table_name	column_index	column_name	column_title	datatype	scale	precision	nullable	default_value	is_auto_inc	fk_table	fk_column_name	is_required	input_type	input_length	onChange	is_data_column	is_display_column	is_key_field	column_text	optionlist_query	url
PR_proteomics_experiment	1	experiment_id	Experiment ID	int	4	0	N		Y							N	N				pkDEFAULT
PR_proteomics_experiment	2	experiment_request_id	Experiment Request ID	int	4	0	Y		N	PR_proteomics_experiment_request	experiment_request_id					N	N				
PR_proteomics_experiment	3	contact_id	Contact	int	4	0	N		N	contact	contact_id	Y	current_contact_id	 		Y	Y	N	PI for this experiment		
PR_proteomics_experiment	4	project_id	Project	int	4	0	N		N	project	project_id	Y	optionlist			Y	Y	N	Project to which the experiment belongs	"SELECT DISTINCT P.project_id,UL.username+' - '+P.name FROM $TB_PROJECT P LEFT JOIN $TB_USER_LOGIN UL ON ( P.PI_contact_id=UL.contact_id ) WHERE P.record_status != 'D' AND P.project_id IN ( $accessible_project_ids ) ORDER BY UL.username+' - '+P.name,P.project_id "	
PR_proteomics_experiment	5	experiment_name	Experiment Title	varchar	100	0	N		N			Y	text	50		Y	Y	N	Title of this experiment		
PR_proteomics_experiment	6	experiment_tag	Experiment Tag	varchar	20	0	N		N			Y	text	20		Y	Y	Y	Short tag (name) of this experiment.  Treat this like a directory/folder name.  Do not use spaces or non-standard characters.		
PR_proteomics_experiment	7	experiment_description	Experiment Description	text	16	0	N		N			Y	textarea	6		Y	Y	N	"Description of this experiment, the sample or samples used, and any other relevant information not contained in the project description or in list-box elements in this form"		
PR_proteomics_experiment	8	experiment_path	Experiment Path	varchar	255	0	N		N			Y	text	50		Y	Y	N	Data path for this experiment (e.g. /data/search/edeutsch/TCells/T_000/human_nci)		
PR_proteomics_experiment	9	organism_id	Organism	int	4	0	N		N			Y	optionlist			Y	Y	N	Organism from which the sample used for this experiment was derived	"SELECT organism_id, organism_name FROM $TB_ORGANISM ORDER BY sort_order,organism_name"	
PR_proteomics_experiment	10	experiment_type_id	Experiment Type	int	4	0	N		N	PR_experiment_type	experiment_type_id	Y	optionlist			Y	Y	N	"Type/class of experiment (e.g. d0/d8 ICAT, etc.)"	"SELECT experiment_type_id, experiment_type_name FROM $TBPR_EXPERIMENT_TYPE ORDER BY sort_order,experiment_type_name"	
PR_proteomics_experiment	11	instrument_id	Instrument	int	4	0	N		N	PR_instrument	instrument_id	Y	optionlist			Y	Y	N	Instrument on which this experiment was performed	"SELECT instrument_id, instrument_name FROM $TBPR_INSTRUMENT ORDER BY sort_order,instrument_name"	
PR_proteomics_experiment	12	gradient_program_id	Gradient Program	int	4	0	Y		N	PR_gradient_program	gradient_program_id	N	optionlist			Y	Y	N	Gradient Program used for this experiment.  Choose MULTIPLE if different programs were used for different msruns within this experiment.	"SELECT gradient_program_id,gradient_program_name FROM $TBPR_GRADIENT_PROGRAM WHERE record_status != 'D'"	
PR_proteomics_experiment	13	column_length	Column Length (cm)	real	4	0	Y		N			N	text	10		Y	Y	N	"Packing length of reverse phase beads column in cm used for this experiment (Do not enter the units in the text box, just the number of cm)"		
PR_proteomics_experiment	14	go_public_date	Go Public Date	datetime	8	0	Y	CURRENT_TIMESTAMP	N			N	text	20		Y	Y	N	Date that this experiment data will go public.  Please use the form 2002-12-31.  Do not enter a date higher than 2030-01-01.		
PR_proteomics_experiment	15	quant_normalization	D0 / D8 Normalization Factor	real	4	0	Y		N			N	text	10		Y	Y	N	"Optional Normalization factor for d0/d8 quantitation ratio.  This will not be known until some data analysis has already been performed.  If ratios that should be calibrated to 1:1 appear as 1.2:1, enter 1.2 here to adjust."		
PR_proteomics_experiment	16	pulldown_protein_name	Pulldown Protein Name	varchar	255	0	Y		N			N	text	50		Y	Y	N	"If this is a pulldown experiment, write in the bait protein here.  This will permit one or more experiments to be properly visualized as a network."		
PR_proteomics_experiment	17	experiment_samples_ids	Experiment Sample IDS	varchar	255	0	Y		N	PR_experiments_samples	experiments_samples_id	N	multilink	4		Y	Y	N	Select all the Samples that were used in this experiment.	"SELECT proteomics_sample_id,  sample_tag FROM $TBPR_PROTEOMICS_SAMPLE  WHERE record_status != 'D' ORDER BY sample_tag"	
PR_proteomics_experiment	18	uri	URI	varchar	255	0	Y		N			N	text	50		Y	Y	N	External web page or other URI		SELF
PR_proteomics_experiment	19	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
PR_proteomics_experiment	20	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_proteomics_experiment	21	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_proteomics_experiment	22	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_proteomics_experiment	23	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_proteomics_experiment	24	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
PR_proteomics_experiment	25	record_status	Record Status	char	1	0	N	N	N							N	N				
PR_gradient_program	1	gradient_program_id	Gradient Program ID	int	4	0	N		Y							N	N				pkDEFAULT
PR_gradient_program	2	project_id	Project	int	4	0	N		N	project	project_id	Y	optionlist			Y	Y	N	Project to which the gradient program belongs	"SELECT DISTINCT P.project_id,UL.username+' - '+P.name FROM $TB_PROJECT P LEFT JOIN $TB_USER_LOGIN UL ON ( P.PI_contact_id=UL.contact_id ) WHERE P.record_status != 'D' AND P.project_id IN ( $accessible_project_ids ) ORDER BY UL.username+' - '+P.name,P.project_id"	
PR_gradient_program	3	gradient_program_name	Program Name	varchar	255	0	N		N			Y	text	50		Y	Y	Y	Title of this gradient program		
PR_gradient_program	4	gradient_program_description	Program Description	varchar	255	0	N		N			Y	textarea	3		Y	Y	N	One-line description of this gradient program		
PR_gradient_program	5	gradient_program_table	Program Data	text	16	0	Y		N			N	textarea	12		Y	Y	N	"Please enter the full gradient program here in the form of three- or four-column data.  Column 1 is the time point in minutes from the beginning of the program.  Column 2 and 3 are buffer A and B settings in percent.  Column 4 is the flow rate in mL/min.  Write no units, just the numbers.  Separate with spaces."		
PR_gradient_program	6	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
PR_gradient_program	7	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_gradient_program	8	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_gradient_program	9	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_gradient_program	10	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_gradient_program	11	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
PR_gradient_program	12	record_status	Record Status	char	1	0	N	N	N							N	N				
PR_gradient_delta	1	gradient_delta_id	Gradient Program Delta ID	int	4	0	N		Y							N	N				pkDEFAULT
PR_gradient_delta	2	gradient_program_id	Gradient Program ID	int	4	0	N		N	PR_gradient_program	gradient_program_id					Y	Y	Y	Gradient Program of which this time point is a part		
PR_gradient_delta	3	gradient_delta_time	Gradient Delta Time Point	real	4	0	N		N							Y	Y	Y	Time point in minutes as the start		
PR_gradient_delta	4	buffer_A_setting_percent	Buffer A Setting Percent	real	4	0	N		N							Y	Y	N	Desired setting of Buffer A in percent (i.e. 0-100) at this timepoint		
PR_gradient_delta	5	buffer_B_setting_percent	Buffer B Setting Percent	real	4	0	N		N							Y	Y	N	Desired setting of Buffer B (currently usually acetonitrile) in percent (i.e. 0-100) at this timepoint		
PR_gradient_delta	6	flow_rate	Flow Rate (mL/min)	real	4	0	N		N							Y	Y	N	"Flow rate in units of mL/min (Do not write units in text box, just the number)"		
PR_fractionation_type	1	fractionation_type_id	Fractionation Type ID	int	4	0	N		Y							N	N				pkDEFAULT
PR_fractionation_type	2	fractionation_type_name	Fractionation Type Name	varchar	100	0	N		N			Y	text	20		Y	Y	Y	Short name of this fractionation type as it will appear in list boxes		
PR_fractionation_type	3	fractionation_type_description	Fractionation Type Description	text	16	0	N		N			Y	textarea	6		Y	Y	N	More complete description of this fractionation type		
PR_fractionation_type	4	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
PR_fractionation_type	5	sort_order	Sort Order	int	4	0	N	10	N			N	text	10		Y	Y	N	Numbers which override alphabetical sorting in a list box		
PR_fractionation_type	6	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_fractionation_type	7	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_fractionation_type	8	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_fractionation_type	9	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_fractionation_type	10	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
PR_fractionation_type	11	record_status	Record Status	char	1	0	N	N	N							N	N				
PR_fraction	1	fraction_id	Fraction ID	int	4	0	N		Y							N	N				pkDEFAULT
PR_fraction	2	experiment_id	Experiment ID	int	4	0	N		N	PR_proteomics_experiment	experiment_id	Y	fixed			Y	Y	Y	Experiment to which this msrun belongs		
PR_fraction	3	fraction_tag	Fraction Tag	varchar	50	0	N		N			Y	fixed			Y	Y	Y	Short tag (name) of this msrun.  This corresponds to the .dat or .raw filename without the extension.  Do not use spaces or non-standard characters.		
PR_fraction	4	fraction_number	Fraction Number	int	4	0	Y		N			N	text	20		Y	Y	N	"This corresponds to serial number of the msrun, sometimes related to the SCX fraction number, but there are no rules yet"		
PR_fraction	5	fraction_date	Fraction Date	datetime	8	0	Y		N			N	fixed			Y	Y	N	Datetime when this msrun was completed		
PR_fraction	6	gradient_program_id	Gradient Program ID	int	4	0	Y		N	PR_gradient_program	gradient_program_id	N	optionlist			Y	Y	N	Gradient Program used for this fraction	"SELECT gradient_program_id,gradient_program_name FROM $TBPR_GRADIENT_PROGRAM WHERE record_status != 'D'"	
PR_fraction	7	column_delay	Column Delay (s)	int	4	0	Y		N			N	text	20		Y	Y	N	Column delay in seconds.  This is the offset between when the pumps claims to be at a given setting and the instrument is seeing the spray at that percentage setting		
PR_fraction	8	fractionation_type_id	Fractionation Type	int	4	0	Y		N	PR_fractionation_type	fractionation_type_id	N	optionlist			Y	Y	N	"Type of fractionation used to creation this fraction (SCX, FFE, etc.)"	"SELECT fractionation_type_id,fractionation_type_name FROM $TBPR_FRACTIONATION_TYPE WHERE record_status != 'D'"	
PR_fraction	9	fraction_centroid	Fraction Centroid	real	4	0	Y		N			N	text	20		Y	Y	N	"Central value of the bin of the changing variable for this particular fraction (in salt concentration units for SCX, pI for FFE, etc.)  Note that if more than one true fraction was combined, use the mean value of all the combined fractions that were actually put into the mass spec for this run"		
PR_fraction	10	fraction_full_width	Fraction Full Width	real	4	0	Y		N			N	text	20		Y	Y	N	"Full width of the bin of the changing variable for this particular fraction (in salt concentration units for SCX, pI for FFE, etc.)  Note that if more than one true fraction was combined, use the total full width of all the combined fractions that were actually put into the mass spec in this run"		
PR_fraction	11	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
PR_fraction	12	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_fraction	13	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_fraction	14	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_fraction	15	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_fraction	16	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
PR_fraction	17	record_status	Record Status	char	1	0	N	N	N							N	N				
PR_msms_spectrum	1	msms_spectrum_id	MS/MS Spectrum ID	int	4	0	N		Y							N	N				pkDEFAULT
PR_msms_spectrum	2	fraction_id	Fraction ID	int	4	0	N		N	PR_fraction	fraction_id					Y	Y	Y	MS Run from which this spectrum comes		
PR_msms_spectrum	3	msms_spectrum_file_root	MS/MS Spectrum File Root	varchar	255	0	N		N							Y	Y	Y	File root of this exactracted spectrum.  This corresponds to the .dta or .out filename without the extension.  Do not use spaces or non-standard characters.		
PR_msms_spectrum	4	start_scan	Start Scan Number	int	4	0	N		N							Y	Y	N	Starting scan number of the MS/MS Spectrum		
PR_msms_spectrum	5	end_scan	End Scan Number	int	4	0	N		N							Y	Y	N	"Ending scan number of the MS/MS Spectrum (if only a single scan, this will be the same as start_scan)"		
PR_msms_spectrum	6	precursor_intensity	Precursor Intensity	real	4	0	Y		N							Y	Y	N	Mass spec intensity of the precursor peptide that is fragmented		
PR_msms_spectrum	7	n_peaks	Number of Peaks	int	4	0	N		N							Y	Y	N	Number of peaks in the spectrum		
PR_msms_spectrum	8	spectrum_score	Spectrum Score	real	4	0	Y		N							Y	Y	N	"Spectrum score, a floating point number of arbitrary scale"		
PR_msms_spectrum	9	score_version	Score Version	varchar	10	0	Y		N							Y	Y	N	Version tag of the software used to score this spectrum		
PR_msms_spectrum	10	scan_time	Scan Time	real	4	0	Y		N							Y	Y	N	Time of the start_scan in seconds after the instrument started counting		
PR_msms_spectrum	11	calc_buffer_percent	Calculated Buffer B Percent	real	4	0	Y		N							Y	Y	N	Calculated percent buffer B (acetonitrile) at the time of this MS/MS spectrum		
PR_msms_spectrum	12	calib_buffer_percent	Calibrated Buffer B Percent	real	4	0	Y		N							Y	Y	N	Calibrated percent buffer B (acetonitrile) at the time of this MS/MS spectrum (not used yet)		
PR_msms_spectrum_peak	1	msms_spectrum_id	MS/MS Spectrum ID	int	4	0	N		N	PR_msms_spectrum	msms_spectrum_id					Y	Y	Y	MS/MS Spectrum to which this peak belongs		
PR_msms_spectrum_peak	2	mass	Peak Mass	float	8	0	N		N							Y	Y	Y	Average mass of this peak		
PR_msms_spectrum_peak	3	intensity	Peak Intensity	real	4	0	N		N							Y	Y	N	Intensity of this peak		
PR_biosequence_set	1	biosequence_set_id	BioSequence Set ID	int	4	0	N		Y							N	N				pkDEFAULT
PR_biosequence_set	2	project_id	Owner Project	int	4	0	N		N	project	project_id	Y	optionlist			Y	Y	N	Project under which this Biosequence Set is organized and for which user privileges is controlled	"SELECT DISTINCT P.project_id,UL.username+' - '+P.name FROM $TB_PROJECT P LEFT JOIN $TB_USER_LOGIN UL ON ( P.PI_contact_id=UL.contact_id ) WHERE P.record_status != 'D' AND P.project_id IN ( $accessible_project_ids ) ORDER BY UL.username+' - '+P.name,P.project_id"	
PR_biosequence_set	3	organism_id	Organism	int	4	0	N		N	organism	organism_id	Y	optionlist			Y	Y	N	Organism to which the BioSequences in this database belong	"SELECT organism_id, organism_name FROM $TB_ORGANISM ORDER BY sort_order,organism_name"	
PR_biosequence_set	4	set_name	Set Name	varchar	100	0	N		N			Y	text	50		Y	Y	N	Name of this BioSequence database		
PR_biosequence_set	5	set_tag	Set Tag	varchar	50	0	N		N			Y	text	20		Y	Y	Y	Short tag (name) of this BioSequence database		
PR_biosequence_set	6	set_description	Set Description	varchar	255	0	N		N			Y	text	50		Y	Y	N	Longer description of this BioSequence database		
PR_biosequence_set	7	set_version	Set Version	varchar	50	0	N		N			Y	text	40		Y	Y	N	Version of this BioSequence database		
PR_biosequence_set	8	polymer_type_id	Polymer Type	int	4	0	N		N	BL_polymer_type	polymer_type_id	Y	optionlist			Y	Y	N	"Polymer type (e.g. protein, DNA, RNA) for the BioSequences in this database"	"SELECT polymer_type_id, polymer_type_name FROM $TBBL_POLYMER_TYPE ORDER BY sort_order,polymer_type_name"	
PR_biosequence_set	9	upload_file	Upload file	varchar	255	0	Y		N			N	file	40		Y	Y	N	File path of this BioSequence database if to be uploaded via the web interface		
PR_biosequence_set	10	set_path	Set Path	varchar	255	0	N		N			Y	text	50		Y	Y	N	File path of this BioSequence database		
PR_biosequence_set	11	source_file_date	Source File Date	datetime	8	0	Y		N			N	text	40		N	N	N	Date of the FASTA file at last update		
PR_biosequence_set	12	uri	URI	varchar	255	0	Y		N			N	text	50		Y	Y	N	External web page or other URI		SELF
PR_biosequence_set	13	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
PR_biosequence_set	14	sort_order	Sort Order	int	4	0	N	10	N			Y	text	20		Y	Y	N	Allows the ordering or ranking of Biosequence Sets which is used to break ties for choosing canonical names.  Lower numbers indicate better rank.		
