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
AT_atlas_build	1	atlas_build_id	Atlas Build ID	int	4	0	N		Y							N	N				pkDEFAULT
AT_atlas_build	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"	
AT_atlas_build	3	atlas_build_name	Atlas Build Name	varchar	255	0	N		N			Y	text	50		Y	Y	Y	Title of this PeptideAtlas build		
AT_atlas_build	4	biosequence_set_id	Biosequence Set	int	4	0	N		N	AT_biosequence_set	biosequence_set_id	Y	optionlist			Y	Y	N	Biosequence set against which this peptide atlas was built	"SELECT biosequence_set_id,set_name FROM $TBAT_BIOSEQUENCE_SET ORDER BY sort_order,set_name"	
AT_atlas_build	5	probability_threshold	Probability Threshold	real	4	0	Y		N			Y	text	10		Y	Y	N	Minimum probability threshold used for build		
AT_atlas_build	6	APD_id	APD ID	int	4	0	Y		N			Y	text	10		Y	Y	N	The peptide_summary_id of the APD		
AT_atlas_build	7	data_path	Data Path	varchar	255	0	N		N			Y	text	50		Y	Y	N	Path to the data relative to base directory		
AT_atlas_build	8	build_date	Build Date	datetime	8	0	N	CURRENT_TIMESTAMP	N			Y	text	20		Y	Y	N	Date that this PeptideAtlas build was started		
AT_atlas_build	9	atlas_build_description	Atlas Build Description	text	16	0	Y		N			N	textarea	10		Y	Y	N	Full description of this PeptideAtlas build		
AT_atlas_build	10	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
AT_atlas_build	11	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_atlas_build	12	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_atlas_build	13	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_atlas_build	14	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_atlas_build	15	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
AT_atlas_build	16	record_status	Record Status	char	1	0	N	N	N							N	N				
AT_default_atlas_build	1	default_atlas_build_id	Default Atlas Build ID	int	4	0	N		Y							N	N				pkDEFAULT
AT_default_atlas_build	2	organism_id	Organism	int	4	0	Y		N	organism	organism_id	N	optionlist			Y	Y	Y	Organism for which this default applies.  Leave empty for overall default	"SELECT organism_id, organism_name FROM $TB_ORGANISM ORDER BY sort_order,organism_name"	
AT_default_atlas_build	3	atlas_build_id	Atlas Build ID	int	4	0	N		N	AT_atlas_build	atlas_build_id	Y	optionlist			Y	Y	Y	Atlas Build that should be the default for this organism	"SELECT atlas_build_id,atlas_build_name FROM $TBAT_ATLAS_BUILD WHERE record_status != 'D' AND project_id IN (  $accessible_project_ids ) ORDER BY atlas_build_name "	
AT_default_atlas_build	4	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
AT_default_atlas_build	5	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_default_atlas_build	6	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_default_atlas_build	7	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_default_atlas_build	8	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_default_atlas_build	9	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
AT_default_atlas_build	10	record_status	Record Status	char	1	0	N	N	N							N	N				
AT_sample	1	sample_id	Sample ID	int	4	0	N		Y							N	N				pkDEFAULT
AT_sample	2	project_id	Owner Project	int	4	0	N		N	project	project_id	Y	optionlist			Y	Y	N	Project under which this Sample 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"	
AT_sample	3	sample_title	Sample Title	varchar	255	0	N		N			Y	textarea	2		Y	Y	Y	Title of this Sample		
AT_sample	4	sample_tag	Sample Tag	varchar	50	0	N		N			Y	text	30		Y	Y	Y	"Short tag (mnenomic) for this sample (e.g., THP1sLPS)"		
AT_sample	5	original_experiment_tag	Original Experiment Tag	varchar	50	0	Y		N			Y	text	30		Y	Y	N	"Short tag (mnenomic) for the original experiment, perhaps superceded with a better name in sample_tag"		
AT_sample	6	sample_date	Sample Date	datetime	8	0	Y	CURRENT_TIMESTAMP	N			N	textdate	20		Y	Y	N	Date on which this sample was prepared	
AT_sample	7	sample_description	Sample Description	text	16	0	Y		N			N	textarea	10		Y	Y	N	Full description of this sample	
AT_sample	8	instrument_model_id	Instrument Model	int	4	0	Y		N	PR_instrument	instrument_id	N	optionlist			Y	Y	N	Instrument (mass spectrometer) manufacturer model name	"SELECT instrument_id,instrument_name FROM $TBPR_INSTRUMENT WHERE record_status != 'D' ORDER BY instrument_name"
