2,D11S4365
ACRV1   56              SP-10,SPACA2,D11S4365

Note: Always use --as-json-lines when piping data from datasets to dataformat