PR_biosequence_set	15	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_biosequence_set	16	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_biosequence_set	17	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_biosequence_set	18	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_biosequence_set	19	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
PR_biosequence_set	20	record_status	Record Status	char	1	0	N	N	N							N	N				
PR_biosequence	1	biosequence_id	BioSequence ID	int	4	0	N		Y							N	N				pkDEFAULT
PR_biosequence	2	biosequence_set_id	BioSequence Set	int	4	0	N		N	PR_biosequence_set	biosequence_set_id					N	N	Y	BioSequence Set to which this BioSequence belongs		pkDEFAULT
PR_biosequence	3	biosequence_name	BioSequence Name	varchar	255	0	N		N			Y	text	50		Y	Y	Y	Name of this BioSequence (generally everything before the first space in a FASTA file header line)		
PR_biosequence	4	biosequence_gene_name	BioSequence Gene Name	varchar	255	0	Y		N			Y	text	20		Y	Y	N	Gene name of this BioSequence if applicable.  Most common gene name if applicable		
PR_biosequence	5	dbxref_id	Database Cross Reference	int	4	0	Y		N	BL_dbxref	dbxref_id					Y	Y	N	Database cross reference for which the accession number applies		pkDEFAULT
PR_biosequence	6	biosequence_accession	BioSequence Accession	varchar	255	0	Y		N			Y	text	50		Y	Y	N	Accession number for this BioSequence in some external database designated above		
PR_biosequence	7	organism_id	Organism	int	4	0	Y		N	organism	organism_id	Y	optionlist			Y	Y	N	Organism to which this BioSequence belongs	"SELECT organism_id, organism_name FROM $TB_ORGANISM ORDER BY sort_order,organism_name"	
PR_biosequence	8	polymer_type_id	Polymer Type	int	4	0	Y		N	BL_polymer_type	polymer_type_id	Y	optionlist			Y	Y	N	"Polymer type (e.g. protein, DNA, RNA) of this BioSequence"	"SELECT polymer_type_id, polymer_type_name FROM $TBBL_POLYMER_TYPE ORDER BY sort_order,polymer_type_name"	
PR_biosequence	9	biosequence_desc	Biosequence Description	varchar	1024	0	N		N			Y	text	40		Y	Y	N	Description of this BioSequence (generally everything after the first space in a FASTA file header line)		
PR_biosequence	10	biosequence_seq	Sequence	text	16	0	Y		N			N	file	40		Y	Y	N	Actual sequence of the BioSequence if known		
PR_biosequence	11	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
PR_biosequence	12	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_biosequence	13	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_biosequence	14	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_biosequence	15	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_biosequence	16	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
PR_biosequence	17	record_status	Record Status	char	1	0	N	N	N							N	N				
PR_biosequence_property_set	1	biosequence_property_set_id	BioSequence Property Set ID	int	4	0	N		Y							N	N				pkDEFAULT
PR_biosequence_property_set	2	biosequence_id	BioSequence ID	int	4	0	N		N	PR_biosequence	biosequence_id					N	N	Y	Biosequence to which this Biosequence property set belongs		pkDEFAULT
PR_biosequence_property_set	3	n_transmembrane_regions	Number of Transmembrane Regions	int	4	0	Y		N							Y	Y	N	Number of transmembrane regions		pkDEFAULT
PR_biosequence_property_set	4	transmembrane_class	Transmembrane Region Class	varchar	10	0	Y		N			Y	text	50		Y	Y	N	"Class of the transmembrane region.  May be 0, TM, A, S, TM_xS based on output from TMHMM and signalP"		
PR_biosequence_property_set	5	transmembrane_topology	Transmembrane Region Topology	varchar	1024	0	Y		N			Y	text	20		Y	Y	N	Coding of which residues belong in the transmembrane regions		
PR_biosequence_property_set	6	has_signal_peptide	Has a Signal Peptide	char	1	0	Y		N			N	text	50		Y	Y	N	"Does this protein have a signal peptide on the end Y/N? (Note that Y means that there is some non-zero probability that it does, not that is necessarily does)"		
PR_biosequence_property_set	7	has_signal_peptide_probability	Probability that it has a Signal Peptide	real	4	0	Y		N			N	text	50		Y	Y	N	Probability that there is a signal peptide on the end as calculated by SignalP		
PR_biosequence_property_set	8	signal_peptide_length	Length of the Signal Peptide	int	4	0	Y		N			N	text	50		Y	Y	N	Length in residues of the signal peptide		
PR_biosequence_property_set	9	signal_peptide_is_cleaved	Signal Peptide gets Cleaved	char	1	0	Y		N			N	text	50		Y	Y	N	Does the signal peptide get cleaved off Y/N?		
PR_biosequence_property_set	10	genome_build	Genome Build	varchar	50	0	Y		N			N	text	50		Y	Y	N	Genome build name for which the following mapping parameters are valid		
PR_biosequence_property_set	11	chromosome	Chromosome	varchar	50	0	Y		N			N	text	50		Y	Y	N	Chromosome in which this mapping occurs		
PR_biosequence_property_set	12	start_in_chromosome	Start Position in Chromosome	int	4	0	Y		N			N	text	20		Y	Y	N	Start position of the biosequence in the chromosome		
PR_biosequence_property_set	13	end_in_chromosome	End Position in Chromosome	int	4	0	Y		N			N	text	20		Y	Y	N	End position of the biosequence in the chromosome		
PR_biosequence_property_set	14	strand	Strand	char	1	0	Y		N			N	text	10		Y	Y	N	"Strand (+,-) of the biosequence in the chromosome"		
PR_biosequence_property_set	15	isoelectric_point	Isoelectric Point	real	4	0	Y		N			N	text	10		Y	Y	N	Isoelectric Point (pI) of the protein		
PR_biosequence_property_set	16	fav_codon_frequency	Favorite Codon Frequency	real	4	0	Y		N			N	text	10		Y	Y	N	Favorite Codon Frequency		
PR_biosequence_property_set	17	duplicate_biosequences	Duplicate Biosequences	varchar	255	0	Y		N			N	text	50		Y	Y	N	Semicolon delimited list of duplicate sequences within the same set		
PR_biosequence_property_set	18	category	Category	varchar	255	0	Y		N			N	text	50		Y	Y	N	Biosequence category		
PR_biosequence_annotation	1	biosequence_annotation_id	Domain Match Type	int	4	0	N		Y							N	N				pkDEFAULT
PR_biosequence_annotation	2	biosequence_id	BioSequence	int	4	0	N		N	PR_biosequence	biosequence_id	Y	fixed			Y	Y	Y	BioSequence to which this annotation belongs		
PR_biosequence_annotation	3	gene_symbol	Gene Symbol	varchar	255	0	Y		N			N	text	50		Y	Y	N	Gene Symbol to describe this protein (e.g. TLR2)		
PR_biosequence_annotation	4	full_gene_name	Full Gene Name	varchar	255	0	Y		N			N	text	50		Y	Y	N	Full name of the gene (e.g. Toll-like Receptor 2)		
PR_biosequence_annotation	5	aliases	BioSequence Aliases	varchar	255	0	Y		N			N	text	50		Y	Y	N	Aliases of this BioSequence.  These are stored as a semi-colon delimited string		
PR_biosequence_annotation	6	former_names	Former BioSequence Names	varchar	255	0	Y		N			N	text	50		Y	Y	N	Former Aliases of this BioSequence.  These are stored as a colon-delimited string		
PR_biosequence_annotation	7	functional_description	Functional Description	text	16	0	Y		N			N	textarea	3		Y	Y	N	Functional description of the protein		
PR_biosequence_annotation	8	EC_numbers	EC Numbers	varchar	255	0	Y		N			N	text	50		Y	Y	N	EC Number(s) that corresponds to this domain.  Separate multiple numbers with a semicolon		
PR_biosequence_annotation	9	biosequence_type	Biosequence Type	varchar	255	0	Y		N			N	text	50		Y	Y	N	Further annotation of biosequence type		
PR_biosequence_annotation	10	category	Category	varchar	255	0	Y		N			N	text	50		Y	Y	N	Category		
PR_biosequence_annotation	11	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
PR_biosequence_annotation	12	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_biosequence_annotation	13	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_biosequence_annotation	14	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_biosequence_annotation	15	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_biosequence_annotation	16	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
PR_biosequence_annotation	17	record_status	Record Status	char	1	0	N	N	N							N	N				
PR_search_batch	1	search_batch_id	Search Batch ID	int	4	0	N		Y							N	N				pkDEFAULT
PR_search_batch	2	experiment_id	Experiment ID	int	4	0	N		N	PR_proteomics_experiment	experiment_id	Y				Y	Y	Y	Experiment to which this search batch belongs		
PR_search_batch	3	biosequence_set_id	BioSequence Set	int	4	0	N		N	PR_biosequence_set	biosequence_set_id	Y				Y	Y	Y	BioSequence Set against which this batch was searched		pkDEFAULT
PR_search_batch	4	data_location	Data Location	varchar	255	0	N		N			Y	text	50		Y	Y	N	Absolute or relative location of the raw data for this search batch		
PR_search_batch	5	search_batch_subdir	Search Batch Subdirectory	varchar	100	0	N		N			Y	text	50		Y	Y	Y	Subdirectory under the experiment where the data for this search resides		
PR_search_batch_parameter	1	search_batch_id	Search Batch ID	int	4	0	N		N	PR_search_batch	search_batch_id					N	N	Y	Search batch to which this search parameter belongs		pkDEFAULT
PR_search_batch_parameter	2	key_order	Key Order	int	4	0	N		N			Y				Y	Y	N	Monotonically increasing number to denote key order		
PR_search_batch_parameter	3	parameter_key	Parameter Key	varchar	100	0	N		N			Y	text	50		Y	Y	Y	The key of the key/value pair		
PR_search_batch_parameter	4	parameter_value	Parameter Value	varchar	255	0	N		N			Y	text	50		Y	Y	N	The value of the key/value pair		
PR_search_batch_parameter_set	1	search_batch_id	Search Batch ID	int	4	0	N		Y	PR_search_batch	search_batch_id					N	N	Y	Search batch to which this set of search parameters belong		pkDEFAULT
PR_search_batch_parameter_set	2	peptide_mass_tolerance	Peptide Mass Tolerance	varchar	100	0	N		N			Y	text	50		Y	Y	N	Peptide Mass Tolerance		
PR_search_batch_parameter_set	3	peptide_ion_tolerance	Peptide Ion Tolerance	varchar	100	0	N		N			Y	text	50		Y	Y	N	Peptide Ion Tolerance		
PR_search_batch_parameter_set	4	etc	and many more	varchar	100	0	N		N			Y	text	50		Y	Y	N	This table is a an unfinished placeholder for a pivoted version of search_batch_parameter.  It will be finished when it seems important to do so.		
PR_search	1	search_id	Search ID	int	4	0	N		Y							N	N				pkDEFAULT
PR_search	2	search_batch_id	Search Batch ID	int	4	0	N		N	PR_search_batch	search_batch_id	Y	fixed			Y	Y	Y	Search Batch to which this search belongs		
PR_search	3	msms_spectrum_id	MS/MS Spectrum ID	int	4	0	N		N	PR_msms_spectrum	msms_spectrum_id	Y	fixed			Y	Y	Y	MS/MS Spectrum that was searched		pkDEFAULT
PR_search	4	file_root	File Root	varchar	255	0	N		N			Y	text	50		Y	Y	N	Root of the filename that was searched.  This is usually in the format of basename.startscan.endscan.assumedcharge		
PR_search	5	start_scan	Start Scan	int	4	0	N		N			Y	text	10		Y	Y	N	Starting scan number		
PR_search	6	end_scan	End Scan	int	4	0	N		N			Y	text	10		Y	Y	N	Ending scan number		
PR_search	7	sample_mass_plus_H	Sample (M+H)+	float	8	0	N		N			Y	text	10		Y	Y	N	Observed mass (M+H)+		
PR_search	8	assumed_charge	Assumed Charge	int	4	0	N		N			Y	text	10		Y	Y	N	Assumed charged for this search (since charge may be unknown)		
PR_search	9	total_intensity	Total Spectrum Intensity	real	4	0	N		N			Y	text	10		Y	Y	N	Total intensity of the spectrum		
PR_search	10	matched_peptides	Number of Matched Peptides	int	4	0	N		N			Y	text	10		Y	Y	N	Number of matched peptides for this search		
PR_search	11	lowest_prelim_score	Lowest Preliminary Score	real	4	0	N		N			Y	text	10		Y	Y	N	Lowest preliminary score by Sequest		
PR_search	12	search_date	Search Date	datetime	8	0	N		N			Y	text	20		Y	Y	N	Date the the spectrum was searched		
PR_search	13	search_elapsed_min	Search Time in Minutes	real	4	0	N		N			Y	text	10		Y	Y	N	Length of time in minutes for the search to complete		
PR_search	14	search_host	Search Hostname	varchar	50	0	N		N			Y	text	50		Y	Y	N	Hostname on which the search was performed		
PR_search_hit	1	search_hit_id	Search Hit ID	int	4	0	N		Y							N	N		Search Hit ID		pkDEFAULT
PR_search_hit	2	search_id	Search ID	int	4	0	N		N	PR_search	search_id					Y	Y	Y	Search ID to which this hit belongs		
PR_search_hit	3	hit_index	Hit Index	int	4	0	N		N							Y	Y	Y	Index number of this hit to denote the order		
PR_search_hit	4	cross_corr_rank	Cross Correlation Rank	int	4	0	N		N							Y	Y	N	Cross Correlation Rank		
PR_search_hit	5	prelim_score_rank	Preliminary Score Rank	int	4	0	N		N							Y	Y	N	Preliminary Score Rank		
PR_search_hit	6	hit_mass_plus_H	Hit (M+H)+	float	8	0	N		N							Y	Y	N	Hit (M+H)+		
PR_search_hit	7	mass_delta	Mass Delta	real	4	0	N		N							Y	Y	N	Mass Delta
PR_search_hit	8	cross_corr	Cross Correlation Score	real	4	0	N		N							Y	Y	N	Cross Correlation Score
PR_search_hit	9	norm_corr_delta	Normalized Correlation Score Delta	real	4	0	N		N							Y	Y	N	Normalized Correlation Score Delta
PR_search_hit	10	prelim_score	Preliminary Score	real	4	0	N		N							Y	Y	N	Preliminary Score
PR_search_hit	11	identified_ions	Number of Identified Ions	int	4	0	N		N							Y	Y	N	Number of Identified Ions
PR_search_hit	12	total_ions	Total Number of Predicted Ions	int	4	0	N		N							Y	Y	N	Total Number of Predicted Ions
PR_search_hit	13	reference	Reference (Protein)	varchar	100	0	N		N							Y	Y	N	Reference (Protein)
PR_search_hit	14	biosequence_id	BioSequence ID	int	4	0	Y		N	PR_biosequence	biosequence_id					Y	Y	N	BioSequence ID
PR_search_hit	15	best_hit_flag	Best Hit Flag	char	1	0	Y		N							Y	Y	N	Best Hit Flag
PR_search_hit	16	additional_proteins	Number of Additional Proteins	int	4	0	N		N							Y	Y	N	Number of Additional Proteins
PR_search_hit	17	peptide	Peptide	varchar	100	0	Y		N							Y	Y	N	Peptide
PR_search_hit	18	peptide_string	Peptide String	varchar	100	0	Y		N							Y	Y	N	Peptide String
PR_search_hit	19	next_dCn	Next Cross Correlation Delta	real	4	0	Y		N							Y	Y	N	Next Cross Correlation Delta
PR_search_hit	20	isoelectric_point	Calculated Isoelectric Point	real	4	0	Y		N							Y	Y	N	Calculated Isoelectric Point
PR_search_hit	21	molecular_weight	Molecular Weight	real	4	0	Y		N							Y	Y	N	Molecular Weight
PR_search_hit	22	probability	Probability	real	4	0	Y		N							Y	Y	N	Probability
PR_search_hit	23	f_score	F Score	real	4	0	Y		N							Y	Y	N	F Score		
PR_search_hit	24	gravy_score	Gravy Score	real	4	0	Y		N							Y	Y	N	Gravy Score		
PR_search_hit_protein	1	search_hit_protein_id	Search Hit Protein ID	int	4	0	N		Y							N	N		Search Hit Protein ID		pkDEFAULT
PR_search_hit_protein	2	search_hit_id	Search Hit ID	int	4	0	N		N	PR_search_hit	search_hit_id					Y	Y	Y	Search Hit ID to which this duplicate protein belongs		
PR_search_hit_protein	3	reference	Reference (Protein)	varchar	100	0	N		N							Y	Y	Y	Reference (Protein)		
PR_search_hit_protein	4	biosequence_id	BioSequence ID	int	4	0	Y		N	PR_biosequence	biosequence_id					Y	Y	N	BioSequence ID		
PR_quantitation	1	quantitation_id	Quantitation ID	int	4	0	N		Y							N	N		Quantitation ID		pkDEFAULT
PR_quantitation	2	search_hit_id	Search Hit ID	int	4	0	N		N	PR_search_hit	search_hit_id					Y	Y	Y	Search Hit ID		
PR_quantitation	3	d0_intensity	d0 Intensity	real	4	0	Y		N							Y	Y	N	d0 Intensity		
PR_quantitation	4	d8_intensity	d8 Intensity	real	4	0	Y		N							Y	Y	N	d8 Intensity		
PR_quantitation	5	d0_first_scan	d0 First Scan	int	4	0	N		N							Y	Y	N	d0 First Scan		
PR_quantitation	6	d0_last_scan	d0 Last Scan	int	4	0	N		N							Y	Y	N	d0 Last Scan		
PR_quantitation	7	d0_mass	d0 Mass	real	4	0	Y		N							Y	Y	N	d0 Mass		
PR_quantitation	8	d8_first_scan	d8 First Scan	int	4	0	N		N							Y	Y	N	d8 First Scan		
PR_quantitation	9	d8_last_scan	d8 Last Scan	int	4	0	N		N							Y	Y	N	d8 Last Scan		
PR_quantitation	10	d8_mass	d8 Mass	real	4	0	Y		N							Y	Y	N	d8 Mass		
PR_quantitation	11	norm_flag	Normalization Flag	int	4	0	Y		N							Y	Y	N	Normalization Flag		
PR_quantitation	12	mass_tolerance	Mass Tolerance	real	4	0	Y		N							Y	Y	N	Mass Tolerance		
PR_quantitation	13	quality_score	Quality Score	real	4	0	Y		N							Y	Y	N	Quality Score		
PR_quantitation	14	manually_changed	Is Manually Changed?	varchar	5	0	Y		N							Y	Y	N	Is Manually Changed?		