AT_sample	9	search_batch_id	Search Batch ID	int	4	0	N		N				fixed			Y	P		Search Batch ID	
AT_sample	10	sample_publication_ids	Sample Publications	varchar	255	0	Y		N	AT_sample_publication	sample_publication_id	N	multilink	4		Y	Y	N	Select all publications that apply to this sample.	"SELECT P.publication_id,P.publication_name FROM $TBAT_PUBLICATION P WHERE P.record_status != 'D' ORDER BY P.publication_name"
AT_sample	11	data_contributors	Data Contributors	text	16	0	Y		N			Y	textarea	10		Y	Y	N	Description of this BioSequence (generally everything after the first space in a FASTA file header line)	
AT_sample	12	primary_contact_email	Primary Email Contact	text	16	0	Y		N			Y	text	40		Y	P	N	Email address of primary contact for data	
AT_sample	13	is_public	Is the dataset publicly available?	char	1	0	Y		N			Y	optionlist			Y	Y	N	Indicates whether the dataset is public	"SELECT option_key,option_value FROM $TB_MISC_OPTION WHERE option_type='yesno' ORDER BY sort_order,option_value"
AT_sample	14	anatomical_site_term	Anatomical Site (not yet used)	varchar	255	0	Y		N			N	optionlist			Y	Y	N	Anatomical site from which this sample was obtained	"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"
AT_sample	15	developmental_stage_term	Developmental Stage (not yet used)	varchar	255	0	Y		N			N	optionlist			Y	Y	N	Developmental stage of the sample donor 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"
AT_sample	16	pathology_term	Pathology (not yet used)	varchar	255	0	Y		N			N	optionlist			Y	Y	N	Pathology of the sample	"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"
AT_sample	17	cell_type_term	Cell Type (not yet used)	varchar	255	0	Y		N			N	optionlist			Y	Y	N	Cell type of the sample	"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"
AT_sample	18	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments	
AT_sample	19	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N			
AT_sample	20	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N			
AT_sample	21	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N			
AT_sample	22	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_sample	23	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
AT_sample	24	record_status	Record Status	char	1	0	N	N	N							N	N				
AT_atlas_build_sample	1	atlas_build_sample_id	Atlas Build Sample ID	int	4	0	N		Y							N	N				pkDEFAULT
AT_atlas_build_sample	2	atlas_build_id	Atlas Build ID	int	4	0	N		N	AT_atlas_build	atlas_build_id					N	N		Associated Atlas Build		
AT_atlas_build_sample	3	sample_id	Sample ID	int	4	0	N		N	AT_sample	sample_id					N	N		Associated Sample		
AT_atlas_build_sample	4	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_atlas_build_sample	5	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_atlas_build_sample	6	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_atlas_build_sample	7	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_atlas_build_sample	8	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
AT_atlas_build_sample	9	record_status	Record Status	char	1	0	N	N	N							N	N				
AT_atlas_build_search_batch	1	atlas_build_search_batch_id	Atlas Build Search Batch ID	int	4	0	N		Y							N	N				pkDEFAULT
AT_atlas_build_search_batch	2	atlas_build_id	Atlas Build ID	int	4	0	N		N	AT_atlas_build	atlas_build_id					N	N		Associated Atlas Build		
AT_atlas_build_search_batch	3	sample_id	Sample ID	int	4	0	N		N	AT_sample	sample_id					N	N		Associated Sample		
AT_atlas_build_search_batch	4	atlas_search_batch_id	Atlas Search Batch ID	int	4	0	N		N	AT_atlas_search_batch	atlas_search_batch_id					N	N		Associated Atlas Search Batch (which can link to a Proteomics Search Batch)		
AT_atlas_build_search_batch	5	n_searched_spectra	Number of Searched spectra	int	4	0	N		N							N	N		Number of spectra searched in this search_batch		
AT_atlas_build_search_batch	6	data_path	Relative Path to search_batch output	varchar	255	0	N		N							N	N		Relative path to the search results		
