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 organism_specialized_build Organism Specialized Build varchar 50 0 Y N N text 40 Y Y Y "If not NULL, a specialized build within this organism, e.g. Human Plasma" AT_default_atlas_build 4 atlas_build_id Atlas Build ID int 4 0 N N AT_atlas_build atlas_build_id Y optionlist Y Y N 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 5 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments AT_default_atlas_build 6 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N AT_default_atlas_build 7 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N AT_default_atlas_build 8 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N AT_default_atlas_build 9 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N AT_default_atlas_build 10 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N AT_default_atlas_build 11 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_accession Sample Accession varchar 255 0 Y N N text 20 Y Y Y stable accession identifier for the sample (e.g. PAe000001) AT_sample 4 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_sample 5 sample_title Sample Title varchar 255 0 N N Y textarea 2 Y Y Y Title of this Sample AT_sample 6 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 7 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 8 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 9 sample_description Sample Description text 16 0 Y N N textarea 10 Y Y N Full description of this sample AT_sample 10 instrument_model_id Instrument Model ID 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 11 search_batch_id Search Batch ID int 4 0 N N fixed Y P Search Batch ID AT_sample 12 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 13 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 14 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 15 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 16 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 17 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 18 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 19 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 20 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments AT_sample 21 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N AT_sample 22 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N AT_sample 23 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N AT_sample 24 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N AT_sample 25 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N AT_sample 26 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 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 4 sample_id Sample ID int 4 0 N N AT_sample sample_id N N Associated Sample AT_atlas_build_search_batch 5 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N AT_atlas_build_search_batch 6 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N AT_atlas_build_search_batch 7 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N AT_atlas_build_search_batch 8 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N AT_atlas_build_search_batch 9 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N AT_atlas_build_search_batch 10 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 sample_id Sample ID int 4 0 N N AT_sample sample_id N N Associated Sample AT_atlas_search_batch 4 n_searched_spectra Number of Searched spectra int 6 0 N N N N Number of spectra searched in this search_batch AT_atlas_search_batch 5 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 6 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 7 pepXML_source_files pepXML Source Files varchar 255 0 N N Y Y comma separated list of one or some xinteract pepXML files used as input for this search_batch AT_atlas_search_batch 8 TPP_version TPP version used in peptide identification scoring varchar 100 0 N N Y Y TPP version used for peptide identification scores AT_atlas_search_batch 9 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N AT_atlas_search_batch 10 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N AT_atlas_search_batch 11 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N AT_atlas_search_batch 12 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N AT_atlas_search_batch 13 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N AT_atlas_search_batch 14 record_status Record Status char 1 0 N N N N N AT_atlas_search_batch_parameter 1 atlas_search_batch_id Atlas Search Batch ID int 4 0 N N AT_atlas_search_batch atlas_search_batch_id