PR_quantitation	15	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N		Date Record Created		
PR_quantitation	16	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N		Record Created By		
PR_quantitation	17	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N		Date Record Modified		
PR_quantitation	18	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N		Record Modified By		
PR_quantitation	19	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N		Owner Group ID		
PR_quantitation	20	record_status	Record Status	char	1	0	N	N	N							N	N		Record Status		
PR_search_hit_annotation	1	search_hit_annotation_id	Search Hit Annotation	int	4	0	N		Y							N	N				pkDEFAULT
PR_search_hit_annotation	2	search_hit_id	Search Hit ID	int	4	0	N		N	PR_search_hit	search_hit_id	Y	fixed			Y	Y	Y	Database ID for the Search Hit to be annotated		
PR_search_hit_annotation	3	annotation_label_id	Annotation Label	int	4	0	N		N	PR_annotation_label	annotation_label_id	Y	scrolloptionlist	6		Y	Y	N	Annotation label to associate with this Search Hit.  A description of how sure the annotater is that this is a correct peptide identification	"SELECT annotation_label_id,label_desc FROM $TBPR_ANNOTATION_LABEL ORDER BY sort_order,label_desc"	
PR_search_hit_annotation	4	annotation_confidence_id	Annotation Confidence	int	4	0	N		N	PR_annotation_confidence	annotation_confidence_id	Y	scrolloptionlist	5		Y	Y	N	Confidence in the above labeling	"SELECT annotation_confidence_id,confidence_desc FROM $TBPR_ANNOTATION_CONFIDENCE ORDER BY sort_order,confidence_desc"	
PR_search_hit_annotation	5	annotation_source_id	Annotation Source	int	4	0	N		N	PR_annotation_source	annotation_source_id	Y	fixedfromlist			Y	Y	N	Source from which this annotation came	"SELECT annotation_source_id,source_desc FROM $TBPR_ANNOTATION_SOURCE ORDER BY sort_order,source_desc"	
PR_search_hit_annotation	6	user_annotation_label_id	User-defined Annotation Label	int	4	0	Y		N	PR_user_annotation_label	user_annotation_label_id	N	scrolloptionlist	6		Y	Y	N	User-defined annotation label to associate with this Search Hit.  This is project-specific	"SELECT user_annotation_label_id,user_annotation_tag FROM $TBPR_USER_ANNOTATION_LABEL WHERE project_id='$project_id' AND record_status !='D' ORDER BY sort_order,user_annotation_tag"	
PR_search_hit_annotation	7	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
PR_search_hit_annotation	8	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_search_hit_annotation	9	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_search_hit_annotation	10	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_search_hit_annotation	11	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_search_hit_annotation	12	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
PR_search_hit_annotation	13	record_status	Record Status	char	1	0	N	N	N							N	N				
PR_annotation_source	1	annotation_source_id	Annotation Source ID	int	4	0	N		Y							N	N				pkDEFAULT
PR_annotation_source	2	source_desc	Annotation Source Name	varchar	100	0	N		N			Y	text	50		Y	Y	Y	Short description of this annotation source		
PR_annotation_source	3	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
PR_annotation_source	4	sort_order	Sort Order	int	4	0	N	10	N							N	N	N	Integer that controls sorting order of the list in a list box		
PR_annotation_source	5	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_annotation_source	6	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_annotation_source	7	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_annotation_source	8	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_annotation_source	9	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
PR_annotation_source	10	record_status	Record Status	char	1	0	N	N	N							N	N				
PR_annotation_label	1	annotation_label_id	Annotation Label ID	int	4	0	N		Y							N	N				pkDEFAULT
PR_annotation_label	2	label_desc	Annotation Label Name	varchar	100	0	N		N			Y	text	50		Y	Y	Y	Short description of this annotation label		
PR_annotation_label	3	annotation_probability	Annotation Probability	real	4	0	Y		N			Y	text	10		Y	Y	N	Probability value for label		
PR_annotation_label	4	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
PR_annotation_label	5	sort_order	Sort Order	int	4	0	N	10	N							N	N	N	Integer that controls sorting order of the list in a list box		
PR_annotation_label	6	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_annotation_label	7	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_annotation_label	8	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_annotation_label	9	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_annotation_label	10	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
PR_annotation_label	11	record_status	Record Status	char	1	0	N	N	N							N	N				
PR_annotation_confidence	1	annotation_confidence_id	Annotation Confidence ID	int	4	0	N		Y							N	N				pkDEFAULT
PR_annotation_confidence	2	confidence_desc	Annotation Confidence Name	varchar	100	0	N		N			Y	text	50		Y	Y	Y	Short description of this annotation confidence label		
PR_annotation_confidence	3	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
PR_annotation_confidence	4	sort_order	Sort Order	int	4	0	N	10	N							N	N	N	Integer that controls sorting order of the list in a list box		
PR_annotation_confidence	5	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_annotation_confidence	6	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_annotation_confidence	7	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_annotation_confidence	8	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_annotation_confidence	9	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
PR_annotation_confidence	10	record_status	Record Status	char	1	0	N	N	N							N	N				
PR_user_annotation_label	1	user_annotation_label_id	User Annotation Label ID	int	4	0	N		Y							N	N				pkDEFAULT
PR_user_annotation_label	2	project_id	Project	int	4	0	N		N	project	project_id	Y	optionlist			Y	Y	Y	Project to which the annotation belongs	"SELECT project_id, name FROM $TB_PROJECT WHERE record_status != 'D' ORDER BY name"	
PR_user_annotation_label	3	user_annotation_tag	Annotation Tag	varchar	100	0	N		N			Y	text	20		Y	Y	Y	Tag for this user annotation.  A tag should be a short (~10 letter) name that makes this category easily recognizable in a table of data		
PR_user_annotation_label	4	user_annotation_desc	Annotation Description	varchar	255	0	N		N			Y	text	50		Y	Y	N	One-line description of this user annotation		
PR_user_annotation_label	5	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
PR_user_annotation_label	6	sort_order	Sort Order	int	4	0	N	10	N							N	N	N			
PR_user_annotation_label	7	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_user_annotation_label	8	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_user_annotation_label	9	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_user_annotation_label	10	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_user_annotation_label	11	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
PR_user_annotation_label	12	record_status	Record Status	char	1	0	N	N	N							N	N				
PR_instrument_type	1	instrument_type_id	Instrument Type ID	int	4	0	N		Y							N	N				pkDEFAULT
PR_instrument_type	2	instrument_type_name	Instrument Type Name	varchar	100	0	N		N			Y	text	20		Y	Y	Y	Short name of this instrument type as it will appear in list boxes		
PR_instrument_type	3	instrument_type_description	Instrument Type Description	varchar	255	0	N		N			Y	text	50		Y	Y	N	More complete description of this instrument type		
PR_instrument_type	4	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
PR_instrument_type	5	sort_order	Sort Order	int	4	0	N	10	N			N	text	10		Y	Y	N	Numbers which override alphabetical sorting in a list box		
PR_instrument_type	6	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_instrument_type	7	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_instrument_type	8	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_instrument_type	9	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_instrument_type	10	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
PR_instrument_type	11	record_status	Record Status	char	1	0	N	N	N							N	N				
PR_instrument	1	instrument_id	Instrument ID	int	4	0	N		Y							N	N				pkDEFAULT
PR_instrument	2	instrument_type_id	Instrument Type	int	4	0	N		N	PR_instrument_type	instrument_type_id	Y	optionlist			Y	Y	N	Type of Instrument	"SELECT instrument_type_id,instrument_type_name FROM $TBPR_INSTRUMENT_TYPE ORDER BY sort_order,instrument_type_name"	
PR_instrument	3	instrument_name	Instrument Name	varchar	100	0	N		N			Y	text	30		Y	Y	Y	Short name of this instrument as it will appear in list boxes		
PR_instrument	4	instrument_description	Instrument Description	varchar	255	0	N		N			Y	text	60		Y	Y	N	More complete description of this instrument		
PR_instrument	5	comment	Comment	text	16	0	Y		N			N	textarea	10		Y	Y	N	Additional comments		
PR_instrument	6	sort_order	Sort Order	int	4	0	N	10	N			N	text	10		Y	Y	N	Numbers which override alphabetical sorting in a list box		
PR_instrument	7	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_instrument	8	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_instrument	9	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_instrument	10	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_instrument	11	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
PR_instrument	12	record_status	Record Status	char	1	0	N	N	N							N	N				
PR_experiment_type	1	experiment_type_id	Experiment Type ID	int	4	0	N		Y							N	N				pkDEFAULT
PR_experiment_type	2	experiment_type_name	Experiment Type Name	varchar	100	0	N		N			Y	text	20		Y	Y	Y	Short name of this experiment type as it will appear in list boxes		
PR_experiment_type	3	experiment_type_description	Experiment Type Description	varchar	255	0	N		N			Y	text	50		Y	Y	N	More complete description of this experiment type		
PR_experiment_type	4	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
PR_experiment_type	5	sort_order	Sort Order	int	2	0	N	10	N			N	text	10		Y	Y	N	Numbers which override alphabetical sorting in a list box		
PR_experiment_type	6	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_experiment_type	7	created_by_id	Record Created By	int	2	0	N	1	N	contact	contact_id					N	N				
PR_experiment_type	8	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_experiment_type	9	modified_by_id	Record Modified By	int	2	0	N	1	N	contact	contact_id					N	N				
PR_experiment_type	10	owner_group_id	Owner Group ID	int	2	0	N	1	N	work_group	work_group_id					N	N				
PR_experiment_type	11	record_status	Record Status	char	1	0	N	N	N							N	N				
PR_request_status	1	request_status_id	Request Status ID	int	2	0	N		Y							N	N				pkDEFAULT
PR_request_status	2	request_status_name	Request Status Name	varchar	100	0	N		N			Y	text	20		Y	Y	Y	Short name of this request status as it will appear in list boxes		
PR_request_status	3	request_status_description	Request Status Description	varchar	255	0	N		N			Y	text	50		Y	Y	N	More complete description of this request status		
PR_request_status	4	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
PR_request_status	5	sort_order	Sort Order	int	2	0	N	10	N			Y	text	10		Y	Y	N	Numbers which override alphabetical sorting in a list box		
PR_request_status	6	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_request_status	7	created_by_id	Record Created By	int	2	0	N	1	N	contact	contact_id					N	N				
PR_request_status	8	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_request_status	9	modified_by_id	Record Modified By	int	2	0	N	1	N	contact	contact_id					N	N				
PR_request_status	10	owner_group_id	Owner Group ID	int	2	0	N	1	N	work_group	work_group_id					N	N				
PR_request_status	11	record_status	Record Status	char	1	0	N	N	N							N	N				
PR_funding_status	1	funding_status_id	Funding Status ID	int	2	0	N		Y							N	N				pkDEFAULT
PR_funding_status	2	funding_status_name	Funding Status Name	varchar	100	0	N		N			Y	text	20		Y	Y	Y	Short name of this funding status as it will appear in list boxes		
PR_funding_status	3	funding_status_description	Funding Status Description	varchar	255	0	N		N			Y	text	50		Y	Y	N	More complete description of this funding status		
PR_funding_status	4	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
PR_funding_status	5	sort_order	Sort Order	int	4	0	N	10	N			Y	text	10		Y	Y	N	Numbers which override alphabetical sorting in a list box		
PR_funding_status	6	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_funding_status	7	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_funding_status	8	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_funding_status	9	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_funding_status	10	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
PR_funding_status	11	record_status	Record Status	char	1	0	N	N	N							N	N				
PR_proteomics_experiment_request	1	experiment_request_id	Experiment Request ID	int	4	0	N		Y							N	N				pkDEFAULT
PR_proteomics_experiment_request	2	contact_id	Requesting Contact	int	4	0	N		N	contact	contact_id	Y	current_contact_id	 		Y	Y	N	Requestor of this experiment		
PR_proteomics_experiment_request	3	PI_contact_id	PI Contact	int	4	0	N		N	contact	contact_id	Y	scrolloptionlist	4		Y	Y	N	PI for this experiment	"SELECT contact_id, last_name+', '+first_name+' ('+organization+')' AS 'name' FROM $TB_CONTACT C JOIN $TB_ORGANIZATION O ON ( C.organization_id = O.organization_id ) ORDER BY last_name,first_name,organization"	
PR_proteomics_experiment_request	4	project_id	Project	int	4	0	N		N	project	project_id	Y	optionlist			Y	Y	N	Project to which the experiment belongs	"SELECT project_id, name + ' ['+budget+']' FROM $TB_PROJECT WHERE PI_contact_id='$contact_id' ORDER BY name"	
PR_proteomics_experiment_request	5	funding_status_id	Funding Status	int	4	0	N		N	PR_funding_status	funding_status_id	Y	optionlist			Y	Y	N	Select the funding status for this experiment or the project with which it is associated	"SELECT funding_status_id,funding_status_name FROM $TBPR_FUNDING_STATUS ORDER BY sort_order,funding_status_name"	
PR_proteomics_experiment_request	6	budget_number	Budget Number	varchar	20	0	N		N			Y	text	20		Y	Y	N	Budget Number which is funding this experiment.  Enter NA if none.  Unfunded experiments must be cleared with Dave Goodlett prior to submission		
PR_proteomics_experiment_request	7	experiment_name	Experiment Title	varchar	100	0	N		N			Y	text	50		Y	Y	N	Title of this experiment	
PR_proteomics_experiment_request	8	experiment_tag	Experiment Tag	varchar	20	0	N		N			Y	text	20		Y	Y	Y	Short tag (name) of this experiment	
PR_proteomics_experiment_request	9	experiment_description	Experiment Description	varchar	255	0	N		N			Y	text	50		Y	Y	N	One-line description of this experiment	
PR_proteomics_experiment_request	10	organism_id	Sample Organism	int	4	0	N		N	organism	organism_id	Y	optionlist			Y	Y	N	Organism from which the sample used for this experiment was derived	"SELECT organism_id, organism_name FROM $TB_ORGANISM ORDER BY sort_order,organism_name"
PR_proteomics_experiment_request	11	experiment_type_id	Experiment Type	int	4	0	N		N	PR_experiment_type	experiment_type_id	Y	optionlist			Y	Y	N	Type of Experiment	"SELECT experiment_type_id,experiment_type_name FROM $TBPR_EXPERIMENT_TYPE ORDER BY sort_order,experiment_type_name"
PR_proteomics_experiment_request	12	instrument_type_id	Instrument Type	int	4	0	N		N	PR_instrument_type	instrument_type_id	Y	optionlist			Y	Y	N	Type of Instrument	"SELECT instrument_type_id,instrument_type_name FROM $TBPR_INSTRUMENT_TYPE ORDER BY sort_order,instrument_type_name"
PR_proteomics_experiment_request	13	initial_search_set_id	Initial Search Set	int	4	0	N		N	PR_biosequence_set	biosequence_set_id	Y	optionlist			Y	Y	N	Select the initial BioSequenceSet ('database') against which SEQUEST should be run	"SELECT biosequence_set_id,set_path FROM $TBPR_BIOSEQUENCE_SET ORDER BY set_path"
PR_proteomics_experiment_request	14	number_of_runs	Number of LCMS runs	varchar	50	0	N		N			Y	text	20		Y	Y	N	"Number of LC/MS runs for this experiment/sample (e.g., 30-50 SCX fractions is typical)"	
PR_proteomics_experiment_request	15	other1_contact_id	Other Contact	int	4	0	N		N	contact	contact_id	N	scrolloptionlist	4		Y	Y	N	You may specify another contact for this experiment.  Confirmation/completion emails will be sent to this person	"SELECT contact_id, last_name+', '+first_name+' ('+organization+')' AS 'name' FROM $TB_CONTACT C JOIN $TB_ORGANIZATION O ON ( C.organization_id = O.organization_id ) ORDER BY last_name,first_name,organization"
PR_proteomics_experiment_request	16	other2_contact_id	Other Contact 2	int	4	0	N		N	contact	contact_id	N	scrolloptionlist	4		Y	Y	N	You may specify another contact for this experiment.  Confirmation/completion emails will be sent to this person	"SELECT contact_id, last_name+', '+first_name+' ('+organization+')' AS 'name' FROM $TB_CONTACT C JOIN $TB_ORGANIZATION O ON ( C.organization_id = O.organization_id ) ORDER BY last_name,first_name,organization"
PR_proteomics_experiment_request	17	request_status_id	Request Status	int	4	0	N		N	PR_request_status	request_status_id	Y	optionlist			Y	Y	N	Status of this request	"SELECT request_status_id,request_status_name FROM $TBPR_REQUEST_STATUS ORDER BY sort_order,request_status_name"
PR_proteomics_experiment_request	18	comment	Comment	text	16	0	Y		N			N	textarea	8		Y	Y	N	Additional comments or notes about this submission or how the experiment should be processed	
PR_proteomics_experiment_request	19	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N			
PR_proteomics_experiment_request	20	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N			
PR_proteomics_experiment_request	21	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N			
PR_proteomics_experiment_request	22	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N			
PR_proteomics_experiment_request	23	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
PR_proteomics_experiment_request	24	record_status	Record Status	char	1	0	N	N	N							N	N				
PR_processing_status	1	processing_status_id	Processing Status ID	int	4	0	N		Y							N	N				pkDEFAULT
PR_processing_status	2	status_tag	Status Tag	varchar	50	0	N		N			Y	text	20		Y	Y	Y	Short tag (name) of this Status entry		
PR_processing_status	3	status_description	Status Description	varchar	255	0	N		N			Y	text	50		Y	Y	N	Longer description of this Status entry		
PR_processing_status	4	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
PR_processing_status	5	sort_order	Sort Order	int	4	0	N	10	N			N	text	10		Y	Y	N	Numbers which override alphabetical sorting in a list box		
PR_processing_status	6	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_processing_status	7	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_processing_status	8	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_processing_status	9	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_processing_status	10	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
PR_processing_status	11	record_status	Record Status	char	1	0	N	N	N							N	N				
PR_raw_data_file	1	raw_data_file_id	Raw Data File ID	int	4	0	N		Y							N	N				pkDEFAULT
PR_raw_data_file	2	file_name	File Name	varchar	255	0	N		N			Y	text	50		Y	Y	Y	Name of the raw data file (no path information)		
PR_raw_data_file	3	file_path	File Path	varchar	255	0	N		N			Y	text	50		Y	Y	N	Current direcotory/folder path of the raw data file		
PR_raw_data_file	4	processing_status_id	Processing Status	int	4	0	N		N			Y	optionlist			Y	Y	N	Current status of the file	"SELECT processing_status_id,status_tag FROM $TBPR_PROCESSING_STATUS ORDER BY sort_order,status_tag"	
PR_raw_data_file	5	file_status_message	File Status Message	varchar	255	0	Y		N			N	text	50		Y	Y	N	Additional message regarding the status of the file		
PR_raw_data_file	6	file_written_date	File Written Date	datetime	8	0	Y		N			N	text	30		Y	Y	N	Date that the file was written		
PR_raw_data_file	7	file_size	File Size	int	4	0	Y		N			N	text	20		Y	Y	N	Size of the file in bytes		
PR_raw_data_file	8	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
PR_raw_data_file	9	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_raw_data_file	10	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_raw_data_file	11	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_raw_data_file	12	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_raw_data_file	13	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
PR_raw_data_file	14	record_status	Record Status	char	1	0	N	N	N							N	N				
PR_query_option	1	query_option_id	Query Option ID	int	4	0	N		Y							N	N				pkDEFAULT
PR_query_option	2	option_type	Option Type	varchar	255	0	N		N			Y	text	50		Y	Y	Y	Type or category of this option		
PR_query_option	3	option_key	Option Key	varchar	255	0	N		N			Y	text	50		Y	Y	Y	Key for this key/value pair option		
PR_query_option	4	option_value	Option Value	varchar	255	0	Y		N			Y	text	50		Y	Y	N	Value of this key/value pair option		
PR_query_option	5	sort_order	Sort Order	int	4	0	N	10	N			N	text	10		Y	Y	N	Numbers which override alphabetical sorting in a list box		
PR_query_option	6	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N			
PR_query_option	7	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N			
PR_query_option	8	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N			
PR_query_option	9	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N			
PR_query_option	10	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N			
PR_query_option	11	record_status	Record Status	char	1	0	N	N	N							N	N			
PR_GetSearchHits	1	input_form_format	Input Form Format									N	optionlist		refreshDocument()	Y	Y	N	Options for level of detail and layout for this input form	"SELECT option_key,option_value FROM $TB_MISC_OPTION WHERE option_type = 'input_form_options' ORDER BY sort_order,option_value"
PR_GetSearchHits	2	search_batch_id	Search Batches									N	multioptionlist	4		Y	Y	N	"Select desired Experiments and Search Batches to include in query.  Multiple items may be selected.  If no items are selected, ALL experiments are searched."	MANUAL