AT_atlas_build_search_batch	7	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_atlas_build_search_batch	8	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_atlas_build_search_batch	9	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_atlas_build_search_batch	10	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_atlas_build_search_batch	11	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
AT_atlas_build_search_batch	12	record_status	Record Status	char	1	0	N	N	N							N	N				
AT_atlas_search_batch	1	atlas_search_batch_id	Atlas Search Batch ID	int	4	0	N		Y							N	N				pkDEFAULT
AT_atlas_search_batch	2	proteomics_search_batch_id	Proteomics Search Batch ID	int	4	0	Y		N							N	N		Associated Proteomics module search_batch_id		
AT_atlas_search_batch	3	n_searched_spectra	Number of Searched spectra	int	4	0	N		N							N	N		Number of spectra searched in this search_batch		
AT_atlas_search_batch	4	data_location	File Path to search_batch output	varchar	255	0	N		N							Y	Y		Absolute or relative location of the raw data for this search batch		
AT_atlas_search_batch	5	search_batch_subdir	Search Batch Subdirectory	varchar	100	0	N		N							Y	Y		Subdirectory under the experiment where the data for this search resides		
AT_atlas_search_batch	6	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_atlas_search_batch	7	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_atlas_search_batch	8	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_atlas_search_batch	9	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_atlas_search_batch	10	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
AT_atlas_search_batch	11	record_status	Record Status	char	1	0	N	N	N							N	N				
AT_peptide	1	peptide_id	Peptide ID	int	4	0	N		Y							N	N				pkDEFAULT
AT_peptide	3	peptide_accession	Peptide Accession	varchar	255	0	N		N			Y	text	20		Y	Y	Y	APD peptide accession number of the the peptide		
AT_peptide	3	peptide_sequence	Peptide Sequence	varchar	255	0	N		N			Y	text	50		Y	Y	N	Sequence of the peptide		
AT_peptide	4	peptide_length	Peptide Length	int	4	0	N		N			Y	text	10		Y	Y	N	Length of the peptide in amino acids		
AT_peptide	5	peptide_isoelectric_point	Isoelectric Point	real	4	0	Y		N			Y	text	10		Y	Y	N	Calculated isoelectric point of the peptide		
AT_peptide_instance	1	peptide_instance_id	Peptide Instance ID	int	4	0	N		Y							N	N				pkDEFAULT
AT_peptide_instance	2	atlas_build_id	Atlas Build	int	4	0	N		N	AT_atlas_build	atlas_build_id	Y	optionlist			Y	Y	Y	Associated Atlas Build		
AT_peptide_instance	3	peptide_id	Peptide	int	4	0	N		N	AT_peptide	peptide_id	Y	optionlist			Y	Y	Y	Peptide		
AT_peptide_instance	4	preceding_residue	Preceding Residue	char	1	0	N		N			Y	text	5		Y	Y	N	Residue (amino acid) immediately preceding the peptide		
AT_peptide_instance	5	following_residue	Following Residue	char	1	0	N		N			Y	text	5		Y	Y	N	Residue (amino acid) immediately following the peptide		
AT_peptide_instance	6	original_protein_name	Original Protein Name	varchar	255	0	N		N			Y	text	5		Y	Y	N	Name of the protein as it was originally identified in the database search		
AT_peptide_instance	7	best_probability	Best Observed Probability	real	4	0	N		N			Y	text	10		Y	Y	N	Best observed PeptideProphet probablity of being correct over all samples		
AT_peptide_instance	8	best_adjusted_probability	Best Adjusted Probability	real	4	0	Y		N			Y	text	10		Y	Y	N	Best probability observed as adjusted by ProteinProphet within all samples		
AT_peptide_instance	9	n_observations	Number of Peptide Observations	int	4	0	N		N			Y	text	10		Y	Y	N	Number of times the peptide was observed in the input samples		
AT_peptide_instance	10	n_genome_locations	Number of Genome Locations Mapped to	int	4	0	N		N			Y	text	10		Y	Y	N	Number of Genome locations for this peptide 		
AT_peptide_instance	11	sample_ids	Samples Observed in	varchar	255	0	N		N			Y	textarea	3		Y	Y	N	Comma-separated list of sample_ids in which which peptide was observed		
AT_peptide_instance	12	is_exon_spanning	Does it span over introns?	char	1	0	Y		N			Y	text	3		Y	Y	N	Comma-separated list of sample_ids in which which peptide was observed		
AT_peptide_instance	13	n_protein_mappings	Number of Proteins for this Peptide 	int	4	0	N		N			Y	text	10		Y	Y	N	Number of distinct accession numbers (proteins) for peptide in Genome		