N N Y Atlas search batch to which this search parameter belongs pkDEFAULT AT_atlas_search_batch_parameter 2 key_order Key Order int 4 0 N N Y Y Y N Monotonically increasing number to denote key order AT_atlas_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 AT_atlas_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 AT_atlas_search_batch_parameter_set 1 atlas_search_batch_id Atlas Search Batch ID int 4 0 N Y AT_atlas_search_batch atlas_search_batch_id N N Y Search batch to which this set of search parameters belong pkDEFAULT AT_atlas_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 AT_atlas_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 AT_atlas_search_batch_parameter_set 4 enzyme Enzyme used in search parameters varchar 100 0 N N Y text 50 Y Y N Enzyme parameter in search AT_atlas_search_batch_parameter_set 5 num_enzyme_termini Num code used in SEQUEST for enzyme termini int 4 0 N N Y text 50 Y Y N Number code used for enzyme termini in SEQUEST params 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 6 molecular_weight Molecular Weight real 4 0 Y N Y text 10 Y Y N Calculated molecular weight of the peptide AT_peptide 7 SSRCalc_relative_hydrophobicity SSRCalc Relative Hydrophobicity real 4 0 Y N Y text 10 Y Y N Calculated hydrophobicity of the peptide using SSRCalc algorithm 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_adjusted_observations Number of Adjusted Observations int 4 0 Y N N text 10 Y Y N Number of adjusted observations AT_peptide_instance 11 n_sibling_peptides Number of Sibling Peptides real 4 0 Y N N text 10 Y Y N Number of sibling peptides AT_peptide_instance 12 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 13 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 14 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 15 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 16 search_batch_ids Search batches varchar 255 0 N N Y textarea 3 Y Y N Comma-separated list of proteomics_search_batch ids AT_peptide_instance 17 is_subpeptide_of superpeptide list varchar 1023 0 Y N N textarea 3 Y Y N Comma-separated list of peptide ids that include this peptide's sequence AT_peptide_instance 18 n_samples Number of Samples Exhibiting Peptide int 4 0 Y N N text 10 Y Y N Number of samples/experiments in which this peptide was observed AT_peptide_instance 19 n_protein_samples Number of Samples Exhibiting Protein int 4 0 Y N N text 10 Y Y N Number of samples/experiments in which the parent protein of this peptide was observed AT_peptide_instance 20 empirical_proteotypic_score Empirical Proteotypic Score real 4 0 Y N N text 10 Y Y N Fraction of samples that exhibit this peptide divided by fraction of samples that exhibit the parent protein AT_peptide_instance 21 predicted_proteotypic_score Predicted Proteotypic Score real 4 0 Y N N text 10 Y Y N Theoretically predicted proteotypic score following Mallick et al. 2006 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 monoisotopic_peptide_mass Monoisotopic Neutral Peptide Mass float 8 0 N N Y text 10 Y Y N Neutral peptide monoisotopic mass AT_modified_peptide_instance 6 average_peptide_mass Average Neutral Peptide Mass float 8 0 N N Y text 10 Y Y N Neutral peptide average mass AT_modified_peptide_instance 7 monoisotopic_parent_mz Monoisotopic Parent m/z float 8 0 N N Y text 10 Y Y N (M+H)+ charged parent ion monoisotopic mass AT_modified_peptide_instance 8 average_parent_mz Average Parent m/z float 8 0 N N Y text 10 Y Y N (M+H)+ charged parent ion average mass AT_modified_peptide_instance 9 best_probability Monoisotopic Neutral Peptide Mass 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 10 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_modified_peptide_instance 11 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 12 n_adjusted_observations Number of Adjusted Observations int 4 0 Y N N text 10 Y Y N Number of adjusted observations AT_modified_peptide_instance 13 n_sibling_peptides Number of Sibling Peptides real 4 0 Y N N text 10 Y Y N Number of sibling peptides AT_modified_peptide_instance 14 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 15 search_batch_ids Search batches varchar 255 0 N N Y textarea 3 Y Y N Comma-separated list of proteomics_search_batch 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 N 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 atlas_build_id Atlas Build ID int 4 0 Y N AT_search_key 6 organism_id Organism int 4 0 Y N AT_search_key 7 resource_name Resource Name varchar 