PR_GetSearchHits	3	probability_constraint	Probability Constraint									N	text	20		Y	Y	N	"Constraint for the probability of being the correct hit.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n"""	
PR_GetSearchHits	4	annotation_status_id	Annotation status constraint									N	optionlist	 		Y	Y	N	Select desired status of annotations to include in result (I.e. display only peptides that have been annotated or have not been annotated at all; leave blank to show either)	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_annotation_status' ORDER BY sort_order,option_value"
PR_GetSearchHits	5	annotation_label_id	Annotation label constraint									N	multioptionlist	5		Y	Y	N	Select desired annotation labels to include (applies only to records that have annotations)	"SELECT annotation_label_id,label_desc FROM $TBPR_ANNOTATION_LABEL ORDER BY sort_order,label_desc"
PR_GetSearchHits	6	xcorr_charge1	XCorr for +1									N	text	20		Y	Y	N	"Constraint for the XCorr value for charge state +1.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"""	
PR_GetSearchHits	7	xcorr_charge2	XCorr for +2									N	text	20		Y	Y	N	"Constraint for the XCorr value for charge state +2.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"""	
PR_GetSearchHits	8	xcorr_charge3	XCorr for +3									N	text	20		Y	Y	N	"Constraint for the XCorr value for charge state +3.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"""	
PR_GetSearchHits	9	delta_xcorr	Delta Xcorr									N	text	20		Y	2	N	"Constraint for the difference in XCorr between the current and next hit.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"""	
PR_GetSearchHits	10	file_root_constraint	file_root Constraint									N	text	40		Y	2	N	Constraint for the file_root. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_GetSearchHits	11	best_hit_constraint	Best Hit Constraint									N	optionlist			Y	1	N	"Constraint for the best hit flag which is set to mark the best hit among the top ones.  The best hit may not be the first one, but can be set or changed"	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_best_hit_options' ORDER BY sort_order,option_value"
PR_GetSearchHits	12	xcorr_rank_constraint	XCorr Rank Constraint									N	text	40		Y	2	N	"Limit for the XCorr Rank value.  Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"""	
PR_GetSearchHits	13	charge_constraint	Charge Constraint									N	optionlist	 		Y	1	N	"Constraint for the charge states to include in the query.  If blank, all states are included"	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_charge_constraint' ORDER BY sort_order,option_value"
PR_GetSearchHits	14	reference_constraint	Reference Constraint									N	text	40		Y	1	N	Constraint for the Protein Reference. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_GetSearchHits	15	biosequence_accession_constraint	Biosequence Accession Constraint									N	text	40		Y	2	N	Constraint for the Biosequence Accession Number corresponding to the reference protein if there is one. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_GetSearchHits	16	description_constraint	Reference Description Constraint									N	text	40		Y	2	N	Constraint for the Protein Description. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_GetSearchHits	17	peptide_constraint	Peptide Constraint									N	text	40		Y	2	N	Constraint for the peptide (regardless of modifications). '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_GetSearchHits	18	peptide_string_constraint	Peptide String Constraint									N	text	40		Y	2	N	Constraint for the peptide string (including modifications and neighboring AAs). '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_GetSearchHits	19	peptide_options	Peptide Options									N	multioptionlist	3		Y	1	N	Various selectable options to further contrain the peptides displayed	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_peptide_options' ORDER BY sort_order,option_value"
PR_GetSearchHits	20	precursor_mass_constraint	Precursor m/z constraint									N	text	40		Y	2	N	"Constraint for the observed precursor m/z (as a single decimal value).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""	
PR_GetSearchHits	21	mass_constraint	Mass constraint									N	text	40		Y	2	N	"Constraint for the theoretical peptide mass (as a single decimal value).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""	
PR_GetSearchHits	22	start_scan_constraint	Start Scan Constraint									N	text	40		Y	2	N	"Constraint for the Start Scan value.  Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"""	
PR_GetSearchHits	23	percent_buffer_b_constraint	% Buffer B (ACN) constraint									N	text	40		Y	2	N	"Constraint for the calculated Percent Buffer B (acetonitrile) (value between 0 and 100).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""	
PR_GetSearchHits	24	isoelectric_point_constraint	pI constraint									N	text	40		Y	2	N	"Constraint for the isoelectric point (pI).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""	
PR_GetSearchHits	25	quantitation_constraint	Quantitation constraint									N	text	40		Y	2	N	"Constraint for the Quantitation (ICAT ratio) as a single decimal value.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""	
PR_GetSearchHits	26	sort_order	Sort Order									N	optionlist	 		Y	Y	N	Desired display sorting order (DESC means descending: highest to lowest)	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_sort_options' ORDER BY sort_order,option_value"
PR_GetSearchHits	27	display_options	Display Options									N	multioptionlist	3		Y	Y	N	Various selectable table display options	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_display_options' ORDER BY sort_order,option_value"
PR_GetSearchHits	28	quantitation_values	Quantitation Values									N	optionlist			Y	1	N	Specify which values to use on which side of the quantitation ratio.  Normally d0/d8.  Use with caution.  This affects both the search constraints as well as display format	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_quant_values' ORDER BY sort_order,option_value"
PR_GetSearchHits	29	quantitation_format	Quantitation Format									N	optionlist			Y	1	N	Display format for the quantitation information	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_quant_format' ORDER BY sort_order,option_value"
PR_GetSearchHits	30	row_limit	Maximum Rows									N	text	10		Y	2	N	"Limit the numbers of rows displayed.  If not provided, default is 1000 rows."	
PR_GetSearch	1	search_batch_id	Search Batches									N	multioptionlist	4		Y	Y	N	"Select desired Experiments and Search Batches to include in query.  Multiple items may be selected.  If no items are selected, ALL experiments are searched."	MANUAL
PR_GetSearch	2	file_root_constraint	file_root Constraint									N	text	40		Y	Y	N	Constraint for the file_root. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_GetSearch	3	sort_order	Sort Order									N	optionlist	 		Y	Y	N	Desired display sorting order (DESC means descending: highest to lowest)	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_sort_options' ORDER BY sort_order,option_value"
PR_GetSearch	4	row_limit	Maximum Rows									N	text	10		Y	Y	N	"Limit the numbers of rows displayed.  If not provided, default is 100 rows."	
PR_BrowseBioSequence	1	biosequence_set_id	BioSequence Sets									N	multioptionlist	4		Y	Y	N	"Select desired BioSequence Sets to include in query.  Multiple items may be selected.  If no items are selected, ALL sets are searched."	"SELECT biosequence_set_id,set_name FROM $TBPR_BIOSEQUENCE_SET ORDER BY sort_order,set_name"
PR_BrowseBioSequence	2	biosequence_name_constraint	Name Constraint									N	text	40		Y	Y	N	Constraint for the BioSequence Name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_BrowseBioSequence	3	biosequence_accession_constraint	Accession Constraint									N	text	40		Y	Y	N	Constraint for the BioSequence Accession Number. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_BrowseBioSequence	4	biosequence_gene_name_constraint	Gene Name Constraint									N	text	40		Y	Y	N	Constraint for the BioSequence Gene Name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_BrowseBioSequence	5	molecular_function_constraint	Molecular Function Constraint									N	text	40		Y	Y	N	Constraint for the GO Molecular Function. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_BrowseBioSequence	6	biological_process_constraint	Biological Process Constraint									N	text	40		Y	Y	N	Constraint for the GO Biological Process. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_BrowseBioSequence	7	cellular_component_constraint	Cellular Component Constraint									N	text	40		Y	Y	N	Constraint for the GO Cellular Component. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_BrowseBioSequence	8	protein_domain_constraint	Protein Domain Constraint									N	text	40		Y	Y	N	Constraint for the InterPro Protein Domain. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_BrowseBioSequence	9	fav_codon_frequency_constraint	Favored Codon Frequency Constraint									N	text	40		Y	Y	N	"Constraint for the favored codon frequency (calculation by Patrick Pedrioli).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n"""	
PR_BrowseBioSequence	10	transmembrane_class_constraint	Transmembrane Class Constraint									N	multioptionlist	3		Y	Y	N	Constraint for the transmembrane class as annotated by TMHMM and SignalP	"SELECT DISTINCT transmembrane_class,transmembrane_class FROM $TBPR_BIOSEQUENCE_PROPERTY_SET ORDER BY transmembrane_class"
PR_BrowseBioSequence	11	n_transmembrane_regions_constraint	Number of Transmembrane Regions Constraint									N	text	40		Y	Y	N	"Constraint for the number of transmembrane regions (based on TMHMM and SignalP calculation by rbonneau).  Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"", ""n +- n"""	
PR_BrowseBioSequence	12	biosequence_seq_constraint	Sequence Constraint									N	text	40		Y	Y	N	Constraint for the actual sequence. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_BrowseBioSequence	13	biosequence_desc_constraint	Description Constraint									N	text	40		Y	Y	N	Constraint for the BioSequence Description. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_BrowseBioSequence	14	sort_order	Sort Order									N	optionlist	 		Y	Y	N	Desired display sorting order (DESC means descending: highest to lowest)	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BBS_sort_options' ORDER BY sort_order,option_value"
PR_BrowseBioSequence	15	gene_annotation_level_constraint	Gene Annotation Level Constraint									N	optionlist			Y	2	N	"Constraint for the hierarchy level of gene annotations to view.  By default, the leaf level annotations are displayed"	"SELECT annotation_hierarchy_level_name,annotation_hierarchy_level_name FROM $TBBL_ANNOTATION_HIERARCHY_LEVEL ORDER BY annotation_hierarchy_level_id"
PR_BrowseBioSequence	16	display_options	Display Options									N	multioptionlist	3		Y	Y	N	Various selectable table display options	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BBS_display_options' ORDER BY sort_order,option_value"
PR_BrowseBioSequence	17	row_limit	Maximum Rows									N	text	10		Y	Y	N	"Limit the numbers of rows displayed.  If not provided, default is 100 rows."	
PR_CompareExperiments	1	input_form_format	Input Form Format									N	optionlist		refreshDocument()	Y	Y	N	Options for level of detail and layout for this input form	"SELECT option_key,option_value FROM $TB_MISC_OPTION WHERE option_type = 'input_form_options' ORDER BY sort_order,option_value"
PR_CompareExperiments	2	search_batch_id	Search Batches									N	multioptionlist	4		Y	Y	N	Select desired Experiments and Search Batches to compare.  You must select at least two items.	MANUAL
PR_CompareExperiments	3	probability_constraint	Probability Constraint									N	text	20		Y	Y	N	"Constraint for the probability of being the correct hit.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n"""	
PR_CompareExperiments	4	annotation_status_id	Annotation status constraint									N	optionlist	 		Y	Y	N	Select desired status of annotations to include in result (I.e. display only peptides that have been annotated or have not been annotated at all; set to blank to be insensitive to annotations)	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_annotation_status' ORDER BY sort_order,option_value"
PR_CompareExperiments	5	annotation_label_id	Annotation Labels									N	multioptionlist	5		Y	Y	N	Select desired annotation labels to include (applies only to records that have annotations)	"SELECT annotation_label_id,label_desc FROM $TBPR_ANNOTATION_LABEL ORDER BY sort_order,label_desc"
PR_CompareExperiments	6	xcorr_charge1	XCorr for +1									N	text	20		Y	Y	N	"Constraint for the XCorr value for charge state +1.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"""	
PR_CompareExperiments	7	xcorr_charge2	XCorr for +2									N	text	20		Y	Y	N	"Constraint for the XCorr value for charge state +2.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"""	
PR_CompareExperiments	8	xcorr_charge3	XCorr for +3									N	text	20		Y	Y	N	"Constraint for the XCorr value for charge state +3.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"""	
PR_CompareExperiments	9	delta_xcorr	Delta Xcorr									N	text	20		Y	2	N	"Constraint for the difference in XCorr between the current and next hit.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"""	
PR_CompareExperiments	10	file_root_constraint	file_root Constraint									N	text	40		Y	2	N	Constraint for the file_root. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_CompareExperiments	11	best_hit_constraint	Best Hit Constraint									N	optionlist			Y	1	N	"Constraint for the best hit flag which is set to mark the best hit among the top ones.  The best hit may not be the first one, but can be set or changed"	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_best_hit_options' ORDER BY sort_order,option_value"
PR_CompareExperiments	12	xcorr_rank_constraint	XCorr Rank Constraint									N	text	40		Y	2	N	"Limit for the XCorr Rank value.  Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"""	
PR_CompareExperiments	13	charge_constraint	Charge Constraint									N	optionlist	 		Y	1	N	"Constraint for the charge states to include in the query.  If blank, all states are included"	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_charge_constraint' ORDER BY sort_order,option_value"
PR_CompareExperiments	14	reference_constraint	Reference									N	text	40		Y	1	N	Constraint for the Protein Reference. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_CompareExperiments	15	description_constraint	Reference Description Constraint									N	text	40		Y	2	N	Constraint for the Protein Description. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_CompareExperiments	16	gene_name_constraint	Gene Name									N	text	40		Y	2	N	Constraint for the Gene Name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_CompareExperiments	17	molecular_function_constraint	GO Molecular Function Constraint									N	text	40		Y	2	N	Constraint for the GO Molecular Function. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_CompareExperiments	18	biological_process_constraint	GO Biological Process Constraint									N	text	40		Y	2	N	Constraint for the GO Biological Process. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_CompareExperiments	19	cellular_component_constraint	GO Cellular Component Constraint									N	text	40		Y	2	N	Constraint for the GO Cellular Component. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_CompareExperiments	20	protein_domain_constraint	Protein Domain Constraint									N	text	40		Y	2	N	Constraint for the InterPro Protein Domain. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_CompareExperiments	21	fav_codon_frequency_constraint	Favored Codon Frequency Constraint									N	text	40		Y	2	N	"Constraint for the favored codon frequency (calculation by Patrick Pedrioli).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n"""	
PR_CompareExperiments	22	transmembrane_class_constraint	Transmembrane Class Constraint									N	multioptionlist	3		Y	2	N	Constraint for the transmembrane class as annotated by TMHMM and SignalP	"SELECT DISTINCT transmembrane_class,transmembrane_class FROM $TBPR_BIOSEQUENCE_PROPERTY_SET ORDER BY transmembrane_class"
PR_CompareExperiments	23	n_transmembrane_regions_constraint	Number of Transmembrane Regions Constraint									N	text	40		Y	2	N	"Constraint for the number of transmembrane regions (based on TMHMM and SignalP calculation by rbonneau).  Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"", ""n +- n"""	
PR_CompareExperiments	24	protein_length_constraint	Protein Length Constraint									N	text	40		Y	2	N	"Constraint for the protein length.  Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"", ""n +- n"""	
PR_CompareExperiments	25	accession_constraint	Accesssion Number									N	text	40		Y	2	N	Constraint for the Accession Number. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_CompareExperiments	26	peptide_constraint	Peptide Constraint									N	text	40		Y	1	N	Constraint for the peptide (regardless of modifications). '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_CompareExperiments	27	peptide_string_constraint	Peptide String Constraint									N	text	40		Y	2	N	Constraint for the peptide string (including modifications and neighboring AAs). '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_CompareExperiments	28	peptide_options	Peptide Options									N	multioptionlist	3		Y	1	N	Various selectable options to further contrain the peptides displayed	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_peptide_options' ORDER BY sort_order,option_value"
PR_CompareExperiments	29	precursor_mass_constraint	Precursor Mass constraint									N	text	40		Y	1	N	"Constraint for the measured precursor mass (as a single decimal value).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""	
PR_CompareExperiments	30	mass_constraint	Mass constraint									N	text	40		Y	2	N	"Constraint for the theoretical peptide mass (as a single decimal value).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""	
PR_CompareExperiments	31	percent_buffer_b_constraint	% Buffer B (ACN) constraint									N	text	40		Y	2	N	"Constraint for the calculated Percent Buffer B (acetonitrile) (value between 0 and 100).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""	
PR_CompareExperiments	32	isoelectric_point_constraint	pI constraint									N	text	40		Y	2	N	"Constraint for the theoretical isoelectric point (pI).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""	
PR_CompareExperiments	33	quantitation_values	Quantitation Values									N	optionlist			Y	1	N	Specify which values to use on which side of the quantitation ratio.  Normally d0/d8.  Use with caution.  This affects both the search constraints as well as display format	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_quant_values' ORDER BY sort_order,option_value"
PR_CompareExperiments	34	quantitation_constraint	Quantitation constraint									N	text	40		Y	2	N	"Constraint for the Quantitation (ICAT ratio) as a single decimal value.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""	
PR_CompareExperiments	35	n_annotations_constraint	# of matches constraint									N	text	10		Y	2	N	"Constraint for the number of entries per row (e.g. use >0 to show only those rows that have at least one match)  Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"""	
PR_CompareExperiments	36	n_in_column_1_constraint	# in Experiment 1 constraint									N	text	10		Y	2	N	"Constraint for the number of entries per row for experiment 1 (e.g. use >0 to show only those rows that have at least one match)  Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n"""	
PR_CompareExperiments	37	n_in_column_2_constraint	# in Experiment 2 constraint									N	text	10		Y	2	N	"Constraint for the number of entries per row for experiment 2 (e.g. use >0 to show only those rows that have at least one match)  Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n"""	
PR_CompareExperiments	38	n_in_column_3_constraint	# in Experiment 3 constraint									N	text	10		Y	2	N	"Constraint for the number of entries per row for experiment 3 (e.g. use >0 to show only those rows that have at least one match)  Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n"""	
PR_CompareExperiments	39	n_in_column_4_constraint	# in Experiment 4 constraint									N	text	10		Y	2	N	"Constraint for the number of entries per row for experiment 4 (e.g. use >0 to show only those rows that have at least one match)  Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n"""	
PR_CompareExperiments	40	n_in_column_5_constraint	# in Experiment 5 constraint									N	text	10		Y	2	N	"Constraint for the number of entries per row for experiment 5 (e.g. use >0 to show only those rows that have at least one match)  Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n"""	
PR_CompareExperiments	41	n_in_column_6_constraint	# in Experiment 6 constraint									N	text	10		Y	2	N	"Constraint for the number of entries per row for experiment 6 (e.g. use >0 to show only those rows that have at least one match)  Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n"""	
PR_CompareExperiments	42	sort_order	Sort Order									N	optionlist	 		Y	Y	N	Desired display sorting order (DESC means descending: highest to lowest)	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'CE_sort_options' ORDER BY sort_order,option_value"
PR_CompareExperiments	43	gene_annotation_level_constraint	Gene Annotation Level Constraint									N	optionlist			Y	2	N	"Constraint for the hierarchy level of gene annotations to view.  By default, the leaf level annotations are displayed"	"SELECT annotation_hierarchy_level_name,annotation_hierarchy_level_name FROM $TBBL_ANNOTATION_HIERARCHY_LEVEL ORDER BY annotation_hierarchy_level_id"
PR_CompareExperiments	44	display_options	Display Options									N	multioptionlist	5		Y	Y	N	Various selectable table display options	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BAP_display_options' ORDER BY sort_order,option_value"
PR_CompareExperiments	45	row_limit	Maximum Rows									N	text	10		Y	2	N	"Limit the numbers of rows displayed.  If not provided, default is 1000 rows."	