AT_peptide_instance	14	search_batch_ids	Search batches	varchar	255	0	N		N			Y	textarea	3		Y	Y	N	Comma-separated list of search_bartch ids		
AT_peptide_instance	15	is_subpeptide_of	superpeptide list	varchar	255	0	Y		N			N	textarea	3		Y	Y	N	Comma-separated list of peptide ids that include this peptide's sequence		
AT_peptide_instance_sample	1	peptide_instance_sample_id	Peptide Instance Sample ID	int	4	0	N		Y							N	N				pkDEFAULT
AT_peptide_instance_sample	2	peptide_instance_id	Peptide Instance ID	int	4	0	N		N	AT_peptide_instance	peptide_instance_id					N	N		Associated Atlas Build		
AT_peptide_instance_sample	3	sample_id	Sample ID	int	4	0	N		N	AT_sample	sample_id					N	N		Associated Sample		
AT_peptide_instance_sample	4	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_peptide_instance_sample	5	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_peptide_instance_sample	6	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_peptide_instance_sample	7	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_peptide_instance_sample	8	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
AT_peptide_instance_sample	9	record_status	Record Status	char	1	0	N	N	N							N	N				
AT_peptide_instance_search_batch	1	peptide_instance_search_batch_id	Peptide Instance Search Batch ID	int	4	0	N		Y							N	N				pkDEFAULT
AT_peptide_instance_search_batch	2	peptide_instance_id	Peptide Instance ID	int	4	0	N		N	AT_peptide_instance	peptide_instance_id					N	N		Associated Atlas Build		
AT_peptide_instance_search_batch	3	atlas_search_batch_id	Atlas Search Batch ID	int	4	0	N		N	AT_atlas_search_batch	atlas_search_batch_id					N	N		Associated Atlas Search Batch		
AT_peptide_instance_search_batch	4	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_peptide_instance_search_batch	5	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_peptide_instance_search_batch	6	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_peptide_instance_search_batch	7	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_peptide_instance_search_batch	8	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
AT_peptide_instance_search_batch	9	record_status	Record Status	char	1	0	N	N	N							N	N				
AT_modified_peptide_instance	1	modified_peptide_instance_id	Modified Peptide Instance ID	int	4	0	N		Y							N	N				pkDEFAULT
AT_modified_peptide_instance	2	peptide_instance_id	Peptide Instance ID	int	4	0	N		N	AT_peptide_instance	peptide_instance_id	Y	text	10		Y	Y	Y	Parent peptide_instance_id		
AT_modified_peptide_instance	3	modified_peptide_sequence	Modified Peptide Sequence	varchar	255	0	N		N			Y	text	50		Y	Y	Y	Sequence of the peptide including modification notations		
AT_modified_peptide_instance	4	peptide_charge	Peptide Charge	int	4	0	N		N			Y	text	10		Y	Y	Y	Charge on the precursor ion		
AT_modified_peptide_instance	5	best_probability	Best Observed Probability	real	4	0	N		N			Y	text	10		Y	Y	N	Best observed PeptideProphet probablity of being correct over all samples		
AT_modified_peptide_instance	6	best_adjusted_probability	Best Adjusted Probability	real	4	0	N		N			Y	text	10		Y	Y	N	Best probability observed as adjusted by ProteinProphet within all samples		
AT_modified_peptide_instance	7	n_observations	Number of Peptide Observations	int	4	0	N		N			Y	text	10		Y	Y	N	Number of times the peptide was observed in the input samples		
AT_modified_peptide_instance	8	sample_ids	Samples Observed in	varchar	255	0	N		N			Y	textarea	3		Y	Y	N	Comma-separated list of sample_ids in which which peptide was observed		
AT_modified_peptide_instance	9	search_batch_ids	Search batches	varchar	255	0	N		N			Y	textarea	3		Y	Y	N	Comma-separated list of search_bartch ids		
AT_modified_peptide_instance_sample	1	modified_peptide_instance_sample_id	Modified Peptide Instance Sample ID	int	4	0	N		Y							N	N				pkDEFAULT
AT_modified_peptide_instance_sample	2	modified_peptide_instance_id	Modified Peptide Instance ID	int	4	0	N		N	AT_modified_peptide_instance	modified_peptide_instance_id					N	N		Associated Atlas Build		
AT_modified_peptide_instance_sample	3	sample_id	Sample ID	int	4	0	N		N	AT_sample	sample_id					N	N		Associated Sample		
