Batch Entrez
Use Batch Entrez to upload a file of GIs or accession
numbers from the Nucleotide or Protein databases, or upload
a list of record identifiers from other Entrez databases.
Tips : Some lists of record identifiers can be tens of
thousands of lines long and 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
systems. Put several thousand record identifiers per file,
left-formatted, and one per line. This may be necessary when
you are loading large numbers of genome records. You can
check the NCBI FTP site locations to download entire genome
records. Also, use GIs rather than 'accession.version'
numbers when making lists for batch entrez to fetch.
Please note that Batch Entrez will check for duplicate
identifiers when reporting results from a list that you have
imported.
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 correct database for
uploaded identifiers when using Batch Entrez, to ensure the
expected records. For example, if you have saved a list of
protein GIs, be sure to select the Protein database.
- Create a file with a list of GI or accession numbers
and save it locally
- Select the database from which the list of accessions
or UIDs originated
- Use the 'Browse' button to select the filename
containing the list of UIDs from your system directory
- Press the Retrieve button and you will 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.
|