PR_CompareMSRuns	1	input_form_format	Input Form Format									N	optionlist		refreshDocument()	Y	Y	N	Options for level of detail and layout for this input form	"SELECT option_key,option_value FROM $TB_MISC_OPTION WHERE option_type = 'input_form_options' ORDER BY sort_order,option_value"
PR_CompareMSRuns	2	search_batch_id	Search Batches									N	multioptionlist	4	refreshDocument()	Y	Y	N	Select desired Experiments and Search Batches to compare.  You must select at least two items.	MANUAL
PR_CompareMSRuns	3	fraction_id	MS Runs									N	multioptionlist	4		Y	Y	N	Select desired MS Runs to compare.  You must select at least two items.	MANUAL
PR_CompareMSRuns	4	probability_constraint	Probability Constraint									N	text	20		Y	Y	N	"Constraint for the probability of being the correct hit.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n"""	
PR_CompareMSRuns	5	annotation_status_id	Annotation status constraint									N	optionlist	 		Y	Y	N	Select desired status of annotations to include in result (I.e. display only peptides that have been annotated or have not been annotated at all; set to blank to be insensitive to annotations)	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_annotation_status' ORDER BY sort_order,option_value"
PR_CompareMSRuns	6	annotation_label_id	Annotation Labels									N	multioptionlist	5		Y	Y	N	Select desired annotation labels to include (applies only to records that have annotations)	"SELECT annotation_label_id,label_desc FROM $TBPR_ANNOTATION_LABEL ORDER BY sort_order,label_desc"
PR_CompareMSRuns	7	xcorr_charge1	XCorr for +1									N	text	20		Y	Y	N	"Constraint for the XCorr value for charge state +1.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"""	
PR_CompareMSRuns	8	xcorr_charge2	XCorr for +2									N	text	20		Y	Y	N	"Constraint for the XCorr value for charge state +2.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"""	
PR_CompareMSRuns	9	xcorr_charge3	XCorr for +3									N	text	20		Y	Y	N	"Constraint for the XCorr value for charge state +3.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"""	
PR_CompareMSRuns	10	delta_xcorr	Delta Xcorr									N	text	20		Y	2	N	"Constraint for the difference in XCorr between the current and next hit.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"""	
PR_CompareMSRuns	11	file_root_constraint	file_root Constraint									N	text	40		Y	2	N	Constraint for the file_root. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_CompareMSRuns	12	best_hit_constraint	Best Hit Constraint									N	optionlist			Y	1	N	"Constraint for the best hit flag which is set to mark the best hit among the top ones.  The best hit may not be the first one, but can be set or changed"	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_best_hit_options' ORDER BY sort_order,option_value"
PR_CompareMSRuns	13	xcorr_rank_constraint	XCorr Rank Constraint									N	text	40		Y	2	N	"Limit for the XCorr Rank value.  Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"""	
PR_CompareMSRuns	14	charge_constraint	Charge Constraint									N	optionlist	 		Y	1	N	"Constraint for the charge states to include in the query.  If blank, all states are included"	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_charge_constraint' ORDER BY sort_order,option_value"
PR_CompareMSRuns	15	reference_constraint	Reference									N	text	40		Y	1	N	Constraint for the Protein Reference. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_CompareMSRuns	16	description_constraint	Reference Description Constraint									N	text	40		Y	2	N	Constraint for the Protein Description. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_CompareMSRuns	17	gene_name_constraint	Gene Name									N	text	40		Y	2	N	Constraint for the Gene Name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_CompareMSRuns	18	molecular_function_constraint	GO Molecular Function Constraint									N	text	40		Y	2	N	Constraint for the GO Molecular Function. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_CompareMSRuns	19	biological_process_constraint	GO Biological Process Constraint									N	text	40		Y	2	N	Constraint for the GO Biological Process. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_CompareMSRuns	20	cellular_component_constraint	GO Cellular Component Constraint									N	text	40		Y	2	N	Constraint for the GO Cellular Component. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_CompareMSRuns	21	protein_domain_constraint	Protein Domain Constraint									N	text	40		Y	2	N	Constraint for the InterPro Protein Domain. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_CompareMSRuns	22	fav_codon_frequency_constraint	Favored Codon Frequency Constraint									N	text	40		Y	2	N	"Constraint for the favored codon frequency (calculation by Patrick Pedrioli).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n"""	
PR_CompareMSRuns	23	transmembrane_class_constraint	Transmembrane Class Constraint									N	multioptionlist	3		Y	2	N	Constraint for the transmembrane class as annotated by TMHMM and SignalP	"SELECT DISTINCT transmembrane_class,transmembrane_class FROM $TBPR_BIOSEQUENCE_PROPERTY_SET ORDER BY transmembrane_class"
PR_CompareMSRuns	24	n_transmembrane_regions_constraint	Number of Transmembrane Regions Constraint									N	text	40		Y	2	N	"Constraint for the number of transmembrane regions (based on TMHMM and SignalP calculation by rbonneau).  Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"", ""n +- n"""	
PR_CompareMSRuns	25	protein_length_constraint	Protein Length Constraint									N	text	40		Y	2	N	"Constraint for the protein length.  Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"", ""n +- n"""	
PR_CompareMSRuns	26	accession_constraint	Accesssion Number									N	text	40		Y	2	N	Constraint for the Accession Number. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_CompareMSRuns	27	peptide_constraint	Peptide Constraint									N	text	40		Y	1	N	Constraint for the peptide (regardless of modifications). '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_CompareMSRuns	28	peptide_string_constraint	Peptide String Constraint									N	text	40		Y	2	N	Constraint for the peptide string (including modifications and neighboring AAs). '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_CompareMSRuns	29	peptide_options	Peptide Options									N	multioptionlist	3		Y	1	N	Various selectable options to further contrain the peptides displayed	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_peptide_options' ORDER BY sort_order,option_value"
PR_CompareMSRuns	30	precursor_mass_constraint	Precursor Mass constraint									N	text	40		Y	1	N	"Constraint for the measured precursor mass (as a single decimal value).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""	
PR_CompareMSRuns	31	mass_constraint	Mass constraint									N	text	40		Y	2	N	"Constraint for the theoretical peptide mass (as a single decimal value).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""	
PR_CompareMSRuns	32	percent_buffer_b_constraint	% Buffer B (ACN) constraint									N	text	40		Y	2	N	"Constraint for the calculated Percent Buffer B (acetonitrile) (value between 0 and 100).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""	
PR_CompareMSRuns	33	isoelectric_point_constraint	pI constraint									N	text	40		Y	2	N	"Constraint for the theoretical isoelectric point (pI).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""	
PR_CompareMSRuns	34	quantitation_values	Quantitation Values									N	optionlist			Y	1	N	Specify which values to use on which side of the quantitation ratio.  Normally d0/d8.  Use with caution.  This affects both the search constraints as well as display format	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_quant_values' ORDER BY sort_order,option_value"
PR_CompareMSRuns	35	quantitation_constraint	Quantitation constraint									N	text	40		Y	2	N	"Constraint for the Quantitation (ICAT ratio) as a single decimal value.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""	
PR_CompareMSRuns	36	n_annotations_constraint	# of matches constraint									N	text	10		Y	2	N	"Constraint for the number of entries per row (e.g. use >0 to show only those rows that have at least one match)  Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"""	
PR_CompareMSRuns	37	n_in_column_1_constraint	# in Experiment 1 constraint									N	text	10		Y	2	N	"Constraint for the number of entries per row for experiment 1 (e.g. use >0 to show only those rows that have at least one match)  Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n"""	
PR_CompareMSRuns	38	n_in_column_2_constraint	# in Experiment 2 constraint									N	text	10		Y	2	N	"Constraint for the number of entries per row for experiment 2 (e.g. use >0 to show only those rows that have at least one match)  Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n"""	
PR_CompareMSRuns	39	n_in_column_3_constraint	# in Experiment 3 constraint									N	text	10		Y	2	N	"Constraint for the number of entries per row for experiment 3 (e.g. use >0 to show only those rows that have at least one match)  Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n"""	
PR_CompareMSRuns	40	n_in_column_4_constraint	# in Experiment 4 constraint									N	text	10		Y	2	N	"Constraint for the number of entries per row for experiment 4 (e.g. use >0 to show only those rows that have at least one match)  Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n"""	
PR_CompareMSRuns	41	n_in_column_5_constraint	# in Experiment 5 constraint									N	text	10		Y	2	N	"Constraint for the number of entries per row for experiment 5 (e.g. use >0 to show only those rows that have at least one match)  Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n"""	
PR_CompareMSRuns	42	n_in_column_6_constraint	# in Experiment 6 constraint									N	text	10		Y	2	N	"Constraint for the number of entries per row for experiment 6 (e.g. use >0 to show only those rows that have at least one match)  Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n"""	
PR_CompareMSRuns	43	sort_order	Sort Order									N	optionlist	 		Y	Y	N	Desired display sorting order (DESC means descending: highest to lowest)	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'CE_sort_options' ORDER BY sort_order,option_value"
PR_CompareMSRuns	44	gene_annotation_level_constraint	Gene Annotation Level Constraint									N	optionlist			Y	2	N	"Constraint for the hierarchy level of gene annotations to view.  By default, the leaf level annotations are displayed"	"SELECT annotation_hierarchy_level_name,annotation_hierarchy_level_name FROM $TBBL_ANNOTATION_HIERARCHY_LEVEL ORDER BY annotation_hierarchy_level_id"
PR_CompareMSRuns	45	display_options	Display Options									N	multioptionlist	5		Y	Y	N	Various selectable table display options	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BAP_display_options' ORDER BY sort_order,option_value"
PR_CompareMSRuns	46	row_limit	Maximum Rows									N	text	10		Y	2	N	"Limit the numbers of rows displayed.  If not provided, default is 1000 rows."	
PR_CompareBySpectrum	1	input_form_format	Input Form Format									N	optionlist		refreshDocument()	Y	Y	N	Options for level of detail and layout for this input form	"SELECT option_key,option_value FROM $TB_MISC_OPTION WHERE option_type = 'input_form_options' ORDER BY sort_order,option_value"
PR_CompareBySpectrum	2	search_batch_id	Search Batches									N	multioptionlist	4		Y	Y	N	Select desired Experiments and Search Batches to compare.  You must select at least two items.	MANUAL
PR_CompareBySpectrum	3	probability_constraint	Overall Probability Constraint									N	text	20		Y	Y	N	"Constraint for the overall probability for all values in the query of being the correct hit.  Careful about how this may conflict with the probability settings below.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n"""	
PR_CompareBySpectrum	4	file_root_constraint	file_root Constraint									N	text	40		Y	Y	N	Constraint for the file_root. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_CompareBySpectrum	5	charge_constraint	Charge Constraint									N	optionlist	 		Y	1	N	"Constraint for the charge states to include in the query.  If blank, all states are included"	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_charge_constraint' ORDER BY sort_order,option_value"
PR_CompareBySpectrum	6	precursor_mass_constraint	Precursor Mass constraint									N	text	40		Y	1	N	"Constraint for the measured precursor mass (as a single decimal value).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""	
PR_CompareBySpectrum	7	percent_buffer_b_constraint	% Buffer B (ACN) constraint									N	text	40		Y	1	N	"Constraint for the calculated Percent Buffer B (acetonitrile) (value between 0 and 100).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""	
PR_CompareBySpectrum	8	probability_in_column_1_constraint	Probability in Experiment 1 constraint									N	text	10		Y	Y	N	"Constraint for the probability for search batch 1 (e.g. use >0 to show only those rows that have at least one match)  Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n"""	
PR_CompareBySpectrum	9	probability_in_column_2_constraint	Probability in Experiment 2 constraint									N	text	10		Y	Y	N	"Constraint for the probability for search batch 2 (e.g. use >0 to show only those rows that have at least one match)  Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n"""	
PR_CompareBySpectrum	10	probability_in_column_3_constraint	Probability in Experiment 3 constraint									N	text	10		Y	Y	N	"Constraint for the probability for search batch 3 (e.g. use >0 to show only those rows that have at least one match)  Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n"""	
PR_CompareBySpectrum	11	probability_in_column_4_constraint	Probability in Experiment 4 constraint									N	text	10		Y	Y	N	"Constraint for the probability for search batch 4 (e.g. use >0 to show only those rows that have at least one match)  Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n"""	
PR_CompareBySpectrum	12	probability_in_column_5_constraint	Probability in Experiment 5 constraint									N	text	10		Y	Y	N	"Constraint for the probability for search batch 5 (e.g. use >0 to show only those rows that have at least one match)  Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n"""	
PR_CompareBySpectrum	13	probability_in_column_6_constraint	Probability in Experiment 6 constraint									N	text	10		Y	Y	N	"Constraint for the probability for search batch 6 (e.g. use >0 to show only those rows that have at least one match)  Allowed syntax: ""n"", ""> n"", "">= n"", ""< n"", ""<= n"", ""n+-n"", ""between n and n"""	
PR_CompareBySpectrum	14	display_options	Display Options									N	multioptionlist	5		Y	Y	N	Various selectable table display options	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'CBS_display_options' ORDER BY sort_order,option_value"
PR_CompareBySpectrum	15	row_limit	Maximum Rows									N	text	10		Y	2	N	"Limit the numbers of rows displayed.  If not provided, default is 1000 rows."	
