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PepcDB files

Last updated: July 16, 2009

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Database files:
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-- pepcTargets.xml.gz - complete list of targets in PepcDB in XML format. 
		        This file includes all target metadata icluding text protocols
                        protein and DNA sequences, and description of experiments.

-- pepcTargets.fasta.gz - protein sequences of PepcDB targets

-- pepcTargetsDNA.fasta.gz - DNA sequences of PepcDB targets. Please note that DNA sequence is 
                             an optional data item in the PepcDB schema. Currently only four centers 
                             provide DNA sequences in addition to the protein sequences. 
                             These are ATCG3D, CESG, NYSGXRC, and SGX

-- pepcTrialSequences.fasta.gz - protein sequences of experimental trials. 
                                 A protein target can be associated with multiple trials or experiments.
                                 The trial sequences might be identical to the target sequences or 
                                 represent truncations, mutations, and other sequence modifications 
                                 introduced to achive experimental goal. 

-- trial_experimental_history.txt - Experimental status history of each reported protein production experiment 
                                    in PepcDB. The file contains dates of  selection, cloning, expression,
                                    purification, crystallization, etc.for each experiment.

-- protein_expression_trials.txt - list of expressed proteins in the PepcDB 
                                   and corresponding expression system:
					- bacteria
					- yeast
					- insect cells
					- cell free

                                   Note: this table lists only those expression trials for which 	
                                         expression system was reported by depositors
		
    Table header:	        
	1.  TargetID
	2.  TrialID
	3.  SG center
	4.  Organism Name
	5.  Organism TaxID
	6.  Protein Sequence => if expressed protein is a complex all protein sequences are included into the string separated by ','
	7.  Status => final status of the experiment
        8.  ProtocolID => expression protocol identifier in the database.
        9.  Expression System => example: bacteria, yeast, insect cells, cell free
        10. Expression Host Strain Code 
        11. Expression Vector
        12. Expression Host TaxID
        13. Specific Expression Details => any specific modifications to expression protocol 
        14. Experiment Stop Info => information if experiment was terminated due experimental failure or other reason
                  
											
Data deposited by each structural genomics center in XML format:

-- CENTER_NAME.xm.gz