AT_modified_peptide_instance_sample	4	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_modified_peptide_instance_sample	5	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_modified_peptide_instance_sample	6	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_modified_peptide_instance_sample	7	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_modified_peptide_instance_sample	8	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
AT_modified_peptide_instance_sample	9	record_status	Record Status	char	1	0	N	N	N							N	N				
AT_modified_peptide_instance_search_batch	1	modified_peptide_instance_search_batch_id	Modified Peptide Instance Search Batch ID	int	4	0	N		Y							N	N				pkDEFAULT
AT_modified_peptide_instance_search_batch	2	modified_peptide_instance_id	Modified Peptide Instance ID	int	4	0	N		N	AT_modified_peptide_instance	modified_peptide_instance_id					N	N		Associated Atlas Build		
AT_modified_peptide_instance_search_batch	3	atlas_search_batch_id	Atlas Search Batch ID	int	4	0	N		N	AT_atlas_search_batch	atlas_search_batch_id					N	N		Associated Atlas Search Batch		
AT_modified_peptide_instance_search_batch	4	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_modified_peptide_instance_search_batch	5	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_modified_peptide_instance_search_batch	6	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_modified_peptide_instance_search_batch	7	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_modified_peptide_instance_search_batch	8	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
AT_modified_peptide_instance_search_batch	9	record_status	Record Status	char	1	0	N	N	N							N	N				
AT_peptide_mapping	1	peptide_mapping_id	Peptide Mapping ID	int	4	0	N		Y							N	N				pkDEFAULT
AT_peptide_mapping	2	peptide_instance_id	Peptide Instance	int	4	0	N		N	AT_peptide_instance	peptide_instance_id	Y	optionlist			Y	Y	Y	Peptide Instance that was mapped		
AT_peptide_mapping	3	matched_biosequence_id	Matched Biosequence	int	4	0	N		N	AT_biosequence	biosequence_id	Y	optionlist			Y	Y	Y	Biosequence to which the peptide was successfully mapped		
AT_peptide_mapping	4	start_in_biosequence	Start Position in Biosequence	int	4	0	N		N			Y	text	10		Y	Y	Y	Start position of the peptide in the matched biosequence		
AT_peptide_mapping	5	end_in_biosequence	End Position in Biosequence	int	4	0	N		N			Y	text	10		Y	Y	N	End position of the peptide in the matched biosequence		
AT_peptide_mapping	6	chromosome	Chromosome	varchar	50	0	N		N			Y	text	50		Y	Y	N	Chromosome in which this mapping occurs		
AT_peptide_mapping	7	start_in_chromosome	Start Position in Chromosome	int	4	0	N		N			Y	text	20		Y	Y	N	Start position of the peptide in the chromosome which the peptide matches the biosequence		
AT_peptide_mapping	8	end_in_chromosome	End Position in Chromosome	int	4	0	N		N			Y	text	20		Y	Y	N	End position of the peptide in the chromosome which the peptide matches the biosequence		
AT_peptide_mapping	9	strand	Strand	char	1	0	N		N			Y	text	10		Y	Y	N	"Strand (+,-) of the peptide in the chromosome"		
AT_biosequence_set	1	biosequence_set_id	BioSequence Set ID	int	4	0	N		Y							N	N				pkDEFAULT
AT_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"	
AT_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"	
AT_biosequence_set	4	set_name	Set Name	varchar	100	0	N		N			Y	text	50		Y	Y	N	Name of this BioSequence database		
AT_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		
AT_biosequence_set	6	set_description	Set Description	varchar	255	0	N		N			Y	text	50		Y	Y	N	Longer description of this BioSequence database		
AT_biosequence_set	7	set_version	Set Version	varchar	50	0	N		N			Y	text	40		Y	Y	N	Version of this BioSequence database		
AT_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"	
AT_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		
AT_biosequence_set	10	set_path	Set Path	varchar	255	0	N		N			Y	text	50		Y	Y	N	File path of this BioSequence database		
AT_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		
AT_biosequence_set	12	uri	URI	varchar	255	0	Y		N			N	text	50		Y	Y	N	External web page or other URI		SELF
AT_biosequence_set	13	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
AT_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.		