PR_SummarizePeptides	1	input_form_format	Input Form Format									N	optionlist		refreshDocument()	Y	Y	N	Options for level of detail and layout for this input form	"SELECT option_key,option_value FROM $TB_MISC_OPTION WHERE option_type = 'input_form_options' ORDER BY sort_order,option_value"
PR_SummarizePeptides	2	search_batch_id	Search Batches									N	multioptionlist	4		Y	Y	N	Select desired Experiments and Search Batches to include in query.  Multiple items may be selected.  At least one must be selected	MANUAL
PR_SummarizePeptides	3	probability_constraint	Probability Constraint									N	text	20		Y	Y	N	"Constraint for the probability of being the correct hit.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n"""	
PR_SummarizePeptides	4	annotation_status_id	Annotation status constraint									N	optionlist	 		Y	Y	N	Select desired status of annotations to include in result (I.e. display only peptides that have been annotated or have not been annotated at all; set to blank to be insensitive to annotations)	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_annotation_status' ORDER BY sort_order,option_value"
PR_SummarizePeptides	5	annotation_label_id	Annotation Labels									N	multioptionlist	5		Y	Y	N	Select desired annotation labels to include (applies only to records that have annotations)	"SELECT annotation_label_id,label_desc FROM $TBPR_ANNOTATION_LABEL ORDER BY sort_order,label_desc"
PR_SummarizePeptides	6	xcorr_charge1	XCorr for +1									N	text	20		Y	Y	N	"Constraint for the XCorr value for charge state +1.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"""	
PR_SummarizePeptides	7	xcorr_charge2	XCorr for +2									N	text	20		Y	Y	N	"Constraint for the XCorr value for charge state +2.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"""	
PR_SummarizePeptides	8	xcorr_charge3	XCorr for +3									N	text	20		Y	Y	N	"Constraint for the XCorr value for charge state +3.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"""	
PR_SummarizePeptides	9	delta_xcorr	Delta Xcorr									N	text	20		Y	2	N	"Constraint for the difference in XCorr between the current and next hit.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"""	
PR_SummarizePeptides	10	file_root_constraint	file_root Constraint									N	text	40		Y	2	N	Constraint for the file_root. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_SummarizePeptides	11	best_hit_constraint	Best Hit Constraint									N	optionlist			Y	1	N	"Constraint for the best hit flag which is set to mark the best hit among the top ones.  The best hit may not be the first one, but can be set or changed"	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_best_hit_options' ORDER BY sort_order,option_value"
PR_SummarizePeptides	12	xcorr_rank_constraint	XCorr Rank Constraint									N	text	40		Y	2	N	"Limit for the XCorr Rank value.  Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"""	
PR_SummarizePeptides	13	charge_constraint	Charge Constraint									N	optionlist	 		Y	1	N	"Constraint for the charge states to include in the query.  If blank, all states are included"	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_charge_constraint' ORDER BY sort_order,option_value"
PR_SummarizePeptides	14	reference_constraint	Reference									N	text	40		Y	1	N	Constraint for the Protein Reference. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_SummarizePeptides	15	description_constraint	Reference Description Constraint									N	text	40		Y	2	N	Constraint for the Protein Description. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_SummarizePeptides	16	gene_name_constraint	Gene Name									N	text	40		Y	2	N	Constraint for the Gene Name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_SummarizePeptides	17	molecular_function_constraint	Molecular Function Constraint									N	text	40		Y	2	N	Constraint for the GO Molecular Function. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_SummarizePeptides	18	biological_process_constraint	Biological Process Constraint									N	text	40		Y	2	N	Constraint for the GO Biological Process. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_SummarizePeptides	19	cellular_component_constraint	Cellular Component Constraint									N	text	40		Y	2	N	Constraint for the GO Cellular Component. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_SummarizePeptides	20	protein_domain_constraint	Protein Domain Constraint									N	text	40		Y	2	N	Constraint for the InterPro Protein Domain. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_SummarizePeptides	21	fav_codon_frequency_constraint	Favored Codon Frequency Constraint									N	text	40		Y	2	N	"Constraint for the favored codon frequency (calculation by Patrick Pedrioli).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n"""	
PR_SummarizePeptides	22	transmembrane_class_constraint	Transmembrane Class Constraint									N	multioptionlist	3		Y	2	N	Constraint for the transmembrane class as annotated by TMHMM and SignalP	"SELECT DISTINCT transmembrane_class,transmembrane_class FROM $TBPR_BIOSEQUENCE_PROPERTY_SET ORDER BY transmembrane_class"
PR_SummarizePeptides	23	n_transmembrane_regions_constraint	Number of Transmembrane Regions Constraint									N	text	40		Y	2	N	"Constraint for the number of transmembrane regions (based on TMHMM and SignalP calculation by rbonneau).  Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"", ""n +- n"""	
PR_SummarizePeptides	24	accession_constraint	Accesssion Number									N	text	40		Y	2	N	Constraint for the Accession Number. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_SummarizePeptides	25	peptide_constraint	Peptide									N	text	40		Y	2	N	Constraint for the peptide (regardless of modifications). '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_SummarizePeptides	26	peptide_string_constraint	Peptide String Constraint									N	text	40		Y	2	N	Constraint for the peptide string (including modifications and neighboring AAs). '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_SummarizePeptides	27	peptide_options	Peptide Options									N	multioptionlist	3		Y	1	N	Various selectable options to further contrain the peptides displayed	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_peptide_options' ORDER BY sort_order,option_value"
PR_SummarizePeptides	28	precursor_mass_constraint	Precursor Mass constraint									N	text	40		Y	1	N	"Constraint for the measured precursor mass (as a single decimal value).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""	
PR_SummarizePeptides	29	mass_constraint	Mass constraint									N	text	40		Y	2	N	"Constraint for the theoretical peptide mass (as a single decimal value).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""	
PR_SummarizePeptides	30	percent_buffer_b_constraint	% Buffer B (ACN) constraint									N	text	40		Y	2	N	"Constraint for the calculated Percent Buffer B (acetonitrile) (value between 0 and 100).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""		
PR_SummarizePeptides	31	isoelectric_point_constraint	pI constraint									N	text	40		Y	2	N	"Constraint for the theoretical isoelectric point (pI).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""		
PR_SummarizePeptides	32	quantitation_values	Quantitation Values									N	optionlist			Y	1	N	Specify which values to use on which side of the quantitation ratio.  Normally d0/d8.  Use with caution.  This affects both the search constraints as well as display format	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_quant_values' ORDER BY sort_order,option_value"	
PR_SummarizePeptides	33	quantitation_constraint	Quantitation constraint									N	text	40		Y	2	N	"Constraint for the Quantitation (ICAT ratio) as a single decimal value.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""		
PR_SummarizePeptides	34	n_annotations_constraint	# of matches constraint									N	text	10		Y	2	N	"Constraint for the number of entries per row (e.g. use >0 to show only those rows that have at least one match)  Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"""		
PR_SummarizePeptides	35	sort_order	Sort Order									N	optionlist	 		Y	Y	N	Desired display sorting order (DESC means descending: highest to lowest)	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BAP_sort_options' ORDER BY sort_order,option_value"	
PR_SummarizePeptides	36	gene_annotation_level_constraint	Gene Annotation Level Constraint									N	optionlist			Y	2	N	"Constraint for the hierarchy level of gene annotations to view.  By default, the leaf level annotations are displayed"	"SELECT annotation_hierarchy_level_name,annotation_hierarchy_level_name FROM $TBBL_ANNOTATION_HIERARCHY_LEVEL ORDER BY annotation_hierarchy_level_id"	
PR_SummarizePeptides	37	display_options	Display Options									N	multioptionlist	5		Y	Y	N	Various selectable table display options	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BAP_display_options' ORDER BY sort_order,option_value"	
PR_SummarizePeptides	38	row_limit	Maximum Rows									N	text	10		Y	2	N	"Limit the numbers of rows displayed.  If not provided, default is 5000 rows."		
PR_SummarizeFractions	1	input_form_format	Input Form Format									N	optionlist		refreshDocument()	Y	Y	N	Options for level of detail and layout for this input form	"SELECT option_key,option_value FROM $TB_MISC_OPTION WHERE option_type = 'input_form_options' ORDER BY sort_order,option_value"	
PR_SummarizeFractions	2	experiment_id	Experiments									N	multioptionlist	4		Y	Y	N	Select desired Experiments to include in query.  Multiple items may be selected.  At least one must be selected	MANUAL	
PR_SummarizeFractions	3	project_id	Project									N	multioptionlist	4		Y	Y	N	Project in which to search for experiments	MANUAL	
PR_SummarizeFractions	4	row_limit	Maximum Rows									N	text	10		Y	2	N	"Limit the numbers of rows displayed.  If not provided, default is 1000 rows."		
PR_protein_summary	1	protein_summary_id	Protein Summary ID	int	4	0	N		Y												pkDEFAULT
PR_protein_summary	2	execution_date	Execution Date	datetime	8	0	Y		N												
PR_protein_summary	3	program_version	Program Version Number	varchar	255	0	Y		N												
PR_protein_summary	4	summary_xml	Summary XML	varchar	255	0	Y		N												
PR_protein_summary_header	1	protein_summary_header_id	Protein Summary Header ID	int	4	0	N		Y												pkDEFAULT
PR_protein_summary_header	2	protein_summary_id	Protein Summary	int	4	0	N		N	PR_protein_summary	protein_summary_id										
PR_protein_summary_header	3	reference_database	Reference Database	varchar	255	0	N		N												
PR_protein_summary_header	4	residue_substitution_list	Residue Substitution List	varchar	255	0	N		N												
PR_protein_summary_header	5	enzyme	Digestion Enzyme	varchar	100	0	Y		N												
PR_protein_summary_header	6	occam_flag	Occam Flag	char	1	0	Y		N												
PR_protein_summary_header	7	groups_flag	Groups Flag	char	1	0	Y		N												
PR_protein_summary_header	8	degen_flag	Degeneracy Flag	char	1	0	Y		N												
PR_protein_summary_header	9	nsp_flag	N Sibling Peptides Flag	char	1	0	Y		N												
PR_protein_summary_header	10	source_files	Source Files	text	16	0	Y		N												
PR_protein_summary_header	11	min_peptide_probability	Minimum Peptide Probability	real	4	0	N		N												
PR_protein_summary_header	12	min_peptide_weight	Minimum Peptide Weight	real	4	0	N		N												
PR_protein_summary_data_filter	1	protein_summary_data_filter_id	Protein Summary Data Filter ID	int	4	0	N		Y												pkDEFAULT
PR_protein_summary_data_filter	2	protein_summary_header_id	Protein Summary Header ID	int	4	0	N		N	PR_protein_summary_header	protein_summary_header_id										
PR_protein_summary_data_filter	3	min_probability	Minimum Probability	real	4	0	N		N												
PR_protein_summary_data_filter	4	sensitivity	Sensitivity	real	4	0	N		N												
PR_protein_summary_data_filter	5	false_positive_error_rate	False Positive Error Rate	real	4	0	N		N												
PR_nsp_information	1	nsp_information_id	NSP Information ID	int	4	0	N		Y												pkDEFAULT
PR_nsp_information	2	protein_summary_header_id	Protein Summary Header ID	int	4	0	N		N	PR_protein_summary_header	protein_summary_header_id										
PR_nsp_information	3	neighboring_bin_smoothing	Neighboring Bin Smoothing	char	1	0	N		N												
PR_nsp_distribution	1	nsp_distribution_id	NSP Distribution ID	int	4	0	N		Y												pkDEFAULT
PR_nsp_distribution	2	nsp_information_id	NSP Information ID	int	4	0	N		N	PR_nsp_information	nsp_information_id										
PR_nsp_distribution	3	bin_no	Neighboring Bin Smoothing	char	1	0	N		N												
PR_nsp_distribution	4	nsp_lower_bound_incl	NSP Lower Bound Inclusive	real	4	0	N		N												
PR_nsp_distribution	5	nsp_upper_bound_excl	NSP Upper Bound Exlusive	real	4	0	N		N												
PR_nsp_distribution	6	pos_freq	Positive Frequency	real	4	0	N		N												
PR_nsp_distribution	7	neg_freq	Negative Frequency	real	4	0	N		N												
PR_nsp_distribution	8	pos_to_neg_ratio	Positive to Negative Frequencies Ratio	real	4	0	N		N												
PR_summary_quantitation	1	summary_quantitation_id	Summary Quantitation ID	int	4	0	N		Y												pkDEFAULT
PR_summary_quantitation	2	ratio_mean	Ratio Mean	real	4	0	N		N												
PR_summary_quantitation	3	ratio_standard_dev	Ratio Standard Deviation	real	4	0	N		N												
PR_summary_quantitation	4	ratio_number_peptides	Number of Peptides in Mean	int	4	0	Y		N												
PR_protein_group	1	protein_group_id	Protein Group ID	int	4	0	N		Y												pkDEFAULT
PR_protein_group	2	protein_summary_id	Protein Summary	int	4	0	N		N	PR_protein_summary	protein_summary_id										
PR_protein_group	3	group_number	Group Number	int	4	0	N		N												
PR_protein_group	4	pseudo_name	Group Pseudoname	varchar	255	0	Y		N												
PR_protein_group	6	probability	Probability	real	4	0	Y		N												
PR_protein_group	7	summary_quantitation_id	Summary Quantitation	int	4	0	Y		N	PR_summary_quantitation	summary_quantitation_id										
PR_protein	1	protein_id	Protein ID	int	4	0	N		Y												pkDEFAULT
PR_protein	2	protein_group_id	Protein Group	int	4	0	N		N	PR_protein_group	protein_group_id										
PR_protein	3	protein_name	Protein Name	varchar	255	0	N		N												
PR_protein	5	probability	Probability	real	4	0	N		N												
PR_protein	6	percent_coverage	Percent Coverage	real	4	0	Y		N												
PR_protein	7	n_indistinguishable_proteins	Number of Indistinguishable Proteins	int	4	0	Y		N												
PR_protein	8	biosequence_id	Biosequence ID	int	4	0	N		N												
PR_protein	9	summary_quantitation_id	Summary Quantitation	int	4	0	Y		N	PR_summary_quantitation	summary_quantitation_id										
PR_protein	10	n_peptides	Number of Peptides	int	4	0	Y		N												
PR_indistinguishable_protein	1	indistinguishable_protein_id	Indistinguishable Protein ID	int	4	0	N		Y												pkDEFAULT
PR_indistinguishable_protein	2	protein_id	Lead Protein	int	4	0	N		N	PR_protein	protein_id										
PR_indistinguishable_protein	3	protein_name	Protein Name	varchar	255	0	N		N												
PR_indistinguishable_protein	4	biosequence_id	Biosequence ID	int	4	0	N		N												
PR_peptide	1	peptide_id	Peptide ID	int	4	0	N		Y												pkDEFAULT
PR_peptide	2	protein_id	Protein	int	4	0	N		N	PR_protein	protein_id										
PR_peptide	3	peptide_sequence	Peptide Sequence	varchar	255	0	N		N												
PR_peptide	4	charge	Charge	int	4	0	N		N												
PR_peptide	6	initial_probability	Initial Probability	real	4	0	N		N												
PR_peptide	7	nsp_adjusted_probability	NSP Adjusted Probability	real	4	0	N		N												
PR_peptide	8	peptide_group_designator	Peptide Twin Designator	varchar	10	0	Y		N												
PR_peptide	9	weight	Weight	real	4	0	N		N												
PR_peptide	10	is_nondegenerate_evidence	Is Nondegenerate Evidence?	char	1	0	N		N												
PR_peptide	11	n_enzymatic_termini	Number of Enzymatic Termini	int	4	0	N		N												
PR_peptide	12	n_sibling_peptides	Number of Sibling Peptides	real	4	0	Y		N												
PR_peptide	13	n_sibling_peptides_bin	Number of Sibling Peptides Bin	int	4	0	N		N												
PR_peptide	14	n_instances	Number of Observed Instances	int	4	0	N		N												
PR_peptide	15	summary_quantitation_id	Summary Quantitation	int	4	0	Y		N	PR_summary_quantitation	summary_quantitation_id										
PR_peptide_parent_protein	1	peptide_parent_protein_id	Peptide Parent Protein ID	int	4	0	N		Y												pkDEFAULT
PR_peptide_parent_protein	2	peptide_id	Peptide	int	4	0	N		N	PR_peptide	peptide_id										
PR_peptide_parent_protein	3	protein_name	Protein Name	varchar	255	0	N		N												
PR_peptide_parent_protein	4	biosequence_id	Biosequence ID	int	4	0	N		N												
PR_indistinguishable_peptide	1	indistinguishable_peptide_id	Indistinguishable Peptide ID	int	4	0	N		Y												pkDEFAULT
PR_indistinguishable_peptide	2	peptide_id	Peptide	int	4	0	N		N	PR_peptide	peptide_id										
PR_indistinguishable_peptide	3	peptide_sequence	Peptide Sequence	varchar	255	0	N		N												
PR_search_batch_protein_summary	1	search_batch_protein_summary_id	Search Batch Protein Summary ID	int	4	0	N		Y												pkDEFAULT
PR_search_batch_protein_summary	2	protein_summary_id	Protein Summary	int	4	0	N		N	PR_protein_summary	protein_summary_id										
PR_search_batch_protein_summary	3	search_batch_id	Search Batch ID	int	4	0	N		N	PR_search_batch	search_batch_id	Y	fixed			Y	Y	Y	Search Batch to which this summary belongs		
PR_search_batch_protein_summary	4	comment	Comment	text	16	0	Y		N												
PR_possible_peptide	1	possible_peptide_id	Possible Peptide ID	int	4	0	N		Y												pkDEFAULT
PR_possible_peptide	2	biosequence_id	BioSequence ID	int	4	0	Y		N	PR_biosequence	biosequence_id					Y	Y	N	BioSequence ID		
PR_possible_peptide	3	mass	Mass	real	4	0	Y		N												
PR_possible_peptide	4	peptide_sequence	Peptide Sequence	varchar	255	0	N		N											
PR_possible_peptide	5	peptide_offset	Peptide Offset	int	4	0	N		N											
PR_possible_peptide	6	preceding_residue	Preceding Residue	char	1	0	N		N											
PR_possible_peptide	7	following_residue	Following Residue	char	1	0	N		N											
PR_possible_peptide	8	n_tryptic_terminii	Number of Tryptic Termini	int	4	0	N		N											
PR_possible_peptide	9	is_cysteine_containing	Is Cytsteine Containing	char	1	0	N		N											
PR_possible_peptide	10	is_unique	Is Unique	char	1	0	N		N											
PR_possible_peptide	11	isoelectric_point	Isoelectric Point	real	4	0	N		N											
PR_BrowsePossiblePeptides	1	input_form_format	Input Form Format									N	optionlist		refreshDocument()	Y	Y	N	Options for level of detail and layout for this input form	"SELECT option_key,option_value FROM $TB_MISC_OPTION WHERE option_type = 'input_form_options' ORDER BY sort_order,option_value"
PR_BrowsePossiblePeptides	2	biosequence_set_id	BioSequence Sets									N	multioptionlist	4		Y	Y	N	"Select desired BioSequence Sets to include in query.  Multiple items may be selected.  If no items are selected, ALL sets are searched."	"SELECT biosequence_set_id,set_name FROM $TBPR_BIOSEQUENCE_SET ORDER BY sort_order,set_name"
PR_BrowsePossiblePeptides	3	biosequence_name_constraint	Name Constraint									N	text	40		Y	Y	N	Constraint for the BioSequence Name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_BrowsePossiblePeptides	4	biosequence_gene_name_constraint	Gene Name Constraint									N	text	40		Y	Y	N	Constraint for the BioSequence Gene Name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_BrowsePossiblePeptides	5	accession_constraint	Accesssion Number									N	text	40		Y	2	N	Constraint for the Accession Number. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_BrowsePossiblePeptides	6	biosequence_seq_constraint	Sequence Constraint									N	text	40		Y	Y	N	Constraint for the actual sequence. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_BrowsePossiblePeptides	7	biosequence_desc_constraint	Description Constraint									N	text	40		Y	Y	N	Constraint for the BioSequence Description. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_BrowsePossiblePeptides	8	molecular_function_constraint	Molecular Function Constraint									N	text	40		Y	2	N	Constraint for the GO Molecular Function. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_BrowsePossiblePeptides	9	biological_process_constraint	Biological Process Constraint									N	text	40		Y	2	N	Constraint for the GO Biological Process. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.		
