Given a file of Entrez accession numbers or other
identifiers, Batch Entrez downloads
the corresponding records.
- Start with a local file containing a list of accession numbers or identifiers
- Select the database corresponding to the type of accession numbers
or identifiers in your input file
- Use the Browse or Choose File... button to select the input file
- Press the Retrieve button to see a list
of document summaries
- Select a format in which to display the data for
viewing, and/or saving
- Select 'Send to file' to save the file.
- To download entire genome records, check the NCBI FTP site, instead of using Batch Entrez.
- Some lists of record identifiers can be tens
of thousands of lines long, so Batch Entrez may not retrieve
all records from one list. Split the list of identifiers
into smaller files using a file splitting software or a file
split command at the command prompt in UNIX or LINUX
- When loading large numbers of genome records, put several thousand record identifiers per file,
one per line, left-adjusted.
- Please note that Batch Entrez will check for duplicate
identifiers when reporting results from a list that you have
- When retrieving a list of Nucleotide
accessions, you must select the specific component database
from which the accessions or GIs were saved. For Nucleotide,
choose either the CoreNucleotide, the EST or the GSS
selection from the database menu. If you have a mixed list
of nucleotide accessions or UIDs, you will need to run the
Batch Entrez search three times. Select the database from
the pull-down menu, CoreNucleotide, EST, and GSS separately.
- In all cases, be certain to select the
database that corresponds to the identifiers you
are uploading. For example, if you have
saved a list of protein accession numbers, be sure to select the Protein