AT_biosequence_set	15	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_biosequence_set	16	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_biosequence_set	17	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_biosequence_set	18	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_biosequence_set	19	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
AT_biosequence_set	20	record_status	Record Status	char	1	0	N	N	N							N	N				
AT_biosequence	1	biosequence_id	BioSequence ID	int	4	0	N		Y							N	N				pkDEFAULT
AT_biosequence	2	biosequence_set_id	BioSequence Set	int	4	0	N		N	AT_biosequence_set	biosequence_set_id					N	N	Y	BioSequence Set to which this BioSequence belongs		pkDEFAULT
AT_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)		
AT_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		
AT_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
AT_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		
AT_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"	
AT_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"	
AT_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)		
AT_biosequence	10	biosequence_seq	Sequence	text	16	0	Y		N			N	file	40		Y	Y	N	Actual sequence of the BioSequence if known		
AT_biosequence	11	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
AT_biosequence	12	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_biosequence	13	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_biosequence	14	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_biosequence	15	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_biosequence	16	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
AT_biosequence	17	record_status	Record Status	char	1	0	N	N	N							N	N				
AT_biosequence_property_set	1	biosequence_property_set_id	BioSequence Property Set ID	int	4	0	N		Y							N	N				pkDEFAULT
AT_biosequence_property_set	2	biosequence_id	BioSequence ID	int	4	0	N		N	AT_biosequence	biosequence_id					N	N	Y	Biosequence to which this Biosequence property set belongs		pkDEFAULT
AT_biosequence_property_set	3	n_transmembrane_regions	Number of Transmembrane Regions	int	4	0	Y		N							Y	Y	N	Number of transmembrane regions		pkDEFAULT
AT_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"		
AT_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		
AT_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)"		
AT_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		
AT_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		
AT_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?		
AT_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		
AT_biosequence_property_set	11	chromosome	Chromosome	varchar	50	0	Y		N			N	text	50		Y	Y	N	Chromosome in which this mapping occurs		
AT_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		
AT_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		
AT_biosequence_property_set	14	strand	Strand	char	1	0	Y		N			N	text	10		Y	Y	N	"Strand (+,-) of the biosequence in the chromosome"		
AT_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		
AT_biosequence_property_set	16	fav_codon_frequency	Favorite Codon Frequency	real	4	0	Y		N			N	text	10		Y	Y	N	Favorite Codon Frequency		
AT_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		
AT_biosequence_property_set	18	category	Category	varchar	255	0	Y		N			N	text	50		Y	Y	N	Biosequence category		
AT_biosequence_annotated_gene	1	biosequence_id	BioSequence ID	int	4	0	N		N	AT_biosequence	biosequence_id					N	N	Y	Biosequence to which this Biosequence property set belongs		
AT_biosequence_annotated_gene	2	annotated_gene_id	Annotated Gene ID	int	4	0	N		N	BL_annotated_gene	annotated_gene_id					N	N	Y	Gene ID associated with Biosequence ID		
AT_biosequence_annotation	1	biosequence_annotation_id	Domain Match Type	int	4	0	N		Y							N	N				pkDEFAULT
AT_biosequence_annotation	2	biosequence_id	BioSequence	int	4	0	N		N	AT_biosequence	biosequence_id	Y	fixed			Y	Y	Y	BioSequence to which this annotation belongs		
AT_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)		
AT_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)		
AT_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		
AT_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		
AT_biosequence_annotation	7	functional_description	Functional Description	text	16	0	Y		N			N	textarea	3		Y	Y	N	Functional description of the protein		
AT_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		
AT_biosequence_annotation	9	biosequence_type	Biosequence Type	varchar	255	0	Y		N			N	text	50		Y	Y	N	Further annotation of biosequence type		
AT_biosequence_annotation	10	category	Category	varchar	255	0	Y		N			N	text	50		Y	Y	N	Category		
AT_biosequence_annotation	11	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
AT_biosequence_annotation	12	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_biosequence_annotation	13	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_biosequence_annotation	14	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_biosequence_annotation	15	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_biosequence_annotation	16	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
AT_biosequence_annotation	17	record_status	Record Status	char	1	0	N	N	N							N	N				
AT_publication	1	publication_id	Publication	int	8	0	N		Y							N	N				pkDEFAULT
AT_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"		