PR_BrowsePossiblePeptides	10	cellular_component_constraint	Cellular Component Constraint									N	text	40		Y	2	N	Constraint for the GO Cellular Component. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.		
PR_BrowsePossiblePeptides	11	protein_domain_constraint	Protein Domain Constraint									N	text	40		Y	2	N	Constraint for the InterPro Protein Domain. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.		
PR_BrowsePossiblePeptides	12	fav_codon_frequency_constraint	Favored Codon Frequency Constraint									N	text	40		Y	2	N	"Constraint for the favored codon frequency (calculation by Patrick Pedrioli).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n"""		
PR_BrowsePossiblePeptides	13	transmembrane_class_constraint	Transmembrane Class Constraint									N	multioptionlist	3		Y	2	N	Constraint for the transmembrane class as annotated by TMHMM and SignalP	"SELECT DISTINCT transmembrane_class,transmembrane_class FROM $TBPR_BIOSEQUENCE_PROPERTY_SET ORDER BY transmembrane_class"	
PR_BrowsePossiblePeptides	14	n_transmembrane_regions_constraint	Number of Transmembrane Regions Constraint									N	text	40		Y	2	N	"Constraint for the number of transmembrane regions (based on TMHMM and SignalP calculation by rbonneau).  Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"", ""n +- n"""		
PR_BrowsePossiblePeptides	15	protein_length_constraint	Protein Length Constraint									N	text	40		Y	2	N	"Constraint for the protein length.  Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"", ""n +- n"""		
PR_BrowsePossiblePeptides	16	peptide_constraint	Peptide Constraint									N	text	40		Y	1	N	Constraint for the peptide (regardless of modifications). '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.		
PR_BrowsePossiblePeptides	17	mass_constraint	Mass Constraint									N	text	40		Y	2	N	"Constraint for the theoretical peptide mass (as a single decimal value).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""		
PR_BrowsePossiblePeptides	18	isoelectric_point_constraint	Isoelectric Point Constraint									N	text	40		Y	2	N	"Constraint for the theoretical peptide pI (isoelectric point).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""		
PR_BrowsePossiblePeptides	19	n_occurrences	Number of Occurrences									N	text	15		Y	1	N	"Constraint for the number of entries per row (only applicable for one of the two Grouping options)  Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"""		
PR_BrowsePossiblePeptides	20	peptide_options	Peptide Options									N	multioptionlist	3		Y	Y	N	Various selectable options to further contrain the peptides displayed	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BPP_peptide_options' ORDER BY sort_order,option_value"	
PR_BrowsePossiblePeptides	21	gene_annotation_level_constraint	Gene Annotation Level Constraint									N	optionlist			Y	2	N	"Constraint for the hierarchy level of gene annotations to view.  By default, the leaf level annotations are displayed"	"SELECT annotation_hierarchy_level_name,annotation_hierarchy_level_name FROM $TBBL_ANNOTATION_HIERARCHY_LEVEL ORDER BY annotation_hierarchy_level_id"	
PR_BrowsePossiblePeptides	22	display_options	Display Options									N	multioptionlist	3		Y	Y	N	Various selectable table display options	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BPP_display_options' ORDER BY sort_order,option_value"	
PR_BrowsePossiblePeptides	23	row_limit	Maximum Rows									N	text	10		Y	Y	N	"Limit the numbers of rows displayed.  If not provided, default is 100 rows."		
PR_publication_category	1	publication_category_id	Publication Category ID	int	4	0	N		Y							N	N				pkDEFAULT
PR_publication_category	2	publication_category_name	Publication Category Name	varchar	100	0	N		N			Y	text	40		Y	Y	Y	Short name of this category as it will appear in list boxes		
PR_publication_category	3	publication_category_description	Publication Category Description	varchar	255	0	N		N			Y	text	50		Y	Y	N	More complete description of this publication category		
PR_publication_category	4	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
PR_publication_category	5	sort_order	Sort Order	int	2	0	N	10	N			N	text	10		Y	Y	N	Numbers which override alphabetical sorting in a list box		
PR_publication_category	6	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_publication_category	7	created_by_id	Record Created By	int	2	0	N	1	N	contact	contact_id					N	N				
PR_publication_category	8	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_publication_category	9	modified_by_id	Record Modified By	int	2	0	N	1	N	contact	contact_id					N	N				
PR_publication_category	10	owner_group_id	Owner Group ID	int	2	0	N	1	N	work_group	work_group_id					N	N				
PR_publication_category	11	record_status	Record Status	char	1	0	N	N	N							N	N				
PR_publication_rating	1	publication_rating_id	Publication Rating ID	int	4	0	N		Y							N	N				pkDEFAULT
PR_publication_rating	2	publication_rating_number	Publication Rating Number	int	4	0	N		N			Y	text	10		Y	Y	Y	Numerical rating of the paper on a scale of 1-10		
PR_publication_rating	3	publication_rating_name	Publication Rating Name	varchar	100	0	N		N			Y	text	40		Y	Y	Y	Short name of this rating level as it will appear in list boxes		
PR_publication_rating	4	publication_rating_description	Publication Rating Description	varchar	255	0	N		N			Y	text	50		Y	Y	N	More complete description of this rating level		
PR_publication_rating	5	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
PR_publication_rating	6	sort_order	Sort Order	int	2	0	N	10	N			N	text	10		Y	Y	N	Numbers which override alphabetical sorting in a list box		
PR_publication_rating	7	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_publication_rating	8	created_by_id	Record Created By	int	2	0	N	1	N	contact	contact_id					N	N				
PR_publication_rating	9	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_publication_rating	10	modified_by_id	Record Modified By	int	2	0	N	1	N	contact	contact_id					N	N				
PR_publication_rating	11	owner_group_id	Owner Group ID	int	2	0	N	1	N	work_group	work_group_id					N	N				
PR_publication_rating	12	record_status	Record Status	char	1	0	N	N	N							N	N				
PR_publication	1	publication_id	Publication ID	int	8	0	N		Y							N	N				pkDEFAULT
PR_publication	2	pubmed_ID	PubMed ID	varchar	50	0	Y		N			N	text	30	refreshDocument()	Y	Y	N	"PubMed ID for this publication.  When this field is changed, the interface fetch the title,author,etc. information for you if the field below this (Publication Name) is empty"		
PR_publication	3	publication_name	Publication Name	varchar	255	0	N		N			Y	text	50		Y	Y	Y	"Friendly name of the citation, e.g. Dewey, Cheetham & Howe (1998)"		
PR_publication	4	keywords	Keywords	varchar	255	0	Y		N			N	text	50		Y	Y	N	A comma-separated list of keywords appropriate when searching for papers of this sort		
PR_publication	5	publication_category_id	Publication Category	int	4	0	Y		N	PR_publication_category	publication_category_id	N	optionlist			Y	Y	N	Broad category within which this publication is classified	"SELECT publication_category_id,publication_category_name FROM $TBPR_PUBLICATION_CATEGORY WHERE record_status != 'D' ORDER BY sort_order,publication_category_name"	
PR_publication	6	publication_rating_id	Publication Rating	int	4	0	Y		N	PR_publication_rating	publication_rating_id	N	optionlist			Y	Y	N	Rating of this paper (typically within the category) given by the person entering this record.  This should be an indication of how worthwhile a read this paper is within the category	"SELECT publication_rating_id,STR(publication_rating_number,5,0)+' - '+publication_rating_name FROM $TBPR_PUBLICATION_RATING WHERE record_status != 'D' ORDER BY sort_order,publication_rating_number DESC,publication_rating_name"	
PR_publication	7	presented_on_date	Presented Date	datetime	8	0	Y		N			N	text	20		Y	Y	N	Date that the publication was presented in a journal club		
PR_publication	8	presented_by_contact_id	Presented By Contact	int	4	0	Y		N	contact	contact_id	N	scrolloptionlist	4		Y	Y	N	Person who presented this paper in a journal club	"SELECT contact_id, last_name+', '+first_name+' ('+organization+')' AS 'name' FROM $TB_CONTACT C JOIN $TB_ORGANIZATION O ON ( C.organization_id = O.organization_id ) ORDER BY last_name,first_name,organization"	
PR_publication	9	title	Title	varchar	255	0	Y		N			N	textarea	2		Y	Y	N	Title of the article		
PR_publication	10	author_list	Author List	varchar	255	0	Y		N			N	textarea	2		Y	Y	N	"Author list in 'Lastname, FIMI' format"		
PR_publication	11	journal_name	Journal Name	varchar	100	0	Y		N			N	text	50		Y	Y	N	Name of the Journal in which the article appears		
PR_publication	12	published_year	Published Year	varchar	10	0	Y		N			N	text	20		Y	Y	N	Year the article was published		
PR_publication	13	volume_number	Volume Number	varchar	50	0	Y		N			N	text	20		Y	Y	N	Volume number of the article		
PR_publication	14	issue_number	Issue Number	varchar	50	0	Y		N			N	text	20		Y	Y	N	Issue number of the article		
PR_publication	15	page_numbers	Page Numbers	varchar	50	0	Y		N			N	text	30		Y	Y	N	Page numbers of the article		
PR_publication	16	publisher_name	Publisher Name	varchar	255	0	Y		N			N	text	40		Y	Y	N	Name of the publisher		
PR_publication	17	editor_name	Editor Name	varchar	255	0	Y		N			N	text	40		Y	Y	N	"Name of the editor, if any"		
PR_publication	18	uri	URI	varchar	255	0	Y		N			N	text	50		Y	Y	N	"URL of other locator for the article, either out on the Internet or in the location Publications repository"		SELF
PR_publication	19	abstract	Abstract	text	16	0	Y		N			N	textarea	4		Y	Y	N	Plain text abstract of the article		
PR_publication	20	full_manuscript_file	Manuscript File Upload	varchar	255	0	Y		N			N	file	40		Y	Y	N	Actual file containing the manuscript (e.g. in PDF format)		uploaded_file
PR_publication	21	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
PR_publication	22	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_publication	23	created_by_id	Record Created By	int	8	0	N		N	contact	contact_id					N	N				
PR_publication	24	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_publication	25	modified_by_id	Record Modified By	int	8	0	N		N	contact	contact_id					N	N				
PR_publication	26	owner_group_id	Owner Group ID	int	8	0	N	1	N	work_group	work_group_id					N	N				
PR_publication	27	record_status	Record Status	char	1	0	N	N	N							N	N			
PR_BrowseProteinSummary	1	input_form_format	Input Form Format									N	optionlist		refreshDocument()	Y	Y	N	Options for level of detail and layout for this input form	"SELECT option_key,option_value FROM $TB_MISC_OPTION WHERE option_type = 'input_form_options' ORDER BY sort_order,option_value"
PR_BrowseProteinSummary	2	search_batch_id	Search Batches									N	multioptionlist	4		Y	Y	N	Select desired Experiments and Search Batches to include in query.  Multiple items may be selected.  At least one must be selected	MANUAL
PR_BrowseProteinSummary	3	protein_group_probability_constraint	Protein Group Probability Constraint									N	text	20		Y	Y	N	"Constraint for the probability of the protein group being present in the sample.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n"""	
PR_BrowseProteinSummary	4	protein_probability_constraint	Protein Probability Constraint									N	text	20		Y	Y	N	"Constraint for the probability of the protein being present in the sample.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n"""	
PR_BrowseProteinSummary	5	annotation_status_id	Annotation status Constraint									N	optionlist	 		Y	Y	N	Select desired status of annotations to include in result (I.e. display only peptides that have been annotated or have not been annotated at all; set to blank to be insensitive to annotations)	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_annotation_status' ORDER BY sort_order,option_value"
PR_BrowseProteinSummary	6	annotation_label_id	Annotation Labels Constraint									N	multioptionlist	5		Y	Y	N	Select desired annotation labels to include (applies only to records that have annotations)	"SELECT annotation_label_id,label_desc FROM $TBPR_ANNOTATION_LABEL ORDER BY sort_order,label_desc"
PR_BrowseProteinSummary	7	reference_constraint	Protein Name Constraint									N	text	40		Y	1	N	Constraint for the Protein Reference. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_BrowseProteinSummary	8	description_constraint	Protein Description Constraint									N	text	40		Y	2	N	Constraint for the Protein Description. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_BrowseProteinSummary	9	gene_name_constraint	Gene Name Constraint									N	text	40		Y	2	N	Constraint for the Gene Name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_BrowseProteinSummary	10	molecular_function_constraint	Molecular Function Constraint									N	text	40		Y	2	N	Constraint for the GO Molecular Function. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_BrowseProteinSummary	11	biological_process_constraint	Biological Process Constraint									N	text	40		Y	2	N	Constraint for the GO Biological Process. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_BrowseProteinSummary	12	cellular_component_constraint	Cellular Component Constraint									N	text	40		Y	2	N	Constraint for the GO Cellular Component. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_BrowseProteinSummary	13	protein_domain_constraint	Protein Domain Constraint									N	text	40		Y	2	N	Constraint for the InterPro Protein Domain. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
PR_BrowseProteinSummary	14	fav_codon_frequency_constraint	Favored Codon Frequency Constraint									N	text	40		Y	2	N	"Constraint for the favored codon frequency (calculation by Patrick Pedrioli).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n"""	
PR_BrowseProteinSummary	15	transmembrane_class_constraint	Transmembrane Class Constraint									N	multioptionlist	3		Y	2	N	Constraint for the transmembrane class as annotated by TMHMM and SignalP	"SELECT DISTINCT transmembrane_class,transmembrane_class FROM $TBPR_BIOSEQUENCE_PROPERTY_SET ORDER BY transmembrane_class"
PR_BrowseProteinSummary	16	n_transmembrane_regions_constraint	Number of Transmembrane Regions Constraint									N	text	40		Y	2	N	"Constraint for the number of transmembrane regions (based on TMHMM and SignalP calculation by rbonneau).  Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"", ""n +- n"""		
PR_BrowseProteinSummary	17	accession_constraint	Accesssion Number Constraint									N	text	40		Y	2	N	Constraint for the Accession Number. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.		
PR_BrowseProteinSummary	18	quantitation_constraint	Quantitation constraint									N	text	40		Y	2	N	"Constraint for the Quantitation (ICAT ratio) as a single decimal value.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""		
PR_BrowseProteinSummary	19	gene_annotation_level_constraint	Gene Annotation Level Constraint									N	optionlist			Y	2	N	"Constraint for the hierarchy level of gene annotations to view.  By default, the leaf level annotations are displayed"	"SELECT annotation_hierarchy_level_name,annotation_hierarchy_level_name FROM $TBBL_ANNOTATION_HIERARCHY_LEVEL ORDER BY annotation_hierarchy_level_id"	
PR_BrowseProteinSummary	20	display_options	Display Options									N	multioptionlist	5		Y	Y	N	Various selectable table display options	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BPS_display_options' ORDER BY sort_order,option_value"	
PR_BrowseProteinSummary	21	row_limit	Maximum Rows									N	text	10		Y	2	N	"Limit the numbers of rows displayed.  If not provided, default is 5000 rows."		
PR_proteomics_sample	1	proteomics_sample_id	Proteomics Sample ID	int	4	0	N		Y			Y				N	N	Y	Proteomics Sample ID		pkDEFAULT
PR_proteomics_sample	2	project_id	Project	int	4	0	N		N	project	project_id	Y	optionlist			Y	Y	N	FK to project.project_id	"SELECT project_id, UL.username + ' - ' + proj.name + ' ( ' + RTRIM(CAST(proj.project_id AS CHAR)) + ' )'   AS name FROM $TB_PROJECT proj JOIN $TB_USER_LOGIN UL ON (proj.PI_contact_id = UL.contact_id)  WHERE proj.project_tag IS NOT NULL AND proj.record_status != 'D' ORDER BY UL.username"	
PR_proteomics_sample	3	sample_tag	Sample Tag	varchar	50	0	N		N			Y	text	50		Y	Y	N	Sample Name.  Keep it short.  Do not use any strange characters like /\*&$() (e.g. NP Epi 03-123)		
PR_proteomics_sample	4	full_sample_name	Full Sample Name	varchar	255	0	Y		N			Y	textarea	3		Y	Y	N	"Full Sample Name.  A longer, less cryptic name should be placed here.  It should be long enough so that someone else can understand quickly the general idea of the sample. (e.g. Epithelial cells FACS sorted from ""normal"" prostate tissue from specimen 03-123)"		
PR_proteomics_sample	5	sample_group_name	Sample Group Name	varchar	50	0	Y		N			N	text	50		Y	Y	N	Sample Group Name.  Name used to group together biological replicates		
PR_proteomics_sample	6	sample_provider_organization_id	Sample Provider	int	4	0	Y		N	organization	organization_id	N	optionlist			Y	Y	N	"Provider of this biomaterial (academic department, research lab, vendor, etc.)"	"SELECT O.organization_id,O.organization FROM $TB_ORGANIZATION O INNER JOIN $TB_ORGANIZATION_TYPE OT ON (O.organization_type_id=OT.organization_type_id) WHERE O.record_status != 'D' ORDER BY organization"	
PR_proteomics_sample	7	organism_id	Organism	int	4	0	Y		N	organism	organism_id	N	optionlist			Y	Y	N	Organism from which the biomaterial was derived	"SELECT organism_id, organism_name FROM $TB_ORGANISM ORDER BY sort_order,organism_name"	
PR_proteomics_sample	8	strain_or_line	Strain or Line	varchar	255	0	Y		N			N	text	50		Y	Y	N	Strain or line of the individual		
PR_proteomics_sample	9	individual	Individual	varchar	255	0	Y		N			N	text	50		Y	Y	N	Identifier or name of the individual organism from which the biomaterial was derived		
PR_proteomics_sample	10	sex_ontology_term_id	Sex	int	4	0	Y		N			N	optionlist			Y	Y	N	Sex of the individual	"SELECT MOT2.MGED_ontology_term_id,MOT2.name FROM $TB_MGED_ONTOLOGY_RELATIONSHIP MOR INNER JOIN $TB_MGED_ONTOLOGY_TERM MOT2 ON ( MOR.subject_term_id = MOT2.MGED_ontology_term_id ) WHERE MOR.object_term_id = 5497 ORDER BY MOT2.name"	
PR_proteomics_sample	11	age	Age	varchar	255	0	Y		N			N	text	50		Y	Y	N	"Age of the individual at the time of harvest of the biomaterial.  Free form text; include units, developmental stage, and reference point as appropriate (e.g., days since planting, years after birth, minutes after death)"	
PR_proteomics_sample	12	organism_part	Organism Part	varchar	255	0	Y		N			N	text	50		Y	Y	N	"Part of the organism's anatomy from the biomaterial was derived, excludes cells. (e.g., tissue, organ, system, or body location)"	
PR_proteomics_sample	13	cell_line	Cell Line	varchar	255	0	Y		N			N	text	50		Y	Y	N	Identifier for the cell line if one was used as a biomaterial	
PR_proteomics_sample	14	cell_type	Cell Type	varchar	255	0	Y		N			N	text	50		Y	Y	N	"Type of cell used as the biomaterial (e.g., epithelial, glial, etc.)"	
