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TargetDB files

Last updated: June 7, 2011

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Database files:
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target.sql - TargetDB tables "target_complex" and "targ_sequence".

These two tables together contain all data items provided by depositors.
Please see target.dtd for details: http://targetdb.sbkb.org/target.dtd

pdbt_id is incremental ID assigned to each target entry at parsing of
the data file provided by depositors. 

Sequence_id is an internal protein sequence id assigned to each distinct sequence in the target
sequence list.
Distinct sequence is a sequence(string) that differs from other
sequences in the database by at least one character.Distinct sequence
is a sequence(string) that differs from other
sequences in the database by at least one character.


targetpdb_info.sql - TargetDB table targetpdb_info

This table represents a list of structures in the PDB that are determined by
SG centers and included into target data file. 

XML files:
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targets.xml 

All targets in TargetDB. The file is built according to the old version of
the TargetDB DTD: target.dtd

targets.xml.zip/targets.xml.gz - zipped files of targets.xml


targetsV2.xml 

All targets in TargetDB. The file is built according to the latest
version of the TargetDB DTD: target.v2.dtd

targetsV2.xml.zip/targetsV2.xml.gz - zipped files of targetsV2.xml


lablist.xml - list of SG laboratory names as provided by depositors.

FASTA files:
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targets.fa.gz 

All target sequences found in TargetDB in FASTA format.

header:
>'target id' $ 'center initials' $ 'sequence_id' $ 'internal database counter' $ 'target sequence number' $ 

example:
>APC094 $ MCSG $ SQ14167 $ PDBT38819 $ 1 $ 


targets_distinct.fa.gz

Distinct targets in FASTA format.
Distinct sequence is a sequence (string) that differs from other
sequences in the database by at least one character.

>header: 'sequence_id'|'SG center initials'_'target_id'

example:
>SQ100000|NESG_YR145

if sequence is reported by more than one SG centers, than header
contains all the 'SG center initials'_'target_id' pairs separated by a
bar.

example:
>SQ154604|NESG_MbR227|NON-SSGCID_MytuD.00010.a


Tab delimited TXT files:
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targets.txt.gz - zipped, tab delimited output of TargetDB tables
"targ_sequence" and "target_complex"

targetpdb_info.txt  - tab delimited output of TargetDB table
"targetpdb_info"

tarDBstructures.txt (List of SG structures) - Tab delimited version of
the table: http://targetdb.sbkb.org/statistics/pdb_targetdb_title.html
This is a parsed version of targetpdb_info table. pdbt_id and method
columns were excluded from this file. Related PDB_ID(s):
PDB_ID(s)that are referenced by the same target in TargetDB.

sg_structures_by_organism.txt - list of SG structures reported to TargetDB by source organism. The organism taxonomy is provided by superkingdom, family, genus, and species name. Superkingdom is represented by NCBI TAX ID: 
2 - bacteria
2157 - archaea
2757 - eukaryota
10232 - virus

lablist.txt - list of SG laboratory names as provided by depositors.

target_experimental_status.txt - List of all targets in the targetdb with dates of 
the experiemtal status update including status selected, cloned, expressed, purified, crystallized, diffraction,
crystal structre, NMR assigned, NMR structure,  work stopped, and In PDB. The file also provides info on the final experimental 
status of a target. Please note that the status dates represent the dates when experimental status
was updated in the targetdb. It may not precisely reflect the date when experiment was initiated
or completed.  

target_taxonomy_mapping.txt - Mapping of target sequences to NCBI taxonomy.

target_uniprot_mapping.txt  - Mapping of targetdb IDs to Uniprot IDs

target_pfam_mapping.txt     - Mapping of targetdb IDs to PFAM IDs


SOFTWARE:
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targetdb_search.pl - perl script that performs TargetDB search. The
output file is the query result in XML format.


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if you have any questions or suggestions please contact:

target-help@sbkb.org