AT_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)"		
AT_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		
AT_publication	9	title	Title	varchar	255	0	Y		N			N	textarea	2		Y	Y	N	Title of the article		
AT_publication	10	author_list	Author List	varchar	255	0	Y		N			N	textarea	2		Y	Y	N	"Author list in 'Lastname, FIMI' format"		
AT_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		
AT_publication	12	published_year	Published Year	varchar	10	0	Y		N			N	text	20		Y	Y	N	Year the article was published		
AT_publication	13	volume_number	Volume Number	varchar	50	0	Y		N			N	text	20		Y	Y	N	Volume number of the article		
AT_publication	14	issue_number	Issue Number	varchar	50	0	Y		N			N	text	20		Y	Y	N	Issue number of the article		
AT_publication	15	page_numbers	Page Numbers	varchar	50	0	Y		N			N	text	30		Y	Y	N	Page numbers of the article		
AT_publication	16	publisher_name	Publisher Name	varchar	255	0	Y		N			N	text	40		Y	Y	N	Name of the publisher		
AT_publication	17	editor_name	Editor Name	varchar	255	0	Y		N			N	text	40		Y	Y	N	"Name of the editor, if any"		
AT_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
AT_publication	19	abstract	Abstract	text	16	0	Y		N			N	textarea	4		Y	Y	N	Plain text abstract of the article		
AT_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
AT_publication	21	comment	Comment	text	16	0	Y		N			N	textarea	4		Y	Y	N	Additional comments		
AT_publication	22	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_publication	23	created_by_id	Record Created By	int	8	0	N		N	contact	contact_id					N	N				
AT_publication	24	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_publication	25	modified_by_id	Record Modified By	int	8	0	N		N	contact	contact_id					N	N				
AT_publication	26	owner_group_id	Owner Group ID	int	8	0	N	1	N	work_group	work_group_id					N	N				
AT_publication	27	record_status	Record Status	char	1	0	N	N	N							N	N				
AT_search_key	1	search_key_id	Search Key ID	int	4	0	N		Y												
AT_search_key	2	search_key_name	Search Key Name	varchar	800	0	N		N												
AT_search_key	3	search_key_type	Search Key Type	varchar	50	0	N		N												
AT_search_key	4	search_key_dbxref_id	Database Cross Reference	int	4	0	Y		N												
AT_search_key	5	organism_id	Organism	int	4	0	Y		N												
AT_search_key	6	resource_name	Resource Name	varchar	255	0	N		N												
AT_search_key	7	resource_type	Resource Type	varchar	50	0	N		N												
AT_search_key	8	resource_url	Resource URL	varchar	255	0	N		N												
AT_search_key	9	resource_n_matches	Resource N Matches	int	4	0	Y		N												
AT_query_option	1	query_option_id	Query Option ID	int	4	0	N		Y							N	N				pkDEFAULT
AT_query_option	2	option_type	Option Type	varchar	255	0	N		N			Y	text	50		Y	Y	Y	Type or category of this option		
AT_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		
AT_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		
AT_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		
AT_query_option	6	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_query_option	7	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_query_option	8	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_query_option	9	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_query_option	10	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
AT_query_option	11	record_status	Record Status	char	1	0	N	N	N							N	N				
AT_sample_publication	1	sample_publication_id	Sample Publication ID	int	4	0	N		Y			Y				N	N	N			pkDEFAULT
AT_sample_publication	2	sample_id	Sample ID	int	4	0	N		N	AT_sample	sample_id	Y				Y	N	Y			
AT_sample_publication	3	publication_id	Publication ID	int	4	0	N		N	AT_publication	publication_id	Y				N	N	Y	Publication ID		
AT_sample_publication	4	date_created	Date Record Created	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_sample_publication	5	created_by_id	Record Created By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_sample_publication	6	date_modified	Date Record Modified	datetime	8	0	N	CURRENT_TIMESTAMP	N							N	N				
AT_sample_publication	7	modified_by_id	Record Modified By	int	4	0	N	1	N	contact	contact_id					N	N				
AT_sample_publication	8	owner_group_id	Owner Group ID	int	4	0	N	1	N	work_group	work_group_id					N	N				
AT_sample_publication	9	record_status	Record Status	char	1	0	N	N	N							N	N				
AT_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 $TBAT_BIOSEQUENCE_SET WHERE project_id IN (  $accessible_project_ids ) ORDER BY sort_order,set_name"	
AT_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.		
AT_BrowseBiosequence	3	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.		
AT_BrowseBiosequence	4	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.		
AT_BrowseBiosequence	5	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.		
AT_BrowseBiosequence	6	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.	
AT_BrowseBiosequence	7	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.	
AT_BrowseBiosequence	8	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"""	
AT_BrowseBiosequence	9	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 $TBAT_BIOSEQUENCE_PROPERTY_SET ORDER BY transmembrane_class"
AT_BrowseBiosequence	10	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"""	
AT_BrowseBiosequence	11	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.	
AT_BrowseBiosequence	12	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.	