255 0 N N AT_search_key 8 resource_type Resource Type varchar 50 0 N N AT_search_key 9 resource_url Resource URL varchar 255 0 N N AT_search_key 10 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 optionlist 4 Y Y N "Select desired Atlas Build to include in query, required." "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 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 5 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 6 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 7 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 8 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 9 n_samples_constraint Number of Different Samples Constraint N text 15 Y Y N "Constraint for the number of different samples in which the peptide was observed. Allowed syntax: ""n"", ""> n"", ""< n"", ""between n and n"", ""n +- n""" AT_GetPeptides 10 empirical_proteotypic_constraint Empirical Proteotypic Score Constraint N text 10 Y Y N "Constraint for the empirical proteotypic score for a peptide. Allowed syntax: ""n.n"", ""> n.n"", ""< n.n"", ""between n.n and n.n"", ""n.n +- n.n""" AT_GetPeptides 11 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 12 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 13 is_exon_spanning_constraint Is Exon Spanning? N optionlist Y Y N Does at least one of the mappings of this peptide span from one exon to another? "SELECT option_key,option_value FROM $TB_MISC_OPTION WHERE option_type='yesno' ORDER BY sort_order,option_value" AT_GetPeptides 14 chromosome_constraint Chromosome Constraint N text 10 Y 1 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 15 start_in_chromosome_constraint Start in Chromosome Constraint N text 20 Y 1 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 16 end_in_chromosome_constraint End in Chromosome Constraint N text 20 Y 1 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 17 strand_constraint Strand N text 5 Y 1 N Constraint for the strand (orientiation) of the chromosome mapping (must be either + or -) AT_GetPeptides 18 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" AT_spectra_description_set 1 spectra_description_set_id Spectra Description Set ID int 4 0 N Y N N pkDEFAULT AT_spectra_description_set 2 atlas_build_id Atlas Build ID int 4 0 N N AT_atlas_build atlas_build_id N N Associated Atlas Build AT_spectra_description_set 3 sample_id Sample ID int 4 0 N N AT_sample sample_id N N Associated Sample AT_spectra_description_set 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_spectra_description_set 5 instrument_model_id Instrument Model ID int 4 0 Y N PR_instrument instrument_id N optionlist Y Y N Instrument (mass spectrometer) manufacturer model id "SELECT instrument_id,instrument_name FROM $TBPR_INSTRUMENT WHERE record_status != 'D' ORDER BY instrument_name" AT_spectra_description_set 6 instrument_model_name Instrument Model Name varchar 100 0 Y N N Y Y N Instrument (mass spectrometer) manufacturer model name AT_spectra_description_set 7 conversion_software_name Conversion Software Name varchar 255 0 N N N N Name of software used in conversion to mzXML AT_spectra_description_set 8 conversion_software_version Conversion Software Version varchar 50 0 N N N N Version of software used in conversion to mzXML AT_spectra_description_set 9 mzXML_schema mzXML Schema varchar 1024 0 N N N N mzXML schema AT_spectra_description_set 10 n_spectra Number of Spectra int 6 0 N N N N Number of spectra AT_spectra_description_set 11 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N AT_spectra_description_set 12 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N AT_spectra_description_set 13 date_modified Date Record Modified datetime 8 0 N CURRENT_TIMESTAMP N N N AT_spectra_description_set 14 modified_by_id Record Modified By int 4 0 N 1 N contact contact_id N N AT_spectra_description_set 15 owner_group_id Owner Group ID int 4 0 N 1 N work_group work_group_id N N AT_spectra_description_set 16 record_status Record Status char 1 0 N N N N N AT_NIST_library 1 NIST_library_id NIST Library ID int 4 0 N Y N N pkDEFAULT AT_NIST_library 2 organism_id Organism int 4 0 Y N organism organism_id N optionlist Y Y N 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_NIST_library 3 comment Comment text 16 0 Y N N textarea 4 Y Y N Additional comments AT_NIST_library 4 date_created Date Record Created datetime 8 0 N CURRENT_TIMESTAMP N N N AT_NIST_library 5 created_by_id Record Created By int 4 0 N 1 N contact contact_id N N AT_NIST_library 6 