PR_proteomics_sample	15	disease_state	Disease State	varchar	255	0	Y		N			N	text	50		Y	Y	N	"Name of the pathology diagnosed in the organism from which the biomaterial was derived.  The disease state is ""normal"" if no disease state has been diagnosed."	
PR_proteomics_sample	16	sample_amount	Amount of Sample	varchar	50	0	Y		N			N	text	50		Y	Y	N	"Amount of sample initally supplied.  Example 1ml, 2kg"	
PR_proteomics_sample	17	proteomics_sample_protocol_ids	Proteomics Sample Protocols	varchar	255	0	Y		N	PR_proteomics_sample_protocol	proteomics_sample_protocol_id	N	multilink	4		Y	Y	N	Select all protocols that apply to this biomaterial.  Describe sequence of protocols in the Treatment Description below	"SELECT protocol_id,P.name FROM $TB_PROTOCOL P LEFT JOIN $TB_PROTOCOL_TYPE PT ON ( P.protocol_type_id=PT.protocol_type_id ) WHERE P.record_status != 'D' ORDER BY P.name"
PR_proteomics_sample	18	protocol_deviations	Protocol Deviations	text	16	0	Y		N			N	textarea	4		Y	Y	N	Describe any deviations from the selected protocols	
PR_proteomics_sample	19	sample_description	Sample Description	text	16	0	Y		N			N	textarea	4		Y	Y	N	Describe the biomaterial briefly	
PR_proteomics_sample	20	sample_preparation_date	Sample Preparation Date	datetime	8	0	Y		N			N	text	30		Y	Y	Y	Date/time the biomaterial was prepared with the described protocols	
PR_proteomics_sample	21	treatment_description	Treatment Description	text	16	0	Y		N			N	textarea	4		Y	Y	N	"Describe the treatment of the biomaterials, including mention of the selected protocols"	
PR_proteomics_sample	22	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional notes	
PR_proteomics_sample	23	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	Y	N		
PR_proteomics_sample	24	created_by_id	Record Created By	int	4	0	N		N	contact	contact_id					N	N	Y		
PR_proteomics_sample	25	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N	N		
PR_proteomics_sample	26	modified_by_id	Record Modified By	int	4	0	N		N	contact	contact_id					N	N	Y		
PR_proteomics_sample	27	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N	Y			
PR_proteomics_sample	28	record_status	Record Status	char	1	0	N	N	N							N	N	N			
PR_proteomics_sample_protocol	1	proteomics_sample_protocol_id	Proteomics Sample Protocol ID	int	4	0	N		Y			Y				N	N	N			pkDEFAULT
PR_proteomics_sample_protocol	2	proteomics_sample_id	Proteomics Sample ID	int	4	0	N		N	PR_proteomics_sample	proteomics_sample_id	Y				Y	N	Y			
PR_proteomics_sample_protocol	3	protocol_id	Protocol ID	int	4	0	N		N	protocol	protocol_id	Y				N	N	Y	Protocol ID		
PR_proteomics_sample_protocol	4	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_proteomics_sample_protocol	5	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_proteomics_sample_protocol	6	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_proteomics_sample_protocol	7	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_proteomics_sample_protocol	8	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
PR_proteomics_sample_protocol	9	record_status	Record Status	char	1	0	N	N	N							N	N				
PR_experiments_samples	1	experiments_samples_id	Experiments Samples ID	int	4	0	N		Y			Y				N	N	Y	Linking table for experiments and proteomic samples		pkDEFAULT
PR_experiments_samples	2	experiment_id	Proteomic Experiment Name	int	4	0	N		N	PR_proteomics_experiment	experiment_id	Y	optionlist			Y	Y	Y	Proteomics Experiment Name tag	MANUAL	
PR_experiments_samples	3	proteomics_sample_id	Proteomics Sample Name	int	4	0	N		N	PR_proteomics_sample	proteomics_sample_id	Y	optionlist			Y	Y	Y	Proteomics Sample Name tag	MANUAL	
PR_experiments_samples	4	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_experiments_samples	5	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_experiments_samples	6	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
PR_experiments_samples	7	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
PR_experiments_samples	8	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
PR_experiments_samples	9	record_status	Record Status	char	1	0	N	N	N							N	N				
APD_peptide_summary	1	peptide_summary_id	Peptide Summary ID	int	4	0	N		Y							N	N				pkDEFAULT
APD_peptide_summary	2	project_id	Project	int	4	0	N		N	project	project_id	Y	optionlist			Y	Y	N	Project to which the peptide summary belongs	"SELECT DISTINCT P.project_id,UL.username+' - '+P.name FROM $TB_PROJECT P LEFT JOIN $TB_USER_LOGIN UL ON ( P.PI_contact_id=UL.contact_id ) WHERE P.record_status != 'D' AND P.project_id IN ( $accessible_project_ids ) ORDER BY UL.username+' - '+P.name,P.project_id"	
APD_peptide_summary	3	peptide_summary_name	Peptide Summary Title	varchar	100	0	N		N			Y	text	50		Y	Y	Y	Title of this peptide summary		
APD_peptide_summary	4	description	Peptide Summary Description	text	16	0	N		N			Y	textarea	4		Y	Y	N	"Description of this APD peptide summary, from where it is derived, etc."		
APD_peptide_summary	5	minimum_probability	Minimum Probability	real	4	0	N		N			Y	text	10		Y	Y	N	Minimum P value for selecting good peptides		
APD_peptide_summary	6	experiment_list	Search Batch ID List	varchar	512	0	N		N			Y	text	50		Y	Y	N	List of search batch ids		
APD_peptide_summary	7	n_experiments	Number of Experiments	int	4	0	N		N			Y	text	10		Y	Y	N	Total number of experiments used for this summary		
APD_peptide_summary	8	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
APD_peptide_summary	9	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
APD_peptide_summary	10	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
APD_peptide_summary	11	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
APD_peptide_summary	12	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
APD_peptide_summary	13	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N	
APD_peptide_summary	14	record_status	Record Status	char	1	0	N	N	N							N	N	
APD_aggregated_peptide	1	peptide_id	APD Peptide ID	int	4	0	N		Y			Y						N
APD_aggregated_peptide	2	peptide_summary_id	APD Peptide Summary ID	int	4	0	N		N	APD_peptide_summary	peptide_summary_id							Y
APD_aggregated_peptide	3	peptide_identifier_id	APD Peptide Identifier ID	int	4	0	N		N	APD_peptide_identifier	peptide_identifier_id							Y
APD_aggregated_peptide	4	biosequence_id	BioSequence ID	int	4	0	N		N	PR_biosequence	biosequence_id							N
APD_aggregated_peptide	5	biosequence_name	BioSequence Name	varchar	255	0	N		N									N
APD_aggregated_peptide	6	peptide	Peptide	varchar	512	0	N		N									N
APD_aggregated_peptide	7	n_peptides	Number of Peptides	int	4	0	N		N									N
APD_aggregated_peptide	8	experiment_list	Search Batch ID List	varchar	255	0	N		N									N
APD_aggregated_peptide	9	n_experiments	Number of Experiments	int	4	0	N		N									N
APD_aggregated_peptide	10	maximum_probability	Maximum Probability	real	4	0	N		N									N
APD_peptide_summary_experiment	1	peptide_summary_id	APD Peptide Summary ID	int	4	0	N		N	APD_peptide_summary	peptide_summary_id							Y
APD_peptide_summary_experiment	2	proteomics_experiment_id	Proteomics Experiment ID	int	4	0	N		N	PR_proteomics_experiment	experiment_id							Y
APD_peptide_identifier	1	peptide_identifier_id	APD Peptide Identifier ID	int	4	0	N		Y									N
APD_peptide_identifier	2	peptide_identifier_str	APD Peptide Identifier (f. ex. PAp12345678)	varchar	50	0	N		N									Y
APD_peptide_identifier	3	peptide	APD Peptide aa sequence	varchar	512	0	N		N									N
APD_modified_peptide	1	modified_peptide_id	Modified Peptide ID	int	4	0	N		Y									N
APD_modified_peptide	2	peptide_id	APD Peptide ID	int	4	0	N		N	APD_aggregated_peptide	peptide_id							Y
APD_modified_peptide	3	peptide_string	APD Peptide String	varchar	512	0	N		N									Y
APD_modified_peptide	4	charge_state	Charge State	int	4	0	N		N									N
APD_modified_peptide	5	n_modified_peptides	Number of Modified Peptides	int	4	0	N		N									N
APD_modified_peptide	6	experiment_list	Experiment List	varchar	255	0	N		N									N
APD_modified_peptide	7	n_experiments	Number of Experiments	int	4	0	N		N									N
APD_modified_peptide	8	maximum_probability	Maximum Probability	real	4	0	N		N									N
APD_modified_peptide	9	calc_peptide_mass	Calculated Peptide Mass	real	4	0	N		N									N
APD_modified_peptide	10	precursor_mass_avg	Avg of Precursor Ion Mass	real	4	0	N		N									N
APD_modified_peptide	11	precursor_mass_stdev	SD of Precorsor Ion Mass	real	4	0	Y		N									N
APD_modified_peptide	12	percent_ACN_avg	Avg of Percent Acetonitrile	real	4	0	Y		N									N
APD_modified_peptide	13	percent_ACN_stdev	SD of Percent Acetonitrile	real	4	0	Y		N									N
APD_modified_peptide	14	pI_avg	Avg pI	real	4	0	Y		N									N
APD_modified_peptide	15	SCX_avg	Avg SCX Value	real	4	0	Y		N									N
APD_peptide_property_type	1	peptide_property_type_id	Peptide Property Type ID	int	4	0	N		Y									N
APD_peptide_property_type	2	peptide_property_type_name	Peptide Property Type Name	varchar	100	0	N		N									Y
APD_peptide_property_type	3	peptipe_property_type_decription	Peptide Property Type Description	text	16	0	Y		N									N
APD_peptide_property_type	4	comment	Comment	text	16	0	Y		N									N
APD_peptide_property_type	5	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N									N
APD_peptide_property_type	6	created_by_id	Record Created By	int	4	0	N		N	contact	contact_id							N
APD_peptide_property_type	7	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N									N
APD_peptide_property_type	8	modified_by_id	Record Modified By	int	4	0	N		N	contact	contact_id							N
APD_peptide_property_type	9	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id							N
APD_peptide_property_type	10	record_status	Record Status	char	1	0	N	N	N									N
APD_modified_peptide_property	1	modified_peptide_property_id	Modified Peptide Property ID	int	4	0	N		Y									N
APD_modified_peptide_property	2	modified_peptide_id	Modified Peptide ID	int	4	0	N		N	APD_modified_peptide	modified_peptide_id							Y
APD_modified_peptide_property	3	peptide_property_type_id	Peptide Property Type ID	int	4	0	N		N	APD_peptide_property_type	peptide_property_type_id							Y
APD_modified_peptide_property	4	min_value	Minimum Value	real	4	0	N		N									N
APD_modified_peptide_property	5	max_value	Maximum Value	real	4	0	N		N									N
APD_modified_peptide_property	6	average_value	Avg Value	real	4	0	N		N									N
APD_modified_peptide_property	7	standard_deviation	SD	real	4	0	Y		N									N		
APD_modified_peptide_property	8	median_value	Mean	real	4	0	Y		N									N		
APD_modified_peptide_property	9	SIQR	SIQR	real	4	0	Y		N									N		
APD_modified_peptide_property	10	N_values	Number of Values	int	4	0	N		N									N		
APD_BrowseAPD	1	input_form_format	Input Form Format									N	optionlist		refreshDocument()	Y	Y	N	Options for level of detail and layout for this input form	"SELECT option_key,option_value FROM $TB_MISC_OPTION WHERE option_type = 'input_form_options' ORDER BY sort_order,option_value"
APD_BrowseAPD	2	peptide_summary_id	APD Summary ID									N	multioptionlist	4		Y	Y	N	Select the desired APD peptide summaries to search.  It is best to select just one.	"SELECT peptide_summary_id,peptide_summary_name FROM $TBAPD_PEPTIDE_SUMMARY WHERE record_status != 'D' ORDER BY peptide_summary_name"
APD_BrowseAPD	3	probability_constraint	Probability Constraint									N	text	20		Y	Y	N	"Constraint for the maximum probability of the peptide.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n"""	
APD_BrowseAPD	4	APD_accession_constraint	APD Accession Number									N	text	20		Y	Y	N	Constraint for the APD peptide accession number (e.g. PAp00002334). '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
APD_BrowseAPD	5	charge_constraint	Charge Constraint									N	optionlist	 		Y	1	N	"Constraint for the charge states to include in the query.  If blank, all states are included"	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_charge_constraint' ORDER BY sort_order,option_value"
APD_BrowseAPD	6	reference_constraint	Protein Name Constraint									N	text	40		Y	1	N	Constraint for the Protein Reference. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
APD_BrowseAPD	7	description_constraint	Reference Description Constraint									N	text	40		Y	2	N	Constraint for the Protein Description. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
APD_BrowseAPD	8	gene_name_constraint	Gene Name Constraint									N	text	40		Y	2	N	Constraint for the Gene Name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
APD_BrowseAPD	9	molecular_function_constraint	Molecular Function Constraint									N	text	40		Y	2	N	Constraint for the GO Molecular Function. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
APD_BrowseAPD	10	biological_process_constraint	Biological Process Constraint									N	text	40		Y	2	N	Constraint for the GO Biological Process. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
APD_BrowseAPD	11	cellular_component_constraint	Cellular Component Constraint									N	text	40		Y	2	N	Constraint for the GO Cellular Component. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
APD_BrowseAPD	12	protein_domain_constraint	Protein Domain Constraint									N	text	40		Y	2	N	Constraint for the InterPro Protein Domain. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
APD_BrowseAPD	13	fav_codon_frequency_constraint	Favored Codon Frequency Constraint									N	text	40		Y	2	N	"Constraint for the favored codon frequency (calculation by Patrick Pedrioli).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n"""	
APD_BrowseAPD	14	transmembrane_class_constraint	Transmembrane Class Constraint									N	multioptionlist	3		Y	2	N	Constraint for the transmembrane class as annotated by TMHMM and SignalP	"SELECT DISTINCT transmembrane_class,transmembrane_class FROM $TBPR_BIOSEQUENCE_PROPERTY_SET ORDER BY transmembrane_class"
APD_BrowseAPD	15	n_transmembrane_regions_constraint	Number of Transmembrane Regions Constraint									N	text	40		Y	2	N	"Constraint for the number of transmembrane regions (based on TMHMM and SignalP calculation by rbonneau).  Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"", ""n +- n"""	
APD_BrowseAPD	16	accession_constraint	Accesssion Number									N	text	40		Y	2	N	Constraint for the Accession Number. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
APD_BrowseAPD	17	peptide_constraint	Peptide									N	text	40		Y	2	N	Constraint for the peptide (regardless of modifications). '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
APD_BrowseAPD	18	peptide_string_constraint	Peptide String Constraint									N	text	40		Y	2	N	Constraint for the peptide string (including modifications and neighboring AAs). '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; no other regexps supported.	
APD_BrowseAPD	19	peptide_options	Peptide Options									N	multioptionlist	3		Y	1	N	Various selectable options to further contrain the peptides displayed	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BSH_peptide_options' ORDER BY sort_order,option_value"
APD_BrowseAPD	20	precursor_mass_constraint	Precursor Mass constraint									N	text	40		Y	1	N	"Constraint for the measured precursor mass (as a single decimal value).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""	
APD_BrowseAPD	21	percent_buffer_b_constraint	% Buffer B (ACN) constraint									N	text	40		Y	2	N	"Constraint for the calculated Percent Buffer B (acetonitrile) (value between 0 and 100).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""	
APD_BrowseAPD	22	isoelectric_point_constraint	pI constraint									N	text	40		Y	2	N	"Constraint for the theoretical isoelectric point (pI).  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""n.n +- n.n"", ""between n.n and n.n"""	
APD_BrowseAPD	23	sort_order	Sort Order									N	optionlist	 		Y	Y	N	Desired display sorting order (DESC means descending: highest to lowest)	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BAPD_sort_options' ORDER BY sort_order,option_value"
APD_BrowseAPD	24	gene_annotation_level_constraint	Gene Annotation Level Constraint									N	optionlist			Y	2	N	"Constraint for the hierarchy level of gene annotations to view.  By default, the leaf level annotations are displayed"	"SELECT annotation_hierarchy_level_name,annotation_hierarchy_level_name FROM $TBBL_ANNOTATION_HIERARCHY_LEVEL ORDER BY annotation_hierarchy_level_id"
APD_BrowseAPD	25	display_options	Display Options									N	multioptionlist	5		Y	Y	N	Various selectable table display options	"SELECT option_key,option_value FROM $TBPR_QUERY_OPTION WHERE option_type = 'BAPD_display_options' ORDER BY sort_order,option_value"
APD_BrowseAPD	26	row_limit	Maximum Rows									N	text	10		Y	2	N	"Limit the numbers of rows displayed.  If not provided, default is 5000 rows."	