AT_BrowseBiosequence	13	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 $TBAT_QUERY_OPTION WHERE option_type = 'BBS_sort_options' ORDER BY sort_order,option_value"
AT_BrowseBiosequence	14	display_options	Display Options									N	multioptionlist	3		Y	Y	N	Various selectable table display options	"SELECT option_key,option_value FROM $TBAT_QUERY_OPTION WHERE option_type = 'BBS_display_options' ORDER BY sort_order,option_value"
AT_BrowseBiosequence	15	row_limit	Maximum Rows									N	text	10		Y	Y	N	"Limit the numbers of rows displayed.  If not provided, default is 100 rows."	
AT_GetPeptides	1	atlas_build_id	Atlas Build									Y	multioptionlist	4		Y	Y	N	Select desired Atlas Builds to include in query.  Multiple items may be selected.  At least one item must be selected.	"SELECT atlas_build_id,atlas_build_name FROM $TBAT_ATLAS_BUILD WHERE record_status != 'D' AND project_id IN (  $accessible_project_ids ) ORDER BY atlas_build_name "
AT_GetPeptides	2	biosequence_name_constraint	Protein Name Constraint									N	text	40		Y	Y	N	Constraint for the Protein Name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; multiple entries may be separated with a  semicolon; Use ! for NOT.	
AT_GetPeptides	3	biosequence_gene_name_constraint	Gene Name Constraint									N	text	40		Y	Y	N	Constraint for the Gene Name. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; multiple entries may be separated with a  semicolon; Use ! for NOT.	
AT_GetPeptides	4	peptide_name_constraint	Peptide Name Constraint									N	text	40		Y	Y	N	Constraint for the Peptide Name (i.e PApxxxxxxxx). '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; multiple entries may be separated with a  semicolon; Use ! for NOT.	
AT_GetPeptides	5	peptide_sequence_constraint	Peptide Sequence Constraint									N	text	40		Y	Y	N	Constraint for the Peptide Sequence. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; multiple entries may be separated with a  semicolon; Use ! for NOT.	
AT_GetPeptides	6	best_probability_constraint	Best Probability Constraint									N	text	15		Y	Y	N	"Constraint for the best observed probability for a peptide.  Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n"""	
AT_GetPeptides	7	n_observations_constraint	Number of Observations Constraint									N	text	10		Y	Y	N	"Constraint for the number of observations for a peptide.  Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"", ""n +- n"""	
AT_GetPeptides	8	chromosome_constraint	Chromosome Constraint									N	text	10		Y	Y	N	Constraint for the Chromosome onto which the peptide was mapped. '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; multiple entries may be separated with a  semicolon; Use ! for NOT.	
AT_GetPeptides	9	start_in_chromosome_constraint	Start in Chromosome Constraint									N	text	20		Y	Y	N	"Constraint for the start position of the peptide in nucleotides along the chromosome.  Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"", ""n +- n"""	
AT_GetPeptides	10	end_in_chromosome_constraint	End in Chromosome Constraint									N	text	20		Y	Y	N	"Constraint for the end position of the peptide in nucleotides along the chromosome.  Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"", ""n +- n"""	
AT_GetPeptides	11	strand_constraint	Strand									N	text	5		Y	Y	N	Constraint for the strand (orientiation) of the chromosome mapping (must be either + or -)	
AT_GetPeptides	12	n_protein_mappings_constraint	Number of Proteins Mapped Constraint									N	text	5		Y	Y	N	Constraint for number of distinct proteins for this peptide ( >=0 )	
AT_GetPeptides	13	n_genome_locations_constraint	Number of Genome Locations Mapped Constraint									N	text	5		Y	Y	N	Constraint for number of genome locations for this peptide ( >=0 )	
AT_GetPeptides	14	is_exon_spanning_constraint	Does Mapping Span Exons Constraint									N	text	5		Y	Y	N	Constraint for whether the peptide spans more than one exon (y or n)	
AT_GetPeptides	15	biosequence_desc_constraint	Description Constraint									N	text	40		Y	Y	N	Constraint for the Protein description (description string from input FASTA file). '%' is wildcard character; '_' is single character wildcard; character range is like '[a-m]'; multiple entries may be separated with a  semicolon; Use ! for NOT.	
AT_GetPeptides	16	display_options	Display Options									N	multioptionlist	3		Y	Y	N	Various selectable table display options	"SELECT option_key,option_value FROM $TBAT_QUERY_OPTION WHERE option_type = 'GP_display_options' ORDER BY sort_order,option_value"