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_NIST_library_spectrum 1 NIST_library_spectrum_id NIST Library Spectrum ID int 4 0 N Y N N pkDEFAULT AT_NIST_library_spectrum 2 NIST_library_id NIST Library ID int 4 0 N N AT_NIST_library NIST_library_id Y N N Y NIST library ID AT_NIST_library_spectrum 3 sequence Amino Acid Sequence varchar 255 0 N N Y text 50 Y Y N Amino acid sequence assigned to the spectrum AT_NIST_library_spectrum 4 modified_sequence Modified Sequence varchar 255 0 Y N N text 50 Y Y N Sequence including modification notations AT_NIST_library_spectrum 5 charge Charge State int 4 0 N N N Y Y N charge AT_NIST_library_spectrum 6 NIST_spectrum_type_id NIST Spectrum Type ID int 4 0 N N AT_NIST_spectrum_type NIST_spectrum_type_id Y N N Y NIST Spectrum Type ID AT_NIST_library_spectrum 7 modifications Modifications varchar 255 0 Y N N text 20 Y Y N Modifications to the amino acid sequence AT_NIST_library_spectrum 8 protein_name Protein Name varchar 255 0 Y N Y text 50 Y Y N Name of this Protein AT_NIST_library_spectrum 9 mz_exact Exact M/Z float 8 0 N N Y text 10 Y Y N (M+H)+ charged parent ion AT_NIST_library_spectrum_peak 1 NIST_library_spectrum_peak_id NIST Library Spectrum Peak ID int 4 0 N Y N N pkDEFAULT AT_NIST_library_spectrum_peak 2 NIST_library_spectrum_id NIST Library Spectrum ID int 4 0 N N AT_NIST_library_spectrum NIST_library_spectrum_id Y Y Y N NIST Library Spectrum in which this peak exists SELECT NIST_library_spectrum_id FROM $TBAT_NIST_library_spectrum ORDER BY sort_order AT_NIST_library_spectrum_peak 3 mz M/Z float 8 0 N N Y text 10 Y Y N Fragment ion M/Z AT_NIST_library_spectrum_peak 4 relative_intensity Relative Intensity int 8 0 N N N N N Intensity of the peak relative to a scale AT_NIST_library_spectrum_peak 5 ion_label Ion Label varchar 255 0 Y N N text 20 Y Y N Fragment ion label AT_NIST_library_spectrum_peak 6 peak_label Peak Label varchar 255 0 Y N N text 20 Y Y N Peak Label AT_NIST_library_spectrum_peak 7 charge Charge State int 4 0 N N N Y Y N charge AT_NIST_spectrum_type 1 NIST_spectrum_type_id NIST Spectrum Type ID int 4 0 N Y N N pkDEFAULT AT_NIST_spectrum_type 2 NIST_spectrum_type_name NIST Spectrum Type Name varchar 50 0 N N Y text 30 Y Y N "Spectrum Type Name (i.e., consensus, replicate, or single)" AT_NIST_spectrum_type 3 NIST_spectrum_type_description NIST Spectrum Type Description varchar 1024 0 N N Y text 30 Y Y N Spectrum Type Description AT_spectrum_identification 1 spectrum_identification_id Spectrum Identification ID int 4 0 N Y N N PkDEFAULT AT_spectrum_identification 2 modified_peptide_instance_id Modified Peptide Instance ID int 4 0 N N AT_modified_peptide_instance modified_peptide_instance_id Y text 10 Y Y Parent modified_peptide_instance_id AT_spectrum_identification 3 probability Probability real 4 0 N N Y text 10 Y Y N PeptideProphet probability for assignment to peptide AT_spectrum_identification 4 spectrum_id Spectrum ID int 4 0 N N AT_spectrum spectrum_id Y text 10 Y Y spectrum_id AT_spectrum_identification 5 atlas_search_batch_id Atlas Search Batch ID int 4 0 N N AT_atlas_search_batch atlas_search_batch_id Y text 10 Y Y atlas_search_batch_id AT_spectrum 1 spectrum_id Spectrum ID int 4 0 N Y N N PkDEFAULT AT_spectrum 2 sample_id Sample ID int 4 0 N N AT_sample sample_id Y text 10 Y Y sample_id AT_spectrum 3 spectrum_name Spectrum Name varchar 50 0 N N Y text 30 Y Y N Spectrum Name AT_spectrum 4 start_scan Start scan number int 4 0 N N N Y Y N Start scan number of MS/MS spectrum AT_spectrum 5 end_scan End scan number int 4 0 N N N Y Y N End scan number of MS/MS spectrum AT_spectrum 6 scan_index Scan Index int 4 0 N N N Y Y N Scan index AT_spectrum_peak 1 spectrum_peak_id Spectrum Peak ID int 4 0 N Y N N PkDEFAULT AT_spectrum_peak 2 spectrum_id Spectrum ID int 4 0 N N AT_spectrum spectrum_id Y text 10 Y Y spectrum_id AT_spectrum_peak 3 mz M/Z float 8 0 N N Y text 10 Y Y N Fragment ion M/Z AT_spectrum_peak 4 relative_intensity Relative Intensity int 8 0 N N N N N Integrated Intensity of the peak profile AT_NIST_library_spectrum_comment 1 NIST_library_spectrum_id NIST library spectrum ID int 4 0 N N AT_NIST_library_spectrum NIST_library_spectrum_id N N Y library spectrum to which this comment belongs pkDEFAULT AT_NIST_library_spectrum_comment 2 parameter_key Parameter Key varchar 100 0 N N Y text 50 Y Y Y The key of the key/value pair AT_NIST_library_spectrum_comment 3 parameter_value Parameter Value varchar 1023 0 N N Y text 50 Y Y N The value of the key/value pair