============
Introduction
============

The files in this directory provide a mapping between the accession.version from
a nucleotide, protein, WGS or TSA sequence record and a taxonomy ID (taxid) from
the NCBI Taxonomy database (http://www.ncbi.nlm.nih.gov/taxonomy/).

Please do not attempt to view the files with a web browser since they contain 
millions of lines.


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Files in this directory
=======================

Two set of files are available for download. 
The first set contains accession to taxid mapping for live sequence records:

nucl_wgs.accession2taxid.gz
TaxID mapping for live nucleotide sequence records of type WGS or TSA.

nucl_gb.accession2taxid.gz
TaxID mapping for live nucleotide sequence records that are not WGS or TSA.

prot.accession2taxid.gz
TaxID mapping for live protein sequence records which have GI identifiers.

prot.accession2taxid.FULL.gz
TaxID mapping for all live protein sequence records, including GI-less WGS proteins

prot.accession2taxid.FULL.NN.gz
TaxID mapping for all live protein sequence records, split into smaller files
containing 400 million rows each.

pdb.accession2taxid.gz
TaxID mapping for all live sequence records at NCBI that have been derived
from RCSB/PDB protein structures. PDB sequences are identified by a
combination of a Molecule-ID and a Chain-ID, so the content of the first
and second columns are not INSDC-like accession numbers. In addition, these
sequences are not formally versioned, so there are no ".Version" values present
in the second column.

The second set of files contains accession to taxid mappings for dead 
(suppressed or withdrawn) sequence records:

dead_nucl.accession2taxid.gz
TaxID mapping for dead nucleotide sequence records that are not WGS or TSA.

dead_wgs.accession2taxid.gz
TaxID mapping for dead nucleotide sequence records of type WGS or TSA.

dead_prot.accession2taxid.gz
TaxID mapping for dead protein sequence records.

All data files are compressed with gzip. They are updated weekly.

Each data file is paired with an md5checksum file which has the same name plus
the suffix .md5. The md5checksum from the md5 file can be used to verify the 
integrity of the data file after it has been downloaded.


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File content
============

All files have four columns separated by a TAB character. The first line in 
each file is a header line:
accession<TAB>accession.version<TAB>taxid<TAB>gi

Columns:
1. Accession
   Accession of the sequence record, without a version. e.g. BA000005
2. Accession.version
   Accession of the sequence record together with the version number. 
   e.g. BA000005.3
   Some dead sequence records do not have any version number in which case the
   value in this column will be the accession followed by a dot. e.g. X53318.
3. TaxId
   Taxonomy identifier of the source organism for the sequence record. e.g. 9606
   If for some reason the source organism cannot be mapped to the taxonomy 
   database, the column will contain 0.
4. GI
   GI of the sequence record. e.g. 55417888
   NCBI is phasing out use of gi numbers, see:
   http://www.ncbi.nlm.nih.gov/news/03-02-2016-phase-out-of-GI-numbers/
   Some sequences such as unannotated WGS and TSA records already lack a GI.
   If a sequence record does not have a GI assigned, the column will contain na.

The content of the files is unsorted.

________________________________________________________________________________
National Center for Biotechnology Information (NCBI)
National Library of Medicine
National Institutes of Health
8600 Rockville Pike
Bethesda, MD 20894, USA
tel: (301) 496-2475
fax: (301) 480-9241
e-mail: info@ncbi.nlm.nih.gov
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